Publications by authors named "B Jesse Shapiro"

1,735 Publications

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A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control.

bioRxiv 2021 Apr 6. Epub 2021 Apr 6.

We report a SARS-CoV-2 lineage that shares N501Y, P681H, and other mutations with known variants of concern, such as B.1.1.7. This lineage, which we refer to as B.1.x (COG-UK sometimes references similar samples as B.1.324.1), is present in at least 20 states across the USA and in at least six countries. However, a large deletion causes the sequence to be automatically rejected from repositories, suggesting that the frequency of this new lineage is underestimated using public data. Recent dynamics based on 339 samples obtained in Santa Cruz County, CA, USA suggest that B.1.x may be increasing in frequency at a rate similar to that of B.1.1.7 in Southern California. At present the functional differences between this variant B.1.x and other circulating SARS-CoV-2 variants are unknown, and further studies on secondary attack rates, viral loads, immune evasion and/or disease severity are needed to determine if it poses a public health concern. Nonetheless, given what is known from well-studied circulating variants of concern, it seems unlikely that the lineage could pose larger concerns for human health than many already globally distributed lineages. Our work highlights a need for rapid turnaround time from sequence generation to submission and improved sequence quality control that removes submission bias. We identify promising paths toward this goal.
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http://dx.doi.org/10.1101/2021.04.05.438352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043452PMC
April 2021

Author Correction: Dense sampling of bird diversity increases power of comparative genomics.

Authors:
Shaohong Feng Josefin Stiller Yuan Deng Joel Armstrong Qi Fang Andrew Hart Reeve Duo Xie Guangji Chen Chunxue Guo Brant C Faircloth Bent Petersen Zongji Wang Qi Zhou Mark Diekhans Wanjun Chen Sergio Andreu-Sánchez Ashot Margaryan Jason Travis Howard Carole Parent George Pacheco Mikkel-Holger S Sinding Lara Puetz Emily Cavill Ângela M Ribeiro Leopold Eckhart Jon Fjeldså Peter A Hosner Robb T Brumfield Les Christidis Mads F Bertelsen Thomas Sicheritz-Ponten Dieter Thomas Tietze Bruce C Robertson Gang Song Gerald Borgia Santiago Claramunt Irby J Lovette Saul J Cowen Peter Njoroge John Philip Dumbacher Oliver A Ryder Jérôme Fuchs Michael Bunce David W Burt Joel Cracraft Guanliang Meng Shannon J Hackett Peter G Ryan Knud Andreas Jønsson Ian G Jamieson Rute R da Fonseca Edward L Braun Peter Houde Siavash Mirarab Alexander Suh Bengt Hansson Suvi Ponnikas Hanna Sigeman Martin Stervander Paul B Frandsen Henriette van der Zwan Rencia van der Sluis Carina Visser Christopher N Balakrishnan Andrew G Clark John W Fitzpatrick Reed Bowman Nancy Chen Alison Cloutier Timothy B Sackton Scott V Edwards Dustin J Foote Subir B Shakya Frederick H Sheldon Alain Vignal André E R Soares Beth Shapiro Jacob González-Solís Joan Ferrer-Obiol Julio Rozas Marta Riutort Anna Tigano Vicki Friesen Love Dalén Araxi O Urrutia Tamás Székely Yang Liu Michael G Campana André Corvelo Robert C Fleischer Kim M Rutherford Neil J Gemmell Nicolas Dussex Henrik Mouritsen Nadine Thiele Kira Delmore Miriam Liedvogel Andre Franke Marc P Hoeppner Oliver Krone Adam M Fudickar Borja Milá Ellen D Ketterson Andrew Eric Fidler Guillermo Friis Ángela M Parody-Merino Phil F Battley Murray P Cox Nicholas Costa Barroso Lima Francisco Prosdocimi Thomas Lee Parchman Barney A Schlinger Bette A Loiselle John G Blake Haw Chuan Lim Lainy B Day Matthew J Fuxjager Maude W Baldwin Michael J Braun Morgan Wirthlin Rebecca B Dikow T Brandt Ryder Glauco Camenisch Lukas F Keller Jeffrey M DaCosta Mark E Hauber Matthew I M Louder Christopher C Witt Jimmy A McGuire Joann Mudge Libby C Megna Matthew D Carling Biao Wang Scott A Taylor Glaucia Del-Rio Alexandre Aleixo Ana Tereza Ribeiro Vasconcelos Claudio V Mello Jason T Weir David Haussler Qiye Li Huanming Yang Jian Wang Fumin Lei Carsten Rahbek M Thomas P Gilbert Gary R Graves Erich D Jarvis Benedict Paten Guojie Zhang

Nature 2021 Apr 8. Epub 2021 Apr 8.

China National GeneBank, BGI-Shenzhen, Shenzhen, China.

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http://dx.doi.org/10.1038/s41586-021-03473-8DOI Listing
April 2021

Elevated rates of horizontal gene transfer in the industrialized human microbiome.

Cell 2021 Apr 31;184(8):2053-2067.e18. Epub 2021 Mar 31.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA. Electronic address:

Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.
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http://dx.doi.org/10.1016/j.cell.2021.02.052DOI Listing
April 2021

Translational activity is uncoupled from nucleic acid content in bacterial cells of the human gut microbiota.

Gut Microbes 2021 Jan-Dec;13(1):1-15

Department of Microbiology & Immunology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.

Changes in bacterial diversity in the human gut have been associated with many conditions, despite not always reflecting changes in bacterial activity. Methods linking bacterial identity to function are needed for improved understanding of how bacterial communities adapt and respond to their environment, including the gut. Here, we optimized bioorthogonal non-canonical amino acid tagging (BONCAT) for the gut microbiota and combined it with fluorescently activated cell sorting and sequencing (FACS-Seq) to identify the translationally active members of the community. We then used this novel technique to compare with other bulk community measurements of activity and viability: relative nucleic acid content and membrane damage. The translationally active bacteria represent about half of the gut microbiota, and are not distinct from the whole community. The high nucleic acid content bacteria also represent half of the gut microbiota, but are distinct from the whole community and correlate with the damaged subset. Perturbing the community with xenobiotics previously shown to alter bacterial activity but not diversity resulted in stronger changes in the distinct physiological fractions than in the whole community. BONCAT is a suitable method to probe the translationally active members of the gut microbiota, and combined with FACS-Seq, allows for their identification. The high nucleic acid content bacteria are not necessarily the protein-producing bacteria in the community; thus, further work is needed to understand the relationship between nucleic acid content and bacterial metabolism in the human gut. Considering physiologically distinct subsets of the gut microbiota may be more informative than whole-community profiling.
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http://dx.doi.org/10.1080/19490976.2021.1903289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8009119PMC
March 2021

A fast and efficient single-stranded genomic library preparation method optimized for ancient DNA.

J Hered 2021 Mar 26. Epub 2021 Mar 26.

Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA.

We present a protocol to prepare extracted DNA for sequencing on the Illumina sequencing platform that has been optimized for ancient and degraded DNA. Our approach, the Santa Cruz Reaction or SCR, uses directional splinted ligation of Illumina's P5 and P7 adapters to convert natively single-stranded DNA and heat denatured double-stranded DNA into sequencing libraries in a single enzymatic reaction. To demonstrate its efficacy in converting degraded DNA molecules, we prepare five ancient DNA extracts into sequencing libraries using the SCR and two of the most commonly used approaches for preparing degraded DNA for sequencing: BEST, which targets and converts double-stranded DNA, and ssDNA2.0, which targets and converts single-stranded DNA. We then compare the efficiency with which each approach recovers unique molecules, or library complexity, given a standard amount of DNA input. We find that the SCR consistently outperforms the BEST protocol in recovering unique molecules and, despite its relative simplicity to perform and low cost per library, has similar performance to ssDNA2.0 across a wide range of DNA inputs. The SCR is a cost- and time-efficient approach that minimizes the loss of unique molecules and makes accessible a taxonomically, geographically, and temporally broader sample of preserved remains for genomic analysis.
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http://dx.doi.org/10.1093/jhered/esab012DOI Listing
March 2021

Ancient plant DNA reveals High Arctic greening during the Last Interglacial.

Proc Natl Acad Sci U S A 2021 Mar;118(13)

Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303.

Summer warming is driving a greening trend across the Arctic, with the potential for large-scale amplification of climate change due to vegetation-related feedbacks [Pearson et al., (3), 673-677 (2013)]. Because observational records are sparse and temporally limited, past episodes of Arctic warming can help elucidate the magnitude of vegetation response to temperature change. The Last Interglacial ([LIG], 129,000 to 116,000 y ago) was the most recent episode of Arctic warming on par with predicted 21st century temperature change [Otto-Bliesner et al., (371), 20130097 (2013) and Post et al., (5), eaaw9883 (2019)]. However, high-latitude terrestrial records from this period are rare, so LIG vegetation distributions are incompletely known. Pollen-based vegetation reconstructions can be biased by long-distance pollen transport, further obscuring the paleoenvironmental record. Here, we present a LIG vegetation record based on ancient DNA in lake sediment and compare it with fossil pollen. Comprehensive plant community reconstructions through the last and current interglacial (the Holocene) on Baffin Island, Arctic Canada, reveal coherent climate-driven community shifts across both interglacials. Peak LIG warmth featured a ∼400-km northward range shift of dwarf birch, a key woody shrub that is again expanding northward. Greening of the High Arctic-documented here by multiple proxies-likely represented a strong positive feedback on high-latitude LIG warming. Authenticated ancient DNA from this lake sediment also extends the useful preservation window for the technique and highlights the utility of combining traditional and molecular approaches for gleaning paleoenvironmental insights to better anticipate a warmer future.
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http://dx.doi.org/10.1073/pnas.2019069118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8020792PMC
March 2021

Conserving intraspecific variation for nature's contributions to people.

Nat Ecol Evol 2021 Mar 1. Epub 2021 Mar 1.

Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, CA, USA.

The rapid loss of intraspecific variation is a hidden biodiversity crisis. Intraspecific variation, which includes the genomic and phenotypic diversity found within and among populations, is threatened by local extinctions, abundance declines, and anthropogenic selection. However, biodiversity assessments often fail to highlight this loss of diversity within species. We review the literature on how intraspecific variation supports critical ecological functions and nature's contributions to people (NCP). Results show that the main categories of NCP (material, non-material, and regulating) are supported by intraspecific variation. We highlight new strategies that are needed to further explore these connections and to make explicit the value of intraspecific variation for NCP. These strategies will require collaboration with local and Indigenous groups who possess critical knowledge on the relationships between intraspecific variation and ecosystem function. New genomic methods provide a promising set of tools to uncover hidden variation. Urgent action is needed to document, conserve, and restore the intraspecific variation that supports nature and people. Thus, we propose that the maintenance and restoration of intraspecific variation should be raised to a major global conservation objective.
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http://dx.doi.org/10.1038/s41559-021-01403-5DOI Listing
March 2021

Million-year-old DNA sheds light on the genomic history of mammoths.

Nature 2021 03 17;591(7849):265-269. Epub 2021 Feb 17.

Centre for Palaeogenetics, Stockholm, Sweden.

Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.
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http://dx.doi.org/10.1038/s41586-021-03224-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116897PMC
March 2021

A Reference Genome Assembly of American Bison, Bison bison bison.

J Hered 2021 Mar;112(2):174-183

USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA.

Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary. Here, we use trio binning of long reads from a bison-Simmental cattle (Bos taurus taurus) male F1 hybrid to sequence and assemble the genome of the American plains bison (Bison bison bison). The male haplotype genome is chromosome-scale, with a total length of 2.65 Gb across 775 scaffolds (839 contigs) and a scaffold N50 of 87.8 Mb. Our bison genome is ~13× more contiguous overall and ~3400× more contiguous at the contig level than the current bison reference genome. The bison genome sequence presented here (ARS-UCSC_bison1.0) will enable new research into the evolutionary history of this iconic megafauna species and provide a new tool for the management of bison populations in federal and commercial herds.
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http://dx.doi.org/10.1093/jhered/esab003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8006816PMC
March 2021

Reintroduction of the archaic variant of in cortical organoids alters neurodevelopment.

Science 2021 02;371(6530)

Department of Pediatrics and Department of Cellular & Molecular Medicine, School of Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA 92037, USA.

The evolutionarily conserved splicing regulator neuro-oncological ventral antigen 1 () plays a key role in neural development and function. also includes a protein-coding difference between the modern human genome and Neanderthal and Denisovan genomes. To investigate the functional importance of an amino acid change in humans, we reintroduced the archaic allele into human induced pluripotent cells using genome editing and then followed their neural development through cortical organoids. This modification promoted slower development and higher surface complexity in cortical organoids with the archaic version of Moreover, levels of synaptic markers and synaptic protein coassociations correlated with altered electrophysiological properties in organoids expressing the archaic variant. Our results suggest that the human-specific substitution in , which is exclusive to modern humans since divergence from Neanderthals, may have had functional consequences for our species' evolution.
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http://dx.doi.org/10.1126/science.aax2537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8006534PMC
February 2021

Is Opioid-Limiting Legislation Effective for Hand Surgery Patients?

Hand (N Y) 2021 Feb 3:1558944720988132. Epub 2021 Feb 3.

Brown University, Providence, RI, USA.

Background: The Rhode Island State Legislature passed the in 2016 to limit opioid prescriptions. We aimed to objectively evaluate its effect on opioid prescribing for hand surgery patients and also identify risk factors for prolonged opioid use.

Methods: A 6-month period (January-June 2016) prior to passage of the law was compared with a period following its implementation (July-December 2017). Thumb carpometacarpal arthroplasty and distal radius fracture fixation were classified as "major surgery" and carpal tunnel and trigger finger release as "minor surgery." Prescription Drug Monitoring Database was used to review controlled substances filled during the study periods.

Results: A total of 1380 patients met our inclusion criteria, with 644 and 736 . Patients undergoing "major surgery" saw a significant decrease in the number of pills issued in the first postoperative prescription (41.1 vs 21.0) and a corresponding decrease in morphine milligram equivalents (MMEs) (318.6 vs 159.2 MMEs) after implementation. A 30% decrease in MMEs was also seen in those undergoing "major surgery" in the first 30 days postoperatively (544.7 vs 381.7 MMEs). Risk factors for prolonged opioid use included male sex and preoperative opioid use.

Conclusions: In Rhode Island, opioid-limiting legislation resulted in a significant decrease in the number of pills and MMEs of the initial prescription and a 30% decrease in total MMEs in the 30-day postoperative period after "major hand surgery." Additional research is needed to explore the association between legislation and clinical outcomes.
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http://dx.doi.org/10.1177/1558944720988132DOI Listing
February 2021

Dire wolves were the last of an ancient New World canid lineage.

Nature 2021 03 13;591(7848):87-91. Epub 2021 Jan 13.

School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.
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http://dx.doi.org/10.1038/s41586-020-03082-xDOI Listing
March 2021

A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus.

J Hered 2021 Mar;112(2):184-191

USDA, ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD.

Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.
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http://dx.doi.org/10.1093/jhered/esab002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8006815PMC
March 2021

Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France.

Curr Biol 2021 Mar;31(5):1072-1083.e10

Centre d'Anthropobiologie et de Génomique de Toulouse CAGT, CNRS UMR 5288, Université Toulouse III Paul Sabatier, Faculté de Médecine Purpan, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France. Electronic address:

The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe. These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry. This transition is documented through extensive ancient genomic data from present-day Britain, Ireland, Iberia, Mediterranean islands, and Germany. It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63), with the exception of one Late Neolithic genome sequenced at 0.05× coverage. This leaves the key transitional period covering ∼3,400-2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400-1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale.
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http://dx.doi.org/10.1016/j.cub.2020.12.015DOI Listing
March 2021

Can Cyanobacterial Diversity in the Source Predict the Diversity in Sludge and the Risk of Toxin Release in a Drinking Water Treatment Plant?

Toxins (Basel) 2021 Jan 1;13(1). Epub 2021 Jan 1.

Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montréal, QC H3C 3A7, Canada.

Conventional processes (coagulation, flocculation, sedimentation, and filtration) are widely used in drinking water treatment plants and are considered a good treatment strategy to eliminate cyanobacterial cells and cell-bound cyanotoxins. The diversity of cyanobacteria was investigated using taxonomic cell counts and shotgun metagenomics over two seasons in a drinking water treatment plant before, during, and after the bloom. Changes in the community structure over time at the phylum, genus, and species levels were monitored in samples retrieved from raw water (RW), sludge in the holding tank (ST), and sludge supernatant (SST). and were predominant species detected in RW by taxonomic cell counts. Shotgun metagenomics revealed that Proteobacteria was the predominant phylum in RW before and after the cyanobacterial bloom. Taxonomic cell counts and shotgun metagenomic showed that the bloom occurred inside the plant. Cyanobacteria and Bacteroidetes were the major bacterial phyla during the bloom. Shotgun metagenomics also showed that , and were the predominant detected cyanobacterial genera in the samples. Conventional treatment removed more than 92% of cyanobacterial cells but led to cell accumulation in the sludge up to 31 times more than in the RW influx. Coagulation/sedimentation selectively removed more than 96% of and . Cyanobacterial community in the sludge varied from raw water to sludge during sludge storage (1-13 days). This variation was due to the selective removal of coagulation/sedimentation as well as the accumulation of captured cells over the period of storage time. However, the prediction of the cyanobacterial community composition in the SST remained a challenge. Among nutrient parameters, orthophosphate availability was related to community profile in RW samples, whereas communities in ST were influenced by total nitrogen, Kjeldahl nitrogen (N- Kjeldahl), total and particulate phosphorous, and total organic carbon (TOC). No trend was observed on the impact of nutrients on SST communities. This study profiled new health-related, environmental, and technical challenges for the production of drinking water due to the complex fate of cyanobacteria in cyanobacteria-laden sludge and supernatant.
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http://dx.doi.org/10.3390/toxins13010025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7823770PMC
January 2021

A mummified Pleistocene gray wolf pup.

Curr Biol 2020 Dec;30(24):R1467-R1468

Government of Yukon, Department of Tourism and Culture, Yukon Palaeontology Program, PO Box 2703, Whitehorse, YT, Y1A 2C6, Canada; Collections and Research, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, ON, K1P 6P4, Canada.

In July 2016, a mummified carcass of an ancient wolf (Canis lupus) pup (specimen YG 648.1) was discovered in thawing permafrost in the Klondike goldfields, near Dawson City, Yukon, Canada (Figure 1A). The wolf pup mummy was recovered along a small tributary of Last Chance Creek during hydraulic thawing that exposed the permafrost sediment in which it was preserved. This mummified wolf pup is important to the local Tr'ondëk Hwëch'in people, who named it Zhùr, meaning 'wolf' in the Hän language of their community. Here, we report detailed morphometric, isotopic, and genetic analyses of Zhùr that reveal details of her appearance, evolutionary relationships to other wolves and short life-history and ecology. Zhùr is the most complete wolf mummy known. She lived approximately 57,000 years ago and died in her den during a collapse of the sediments. During her short life, she ate aquatic resources, and is related to ancient Beringian and Russian gray wolves and her clade is basal to all living gray wolves. VIDEO ABSTRACT.
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http://dx.doi.org/10.1016/j.cub.2020.11.011DOI Listing
December 2020

Ten strategies for a successful transition to remote learning: Lessons learned with a flipped course.

Ecol Evol 2020 Nov 16;10(22):12620-12634. Epub 2020 Oct 16.

Department of Ecology and Evolutionary Biology University of California Los Angeles Los Angeles CA USA.

Transitioning from in-person to remote learning can present challenges for both the instructional team and the students. Here, we use our course "Biodiversity in the Age of Humans" to describe how we adapted tools and strategies designed for a flipped classroom to a remote learning format. Using anonymous survey data collected from students who attended the course either in-person (2019) or remotely (2020), we quantify student expectations and experiences and compare these between years. We summarize our experience and provide ten "tips" or recommendations for a transition to remote learning, which we divide into three categories: (a) precourse instructor preparation; (b) outside of class use of online materials; and (c) during class student engagement. The survey results indicated no negative impact on student learning during the remote course compared to in-person instruction. We found that communicating with students and assessing specific needs, such as access to technology, and being flexible with the structure of the course, simplified the transition to remote instruction. We also found that short, pre-recorded videos that introduce subject materials were among the most valuable elements for student learning. We hope that instructors of undergraduate ecology and evolution courses can use these recommendations to help establish inclusive online learning communities that empower students to acquire conceptual knowledge and develop scientific inquiry and literacy skills.
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http://dx.doi.org/10.1002/ece3.6760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7679550PMC
November 2020

Efficacy of an Educational Intervention on the Hydration of Indoor College Athletes.

J Athl Train 2020 Nov 25. Epub 2020 Nov 25.

Director, Associate Professor, Barry University,

Context: Research focusing on improving hydration status and knowledge in indoor female athletes is limited. Previous research has demonstrated hydration education is an optimal tool for improving the hydration status of athletes.

Objective: To assess hydration status and fluid intake of collegiate female indoor athletes before and after a one-time educational intervention.

Design: Controlled field study Setting: Collegiate women's volleyball and basketball practices Participants: Twenty-five female collegiate volleyball and basketball athletes (21±1years; 173.5±8.7cm, 72.1±10.0kg) were assessed during six days of practices.

Intervention(s): Participants' hydration status and habits were monitored for 3 practice days before undergoing a hydration educational intervention. Post-intervention, participants were observed for 3 more practice days.

Main Outcome Measures: Change in body mass (BM), fluid consumed, urine specific gravity (USG), urine color (Ucol), and sweat rate were recorded for 6 practice days. Participants completed a hydration knowledge questionnaire (HAQ) before and after the intervention to assess changes.

Results: Three-day mean USG and Ucol were considered euhydrated pre-practice (USG 1.015±0.006, Ucol 4±1) and remained euhydrated post-practice (USG 1.019±0.005, Ucol 5±2) during the pre-intervention period. Decreases in pre-practice Ucol (p<.01) and increases (p<.01) in hydration knowledge were found post-intervention. Basketball athletes had greater BM losses from pre- to post-practice compared to volleyball (p=.000). Significant increases were found overall when comparing pre- and post-practice measures of USG and Ucol in pre-intervention period (p=.000, p=.001) and post-intervention period (p=.001, p=.000). No correlation was found between hydration knowledge and physiological indices of hydration and fluid intake.

Conclusions: Overall, female collegiate indoor athletes were hydrated and knowledgeable of hydration. Variability in findings indicates further research is needed with this sport; clinically, attention should be given to individualized needs of each athlete. More research is needed to determine if a one-time educational intervention may be an effective tool for improving overall hydration in this population.
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http://dx.doi.org/10.4085/1062-6050-0495.19DOI Listing
November 2020

Does diversity beget diversity in microbiomes?

Elife 2020 11 20;9. Epub 2020 Nov 20.

Département de sciences biologiques, Université de Montréal, Montreal, Canada.

Microbes are embedded in complex communities where they engage in a wide array of intra- and inter-specific interactions. The extent to which these interactions drive or impede microbiome diversity is not well understood. Historically, two contrasting hypotheses have been suggested to explain how species interactions could influence diversity. 'Ecological Controls' (EC) predicts a negative relationship, where the evolution or migration of novel types is constrained as niches become filled. In contrast, 'Diversity Begets Diversity' (DBD) predicts a positive relationship, with existing diversity promoting the accumulation of further diversity via niche construction and other interactions. Using high-throughput amplicon sequencing data from the Earth Microbiome Project, we provide evidence that DBD is strongest in low-diversity biomes, but weaker in more diverse biomes, consistent with biotic interactions initially favouring the accumulation of diversity (as predicted by DBD). However, as niches become increasingly filled, diversity hits a plateau (as predicted by EC).
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http://dx.doi.org/10.7554/eLife.58999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7755399PMC
November 2020

Highly accurate long-read HiFi sequencing data for five complex genomes.

Sci Data 2020 11 17;7(1):399. Epub 2020 Nov 17.

Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA.

The PacBio HiFi sequencing method yields highly accurate long-read sequencing datasets with read lengths averaging 10-25 kb and accuracies greater than 99.5%. These accurate long reads can be used to improve results for complex applications such as single nucleotide and structural variant detection, genome assembly, assembly of difficult polyploid or highly repetitive genomes, and assembly of metagenomes. Currently, there is a need for sample data sets to both evaluate the benefits of these long accurate reads as well as for development of bioinformatic tools including genome assemblers, variant callers, and haplotyping algorithms. We present deep coverage HiFi datasets for five complex samples including the two inbred model genomes Mus musculus and Zea mays, as well as two complex genomes, octoploid Fragaria × ananassa and the diploid anuran Rana muscosa. Additionally, we release sequence data from a mock metagenome community. The datasets reported here can be used without restriction to develop new algorithms and explore complex genome structure and evolution. Data were generated on the PacBio Sequel II System.
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http://dx.doi.org/10.1038/s41597-020-00743-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7673114PMC
November 2020

Dense sampling of bird diversity increases power of comparative genomics.

Authors:
Shaohong Feng Josefin Stiller Yuan Deng Joel Armstrong Qi Fang Andrew Hart Reeve Duo Xie Guangji Chen Chunxue Guo Brant C Faircloth Bent Petersen Zongji Wang Qi Zhou Mark Diekhans Wanjun Chen Sergio Andreu-Sánchez Ashot Margaryan Jason Travis Howard Carole Parent George Pacheco Mikkel-Holger S Sinding Lara Puetz Emily Cavill Ângela M Ribeiro Leopold Eckhart Jon Fjeldså Peter A Hosner Robb T Brumfield Les Christidis Mads F Bertelsen Thomas Sicheritz-Ponten Dieter Thomas Tietze Bruce C Robertson Gang Song Gerald Borgia Santiago Claramunt Irby J Lovette Saul J Cowen Peter Njoroge John Philip Dumbacher Oliver A Ryder Jérôme Fuchs Michael Bunce David W Burt Joel Cracraft Guanliang Meng Shannon J Hackett Peter G Ryan Knud Andreas Jønsson Ian G Jamieson Rute R da Fonseca Edward L Braun Peter Houde Siavash Mirarab Alexander Suh Bengt Hansson Suvi Ponnikas Hanna Sigeman Martin Stervander Paul B Frandsen Henriette van der Zwan Rencia van der Sluis Carina Visser Christopher N Balakrishnan Andrew G Clark John W Fitzpatrick Reed Bowman Nancy Chen Alison Cloutier Timothy B Sackton Scott V Edwards Dustin J Foote Subir B Shakya Frederick H Sheldon Alain Vignal André E R Soares Beth Shapiro Jacob González-Solís Joan Ferrer-Obiol Julio Rozas Marta Riutort Anna Tigano Vicki Friesen Love Dalén Araxi O Urrutia Tamás Székely Yang Liu Michael G Campana André Corvelo Robert C Fleischer Kim M Rutherford Neil J Gemmell Nicolas Dussex Henrik Mouritsen Nadine Thiele Kira Delmore Miriam Liedvogel Andre Franke Marc P Hoeppner Oliver Krone Adam M Fudickar Borja Milá Ellen D Ketterson Andrew Eric Fidler Guillermo Friis Ángela M Parody-Merino Phil F Battley Murray P Cox Nicholas Costa Barroso Lima Francisco Prosdocimi Thomas Lee Parchman Barney A Schlinger Bette A Loiselle John G Blake Haw Chuan Lim Lainy B Day Matthew J Fuxjager Maude W Baldwin Michael J Braun Morgan Wirthlin Rebecca B Dikow T Brandt Ryder Glauco Camenisch Lukas F Keller Jeffrey M DaCosta Mark E Hauber Matthew I M Louder Christopher C Witt Jimmy A McGuire Joann Mudge Libby C Megna Matthew D Carling Biao Wang Scott A Taylor Glaucia Del-Rio Alexandre Aleixo Ana Tereza Ribeiro Vasconcelos Claudio V Mello Jason T Weir David Haussler Qiye Li Huanming Yang Jian Wang Fumin Lei Carsten Rahbek M Thomas P Gilbert Gary R Graves Erich D Jarvis Benedict Paten Guojie Zhang

Nature 2020 11 11;587(7833):252-257. Epub 2020 Nov 11.

China National GeneBank, BGI-Shenzhen, Shenzhen, China.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity. Sparse taxon sampling has previously been proposed to confound phylogenetic inference, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.
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http://dx.doi.org/10.1038/s41586-020-2873-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759463PMC
November 2020

Larger Initial Opioid Prescriptions Following Total Joint Arthroplasty Are Associated with Greater Risk of Prolonged Use.

J Bone Joint Surg Am 2021 Jan;103(2):106-114

Department of Orthopaedic Surgery (D.B.C.R., K.N.S., E.A., E.M.C., and A.H.D.), Warren Alpert Medical School of Brown University (J.H.R. and B.H.S.), Providence, Rhode Island.

Background: The ongoing U.S. opioid epidemic threatens quality of life and poses substantial economic and safety burdens to opioid abusers and their communities, physicians, and health-care systems. Public health experts have argued that prescription opioids are implicated in this epidemic; however, opioid dosing following surgical procedures remains controversial. The purpose of this study was to evaluate the relationship between initial opioid prescribing following total hip arthroplasty (THA) and total knee arthroplasty (TKA) and the risk and quantity of long-term opioid use.

Methods: Patients undergoing THA or TKA from January 1, 2016, to June 30, 2016, were identified. Preoperative 30-day opioid and benzodiazepine exposures were evaluated using the Rhode Island Prescription Drug Monitoring Program. Cumulative morphine milligram equivalents (MMEs) in the postoperative inpatient stay, initial outpatient opioid prescription, and prescriptions filled from 31 to 90 days (prolonged use) and 91 to 150 days (chronic use) following the surgical procedure were calculated. Regression analyses evaluated the association between the initial postoperative opioid dosing and prolonged or chronic use, controlling for demographic characteristics, procedure, preoperative opioid and benzodiazepine exposures, anesthesia type, and use of a peripheral nerve block.

Results: A total of 507 patients (198 who underwent a THA and 309 who underwent a TKA) were identified. Increased inpatient opioid dosing (odds ratio [OR], 1.49 per 1 standard deviation increase in inpatient opioid MMEs; p = 0.001) and increased dosing in the first outpatient prescription (OR, 1.26 per 1 standard deviation increase in initial outpatient prescription MMEs; p = 0.049) were each independently associated with an increased risk of prolonged opioid use. Additionally, increased inpatient dosing postoperatively was strongly associated with a greater risk of chronic use (OR, 1.77 per 1 standard deviation increase in inpatient MMEs; p < 0.001). Among the 30% (151 of 507) of patients requiring prolonged postoperative opioids, each 1-MME increase in the initial outpatient prescription dose was associated with a 0.997-MME increase in quantity filled during the prolonged period (p < 0.001). Among the 14% (73 of 507) of patients requiring chronic opioids, every 1-MME increase in the initial outpatient dose was associated with a 1.678-MME increase in chronic opioid dosing (p = 0.008).

Conclusions: Increased opioid dosing in the early postoperative period following total joint arthroplasty (TJA) is associated with an increased risk of extended opioid use. A dose-dependent relationship between initial outpatient dosing and greater future quantities consumed by those with prolonged usage and those with chronic usage was noted. This study suggests that providers should attempt to minimize inpatient and early outpatient opioid utilization following TJA. Multimodal pain management strategies may be employed to assist in achieving adequate pain control while minimizing opioid utilization.

Level Of Evidence: Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
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http://dx.doi.org/10.2106/JBJS.20.00732DOI Listing
January 2021

A safety evaluation of aripiprazole in the treatment of schizophrenia.

Expert Opin Drug Saf 2020 Dec 16;19(12):1529-1538. Epub 2020 Oct 16.

Department of Psychiatry and Human Behavior, UC Irvine Medical Center , Orange, CA, USA.

Introduction: Aripiprazole is a third generation antipsychotic approved by the US Food and Drug Administration (FDA) for the treatment of schizophrenia. Aripiprazole is available as oral and long-acting injectable (LAI) depot formulations, with a unique mechanism of action comprising partial D and serotonin 5-HT agonism and antagonism at serotonin 5-HT receptors.

Areas Covered: We review short-and-long-term clinical trials, meta-analyses of clinical trials and product information pertaining to the safety and efficacy of aripiprazole in adults with schizophrenia. Formulations of aripiprazole reviewed include oral aripiprazole, Aripiprazole monohydrate LAI (Abilify Maintena©) and Aripiprazole lauroxil LAI (Aristada©). Clinical studies and product information were collected from PubMed, Psychinfo, Embase, and other web sources.

Expert Opinion: Aripiprazole is a generally well-tolerated third-generation antipsychotic with low rates of motor side effects and metabolic adverse effects that occur commonly with several alternative antipsychotics. Akathisia and tremor appear to occur at higher rates with aripiprazole compared to placebo but are still generally uncommon with incidences of 10-11% or less. Uniquely, aripiprazole treatment is associated with reduced serum prolactin levels and QT interval. A variety of LAI options with dosing intervals as infrequent as every 8 weeks provide a compelling reason to select aripiprazole in patients with limited oral treatment adherence.
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http://dx.doi.org/10.1080/14740338.2020.1832990DOI Listing
December 2020

Role of child neurologists and neurodevelopmentalists in the diagnosis of cerebral palsy: A survey study.

Neurology 2020 11 12;95(21):962-972. Epub 2020 Oct 12.

From the Department of Neurology (B.R.A., T.S.P.), Division of Pediatric Neurology, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO; Departments of Pediatrics and Neurology/Neurosurgery (M.S.), Montreal Children's Hospital, McGill University, Montreal, Quebec, Canada; Division of Pediatric Neurology (J.L.Wilson, B.R.), Oregon Health & Science University, Portland, OR; Department of Pediatrics (Y-M.K.), Division of Pediatric Neurology, Loma Linda University School of Medicine, Loma Linda, CA; Stanford University School of Medicine (J.A.O.), Palo Alto, CA; Departments of Child Health (M.C.K.), Neurology & Genetics, University of Arizona College of Medicine, Phoenix, AZ; Program in Neuroscience (M.C.K.), Arizona State University, Tempe, AZ; Pediatric Movement Disorders Program and Neurogenetics Research Program (M.C.K.), Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ; Department of Paediatrics (M.F.), Monash University, Melbourne, Australia; Department of Pediatrics (J.L.Waugh), Division of Pediatric Neurology and Department of Neurology and Neurotherapeutics, University of Texas Southwestern, Dallas, TX; Department of Neurology and Developmental Medicine (B.S.), The Kennedy Krieger Institute, Baltimore, MD; Louisiana State University Health Sciences Center New Orleans and Children's Hospital of New Orleans (A.T.), New Orleans, LA.

Objective: To contextualize the role of child neurologists and neurodevelopmentalists (CNs/NDDs) in cerebral palsy (CP) care, we review the changing landscape of CP diagnosis and survey stakeholder CNs/NDDs regarding their roles in CP care.

Methods: The optimal roles of the multiple specialties involved in CP care are currently unclear, particularly regarding CP diagnosis. We developed recommendations regarding the role of CNs/NDDs noting (1) increasing complexity of CP diagnosis given a growing number of genetic etiologies and treatable motor disorders that can be misdiagnosed as CP and (2) the views of a group of physician stakeholders (CNs/NDDs from the Child Neurology Society Cerebral Palsy Special Interest Group).

Results: CNs/NDDs felt that they were optimally suited to diagnose CP. Many (76%) felt that CNs/NDDs should always be involved in CP diagnosis. However, 42% said that their patients with CP were typically not diagnosed by CNs/NDDs, and 18% did not receive referrals to establish the diagnosis of CP at all. CNs/NDDs identified areas of their expertise critical for CP diagnosis including knowledge of the neurologic examination across development and early identification of features atypical for CP. This contrasts with their views on CP management, where CNs/NDDs felt that they could contribute to the medical team, but were necessary primarily when neurologic coexisting conditions were present.

Discussion: Given its increasing complexity, we recommend early referral for CP diagnosis to a CN/NDD or specialist with comparable expertise. This contrasts with current consensus guidelines, which either do not address or do not recommend specific specialist referral for CP diagnosis.
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http://dx.doi.org/10.1212/WNL.0000000000011036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7734737PMC
November 2020

SBML Level 3: an extensible format for the exchange and reuse of biological models.

Mol Syst Biol 2020 08;16(8):e9110

Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.
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http://dx.doi.org/10.15252/msb.20199110DOI Listing
August 2020

Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.

Curr Biol 2020 Oct 13;30(19):3871-3879.e7. Epub 2020 Aug 13.

Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden. Electronic address:

Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1-3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations [2]. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species' extinction. Analysis of the nuclear genome from a ∼18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans [4]. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the Bølling-Allerød interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.
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http://dx.doi.org/10.1016/j.cub.2020.07.046DOI Listing
October 2020

A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities.

ISME J 2020 12 7;14(12):3011-3023. Epub 2020 Aug 7.

Department of Biology, Concordia University, Montréal, QC, Canada.

Lakes play a pivotal role in ecological and biogeochemical processes and have been described as "sentinels" of environmental change. Assessing "lake health" across large geographic scales is critical to predict the stability of their ecosystem services and their vulnerability to anthropogenic disturbances. The LakePulse research network is tasked with the assessment of lake health across gradients of land use on a continental scale. Bacterial communities are an integral and rapidly responding component of lake ecosystems, yet large-scale responses to anthropogenic activity remain elusive. Here, we assess the ecological impact of land use on bacterial communities from over 200 lakes covering more than 660,000 km across Eastern Canada. In addition to community variation between ecozones, land use across Eastern Canada also appeared to alter diversity, community composition, and network structure. Specifically, increasing anthropogenic impact within the watershed lowered diversity. Likewise, community composition was significantly correlated with agriculture and urban development within a watershed. Interaction networks showed decreasing complexity and fewer keystone taxa in impacted lakes. Moreover, we identified potential indicator taxa of high or low lake water quality. Together, these findings point to detectable bacterial community changes of largely unknown consequences induced by human activity within lake watersheds.
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http://dx.doi.org/10.1038/s41396-020-0733-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7784917PMC
December 2020

Impact of raising serum myoglobin on resuscitation of trauma patients with high injury severity score (ISS).

Surg Open Sci 2020 Apr 11;2(2):81-84. Epub 2020 Jan 11.

Department of Trauma Surgery, & Department of Clinical & Academic Research, Ascension Genesys Hospital, Grand Blanc, MI 48439, USA.

Introduction: Recent studies recommend limiting the amount of crystalloid perfused during resuscitation for trauma patients. Severely injured patients sustain extensive muscle damage with subsequent high serum myoglobin levels precipitating acute renal injury if not treated immediately. To timely identify patients at risk of acute renal injury, we proposed determining the strength of the correlation between the American College of Surgeons-defined injury severity score with serum and urine myoglobin level in the early hours of arrival to the emergency department to determine the patient at higher risk of raising serum myoglobin level and subsequent renal injury.

Method: A retrospective analysis was conducted at a 400-bed community teaching hospital with a level 2 trauma section and annual admission of 750-800 patients using the data in the trauma registry (2010-2017). Patients with an injury severity score of 15 or above were selected, and Student test and Pearson correlation 2-tailed analysis were used to identify the relationship with serum myoglobin.

Result: There were 306 patients total, with 200 men (70.3%) and 106 women (29.7%) and a mean age of 60.64 (SD = 23.6) (range 18-96) years. The mean injury severity score was 22.3 (SD = 8.5) (range 16-75). The median level of serum myoglobin in the first 24 hours of admission was 848.56 ng/mL (range 22-11,197). There was a strong and significant correlation between the 2 variables ( = 0.397,  < .0001).

Conclusion: The appearance of urine myoglobin with serum level of 39 ng/mL suggests that with higher injury severity score, the potential for acute kidney injury is likely and should be addressed early in the patient management.
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http://dx.doi.org/10.1016/j.sopen.2019.12.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7391883PMC
April 2020

Author Correction: 863 genomes reveal the origin and domestication of chicken.

Cell Res 2020 Sep;30(9):824-825

State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41422-020-0380-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7609341PMC
September 2020

Traumatic Brain Injury in the Elderly: Can We Reduce Readmissions? : A Community Hospital Experience.

Am Surg 2020 Dec 8;86(12):1647-1650. Epub 2020 Jul 8.

2974 Genesys Trauma Services, Ascension Genesys Medical Center, Grand Blanc, MI, USA.

Background: Traumatic brain injury (TBI) is a leading cause of mortality and long-term morbidity in trauma patients, with a growing incidence among the elderly. Injury-related disability has many costs, and rehospitalization is a significant part of that. The current study was carried out in an elderly population with TBI to identify risk factors and measures associated with rehospitalization.

Methods: We performed a retrospective analysis of 299 patients with a primary diagnosis of TBI admitted between 2016 and 2018. Variables selected for analysis encompassed the following: patient age, sex, comorbidities, diagnosis, length of stay, use of anticoagulants, 6-month readmission rate, and diagnosis for readmission. Chi-square analysis was used to identify potential risk factors, and multiple regression analysis was conducted to model the relationship.

Results: 209 patients met inclusion criteria, with a mean age of 69 years (SD ± 18.6 years), with (51.5%) males and (48.5%) females. 188 (62.9%) patients were on anticoagulant therapy. 120 patients were discharged to home (40.1%). 79 patients (26.4%) were readmitted within 6 months of discharge, the majority of whom (48 patients, 60.8%) presented with a subdural hematoma (SDH). 38 readmitted patients (49%) came from home, and 57 patients (80%) were on anticoagulant therapy.

Conclusion: In elderly patients with TBI, discharge to a home setting correlates with a higher risk of readmission within 6 months, a majority with a diagnosis of recurrent SDH. Anticoagulant therapy and frequent past readmissions also correlated with a higher risk of subsequent readmission.
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http://dx.doi.org/10.1177/0003134820933560DOI Listing
December 2020