bluuebunny/crossref_metadata_2025_split huggingface dataset:
Responses to Temperatures of DifferentDrosophilaSpecies
Authors: Huda Ainul , Vaden Thomas J. , Omelchenko Alisa A. , Castaneda Allison N. , Ni Lina 
Published: October 2021

AbstractTemperature is a critical environmental variable that affects the distribution, survival, and reproduction of most animals. Although temperature receptors have been identified in different animals, how these receptors respond to temperatures is largely unknown. Here we use modified single-fly thermotactic assays to analyze movements and temperature preferences of nineDrosophilaspecies. The ability/inclination to move varies among these species and at different temperatures. Importantly, different species prefer various ranges of temperatures. While wild-typeD. melanogasterflies avoid the warm temperature in the warm avoidance assay and the cool temperature in the cool avoidance assay,D. bipectinataandD. yakubaavoid neither warm nor cool temperatures andD. biarmipesandD. mojavensisdo not avoid the warm temperature in the warm avoidance assay. These results demonstrate thatDrosophilaspecies have different mobilities and temperature preferences, thereby benefiting the research on molecular mechanisms of temperature responsiveness.Summary statementThe ability to move and the preference for temperatures vary among fly species when flies are exposed to steep temperature gradients.
Characterization of wheat lacking B-type starch granules
Authors: Saccomanno Benedetta , Berbezy Pierre , Findlay Kim , Shoesmith Jennifer , Uauy Cristobal , Viallis Bruno , Trafford Kay 
Published: October 2021

ABSTRACTThe physicochemical and agronomic properties of a new form of bread wheat, lacking B-type starch granules (BlessT) were assessed. Three BlessT mutant lines, made by combining homoeologous deletions ofBGC1, a gene responsible for the control of B-granule content were compared with two sibling lines with normal starch phenotype and the parent line, cv. Paragon. Quantification of starch granule size and number in developing grain confirmed the lack of small, B-type starch granules throughout development in BlessT. Most starch, flour, grain and loaf characteristics did not vary between BlessT and the wild type sibling controls. However, BlessT starches had higher water absorption, reduced grain hardness and higher protein content, and dough made from BlessT flour required more water and had increased elasticity. Despite the lack of B-granules, BlessT lines do not display a significant decrease in total starch content suggesting that it should be possible to produce commercial wheat varieties that lack B-type starch granules without compromising yield. These findings support the potential utility of this novel type of wheat as a specialist crop in applications ranging from bread making and alcohol production to improved industrial starch products.
Volatile social environments can favour investments in quality over quantity of social relationships
Authors: Aubier Thomas G. , Kokko Hanna 
Published: October 2021

ABSTRACTCooperation does not occur in a vacuum: interactions develop over time in social groups that undergo demographic changes. Intuition suggests that stable social environments favour developing few but strong reciprocal relationships (a ‘focused’ strategy), while volatile social environments favour the opposite: more but weaker social relationships (a ‘diversifying’ strategy). We model reciprocal investments under a quality-quantity tradeoff for social relationships. We find that volatility, counterintuitively, can favour a focused strategy. This result becomes explicable through applying the theory of antagonistic pleiotropy, originally developed for senescence, to social life. Diversifying strategies show superior performance later in life, but with costs paid at young ages while the social network is slowly being built. Under volatile environments, many individuals die before reaching sufficiently old ages to reap the benefits. Social strategies that do well early in life are then favoured: a focused strategy leads individuals to form their first few social bonds quickly and to make strong use of existing bonds. Our model highlights the importance of pleiotropy and population age structure for the evolution of cooperative strategies and other social traits, and shows that it is not sufficient to reflect on the fate of survivors only, when evaluating the benefits of social strategies.
THE SPLICING FACTOR PTBP1 REPRESSES TP63 γ ISOFORM PRODUCTION IN SQUAMOUS CELL CARCINOMA
Authors: Taylor William , Reboutier David , Paillard Luc , Méreau Agnès , Audic Yann 
Published: October 2021

ABSTRACTThe TP63 gene encodes the transcription factor p63. It is frequently amplified or overexpressed in squamous cell carcinomas. Owing to alternative splicing, p63 has multiple isoforms called α, β, γ and δ. The regulatory functions of p63 may be isoform-specific. The α isoform inhibits the epithelial to mesenchymal transition (EMT) and controls apoptosis, while the γ isoform promotes EMT. Here, we observed in TCGA data that a high ratio of the TP63γ isoform to the other isoforms is a pejorative factor for the survival of patients with head and neck squamous cell carcinoma (HNSCC). We therefore addressed the regulation of the γ isoform. In several tissues (GTEX data), the expression of the RNA-binding protein PTBP1 (polypyrimidine tract binding protein 1) is negatively correlated with the abundance of TP63γ. Accordingly, we demonstrated that PTBP1 depletion in HNSCC cell lines leads to an increase in abundance of the γ isoform. By RNA immunoprecipitation and in vitro interaction assays, we showed that PTBP1 directly binds to TP63 pre-mRNA in close proximity to the TP63γ-specific exon. The region around the TP63γ-specific exon was sufficient to elicit a PTBP1-dependent regulation of alternative splicing in a splice reporter minigene assay. Finally, we demonstrated that the regulation of TP63γ production by PTBP1 is conserved in amphibians, revealing that it encounters a strong evolutionary pressure. Together, these results identify TP63γ as a prognostic marker in HNSCC, and identify PTBP1 as a direct negative regulator of its production.
Dynamic DNA methylation changes in the COMT gene promoter region in response to mental stress and its modulation by transcranial direct current stimulation
Authors: Wiegand Ariane , Blickle Arne , Brückmann Christof , Weller Simone , Nieratschker Vanessa , Plewnia Christian 
Published: October 2021

AbstractChanges in epigenetic modifications present a mechanism how environmental factors like the experience of stress can alter gene regulation. While stress-related disorders have consistently been associated with differential DNA methylation, little is known about the time scale in which these alterations emerge. We investigated dynamic DNA methylation changes in whole blood of 42 healthy male individuals in response to a stressful cognitive task, its association with concentration changes in cortisol and its modulation by transcranial direct current stimulation (tDCS). We observed a continuous increase in COMT promotor DNA methylation which correlated with higher saliva cortisol levels and was still detectable one week later. However, this lasting effect was suppressed by concurrent activity-enhancing anodal tDCS to the dorsolateral prefrontal cortex. Our findings support the significance of gene-specific DNA methylation in whole blood as potential biomarkers for stress-related disorders. Moreover, they suggest alternative molecular mechanisms possibly involved in lasting behavioral effects of tDCS.
Oligogenic combinations of rare variants influence specific phenotypes in complex disorders
Authors: Pounraja Vijay Kumar , Girirajan Santhosh 
Published: October 2021

ABSTRACTGenetic studies of complex disorders such as autism and intellectual disability (ID) are often based on enrichment of individual rare variants or their aggregate burden in affected individuals compared to controls. However, these studies overlook the influence of combinations of rare variants that may not be deleterious on their own due to statistical challenges resulting from rarity and combinatorial explosion when enumerating variant combinations, limiting our ability to study oligogenic basis for these disorders. We present a framework that combines the apriori algorithm and statistical inference to identify specific combinations of mutated genes associated with complex phenotypes. Our approach overcomes computational barriers and exhaustively evaluates variant combinations to identify non-additive relationships between simultaneously mutated genes. Using this approach, we analyzed 6,189 individuals with autism and identified 718 combinations significantly associated with ID, and carriers of these combinations showed lower IQ than expected in an independent cohort of 1,878 individuals. These combinations were enriched for nervous system genes such asNINandNGF, showed complex inheritance patterns, and were depleted in unaffected siblings. We found that an affected individual can carry many oligogenic combinations, each contributing to the same phenotype or distinct phenotypes at varying effect sizes. We also used this framework to identify combinations associated with multiple comorbid phenotypes, including mutations ofCOL28A1andMFSD2Bfor ID and schizophrenia andABCA4, DNAH10andMC1Rfor ID and anxiety/depression. Our framework identifies a key component of missing heritability and provides a novel paradigm to untangle the genetic architecture of complex disorders.SIGNIFICANCEWhile rare mutations in single genes or their collective burden partially explain the genetic basis for complex disorders, the role of specific combinations of rare variants is not completely understood. This is because combinations of rare variants are rarer and evaluating all possible combinations would result in a combinatorial explosion, creating difficulties for statistical and computational analysis. We developed a data mining approach that overcomes these limitations to precisely quantify the influence of combinations of two or more mutated genes on a specific clinical feature or multiple co-occurring features. Our framework provides a new paradigm for dissecting the genetic causes of complex disorders and provides an impetus for its utility in clinical diagnosis.
Short ‘1.2× genome’ infectious clone initiates deltavirus replication in Boa constrictor cells
Authors: Szirovicza Leonora , Hetzel Udo , Kipar Anja , Hepojoki Jussi 
Published: October 2021

ABSTRACTHuman hepatitis D virus (HDV), discovered in 1977, represented the sole known deltavirus for decades. The dependence on hepatitis B virus (HBV) co-infection and its glycoproteins for infectious particle formation led to the assumption that deltaviruses are human-only pathogens. However, since 2018, several reports have described identification of HDV-like agents from various hosts but without co-infecting hepadnaviruses. Indeed, we demonstrated that Swiss snake colony virus 1 (SwSCV-1) uses arenaviruses as the helper for infectious particle formation, thus shaking the dogmatic alliance with hepadnaviruses for completing deltavirus life cycle. In vitro systems enabling helper virus-independent replication are key for studying the newly discovered deltaviruses. Others and we have successfully used constructs containing multimers of the deltavirus genome for the replication of various deltaviruses via transfection in cell culture. Here, we report the establishment of deltavirus infectious clones with 1.2× genome inserts bearing two copies of the genomic and antigenomic ribozymes. We used SwSCV-1 as the model to compare the ability of the previously reported “2× genome” and the “1.2× genome” plasmid constructs/infectious clones to initiate replication in cell culture. Using immunofluorescence, qRT-PCR, immuno- and northern blotting, we found the 2× and 1.2× genome clones to similarly initiate deltavirus replication in vitro and both induced a persistent infection of snake cells. We hypothesize that duplicating the ribozymes facilitates the cleavage of genome multimers into unit-length pieces during the initial round of replication. The 1.2× genome constructs enable easier introduction of modifications required for studying deltavirus replication and cellular interactions.IMPORTANCEHepatitis D virus (HDV) is a satellite virus infecting humans with strict association to hepatitis B virus (HBV) co-infection because HBV glycoproteins can mediate infectious HDV particle formation. For decades, HDV was the sole representative of deltaviruses, which had led to hypotheses suggesting that it evolved in humans, the only known natural host. Recent sequencing studies have led to the discovery of HDV-like sequences across a wide range of species, representing a paradigm shift in deltavirus evolution. Molecular biology tools such as infectious clones, which enable initiation of deltavirus infection without helper virus, are key to demonstrate that the recently found deltaviruses are capable of independent replication. Such tools will enable identification of the potential helper viruses. Here, we report a 1.2× genome copy strategy for designing plasmid-based infectious clones to study deltaviruses and to demonstrate that plasmid delivery into cultured snake cells sufficiently initiates replication of different deltaviruses.
Membrane remodeling due to mixture of multiple types of curvature proteins
Authors: Kumar Gaurav , Srivastava Anand 
Published: October 2021

AbstractWe present an extension of the Monte Carlo based mesoscopic membrane model, where the membrane is represented as a dynamically triangulated surface and the proteins are modeled as anisotropic inclusions formulated as in-plane nematic field variables adhering to the deformable elastic sheet. In the extended model, we have augmented the Hamiltonian to study membrane deformation due to a mixture of multiple types of curvature generating proteins. This feature opens the door for understanding how multiple kinds of curvature-generating proteins may be working in a coordinated manner to induce desired membrane morphologies. For example, among other things, we study membrane deformations and tubulation due to a mixture of positive and negative curvature proteins as mimics of various proteins from BAR domain family. We also study the effect membrane anisotropy, which manifest as membrane localization and differential binding affinity of a given curvature protein, leading to insights into the tightly regulated cargo sorting and transport processes. Our simulation results show different morphology of deformed vesicles that depend on the curvatures and number of the participating proteins as well as on the protein-protein and membrane-proteins interactions.SignificanceMembrane remodeling requires highly orchestrated interactions between several types of lipids and curvature proteins. Experimentally probing the membrane deformation intermediates is non-trivial. For example, it is not known exactly how two or more different kinds of BAR domain proteins work in concert to induce and stabilize certain membrane curvatures. In this work, we use mesoscopic continuum modeling and explore the factors that induce and stabilize a range of membrane deformation due to a mixture of positive and negative curvature proteins.
Identification and validation of a non-genetically encoded vulnerability to XPO1 inhibition in malignant rhabdoid tumors – expanding patient-driven discovery beyond the N-of-1
Authors: Marks Lianna J. , Diolaiti Daniel , Mundi Prabhjot , Gaviria Ervin S. , Rainey Allison R. , Yamashiro Darrell J. , Fazlollahi Ladan , Hosoi Hajime , Katsumi Yoshiki , Kuwahara Yasumichi , Dela Cruz Filemon S. , Califano Andrea , Kung Andrew L. 
Published: October 2021

AbstractMalignant rhabdoid tumors (MRTs) are rare, aggressive pediatric solid tumors, characterized by a 22q11 deletion that inactivates the SMARCB1 gene. Outcomes remain poor despite multimodality treatment. MRTs are among the most genomically stable cancers and lack therapeutically targetable genetic mutations. We utilized metaVIPER, an extension of the Virtual Inference of Protein-activity by Enriched Regulon (VIPER) algorithm, to computationally infer activated druggable proteins in the tumor of an eight month old patient and then expanded the analysis to TCGA and TARGET cohorts.In vitrostudies were performed on a panel of MRT and atypical teratoid/rhabdoid tumor cell lines. Two patient-derived xenograft (PDX) mouse models of MRT were used forin vivoefficacy studies. MetaVIPER analysis from the patient’s tumor identified significantly high inferred activity of nuclear export protein Exportin-1 (XPO1). Expanded metaVIPER analysis of TCGA and TARGET cohorts revealed consistent elevations in XPO1 inferred activity in MRTs compared to other cancer types. All MRT cell lines demonstrated baseline activation of XPO1. MRT cell lines demonstratedin vitrosensitivity to the XPO1 inhibitor, selinexor which led to cell cycle arrest and induction of apoptosis. Targeted inhibition of XPO1 in patient-derived xenograft models of MRT using selinexor resulted in abrogation of tumor growth. Selinexor demonstrates efficacy in preclinical models of MRT. These results support investigation of selinexor in a phase II study in children with MRT and illustrate the importance of an N-of-1 approach in driving discovery beyond the single patient.Statement of Translational RelevanceWe describe the patient-driven discovery of XPO1 activation as a non-genetically encoded vulnerability in MRTs. The application of metaVIPER analysis to tumors lacking actionable oncogenic alterations represents a novel approach for identifying potential therapeutic targets and biomarkers of response. Our preclinical validation of selinexor confirms XPO1 inhibition as a promising therapeutic strategy for the treatment of MRT.
Mechanistic Model of Telomere Length Homeostasis in Yeast
Authors: Singh Ghanendra , Sriram K. 
Published: October 2021

AbstractCells maintain homeostatic telomere length, and this homeostatic disruption leads to various types of diseases. Presently, it is not clear how telomeres achieve homeostasis. One of the prevailing hypotheses is a protein-counting model with a built-in sensor mechanism that counts proteins that directly regulate the telomeric length. However, it does not explain telomere length regulation at the mechanistic level. Here, we present a mathematical model based on the underlying molecular mechanisms of length regulation needed to establish telomere length homeostasis in yeast. We perform both deterministic and stochastic simulations to validate the models with the experimental data of Teixeira et al., rate-balance plot, and phase plane analysis to understand the nature of dynamics exhibited by the models. For global analysis, we constructed bifurcation diagrams. The model explains the role of negative and positive feedback loops and a delay between telomerase and telomere-bound proteins, leading to oscillations in telomere length. We map these in-silico results to Teixeira’s proposition of telomeres making a transition between extendible and non-extendible states.
Dual medial prefrontal cortex and hippocampus projecting neurons in the paraventricular nucleus of the thalamus
Authors: Viena Tatiana D. , Rasch Gabriela E. , Allen Timothy A. 
Published: October 2021

AbstractThe paraventricular nucleus (PVT) of the midline thalamus is a critical higher-order cortico-thalamo-cortical integration site that plays a critical role in various behaviors including reward seeking, cue saliency, and emotional memory. Anatomical studies have shown that PVT projects to both medial prefrontal cortex (mPFC) and hippocampus (HC). However, dual mPFC-HC projecting neurons which could serve a role in synchronizing mPFC and HC activity during PVT-dependent behaviors, have not been explored. Here we used a dual retrograde adenoassociated virus (AAV) tracing approach to characterize the location and proportion of different projection populations that send collaterals to mPFC and/or ventral hippocampus (vHC). Additionally, we examined the distribution of calcium binding proteins calretinin (CR) and calbindin (CB) with respect to these projection populations PVT. We found that PVT contains separate populations of cells that project to mPFC, vHC, and those that innervate both regions. Interestingly, dual mPFC-HC projecting cells expressed neither CR or CB. Topographically, mPFC- and vHC-projecting CB+ and CR+ cells clustered around dual projecting neurons in PVT. These results are consistent with the features of dual mPFC-vHC projecting cells in the nucleus reuniens (RE) and suggestive of a functional mPFC-PVT-vHC system that may support mPFC-vHC interactions in PVT-dependent behaviors.
BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data
Authors: Steenwyk Jacob L. , Buida Thomas J. , Gonçalves Carla , Goltz Dayna C. , Morales Grace , Mead Matthew E. , LaBella Abigail L. , Chavez Christina M. , Schmitz Jonathan E. , Hadjifrangiskou Maria , Li Yuanning , Rokas Antonis 
Published: October 2021

AbstractBioinformatic analysis—such as genome assembly quality assessment, alignment summary statistics, relative synonymous codon usage, paired-end aware quality trimming and filtering of sequencing reads, file format conversion, and processing and analysis—is integrated into diverse disciplines in the biological sciences. Several command-line pieces of software have been developed to conduct some of these individual analyses; however, the lack of a unified toolkit that conducts all these analyses can be a barrier in workflows. To address this obstacle, we introduce BioKIT, a versatile toolkit for the UNIX shell environment with 40 functions, several of which were community-sourced, that conduct routine and novel processing and analysis of genome assemblies, multiple sequence alignments, coding sequences, sequencing data, and more. To demonstrate the utility of BioKIT, we assessed the quality and characteristics of 901 eukaryotic genome assemblies, calculated alignment summary statistics for 10 phylogenomic data matrices, determined relative synonymous codon usage across 171 fungal genomes including those that use alternative genetic codes, and demonstrate that a novel metric, gene-wise relative synonymous codon usage, can accurately estimate gene-wise codon optimization. BioKIT will be helpful in facilitating and streamlining sequence analysis workflows. BioKIT is freely available under the MIT license from GitHub (https://github.com/JLSteenwyk/BioKIT), PyPi (https://pypi.org/project/jlsteenwykbiokit/), and the Anaconda Cloud (https://anaconda.org/jlsteenwyk/jlsteenwyk-biokit). Documentation, user tutorials, and instructions for requesting new features are available online (https://jlsteenwyk.com/BioKIT).