Culture

Small and medium-sized manufacturing enterprises (SMEs) face many obstacles and difficulties (economic, technical, cultural, etc.) when it comes to implementing Industry 4.0. "These are transition processes that are economically costly, and in which SMEs often come up against technical and cultural problems, as they are not cognizant of how to make this transition, or of the benefits their companies stand to gain by implementing Industry 4.0," explained the UPV/EHU pre-doctoral researcher Víctor Ramírez-Durán.

While several pieces of work address the incorporating of Industry 4.0 technologies into the sphere of product lifecycle and supply chain, which SMEs could use as a reference, this is not the case as far as the customer life cycle in concerned. In this respect, in a piece of work conducted by the UPV/EHU's BDI research group, a methodology has been developed to assist professionals in SME software departments in the task of creating new software services aligned with Industry 4.0; using low-cost options, this would enable them to change the way customers interact with companies and the experiences they have while interacting with them. "Industry 4.0 technologies can help to better understand customers, improve their experience when interacting with products, and facilitate enhanced after-sales support," said Ramirez, author of the work.

Semantic technologies and 3D visualization

The proposed methodology describes a series of well-specified phases and activities that are easy to understand and implement, and which can make this transition possible by using minimal financial resources and taking advantage of new technologies. "With this methodology, it is possible to identify the shortcomings that a company may have with regard to customers, and to analyse how services can be generated in a way that would improve how the customer is treated. The methodology is general; i.e. it does not say which services need to be implemented but helps to spot the shortcomings that can be remedied by generating new services," says Ramírez.

The methodology is mainly based on the use of semantic technologies and 3D visualization. Semantic technologies, in this case ontologies -a network or system that specifies the existing relationships between the concepts of a domain or area of knowledge- provide a high degree of flexibility for the description of knowledge, and also facilitate inference and reasoning processes that are difficult to achieve using traditional databases. On the other hand, 3D visualization technologies offer improved visual representation including better graphics and navigation controls, allowing the user to enjoy an enhanced, interactive experience.

As the researcher explained, this methodology could be used, for example, to create an improved catalogue of a company's products through the 3D visualization of models and advanced navigation options, "with precise descriptions and characteristics of different parts of the model. It could also be used to create a search module which suggests to the customer which product he or she needs". Another of the examples highlighted by Ramírez could be a virtual technician to improve customer service once the product has been purchased. However, Ramírez pointed out that "the methodology is designed in a practical way so that each company can carry out an analysis allowing it to solve a range of problems in relation to its customers. All these benefits will improve the relationship between the customer and the company and achieve a high degree of customer loyalty".

Additional information

Víctor Julio Ramírez-Durán is a pre-doctoral researcher in the Department of Computer Languages and Systems (LSI) of the Faculty of Informatics of the UPV/EHU. His thesis supervisors are the lecturer Idoia Berges and the professor Arantza Illarramendi.

NEW YORK, NY (April 29, 2021) - In a new resource for the scientific community, published today in Nature Biotechnology, researchers in the lab of Neville Sanjana, PhD, at the New York Genome Center (NYGC) and New York University (NYU) developed CRISPR-sciATAC, a novel integrative genetic screening platform that jointly captures CRISPR gene perturbations and single-cell chromatin accessibility genome-wide. With this technology, they profile changes in genome organization and create a large-scale atlas of how loss of individual chromatin-altering enzymes impacts the human genome. The new method harnesses the programmability of the gene editing system CRISPR to knock-out nearly all chromatin-related genes in parallel, offering researchers deeper insights into the role of DNA accessibility in cancer and in rare diseases involving chromatin.

Recent advances in single-cell technologies have given scientists the ability to profile chromatin, the complex of DNA and proteins that resides within the nucleus of individual cells. Chromatin is often called the "gatekeeper" of the genome because its proteins act as packaging elements for the DNA, either promoting or refusing access to it. This controls gene expression processes in the cell, such as turning on or off specific genes. Changes in the chromatin landscape have been linked to diverse human traits and diseases, most notably cancer.

In an initial demonstration of CRISPR-sciATAC, the Sanjana Lab team designed a CRISPR library to target 20 chromatin-modifying genes that are commonly mutated in different cancers, including breast, colon, lung and brain cancers. Many of these enzymes act as tumor suppressors and their loss results in global changes in chromatin accessibility. For example, the group showed that loss of the gene EZH2, which encodes a histone methytransferase, resulted in an increase in gene expression across several previously silenced developmental genes.

"The scale of CRISPR-sciATAC makes this dataset very unique. Here, in a uniform genetic background, we have accessibility data capturing the impact of every chromatin-related gene. This provides a detailed map between each gene and how its loss impacts genome organization with single-cell resolution," said Dr. Noa Liscovitch-Brauer, a postdoctoral fellow in Sanjana's lab at the New York Genome Center and NYU and the study's co-first author.

In total, the team targeted more than 100 chromatin-related genes and developed a "chromatin atlas" that charts how the genome changes in response to loss of these proteins. The atlas shows that different subunits within each of the 17 chromatin remodeling complexes targeted can have different effects on genome accessibility. Surprisingly, nearly all of these complexes have subunits where loss triggers increased accessibility and other subunits with the opposite effect. Overall, the greatest disruption in transcription factor binding sites, which are important functional elements in the genome, was observed after loss of AT-rich interactive domain-containing protein 1A (ARID1A), a member of the BAF complex. Mutations in BAF complex proteins are estimated to be involved in 1 out of every 5 cancers.

In addition to the CRISPR-sciATAC method, the team also developed a suite of computational methods to map the dynamic movements of the nucleosomes, which are the protein clusters that DNA is wrapped around. When there are more nucleosomes, the DNA is tightly wound and less available to bind transcription factors. This is exactly what the team found at specifical transcription factor binding sites involved in cell proliferation after CRISPR knock-out of ARID1A. When targeting a different chromatin-modifying enzyme, these same sites underwent an expansion in nucleosome spacing, demonstrating the dynamics of nucleosome positioning at specific sites in the genome. The CRISPR-sciATAC method allowed the team to systematically explore this genome plasticity for multiple chromatin-modifying enzymes and transcription factor binding sites.

"We really focused on making CRISPR-sciATAC an accessible technique -- we wanted it to be something that any lab could do. We produced most of the key enzymes in-house and used simple methods for single-cell isolation that do not require microfluidics or single-cell kits," said Dr. Antonino Montalbano, a former postdoctoral fellow in Sanjana's lab at the New York Genome Center and NYU and the study's co-first author.

To develop the CRISPR-sciATAC technology, the researchers used a mix of human and mouse cells to create a tagging/identification process that allowed them to split and barcode the nuclei of cells as well as capture the single-guide RNAs required for CRISPR targeting. The work builds off prior single-cell combinatorial indexing ATAC-seq (sciATAC-seq) work from Dr. Jay Shendure at the University of Washington and other groups developing new single-cell genomics methods. CRISPR-sciATAC also uses an unique, easy-to purify transposase that was developed in the NYGC's Innovation Technology Lab. A key technical hurdle was optimizing experimental conditions to simultaneously capture the CRISPR guide RNAs and genome fragments for accessibility profiling while also keeping the nuclear envelope of each cell intact.

"Integrating chromatin accessibility profiling into the genome-wide CRISPR screens provides a new lens for us to understand gene regulation," said Dr. Sanjana, Core Faculty Member, NYGC, Assistant Professor of Biology, NYU, and Assistant Professor of Neuroscience and Physiology, NYU Grossman School of Medicine, the study's senior author. "With CRISPR-sciATAC, we have a comprehensive view into how specific chromatin-modifying enzymes and complexes change accessibility and orchestrate the interactions that control gene expression. Chromatin sets the stage for gene expression, and here we can measure the impact of different mutations on chromatin rapidly. We hope this atlas will be a broadly useful resource for the community and that CRISPR-sciATAC will be used to produce similar atlases in other biological systems and disease contexts."

Researchers at University of California San Diego School of Medicine have discovered one way in which SARS-CoV-2, the coronavirus that causes COVID-19, hijacks human cell machinery to blunt the immune response, allowing it to establish infection, replicate and cause disease.

In short, the virus' genome gets tagged with a special marker by a human enzyme that tells the immune system to stand down, while at the same time ramping up production of the surface proteins that SARS-CoV-2 uses as a "doorknob" to enter cells.

The study, published April 22, 2021 in Cell Reports, helps lay the groundwork for new anti-viral immunotherapies -- treatments that work by boosting a patient's immune system, rather than directly killing the virus.

"It's very smart of this virus to use host machinery to simultaneously go into stealth mode and get inside more cells," said Tariq Rana, PhD, professor and chief of the Division of Genetics in the Department of Pediatrics at UC San Diego School of Medicine and Moores Cancer Center. "The more we know about how the virus establishes itself in the body, the better equipped we are to disrupt it."

In human cells, genes (DNA) are transcribed into RNA, which is then translated into proteins, the molecules that make up the majority of cells. But it's not always so straightforward. Cells can chemically modify RNA to influence protein production. One of these modifications is the addition of methyl groups to adenosine, one of the building blocks that make up RNA. Known as N6-methyladenosine (m6A), this modification is common in humans and other organisms, including viruses.

In contrast to humans, the entire genomes of some viruses, including SARS-CoV-2, are made up of RNA instead of DNA. And rather than carry around the machinery to translate that into proteins, the coronavirus gets human cells to do the work.

Rana and his team previously discovered that m6A plays an important role in HIV and Zika virus infections. In their latest study, the researchers discovered that the human enzyme METTL3 adds methyl groups to introduce m6A in SARS-CoV-2's RNA. That modification prevents the virus' RNA from triggering inflammatory molecules known as cytokines. To the team's surprise, METTL3's activity also led to increased expression of pro-viral genes -- those that encode proteins needed for SARS-CoV-2 replication and survival, such as ACE2, the cell surface receptor that the virus uses to enter human cells.

"It remains to be seen why our cells help the virus out like this," Rana said.

When the team removed METTL3 from cells in the laboratory, using gene silencing or other methods, they saw the reverse -- a pro-inflammatory molecule known as RIG1 binds the viral RNA, more inflammatory cytokines were produced, and pro-viral genes were inhibited. Ultimately, inhibiting METTL3 suppressed viral replication.

To see how this mechanism plays out in the real world, the team compared post-mortem lung samples from COVID-19 patients and healthy lung biopsies. In patients who had died from severe COVID-19, the team found, METTL3 expression was lower and inflammatory genes were elevated. That makes sense in later stages of COVID-19, Rana said, because cytokine storm -- the excessive activation of the patient's own immune system -- is known to worsen the disease.

"It's like there are two phases of the infection -- in the first, the virus needs METTL3 to help it evade the immune response," he said, "but in the second phase, once the virus is replicating like crazy, it's better to downregulate METTL3."

Rana's team is now validating their findings in animal models, and developing METTL3 inhibitors to test as potential experimental therapies for COVID-19.

"We hope that by manipulating m6A levels in the virus, we might be able to time the innate immune response in a way that benefits patients with COVID19, especially for the mild or moderate patients who haven't developed cytokine storm," Rana said. "The challenge is that cells have many other enzymes like METTL3, known as methyltransferases, so inhibiting it would need to be done very specifically, at a specific time."

The burden of student loans in the U.S. continues to grow unabatedly, currently accounting for a total of $1.7 trillion in household debt among nearly 45 million borrowers. "The introduction of income-based repayment over the past decade has made student loans rather complicated products," Paolo Guasoni of Dublin City University said. As borrowers navigate this complex process, they face long-term consequences; people with student debt are less likely to own homes or become entrepreneurs, and generally postpone their enrollment in graduate or professional studies. Though legislative reform is necessary to combat this problem on a grand scale, individual borrowers can take steps to repay their loans with minimal long-term costs.

In a paper that published in April in the SIAM Journal on Financial Mathematics, Guasoni--along with Yu-Jui Huang and Saeed Khalili (both of the University of Colorado, Boulder)--developed a strategy for minimizing the overall cost of repaying student loans. "In the literature, we found mostly empirical studies discussing what borrowers are doing," Huang said. "But what we wanted to know was rather, how should a borrower repay to minimize debt burden?"

Students become responsible for repaying their loans a few months after they graduate or unenroll, and must contend with the loan growing at a national fixed interest rate. One option for borrowers is to repay their balances in full by a fixed maturity -- the date at which a loan's final payment is due. Another is to enroll in an income-based scheme, in which monthly payments are only due if the borrower has an income above a certain subsistence threshold. If payments are required, they are proportional to the amount the borrower makes above that threshold. After roughly 20 to 25 years, any remaining balance is forgiven but taxed as ordinary income. "The tension is between postponing payments until forgiveness and letting interest swell the loan balance over time," Guasoni said. The tax cost of delaying payments increases exponentially with longer timeframes until forgiveness, potentially offsetting the supposed savings.

The intuitive approach for many borrowers may be to pay off small loans as quickly as possible, since even minimum payments would extinguish the balance by the end of its term, making forgiveness irrelevant. Similarly, one may wish to minimize the payments for a large loan through an income-based scheme, especially if the loan will be forgiven in a few years anyway. However, the situation is not always as simple as it seems. "The counterintuitive part is that, if your loan is large and forgiveness is far away, it may be better to maximize payments over the first few years to keep the loan balance from exploding," Huang said. "Then you can switch to income-based repayment and take advantage of forgiveness."

To investigate what is truly the optimal way to pay back a student loan, the authors created a mathematical model of a borrower who took out a federal student loan--the most common type of student loan--with a constant interest rate. The model assumes that the borrower is able to repay the loan under its original term and even possibly make additional payments; otherwise, they would have no choice but to enroll in an income-based scheme. Quickly paying off the loan leads to lower costs from compounding interest. However, the borrower's motivation to do so is contradicted by the possibility of the remaining balance being forgiven and taxed in the future, which encourages them to delay payment until the forgiveness date.

The mathematical model revealed several possible approaches for a borrower who wishes to minimize the overall cost of their loan. "The optimal strategy is to either (i) repay the loan as quickly as possible [if the initial balance is sufficiently low], or (ii) maximize payments up to a critical horizon (possibly now) and then minimize them through income-based repayment," Guasoni said. The critical horizon occurs when the benefits of forgiveness begin to outweigh the compounding costs of interest on the loan balance. For large loans with a high interest rate--which are common for professional degrees--the savings from the strategy of high initial payments followed by enrollment in an income-based scheme can be substantial, for those that are able to afford such a plan.

The authors provided an example of a dental school graduate with a balance of $300,000 in Direct PLUS loans that carry an interest rate of 7.08 percent (according to the American Dental Education Association, 83 percent of dental school graduates have student loan debt, with an average balance of $292,169). This graduate has a starting salary of $100,000 that will grow four percent annually, and is able to repay at most 30 percent of the income that they make above the subsistence level. If they kept up such maximal payments, they would repay the loan in less than 20 years with a total cost of $512,000.

The example graduate could also immediately enroll in income-based repayment, paying only 10 percent of the income that they make above subsistence. After 25 years, their balance would equal $1,053,000 due to compounding interest. This balance would be forgiven and taxed as income at a 40 percent rate, yielding a total cost of $524,000. Alternatively, the graduate could use the authors' suggested strategy and repay 30 percent of their income above subsistence for around nine years, then switch to the income-based repayment scheme. The remaining balance to be forgiven after 25 years would then be $462,000, leading to a total cost from payments and tax of $490,000 -- the lowest of all the strategies. The reduction in the balance through multiple years of high payments curbs the balance's ensuing growth during the period of minimum payments.

Future research could further explore the more complicated factors of student debt repayment. The authors' model is deterministic -- it does not account for the fact that the interest rates could potentially change in the future. However, interest rates can increase or decrease, which may compel borrowers to refinance or delay payments. Further work is necessary to determine the influence of such changes on optimal debt repayment.

This research illuminated the way in which borrowers' choices in their loan repayments can have a sizable impact on overall costs, especially given compounding interest. "If you have student loans, you should consider your specific options carefully and see what the total cost would be under different strategies," Guasoni said. Huang agreed, noting that their proposed strategy may be especially beneficial for the large loans that are often held by law and dental school graduates. "Each loan is slightly different," he said. "Our model does not capture every possible detail, but it helps to focus the attention on two possibilities: quickest full repayment or enrollment in an income-based scheme, possibly after a period of high payments." A careful, mathematical consideration of the approach to loan repayment can help borrowers make decisions that will benefit them in the years to come.

Source article: Guasoni, P., Huang, Y.-J., & Khalili, S. (2021). American student loans: Repayment and valuation. SIAM J. Finan. Math., 12(2), SC-16-SC-30.

Hydrogen as a clean, renewable alternative to fossil fuels is part of a sustainable-energy future, and very much already here. However, lingering concerns about flammability have limited widespread use of hydrogen as a power source for electric vehicles. Previous advances have minimized the risk, but new research from the University of Georgia now puts that risk in the rearview mirror.

Hydrogen vehicles can refuel much more quickly and go farther without refueling than today's electric vehicles, which use battery power. But one of the final hurdles to hydrogen power is securing a safe method for detecting hydrogen leaks.

A new study published in Nature Communications documents an inexpensive, spark-free, optical-based hydrogen sensor that is more sensitive -- and faster -- than previous models.

"Right now, most commercial hydrogen sensors detect the change of an electronic signal in active materials upon interaction with hydrogen gas, which can potentially induce hydrogen gas ignition by electrical sparking," said Tho Nguyen, associate professor of physics in the Franklin College of Arts and Sciences, a co-principal investigator on the project. "Our spark-free optical-based hydrogen sensors detect the presence of hydrogen without electronics, making the process much safer."

Not just for cars

Hydrogen power has many more applications than powering electric vehicles, and flammability mitigating technologies are critical. Robust sensors for hydrogen leak detection and concentration control are important in all stages of the hydrogen-based economy, including production, distribution, storage and utilization in petroleum processing and production, fertilizer, metallurgical applications, electronics, environmental sciences, and in health and safety-related fields.

The three key problems associated with hydrogen sensors are response time, sensitivity, and cost. Current mainstream technology for H2 optical sensors requires an expensive monochromator to record a spectrum, followed by analyzing a spectral shift comparison.

"With our intensity-based optical nano sensors, we go from detection of hydrogen at around 100 parts-per-million to 2 parts-per-million, at a cost of a few dollars for a sensing chip," Tho said. "Our response time of .8 seconds is 20% faster than the best available optical device reported in the literature right now."

How it works

The new optical device relies on the nanofabrication of a nanosphere template covered with a Palladium Cobalt alloy layer. Any hydrogen present is quickly absorbed, then detected by an LED. A silicon detector records the intensity of the light transmitted.

"All metals tend to absorb hydrogen, but by finding the suitable elements with a right balance in the alloy and engineering the nanostructure to amplify subtle changes in light transmission after hydrogen absorption, we were able to set a new benchmark for how fast and sensitive these sensors can be," said George Larsen, a senior scientist at Savannah River National Laboratory and co-principal investigator on the project. "All while keeping the sensor platform as simple as possible."

Study Take-Aways

Unprecedented novel discoveries have implications for characterizing biodiversity for all life, conservation, and human health and disease.

o This finding provides novel avenues of research to increase immune defenses, particularly relevant for emerging infectious diseases, such as the current COVID-19 pandemic.

The flagship paper presented whole genome sequence analyses of 16 vertebrate species to illustrate high quality, near error free, near complete, low cost reference genome assemblies.

o Though near 400 species have been sequenced at some level, the quality today reflects a quantum leap in precision sequence details and discovery.

FORT LAUDERDALE/DAVIE, Fla. - Two decades ago, the full genome sequence of humankind was released. It was funded by international government and philanthropic sources at a cost of billions of dollars.

Fast forward to 2008 and, driven by the need for better genome understanding and the precipitous drop in sequencing costs, the Genome 10K Community of Scientists (G10K) was established to promote and ensure the genome analysis of 10,000 species of vertebrates. The G10K-sponsored Vertebrate Genomes Project embraced dramatic improvements in sequencing bio-technologies in the last few years to expand production of high-quality reference genome assemblies for all ~70,000 living vertebrates in the coming years.

Today, the G10K sponsored Vertebrate Genomes Project (VGP) announces their flagship study and associated publications focused on genome assembly quality and standardization for the field of genomics. This study includes 16 diploid high-quality, near error-free, and near complete vertebrate reference genome assemblies for species across all taxa with backbones (i.e., mammals, amphibians, birds, reptiles, and fishes) from five years of piloting the first phase of the VGP project.

In a special issue of Nature, along with simultaneous companion papers published in other scientific journals, the VGP details numerous technological improvements based on these 16 genome assemblies. In this new study, the VGP demonstrates the feasibility of setting and achieving high-quality reference genome quality metrics using state-of-the-art automated approach of combining long-read and long-range chromosome scaffolding approaches with novel algorithms that put the pieces of the genome assembly puzzle together. To date, the current VGP pipelines have led to the submission of 129 diploid assemblies representing the most complete and accurate versions of those species to date, and is on the path to generating thousands of genome assemblies, demonstrating feasibility in not only quality standardization but also scale.

Some of the animals that were part of this study included, but were not limited to:

Mammals: Pale spear-nosed bat, Egyptian fruit bat; Canada lynx; vaquita; platypus;

Birds: Zebra finch; kakapo; Anna's hummingbird;

Reptile: Goode's thornscrub tortoise;

Fish: Zig-zag eel; climbing perch; blunt-snouted clingfish.

"When we first started the G10K idea, we gathered a small handful of diverse field zoologists together with genome-centric computer scientists, pledging to work together to develop genome sequence data for thousands of the world's vertebrates," said Stephen O'Brien, Ph.D., a professor and research scientist at Nova Southeastern University's (NSU) Halmos College of Arts and Sciences. "We wanted to offer a gift for the next generation of genome scientists. Today the dream of genome empowerment of so many living species took a giant leap forward."

O'Brien is the co-founder of the Genome 10K Consortium, the Chief Scientific Officer at the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia and is a member of the National Academy of Sciences.

The G10K-VGP's approach combines assembly pipelines with manual curation to fix misassemblies, major gaps, and other errors, which informs the iterative development of better algorithms. For example, the VGP helped reveal high levels of false gene duplications, losses or gains, due mostly to algorithms not properly separating maternal and paternal chromosomes. One solution includes a trio binning approach of using DNA from the parents to separate out the paternal and maternal sequences in the offspring. For cases where parental data is unavailable, another solution developed by the VGP and collaborators is an algorithm called FALCON-Phase that reduces the computational complexity of phasing maternal and paternal DNA sequences at chromosome scale.

"When I was asked to take on leadership of the G10K-VGP in 2015, I emphasized the need to work with technology partners and genome assembly experts on approaches that produce the highest quality data possible, as it was taking months per gene for my students and postdocs to correct gene structure and sequences for their experiments, which was causing errors in our biological studies", said Erich Jarvis, lead of the VGP sequencing hub at The Rockefeller University, Chair of the G10K and a Howard Hughes Medical Institute Investigator. "For me this was not only a practical mission, but a moral imperative."

Kerstin Howe, lead of the curation team at the Wellcome Sanger Institute in the UK, said: "Our new approach to produce structurally validated, chromosome-level genome assemblies at scale will be the foundation of ground-breaking insights in comparative and evolutionary genomics."

"It truly was a challenge to design a pipeline applicable to highly diverged genomes - our largest genome, 5GB in size, broke almost every tool commonly used in assembly processes," said Arang Rhie, from the National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, who is the first author of the flagship paper. "The extreme level of heterozygosity or repeat contents posed a big challenge. This is just the beginning; we are continuously improving our pipeline in response to new technology improvements."

Adam Phillippy, chair of the VGP genome assembly and informatics working group of more than 100 members and head of the Genome Informatics Section of the National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA, added: "Completing the first vertebrate reference genome, human, took over 10 years and $3 billion dollars. Thanks to continued research and investment in DNA sequencing technology over the past 20 years, we can now repeat this amazing feat multiple times per day for just a few thousand dollars per genome."

Specific to conservation and in collaboration with the Māori in New Zealand and officials in Mexico, genomic analyses of the kākāp?, a flightless parrot, and the vaquita, a small porpoise and the most endangered marine mammal, respectively, suggest evolutionary and demographic histories of purging harmful mutations in the wild. The implication of these long-term small population sizes at genetic equilibrium gives hope for these species' survival.

Richard Durbin, a Professor at the University of Cambridge and lead of the VGP sequencing hub at the Wellcome Sanger Institute in the UK, said: "These studies mark the start of a new era of genome sequencing that will accelerate over the next decade to enable genomic applications across the whole tree of life, changing our scientific interactions with the living world."

The G10K-VGP consortia involves hundreds of international scientists working together from more than 50 institutions in 12 different countries since the VGP was initiated in 2016 and is exemplary in its scientific cooperation, extensive infrastructure, and collaborative leadership. Additionally, as the first large-scale eukaryotic genomes project to produce reference genome assemblies meeting a specific minimum quality standard, the VGP has thus become a working model for other large consortia, including the Bat 1K, Global Invertebrate Genome Aliance-GIGA, Pan Human Genome Project, Earth BioGenome Project, Darwin Tree of Life, and European Reference Genome Atlas, among others.

"The VGP project is at the vanguard of the creation of a genomic catalog in analogy with Linnaeus' classification of life, said Gene Myers, lead of the VGP sequencing hub at the Max Planck Institute in Dresden, Germany. "I and my colleagues in Dresden are excited to be contributing superb genome reconstructions with the funding of the Max-Planck Society of Germany."

As a next step, the VGP will continue to work collaboratively across the globe and with other consortia to complete Phase 1 of the project, approximately one representative species per 260 vertebrate orders separated by a minimum of 50 million years from a common ancestor with other species in Phase 1. The VGP intends to create comparative genomic resources with these 260 species, including reference-free whole genome alignments, that will provide a means to understand the detailed evolutionary history of these species and create consistent gene annotations. Genome data are primarily generated at three sequencing hubs that have invested in the mission of the VGP including The Rockefeller University's Vertebrate Genome Lab, New York, USA; Wellcome Sanger Institute, UK; and Max Planck Institute, Germany.

Phase 2 will focus on representative species from each vertebrate family and is currently in the progress of sample identification and fundraising. The VGP has an open-door policy and welcomes others to join its efforts, ranging from fundraising and sample collection to generating genome assemblies or including their own genome assemblies that meet the VGP metrics as part of our overall mission.

The VGP collaborated with and tested many protocols from genome sequencing companies, some of whose scientists are also co-authors of the flagship study, including from Pacific Biosciences, Oxford Nanopore Technologies, Illumina, Arima Genomics, Phase Genomics, and Dovetail Genomics. The VGP also collaborated with DNAnexus and Amazon to generate a publicly available VGP assembly pipeline and host the genomic data in the Genome Ark database. The genomes, annotations and alignments are also available in international public genome browsing and analyses databases, including the National Center for Biotechnology Information Genome Data Viewer, Ensembl genome browser, and UC Santa Cruz Genomics Institute Genome Browser. All data are open source and publicly available under the G10K data use policies.

Other novel biological discoveries from the 16 genomes in the flagship paper, and 25 genomes total from over 20 papers in this first wave of publications include:

Corrections of false gene or chromosome losses, where previous assemblies missed between 30% to 50% of GC-rich protein-coding gene regulatory regions, which were considered to belong to the 'dark matter' of the genome;

Newly identified chromosomes in the zebra finch and platypus;

Complete and error free mitochondrial genomes for most species, some generated in single molecule sequences without the need for assembly;

Wild sex chromosome evolution in monotreme mammals and birds;

Genetic variations between humans and marmosets that have implications for marmosets as an emerging non-human primate model system for biomedical research;

Lineage-specific changes shaping the evolution of bird and mammal genomes: duck, emu and platypus and echidna; and

Proposal for a universal evolution-based revised nomenclature for the oxytocin and vasotocin ligand and receptor families.

As state and local policymakers and politicians made the decision to enact stay-at-home orders last March in response to the coronavirus pandemic, a recent study found that more stringent public health measures put in place directly correlated with lower virus case numbers during the first two months of the pandemic.

The study, "More Stringent Measures Against Covid-19 Are Associated With Lower Cases and Deaths in Florida and Miami-Dade," was recently published in the American Journal of Emergency Medicine.

Utilizing The New York Times' GitHub repository of cases and deaths and the COVID-19 Government Response Stringency Index developed by Oxford University's Blavatnik School of Government for the period between March 11, 2020 and March 26, 2021, the researchers found that mitigation efforts to reduce the spread of infection, hospitalizations, and death--including the closure of schools and businesses, the adoption of social distancing measures, the use of facial coverings, and stay-at-home orders--were effective in keeping the overall COVID-19 case count and deaths lower than they would not have been had these efforts not been implemented.

"As we analyzed the data, it was striking to us how the adoption of more stringent policy measures aimed at reducing the spread of COVID-19 infection largely coincided with fewer cases and deaths," said Alex R. Piquero, chair and professor in the Department of Sociology and Arts & Sciences Distinguished Scholar at the University of Miami and corresponding author on the study.

Once the stringencies were loosened, however, researchers noted an initial surge in transmission in the period between the Memorial Day and Independence Day holidays. As statewide stringencies reached their lowest enforcement during October 2020, a second surge in coronavirus cases was seen immediately after.

Any changes in the stringency index were predictive of changes in the incidence of coronavirus cases 10 to 17 days later, the researchers noted.

The image of rows of chairs and desks facing a teacher at a blackboard has been a reality for decades. However, research reveals that this way of organizing the classroom furniture in schools is not the best way for favouring the learning process. Especially if the needs of 21st-century students are taken into account, who, according to the OECD, require a social environment that fosters autonomy, flexibility, decision-making capacity and the connection of knowledge by individual students or through teamwork.

It is also the opinion of 6 out of every 10 teachers that changing the design of the classroom is key to improving learning. This was the result of a recent study conducted by researchers of the Universitat Oberta de Catalunya (UOC), Universitat Autònoma de Barcelona (UAB), Universitat de Barcelona (UB), Universitat de Vic (UVic) and Universidad Simón Bolívar (USB), in which 847 preschool, primary and secondary school teachers from 40 schools participated. "We assume that's what the spaces should be like without giving it much thought or without connecting what we're innovating in terms of methodology with the place in which we're going to put that into practice," said Guillermo Bautista, member of the Smart Classroom Project research group of the UOC and principal investigator in this study. That's why we need to make the Smart Learning Space a reality: "a space that meets any learning need or proposal, that is flexible and not zoned, in which physical and psychological well-being are prioritized as the foundations upon which the learning activity can take place, in which the pupils play a proactive and autonomous role," said Bautista.

Several studies have already acknowledged the benefits of a suitably-designed classroom. This was one of the reasons why the Consorci d'Educació de Barcelona started replacing the furniture in 487 classrooms a few weeks ago, whilst also reorganizing the spaces to obtain motivating environments that encourage discovery. And, as the authors of the UOC-led study point out, it's that the skills and learning needs of today's pupils not only oblige us to rethink our teaching practices or the inclusion of digital resources, they also require changes in the learning spaces in general.

Guillermo Bautista demonstrates this with an example: as he explains, science tells us that we learn better and more by collaborating, and therefore the space must favour this collaboration and interaction, also taking into account what research tells us about collaborative learning. If we organize the activity with groups of four students based on a challenge or a project, it would be logical that the space should be suitable to enable the group to collaborate and also enable a certain amount of autonomy for using the resources it needs, for moving, looking around, experimenting, and self-organizing, etc. "This means that not all of the groups will be doing the same thing at the same time, and the same resources will not be necessary for everyone. The activity in the classroom is diverse and the space must constantly respond to this organizational diversity of use, resources, movements," he explained.

However, the strong assumption upheld for decades that the classroom is as it is, has resulted in us proposing few changes. And when these are finally being proposed, the direction of these changes is not easy to decide upon, "and that is why our research is necessary, to help establish criteria so that the space is changed with guarantees," he said.

Changes in the design of secondary school classrooms also

Currently, most teachers negatively rate the organization of the environment in their classroom. This is one of the findings of the study, whereby low or moderate scores were obtained regarding the suitability of current classrooms to serve as comprehensive learning spaces. But differences exist between the different levels of education, as the design of preschool and primary education learning spaces is generally more flexible, collaborative and personal, affirm the authors of the study, who point to a possible reason for this scenario. "It is precisely in the infant and primary stages where teaching trends such as those applied since the early 20th century (in which the spaces, their layout, furniture, etc. were already linked to clear educational meanings) have been most present and usually more visible," said Angelina Sánchez-Martí, researcher of the Smart Classroom Project and Serra Húnter professor at the Universitat Autònoma de Barcelona.

On the other hand, the traditional layout of the spaces is much more established among secondary school centres and teachers. That's why the authors of the study positively value the fact that during the study it was confirmed that there are teachers and centres from this stage of education who are aware that their spaces do not correspond with the methodologies that they want to implement. "The Smart Spaces that we have implemented as part of the research are co-designed, applying a thoroughness, rigorousness, and seeking to meet the highest objectives and results for learning proposed by each centre. And these spaces are needed in all of the stages," said Bautista.

Another result to highlight is that the teachers are especially critical when it comes to appraising the integration of technology in the classrooms. But in the opinion of the authors of the study, this data is not surprising as "it is precisely the new technologies that are threatening the traditional times and spaces, and therefore demand great flexibility and a constant adaptation to change, as well as a reformulation of the learning spaces", said Sánchez-Martí. She added that the possibilities that technological integration offers in terms of creating new ways to relate and learn "completely clashes with the very standardized design derived from the idea that schools must be based on classrooms per se, when this does not necessarily have to be the case."

ROCHESTER, Minn. -- The Mayo Clinic data scientists who developed highly accurate computer modeling to predict trends for COVID-19 cases nationwide have new research that shows how important a high rate of vaccination is to reducing case numbers and controlling the pandemic.

Vaccination is making a striking difference in Minnesota and keeping the current level of positive cases from becoming an emergency that overwhelms ICUs and leads to more illness and death, according to a study published in Mayo Clinic Proceedings. The study, entitled "Quantifying the Importance of COVID-19 Vaccination to Our Future Outlook," outlines how Mayo's COVID-19 predictive modeling can assess future trends based on the pace of vaccination, and how vaccination trends are crucial to the future course of the pandemic.

The Mayo researchers estimate that a peak of more than 800 patients would be in hospital ICUs in Minnesota this spring if no vaccines had been developed. The projections take into account new variants of the SARS-CoV-2 virus as well as current public health measures and masking standards.

The predicted ICU census levels would be more than double the number of Minnesota COVID-19 patients who were hospitalized in ICUs on Dec. 1, at the height of the most recent surge last year.

"It is difficult to untangle how much of this elevated rate of spread right now is due to new variants as opposed to changes in social behavior," the authors say, but "regardless of the reason, the absence of vaccinations in the current environment would have been likely to result in by far the largest surge to date."

If Minnesota had achieved vaccination of 75% of the population by early April, the study estimates that the 7-day average of cases per 100,000 residents, the number of COVID-19 patients hospitalized and the number in ICUs would plummet by early July. "According to the model, this level of vaccination would completely suppress the growth (even in the face of the recent elevated spread rate) and immediately drive cases and hospitalizations down to very low levels," the authors say.

The Mayo Clinic study was led by Curtis Storlie, Ph.D., and Sean Dowdy, M.D., whose team developed the computer model for forecasting COVID-19's impact on hospital usage that has helped guide Mayo's response to the pandemic. Mayo Clinic's predictive modeling also has been shared with Minnesota public health leadership to help inform critical decisions over the past year.

Mayo Clinic's forecasting of COVID-19 trends nationally is available online at the Mayo Clinic COVID-19 Resource Center. The Coronavirus Map tracking tool has county-by-county information on COVID-19 cases and trends nationwide.

When the pandemic emerged last year, Mayo Clinic data scientists developed predictive modeling to assess when and where COVID-19 hot spots would occur. The model accurately predicted the timing and magnitude of COVID-19 case and hospitalization surges, which enabled Mayo Clinic to prepare and assure it could provide the best care while keeping patients and staff safe.

The United Kingdom government plans to implement mass scale population testing for SARS-CoV-2 infection using Lateral Flow Devices (LFDs), yet the devices' sensitivity is unknown. A study published in the open access journal PLOS Biology by Alan McNally at University of Birmingham, UK, and colleagues suggests while LFDs are highly effective in identifying SARS-CoV-2 in individuals with high quantities of viral RNA present on the test swab, they are inaccurate at diagnosing infections in individuals with lower viral loads.

LFDs are increasingly used to increase testing capacity and screen asymptomatic populations for SARS-CoV-2 infection in mass surveillance programs, yet there are few data indicating the performance of these devices. To determine the sensitivity of LFDs, researchers tested the nasopharyngeal swabs of 8,000 university students using the devices. Next, they validated all positive samples and randomly selected 720 negative samples out of 7,187 negatives for validation.

Using reverse transcription PCR tests, the authors estimated the true COVID-19 prevalence rate and compared it to LFD test results. The researchers were able to determine the LFDs' accuracy rate for different levels of virus, finding that while the test was able to detect infections in samples with higher levels of viral RNA at a 100% accuracy rate, the test's performance dropped significantly in samples with lower viral loads.

The results suggest that for individuals in the very early or very late stages of infection, LFDs are likely to produce a false negative result, pointing to the need for frequent testing. A limitation of the study was that emergent variants and their potential effects on LFDs' sensitivity with asymptomatic cases were not considered within the scope of the study. Independent research suggests that both the UK and South African variants can be reliably detected, but further studies are needed to determine whether the LFDs can detect infections at the same viral loads as with the SARS-CoV-2 strain examined in the current research.

According to the authors, "When used regularly, LFDs can be a highly effective tool in reducing overall community burden. We would strongly recommend that Lateral Flow Device testing is used to screen people at a very regular frequency, and that a negative result should not be used to determine that someone is free from SARS-CoV-2 infection. As such LFDs should not be used as a test-to-do"

Forget diamonds--plastic is forever. It takes decades, or even centuries, for plastic to break down, and nearly every piece of plastic ever made still exists in some form today. We've known for a while that big pieces of plastic can harm wildlife--think of seabirds stuck in plastic six-pack rings--but in more recent years, scientists have discovered microscopic bits of plastic in the water, soil, and even the atmosphere. To learn how these microplastics have built up over the past century, researchers examined the guts of freshwater fish preserved in museum collections; they found that fish have been swallowing microplastics since the 1950s and that the concentration of microplastics in their guts has increased over time.

"For the last 10 or 15 years it's kind of been in the public consciousness that there's a problem with plastic in the water. But really, organisms have probably been exposed to plastic litter since plastic was invented, and we don't know what that historical context looks like," says Tim Hoellein, an associate professor of biology at Loyola University Chicago and the corresponding author of a new study in Ecological Applications. "Looking at museum specimens is essentially a way we can go back in time."

Caleb McMahan, an ichthyologist at the Field Museum, cares for some two million fish specimens, most of which are preserved in alcohol and stored in jars in the museum's underground Collections Resource Center. These specimens are more than just dead fish, though--they're a snapshot of life on Earth. "We can never go back to that time period, in that place," says McMahan, a co-author of the paper.

Hoellein and his graduate student Loren Hou were interested in examining the buildup of microplastics in freshwater fish from the Chicagoland region. They reached out to McMahan, who helped identify four common fish species that the museum had chronological records of dating back to 1900: largemouth bass, channel catfish, sand shiners, and round gobies. Specimens from the Illinois Natural History Survey and University of Tennessee also filled in sampling gaps.

"We would take these jars full of fish and find specimens that were sort of average, not the biggest or the smallest, and then we used scalpels and tweezers to dissect out the digestive tracts," says Hou, the paper's lead author. "We tried to get at least five specimens per decade."

To actually find the plastic in the fishes' guts, Hou treated the digestive tracts with hydrogen peroxide. "It bubbles and fizzes and breaks up all the organic matter, but plastic is resistant to the process," she explains.

The plastic left behind is too tiny to see with the naked eye, though: "It just looks like a yellow stain, you don't see it until you put it under the microscope," says Hou. Under the magnification, though, it's easier to identify. "We look at the shape of these little pieces. If the edges are frayed, it's often organic material, but if it's really smooth, then it's most likely microplastic." To confirm the identity of these microplastics and determine where they came from, Hou and Hoellein worked with collaborators at the University of Toronto to examine the samples using Raman spectroscopy, a technique that uses light to analyze the chemical signature of a sample.

The researchers found that the amount of microplastics present in the fishes' guts rose dramatically over time as more plastic was manufactured and built up in the ecosystem. There were no plastic particles before mid-century, but when plastic manufacturing was industrialized in the 1950s, the concentrations skyrocketed.

"We found that the load of microplastics in the guts of these fishes have basically gone up with the levels of plastic production," says McMahan. "It's the same pattern of what they're finding in marine sediments, it follows the general trend that plastic is everywhere."

The analysis of the microplastics revealed an insidious form of pollution: fabrics. "Microplastics can come from larger objects being fragmented, but they're often from clothing," says Hou--whenever you wash a pair of leggings or a polyester shirt, tiny little threads break off and get flushed into the water supply.

"It's plastic on your back, and that's just not the way that we've been thinking about it," says Hoellein. "So even just thinking about it is a step forward in addressing our purchases and our responsibility."

It's not clear how ingesting these microplastics affected the fish in this study, but it's probably not great. "When you look at the effects of microplastic ingestion, especially long term effects, for organisms such as fish, it causes digestive tract changes, and it also causes increased stress in these organisms," says Hou.

While the findings are stark--McMahan described one of the paper's graphs showing the sharp rise in microplastics as "alarming"--the researchers hope it will serve as a wake-up call. "The entire purpose of our work is to contribute to solutions," says Hoellein. "We have some evidence that public education and policies can change our relationship to plastic. It's not just bad news, there's an application that I think should give everyone a collective reason for hope."

The researchers say the study also highlights the importance of natural history collections in museums. "Loren and I both love the Field Museum but don't always think about it in terms of its day-to-day scientific operations," says Hoellein. "It's an incredible resource of the natural world, not just as it exists now but as it existed in the past. It's fun for me to think of the museum collection sort of like the voice of those long dead organisms that are still telling us something about the state of the world today."

"You can't do this kind of work without these collections," says McMahan. "We need older specimens, we need the recent ones, and we're going to need what we collect in the next 100 years."

Boulder, Colo., USA: Thirty-one new articles were published online ahead of
print for Geology in April. Topics include shocked zircon from the
Chicxulub impact crater; the Holocene Sonoran Desert; the architecture of
the Congo Basin; the southern Death Valley fault; missing water from the
Qiangtang Basin; sulfide inclusions in diamonds; how Himalayan collision
stems from subduction; ghost dune hollows; and the history of the Larsen C Ice Shelf. These Geology articles are online at

https://geology.geoscienceworld.org/content/early/recent

.

Nonlinear fault damage zone scaling revealed through analog modeling

Sylvain Mayolle; Roger Soliva; Stéphane Dominguez; Christopher Wibberley;
Yannick Caniven

Abstract:
Fault damage zones strongly influence fluid flow and seismogenic behavior
of faults and are thought to scale linearly with fault displacement until
reaching a threshold thickness. Using analog modeling with different
frictional layer thicknesses, we investigate damage zone dynamic evolution
during normal fault growth. We show that experimental damage zone growth
with displacement is not linear but progressively tends toward a threshold
thickness, being larger in the thicker models. This threshold thickness
increases significantly at fault segment relay zones. As the thickness
threshold is approached, the failure mode progressively transitions from
dilational shear to isochoric shear. This process affects the whole layer
thickness and develops as a consequence of fault segment linkage as
inferred in nature when the fault matures. These findings suggest that
fault damage zone widths are limited both by different scales of mechanical
unit thickness and the evolution of failure modes, ultimately controlled in
nature by lithology and deformation conditions.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48760.1/596503/Nonlinear-fault-damage-zone-scaling-revealed

History of the Larsen C Ice Shelf

reconstructed from sub–ice shelf and offshore sediments

J.A. Smith; C.-D. Hillenbrand; C. Subt; B.E. Rosenheim; T. Frederichs ...

Abstract:
Because ice shelves respond to climatic forcing over a range of time
scales, from years to millennia, an understanding of their long-term
history is critically needed for predicting their future evolution. We
present the first detailed reconstruction of the Larsen C Ice Shelf (LCIS),
eastern Antarctic Peninsula (AP), based on data from sediment cores
recovered from below and in front of the ice shelf. Sedimentologic and
chronologic information reveals that the grounding line (GL) of an expanded
AP ice sheet had started its retreat from the midshelf prior to 17.7 ± 0.53
calibrated (cal.) kyr B.P., with the calving line following ~6 k.y. later.
The GL had reached the inner shelf as early as 9.83 ± 0.85 cal. kyr B.P.
Since ca. 7.3 ka, the ice shelf has undergone two phases of retreat but
without collapse, indicating that the climatic limit of LCIS stability was
not breached during the Holocene. Future collapse of the LCIS would
therefore confirm that the magnitudes of both ice loss along the eastern AP
and underlying climatic forcing are unprecedented during the past 11.5 k.y.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48503.1/596504/History-of-the-Larsen-C-Ice-Shelf-reconstructed

Confirmation of slow Ti diffusion in quartz by diffusion couple
experiments and evidence from natural samples

Andreas Audétat; Nobuyoshi Miyajima; Dorothea Wiesner; Jean-Nicolas Audinot

Abstract:
Titanium diffusion profiles in natural quartz crystals have become an
increasingly popular tool to reconstruct the time scales of various
magmatic, metamorphic, and hydrothermal processes. However, the original
calibration of Ti diffusion rates in quartz has recently been challenged,
and diffusivities were found to be about three orders of magnitude lower.
We performed annealing experiments on crystal-crystal diffusion couples
consisting of Ti-free synthetic quartz seeds over which Ti-rich quartz
(100–3000 μg/g Ti) was grown hydrothermally. The annealing experiments were
performed at 1000–1600 °C and 0.1 MPa to 2.0 GPa, and they lasted for 3–84
days. The resulting diffusion profiles were mapped by cathodoluminescence
(CL), transmission electron microscope–energy-dispersive X-ray spectroscopy
(TEM-EDXS), and, for the first time, by helium ion microscope–secondary ion
mass spectrometry (HIM-SIMS). Obtained diffusion coefficients range from
values similar to the lower range in previous research to values up to two
orders of magnitude lower. In addition, inversely zoned quartz and sanidine
phenocrysts in a natural rhyolite were studied. Comparison of the diffusion
profiles suggests that at ~735 °C, the Ti diffusivity in quartz is ~1.5 and
3.0 orders of magnitude lower than that of Ba and Sr, respectively, in
sanidine. The combined evidence confirms that Ti diffusion in quartz is
very slow, potentially even slower than proposed earlier. Consequently,
previous time scales derived from Ti diffusion profiles in quartz are
likely orders of magnitude too short, and further experiments are necessary
to fully clarify the issue.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48785.1/596505/Confirmation-of-slow-Ti-diffusion-in-quartz-by

Did accretion of the Caribbean oceanic plateau drive rapid crustal
thickening in the northern Andes?

Sarah W.M. George; Brian K. Horton; Cristian Vallejo; Lily J. Jackson; E.
Gabriela Gutierrez

Abstract:
The onset of orogenic shortening in the northern Andes Mountains coincided
with latest Cretaceous accretion of the Caribbean oceanic plateau. We
present isotopic data (εHf in zircon and εNd) coupled with arc position to
test whether accretion led to abrupt crustal thickening in the northern
Andes of Ecuador and Colombia. A rapid isotopic excursion toward more
evolved crustal compositions was synchronous with ca. 75–70 Ma collision in
Ecuador and preceded a similar deviation in Colombia at ca. 70–55 Ma. The
rapid but diachronous shift to more evolved isotopic signatures is
attributed to progressive northward accretion of the oceanic plateau and
associated thickening of continental crust. We emphasize the effects of
accretion on the magmatic evolution of Cordilleran-type margins, initially
provoking shortening and crustal thickening, and ultimately providing a
substrate for subsequent arcs.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48509.1/596506/Did-accretion-of-the-Caribbean-oceanic-plateau

How Himalayan collision stems from subduction

M. Soret; K.P. Larson; J. Cottle; A. Ali

Abstract:
The mechanisms and processes active during the transition from continental
subduction to continental collision at the plate interface are largely
unknown. Rock records of this transition are scarce, either not exposed or
obliterated during subsequent events. We examine the tectono-metamorphic
history of Barrovian metamorphic rocks from the western Himalayan orogenic
wedge. We demonstrate that these rocks were buried to amphibolite-facies
conditions from ≤47 Ma to 39 ± 1 Ma, synchronously with the formation (46
Ma) and partial exhumation (45–40 Ma) of the ultrahigh-pressure eclogites.
This association indicates that convergence during continental subduction
was accommodated via development of a deep orogenic wedge built through
successive underplating of continental material, including the partially
exhumed eclogites, likely in response to an increase in interplate
coupling. This process resulted in the heating of the subduction interface
(from ~7 to ~20 °C/km) through advective and/or conductive heat transfer.
Rapid cooling of the wedge from 38 Ma, coeval with the formation of a
foreland basin, are interpreted to result from indentation of a promontory
of thick Indian crust.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48803.1/596507/How-Himalayan-collision-stems-from-subduction

Mud in sandy riverbed deposits as a proxy for ancient fine-sediment
supply

N. Wysocki; E. Hajek

Abstract:
The amount of silt and clay available to rivers reflects source-terrain
composition and weathering and can be a primary control on the form and
dynamics of channel networks. Fine sediment also affects the permeability
of buried fluvial reservoirs. Despite this significance, there is currently
a lack of methods for reconstructing how much fine sediment was transported
by ancient rivers. Mud accumulations in sandy river deposits are often
interpreted as indicators of variable flow conditions; however, these
deposits may present an opportunity to constrain how much fine sediment was
transported through ancient rivers. We report results from a series of
experiments designed to evaluate how much clay and silt are preserved in
sandy riverbed deposits under constant and variable discharge conditions.
Our results demonstrate that (1) mud deposits, including drapes and lenses,
form readily under constant, high-discharge conditions, (2) the amount of
fine sediment recovered from bed-material deposits increases as
fine-sediment supply increases, and (3) fine-sediment retention is higher
during bed aggradation than during bypass conditions. These results
indicate that the net retention of clay and silt in sandy riverbed deposits
may be a simple but powerful proxy for comparing the overall amount of fine
sediment supplied to ancient rivers.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48251.1/596508/Mud-in-sandy-riverbed-deposits-as-a-proxy-for

Subduction of the Izanagi-Pacific Ridge–transform intersection at the
northeastern end of the Eurasian plate

Toru Yamasaki; Gen Shimoda; Kenichiro Tani; Jinichiro Maeda; Futoshi
Nanayama

Abstract:
Recent reconstructions of global plate motions suggest that the
Izanagi-Pacific Ridge was subducted along the eastern margin of Eurasia at
ca. 50 Ma. In the Hidaka magmatic zone (HMZ), which was located at the
northeastern end of the Eurasian plate, three magmatic pulses occurred
(46–45, 40–36, and 19–18 Ma). We report whole-rock geochemical and Sr-Nd-Pb
isotopic data for 36 Ma high-Sr/Y (adakitic) rocks from the HMZ and show
that these rocks formed by partial melting of oceanic crust and were
emplaced as near-trench intrusions during ridge subduction. We reevaluate
the nature of plutonic rocks in the HMZ and show that both the 46–45 and
40–36 Ma granitoids have essentially identical geochemical features. The
distribution of plutons and magmatic cessation between 45 and 40 Ma are
best explained by subduction of a ridge-transform intersection with a large
offset of the ridge axis. The boundary between the Eocene granitoids
corresponds to the position of a paleo–transform fault, and adakitic
magmatism was caused by partial melting triggered by slab tearing at an
overlapping spreading center. The paleoridge-transform configuration
coincides with the locations of later large faults and a peridotite body.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48611.1/596509/Subduction-of-the-Izanagi-Pacific-Ridge-transform

Climatically driven instability of marine methane hydrate along a
canyon-incised continental margin

Richard J. Davies; Miguel Ángel Morales Maqueda; Ang Li; Mark Ireland

Abstract:
Establishing how past climate change affected the stability of marine
methane hydrate is important for our understanding of the impact of a
future warmer world. As oceans shallow toward continental margins, the base
of the hydrate stability zone also shallows, and this delineates the
feather edge of marine methane hydrate. It is in these rarely documented
settings that the base of the hydrate stability zone intersects the seabed
and hydrate can crop out where it is close to being unstable and most
susceptible to dissociation due to ocean warming. We show evidence for a
seismically defined outcrop zone intersecting canyons on a canyon-incised
margin offshore of Mauritania. We propose that climatic, and hence ocean,
warming since the Last Glacial Maximum as well as lateral canyon migration,
cutting, and filling caused multiple shifts of the hydrate stability field,
and therefore hydrate instability and likely methane release into the
ocean. This is particularly significant because the outcrop zone is longer
on canyon-incised margins than on less bathymetrically complex submarine
slopes. We propose considerably more hydrate will dissociate in these
settings during future ocean warming, releasing methane into the world’s
oceans.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48638.1/596510/Climatically-driven-instability-of-marine-methane

Enhanced Quaternary exhumation in the Namche Barwa syntaxis, eastern
Himalaya

Rong Yang; Frédéric Herman; Ting Liu; Rabiul Haque Biswas; Maria Giuditta
Fellin ...

Abstract:
The Namche Barwa syntaxis in the eastern Himalaya is rapidly evolving in
terms of its tectonics and topography. Here we constrain the exhumation
history of the Yigong River to the immediate north of the syntaxis across
different time scales using a multidisciplinary approach. Our new
thermochronometric data reveal an acceleration of exhumation rates since 2
Ma in the downstream of the Yigong. Cosmogenic nuclides and
thermoluminescence thermochronometry analyses confirm persistent rapid
exhumation in the lower Yigong over the Quaternary with further increased
exhumation in the last 100 ka. Together with the analysis of the morphology
of the Yigong River profile, we interpret that northward expansion of the
syntaxis together with capture of the Yigong by the Yarlung Tsangpo River
during this expansion is responsible for the exhumation history of the
Yigong River in the Quaternary.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48595.1/596325/Enhanced-Quaternary-exhumation-in-the-Namche-Barwa

Protogenetic sulfide inclusions in diamonds date the diamond formation
event using Re-Os isotopes

M.G. Pamato; D. Novella; D.E. Jacob; B. Oliveira; D.G. Pearson ...

Abstract:
Sulfides are the most abundant inclusions in diamonds and a key tool for
dating diamond formation via Re-Os isotopic analyses. The manner in which
fluids invade the continental lithospheric mantle and the time scale at
which they equilibrate with preexisting (protogenetic) sulfides are poorly
understood yet essential factors to understanding diamond formation and the
validity of isotopic ages. We investigated a suite of sulfide-bearing
diamonds from two Canadian cratons to test the robustness of Re-Os in
sulfide for dating diamond formation. Single-crystal X-ray diffraction
(XRD) allowed determination of the original monosulfide solid-solution
(Mss) composition stable in the mantle, indicating subsolidus conditions of
encapsulation, and providing crystallographic evidence supporting a
protogenetic origin of the inclusions. The results, coupled with a
diffusion model, indicate Re-Os isotope equilibration is sufficiently fast
in sulfide inclusions with typical grain size, at mantle temperatures, for
the system to be reset by the diamond-forming event. This confirms that
even if protogenetic, the Re-Os isochrons defined by these minerals likely
reflect the ages of diamond formation, and this result highlights the power
of this system to date the timing of fluid migration in mantle lithosphere.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48651.1/596326/Protogenetic-sulfide-inclusions-in-diamonds-date

New statistical quantification of the impact of active deformation on
the distribution of submarine channels

Marco Pizzi; Alexander C. Whittaker; Lidia Lonergan; Mike Mayall; W. Hamish
Mitchell

Abstract:
Submarine channel systems play a crucial role in governing the delivery of
sediments and pollutants such as plastics from the shelf edge to deep
water. Understanding their distribution in space and time is important for
constraining the locus, magnitude, and characteristics of deep-water
sedimentation and for predicting stratigraphic architectures and
depositional facies. Using three-dimensional seismic reflection data
covering the outer fold-and-thrust belt of the Niger Delta, we determined
the pathways of Miocene to Pliocene channels that crossed, at 173
locations, 11 fold-thrust structures for which the temporal and spatial
evolution of strain rates has been constrained over a period of 11 m.y. We
use a statistical approach to quantify strain and shortening rate
distributions recorded where channels have crossed structures compared to
the fault array as a whole. Our results prove unambiguously that these
distributions are different. The median strain rate where channels cross
faults is <0.6%/m.y. (~40 m/m.y.), 2.5× lower than the median strain
rate of active fault segments (1.5%/m.y.) with a marked reduction in the
number of channel-fault crossings where fault strain rates are >1%/m.y.
Our results quantify the sensitivity of submarine channels to active
deformation at a population level for the first time and enable us to
predict the temporal and spatial routing of submarine channels affected by
structurally driven topography.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48698.1/596327/New-statistical-quantification-of-the-impact-of

Paleozoic evolution of crustal thickness and elevation in the northern
Appalachian orogen, USA

Ian W. Hillenbrand; Michael L. Williams

Abstract:
The Acadian and Neoacadian orogenies are widely recognized, yet poorly
understood, tectono-thermal events in the New England Appalachian Mountains
(USA). We quantified two phases of Paleozoic crustal thickening using
geochemical proxies. Acadian (425–400 Ma) crustal thickening to 40 km
progressed from southeast to northwest. Neoacadian (400–380 Ma) crustal
thickening was widely distributed and varied by 30 km (40–70 km) from north
to south. Doubly thickened crust and paleoelevations of 5 km or more
support the presence of an orogenic plateau at ca. 380–330 Ma in southern
New England. Neoacadian crustal thicknesses show a strong correlation with
metamorphic isograds, where higher metamorphic grade corresponds to greater
paleo-crustal thickness. We suggest that the present metamorphic field
gradient was exposed through erosion and orogenic collapse influenced by
thermal, isostatic, and gravitational properties related to Neoacadian
crustal thickness. Geobarometry in southern New England underestimates
crustal thickness and exhumation, suggesting the crust was thinned by
tectonic as well as erosional processes.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48705.1/596328/Paleozoic-evolution-of-crustal-thickness-and

Diapiric relamination of the Orocopia Schist (southwestern U.S.) during
low-angle subduction

James B. Chapman

Abstract:
The Orocopia Schist and related schists are sediments subducted during the
Laramide orogeny and are thought to have been underplated as a laterally
extensive layer at the base of the crust in the southwestern United States
Cordillera. This concept is hard to reconcile with the existence of
continental mantle lithosphere in southeastern California and western
Arizona. Analytical solutions and numerical modeling suggest that the
Orocopia Schist may have ascended through the mantle lithosphere as
sediment diapirs or subsolidus crustal plumes to become emplaced in the
middle to lower crust. Modeled time-temperature cooling paths are
consistent with the exhumation history of the Orocopia Schist and explain
an initial period of rapid cooling shortly after peak metamorphism. The
Orocopia Schist represents a potential example of relaminated sediment
observable at the surface.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48647.1/596330/Diapiric-relamination-of-the-Orocopia-Schist

Annually resolved sediments in the classic Clarkia lacustrine deposits
(Idaho, USA) during the middle Miocene Climate Optimum

Daianne Höfig; Yi Ge Zhang; Liviu Giosan; Qin Leng; Jiaqi Liang ...

Abstract:
The world-renowned Miocene Clarkia paleolake in northern Idaho (USA) is
closely associated with Columbia River Basalt Group volcanism. The flood
basalt dammed a local drainage system to form the paleolake, which
preserved a plant fossil Lagerstätte in its deposits. However, the
precise age and temporal duration of the lake remain unsettled. We present
the first unequivocal U-Pb zircon ages from interbedded volcanic ashes at
the P-33 type location, constraining the deposition to 15.78 ± 0.039 Ma.
Using micro–X-ray fluorescence and petrographic and spectral analyses, we
establish the annual characteristics of laminations throughout the
stratigraphic profile using the distribution of elemental ratios, mineral
assemblages, and grain-size structures, as well as organic and fossil
contents. Consequently, the ~7.5-m-thick varved deposit at the type
location P-33 represents ~840 yr of deposition, coincident with the end of
the main phase of Columbia River Basalt Group eruptions during the Miocene
Climate Optimum. The timing and temporal resolution of the deposit offer a
unique opportunity to study climate change in unprecedented detail during
global warming associated with carbon-cycle perturbations.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48901.1/596161/Annually-resolved-sediments-in-the-classic-Clarkia

The carbonate compensation depth in the South Atlantic Ocean since the
Late Cretaceous

Adriana Dutkiewicz; R. Dietmar Müller

Abstract:
Deep-sea carbonate deposition is a complex process that is encapsulated in
the carbonate compensation depth (CCD)—a facies boundary separating
calcareous sediments from non-carbonates. Knowing how the CCD has varied
over time is important for understanding and predicting the distribution of
seafloor sediments and assessing their role in the global carbon cycle. We
focus on the South Atlantic Ocean where the most recent CCD curve is based
on Deep Sea Drilling Project (DSDP) Leg 73 sites drilled in 1980 in the
South Atlantic Ocean. We compute the South and central South Atlantic CCD
from the Late Cretaceous to the present day using updated age models from
45 DSDP and Ocean Drilling Program sites and backtracking with
lithology-specific decompaction, eustasy, and dynamic topography. Our
models extend further back in time and show more fluctuations than previous
reconstructions, with the CCD varying by hundreds of meters during a span
of 2–3 m.y. The addition of eustasy and dynamic topography deepens the CCD
by as much as 500 m between 74 Ma and 45 Ma, and by ~200 m during the
Cenozoic. The central South Atlantic CCD diverges from the average South
Atlantic CCD during the Eocene and Miocene, when it was ~1 km shallower.
These regional deviations may be due to changes in primary productivity
and/or carbonate dissolution leading to reduced carbonate accumulation
rates. Our CCD curves highlight the importance of regional processes in
carbonate deposition across the South Atlantic and provide improved
constraints for the modeling of geochemical cycles.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48404.1/596162/The-carbonate-compensation-depth-in-the-South

Transient Permian-Triassic euxinia in the southern Panthalassa deep
ocean

S.E. Grasby; D.P.G. Bond; P.B. Wignall; R. Yin; L.J. Strachan ...

Abstract:
Both the duration and severity of deep-water anoxic conditions across the
Permian-Triassic mass extinction (PTME) are controversial. Panthalassa
Ocean circulation models yield varying results, ranging from a
well-ventilated deep ocean to rapidly developing northern-latitude, but not
southern-latitude, anoxia in response to Siberian Traps–driven global
warming. To address this uncertainty, we examined a southern-paleolatitude
pelagic record. Trace metal and pyrite framboid data suggest bottom-water
euxinic conditions developed in the southern Panthalassa Ocean at the PTME,
coincident with enhanced volcanic activity indicated by Hg geochemistry.
While a global ocean euxinic event at the PTME placed extraordinary stress
on marine life, southern surface waters appear to have recovered more
quickly as radiolarian populations returned several million years before
they did in northern Panthalassa.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48928.1/596163/Transient-Permian-Triassic-euxinia-in-the-southern

Water transfer to the deep mantle through hydrous, Al-rich silicates in
subduction zones

Jörg Hermann; Shayne Lakey

Abstract:
Constraining deep-water recycling along subduction zones is a first-order
problem to understand how Earth has maintained a hydrosphere over billions
of years that created conditions for a habitable planet. The
pressure-temperature stability of hydrous phases in conjunction with slab
geotherms determines how much H2O leaves the slab or is
transported to the deep mantle. Chlorite-rich, metasomatic rocks that form
at the slab-mantle interface at 50–100 km depth represent an unaccounted, H 2O-rich reservoir in subduction processes. Through a series of
high-pressure experiments, we investigated the fate of such chlorite-rich
rocks at the most critical conditions for subduction water recycling (5–6.2
GPa, 620–800 °C) using two different natural ultramafic compositions. Up to
5.7 GPa, 740 °C, chlorite breaks down to an anhydrous peridotite
assemblage, and H2O is released. However, at higher pressures
and lower temperatures, a hydrous Al-rich silicate (11.5 Å phase) is an
important carrier to enable water transfer to the deep mantle for cold
subduction zones. Based on the new phase diagrams, it is suggested that the
deep-water cycle might not be in secular equilibrium.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article/doi/10.1130/G48658.1/596165/Water-transfer-to-the-deep-mantle-through-hydrous

Eruption risks from covert silicic magma bodies

Shane M. Rooyakkers; John Stix; Kim Berlo; Maurizio Petrelli; Freysteinn
Sigmundsson

Abstract:
Unintentional encounters with silicic magma at ~2–2.5 km depth have
recently occurred during drilling at three volcanoes: Kilauea (Hawaii),
Menengai (Kenya), and Krafla (Iceland). Geophysical surveys had failed to
warn about shallow magma before each encounter, and subsequent surveys at
Krafla have been unable to resolve the size or architecture of its silicic
magma body. This presents a conundrum for volcano monitoring: Do such
shallow “covert” magma bodies pose an eruption risk? Here, we show that
Krafla’s most recent explosive eruption, a mixed hydrothermal-magmatic
event in 1724 C.E. that formed the Víti maar, involved rhyolite essentially
indistinguishable in composition from magma encountered during drilling in
2009. Streaks of quenched basalt in some Víti pumices provide direct
evidence for interaction between co-erupted rhyolitic and basaltic magmas,
but crystals in these pumices show no evidence for late-stage heating or
re-equilibration with more mafic melt, implying mixing time scales of at
most several hours. Covert silicic magma thus presents an eruption risk at
Krafla and may be mobilized with little warning. Difficulties in resolving
magma bodies smaller than ~1 km3 with geophysical surveys mean
that covert silicic magma may exist at many other volcanoes and should be
considered in hazard and risk assessments.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48697.1/596166/Eruption-risks-from-covert-silicic-magma-bodies

Ghost-dune hollows of the eastern Snake River Plain, Idaho: Their
genesis, evolution, and relevance to Martian ghost-dune pits

David R. Gaylord; Tammy M. Rittenour; Paul K. Link; Brent D. Turrin; Mel A.
Kuntz

Abstract:
Ghost-dune hollows on the eastern Snake River Plain (ESRP), Idaho, USA, are
topographically inverted, crescent-shaped depressions that record the
partial encasement of sand dunes by ca. 61 ka basalt lava flows. Deflation
of these “ghost” sand dunes produced approximately two dozen, 5–10-m-deep
ghost-dune hollows now incompletely filled with pedogenically altered
eolian and colluvial sediment. Optically stimulated luminescence (OSL) and 40Ar/39Ar ages constrain a ghost-dune hollow model
that illuminates the late Pleistocene to Holocene environmental and climate
history of the ESRP. Detrital zircon analyses indicate sand-dune supply
routes changed following the burial of Pleistocene Henrys Fork (tributary
of the Snake River) alluvium by ca. 70 ka basalt flows. Removal of Henrys
Fork alluvium from the eolian supply system made Lake Terreton sediment the
primary source for later ESRP sand dunes. Such sediment supply changes
highlight the potential impacts of effusive volcanism on sand-dune
histories and landscapes. Our results support stratigraphic and sedimentary
modeling of comparable ghost-dune “pit” deposits older than ca. 2 Ga on
Mars that may have served as refugia for early life on that planet.
Analogous ancient ghost-dune hollow deposits on Earth may also have served
as early life refugia.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48645.1/596167/Ghost-dune-hollows-of-the-eastern-Snake-River

Controls on the origin and evolution of deep-ocean trench-axial
channels

Adam D. McArthur; Daniel E. Tek

Abstract:
The type and volume of sediment entering subduction zones affects the style
of plate-boundary deformation and thus sedimentary and tectonic cycles.
Because submarine channels significantly increase the transport efficiency
of turbidity currents, their presence or absence in subduction trenches is
a primary control on trench fill. To date, comprehensive architectural
characterization of trench-axial channels has not been possible,
undermining efforts to identify the factors controlling their initiation
and evolution. Here, we describe the evolution of the Hikurangi Channel,
which traverses the Hikurangi Trench, offshore New Zealand. Analysis of
two- and three-dimensional seismic data reveals that the channel was
present only during the last ~3.5 m.y. of the ~27 m.y. of the trench’s
existence; its inception and propagation resulted from increased sediment
supply to the trench following amplified hinterland exhumation. To test if
the controls on the evolution of the Hikurangi Channel are universal,
multivariate statistical analysis of the geomorphology of subduction
trenches globally is used to investigate the formative conditions of axial
channels in modern trenches. Terrigenous sediment supply and thickness of
sediment cover in a trench are the dominant controls; subsidiary factors
such as trench length and rugosity also contribute to the conditions
necessary for trench-axial channel development. Axial channels regulate
sediment distribution in trenches, and this varies temporally and spatially
as a channel propagates along a trench. The presence of a trench-axial
channel affects plate-boundary mechanics and has implications for the style
of subduction-margin deformation.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48612.1/596024/Controls-on-the-origin-and-evolution-of-deep-ocean

Joint inversion of surface wave and gravity data reveals subbasin
architecture of the Congo Basin

A. Raveloson; A. Nyblade; R. Durrheim

Abstract:
We investigated the architecture of the greater Congo Basin, one of the
largest and least-well-studied sedimentary basins on any continent.
Seismograms from a large number of M > 4.5 earthquakes within and
surrounding the African plate were used to make event-to-station Rayleigh
wave group velocity measurements between periods of 5 and 100 s. Group
velocities for discrete periods across the basin, obtained by inverting the
event-station measurements, were jointly modeled with gravity data to
obtain a three-dimensional S-wave and density model of the basin. The model
corroborates the existence of two previously suggested subbasins, one to
the north and one to the south, each ~8 km deep and separated by an
east-west structural high. Our results favor a salt tectonics origin for
the structural high but cannot rule out uplifted basement rock. The
northern subbasin is offset to the west from the southern subbasin,
consistent with previous studies suggesting sinistral motion along basement
faults during periods of transpressional tectonics in late
Neoproterozoic–early Paleozoic times.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48408.1/596025/Joint-inversion-of-surface-wave-and-gravity-data

Hydrothermal recycling of sedimentary ammonium into oceanic crust and
the Archean ocean at 3.24 Ga

E.E. Stüeken; T.J. Boocock; A. Robinson; S. Mikhail; B.W. Johnson

Abstract:
The Archean ocean supported a diverse microbial ecosystem, yet studies
suggest that seawater was largely depleted in many essential nutrients,
including fixed nitrogen. This depletion was in part a consequence of
inefficient nutrient recycling under anoxic conditions. Here, we show how
hydrothermal fluids acted as a recycling mechanism for ammonium (NH 4+) in the Archean ocean. We present elemental and
stable isotope data for carbon, nitrogen, and sulfur from shales and
hydrothermally altered volcanic rocks from the 3.24 Ga Panorama district in
Western Australia. This suite documents the transfer of NH4 + from organic-rich sedimentary rocks into underlying
sericitized dacite, similar to what is seen in hydrothermal systems today.
On modern Earth, hydrothermal fluids that circulate through sediment
packages are enriched in NH4+ to millimolar
concentrations because they efficiently recycle organic-bound N. Our data
show that a similar hydrothermal recycling process dates back to at least
3.24 Ga, and it may have resulted in localized centers of enhanced
biological productivity around hydrothermal vents. Last, our data provide
evidence that altered oceanic crust at 3.24 Ga was enriched in nitrogen,
and, when subducted, it satisfies the elemental and isotopic source
requirements for a low-N, but 15N-enriched, deep mantle nitrogen
reservoir as sampled by mantle plumes.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48844.1/596026/Hydrothermal-recycling-of-sedimentary-ammonium

Missing water from the Qiangtang Basin on the Tibetan Plateau

Bin Yong; Chi-Yuen Wang; Jiansheng Chen; Jiaqi Chen; D.A. Barry ...

Abstract:
The Qiangtang Basin is a large endorheic basin in the inner part of the
Tibetan Plateau, and has been thought to be a dry region in contrast with
the surrounding wet outer region that feeds all the major Asian rivers.
Combining surface hydrological data with modeling and satellite data from
2002 to 2016 CE, our study reveals that an enormous amount of water, ~54 ±
4 km3, is unaccounted for annually in the Qiangtang Basin. The
amount of missing water is comparable to the total annual discharge of the
Yellow River. Data from the Gravity Recovery and Climate Experiment (GRACE)
satellite mission show little increase of local terrestrial water storage.
Thus, the missing water must have flowed out of the basin through
underground passages. Interpreting this result in the context of recent
seismic and geological studies of Tibet, we suggest that a significant
amount of meteoric water in the Qiangtang Basin leaks out by way of
groundwater flow through deep normal faults and tensional fractures along
the nearly north-south rift valleys that are oriented subnormal to and
cross the surficial hydrological divide on the southern margin of the
basin. Cross-basin groundwater outflow of such a magnitude defies the
traditional view of a basin-scale water cycle and leads to a very different
picture from the previous hydrological view of the Qiangtang Basin. This
finding calls for major rethinking of the regional water balance.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48561.1/596027/Missing-water-from-the-Qiangtang-Basin-on-the

Alternating wet and dry depositional environments recorded in the
stratigraphy of Mount Sharp at Gale crater, Mars

W. Rapin; G. Dromart; D. Rubin; L. Le Deit; N. Mangold ...

Abstract:
The Curiosity rover is exploring Hesperian-aged stratigraphy in Gale
crater, Mars, where a transition from clay-bearing units to a layered
sulfate-bearing unit has been interpreted to represent a major
environmental transition of unknown character. We present the first
description of key facies in the sulfate-bearing unit, recently observed in
the distance by the rover, and propose a model for changes in depositional
environments. Our results indicate a transition from lacustrine mudstones
into thick aeolian deposits, topped by a major deflation surface, above
which strata show architectures likely diagnostic of a subaqueous
environment. This model offers a reference example of a depositional
sequence for layered sulfate-bearing strata, which have been identified
from orbit in other locations globally. It differs from the idea of a
monotonic Hesperian climate change into long-term aridity on Mars and
instead implies a period characterized by multiple transitions between
sustained drier and wetter climates.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48519.1/596028/Alternating-wet-and-dry-depositional-environments

Evidence for 40–41 km of dextral slip on the southern Death Valley
fault: Implications for the Eastern California shear zone and
extensional tectonics

Terry L. Pavlis; Ghislain Trullenque

Abstract:
Recognition of a pair of pre-Neogene markers together with analysis of
published data indicate ~40 km of dextral slip across the southern Death
Valley fault zone, California, USA. Stratigraphic overlaps on fault rocks
indicate much of the dextral slip predates the late Miocene, placing a
significant fraction of the dextral slip in the same time window as
regional extension and challenging interpretations that the modern
strike-slip system became active post–6–3 Ma. However, these results are
consistent with regional evidence that dextral transtension began by ca. 12
Ma.

View article:
https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48528.1/596029/Evidence-for-40-41-km-of-dextral-slip-on-the

A metasedimentary source of gold in Archean orogenic gold deposits

Iain K. Pitcairn; Nikolaos Leventis; Georges Beaudoin; Stephane Faure; Carl
Guilmette ...

Abstract:
The sources of metals enriched in Archean orogenic gold deposits have long
been debated. Metasedimentary rocks, which are generally accepted as the
main metal source in Phanerozoic deposits, are less abundant in Archean
greenstone belts and commonly discounted as a viable metal source for
Archean deposits. We report ultralow-detection-limit gold and trace-element
concentrations from a suite of metamorphosed sedimentary rocks from the
Abitibi belt and Pontiac subprovince, Superior Province, Canada. Systematic
decreases in the Au content with increasing metamorphic grade indicate that
Au was mobilized during prograde metamorphism. Mass balance calculations
show that over 10 t of Au, 30,000 t of As, and 600 t of Sb were mobilized
from 1 km3 of Pontiac subprovince sedimentary rock metamorphosed
to the sillimanite metamorphic zone. The total gold resource in orogenic
gold deposits in the southern Abitibi belt (7500 t Au) is only 3% of the Au
mobilized from the estimated total volume of high-metamorphic-grade Pontiac
sedimentary rock in the region (25,000 km3), indicating that
sedimentary rocks are a major contributor of metals to the orogenic gold
deposits in the southern Abitibi belt.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48587.1/596030/A-metasedimentary-source-of-gold-in-Archean

Similar curvature-to-width ratios for channels and channel belts:
Implications for paleo-hydraulics of fluvial ridges on Mars

Alistair T. Hayden; Michael P. Lamb; Alexander J. Carney

Abstract:
The surface of Mars contains abundant sinuous ridges that appear similar to
river channels in planform, but they stand as topographic highs. Ridges
have similar curvature-to-width ratios as terrestrial meandering rivers,
which has been used to support the hypothesis that ridges are inverted
channels that directly reflect channel geometry. Anomalously wide ridges,
in turn, have been interpreted as evidence for larger rivers on Mars
compared to Earth. However, an alternate hypothesis is that ridges are
exhumed channel-belt deposits—a larger zone of relatively coarse-grained
deposits formed from channel lateral migration and aggradation. Here, we
measured landform wavelength, radius of curvature, and width to compare
terrestrial channels, terrestrial channel belts, and martian ridges. We
found that all three landforms follow similar scaling relations, in which
ratios of radius of curvature to width range from 1.7 to 7.3, and
wavelength-to-width ratios range from 5.8 to 13. We interpret this
similarity to be a geometric consequence of a sinuous curved line of finite
width. Combined with observations of ridge-stacking patterns, our results
suggest that wide ridges on Mars could indicate fluvial channel belts that
formed over significant time rather than anomalously large rivers.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48370.1/595962/Similar-curvature-to-width-ratios-for-channels-and

Outer forearc uplift and exhumation during high-flux magmatism:
Evidence from detrital zircon geochemistry of the Nacimiento forearc
basin, California, USA

Scott M. Johnston; Andrew R.C. Kylander-Clark

Abstract:
We present new coupled detrital zircon trace-element and U–Pb age data from
Valanginian–Santonian strata of the Nacimiento forearc basin (California,
USA) to enhance provenance discrimination and investigate the evolution of
the late Mesozoic California margin. Our data document at least five
different Jurassic–earliest Cretaceous zircon populations with variable
U/Yb ratios, and zircon that displays systematically increasing U/Yb from
130 to 80 Ma. Based on the presence of a distinctive population of
geochemically primitive, 168–157 Ma low-U/Yb zircon that is found in
Albian–Lower Cenomanian strata but not in older Valanginian strata, we
infer a period of uplift and Albian–early Cenomanian erosion of forearc
basement (the Coast Range ophiolite) that was coincident with increasing
Cordilleran arc magmatic flux.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48627.1/595963/Outer-forearc-uplift-and-exhumation-during-high

Shutting down dust emission during the middle Holocene drought in the
Sonoran Desert, Arizona, USA

Guy Tau; Onn Crouvi; Yehouda Enzel; Nadya Teutsch; Paul Ginoux ...

Abstract:
Long-term relationships between climate and dust emission remain unclear,
with two prevailing but opposite hypotheses for effects of climate shifts:
(1) increased dust emission due to increasing aridity imposing a vegetation
change, or (2) decreased dust emission due to increasing aridity which
imposes less stormy climate and reduced sediment supply. Here we test these
hypotheses by analyzing an ~11-m-long core archiving Holocene dust trapped
in Montezuma Well, a natural sinkhole in Arizona (southwestern United
States), alongside current dust sources and transport pathways. Major
elements indicate that Montezuma Well sediments originate from two end
members: local carbonate bedrock and external siliceous dust. Core
sediments are similar to the adjacent siliceous soils accumulated atop the
bedrock, pointing to their eolian origin. Particle-size distributions
reveal fine dust transported during winter from the northwestern Sonoran
Desert and the Mojave Desert and coarse dust transported during summer from
the southwestern Sonoran Desert, similar to current climate systems and
dust pathways. A survey of potential dust sources indicates that current
summer and winter dust sources in the Sonoran Desert are under a
supply-limited state. Dust fluxes were higher during wetter phases of the
Holocene when winter sources dominated. During the middle Holocene drought,
dust fluxes were minimal and dominated by summer sources until dust input
ceased as drought conditions did not produce enough floods to refill
sources with sediments. We propose that in the Sonoran Desert, dust
emission is strongly connected with climate, increasing during humid
intervals and enhanced by fluvial sediment replenishment at dust sources.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48550.1/595964/Shutting-down-dust-emission-during-the-middle

Extensive decentralized hydrogen export from the Atlantis Massif

Susan Q. Lang; Marvin D. Lilley; Tamara Baumberger; Gretchen L. Früh-Green;
Sharon L. Walker ...

Abstract:
Hydrogen is an important energy source for subsurface microbial
communities, but its availability beyond the flow focused through
hydrothermal chimneys is largely unknown. We report the widespread export
of H2 across the Atlantis Massif oceanic core complex (30°N,
Mid-Atlantic Ridge; up to 44 nM), which is distinct from the
circulation system feeding the Lost City Hydrothermal Field (LCHF) on the
massif’s southern wall. Methane (CH4) abundances are generally
low to undetectable (<3 nM) in fluids that are not derived from
the LCHF. Reducing fluids exit the seafloor over a wide geographical area
and depth range, including the summit of the massif and along steep areas
of mass wasting east of the field. The depth of the fluids in the water
column and their H2/CH4 ratios indicate that some are
sourced separately from the LCHF. We argue that extensive H2
export is the natural consequence of fluid flow pathways strongly
influenced by tectonic features and the volume and density changes that
occur when ultramafic rocks react to form serpentinites, producing H 2 as a by-product. Furthermore, the circulation of H2
-rich fluids through uplifted mantle rocks at moderate temperatures
provides geographically expansive and stable environmental conditions for
the early evolution of biochemical pathways. These results provide insight
into the spatial extent of H2- and CH4-bearing fluids
associated with serpentinization, independent of the focused flow emanating
from the LCHF.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48322.1/595965/Extensive-decentralized-hydrogen-export-from-the

Shock-deformed zircon from the Chicxulub impact crater and implications
for cratering process

Jiawei Zhao; Long Xiao; Zhiyong Xiao; Joanna V. Morgan; Gordon R. Osinski
...

Abstract:
Large impact structures with peak rings are common landforms across the
solar system, and their formation has implications for both the interior
structure and thermal evolution of planetary bodies. Numerical modeling and
structural studies have been used to simulate and ground truth peak-ring
formative mechanisms, but the shock metamorphic record of minerals within
these structures remains to be ascertained. We investigated impact-related
microstructures and high-pressure phases in zircon from melt-bearing
breccias, impact melt rock, and granitoid basement from the Chicxulub peak
ring (Yucatán Peninsula, Mexico), sampled by the International Ocean
Discovery Program (IODP)/International Continental Drilling Project
(IODP-ICDP) Expedition 364 Hole M0077A. Zircon grains exhibit shock
features such as reidite, zircon twins, and granular zircon including
“former reidite in granular neoblastic” (FRIGN) zircon. These features
record an initial high-pressure shock wave (>30 GPa), subsequent
relaxation during the passage of the rarefaction wave, and a final heating
and annealing stage. Our observed grain-scale deformation history agrees
well with the stress fields predicted by the dynamic collapse model, as the
central uplift collapsed downward-then-outward to form the peak ring. The
occurrence of reidite in a large impact basin on Earth represents the first
such discovery, preserved due to its separation from impact melt and rapid
cooling by the resurging ocean. The coexistence of reidite and FRIGN zircon
within the impact melt–bearing breccias indicates that cooling by seawater
was heterogeneous. Our results provide valuable information on when
different shock microstructures form and how they are modified according to
their position in the impact structure, and this study further improves on
the use of shock barometry as a diagnostic tool in understanding the
cratering process.

View article:

https://pubs.geoscienceworld.org/gsa/geology/article-abstract/doi/10.1130/G48278.1/595966/Shock-deformed-zircon-from-the-Chicxulub-impact

The genome of single-celled plankton, known as dinoflagellates, is organized in an incredibly strange and unusual way, according to new research. The findings lay the groundwork for further investigation into these important marine organisms and dramatically expand our picture of what a eukaryotic genome can look like.

Researchers from KAUST, the U.S. and Germany have investigated the genomic organization of the coral-symbiont dinoflagellate Symbiodinium microadriaticum. The S. microadriaticum genome had already been sequenced and assembled into segments known as scaffolds but lacked a chromosome-level assembly.

The team used a technique known as Hi-C to detect interactions in the dinoflagellate's chromatin, the combination of DNA and protein that makes up a chromosome. By analyzing these interactions, they could figure out how the scaffolds were connected together into chromosomes, giving them a view into the spatial and structural organization of the genome.

A striking finding was that the genes in the genome tended to be organized in alternating unidirectional blocks. "That's really, really different to what you see in other organisms," says Octavio Salazar, a Ph.D. student in Manuel Aranda's group at KAUST and one of the lead authors of the study. The orientation of genes on a chromosome is usually random. In this case, however, genes were consistently oriented one way and then the other, with the boundaries between blocks showing up clearly in the chromatin interaction data.

"Nature can work in a completely different way than we thought."

This organization is also reflected in the three-dimensional structure of the genome, which the team inferred comprises rod-shaped chromosomes that fold into structural domains at the boundaries where gene blocks converge. Even more intriguingly, this structure appears to be dependent on transcriptional activity. When the researchers treated cells with a chemical that blocks gene transcription, the structural domains disappeared.

This unusual link is consistent with another strange fact about dinoflagellates -- they have very few transcription factors in their genome and do not seem to respond to environmental changes by altering gene expression. They may use gene dosage to control expression and adapt to the environment by losing or gaining chromosomes or perhaps via epigenetic structural modifications. The researchers plan to explore all of these questions.

Another open question is the origin of this exceptional genome structure. Dinoflagellates produce very few histones, the proteins used by other eukaryotes to structure their DNA, instead using viral proteins incorporated into their genome long ago. The extraordinary genome structure and genetic regulation may be a consequence of how these viral proteins work, but that remains to be confirmed.

The dinoflagellate genome defies the expectation and dogmas built from studying other eukaryotes. "It shows that nature can work in a completely different way than we thought," says Salazar. "There are so many possibilities for what could have happened as life evolved."

DURHAM, N.C. - Mantis shrimp don't need baby food. They start their life as ferocious predators who know how to throw a lethal punch.

A new study appearing April 29 in the Journal of Experimental Biology shows that larvae of the Philippine mantis shrimp (Gonodactylaceus falcatus) already display the ultra-fast movements for which these animals are known, even when they are smaller than a short grain of rice.

Their ultra-fast punching appendages measure less than 1 mm, and develop right when the larva exhausts its yolk reserves, moves away from its nest and out into the big wide sea. It immediately begins preying on organisms smaller than a grain of sand.

Although they accelerate their arms almost 100 times faster than a Formula One car, Philippine mantis shrimp larvae are slower than larger adults, which goes against the theoretical expectation that smaller is always faster.

"They're producing amazing speeds and impressive accelerations relative to their body size, but they're not as fast as adults," said Jacob Harrison, a PhD candidate in biology at Duke University and lead author of the study.

Mantis shrimps achieve their ultra-fast movements through a tiny spring-actuated mechanism hidden in their punching appendage. A muscle contracts, deforming a tiny segment of their exoskeleton -the rigid cuticle that covers their body. This contraction allows elastic energy to be stored in the locked joint. Once the latch releases, the exoskeleton springs back into its natural position, violently propelling the appendage forward with ultra-fast speeds.

Engineering and physics models predict that smaller organisms, who have a smaller mass to displace, will be faster than larger, heavier, organisms. Mantis shrimp larvae show that biology doesn't always follow the theory.

"Theoretically, they should be producing the highest acceleration," said Harrison, "but we don't find that."

Harrison explains that this discrepancy may be due to multiple factors. The larvae muscles may be too small to effectively load a very stiff spring, or the water resistance at their small size may be too high for their punches to reach the speed that larger individuals reach, among other possibilities.

"There are limitations to these spring and latch structures that we don't fully understand," said Harrison. "But whenever biology moves away from theoretical models it highlights some pretty interesting areas for us to learn."

Mantis shrimp larvae are an interesting system not only due to their small size, but also due to their color, or lack thereof.

Adult mantis shrimps have opaque exoskeletons, rendering the inner working of their spring-latch mechanisms impossible to observe in action. The exoskeleton of larvae, however, is much thinner and fully transparent, allowing researchers to see precisely how these animals manage to store so much elastic energy in their tiny appendages simply by watching them through a microscope.

"One of the trickiest parts of researching spring-actuated mechanisms is that a lot of those elements are working inside the animal. We can look outside of the animal and see the behavior, measure the kinematics, dissect the animal, and say the mechanism looks like it works like this, but there are always levels of assumption," said Harrison.

"(Transparency) sets up larval mantis shrimps as systems where we can look at how each of these elements work in concert together," said Harrison. "It removes assumptions and allows us to understand it on a finer scale."

Larval mantis shrimps are therefore doubly interesting. They highlight discrepancies between physics and biology, and also offer a true window into a better understanding of the mechanism behind ultra-fast movements.

"When something doesn't match your predictions, the first gut reaction is always to be incredibly frustrated, but this is actually what highlights new areas of research," said Harrison.

In a novel effort to combat COVID-19 misinformation, a group of women researchers, including nurse scientists from the University of Pennsylvania School of Nursing (Penn Nursing), launched the Dear Pandemic social media campaign in March 2020. It delivers curated, comprehensive, and timely information about the COVID-19 pandemic in a question-and-answer format. Complex topics such as COVID-19 aerosol transmission, risk reduction strategies to avoid infection, and excess mortality are explained in common language and shared widely.

Now with more than 100,000 followers and accounts on Facebook, Twitter, and Instagram, the campaign has an international and multilingual impact offering important public health insight via social media. An article in the journal Public Health Nursing describes how the campaign is combating misinformation about COVID-19.

"Dear Pandemic has demonstrated that consistently publishing high-quality content outside a peer-reviewed venue can result in incredible impact--personal behavior change, informed nodes of trust to further disseminate factual information, and resources for community providers navigating constantly evolving knowledge," says Penn Nursing's Ashley Z. Ritter, PhD, CRNP, the article's lead author.

Dear Pandemic is an example of necessary low-barrier information exchange with the public and a tool for community providers like nurses to stay informed of breaking news. Increased engagement of nurses in endeavors like Dear Pandemic amplifies the impact of collective interdisciplinary efforts to educate the public, contain misinformation, and motivate individual and systemic action, the article explains.

"Now is the time for nurses to flex their communication and trust muscles in both traditional and innovative ways to advance the health of the public through trusted, actionable messaging in addition to exceptional patient care," says co-author Shoshana Aronowitz, PhD, CRNP, a Fellow of the National Clinician Scholars Program.