bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limb, joint and pelvic kinematic control in the quail coping with step perturbations
Authors: Andrada Emanuel , Mothes Oliver , Stark Heiko , Tresch Matthew C. , Denzler Joachim , Fischer Martin S. , Blickhan Reinhard 
Published: January 2022

AbstractSmall cursorial birds display remarkable walking skills and can negotiate complex and unstructured terrains with ease. The neuromechanical control strategies necessary to adapt to these challenging terrains are still not well understood. Here, we analyzed the 2D- and 3D pelvic and leg kinematic strategies employed by the common quail to negotiate visible step-up and step-down perturbations of 1 cm, 2.5 cm, and 5 cm. We used biplanar fluoroscopy to accurately describe joint positions in three dimensions and performed semi-automatic landmark localization using deep learning.Quails negotiated vertical perturbations without major problems and rapidly regained steady-state locomotion. When coping with step-up perturbations, the quail mostly adapted the trailing limb to permit the leading leg to step on the elevated substrate in a similar way as it did during level locomotion. When the quail negotiated step-down perturbations, both legs showed significant adaptations. For small and moderate perturbations (not inducing aerial running) the quail kept the function of the distal joints (i.e., their kinematic pattern) largely unchanged during uneven locomotion, and most changes occurred in proximal joints. The hip regulated leg length, while the distal joints maintained the spring-damped limb patterns. However, to negotiate the largest visible step perturbations, more dramatic kinematic alterations were observed. For these large perturbations, all joints contributed to leg lengthening/ shortening in the trailing leg and both the trailing and leading legs stepped more vertically and less abducted. This indicates a shift from a dynamic walking program to strategies that are focused on maximizing safety.
Tissue fibroblasts are a critical source of prostacyclin and anti-thrombotic protection
Authors: Mitchell Jane A. , Vinokurova Maria , Lopes-Pires Maria Elisa , Shala Fisnik , Armstrong Paul C. , Ahmetaj-Shala Blerina , Elghazouli Youssef , Liu Bin , Zhou Yingbi , Hao Chuan-ming , Herschman Harvey R. , Kirkby Nicholas S. 
Published: January 2022

AbstractProstacyclin is one of the bodies fundamental signalling pathways. It has long been considered principally anti-thrombotic hormone derived from the vascular endothelium. The role of non-vascular sources in prostacyclin synthesis has not been systematically evaluated, however, due to a lack of tools resulting in an underappreciation of its role in other contexts. Here we used cellspecific knockout mice and human tissues to show that lung, and other tissues, are powerful producers of prostacyclin independent of their vascular components. Instead, in mice and humans, lung prostacyclin synthesis is associated with fibroblasts. The fibroblast-derived prostaglandins enter the circulation and provide systemic anti-thrombotic protection. These observations define a new paradigm in prostacyclin biology in which fibroblast/non-vascular-derived prostacyclin works in parallel with endothelium-derived prostaglandins to control cardiovascular health and potentially a broad range of other biology. These results may explain how local diseases of the lung and elsewhere result in cardiovascular risk.
Pathological relevance of post-translationally modified alpha-synuclein (pSer87, pSer129, nTyr39) in idiopathic Parkinson’s disease and Multiple System Atrophy
Authors: Sonustun Berkiye , Altay Firat M , Strand Catherine , Hondhamuni Geshanthi , Warner Thomas T , Lashuel Hilal A , Bandopadhyay Rina 
Published: January 2022

AbstractAggregated alpha-synuclein (α-synuclein) is the main component of Lewy bodies (LBs), Lewy neurites (LNs), and glial cytoplasmic inclusions (GCIs), which are pathological hallmarks of idiopathic Parkinson’s disease (IPD) and multiple system atrophy (MSA), respectively. Initiating factors that culminate in forming LBs/LNs/GCIs remain elusive. Several species of α-synuclein exist, including phosphorylated and nitrated forms. It is unclear which α-synuclein post-translational modifications (PTMs) appear within aggregates throughout disease pathology. Herein we aimed to establish the predominant α–synuclein PTMs in post-mortem IPD and MSA pathology using immunohistochemistry. We examined the patterns of three α-synuclein PTMs (pS87, pS129, nY39) simultaneously in pathology-affected regions of 15 PD, 5 MSA, 6 neurologically normal controls. All antibodies recognized LBs, LNs, and GCIs, albeit to a variable extent. pS129 α-synuclein antibody was particularly immunopositive for LNs and synaptic dot-like structures followed by nY39 α-synuclein antibody. GCIs, neuronal inclusions, and small threads were positive for nY39 α-synuclein in MSA. Quantification of the LB scores revealed that pS129 α-synuclein was the dominant and earliest α-synuclein PTM followed by nY39 α-synuclein, while lower amounts of pSer87 α-synuclein appeared later in disease progression in PD. These results may have implications for novel biomarker and therapeutic developments.
Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers
Authors: Irber Luiz , Brooks Phillip T. , Reiter Taylor , Pierce-Ward N. Tessa , Hera Mahmudur Rahman , Koslicki David , Brown C. Titus 
Published: January 2022

AbstractThe identification of reference genomes and taxonomic labels from metagenome data underlies many microbiome studies. Here we describe two algorithms for compositional analysis of metagenome sequencing data. We first investigate the FracMinHash sketching technique, a derivative of modulo hash that supports Jaccard containment estimation between sets of different sizes. We implement FracMinHash in the sourmash software, evaluate its accuracy, and demonstrate large-scale containment searches of metagenomes using 700,000 microbial reference genomes. We next frame shotgun metagenome compositional analysis as the problem of finding a minimum collection of reference genomes that “cover” the known k-mers in a metagenome, a minimum set cover problem. We implement a greedy approximate solution using FracMinHash sketches, and evaluate its accuracy for taxonomic assignment using a CAMI community benchmark. Finally, we show that the minimum metagenome cover can be used to guide the selection of reference genomes for read mapping. sourmash is available as open source software under the BSD 3-Clause license at github.com/dib-lab/sourmash/.
Inflammatory CD4/CD8 double positive human T cells arise from reactive CD8 T cells and are sufficient to mediate GVHD pathology
Authors: Hess Nicholas J. , Turicek David P. , Riendeau Jeremiah , McIlwain Sean J. , Guzman Emmanuel Contreras , Nadiminti Kalyan , Hudson Amy , Callander Natalie S. , Skala Melissa C. , Gumperz Jenny E. , Hematti Peiman , Capitini Christian M. 
Published: January 2022

AbstractAn important paradigm in allogeneic hematopoietic cell transplantations (allo-HCTs) is the prevention of graft-vs-host disease (GVHD) while preserving the graft-vs-leukemia (GVL) activity of donor T cells. From an observational clinical study of adult allo-HCT recipients, we identified a CD4+/CD8+ double positive T cell (DPT) population, not present in starting grafts, whose presence was predictive of ≥ grade 2 GVHD. Using an established xenogeneic transplant model, we reveal that the DPT population develop from antigen stimulated CD8 T cells which become transcriptionally, metabolically and phenotypically distinct from single-positive CD4 and CD8 T cells. Isolated DPTs were sufficient to mediate xeno-GVHD pathology when re-transplanted into naive mice but provided no survival benefit when mice were challenged with a human B-ALL cell line. Overall, this study reveals human DPTs as a T cell population directly involved with GVHD pathology.One Sentence SummaryHuman CD4+/CD8+ double positive T cells (DPTs) mediate xenogeneic GVHD but possess limited GVL activity.
Temperature-dependent genetics of thermotolerance between yeast species
Authors: Abrams Melanie B. , Brem Rachel B. 
Published: January 2022

AbstractMany traits of industrial and basic biological interest arose long ago, and manifest now as fixed differences between a focal species and its reproductively isolated relatives. In these systems, extant individuals can hold clues to the mechanisms by which phenotypes evolved in their ancestors. We harnessed yeast thermotolerance as a test case for such molecular-genetic inferences. In viability experiments, we showed that extant Saccharomyces cerevisiae survived at temperatures where cultures of its sister species S. paradoxus died out. Then, focusing on loci that contribute to this difference, we found that the genetic mechanisms of high-temperature growth changed with temperature. We also uncovered an enrichment of low-frequency variants at thermotolerance loci in S. cerevisiae population sequences, suggestive of a history of non-neutral selective forces acting at these genes. We interpret our results in light of a model of gradual acquisition of thermotolerance in the S. cerevisiae lineage by positive selection along a temperature cline. We propose that in an ancestral S. cerevisiae population, alleles conferring defects at a given temperature would have been resolved by adaptive mutations, expanding the range and setting the stage for further temperature advances. Together, our results and interpretation underscore the power of genetic approaches to explore how an ancient trait came to be.
Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling
Authors: Batzilla Alina , Lu Junyan , Kivioja Jarno , Putzker Kerstin , Lewis Joe , Zenz Thorsten , Huber Wolfgang 
Published: January 2022

AbstractThe development of cancer therapies may be improved by the discovery of tumor-specific molecular dependencies. The requisite tools include genetic and chemical perturbations, each with its strengths and limitations. Drug perturbations can be readily applied to primary cancer samples at a large scale, but mechanistic understanding of hits and further pharmaceutical development is often complicated by the fact that a small compound has a range of affinities to multiple proteins.To computationally infer the molecular dependencies of individual cancers from their ex-vivo drug sensitivity profiles, we developed a mathematical model that deconvolutes these data using measurements of protein-drug affinity profiles.Our method, DepInfeR, correctly identified known dependencies, including EGFR dependence in Her2+ breast cancer cell line, FLT3 dependence in AML tumors with FLT3-ITD mutations and the differential dependencies on the B-cell receptor pathway in two major subtypes of chronic lymphocytic leukemia (CLL). Furthermore, our method uncovered new subgroup-specific dependencies, including a previously unreported dependence of high-risk CLL on Checkpoint kinase 1 (CHEK1). The method also produced a more accurate map of the molecular dependencies in a heterogeneous set of 117 CLL samples.The ability to deconvolute polypharmacological phenotypes into underlying causal molecular dependencies should increase the utility of high-throughput drug response assays for functional precision oncology.
Optimization of an unscented Kalman filter for an embedded platform
Authors: Graybill Philip P. , Gluckman Bruce J. , Kiani Mehdi 
Published: January 2022

AbstractThe unscented Kalman filter (UKF) is finding increased application in biological fields. While realizing a complex UKF system in a low-power embedded platform offers many potential benefits including wearability, it also poses significant design challenges. Here we present a method for optimizing a UKF system for realization in an embedded platform. The method seeks to minimize both computation time and error in UKF state reconstruction and forecasting. As a case study, we applied the method to a model for the rat sleep-wake regulatory system in which 432 variants of the UKF over six different variables are considered. The optimization method is divided into three stages that assess computation time, state forecast error, and state reconstruction error. We apply a cost function to variants that pass all three stages to identify a variant that computes 27 times faster than the reference variant and maintains required levels of state estimation and forecasting accuracy. We draw the following insights: 1) process noise provides leeway for simplifying the model and its integration in ways that speed computation time while maintaining state forecasting accuracy, 2) the assimilation of observed data during the UKF correction step provides leeway for simplifying the UKF structure in ways that speed computation time while maintaining state reconstruction accuracy, and 3) the optimization process can be accelerated by decoupling variables that directly impact the underlying model from variables that impact the UKF structure.Author summaryPowerful statistical tools can be used to estimate unmeasured information in biological systems and predict the system’s future state. Translating these tools from a desktop computer to small, wearable or implantable platforms can unlock many benefits, but presents many design challenges, because tradeoffs between computational simplicity and system accuracy must be balanced. We present an approach to translating one such widely used statistical tool, the unscented Kalman filter, from a desktop computer to a miniature device. We demonstrate the approach with a case study centering on the neural circuits governing the mammalian sleep-wake cycle. By exploiting uncertainty in the biology being estimated and the corrective influence of biological measurements, we arrive at a design that is easily computable on the miniature device and maintains a high level of accuracy. We anticipate that our approach will aid others in designing such miniaturized systems for a broad range of applications.
PVT1, a YAP1 dependent stress responsive lncRNA drives ovarian cancer metastasis and chemoresistance
Authors: Tabury Kevin , Monavarian Mehri , Listik Eduardo , Shelton Abigail K. , Choi Alex Seok , Quintens Roel , Arend Rebecca , Hempel Nadine , Miller C. Ryan , Györrfy Balázs , Mythreye Karthikeyan 
Published: January 2022

AbstractMetastatic growth of ovarian cancer cells into the peritoneal cavity requires adaptation to various cellular stress factors to facilitate cell survival and growth. Here we demonstrate the role of PVT1, one such stress induced long non-coding RNA, in ovarian cancer growth and metastasis. PVT1 is an amplified and overexpressed lncRNA in ovarian cancer with strong predictive value for survival and response to targeted therapeutics. We find that expression of PVT1 is regulated by ovarian tumor cells in response to cellular stress, particularly loss of cell-cell contacts and changes in matrix rigidity occurring in a YAP1 dependent manner. Induction of PVT1 promotes tumor cell survival, growth, and migration. Conversely, reducing PVT1 levels robustly abrogates metastatic behavior and tumor cell dissemination in cell lines and syngeneic transplantation modelsin vivo. We find that reducing PVT1 causes widespread transcriptome changes leading to alterations in cellular stress response and metabolic pathways including doxorubicin metabolism, which directly impacts chemosensitivity. Together, these findings implicate PVT1 as a promising therapeutic target to suppress metastasis and avoid chemoresistance in ovarian cancer.SUMMARY BLURBPVT1 is a stress-responsive IncRNA regulated by YAP1, leading to increased ovarian cancer metastasis and chemoresistance, making PVT1 a promising therapeutic target.
Evolutionary adaptation to juvenile malnutrition impacts adult metabolism and impairs adult fitness inDrosophila
Authors: Erkosar Berra , Dupuis Cindy , Cavigliasso Fanny , Savary Loriane , Kremmer Laurent , Gallart-Ayala Hector , Ivanisevic Julijana , Kawecki Tadeusz J. 
Published: January 2022

AbstractJuvenile undernutrition has lasting effects on adult metabolism of the affected individuals, but it is unclear how adult physiology is shaped over evolutionary time by natural selection driven by juvenile undernutrition. We combined RNAseq, targeted metabolomics and genomics to study the consequences of evolution under juvenile undernutrition for metabolism of reproductively active adult females ofDrosophila melanogaster. Compared to Control populations maintained on standard diet, Selected populations maintained for over 230 generations on a nutrient-poor larval diet evolved major changes in adult gene expression and metabolite abundance, in particular affecting amino-acid and purine metabolism. The evolved differences in adult gene expression and metabolite abundance between Selected and Control populations were positively correlated with the corresponding differences previously reported for Selected versus Control larvae. This implies that genetic variants affect both stages similarly. Even when well fed, the metabolic profile of Selected flies resembled that of flies subject to starvation. Finally, Selected flies had lower reproductive output than Controls even when both were raised under the conditions under which the Selected populations evolved. These results imply that evolutionary adaptation to juvenile undernutrition has large pleiotropic consequences for adult metabolism, and that they are costly rather than adaptive for adult fitness. Thus, juvenile and adult metabolism do not appear to evolve independently from each other even in a holometabolous species where the two life stages are separated by a complete metamorphosis.
HIV and FIV glycoproteins increase cellular tau pathology via cGMP-dependent kinase II activation
Authors: Sathler Matheus F. , Doolittle Michael J. , Cockrell James A. , Nadalin India R. , Hofmann Franz , VandeWoude Sue , Kim Seonil 
Published: January 2022

AbstractAs the development of combination antiretroviral therapy (cART) against human immunodeficiency virus (HIV) drastically improves the lifespan of individuals with HIV, many are now entering the prime age when Alzheimer’s disease (AD)-like symptoms begin to manifest. Hyperphosphorylated tau, a known AD pathological characteristic, has been prematurely increased in the brains of HIV-infected patients as early as in their 30s and is increased with age. This thus suggests that HIV infection may lead to accelerated AD phenotypes. However, whether HIV infection causes AD to develop more quickly in the brain is not yet fully determined. Interestingly, we have previously revealed that viral glycoproteins, HIV gp120 and feline immunodeficiency virus (FIV) gp95, induce neuronal hyperexcitation via cGMP-dependent kinase II (cGKII) activation in cultured hippocampal neurons. Here, we use cultured mouse cortical neurons to demonstrate that HIV gp120 and FIV gp95 are sufficient to increase cellular tau pathology, including intracellular tau hyperphosphorylation and tau release to the extracellular space. We further reveal that viral glycoprotein-induced cellular tau pathology requires cGKII activation. Together, HIV infection likely accelerates AD-related tau pathology via cGKII activation.
Evolution of a cis-acting SNP that controls Type VI Secretion in Vibrio cholerae
Authors: Ng Siu Lung , Kammann Sophia , Steinbach Gabi , Hoffmann Tobias , Yunker Peter J , Hammer Brian K. 
Published: January 2022

AbstractMutations in regulatory mechanisms that control gene expression contribute to phenotypic diversity and thus facilitate the adaptation of microbes and other organisms to new niches. Comparative genomics can be used to infer rewiring of regulatory architecture based on large effect mutations like loss or acquisition of transcription factors but may be insufficient to identify small changes in non-coding, intergenic DNA sequence of regulatory elements that drive phenotypic divergence. In human-derived Vibrio cholerae, the response to distinct chemical cues triggers production of multiple transcription factors that can regulate the Type VI Secretion System (T6), a broadly distributed weapon for interbacterial competition. However, to date, the signaling network remains poorly understood because no regulatory element has been identified for the major T6 locus. Here we identify a conserved cis-acting single nucleotide polymorphism (SNP) controlling T6 transcription and activity. Sequence alignment of the T6 regulatory region from diverse V. cholerae strains revealed conservation of the SNP that we rewired to interconvert V. cholerae T6 activity between chitin-inducible and constitutive states. This study supports a model of pathogen evolution through a non-coding cis-regulatory mutation and preexisting, active transcription factors that confers a different fitness advantage to tightly regulated strains inside a human host and unfettered strains adapted to environmental niches.ImportanceOrganisms sense external cues with regulatory circuits that trigger the production of transcription factors, which bind specific DNA sequences at promoters (“cis” regulatory elements) to activate target genes. Mutations of transcription factors or their regulatory elements create phenotypic diversity, allowing exploitation of new niches. Waterborne pathogen Vibrio cholerae encodes the Type VI Secretion System “nanoweapon” to kill competitor cells when activated. Despite identification of several transcription factors, no regulatory element has been identified in the promoter of the major Type VI locus, to date. Combining phenotypic, genetic, and genomic analysis of diverse V. cholerae strains, we discovered a single nucleotide polymorphism in the Type VI promoter that switches its killing activity between a constitutive state beneficial outside hosts and an inducible state for constraint in a host. Our results support a role for non-coding DNA in adaptation of this pathogen.
Germline-soma Supply Mitochondria for mtDNA Inheritance in Mouse Oogenesis
Authors: Sha Hongying , Ye Zhao , Ye Zhen , Shi Sanbao , Pan Jianxin , Dong Xi , Zhao Yao 
Published: January 2022

AbstractMaternal transmission paradigm of mtDNA remains controversial in mammalian oogenesis. Germline-soma-to-oocyte communication by numerous transzonal nanotubes (TZTs) reminds whether intercellular mitochondrial transfer is associated with maternal inheritance. Here, we found that mouse oocytes egocentrically receive mitochondria via TZTs, which projected from germline-soma, to achieve 105copies, instead ofde novosynthesis of mtDNA subpopulation in growing oocytes.De novoassembled TZTs amongst germline-soma and oocytes accumulated mtDNA amounts of the oocytesin vitro. However, mitochondrial supplement from germline-soma gradually diminished along with oocyte growth and was terminated by meiosis resumption, in line with a decrease in the proportion of germline-soma with thriving mtDNA replication and FSH capture capability. Thus, germline-soma-to-oocyte mitochondrial transfer is responsible for mammalian mtDNA inheritance as well as oogenesis and aging.One-sentence summariesThe maternal mtDNA transmission accompanied by oogenesis is inseparable from germline-soma mitochondrial transport.