bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trends in Pacific Canadian groundfish stock status
Authors: Anderson Sean C. , Connors Brendan M. , English Philina A. , Forrest Robyn E. , Haigh Rowan , Holt Kendra R. 
Published: December 2021

AbstractWe assembled estimated biomass (B) time series from stock assessments for 24 Pacific Canadian groundfish stocks and modelled average and stock status through 2020 based on biomass relative to each stock’s (1) Limit Reference Point (B/LRP), (2) Upper Stock Reference (B/USR), and (3) biomass at maximum sustainable yield (B/BMSY). The overall mean B/LRP in 2020 was 3.2 (95% credible interval [CI]: 2.6–3.9). The overall mean B/USR and B/BMSY in 2020 was 1.5 (95% CI: 1.3–1.9) and 1.4 (95% CI: 1.1–1.7), respectively. Average stock status declined from 1950 to around 2000 and has remained relatively stable since then. The change around 2000 followed the implementation of ITQs (individual transferable quotas) for the trawl fleet and the commencement of the synoptic trawl surveys. As of their last assessment, four stocks (Strait of Georgia Lingcod [Area 4B], coastwide Bocaccio, and inside and outside Quillback Rockfish) had a greater than 5% probability of being below their LRP (i.e., in the “ critical zone”); Pacific Cod in Area 3CD had a 4.6% probability. Roughly one-third of stocks had a greater than 1 in 4 chance of being below their USR (i.e., in the “ cautious zone”). Conversely, two-thirds of assessed groundfish stocks had a high (>75%) probability of being above the USR (i.e., in the “ healthy zone”).
Milking it for all it’s worth: The effects of environmental enrichment on maternal nurturance, lactation quality, and offspring social behavior
Authors: DeRosa Holly , Caradonna Salvatore G. , Tran Hieu , Marrocco Jordan , Kentner Amanda C. 
Published: December 2021

AbstractBreastfeeding confers robust benefits to offspring development in terms of growth, immunity, and neurophysiology. Similarly, improving environmental complexity (i.e., environmental enrichment; EE) contributes developmental advantages to both humans and laboratory animal models. However, the impact of environmental context on maternal care and milk quality has not been thoroughly evaluated, nor are the biological underpinnings of EE on offspring development understood. Here, Sprague-Dawley rats were housed and bred in either EE or standard-housed (SD) conditions. EE dams gave birth to a larger number of pups, and litters were standardized and cross-fostered across groups on postnatal day (P)1. Maternal milk samples were then collected on P1 (transitional milk phase) and P10 (mature milk phase) for analysis. While EE dams spent less time nursing, postnatal enrichment exposure was associated with heavier offspring bodyweights. Milk from EE mothers had increased triglyceride levels, a greater microbiome diversity, and a significantly higher abundance of bacterial families related to bodyweight and energy metabolism. These differences reflected comparable transcriptomic changes at the genome-wide level. In addition to changes in lactational quality, we observed elevated levels of cannabinoid receptor 1 in the hypothalamus of EE dams, and sex- and time-dependent effects of EE on offspring social behavior. Together, these results underscore the multidimensional impact of the combined neonatal and maternal environments on offspring development and maternal health. Moreover, they highlight potential deficiencies in the use of “gold standard” laboratory housing in the attempt to design translationally relevant animal models in biomedical research.Significance StatementMaternal care quality is different between environmentally enriched (EE) and standard laboratory housed (SD) dams. SD rat dams spend more time nursing their young. This may result in overfeeding which can program offspring neural stress responses. Alternatively, metabolic differences in milk may affect neurodevelopmental outcomes, which are different between EE and SD animals. To test this, we evaluated milk and offspring behavior. Milk from EE dams had elevated triglyceride levels and microbiome diversity. EE offspring had heavier body weights and increased social behavior which was lost with crossfostering into SD housing. These data identify potential deficiencies in the quality of “gold standard” laboratory housing and its impact on the welfare and design of translationally relevant animal models in biomedical research.
High-performance Saccharomyces cerevisiae-based biosensor for heavy metal detection
Authors: Fan Cong , Zhang Danli , Mo Qiwen , Yuan Jifeng 
Published: December 2021

ABSTRACTHeavy metals, i.e., Cu(II), are harmful to the environment. There is an increasing demand to develop inexpensive detection methods for heavy metals. Here, we developed a yeast biosensor with reduced-noise and improved signal output for potential on-site copper ion detection. The copper-sensing circuit was achieved by employing a secondary genetic layer to control the galactose-inducible (GAL) system in Saccharomyces cerevisiae. The reciprocal control of the Gal4 activator and Gal80 repressor under copper-responsive promoters resulted in a low-noise and ultrasensitive yeast biosensor for the copper ion detection. Furthermore, we developed a betaxanthin-based colorimetric assay, as well as 2-phenylethanol and styrene-based olfactory outputs for the copper ion detection. Notably, our engineered yeast sensor confers a narrow range switch-like behavior, which can give a “yes/no” response when coupled with betaxanthin-based visual phenotype. Taken together, we envision that the design principle established here might be applicable for developing other sensing systems for various chemical detections.IMPORTANCEThe accumulation of heavy metals in the environment led to an imbalance with environmental and ecological impacts, and there is an increasing demand for inexpensive methods that permit on-site detection of heavy metals. In this study, a yeast biosensor with reduced-noise and improved signal output was developed. We used a betaxanthin-based colorimetric assay for monitoring the copper contamination in water samples, which confers a switch-like behavior with a “yes/no” response. In addition, we also explored the 2-phenylethanol and styrene-based outputs for copper detection, which might be useful for olfactory detection of heavy metals.
Distinct promoter regions of the oxytocin receptor gene are hypomethylated in Prader-Willi syndrome and in Prader-Willi syndrome associated psychosis
Authors: Heseding Hannah Marie , Jahn Kirsten , Eberlein Christian K. , Wieting Jelte , Maier Hannah B. , Proskynitopoulos Phileas , Glahn Alexander , Bleich Stefan , Frieling Helge , Deest Maximilian 
Published: December 2021

AbstractBackgroundPrader-Willi syndrome (PWS) is a rare neurodevelopmental disorder caused by a loss of usually paternally expressed, maternally imprinted genes located on chromosome 15q11-q13. Individuals with PWS display a specific behavioral phenotype and have a higher susceptibility than the general population for certain psychiatric conditions, especially psychosis. An impairment of the oxytocin system has been described in Prader-Willi syndrome, but has not yet been investigated on the epigenetic level. Recent studies have pointed out altered methylation patterns of the oxytocin receptor gene (OXTR) in various psychiatric disorders, including psychosis.MethodsIn this study, we investigated methylation rates of CpG dinucleotides in the promoter region of the oxytocin receptor gene via bisulfite-sequencing using DNA extracted from peripheral blood samples of 31 individuals with PWS and 14 controls matched for age, sex and BMI.ResultsIndividuals with PWS show significantly lower methylation in the intron 1 region of the OXTR than neurotypical controls (p=0.012). Furthermore, male PWS subjects with psychosis show significantly lower methylation of the OXTR exon 1 region than those without psychosis (p=0.002). Transcription factor binding site analysis revealed E2F1 as a transcription factor potentially binding to the exon 1 region. E2F1 is physiologically regulated by Necdin, an anti-apoptotic protein whose corresponding gene is located within the PWS locus.ConclusionThis study provides evidence of a disruption of the Oxytocin system on an epigenetic level in PWS in general and in individuals with PWS and psychosis.
Selection-driven adaptation to the extreme Antarctic environment in the Emperor penguin
Authors: Pirri Federica , Ometto Lino , Fuselli Silvia , Fernandes Flávia A. N. , Ancona Lorena , Le Bohec Céline , Zane Lorenzo , Trucchi Emiliano 
Published: December 2021

AbstractThe eco-evolutionary history of penguins is profoundly influenced by their shift from temperate to cold environments. Breeding only in Antarctica during the winter, the Emperor penguin appears as an extreme outcome of this process, with unique features related to insulation, heat production and energy management. However, whether this species actually diverged from a less cold-adapted ancestor, thus more similar in ecology to its sister species, the King penguin, is still an open question. As the Antarctic niche shift likely resulted in vast changes in selective pressure experienced by the Emperor penguin, the identification and relative quantification of the genomic signatures of selection, unique to each of these sister species, could answer this question. Applying a suite of phylogeny-based methods on 7,651 orthologous gene alignments of seven penguins and 13 other birds, we identified a set of candidate genes showing significantly different selection regimes either in the Emperor or in the King penguin lineage. Our comparative approach unveils a more pervasive selection shift in the Emperor penguin, supporting the hypothesis that its extreme cold adaptation is a derived state from a more King penguin-like ecology. Among the candidate genes under selection in the Emperor penguin, four genes (TRPM8, LEPR, CRB1, and SFI1) were identified before in other cold adapted vertebrates, while, on the other hand, 161 genes can be assigned to functional pathways relevant to cold adaptation (e.g., cardiovascular system, lipid, fatty acid and glucose metabolism, insulation, etc.). Our results show that extreme cold adaptation in the Emperor penguin largely involved unique genetic options which, however, affect metabolic and physiological traits common to other cold-adapted homeotherms.
A comprehensive examination of ACE-2 receptor and prediction of spike glycoprotein and ACE-2 interaction based on in silico analysis of ACE-2 receptor
Authors: Özgentürk Nehir Özdemir , Aktaş Emre 
Published: December 2021

AbstractACE-2 receptor plays a vital role not only in the SARS-CoV-induced epidemic but also in some diseases. Studies have been carried out on the interactions of ACE-2-SARS-CoV proteins. However, comprehensive research has not been conducted on ACE2 protein by using bioinformatic tools. The present study especially two places, G104 and L108 points, which are effective in protecting the structure of the ACE-2 protein, play a critical role in the biological functioning of this protein, and play an essential role in determining the chemicalphysical properties of this protein, and play a crucial role for ACE-2 protein-SARS CoV surface glycoprotein, were determined. It was also found that the G104 and L108 regions were more prone to possible mutations or deletions than the other ACE-2 protein regions. Moreover, it was determined that all possible mutations or deletions in these regions affect the chemical-physical properties, biological functions, and structure of the ACE-2 protein. Having a negative GRAVY value, one transmembrane helix, a significant molecular weight, a long-estimated half-life as well as most having unstable are results of G104 and L108 points mutations or deletions. Finally, it was determined that LQQNGSSVLS, which belong to the ACE-2 protein, may play an active role in binding the spike protein of SARS-CoV. All possible docking score results were estimated. It is thought that this study will bring a different perspective to ACE-2 _SARS-CoV interaction and other diseases in which ACE-2 plays an important role and will also be an essential resource for studies on ACE-2 protein.
From Deer-to-Deer: SARS-CoV-2 is efficiently transmitted and presents broad tissue tropism and replication sites in white-tailed deer
Authors: Martins Mathias , Boggiatto Paola M. , Buckley Alexandra , Cassmann Eric D. , Falkenberg Shollie , Caserta Leonardo C. , Fernandes Maureen H.V. , Kanipe Carly , Lager Kelly , Palmer Mitchell V. , Diel Diego G. 
Published: December 2021

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) in humans, has a broad host range, and is able to infect domestic and wild animal species. Notably, white-tailed deer (WTD, Odocoileus virginianus), the most widely distributed cervid species in the Americas, were shown to be highly susceptible to SARS-CoV-2 in challenge studies and reported natural infection rates approaching 40% in free-ranging WTD in the U.S. Thus, understanding the infection and transmission dynamics of SARS-CoV-2 in WTD is critical to prevent future zoonotic transmission to humans and for implementation of effective disease control measures. Here, we demonstrated that following intranasal inoculation with SARS-CoV-2, WTD fawns shed infectious virus up to day 5 post-inoculation (pi), with high viral loads shed in nasal and oral secretions. This resulted in efficient deer-to-deer transmission on day 3 pi. Consistent a with lack of infectious SARS-CoV-2 shedding after day 5 pi, no transmission was observed to contact animals added on days 6 and 9 pi. We have also investigated the tropism and sites of SARS-CoV-2 replication in adult WTD. Infectious virus was recovered from respiratory-, lymphoid-, and central nervous system tissues, indicating broad tissue tropism and multiple sites of virus replication. The study provides important insights on the infection and transmission dynamics of SARS-CoV-2 in WTD, a wild animal species that is highly susceptible to infection and with the potential to become a reservoir for the virus in the field.Author summaryThe high susceptibility of white-tailed deer (WTD) to SARS-CoV-2, their ability to transmit the virus to other deer, and the recent findings suggesting widespread SARS-CoV-2 infection in wild WTD populations in the U.S. underscore the need for a better understanding of the infection and transmission dynamics of SARS-CoV-2 in this potential reservoir species. Here we investigated the transmission dynamics of SARS-CoV-2 over time and defined the major sites of virus replication during the acute phase of infection. Additionally, we assessed the evolution of the virus as it replicated and transmitted between animals. The work provides important information on the infection dynamics of SARS-CoV-2 in WTD, an animal species that - if confirmed as a new reservoir of infection - may provide many opportunities for exposure and potential zoonotic transmission of the virus back to humans.
The effect of constraining mediolateral ankle moments and foot placement on the use of the counter-rotation mechanism during walking
Authors: van den Bogaart Maud , Bruijn Sjoerd M. , Spildooren Joke , van Dieën Jaap H. , Meyns Pieter 
Published: December 2021

AbstractStability during walking can be maintained by shifts of the Center of Pressure through modulation of foot placement and ankle moments (CoP-mechanism). An additional mechanism to stabilize gait, is the counter-rotation mechanism i.e. changing the angular momentum of segments around the Center of Mass (CoM) to change the direction of the ground reaction force. It is unknown if and how humans use the counter-rotation mechanism to control the CoM during walking and how this interacts with the CoP-mechanism. Thirteen healthy adults walked on a treadmill, while full-body kinematic and force plate data were obtained. The contributions of the CoP and the counter-rotation mechanisms to control the CoM were calculated during steady-state walking, walking on LesSchuh, i.e. constraining mediolateral CoP shifts underneath the stance foot and walking on LesSchuh at 50% of normal step width, constraining both foot placement and ankle mechanisms (LesSchuh50%). A decreased magnitude of within-stride control by the CoP-mechanism was compensated for by an increased magnitude of within-stride control by the counter-rotation mechanism during LesSchuh50% compared to steady-state walking. This suggests that the counter-rotation mechanism is used to stabilize gait when needed. However, the mean contribution of the counter-rotation mechanism over strides did not increase during LesSchuh50% compared to steady-state walking. The CoP-mechanism was the main contributor to the total CoM acceleration. The use of the counter-rotation mechanism may be limited because angular accelerations ultimately need to be reversed and because of interference with other task constraints, such as head stabilization and preventing interference with the gait pattern.
Adaptive strategies under prolonged starvation and role of slow growth in bacterial fitness
Authors: Nandy Pabitra 
Published: December 2021

1.AbstractAdaptive evolution has the power to illuminate genetic mechanisms under a pre-defined set of selection factors in a controlled environment. Laboratory evolution of bacteria under long-term starvation has gained importance in recent years because of its ability to uncover adaptive strategies to overcome prolonged nutrient limitation- a condition thought to be encountered often by natural microbial isolates. In this evolutionary paradigm, bacteria are maintained in an energy-restricted environment in the growth phase called as long-term stationary phase or LTSP. This phase is characterized by a stable viable population size and highly dynamic genetic changes. Multiple independent iterations of LTSP evolution experiments have given rise to mutants that are slow-growing compared to the ancestor. Although the antagonistic regulation between rapid growth and stress response is fairly well-known in bacteria (especiallyEscherichia coli), the reason behind the growth deficit of many LTSP-adapted mutants has not been explored in detail. In this review, I revisit the trade-off between growth and stress response and delve into the regulatory mechanisms currently known to control growth under nutrient deficiency. Focusing on the theme of “sigma-factor competition” I try to search for the evolutionary reasoning of slow growth amongst mutants adapted to prolonged starvation. Additionally, I present novel experimental data indicating the dynamics of four such slow-growing variants that evolved during a 30-day long LTSP evolution experiment withEscherichia coli.
Population genomic analysis of the speckled dace species complex (Rhinichthys osculus) identifies three species-level lineages in California
Authors: Su Yingxin , Moyle Peter B. , Campbell Matthew A. , Finger Amanda J. , O’Rourke Sean M. , Baumsteiger Jason , Miller Michael R. 
Published: December 2021

AbstractThe speckled dace (Rhinichthys osculus) is small cyprinid fish that is widespread in the Western USA. Currently treated as a single species, speckled dace consists of multiple evolutionary lineages that can be recognized as species and subspecies throughout its range. Recognition of taxonomic distinctiveness of speckled dace populations is important for developing conservation strategies. In this study, we collected samples of speckled dace from 38 locations in the American West, with a focus on California. We used RAD sequencing to extract thousands of SNPs across the genome from samples to identify genetic differences among seven California populations informally recognized as speckled dace subspecies: Amargosa, Owens, Long Valley, Lahontan, Klamath, Sacramento, and Santa Ana speckled dace. We performed principal component analysis, admixture analysis, estimated pairwise Fst, and constructed a phylogeny to explore taxonomic relationships among these groups and test if these subspecies warrant formal recognition. Our analyses show that the seven subspecies fit into three major lineages equivalent to species: western (Sacramento-Klamath), Santa Ana, and Lahontan speckled dace. Death Valley speckled dace were determined to be two lineages (Amargosa and Long Valley) within Lahontan speckled dace. Western and Lahontan speckled dace lineages had branches that can be designated as subspecies. These designations fit well with the geologic history of the region which has promoted long isolation of populations. This study highlights the importance of genetic analysis for conservation and management of freshwater fishes.
RNA binding protein RBM3 augments kissing loop formation with lncRNAs to enhance translational control
Authors: Sayed Afreen Asif Ali , Choudhury Sonali , Subramaniam Dharmalingam , Gunewardena Sumedha , Ponnurangam Sivapriya , Dandawate Prasad , Tawfik Ossama , Standing David , Padhye Subhash B. , Li Linheng , Iwakuma Tomoo , Umar Shahid , Jensen Roy A. , Thomas Sufi Mary , Anant Shrikant 
Published: December 2021

AbstractIt is becoming apparent that translational regulation involves the coordinated actions of RNA binding proteins (RBPs) and non-coding RNAs. For efficient translation, mRNA needs to be circularized, which is catalyzed by RNA binding proteins and translation factors. However, the role of lncRNAs in the process is not yet defined. We first performed RNA-seq and RNA- immunoprecipitation coupled-Seq and identified LSAMP-3 and Flii-1. Moreover, modeling studies suggest enhanced kissing loop interactions including of transcripts that encode angiogenesis and epithelial mesenchymal transition. While intestinal epithelial cell specific RBM3 transgenic mice showed increased LSAMP-3 and Flii-1, this was reduced in knockout mice. Also, RBM3 overexpression increased tumor xenograft growth, this was suppressed by knockdown of the lncRNAs. Also, knockdown of endogenous RBM3 reduced lncRNA levels and tumor xenograft growth. In addition, it reduced colitis-associated cancers. We propose that RBPs such as RBM3 mediate their function through regulatory lncRNAs that enable circularization to control translation.
Genomic determinants of Furin cleavage in diverse European SARS-related bat coronaviruses
Authors: Sander Anna-Lena , Moreira-Soto Andres , Yordanov Stoian , Toplak Ivan , Balboni Andrea , Ameneiros Ramón Seage , Corman Victor , Drosten Christian , Drexler Jan Felix 
Published: December 2021

AbstractThe furin cleavage site in SARS-CoV-2 is unique within the Severe acute respiratory syndrome–related coronavirus (SrC) species. We re-assessed diverse SrC from European horseshoe bats and reveal molecular determinants such as purine richness, RNA secondary structures and viral quasispecies potentially enabling furin cleavage. Furin cleavage thus likely emerged from the SrC bat reservoir via molecular mechanisms conserved across reservoir-bound RNA viruses, supporting a natural origin of SARS-CoV-2.