bluuebunny/crossref_metadata_2025_split huggingface dataset:
CommensalBacillus subtilisfrom cow milk inhibitsStaphylococcus aureusbiofilm formation and mastitis in mice
Authors: Qiu Min , Feng Lianjun , Zhao Caijun , Gao Siyuan , Bao Lijuan , Zhao Yihong , Fu Yunhe , Hu Xiaoyu 
Published: June 2022

AbstractThe colonization and virulence production of Staphylococcus aureus (S. aureus), a known pathogen that induces mastitis, depend on its quorum-sensing (QS) system and biofilm formation. It has been reported that Bacillus can inhibit the QS system of S. aureus, thereby reducing S. aureus colonization in the intestine. However, whether Bacillus affects S. aureus biofilm formation and consequent colonization during mastitis is still unknown. In this study, the differences in the colonization of S. aureus and Bacillus were first analyzed by isolating and culturing bacteria from milk samples. It was found that the colonization of Bacillus and S. aureus in cow mammary glands was negatively correlated. Secondly, we found that although Bacillus did not affect S. aureus growth, it inhibited the biofilm formation of S. aureus by interfering its QS signaling. The most significant anti-biofilm effect was found in Bacillus subtilis H28 (B. subtilis H28). Finally, we found that B. subtilis H28 treatment alleviated S. aureus-induced mastitis in a mice model. Our results rerealed that bovine milk derived commensal Bacillus inhibited S. aureus colonization and alleviated S. aureus-induced mastitis by influencing biofilm formation, suggesting a potential targeted strategy to limit the colonization of S. aureus in vivo.
From blood to stress—my life investigating cell differentiation
Authors: Breitenbach Michael , Cooper Terrance G 
Published: June 2022

AbstractThis short retrospective covers more than 50 years of research. I spent most of it doing yeast genetics and genetic engineering. It has been my great privilege to be part of the international group of yeast genetics researchers. With many of them named in this retrospective, I am connected in lifelong friendships and the same is true for my students and collaborators. The question which we wanted to ask is “How does the genome of the cell and cell differentiation adapt to changing and stressful environmental conditions?” The two examples we studied were sporulation and pseudohyphal growth. Both forms of differentiation are triggered by the stress of starvation. In the pathway of regulation of pseudohyphal growth, a yeast NADPH oxidase (discovered by our group) plays a major role.
Ancestral State Reconstructions Trace Mitochondria But Not Phagocytosis to the Last Eukaryotic Common Ancestor
Authors: Bremer Nico , Tria Fernando D. K. , Skejo Josip , Garg Sriram G. , Martin William F. 
Published: June 2022

AbstractTwo main theories have been put forward to explain the origin of mitochondria in eukaryotes: phagotrophic engulfment (undigested food) and microbial symbiosis (physiological interactions). The two theories generate mutually exclusive predictions about the order in which mitochondria and phagocytosis arose. To discriminate the alternatives, we have employed ancestral state reconstructions (ASR) for phagocytosis as a trait, phagotrophy as a feeding habit, the presence of mitochondria, the presence of plastids, and the multinucleated organization across major eukaryotic lineages. To mitigate the bias introduced by assuming a particular eukaryotic phylogeny, we reconstructed the appearance of these traits across 1789 different rooted gene trees, each having species from opisthokonts, mycetozoa, hacrobia, excavate, archeplastida, and Stramenopiles, Alveolates and Rhizaria. The trees reflect conflicting relationships and different positions of the root. We employed a novel phylogenomic test that summarizes ASR across trees which reconstructs a last eukaryotic common ancestor that possessed mitochondria, was multinucleated, lacked plastids, and was non-phagotrophic as well as non-phagocytic. This indicates that both phagocytosis and phagotrophy arose subsequent to the origin of mitochondria, consistent with findings from comparative physiology. Furthermore, our ASRs uncovered multiple origins of phagocytosis and of phagotrophy across eukaryotes, indicating that, like wings in animals, these traits are useful but neither ancestral nor homologous across groups. The data indicate that mitochondria preceded the origin of phagocytosis, such that phagocytosis cannot have been the mechanism by which mitochondria were acquired.
The Evolution of Widespread Recombination Suppression on the Dwarf Hamster (Phodopus) X Chromosome
Authors: Moore Emily C. , Thomas Gregg W. C. , Mortimer Sebastian , Kopania Emily E. K. , Hunnicutt Kelsie E. , Clare-Salzler Zachary J. , Larson Erica L. , Good Jeffrey M. 
Published: June 2022

Abstract
The X chromosome of therian mammals shows strong conservation among distantly related species, limiting insights into the distinct selective processes that have shaped sex chromosome evolution. We constructed a chromosome-scale de novo genome assembly for the Siberian dwarf hamster (Phodopus sungorus), a species reported to show extensive recombination suppression across an entire arm of the X chromosome. Combining a physical genome assembly based on shotgun and long-range proximity ligation sequencing with a dense genetic map, we detected widespread suppression of female recombination across ∼65% of the Phodopus X chromosome. This region of suppressed recombination likely corresponds to the Xp arm, which has previously been shown to be highly heterochromatic. Using additional sequencing data from two closely related species (P. campbelli and P. roborovskii), we show that recombination suppression on Xp appears to be independent of major structural rearrangements. The suppressed Xp arm was enriched for several transposable element families and de-enriched for genes primarily expressed in placenta, but otherwise showed similar gene densities, expression patterns, and rates of molecular evolution when compared to the recombinant Xq arm. Phodopus Xp gene content and order was also broadly conserved relative to the more distantly related rat X chromosome. These data suggest that widespread suppression of recombination has likely evolved through the transient induction of facultative heterochromatin on the Phodopus Xp arm without major changes in chromosome structure or genetic content. Thus, substantial changes in the recombination landscape have so far had relatively subtle influences on patterns of X-linked molecular evolution in these species.
Expression Plasticity of Transposable Elements Is Highly Associated with Organismal Re-adaptation to Ancestral Environments
Authors: Liu Yan-Nan , Chen Rong-Mei , Pu Qi-Ting , Nneji Lotanna M. , Sun Yan-Bo 
Published: June 2022

Abstract
Understanding the roles of phenotypic plasticity in adaptive evolution has gained recognition for decades. Studies involving multiple taxa have shown that gene expression plasticity serves as “long-term memory” to facilitate re-adaptations to ancestral environments. Nevertheless, the general pattern and the underlying genetic basis of expression plasticity remain unclear. The transposable elements (TEs) play crucial roles in gene expression regulation and are widely distributed within the genome. Given this, we re-analyzed the transcriptomic data of chicken (Gallus gallus) generated from a reciprocal transplant experiment to examine whether expression shifts of TEs are involved in the re-adaptation process. Similar to the protein-coding genes, the plastic changes of TEs overwhelmingly exceed the genetic changes in the re-adaptation process. Further, the associated TEs co-expressed with diverse genes to perform a regulatory activity. Thus, our study supports the general function of phenotypic plasticity in adaptive evolution, and suggests a regulatory functions of TEs in this process.
Long-term Risk of Herpes Zoster Infection in Patients With Ulcerative Colitis Receiving Tofacitinib
Authors: Winthrop Kevin L , Vermeire Séverine , Long Millie D , Panés Julian , Ng Siew C , Kulisek Nicole , Mundayat Rajiv , Lawendy Nervin , Vranic Ivana , Modesto Irene , Su Chinyu , Melmed Gil Y 
Published: June 2022

Abstract

Background
Tofacitinib is an oral, small molecule Janus kinase inhibitor for the treatment of ulcerative colitis (UC). We report herpes zoster (HZ) incidence and risk factors in the tofacitinib UC clinical program (up to 7.8 years).

Methods
Proportions and incidence rates (IRs; unique patients with events/100 patient-years) of HZ were evaluated in 4 cohorts: Induction (phase 2 and 3 induction study data), Maintenance (phase 3 maintenance study data), Overall (data from all phase 2, 3, and open-label, long-term extension studies), and Overall plus interim 6-month phase 3b and 4 data. Herpes zoster risk factors were assessed by Cox regression analysis.

Results
In the Induction and Maintenance Cohorts, IRs for HZ (nonserious and serious) were numerically higher with tofacitinib 10 mg twice daily (BID) vs placebo and tofacitinib 10 vs 5 mg BID, respectively. With all tofacitinib doses (5 or 10 mg BID), IRs (95% confidence intervals) for HZ in the Overall and Overall plus phase 3b/4 Cohorts (total exposure, 2814.4 and 2999.7 patient-years, respectively) were 3.38 (2.73-4.15) and 3.30 (2.67-4.04), respectively. In the Overall plus phase 3b/4 Cohort, &gt;90% of HZ were nonserious; &gt;90% were mild/moderate; &gt;90% resolved without discontinuing tofacitinib; 0.6% of patients had multiple HZ events. Herpes zoster IRs were stable when analyzed by 6-month intervals up to &gt;30 months. Herpes zoster risk factors included older age, lower weight, geographic region, and prior tumor necrosis factor inhibitor (TNFi) failure.

Conclusions
Most HZ events were mild/moderate. Herpes zoster IRs remained stable over 7.8 years of exposure. Older age, lower weight, geographic region, and prior TNFi failure were associated with increased HZ risk.

ClinicalTrials.gov
NCT00787202;NCT01465763;NCT01458951;NCT01458574;NCT01470612;NCT03281304
When Defenses Fail: Atelopus zeteki Skin Secretions Increase Growth of the Pathogen Batrachochytrium dendrobatidis
Authors: Gass Jordan , Voyles Jamie 
Published: June 2022

Abstract
To combat the threat of emerging infectious diseases in wildlife, ecoimmunologists seek to understand the complex interactions among pathogens, their hosts, and their shared environments. The cutaneous fungal pathogen Batrachochytrium dendrobatidis (Bd), has led to the decline of innumerable amphibian species, including the Panamanian golden frog (Atelopus zeteki). Given that Bd can evade or dampen the acquired immune responses of some amphibians, nonspecific immune defenses are thought to be especially important for amphibian defenses against Bd. In particular, skin secretions constitute a vital component of amphibian innate immunity against skin infections, but their role in protecting A. zeteki from Bd is unknown. We investigated the importance of this innate immune component by reducing the skin secretions from A. zeteki and evaluating their effectiveness against Bd in vitro and in vivo. Following exposure to Bd in a controlled inoculation experiment, we compared key disease characteristics (e.g., changes in body condition, prevalence, pathogen loads, and survival) among groups of frogs that had their skin secretions reduced and control frogs that maintained their skin secretions. Surprisingly, we found that the skin secretions collected from A. zeteki increased Bd growth in vitro. This finding was further supported by infection and survival patterns in the in vivo experiment where frogs with reduced skin secretions tended to have lower pathogen loads and survive longer compared to frogs that maintained their secretions. These results suggest that the skin secretions of A. zeteki are not only ineffective at inhibiting Bd but may enhance Bd growth, possibly leading to greater severity of disease and higher mortality in this highly vulnerable species. These results differ from those of previous studies in other amphibian host species that suggest that skin secretions are a key defense in protecting amphibians from developing severe chytridiomycosis. Therefore, we suggest that the importance of immune components cannot be generalized across all amphibian species or over time. Moreover, the finding that skin secretions may be enhancing Bd growth emphasizes the importance of investigating these immune components in detail, especially for species that are a conservation priority.
Metabarcoding Approaches in Amphibian Disease Ecology: Disentangling the Functional Contributions of Skin Bacteria on Disease Outcome
Authors: Longo Ana V 
Published: June 2022

Abstract
Molecular technologies have revolutionized the field of wildlife disease ecology, allowing the detection of outbreaks, novel pathogens, and invasive strains. In particular, metabarcoding approaches, defined here as tools used to amplify and sequence universal barcodes from a single sample (e.g., 16S rRNA for bacteria, ITS for fungi, 18S rRNA for eukaryotes), are expanding our traditional view of host–pathogen dynamics by integrating microbial interactions that modulate disease outcome. Here, I provide an analysis from the perspective of the field of amphibian disease ecology, where the emergence of multi-host pathogens has caused global declines and species extinctions. I reanalyzed an experimental mesocosm dataset to infer the functional profiles of the skin microbiomes of coqui frogs (Eleutherodactylus coqui), an amphibian species that is consistently found infected with the fungal pathogen Batrachochytrium dendrobatidis and has high turnover of skin bacteria driven by seasonal shifts. I found that the metabolic activities of microbiomes operate at different capacities depending on the season. Global enrichment of predicted functions was more prominent during the warm-wet season, indicating that microbiomes during the cool-dry season were either depauperate, resistant to new bacterial colonization, or that their functional space was more saturated. These findings suggest important avenues to investigate how microbes regulate population growth and contribute to host physiological processes. Overall, this study highlights the current challenges and future opportunities in the application of metabarcoding to investigate the causes and consequences of disease in wild systems.
Revisiting TSHβ’s Role in Avian Seasonal Reproduction, Insights, and Challenges from Mammalian Models
Authors: Pérez Jonathan H 
Published: June 2022

Abstract
The core neuroendocrine pathways regulating seasonal reproduction in vertebrates were characterized over a decade ago. This has led to the development of a “consensus” model of seasonal reproduction that appears to be largely conserved across mammals, birds, amphibians, reptile and fish. This model centers around the photoinduced increase in TSHβ expression in the pars tuberalis of the anterior pituitary gland as the key transducer of photic information from sensory cells to the critical switch in hypothalamic deiodinase enzyme expression that drives changes in localized thyroid hormone signaling. These changes in localized thyroid hormone signaling in the medial basal hypothalamus ultimately activate the reproductive axis. This model has in turn, been consistently supported by studies in a variety of taxa. As such, it has become the standard against which subsequent work is compared, particularly in the non-mammalian literature. However, as new studies move away from the handful of canonical model systems and begin to explore the effects of naturalistic rather than artificial photoperiod manipulations, a more nuanced picture has begun to emerge. Yet, progress in elucidating the detailed events of reproductive photostimulation has been uneven across the research community. In this perspective, I draw on emerging data from studies in free living animals that challenges some of the established assumptions of the avian consensus model of reproduction. Specifically, the role of TSHβ and its dissociation from deiodinase signaling. I then discuss how these apparently surprising findings can be contextualized within the context of the mammalian seasonal literature. In turn, this ability to contextualize from the mammalian literature highlights the breadth of the current gap versus our understanding of the molecular neuroendocrine mechanisms of seasonality in mammals versus birds and other non-mammalian seasonal breeders.
Different Traits at Different Rates: The Effects of Dynamic Strain Rate on Structural Traits in Biology
Authors: Anderson Philip S L , Kawano Sandy M 
Published: June 2022

AbstractPhenotypic diversity is influenced by physical laws that govern how an organism's morphology relates to functional performance. To study comparative organismal biology, we need to quantify this diversity using biological traits (definable aspects of the morphology, behavior, and/or life history of an organism). Traits are often assumed to be immutable properties that need to be measured only a single time in each adult. However, organisms often experience changes in their biotic and abiotic environments that can alter trait function. In particular, structural traits represent the physical capabilities of an organism and may be heavily influenced by the rate at which they are exposed to physical demands (“loads”). For instance, materials tend to become more brittle when loaded at faster rates which could negatively affect structures trying to resist those loads (e.g., brittle materials are more likely to fracture). In the following perspective piece, we address the dynamic properties of structural traits and present case studies that demonstrate how dynamic strain rates affect the function of these traits in diverse groups of organisms. First, we review how strain rate affects deformation and fracture in biomaterials and demonstrate how these effects alter puncture mechanics in systems such as snake strikes. Second, we discuss how different rates of bone loading affect the locomotor biomechanics of vertebrates and their ecology. Through these examinations of diverse taxa and ecological functions, we aim to highlight how rate-dependent properties of structural traits can generate dynamic form–function relationships in response to changing environmental conditions. Findings from these studies serve as a foundation to develop more nuanced ecomechanical models that can predict how complex traits emerge and, thereby, advance progress on outlining the Rules of Life.
Invasive Widow Spiders Perform Differently at Low Temperatures from Conspecifics from the Native Range
Authors: Mowery Monica A , Anthony Susan E , Dorison Alexandra N , Mason Andrew C , Andrade Maydianne C B 
Published: June 2022

Abstract
Temperature challenges are one of the leading abiotic causes of success or failure of non-native species in a novel environment, and this is particularly true for low temperatures. Establishing and reproducing in a novel thermal environment can alter survival, behavior, and traits related to fitness. It has been proposed that plasticity or adaptation of thermal tolerance may allow an introduced species to thrive, or that successful invaders may be those with a thermal breadth in their native habitat that encompasses their new environment. Here, we tested these hypotheses using native and invasive populations of Australian redback spiders (Latrodectus hasselti). We measured how exposure to temperatures common to invasive and native range habitats (exposure to 15 and 25°C, respectively) affected behavioral and life-history traits and trade-offs that may underlie fitness in an invasive population detected in 1995 in Japan and a native population from Australia. We found that the critical thermal minimum (CTmin) was higher in the invasive population from Japan than in the native population, but critical thermal maximum (CTmax) did not differ between populations. Compared to the invasive population, eggs from the native population had a longer development time and lower hatching success at 15°C. Both populations performed equally well at 25°C, as measured by egg development time and hatching success. Invasive juveniles tested at 15°C were faster to explore a novel environment and bolder compared to those tested at 25°C. In comparison, the native population showed faster average exploration, with no differences in boldness or exploration at the two development or testing temperatures. Overall, L. hasselti from Japan maintained hatching success and development across a wider temperature range than the native population, indicating greater thermal breadth and higher behavioral plasticity. These results support the importance of plasticity in thermal tolerance and behavior for a successful invasion under novel environmental temperatures.
Aripiprazole and Risperidone Present Comparable Long-Term Metabolic Profiles: Data From a Pragmatic Randomized Controlled Trial in Drug-Naïve First-Episode Psychosis
Authors: Vázquez-Bourgon Javier , Ortiz-García de la Foz Víctor , Gómez-Revuelta Marcos , Mayoral-van Son Jacqueline , Juncal-Ruiz María , Garrido-Torres Nathalia , Crespo-Facorro Benedicto 
Published: June 2022

Abstract

Objective
Aripiprazole and risperidone are 2 of the most used second-generation antipsychotics (SGAs) worldwide. Previous evidence shows a similar effect of these SGAs on weight and metabolic changes in the short term. However, a longer period is necessary for a better assessment of the SGA´s metabolic profile. We aimed to compare the long-term (1-year) metabolic profile of these 2 antipsychotics on a sample of drug-naïve first episode-psychosis (FEP) patients.

Methods
A total 188 drug-naïve patients, suffering from a first episode of non-affective psychosis (FEP), were randomly assigned to treatment with either aripiprazole or risperidone. Weight and glycemic/lipid parameters were recorded at baseline and after 1-year follow-up.

Results
We observed significant weight increments in both groups (9.2 kg for aripiprazole and 10.5 kg for risperidone) after 1 year of treatment. Despite this, weight and body mass index changes did not significantly differ between treatment groups (P &gt; .05). Similarly, both treatment groups presented similar metabolic clinical impact with a comparable increase in the proportion of participants meeting criteria for metabolic disorders such as obesity or hypercholesterolemia, but not for metabolic syndrome (Δ9.2% vs Δ4.3%) or hypertriglyceridemia (Δ21.9% vs Δ8.0%), where aripiprazole showed worse outcomes than risperidone.

Conclusion
This study shows that aripiprazole and risperidone share a similar long-term metabolic profile. After 1 year of antipsychotic treatment, drug-naïve FEP patients in both treatment groups presented a significant increase in weight and metabolic changes, leading to a greater prevalence of metabolic disorders.
Corrigendum to: “Growth of Unbounded Subsets in Nilpotent Groups, Random Mapping Statistics, and Geometry of Group Laws”
Authors: Greenfeld Be’eri , Lavner Hagai 
Published: June 2022

Abstract
We fix Lemma 6.2 in our recent paper [1] and correct the constants derived from it, appearing in Theorems 1.1, 1.3, and 1.4 and Corollary 6.5.
Supercuspidal Support of Irreducible Modulo ℓ-Representations of SLn(F)
Authors: Cui Peiyi 
Published: June 2022

Abstract
Let $p$ be a prime number and $k$ an algebraically closed field with characteristic $\ell \neq p$. We show that the supercuspidal support of irreducible smooth $k$-representations of Levi subgroups $\textrm {M}^{\prime}$ of $\textrm {SL}_n(F)$ is unique up to $\textrm {M}^{\prime}$-conjugation, where $F$ is either a finite field of characteristic $p$ or a non-Archimedean locally compact field of residual characteristic $p$.