bluuebunny/crossref_metadata_2025 huggingface dataset:
Determining insulin sensitivity from glucose tolerance tests in Iberian and Landrace pigs
Authors: Rodríguez-López JM , Lachica M , González-Valero L , Fernández-Fígares I
Published: December 2019

As insulin sensitivity may help to explain divergences in growth and body composition between native and modern breeds, metabolic responses to glucose infusion were measured using an intra-arterial glucose tolerance test (IAGTT). Iberian (n = 4) and Landrace (n = 5) barrows (47.0 ± 1.2 kg BW), fitted with a permanent carotid artery catheter were injected with glucose (500 mg/kg BW) and blood samples collected at −10, 0, 5, 10, 15, 20, 25, 30, 45, 60, 90, 120 and 180 min following glucose infusion. Plasma samples were analysed for insulin, glucose, lactate, triglycerides, cholesterol, creatinine, albumin and urea. Insulin sensitivity indices were calculated and analyed. Mean plasma glucose, creatinine and cholesterol concentrations were lower (P< 0.01) in Iberian (14, 68 and 22%, respectively) compared with Landrace pigs during the IAGTT. However, mean plasma insulin, lactate, triglycerides and urea concentrations were greater (P< 0.001) in Iberian (50, 35, 18 and 23%, respectively) than in Landrace pigs. Iberian pigs had larger area under the curve (AUC) of insulin (P< 0.05) and lactate (P< 0.1), and smaller (P< 0.05) AUC for glucose 0-60 min compared with Landrace pigs. Indices for estimating insulin sensitivity in fasting conditions indicated improved β-cell function in Iberian compared with Landrace pigs, but no difference (P> 0.10) in calculated insulin sensitivity index was found after IAGTT between breeds. A time response (P< 0.05) was obtained for insulin, glucose and lactate so that maximum concentration was achieved 10 and 15 min post-infusion for insulin (Iberian and Landrace pigs, respectively), immediately post-infusion for glucose, and 20 min post-infusion for lactate, decreasing thereafter until basal levels. There was no time effect for the rest of metabolites evaluated. In conclusion, growing Iberian pigs challenged with an IAGTT showed changes in biochemical parameters and insulin response that may indicate an early stage of insulin resistance.
Spatial Areas of Genotype Probability (SPAG): predicting the spatial distribution of adaptive genetic variants under future climatic conditions
Authors: Rochat Estelle , Joost Stéphane
Published: December 2019

In a context of rapid global change, one of the key components for the survival of species is their genetic adaptive potential. Many methods have been developed to identify adaptive genetic variants, but few tools were made available to integrate this knowledge into conservation management. We present here the SPatial Areas of Genotype probability (SPAG), using genotype-environment logistic associations to map the probability of finding beneficial variants in a study area. We define a univariate model predicting the spatial distribution of a single genotype, and three multivariate models allowing the integration of several genotypes, potentially associated with various environmental variables. We then integrate climate change projections to map the corresponding future distribution of genotypes. The analysis of the mismatch between current and future SPAGs makes it possible to identify a) populations that are better adapted to the future climate through the presence of genetic variants able to cope with future conditions, and b) vulnerable populations where genotype(s) of interest are not frequent enough for the individuals to adapt to the future climate. We validate the SPAG approach using simulations and we use it to study the potential adaptation of 161 Moroccan and 382 European goats to the bioclimatic conditions. In Morocco, using whole genome sequence data, we identify seven genomic regions strongly associated with the precipitation seasonality (WorldClim database). The predicted shift in SPAGs under a strong climate change scenario for 2070 highlights goat populations likely to be threatened by the expected increase in precipitation variation in the future. In Europe, we find genomic regions associated with low precipitation, the shift in SPAGs highlighting vulnerable populations not adapted to the very dry conditions expected in 2070. The SPAG methodology is successfully validated using cross-validations and provides an efficient tool to take the adaptive potential into account in general conservation frameworks.
Oligodendrocytes support axonal transport and maintenance via exosome secretion
Authors: Frühbeis Carsten , Kuo-Elsner Wen Ping , Müller Christina , Barth Kerstin , Peris Leticia , Tenzer Stefan , Möbius Wiebke , Werner Hauke B. , Nave Klaus-Armin , Fröhlich Dominik , Krämer-Albers Eva-Maria
Published: December 2019

Neurons extend long axons that require maintenance and are susceptible to degeneration. Long-term integrity of axons depends on intrinsic mechanisms including axonal transport and extrinsic support from adjacent glial cells. The mechanisms of support provided by myelinating oligodendrocytes to underlying axons are only partly understood. Oligodendrocytes release extracellular vesicles (EVs) with properties of exosomes, which upon delivery to neurons improve neuronal viability in vitro. Here, we show that oligodendroglial exosome secretion is impaired in two mouse mutants exhibiting secondary axonal degeneration due to oligodendrocyte-specific gene defects. Wildtype oligodendroglial exosomes support neurons by improving the metabolic state and promoting axonal transport in nutrient deprived neurons. Mutant oligodendrocytes release less exosomes that share a common signature of underrepresented proteins. Notably, mutant exosomes lack the ability to support nutrient deprived neurons and to promote axonal transport. Together, these findings indicate that glia to neuron exosome transfer promotes neuronal long-term maintenance by facilitating axonal transport, providing a novel mechanistic link between myelin diseases and secondary loss of axonal integrity.
Stimulus-choice (mis)alignment in primate MT cortex
Authors: Zhao Yuan , Yates Jacob L. , Levi Aaron J. , Huk Alexander C. , Park Il Memming
Published: December 2019

For stimuli near perceptual threshold, the trial-by-trial activity of single neurons in many sensory areas is correlated with the animal’s perceptual report. This phenomenon has often been attributed to feedforward readout of the neural activity by the downstream decision-making circuits. The interpretation of choice-correlated activity is quite ambiguous, but its meaning can be better understood in the light of population-wide correlations among sensory neurons. Using a statistical nonlinear dimensionality reduction technique on single-trial ensemble recordings from the middle temporal area during perceptual-decision-making, we extracted low-dimensional neural tra jectories that captured the population-wide fluctuations. We dissected the particular contributions of sensory-driven versus choice-correlated activity in the low-dimensional population code. We found that the neural trajectories strongly encoded the direction of the stimulus in single dimension with a temporal signature similar to that of single MT neurons. If the downstream circuit were optimally utilizing this information, choice-correlated signals should be aligned with this stimulus encoding dimension. Surprisingly, we found that a large component of the choice information resides in the subspace orthogonal to the stimulus representation inconsistent with the optimal readout view. This misaligned choice information allows the feedforward sensory information to coexist with the decision-making process. The time course of these signals suggest that this misaligned contribution likely is feedback from the downstream areas. We hypothesize that this non-corrupting choice-correlated feedback might be related to learning or reinforcing sensory-motor relations in the sensory population.

Author summary

In sensorimotor decision-making, internal representation of sensory stimuli is utilized for the generation of appropriate behavior for the context. Therefore, the correlation between variability in sensory neurons and perceptual decisions is sometimes explained by a causal, feedforward role of sensory noise in behavior. However, this correlation could also originate via feedback from decision-making mechanisms downstream of the sensory representation. This cannot be resolved by analyzing single unit responses, but requires a population level analysis. Area MT contains both sensory and choice information and is known to be the key sensory area for visual motion perception. Thus the decision-making process may be corrupting the sensory representation. However, we find that the sensory stimuli and choice variables are separate at the population level,contradicting the previous interpretations based on single unit recordings. This new insight postulates how neural systems can maintain a mixed representation while allows learning and adaptation.
A four-step regulatory cascade controls bistable transfer competence development of the integrative and conjugative element ICEclcinPseudomonas
Authors: Carraro Nicolas , Richard Xavier , Sulser Sandra , Delavat François , Mazza Christian , van der Meer Jan Roelof
Published: December 2019

Genetic bistability controls different phenotypic programs in defined subpopulations of genetically identical bacteria. Conjugative transfer of the integrative and conjugative element ICEclcinPseudomonasrequires development of a transfer competence state in stationary phase, but this state arises only in 3-5% of individual cells. The mechanisms controlling and underlying the bistable switch between non-active and transfer competence cells have long remained enigmatic. Using a variety of genetic tools combined with stochastic modeling, we characterize here the factors and overall network architecture controlling bistable ICEclcactivation of transfer competence. Two new key regulators (BisR and BisDC) were uncovered, that link the hierarchical cascade of ICEclctransfer competence activation to in total four regulatory nodes. The final activator complex named BisDC drives a positive feedback on its own transcription, and directly controls the “late” ICE promoters for excision and transfer. Stochastic mathematical modeling conceptually explained the arisal and maintenance of bistability by the feedback loop, and demonstrated its importance to guarantee consistent prolonged downstream output in activated cells. A minimized gene set allowing controllable bistable output in aPseudomonas putidain absence of the ICEclclargely confirmed model predictions. Phylogenetic analyses further showed that the two new ICEclcregulatory factors are widespread among putative ICEs found inGamma- andBeta- proteobacteria, highlighting the conceptual importance of our findings for the behaviour of this wide family of conjugative elements.

Author summary

Integrative and conjugative elements (ICEs) are mobile genetic elements present in virtually every bacterial species, which can confer adaptive functions to their host, such as antibiotic resistance or xenometabolic pathways. Integrated ICEs maintain by replication along with the genome of their bacterial host, but in order to transfer, the ICE excises and conjugates into a new recipient cell. Single-cell studies on a unique but widely representative ICE model fromPseudomonas(ICEclc) showed that transfer only occurs from a small dedicated subpopulation of cells that arises during stationary phase conditions. This bistable subpopulation differentiation is highly significant for ICE behaviour and fitness, but how it is regulated has remained largely unknown. The present work unveiled the architecture of the ICEclctransfer competence regulation, and showed its widespread occurrence among ICEs of the same family. Stochastic mathematical modeling explained how bistability is generated and maintained, prolonging the capacity of stationary phase cells to complete all stages of ICE activation.
PolyQ-independent toxicity associated with novel translational products from CAG repeat expansions
Authors: Rudich Paige D. , Watkins Simon , Lamitina Todd
Published: December 2019

Expanded CAG nucleotide repeats are the underlying genetic cause of at least 14 incurable diseases, including Huntington’s disease (HD). The toxicity associated with many CAG repeat expansions is thought to be due to the translation of the CAG repeat to create a polyQ protein, which forms toxic oligomers and aggregates. However, recent studies show that HD CAG repeats undergo a non-canonical form of translation calledRepeat-associatednon-AUG dependent (RAN) translation. RAN translation of the CAG sense and CUG anti-sense RNAs produces six distinct repeat peptides: polyalanine (polyAla, from both CAG and CUG repeats), polyserine (polySer), polyleucine (polyLeu), polycysteine (polyCys), and polyglutamine (polyGln). The toxic potential of individual CAG-derived RAN polypeptides is not well understood. We developed pureC. elegansprotein models for each CAG RAN polypeptide using codon-varied expression constructs that preserve RAN protein sequence but eliminate repetitive CAG/CUG RNA. While all RAN polypeptides formed aggregates, only polyLeu was consistently toxic across multiple cell types. In GABAergic neurons, which exhibit significant neurodegeneration in HD patients, codon-varied (Leu)38, but not (Gln)38, caused substantial neurodegeneration and motility defects. Our studies provide the firstin vivoevaluation of CAG-derived RAN polypeptides and suggest that polyQ-independent mechanisms, such as RAN-translated polyLeu peptides, may have a significant pathological role in CAG repeat expansion disorders.
Effect of intensity of agronomic practices on the yield of two breeding types of winter oilseed rape cultivars
Authors: Wójtowicz Marek , Wójtowicz Andrzej , Jajor Ewa , Korbas Marek , Wielebski Franciszek
Published: December 2019

The effect of three fungicide treatment programmes and the level of spring nitrogen fertilisation on the seed yield of two types of cultivars ofBrassica napusL. sown at two different seeding rates was studied in a field experiment carried out in a split-split-plot design. The subject of the study was an open-pollinated cultivar (Casoar) and a restored hybrid cultivar (Visby). Three plant protection programmes, two levels of spring nitrogen fertilisation (160 and 220 kg N·ha-1), and two different seeding rates for each cultivar (Visby—50 and 70 seeds·m-2; Casoar—60 and 80 seeds·m-2) were included. The most intensive protection programme comprised three fungicide treatments: first in autumn at the six-leaves-unfolded stage—BBCH 16, second in spring at the stem elongation stage—BBCH 33, and third at the full flowering stage—BBCH 65. One of two less intensive programmes of plant protection included fungicide application in autumn at the six-leaves-unfolded stage—BBCH 16 and at the full flowering stage—BBCH 65, while the second included fungicide application in spring at the stem elongation stage—BBCH 33 and at the full flowering stage—BBCH 65.

The effectiveness of the protection programmes and nitrogen fertilisation was influenced by the intensity of abiotic stress factors. However, the average yield from the plots protected against pathogens was significantly higher than that from the untreated plots. The increase of nitrogen fertilisation from 160 to 220 kg·ha-1also caused significant increase of average seed yield. The yield of cultivar Visby was higher and less dependent on the seeding rate compared to cultivar Casoar. Cultivars responded similarly to plant protection programmes and the rate of nitrogen fertilisation in spring. Higher yields of Visby cultivar can be attributed to the higher number of seeds per silique and the higher number of siliques per m2.
Bmal1 integrates mitochondrial metabolism and macrophage activation
Authors: Alexander Ryan K. , Liou Yae-Huei , Knudsen Nelson H. , Starost Kyle A. , Xu Chuanrui , Hyde Alexander L. , Liu Sihao , Jacobi David , Liao Nan-Shih , Lee Chih-Hao
Published: December 2019

Metabolic pathways and inflammatory processes are under circadian regulation. While rhythmic immune cell recruitment is known to impact infection outcomes, whether the circadian clock modulates immunometabolism remains unclear. We find the molecular clock Bmal1 is induced by inflammatory stimulants, including Ifn-γ/lipopolysaccharide (M1) and tumor conditioned medium, to maintain mitochondrial metabolism under these metabolically stressed conditions in mouse macrophages. Upon M1 stimulation, myeloid-specificBmal1knockout (M-BKO) renders macrophages unable to sustain mitochondrial function, enhancing succinate dehydrogenase (SDH)-mediated mitochondrial ROS production and Hif-1α-dependent metabolic reprogramming and inflammatory damage. In tumor-associated macrophages, the aberrant Hif-1α activation and metabolic dysregulation by M-BKO contribute to an immunosuppressive tumor microenvironment. Consequently, M-BKO increases melanoma tumor burden, while administrating an SDH inhibitor dimethyl malonate suppresses tumor growth. Therefore, Bmal1 functions as a metabolic checkpoint integrating macrophage mitochondrial metabolism, redox homeostasis and effector functions. This Bmal1-Hif-1α regulatory loop may provide therapeutic opportunities for inflammatory diseases and immunotherapy.
Epiphytic Microbiome of Grapes Berries Varies Between Phenological Timepoints, Growing Seasons and Regions
Authors: Hall Megan E. , O’Bryon Isabelle , Wilcox Wayne F. , Osier Michael V. , Cadle-Davidson Lance
Published: December 2019

Extensive research into the microbial ecology of grapes near harvest, with a primary focus on yeasts, has improved our understanding of some components of variation that influence grapevine terroir. Metagenomic tools enable a broader exploration of the plant microbiome and components of variability due to such factors as year, location, management, and phenological stage. In 2014, to characterize the microbial changes of the grape surface over the course of the growing season in the Finger Lakes region of New York, we examined the epiphytic microbiome of grapes at five key phenological stages: pea-sized, bunch closure, Veraison, 15 Brix and harvest. This experiment was repeated in two subsequent years in the Finger Lakes, New York in 2015, and in Tasmania, Australia in 2016, to examine variability of regional terroir. We found significant shifts in taxa presence and relative taxa abundance between phenological timepoints, and determined that the epiphytic microbiome differed significantly not just between regions but also within a single region from one year to the next. These findings call into question the role of the phytobiome in the expression of terroir, as the phytobiome is dynamically responding to its environment, within and between years and locations. On the berry surface in particular, these dynamics are complicated by weather and management. Understanding that the grape surface microbiome is consistently changing may influence how we manage the berry epiphytic microbiome, potentially affecting disease management and vinification decisions.
MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data
Authors: Shahryary Yadollah , Hazarika Rashmi R. , Johannes Frank
Published: December 2019

Background:

Whole-Genome Bisulfite Sequencing (WGBS) is a Next Generation Sequencing (NGS) technique for measuring DNA methylation at base resolution. Continuing drops in sequencing costs are beginning to enable high-throughput surveys of DNA methylation in large samples of individuals and/or single cells. These surveys can easily generate hundreds or even thousands of WGBS datasets in a single study. The efficient pre-processing of these large amounts of data poses major computational challenges and creates unnecessary bottlenecks for downstream analysis and biological interpretation.

Results:

To offer an efficient analysis solution, we present MethylStar, a fast, stable and flexible pre-processing pipeline for WGBS data. MethylStar integrates well-established tools for read trimming, alignment and methylation state calling in a highly parallelized environment, manages computational resources and performs automatic error detection. MethylStar offers easy installation through a dockerized container with all preloaded dependencies and also features a user-friendly interface designed for experts/non-experts. Application of MethylStar to WGBS from human, maize and Arabidopsis shows that it outperforms existing pre-processing pipelines in terms of speed and memory requirements.

Conclusions:

MethylStar is a fast, stable and flexible pipeline for high-throughput pre-processing of bulk or single-cell WGBS data. Its easy installation and user-friendly interface should make it a useful resource for the wider epigenomics community. MethylStar is distributed under GPL-3.0 license and source code is publicly available for download from githubhttps://github.com/jlab-code/MethylStar. Installation through a docker image is available fromhttp://jlabdata.org/methylstar.tar.gz
DHX9-dependent recruitment of BRCA1 to RNA is required to promote DNA end resection in homologous recombination
Authors: Chakraborty Prasun , Hiom Kevin
Published: December 2019

DExD/H-box helicase 9 (DHX9/RNA helicaseA) is ubiquitously expressed ATP-dependent helicase that unwinds a variety of complex DNA and RNA secondary structures, suggesting it might have a role in DNA replication and the repair of DNA damage. Here we identify a pivotal role for DHX9 in homologous recombination (HR). Cells that are deficient in DHX9 are impaired in the generation of single stranded DNA (ssDNA) by DNA end resection. Consequently these cells fail to recruit RPA and RAD51 to sites of DNA damage and are hypersensitive to treatment with the DNA damaging agents camptothecin and Olaparib. A critical early step in the initiation of HR is the recruitment of BRCA1 mediator protein to DNA damage to promote DNA resection. We show here that recruitment of BRCA1 to DNA damage foci is dependent on its interaction with DHX9 to form the BRCA1-D complex, which binds to nascent RNA. Together our data identify a pivotal role for DHX9 in homologous recombination and highlight the important contribution of RNA in the recruitment of BRCA1 to DNA damage for the repair of DNA breaks
Alpha synuclein aggresomes inhibit ciliogenesis and multiple functions of the centrosome
Authors: Iqbal Anila , Baldrighi Marta , Murdoch Jennifer N. , Fleming Angeleen , Wilkinson Christopher J.
Published: December 2019

Protein aggregates are the pathogenic hallmarks of many different neurodegenerative diseases and include the Lewy bodies found in Parkinson’s disease. Aggresomes are closely-related cellular accumulations of misfolded proteins. They develop in a juxtanuclear position, adjacent to the centrosome, the microtubule organizing centre of the cell, and share some protein components. Despite the long-standing observation that aggresomes/Lewy bodies and the centrosome sit side-by-side in the cell, no studies have been done to see whether these protein accumulations impede the organelle function. We investigated whether the formation of aggresomes affected key centrosome functions: its ability to organize the microtubule network and to promote cilia formation. We find that when aggresomes are present, neuronal cells are unable to organise their microtubule network. New microtubules are not nucleated and extended, and the cells fail to respond to polarity cues. Since dopaminergic neurons are polarised, ensuring correct localisation of organelles and the effective intracellular transport of neurotransmitter vesicles, loss of centrosome activity could contribute to loss of dopaminergic function and neuronal cell death in Parkinson’s disease. In addition, we provide evidence that many cell types, including dopaminergic neurons, cannot form cilia when aggresomes are present, which would affect their ability to receive extracellular signals.
Vargas: heuristic-free alignment for assessing linear and graph read aligners
Authors: Darby Charlotte A. , Gaddipati Ravi , Schatz Michael C. , Langmead Ben
Published: December 2019

Read alignment is central to many aspects of modern genomics. Most aligners use heuristics to accelerate processing, but these heuristics can fail to find the optimal alignments of reads. Alignment accuracy is typically measured through simulated reads; however, the simulated location may not be the (only) location with the optimal alignment score. Vargas implements a heuristic-free algorithm guaranteed to find the highest-scoring alignment for real sequencing reads to a linear or graph genome. With semiglobal and local alignment modes and affine gap and quality-scaled mismatch penalties, it can implement the scoring functions of commonly used aligners to calculate optimal alignments. While this is computationally intensive, Vargas uses multi-core parallelization and vectorized (SIMD) instructions to make it practical to optimally align large numbers of reads, achieving a maximum speed of 456 billion cell updates per second. We demonstrate how these “gold standard” Vargas alignments can be used to improve heuristic alignment accuracy by optimizing command-line parameters in Bowtie 2, BWA-MEM, and vg to align more reads correctly. Source code implemented in C++ and compiled binary releases are available athttps://github.com/langmead-lab/vargasunder the MIT license.
A community-maintained standard library of population genetic models
Authors: Adrion Jeffrey R. , Cole Christopher B. , Dukler Noah , Galloway Jared G. , Gladstein Ariella L. , Gower Graham , Kyriazis Christopher C. , Ragsdale Aaron P. , Tsambos Georgia , Baumdicker Franz , Carlson Jedidiah , Cartwright Reed A. , Durvasula Arun , Gronau Ilan , Kim Bernard Y. , McKenzie Patrick , Messer Philipp W. , Noskova Ekaterina , Ortega-Del Vecchyo Diego , Racimo Fernando , Struck Travis J. , Gravel Simon , Gutenkunst Ryan N. , Lohmueller Kirk E. , Ralph Peter L. , Schrider Daniel R. , Siepel Adam , Kelleher Jerome , Kern Andrew D.
Published: December 2019

The explosion in population genomic data demands ever more complex modes of analysis, and increasingly these analyses depend on sophisticated simulations. Recent advances in population genetic simulation have made it possible to simulate large and complex models, but specifying such models for a particular simulation engine remains a difficult and error-prone task. Computational genetics researchers currently re-implement simulation models independently, leading to inconsistency and duplication of effort. This situation presents a major barrier to empirical researchers seeking to use simulations for power analyses of upcoming studies or sanity checks on existing genomic data. Population genetics, as a field, also lacks standard benchmarks by which new tools for inference might be measured. Here we describe a new resource,stdpopsim, that attempts to rectify this situation.Stdpopsimis a community-driven open source project, which provides easy access to a growing catalog of published simulation models from a range of organisms and supports multiple simulation engine backends. This resource is available as a well-documented python library with a simple command-line interface. We share some examples demonstrating howstdpopsimcan be used to systematically compare demographic inference methods, and we encourage a broader community of developers to contribute to this growing resource.
A full-proteome, interaction-specific characterization of mutational hotspots across human cancers
Authors: Chen Siwei , Liu Yuan , Zhang Yingying , Wierbowski Shayne D. , Lipkin Steven M. , Wei Xiaomu , Yu Haiyuan
Published: December 2019

Rapid accumulation of cancer genomic data has led to the identification of an increasing number of mutational hotspots with uncharacterized significance. Here we present a biologically-informed computational framework that characterizes the functional relevance of all 1,107 published mutational hotspots identified in ∼25,000 tumor samples across 41 cancer types in the context of a human 3D interactome network, in which the interface of each interaction is mapped at residue resolution. Hotspots reside in network hub proteins and are enriched on protein interaction interfaces, suggesting that alteration of specific protein-protein interactions is critical for the oncogenicity of many hotspot mutations. Our framework enables, for the first time, systematic identification of specific protein interactions affected by hotspot mutations at the full proteome scale. Furthermore, by constructing a hotspot-affected network that connects all hotspot-affected interactions throughout the whole human interactome, we uncover genome-wide relationships among hotspots and implicate novel cancer proteins that do not harbor hotspot mutations themselves. Moreover, applying our network-based framework to specific cancer types identifies clinically significant hotspots that can be used for prognosis and therapy targets. Overall, we demonstrate that our framework bridges the gap between the statistical significance of mutational hotspots and their biological and clinical significance in human cancers.
Transfer of antigen-encoding bone marrow under immune-preserving conditions deletes mature antigen-specific B cells in recipients and inhibits antigen-specific antibody production
Authors: Brooks Jeremy F. , Davies Janet M. , Wells James W. , Steptoe Raymond J.
Published: December 2019

Pathological activation and collaboration of T and B cells underlies pathogenic autoantibody responses. Existing treatments for autoimmune disease cause non-specific immunosuppression and induction of antigen-specific tolerance remains an elusive goal. Many immunotherapies aim to manipulate the T-cell component of T-B interplay but few directly target B cells. One possible means to specifically target B cells is the transfer of gene-engineered BM that, once engrafted, gives rise to widespread specific and tolerogenic antigen expression within the hematopoietic system. Gene-engineered bone marrow encoding ubiquitous ovalbumin expression was transferred after low-dose (300cGy) immune-preserving irradiation. B-cell responsiveness was monitored by analyzing ovalbumin-specific antibody production after immunization with ovalbumin/complete Freund’s adjuvant. Ovalbumin-specific B cells and their response to immunization were analyzed using multi-tetramer staining. When antigen-encoding bone marrow was transferred under immune-preserving conditions, cognate antigen-specific B cells were purged from the recipient’s pre-existing B cell repertoire as well as the repertoire that arose after bone marrow transfer. OVA-specific B-cell deletion was apparent within the established host B-cell repertoire as well as that developing after gene-engineered bone marrow transfer. OVA-specific antibody production was substantially inhibited by transfer of OVA-encoding BM and activation of OVA-specific B cells, germinal centre formation and subsequent OVA-specific plasmablast differentiation were all inhibited. Low levels of gene-engineered bone marrow chimerism were sufficient to limit antigen-specific antibody production. These data show that antigen-specific B cells within an established B-cell repertoire are susceptible tode novotolerance induction and this can be achieved by transfer of gene-engineered bone marrow. This adds further dimensions to the utility of antigen-encoding bone marrow transfer as an immunotherapeutic tool.
Compensatory guaiacyl lignin biosynthesis at the expense of syringyl lignin in4CL1-knockout poplar
Authors: Tsai Chung-Jui , Xu Peng , Xue Liang-Jiao , Hu Hao , Nyamdari Batbayar , Naran Radnaa , Zhou Xiaohong , Goeminne Geert , Gao Ruili , Gjersing Erica , Dahlen Joseph , Pattathil Sivakumar , Hahn Michael G. , Davis Mark F. , Ralph John , Boerjan Wout , Harding Scott A.
Published: December 2019

The lignin biosynthetic pathway is highly conserved in angiosperms, yet pathway manipulations give rise to a variety of taxon-specific outcomes. Knockout of lignin-associated4-coumarate:CoA ligases(4CLs) in herbaceous species mainly reduces guaiacyl (G) lignin and enhances cell wall saccharification. Here we show that CRISPR-knockout of4CL1inPopulus tremula×albapreferentially reduced syringyl (S) lignin, with negligible effects on biomass recalcitrance. Concordant with reduced S-lignin was downregulation offerulate 5-hydroxylases(F5Hs). Lignification was largely sustained by 4CL5, a low-affinity paralog of 4CL1 typically with only minor xylem expression or activity. Levels of caffeate, the preferred substrate of 4CL5, increased in line with significant upregulation ofcaffeoyl shikimate esterase1. Upregulation ofcaffeoyl-CoA O-methyltransferase1and downregulation ofF5Hsare consistent with preferential funneling of 4CL5 products toward G-lignin biosynthesis at the expense of S-lignin. Thus, transcriptional and metabolic adaptations to4CL1-knockout appear to have enabled 4CL5 catalysis at a level sufficient to sustain lignification. Finally, genes involved in sulfur assimilation, the glutathione-ascorbate cycle and various antioxidant systems were upregulated in the mutants, suggesting cascading responses to perturbed thioesterification in lignin biosynthesis.

One sentence summary

Knockout of lignin-associated4CL1inPopulusreveals a 4CL5-dependent, caffeate-modulated compensatory pathway for lignification with links to thiol redox balance and sulfur assimilation.
Self-regulation of single-stranded DNA wrapping dynamics byE. coliSSB promotes both stable binding and rapid dissociation
Authors: Naufer M. Nabuan , Morse Michael , Möller Guðfríður Björg , McIsaac James , Rouzina Ioulia , Beuning Penny J. , Williams Mark C.
Published: December 2019

E. coliSSB (EcSSB) is a model protein for studying functions of single-stranded DNA (ssDNA) binding proteins (SSBs), which are critical in genome maintenance.EcSSB forms homotetramers that wrap ssDNA in multiple conformations in order to protect these transiently formed regions during processes such as replication and repair. Using optical tweezers, we measure the binding and wrapping of a single long ssDNA substrate under various conditions and free protein concentrations. We show thatEcSSB binds in a biphasic manner, where initial wrapping events are followed by unwrapping events as protein density on the substrate passes a critical saturation. Increasing freeEcSSB concentrations increase the fraction ofEcSSBs in less-wrapped conformations, including a previously uncharacterizedEcSSB8bound state in which ∼8 nucleotides of ssDNA are bound by a single domain of the tetramer with minimal substrate deformation. When the ssDNA is over-saturated withEcSSB, stimulated dissociation rapidly removes excessEcSSB, leaving an array of stably-wrappedEcSSB-ssDNA complexes. We develop a multi-step kinetic model in whichEcSSB tetramers transition through multiple wrapped conformations which are regulated through nearest neighbor interactions and ssDNA occupancy. These results provide a mechanism through which otherwise stably bound and wrappedEcSSB tetramers can be rapidly removed from an ssDNA substrate to allow for DNA maintenance and replication functions while still fully protecting ssDNA over a wide range of protein concentrations.
HSI2/VAL1 and HSL1/VAL2 function redundantly to regulate seed dormancy by controllingDOG1expression in Arabidopsis
Authors: Chen Naichong , Wang Hui , Abdelmageed Haggag , Veerappan Vijaykumar , Tadege Million , Allen Randy D.
Published: December 2019

DELAY OF GERMINATION1(DOG1) represents a major quantitative locus for the genetic regulation of seed dormancy in Arabidopsis. Accumulation of DOG1 in seeds leads to deep dormancy and delayed germination. Here, we report that the conserved B3 DNA binding domains of the transcriptional repressors HIGH-LEVEL EXPRESSION OF SUGAR INDICIBLE GENE2/ VIVIPAROUS-1/ABSCISIC ACID INSENSITIVE 3-LIKE1 (HSI2/VAL1) and HSI2-LIKE1/ VIVIPAROUS-1/ABSCISIC ACID INSENSITIVE 3-LIKE2 (HSL1/VAL2), which play critical roles in the developmental transition from seed maturation to seedling growth, interact with RY elements in theDOG1proximal promoter leading to repression ofDOG1transcription during germination and seedling establishment.DOG1expression is partially de-repressed inhsi2/val1(hsi2-2) but not inhsl1/val2(hsl1-1) knockout mutants and is strongly upregulated in ahsi2/val1 hsl1/val2double mutant, indicating that HSI2/VAL1 and HSL1/VAL2 act redundantly to repressDOG1expression. HSI2/VAL1 and HSL1/VAL2 form homo- and hetero-dimersin vivo, and dimerization is dependent on the HSI2/VAL1 PHD-like domain. Complementation ofhsi2-2with HSI2/VAL1 harboring a disrupted plant homeodomain (PHD)-like domain results in stronger de-repression ofDOG1expression than thehsi2-2knockout, indicating that the PHD-like domain plays a critical role in mediating functional interactions between HSI2/VAL1 and HSL1/VAL2. Both HSI2/VAL1 and HSL1/VAL2 interact with components of polycomb repressive complex 2 (PRC2), including CURLY LEAF and MULTICOPY SUPPRESSOR OF IRA1 (MSI1), along with LIKE HETERCHROMATIN PROTEIN 1 (LHP1), which are involved in the deposition and expansion of histone H3 lysine 27 trimethylation (H3K27me3) marks in repressive chromatin. Thus, HSI2/VAL1 HSL1/VAL2-dependent recruitment of PRC2 leads to silencing ofDOG1through the deposition of H3K27me3.
Coarse-Grained Modelling of DNA Plectoneme Pinning in the Presence of Base-Pair Mismatches
Authors: Desai Parth Rakesh , Brahmachari Sumitabha , Marko John F. , Das Siddhartha , Neuman Keir C.
Published: December 2019

Damaged or mismatched DNA bases result in the formation of physical defects in double-stranded DNA.In vivo, defects in DNA must be rapidly and efficiently repaired to maintain cellular function and integrity. Defects can also alter the mechanical response of DNA to bending and twisting constraints, both of which are important in defining the mechanics of DNA supercoiling. Here, we use coarse-grained molecular dynamics (MD) simulation and supporting statistical-mechanical theory to study the effect of mismatched base pairs on DNA supercoiling. Our simulations show that plectoneme pinning at the mismatch site is deterministic under conditions of relatively high force (> 2 pN) and high salt concentration (> 0.5 M NaCl). Under physiologically relevant conditions of lower force (0.3 pN) and lower salt concentration (0.2 M NaCl), we find that plectoneme pinning becomes probabilistic and the pinning probability increases with the mismatch size. These findings are in line with experimental observations. The simulation framework, validated with experimental results and supported by the theoretical predictions, provides a way to study the effect of defects on DNA supercoiling and the dynamics of supercoiling in molecular detail.
A burst in T cell receptor translation mediated by eIF3 interactions with T cell receptor mRNAs
Authors: De Silva Dasmanthie , Ferguson Lucas , Smith Benjamin E. , Chin Grant H. , Apathy Ryan A. , Roth Theodore L. , Kudla Marek , Marson Alexander , Ingolia Nicholas T. , Cate Jamie H. D.
Published: December 2019

Activation of T cells requires a global surge in cellular protein synthesis, accompanied by a large increase in translation initiation1–4. A central component of the translation initiation machinery–the multi-subunit eukaryotic initiation factor 3 (eIF3)–is rapidly turned on when quiescent T cells are stimulated3. However, the precise role eIF3 plays in activated T cells is not known. Using a global transcriptome crosslinking approach, we show human eIF3 interacts with a distinct set of mRNAs in activated Jurkat cells. A subset of these mRNAs, including those encoding the T cell receptor (TCR) subunits TCRA and TCRB, crosslink to eIF3 across the entire length of the mRNA. TheTCRAandTCRBmRNAs do not co-localize with translationally repressed environments of P-bodies or stress granules but form distinct granules, potentially acting as translation “hot-spots.” T cell activation through CD28 causes a burst of TCR translation controlled by elements in the 3’-untranslated regions (3’-UTRs) of theTCRAandTCRBmRNAs that directly contact eIF3 and that are required for T cell activity. These results highlight a new role for eIF3 in regulating the translation dynamics of the TCR and provide insights that can guide the engineering of T cells used in cell immunotherapy applications.
Regionally divergent drivers of historical diversification in the late Quaternary in a widely distributed generalist species, the common pheasantPhasianus colchicus
Authors: Liu Simin , Liu Yang , Jelen Edouard , Alibadian Mansour , Yao Cheng-Te , Li Xintong , Kayvanfar Nasrin , Wang Yutao , Vahidi Farhad , Han Jianlin , Sundev Gombobaatar , Zhang Zhengwang , Schweizer Manuel
Published: December 2019

Aim

Historical factors such as Pleistocene climate cycles and associated environmental changes have influenced the phylogeographic structure and demographic dynamics of many species. Resulting patterns not only depend on species’ life-history but also vary regionally. Consequently, different populations of species with large ranges over different biomes might have experienced divergent drivers of diversification and show different population histories. Such a representative species is the common pheasantPhasianus colchicus, an ecological generalist with a wide distribution in the Palearctic and at the edge of the Oriental region. We aimed at identifying distinct phylogeographic lineages of the common pheasant and investigating their evolutionary trajectories.

Study location

Asia

Methods

We used coalescent approaches to describe the phylogeographic structure and to reconstruct the spatio-temporal diversification and demographic history of the common pheasant based on a comprehensive geographic sampling of 265 individuals genotyped at seven nuclear and two mitochondrial loci.

Results

The common pheasant diversified during the late Pleistocene into eight distinct evolutionary lineages which only partly correspond to traditional morphological groups. It originated at the edge of the Qinghai-Tibetan plateau and spread from there to East and Central Asia. Only the widely distributed genetically uniform lowland lineage of East Asia showed a recent range and population expansion, starting during last glacial. More phylogeographic structure was found elsewhere with lineages showing no signs of recent range expansions. One lineage of subtropical south-central China this is the result of long-term isolation in a climatically stable and topographically complex region. In others from arid Central Asia and China, demographic and range expansions were impeded by repeated population fragmentation during dry glacial and recent aridification. Given such a phylogeographic structure and demographic scenarios among lineages, we proposed split the range-wide common pheasant into three species.

Main conclusions

Spatio-temporal phylogeographic frameworks of widespread species complexes such as the common pheasant provide valuable opportunities to identify regionally divergent drivers of diversification.
Elongation of stigmatic papillae induced by heat stress is associated with disturbance of pollen attachment inArabidopsis thaliana
Authors: Katano Kazuma , Oi Takao , Suzuki Nobuhiro
Published: December 2019

ABSTRUCT

Heat stress can seriously impact on yield production and quality of crops. Many studies uncovered the molecular mechanisms that regulate heat stress responses in plants. Nevertheless, effects of heat stress on the morphology of plants were still not extensively studied. In this study, we observed the detailed morphological changes of reproductive organs inArabidopsis thalianacaused by heat stress. Larger area of stigma, and shorter length of anthers, filaments and petals were observed in plants subjected to heat stress compared to those under controlled conditions. Scanning electron microscopy (SEM) observation showed that length of stigmatic papillae without pollens seemed to be longer than that with pollens. In addition, classification of stigmas based on pollen attachment patterns together with artificial pollination assay revealed that pollen attachment onto stigma was clearly decreased by heat stress, and indicated that heat induced elongation of stigmatic papillae might be associated with disturbance of pollen attachment onto stigma. Furthermore, histochemical staining experiments revealed that crosstalk between Ca2+and NO derived from pollens and O2−derived from stigma might be associated with morphological alteration of stigma.
Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavagein vivo
Authors: Yang Minglei , Woolfenden Hugh C. , Zhang Yueying , Fang Xiaofeng , Liu Qi , Vigh Maria Louisa , Cheema Jitender , Yang Xiaofei , Norris Matthew , Yu Sha , Carbonell Alberto , Brodersen Peter , Wang Jiawei , Ding Yiliang
Published: December 2019

MicroRNA (miRNA)-mediated cleavage is involved in numerous essential cellular pathways. miRNAs recognize target RNAs via sequence complementarity. In addition to complementarity,in vitroandin silicostudies have suggested that RNA structure may influence the accessibility of mRNAs to miRNA-Induced Silencing Complexes (miRISCs), thereby affecting RNA silencing. However, the regulatory mechanism of mRNA structure in miRNA cleavage remains elusive. Here, we investigated the role ofin vivoRNA secondary structure in miRNA cleavage by developing the new CAP-STRUCTURE-seq method to capture the intact mRNA structurome inArabidopsis thaliana. This approach revealed that miRNA target sites were not structurally accessible for miRISC binding prior to cleavagein vivo. Instead, the unfolding of the target site structure is the primary determinant for miRISC activityin vivo. Notably, we found that the single-strandedness of the two nucleotides immediately downstream of the target site, named Target Adjacent structure Motif (TAM), can promote miRNA cleavage but not miRNA binding, thus decoupling target site binding from cleavage. Our findings demonstrate that mRNA structurein vivocan regulate miRNA cleavage, providing evidence of mRNA structure-dependent regulation of biological processes.
Prioritization of enhancer mutations by combining allele-specific chromatin accessibility with deep learning
Authors: Atak Zeynep Kalender , Taskiran Ibrahim Ihsan , Flerin Christopher , Mauduit David , Minnoye Liesbeth , Hulsemans Gert , Christiaens Valerie , Ghanem Ghanem-Elias , Wouters Jasper , Aerts Stein
Published: December 2019

Brief Abstract

Prioritization of non-coding genome variation benefits from explainable AI to predict and interpret the impact of a mutation on gene regulation. Here we apply a specialized deep learning model to phased melanoma genomes and identify functional enhancer mutations with allelic imbalance of chromatin accessibility and gene expression.