bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Arabidopsis HOP2 Gene Has a Role in Preventing illegitimate Exchanges between Nonhomologous Chromosomes
Authors: Farahani-Tafreshi Yisell , Wei Chun , Gan Peilu , Daradur Jenya , Riggs C. Daniel , Hasenkampf Clare A. 
Published: August 2021

ABSTRACTMeiotic homologous chromosomes pair up and undergo crossing over. In many eukaryotes both intimate pairing and crossing over require the induction of double stranded breaks (DSBs) and subsequent repair via Homologous Recombination (HR). In these organisms, two key proteins are the recombinases RAD51 and DMC1. Recombinase-modulators HOP2 and MND1 have been identified as proteins that assist RAD51 and DMC1 and are needed to promote stabilized pairing. We have probed the nature of the genetic lesions seen in hop2 mutants and looked at the role of HOP2 in the fidelity of genetic exchanges. Using γH2Ax as a marker for unrepaired DSBs we found that hop2-1 and mnd1 mutants have different appearance/disappearance for DSBs than wild type, but all DSBs are repaired by mid-late pachytene. Therefore, the bridges and fragments seen from metaphase I onward are due to mis-repaired DSBs, not unrepaired ones. Studying Arabidopsis haploid meiocytes we found that wild type haploids produced the expected five univalents, but hop2-1 haploids suffered many illegitimate exchanges that were stable enough to produce bridged chromosomes during segregation. Our results suggest that HOP2 has a significant active role in preventing nonhomologous associations. We also found evidence that HOP2 plays a role in preventing illegitimate exchanges during repair of radiation-induced DSBs in rapidly dividing petal cells. Thus, HOP2 plays both a positive role in promoting homologous chromosome synapsis and a separable role in preventing nonhomologous chromosome exchanges. Possible mechanisms for this second important role are discussed.SIGNIFICANCE STATEMENTThe fidelity of Homologous Recombination (HR) during meiosis is essential to the production of viable gametes and for maintaining genome integrity in vegetative cells. HOP2 is an important protein for accurate meiotic HR in plants. We find high levels of illegitimate repairs between nonhomologous chromosomes during meiosis and in irradiated petal cells in HOP2 mutants. We consider mechanisms of how this second role might be accomplished.
The ethanol tolerance in Saccharomyces cerevisiae under a phenomics perspective
Authors: Wolf Ivan Rodrigo , Marques Lucas Farinazzo , de Almeida Lauana Fogaça , Lázari Lucas Cardoso , de Moraes Leonardo Nazário , Cardoso Luiz Henrique , de Oliveira Alves Camila Cristina , Nakajima Rafael Takahiro , Schnepper Amanda Piveta , de Assis Golim Marjorie , Cataldi Thais Regiani , Nijland Jeroen G. , Pinto Camila Moreira , Fioretto Matheus Naia , Almeida Rodrigo Oliveira , Driessen Arnold J. M. , Simōes Rafael Plana , Labate Mônica Veneziano , Grotto Rejane Maria Tommasini , Labate Carlos Alberto , Junior Ary Fernandes , Justulin Luís Antonio , Coan Rafael Luiz Buogo , Ramos Érica , Furtado Fabiana Barcelos , Martins Cesar , Valente Guilherme Targino 
Published: August 2021

AbstractEthanol (EtOH) is a substantial stressor for Saccharomyces cerevisiae. Data integration from strains with different phenotypes, including EtOH stress-responsive lncRNAs, are still not available. We covered these issues seeking systems modifications that drive the divergences between higher (HT) and lower (LT) EtOH tolerant strains under their highest stress conditions. We showed that these phenotypes are neither related to high viability nor faster population rebound after stress relief. LncRNAs work on many stress-responsive systems in a strain-specific manner promoting the EtOH tolerance. Cells use membraneless RNA/protein storage and degradation systems to endure the stress harming, and lncRNAs jointly promote EtOH tolerance. CTA1 and longevity are primer systems promoting phenotype-specific gene expression. The lower cell viability and growth under stress is a byproduct of sphingolipids and inositol phosphorylceramide dampening, acerbated in HTs by sphinganine, ERG9, and squalene overloads; LTs diminish this harm by accumulating inositol 1-phosphate. The diauxic shift drives an EtOH buffering by promoting an energy burst under stress, mainly in HTs. Analysis of mutants showed genes and lncRNAs in three strains critical for their EtOH tolerance. Finally, longevity, peroxisome, energy and lipid metabolisms, RNA/protein degradation and storage systems are the main pathways driving the EtOH tolerance phenotypes.
The lesser Pacific striped octopus, Octopus chierchiae: an emerging laboratory model for the study of octopuses
Authors: Grearson Anik G. , Dugan Alison , Sakmar Taylor , Dölen Gül , Gire David H. , Sivitilli Dominic M. , Niell Cristopher M. , Caldwell Roy L. , Wang Z. Yan , Grasse Bret 
Published: August 2021

AbstractCephalopods have the potential to become useful experimental models in various fields of science, particularly in neuroscience, physiology, and behavior. Their complex nervous systems, intricate color- and texture-changing body patterns, and problem-solving abilities have attracted the attention of the biological research community, while the high growth rates and short life cycles of some species render them suitable for laboratory culture. Octopus chierchiae is a small octopus native to the central Pacific coast of North America whose predictable reproduction, short time to maturity, small adult size, and ability to lay multiple egg clutches (iteroparity) make this species ideally suited to laboratory culture. Here we describe novel methods for culture of O. chierchiae, with emphasis on enclosure designs, feeding regimes, and breeding management. Our results demonstrate the feasibility of multigenerational culture of O. chierchiae. Specifically, O. chierchiae bred in the laboratory grows from a 3.5-millimeter mantle length at hatching to an adult mantle length of approximately 20-30 millimeters in 250-300 days, with 14-15% survivorship to over 400 days of age in first and second generations. O. chierchiae sexually matures at around an estimated six months of age and, unlike most octopus species, can lay multiple clutches of eggs, approximately every 30-90 days. Eggs are large and hatchlings emerge as direct developing octopuses. Based on these results, we propose that O. chierchiae possesses both the practical and biological features needed for a model octopus that can be cultured repeatedly to address a wide range of fundamental biological questions.
Mucin-mimetic action of capsaicin improves high fat diet-induced gut barrier dysfunction in mice colon
Authors: Kumar Vijay , Kumar Vibhu , Mahajan Neha , Kaur Jasleen , Devi Kirti , Dharavath Ravinder Naik , Singh Ravindra Pal , Kondepudi Kanthi Kiran , Bishnoi Mahendra 
Published: August 2021

ABSTRACTThe gut barrier – including tight junction proteins and mucus layers, is the first line of defense against physical, chemical, or pathogenic incursions. This barrier is compromised in various health disorders. Capsaicin, a dietary agonist of Transient receptor potential vanilloid 1 (TRPV1) channel, is reported to alleviate the complications of obesity. While its mode of action is well established to enhance energy expenditure, metabolism and prevent dysbiosis, the more local effects on the host gut – particularly the gut barrier and mucus system remain elusive.We employed a diet-induced obesity model to investigate the effect of capsaicin on the gut barrier and mucus production and to understand the involvement of mucus, bacteria, and TRPV1 in these phenomena. Mucin feeding reflected most of the effects produced by capsaicin, indicating that mucus modulation by capsaicin plays a crucial role in its anti-obesity effects. Capsaicin, bacteria and the host mucus system seem to act in a cyclic cascade involving TRPV1, which can be activated by capsaicin and various bacteria. These findings provide new insight into the role of TRPV1 in maintaining a healthy gut environment.HIGHLIGHTSExogenous mucin feeding produced anti-obesity effects similar to capsaicin in mice.Mucin and capsaicin improved TJP expression, intestinal permeability and gut microbial diversity.Capsaicin modulated bacterial diversity in vitro, independently of the host.Probiotic bacteria and butyrate activated TRPV1 in transfected HEK cells.Anti-obesity action of capsaicin is not exclusive to TRPV1 agonism.Capsaicin’s action as colonic mucus secretagogue – plays a crucial part in its anti-obesity benefits.
Functional multi-omics reveals genetic and pharmacologic regulation of surface CD38 in multiple myeloma
Authors: Choudhry Priya , Kasap Corynn , Patiño-Escobar Bonell , Gugliemini Olivia , Geng Huimin , Sarin Vishesh , Kang Amrik , Kishishita Audrey , Rampersaud Sham , Sarah Letitia , Lin Yu-Hsiu T. , Paranjape Neha , Ramkumar Poornima , Patton Jonathan C. , Marcoulis Makeba , Wang Donghui , Phojanakong Paul , Steri Veronica , Hann Byron , Barwick Benjamin G. , Kampmann Martin , Wiita Arun P. 
Published: August 2021

AbstractCD38 is a surface ectoenzyme expressed at high levels on myeloma plasma cells and is the target for the monoclonal antibodies (mAbs) daratumumab and isatuximab. Pre-treatment CD38 density on tumor cells is an important determinant of mAb efficacy. Several small molecules have been found to increase tumor surface CD38, with the goal of boosting mAb efficacy in a co-treatment strategy. Numerous other CD38-targeting therapeutics are currently in preclinical or clinical development. Here we sought to extend our currently limited insight into CD38 surface expression by using a multi-omics approach. Genome-wide CRISPR-interference screens integrated with patient-centered epigenetic analysis confirmed known regulators of CD38, such as RARA, while revealing XBP1 and SPI1 as other key transcription factors governing surface CD38 levels. CD38 knockdown followed by cell surface proteomics demonstrated no significant remodeling of the myeloma “surfaceome” after genetically-induced loss of this antigen. Integrated transcriptome and surface proteome data confirmed high specificity of all-trans retinoic acid in upregulating CD38 in contrast to broader effects of azacytidine and panobinostat. Finally, unbiased phosphoproteomics identified inhibition of MAP kinase pathway signaling in tumor cells after daratumumab treatment. Our work provides a resource to design strategies to enhance efficacy of CD38-targeting immunotherapies in myeloma.
Protist.guru: a comparative transcriptomics database for the protist kingdom
Authors: Villanueva Erielle Marie Fajardo , Lim Peng Ken , Lim Jolyn Jia Jia , Lim Shan Chun , Lau Pei Yi , Koh Kenny Ting Sween , Tan Emmanuel , Kairon Ryanjit Singh , See Wei An , Liao Jian Xiang , Hee Ker Min , Vijay Varsheni , Maitra Ishani , Boon Chong Jun , Fo Kevin , Wang Yee Tat , Jaya Ryan , Hew Li Anne , Lim Yong Yee , Lee Wei Quan , Lee Zhi Qi , Foo Herman , Lopes dos Santos Adriana , Mutwil Marek 
Published: August 2021

AbstractSummaryDuring the last few decades, the study of microbial ecology has been enabled by molecular and genomic data. DNA sequencing has revealed the surprising extent of microbial diversity and how microbial processes run global ecosystems. However, significant gaps in our understanding of the microbial world remain, and one example is that microbial eukaryotes, or protists, are still neglected. To address this gap, we used gene expression data from 15 distinct protist species to create protist.guru: an online database equipped with tools for identifying functional co-expression networks, gene families, and enriched gene clusters. Here, we show how our database can be used to reveal genes involved in essential pathways, such as the synthesis of secondary carotenoids in Haematococcus lacustris. We expect protist.guru to serve as a valuable resource for protistologists, as well as a catalyst for discoveries and new insights into the biological processes of microbial eukaryotes.AvailabilityThe database and co-expression networks are freely available from http://protist.guru/. The expression matrices and sample annotations are found in the supplementary data.
NO-stressed Y. pseudotuberculosis have decreased cell division rates in the mouse spleen
Authors: Liu Bessie , Braza Rezia Era D. , Cotten Katherine L. , Davidson Robert K. , Davis Kimberly M. 
Published: August 2021

AbstractFluorescence dilution approaches can detect bacterial cell division events, and can detect if there are differential rates of cell division across individual cells within a population. This approach typically involves inducing expression of a fluorescent protein, and then tracking partitioning of fluorescence into daughter cells. However, fluorescence can be diluted very quickly within a rapidly replicating population, such as pathogenic bacterial populations replicating within host tissues. To overcome this limitation, we have generated two revTetR reporter constructs, where either mCherry or yellow fluorescent protein (YFP) is constitutively expressed, and repressed by addition of tetracyclines, resulting in fluorescence dilution within defined timeframes. We show that fluorescent signals are diluted in replicating populations, and that signal accumulates in growth-inhibited populations, including during nitric oxide exposure. Furthermore, we show that tetracyclines can be delivered to the mouse spleen during Yersinia pseudotuberculosis infection, and defined a drug concentration that results in even exposure of cells to tetracyclines. We then used this system to visualize bacterial cell division within defined timeframes post-inoculation. We detected growth attenuation of the revTetR-mCherry strains within mouse tissues, however data suggested heightened NO exposure correlated with heightened mCherry signal. We were able to restore normal bacterial growth with revTetR-YFP, and use this strain to show that heightened NO exposure correlated with heightened YFP signal, indicating decreased cell division rates within this subpopulation in vivo. This revTetR reporter will provide a critical tool for future studies to identify and isolate slowly replicating bacterial subpopulations from host tissues.
Optical nanoscopy reveals SARS-CoV-2-induced remodeling of human airway cells
Authors: Nijenhuis Wilco , Damstra Hugo G.J. , van Grinsven Emma J. , Iwanski Malina K. , Praest Patrique , Soltani Zahra E. , van Grinsven Mariëlle M.P. , Brunsveld Jesse E. , de Kort Theun , Rodenburg Lisa W. , de Jong Dorien C.M. , Raeven Henriette H.M. , Spelier Sacha , Amatngalim Gimano D. , Akhmanova Anna , Nijhuis Monique , Lebbink Robert Jan , Beekman Jeffrey M. , Kapitein Lukas C. 
Published: August 2021

AbstractA better understanding of host cell remodeling by the coronavirus SARS-CoV-2 is urgently needed to understand viral pathogenesis and guide drug development. Expression profiling and electron microscopy have frequently been used to study virus-host interactions, but these techniques do not readily enable spatial, sub-cellular and molecular analysis of specific cellular compartments. Here, we use diffraction-unlimited fluorescence microscopy to analyze how SARS-CoV-2 infection exploits and repurposes the subcellular architecture of primary human airway cells. Using STED nanoscopy, we detect viral entry factors along the motile cilia of ciliated cells and visualize key aspects of the viral life cycle. Using Tenfold Robust Expansion (TREx) microscopy, we analyze the extensively remodeled three-dimensional ultrastructure of SARS-CoV-2-infected ciliated cells and uncover Golgi fragmentation, emergence of large and atypical multivesicular bodies enclosing viral proteins, ciliary clustering, and remodeling of the apical surface. These results demonstrate a broadly applicable strategy to study how viruses reorganize host cells with spatial and molecular specificity and provide new insights into SARS-CoV-2 infection in primary human cell models.
A TIR-1/SARM1 phase transition underlies p38 immune pathway activation in theC. elegansintestine
Authors: Peterson Nicholas D. , Icso Janneke D. , Salisbury J. Elizabeth , Rodríguez Tomás , Thompson Paul R. , Pukkila-Worley Read 
Published: August 2021

ABSTRACTIntracellular signaling regulators can be concentrated into membrane-free, higher-ordered protein assemblies to initiate protective responses during stress — a process known as phase transition. Here, we show that a phase transition of theCaenorhabditis elegansToll/interleukin-1 receptor domain protein (TIR-1), an NAD+glycohydrolase homologous to mammalian sterile alpha and TIR motif-containing 1 (SARM1), underlies p38 PMK-1 immune pathway activation inC. elegansintestinal epithelial cells. Through visualization of fluorescently labeled TIR-1/SARM1 protein, we demonstrate for the first time that physiologic stresses, both pathogen and non-pathogen, induce multimerization of TIR-1/SARM1 into visible puncta within intestinal epithelial cells.In vitroenzyme kinetic analyses revealed that, like mammalian SARM1, the NAD+glycohydrolase activity ofC. elegansTIR-1 is dramatically potentiated by protein oligomerization and a phase transition. Accordingly,C. eleganswith genetic mutations that specifically block either multimerization or the NAD+glycohydrolase activity of TIR-1/SARM1 fail to induce p38 PMK phosphorylation, are unable to increase immune effector expression, and are dramatically susceptible to bacterial infection. Finally, we demonstrate that the TIR-1/SARM1 phase transition is modified by dietary cholesterol, revealing a new adaptive response that allows a metazoan host to anticipate pathogen threats during micronutrient deprivation, a time of relative susceptibility to infection. When cholesterol is limited, TIR-1/SARM1 oligomerizes into puncta in intestinal epithelial cells and engages its NAD+glycohydrolase activity, which increases p38 PMK-1 phosphorylation, and primes immune effector induction in a manner that promotes pathogen clearance from the intestine during a subsequent infection. Thus, a phase transition of TIR-1/SARM1 as a prerequisite for its NAD+glycohydrolase activity is strongly conserved across millions of years of evolution and is essential for diverse physiological processes in multiple cell types.
Balancing conservation priorities for grassland and forest specialist bird communities in agriculturally dominated landscapes
Authors: de Zwaan Devin R. , Alavi Niloofar , Mitchell Greg W. , Lapen David R. , Duffe Jason , Wilson Scott 
Published: August 2021

AbstractEffective conservation planning often requires difficult decisions when at-risk species inhabit economically valuable landscapes or if the needs of multiple threatened species do not align. In the agriculture-dominated landscape of eastern Ontario and southwestern Quebec, Canada, conflicting habitat requirements exist between threatened grassland birds benefiting from certain agriculture practices and those of a diverse woodland bird community dependent on forest recovery. Using multi-scale species distribution models with Breeding Bird Survey (BBS) data, we assessed habitat suitability for 8 threatened grassland and forest specialists within this region. We also identified landscapes that jointly maximize occurrence of the 8 focal species and diversity of the overall grassland and forest communities. Influential habitat associations differed among species at the territory (200m radius) and landscape level (1km), highlighting the importance of considering multiple spatial scales. Species diversity was maximized when forest or grassland/pasture cover approached 40–50%, indicating a positive response to land cover heterogeneity. We identified species diversity hotspots near Lake Huron, as well as along the shore and southeast of the St. Lawrence River. These areas represent mosaic landscapes, balancing forest patches, wetland, grassland/pasture, and row crops such as corn, soybean, and cereals. Despite drastic landscape changes associated with agroecosystems, we demonstrate that targeted habitat protection and enhancement that prioritizes land cover diversity can maximize protection of bird communities with directly contrasting needs. We highlight multiple pathways to achieve this balance, including forest retention or separating row crops with hedgerows and wooded fence-lines, improving flexibility in conservation approaches.
A Cell Culture Model of BK Polyomavirus Persistence, Genome Recombination, and Reactivation
Authors: Zhao Linbo , Imperiale Michael J. 
Published: August 2021

AbstractBK Polyomavirus (BKPyV) is a small non-enveloped DNA virus that establishes a ubiquitous, asymptomatic, and lifelong persistent infection in at least 80% of the world’s population. In some immunosuppressed transplant recipients, BKPyV reactivation causes polyomavirus-associated nephropathy and hemorrhagic cystitis. We report a novel in vitro model of BKPyV persistence and reactivation using a BKPyV natural host cell line. In this system, viral genome loads remain constant for various times post-establishment of persistent infection, during which BKPyV undergoes extensive random genome recombination. Certain recombination events result in viral DNA amplification and protein expression, resulting in production of viruses with enhanced replication ability.ImportanceBK polyomavirus (BKPyV) generally establishes a persistent subclinical infection in healthy individuals but can cause severe disease in transplant recipients. While an in vitro model to study acute replication exists, no practical model with which to study BKPyV persistence is currently available. We established a BKPyV persistence model in cell culture. Our model reveals that the virus can persist for varying periods of time before random recombination of the viral genome leads to enhanced replication.
Seipin forms a flexible cage at lipid droplet formation sites
Authors: Arlt Henning , Sui Xuewu , Folger Brayden , Adams Carson , Chen Xiao , Remme Roman , Hamprecht Fred A. , DiMaio Frank , Liao Maofu , Goodman Joel M. , Farese Robert V. , Walther Tobias C. 
Published: August 2021

SUMMARYLipid droplets (LDs) form in the endoplasmic reticulum by phase separation of neutral lipids. This process is facilitated by the seipin protein complex, which consists of a ring of seipin monomers, with yet unclear function. Here, we report a structure of yeast seipin based on cryo-electron microscopy and structural modeling data. Seipin forms a decameric, cage-like structure with the lumenal domains forming a stable ring at the cage floor and transmembrane segments forming the cage sides and top. The transmembrane segments interact with adjacent monomers in two distinct, alternating conformations. These conformations result from changes in switch regions, located between the lumenal domains and the transmembrane segments, that are required for seipin function. Our data suggest a model for LD formation in which a closed seipin cage enables TG phase separation and subsequently switches to an open conformation to allow LD growth and budding.