bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative phylogenomic patterns in the Baja California avifauna, their conservation implications, and the stages in lineage divergence
Authors: Vázquez-Miranda Hernán , Zink Robert M. , Pinto Brendan J. 
Published: August 2021

AbstractComparative phylogeography explores the historical congruence of co-distributed species to understand the factors that led to their current genetic and phenotypic structures. Even species that span the same biogeographic barrier can exhibit different phylogeographic structures owing to differences in effective population sizes, marker bias, and dispersal abilities. The Baja California peninsula and adjacent desert regions include several biogeographic barriers that have left phylogeographic patterns in some but not all species. We found that mitochondrial DNA, single nuclear genes, and genome-wide SNP data sets show largely concordant phylogeographic patterns for four bird species along the Baja California peninsula and adjacent mainland: cactus wren, Gila woodpecker, California gnatcatcher, and LeConte’s thrasher. The cactus wren and LeConte’s thrasher show a concordant historical division at or near the Vizcaíno Desert in north-central Baja California, the Gila woodpecker appears to be at an intermediate stage of divergence, and the California gnatcatcher lacks notable phylogeographic structure. None of these four species are classified taxonomically in a way that captures their evolutionary history with the exception of the LeConte’s thrasher. We also present mtDNA data on small samples of ten other species that span the Vizcaíno Desert, with five showing no apparent division, and five species from the Sierra de la Laguna, all of which appear differentiated. Reasons for contrasting phylogeographic patterns should be explored further with genomic data to test the extent of concordant phylogeographic patterns. The evolutionary division at the Vizcaíno desert is well known in other vertebrate species, and our study further corroborates the extent, profound effect and importance of this biogeographic boundary. The areas north and south of the Vizcaíno Desert, which contains considerable diversity, should be recognized as historically significant areas for conservation.
In the Line of Fire: Debris Throwing by Wild Octopuses
Authors: Godfrey-Smith Peter , Scheel David , Chancellor Stephanie , Linquist Stefan , Lawrence Matthew 
Published: August 2021

ABSTRACTWild octopuses at an Australian site frequently propel shells, silt, and algae through the water by releasing these materials from their arms while creating a forceful jet from the siphon held under the arm web. These “throws” occur in several contexts, including interactions with conspecifics, and material thrown in conspecific contexts frequently hits other octopuses. Some throws appear to be targeted on other individuals and play a social role, as suggested by several kinds of evidence. Such throws were significantly more vigorous and more often used silt, rather than shells or algae, and high vigor throws were significantly more often accompanied by uniform or dark body patterns. Some throws were directed differently from beneath the arms and such throws were significantly more likely to hit other octopuses. Throws targeted at other individuals in the same population, as these appear to be, are the least common form of nonhuman throwing.
Breeding displacement in gray wolves(Canis lupus): Three males usurp breeding position and pup rearing from a neighboring pack in Yellowstone National Park
Authors: SunderRaj Jeremy D. , Rabe Jack W. , Cassidy Kira A. , McIntyre Rick , Stahler Daniel R. , Smith Douglas W. 
Published: August 2021

AbstractGray Wolves(Canis lupus)are territorial, group living carnivores that live in packs typically consisting of a dominant breeding pair and their offspring. Breeding tenures are relatively short and competitive, with vacancies usually occurring following a breeder’s death, and are often filled by unrelated immigrants or by relatives of the previous breeder. The frequency and conditions of active breeder displacements are poorly understood. Position changes in the dominance hierarchy are common yet rarely documented in detail. We describe a turnover in male breeding position in a wolf pack by males from a neighboring pack in mid-summer 2016 in Yellowstone National Park. Over the course of two months, three males from the Mollie’s pack displaced the breeding male of the neighboring Wapiti Lake pack, joined the pack’s two adult females, and subsequently raised the previous male’s four approximately three-month old pups. In the four years following the displacement (2017 to 2020), at least one of the intruding males has successfully bred with the dominant female and most years with a subordinate female (who was one of the pups at the time of displacement). The pack reared pups to adulthood each year. Male breeding displacements are likely influenced by male-male competition and female mate choice. These changes are the result of individuals competing to improve breeding position and may lead to increased pack stability and greater reproductive success. We report in detail on the behavior of a closely observed breeding displacement and we discuss the adaptive benefits of the change.
RRNPP_detector: a tool to detect RRNPP quorum sensing systems in chromosomes, plasmids and phages of gram-positive bacteria
Authors: Bernard Charles , Li Yanyan , Bapteste Eric , Lopez Philippe 
Published: August 2021

ABSTRACTGram-positive bacteria (e.g. Firmicutes) and their mobile genetic elements (plasmids, bacteriophages) encode peptide-based quorum sensing systems (QSSs) that regulate behavioral transitions in a density-dependent manner. In their simplest form, termed “RRNPP”, these QSSs are composed of two adjacent genes: a communication propeptide and its cognate intracellular receptor. Despite the prime importance of RRNPP QSSs in the regulation of key biological pathways such as virulence, sporulation or biofilm formation in bacteria, conjugation in plasmids or lysogeny in temperate bacteriophages, no tools exist to predict their presence in target genomes/mobilomes. Here, we introduce RRNPP_detector, a software to predict RRNPP QSSs in chromosomes, plasmids and bacteriophages of gram-positive bacteria, available at https://github.com/TeamAIRE/RRNPP_detector. RRNPP_detector does not rely on homology searches but on a signature of multiple criteria, which are common between distinct families of experimentally-validated RRNPP QSSs. Because this signature is generic while specific to the canonical mechanism of RRNPP quorum sensing, it enables the discovery of novel RRNPP QSSs and thus of novel “languages” of biocommunication. Applying RRNPP_detector against complete genomes of viruses and Firmicutes available on the NCBI, we report a potential 7.5-fold expansion of RRNPP QSS diversity, alternative secretion-modes for certain candidate QSS propeptides, ‘bilingual’ bacteriophages and plasmids, as well as predicted chromosomal and plasmidic Biosynthetic-Gene-Clusters regulated by QSSs.
Spatial and Temporal Consistency of Brain Networks for different Multi-Echo fMRI Combination Methods
Authors: Pilmeyer J. , Hadjigeorgiou G. , Lamerichs R. , Breeuwer M. , Aldenkamp A.P. , Zinger S. 
Published: August 2021

AbstractThe application of multi-echo functional magnetic resonance imaging (fMRI) studies has considerably increased in the last decade due to its superior BOLD sensitivity compared to single-echo fMRI. Various methods have been developed that combine the fMRI time-series derived at different echo times to improve the data quality. Here we evaluated three multi-echo combination schemes, i.e. ‘optimal combination’ (T2*-weighted), temporal Signal-to-Noise Ratio (tSNR) weighted, and temporal Contrast-to-Noise Ratio (tCNR) weighted combination. For the first time, the effect of these multi-echo combinations on functional resting-state networks was assessed in the temporal and spatial domain, and compared to networks derived from the second echo (35 ms) functional images. Sixteen healthy volunteers were scanned during a 5 minutes resting-state fMRI session. After obtaining the networks, several temporal and spatial metrics were calculated for their time-series and spatial maps. Our results showed that, compared to the second echo network time-series, the Pearson correlation and root mean square error were the most consistent for the optimal combination time-series and the least with those derived from tSNR-weighted combination. The frequency analysis further suggested that the time-series from the tSNR-weighted combination method reduced hardware- and physiological-related artifacts as reflected by the reduced power for the associated frequencies in almost all networks. Moreover, the spatial stability and extent of the networks significantly increased after multi-echo combination, primarily for the optimal combination, followed by the tSNR-weighted combination. The performance of the tCNR-weighted combination lacked robustness and instead varied remarkedly between resting-state networks in both the temporal and spatial domain. The results highlight the benefits of multi-echo sequences on resting-state networks as well as the importance of adjusting the choice of multi-echo combination method to the research question and domain of interest.
Sharks, Lies, and Videotape: A content analysis of 32 years of Shark Week documentaries
Authors: Whitenack Lisa B. , Mickley Brady L. , Saltzman Julia , Kajiura Stephen M. , Macdonald Catherine C. , Shiffman David S. 
Published: August 2021

AbstractDespite evidence of their importance to marine ecosystems, at least 25% of all chondrichthyan species are estimated or assessed as threatened with extinction. In addition to the logistical difficulties of effectively conserving wide-ranging marine species, shark conservation is believed to have been hindered in the past by public perceptions of sharks as dangerous to humans. Shark Week is a high-profile, international programming event that has potentially enormous influence on public perceptions of sharks, shark research, shark researchers, and shark conservation. However, Shark Week has received regular criticism for poor factual accuracy, fearmongering, bias, and inaccurate representations of science and scientists. This research analyzes the content and titles of Shark Week episodes across its entire 32 years of programming to determine if there are trends in species covered, research techniques featured, expert identity, conservation messaging, type of programming, and portrayal of sharks. We analyzed titles from 272 episodes (100%) of Shark Week programming and the content of all available (201; 73.9%) episodes. Our data demonstrate that the majority of episodes are not focused on shark bites, although such shows are common and many Shark Week programs frame sharks around fear, risk, and adrenaline. While anecdotal descriptions of disproportionate attention to particular charismatic species (e.g. great whites, bull sharks, and tiger sharks) are accurate and supported by data, 79 shark species have been featured briefly at least once. Shark Week’s depictions of research and of scientists are biased towards a small set of (typically visual and expensive) research methodologies and (mostly white, mostly male) scientists, including presentation of many white male non-scientists as experts. While sharks are more often portrayed negatively than positively, limited conservation messaging does appear in 53% of episodes analyzed. Results suggest that as a whole, while Shark Week is likely contributing to the collective perception of sharks as monsters, even relatively small alterations to programming decisions could substantially improve the presentation of sharks and shark science and conservation issues.
Integration of RT-LAMP and Microfluidic Technology for Detection of SARS-CoV-2 in Wastewater as an Advanced Point-of-care Platform
Authors: Donia Ahmed , Shahid Muhammad Furqan , Hassan Sammer-ul , Shahid Ramla , Ahmad Aftab , Javed Aneela , Nawaz Muhammad , Yaqub Tahir , Bokhari Habib 
Published: August 2021

AbstractDevelopment of lab-on-a-chip (LOC) system based on integration of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and microfluidic technology is expected to speed up SARS-CoV-2 diagnostics allowing early intervention. In the current work, reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and RT-LAMP assays were performed on extracted RNA of 7 wastewater samples from COVID-19 hotspots. RT□LAMP assay was also performed on wastewater samples without RNA extraction. Current detection of SARS-CoV-2 is mainly by RT-qPCR of ORF (ORF1ab) and N genes so we targeted both to find the best surrogate marker for SARS-CoV-2 detection. We also performed RT-LAMP with/without RNA extraction inside microfluidic device to target both genes. Positivity rates of RT-qPCR and RT-LAMP performed on extracted RNA were 100.0% (7/7) and 85.7% (6/7), respectively. RT-qPCR results revealed that all 7 wastewater samples were positive for N gene (Ct range 37-39), and negative for ORF1ab, suggesting that N gene could be used as a surrogate marker for detection of SARS-CoV-2. RT-LAMP of N and ORF (ORF1a) genes performed on wastewater samples without RNA extraction indicated that all 7 samples remains pink (negative). The color remains pink in all microchannels except microchannels which subjected to RT-LAMP for targeting N region after RNA extraction (yellow color) in 6 out of 7 samples. This study shows that SARS-CoV-2 was successfully detected from wastewater samples using RT-LAMP in microfluidic chips.
Ubiquitin modulates 26S proteasome conformational dynamics and promotes substrate degradation
Authors: Jonsson Erik , Htet Zaw Min , Bard Jared A.M. , Dong Ken C. , Martin Andreas 
Published: August 2021

SUMMARYThe 26S proteasome is the major ATP-dependent protease in eukaryotic cells, where it catalyzes the degradation of thousands of proteins for general homeostasis and the control of vital processes. It specifically recognizes appropriate substrates through attached ubiquitin chains and uses its ATPase motor for mechanical unfolding and translocation into a proteolytic chamber. Here, we used single-molecule Förster Resonance Energy Transfer (FRET) measurements to provide unprecedented insights into the mechanisms of selective substrate engagement, ATP-dependent degradation, and the regulation of these processes by ubiquitin chains. Our assays revealed the proteasome conformational dynamics and allowed monitoring individual substrates as they progress through the central channel during degradation. We found that rapid transitions between engagement- and processing-competent conformations of the proteasome control substrate access to the ATPase motor. Ubiquitin-chain binding functions as an allosteric regulator to slow these transitions, stabilize the engagement-competent state, and facilitate degradation initiation. The global conformational transitions cease upon substrate engagement, and except for apparent motor slips when encountering stably folded domains, the proteasome remains in processing-competent states for substrate translocation and unfolding, which is further accelerated by ubiquitin chains. Our studies revealed the dependence of ATP-dependent substrate degradation on the conformational dynamics of the proteasome and its allosteric regulation by ubiquitin chains, which ensure substrate selectivity and prioritization in a crowded cellular environment.
Unraveling Fe(II)-oxidizing mechanisms in a facultative Fe(II) oxidizer Sideroxydans lithotrophicus ES-1 via culturing, transcriptomics, and RT-qPCR
Authors: Zhou Nanqing , Keffer Jessica L. , Polson Shawn W. , Chan Clara S. 
Published: August 2021

AbstractSideroxydans lithotrophicus ES-1 grows autotrophically either by Fe(II) oxidation or thiosulfate oxidation, in contrast to most other neutrophilic Fe(II)-oxidizing bacteria (FeOB) isolates. This provides a unique opportunity to explore the physiology of a facultative FeOB and constrain the genes specific to Fe(II) oxidation. We compared the growth of S. lithotrophicus ES-1 on Fe(II), thiosulfate, and both substrates together. While initial growth rates were similar, thiosulfate-grown cultures had higher yield with or without Fe(II) present, which may give ES-1 an advantage over obligate FeOB. To investigate the Fe(II) and S oxidation pathways, we conducted transcriptomics experiments, validated with RT-qPCR. We explored the long-term gene expression response at different growth phases (over days-week) and expression changes during a short-term switch from thiosulfate to Fe(II) (90 min). The dsr and sox sulfur oxidation genes were upregulated in thiosulfate cultures. The Fe(II) oxidase gene cyc2 was among the top expressed genes during both Fe(II) and thiosulfate oxidation, and addition of Fe(II) to thiosulfate-grown cells caused an increase in cyc2 expression. These results support the role of Cyc2 as the Fe(II) oxidase and suggest that ES-1 maintains readiness to oxidize Fe(II) even in the absence of Fe(II). We used gene expression profiles to further constrain the ES-1 Fe(II) oxidation pathway. Notably, among the most highly upregulated genes during Fe(II) oxidation were genes for alternative complex III, reverse electron transport and carbon fixation. This implies a direct connection between Fe(II) oxidation and carbon fixation, suggesting that CO2 is an important electron sink for Fe(II) oxidation.ImportanceNeutrophilic FeOB are increasingly observed in various environments, but knowledge of their ecophysiology and Fe(II) oxidation mechanisms is still relatively limited. Sideroxydans are widely observed in aquifers, wetlands, and sediments, and genome analysis suggests metabolic flexibility contributes to their success. The type strain ES-1 is unusual amongst neutrophilic FeOB isolates as it can grow on either Fe(II) or a non-Fe(II) substrate, thiosulfate. Almost all our knowledge of neutrophilic Fe(II) oxidation pathways comes from genome analyses, with some work on metatranscriptomes. This study used culture-based experiments to test the genes specific to Fe(II) oxidation in a facultative FeOB and refine our model of the Fe(II) oxidation pathway. We gained insight into how facultative FeOB like ES-1 connect Fe, S, and C biogeochemical cycling in the environment, and suggest a multi-gene indicator would improve understanding of Fe(II) oxidation activity in environments with facultative FeOB.
Heterogeneity of the Cancer Cell Line Metabolic Landscape
Authors: Shorthouse David , Bradley Jenna , Critchlow Susan E. , Bendtsen Claus , Hall Benjamin A 
Published: August 2021

ABSTRACTThe unravelling of the complexity of cellular metabolism is in its infancy. Cancer-associated genetic alterations may result in changes to cellular metabolism that aid in understanding phenotypic changes, reveal detectable metabolic signatures, or elucidate vulnerabilities to particular drugs. To understand cancer-associated metabolic transformation we performed untargeted metabolite analysis of 173 different cancer cell lines from 11 different tissues under constant conditions for 1099 different species using liquid chromatography-mass spectrometry (LC-MS). We correlate known cancer-associated mutations and gene expression programs with metabolic signatures, generating novel associations of known metabolic pathways with known cancer drivers. We show that metabolic activity correlates with drug sensitivity and use metabolic activity to predict drug response and synergy. Finally, we study the metabolic heterogeneity of cancer mutations across tissues, and find that genes exhibit a range of context specific, and more general metabolic control.
An early Shh-H2O2 feedback loop controls the progression of the regenerative program during adult zebrafish fin regeneration
Authors: Thauvin Marion , de Sousa Rodolphe Matias , Alves Marine , Volovitch Michel , Vriz Sophie , Rampon Christine 
Published: August 2021

AbstractReactive oxygen species (ROS), originally classified as toxic molecules, have attracted increasing interest given their actions in cell signaling. Among these molecules, Hydrogen peroxide (H2O2) is the major ROS produced by cells and acts as a second messenger to modify redox-sensitive proteins or lipids. After amputation, tight spatiotemporal regulation of ROS is required first for wound healing and later to initiate the regenerative program. However, the mechanisms carrying out this sustained ROS production and their integration with signaling pathways are still poorly understood. We focused on the early dialog between H2O2 and Sonic Hedgehog (Shh) during fin regeneration. We demonstrate that H2O2 controls Shh expression and that Shh in turn regulates the H2O2 level via a canonical pathway. Moreover, this tightly controlled feedback loop changes during the successive phases of the regenerative program. Dysregulation of the Hedgehog pathway has been implicated in several developmental syndromes, diabetes and cancer. These data support the existence of a very early feedback loop between Shh and H2O2 that might be more generally involved in various physiological or pathological processes. These new findings pave the way to improve regenerative processes, particularly in vertebrates.
Comparative Molecular Genomic Analyses of a Spontaneous Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer
Authors: Lermi Nejla Ozirmak , Gray Stanton B. , Bowen Charles M. , Reyes-Uribe Laura , Dray Beth K. , Deng Nan , Harris R. Alan , Raveendran Muthuswamy , Benavides Fernando , Hodo Carolyn L. , Taggart Melissa W. , Maresso Karen Colbert , Sinha Krishna M. , Rogers Jeffrey , Vilar Eduardo 
Published: August 2021

AbstractColorectal cancer (CRC) remains the third most common cancer in the US with 15% of cases displaying Microsatellite Instability (MSI) secondary to Lynch Syndrome (LS) or somatic hypermethylation of the MLH1 promoter. A cohort of rhesus macaques from our institution developed spontaneous mismatch repair deficient (MMRd) CRC with a notable fraction harboring a pathogenic germline mutation in MLH1 (c.1029C<G, p.Tyr343Ter). Our study incorporated a detailed molecular characterization of rhesus CRC for cross-comparison with human MMRd CRC. We performed PCR-based MSI testing, transcriptomic analysis, and reduced-representation bisulfite sequencing (RRBS) of rhesus CRC (n=41 samples) using next-generation sequencing (NGS). Systems biology pipelines were used for gene set enrichment analysis (GSEA) for pathway discovery, consensus molecular subtyping (CMS), and somatic mutation profiling. Overall, the majority of rhesus tumors displayed high levels of MSI (MSI-high) and differential gene expression profiles that were consistent with known deregulated pathways in human CRC. DNA methylation analysis exposed differentially methylated patterns among MSI-H, MSI-L (MSI-low)/MSS (MS-stable) and LS tumors with MLH1 predominantly inactivated among sporadic MSI-H CRCs. The findings from this study support the use of rhesus macaques as the preferred animal model to study carcinogenesis, develop immunotherapies and vaccines, and implement chemoprevention approaches pertinent to sporadic MSI-H and LS CRC in humans.