bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anti-diabetic effects ofHolarrhena antidysentricaextracts: Results from a Longitudinal Meta-analysis
Authors: Divya C. A. , Dhar Sujan K , Shantaram Manjula , Das Manjula 
Published: February 2021

AbstractBackgroundHolarrhena antidysenterica(HA), a twining shrub belonging to the Apocynaceae family is found in tropical regions of Africa and over a large part of Asia including India, Philippines and Malayan Peninsula. In Indian traditional system of medicine, HA has been used to treat gastric ailments, for wound healing and also to improve glycaemic control. Glucose lowering activity of HA root, bark, seed, leaf and fruit extract in different parts of India as well as in Chinese traditional medicine is widely reported.PurposeIn the meta-analysis reported in this article, we summarize glucose-lowering effects of HA extracts from different plant parts as reported in multiple studies involving animal models of diabetes. Our analysis helps to quantify the glucose-lowering effect of HA in comparison with standard diabetes drugs. The analysis also sheds light on differential efficacy levels of HA extracted from different plant parts.Study designThe meta-analysis was carried out following PRISMA guidelines. Literature was searched to identify studies published between years 2011 to 2019 reporting glucose-lowering effects of HA extract on rodent models of diabetes.MethodsLongitudinal meta-analysis was carried out on time-course data extracted from selected studies to calculate standardized mean change of glucose value from day 1 to days 7, 14 and 21 post-treatment by HA extract or standard anti-diabetic drug. Subgroup analysis was carried out for studies reporting effects of HA on leaf and seed extracts. Standardized mean difference in levels of cholesterol, triglycerides and serum total protein between treatment and control groups were also assessed.ResultsWe shortlisted nine articles to be used for this meta-analysis. Summarized standardized mean changes of glucose value between day 1 and day 21 post-treatment indicated glucose-lowering effects of HA extracts to be marginally lower but comparable to that of standard anti-diabetic drugs like Glibenclamide or Sitagliptin. However, subgroup analysis revealed seed extracts of HA to be more potent than leaf extracts or even standard drugs. Effects of the extract on levels of cholesterol, triglyceride and serum total protein was also commensurate with its glucose-lowering property.ConclusionsOur results, summarized over multiple studies, present a clear quantitative assessment of the anti-diabetic property of HA, in particular the seed extracts compared to standard anti-diabetic drugs. Further differential analysis of the seed extracts will be useful to arrive at a herbal formulation with superior anti-diabetic property and possibly lesser side effects than chemical entities.
Exploring the interspecific interactions and the metabolome of the soil isolateHylemonella gracilis
Authors: Tyc Olaf , Kulkarni Purva , Ossowicki Adam , Tracanna Vittorio , Medema Marnix H. , van Baarlen Peter , van IJcken W.F.J. , Verhoeven Koen J. F. , Garbeva Paolina 
Published: February 2021

AbstractMicrobial community analysis of aquatic environments showed that an important component of its microbial diversity consists of bacteria with cell sizes of ~0.1 μm. Such small bacteria can show genomic reductions and metabolic dependencies with other bacteria. However, so far no study investigated if such bacteria exist in terrestrial environments like e.g. soil.Here, we isolated soil bacteria that passed through a 0.1 μm filter, by applying a novel isolation and culturing approach. The complete genome of one of the isolates was sequenced and the bacterium was identified asHylemonella gracilis. A set of co-culture assays with phylogenetically distant soil bacteria with different cell and genome sizes was performed. The co-culture assays revealed thatH. gracilisgrows better when interacting with other soil bacteria likePaenibacillussp. AD87and Serratia plymuthica. Transcriptomics and metabolomics showed thatH. graciliswas able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct cell-cell contact.Our study indicates that bacteria are present in the soil that can pass through a 0.1 μm filter. These bacteria may have been overlooked in previous research on soil microbial communities. Such small bacteria, exemplified here byH. gracilis,are able to induce transcriptional and metabolomic changes in other bacteria upon their interactions in soil. In vitro, the studied interspecific interactions allowed utilization of growth substrates that could not be utilized by monocultures, suggesting that biochemical interactions between substantially different sized soil bacteria may contribute to the symbiosis of soil bacterial communities.ImportanceAnalysis of aquatic microbial communities revealed that parts of its diversity consist of bacteria with cell sizes of ~0.1 μm. Such bacteria can show genomic reductions and metabolic dependencies with other bacteria. So far, no study investigated if such bacteria exist in terrestrial environments e.g. soil. By applying a novel isolation method, we show that such bacteria also exist in soil. The isolated bacteria was identified asHylemonella gracilis.Co-culture assays with phylogenetically different soil bacteria revealed thatH. gracilisgrows better when co-cultured with other soil bacteria. Transcriptomics and metabolomics showed thatH. graciliswas able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct contact. Our study revealed that bacteria are present in soil that can pass through 0.1 μm filters. Such bacteria may have been overlooked in previous research on soil microbial communities and may contribute to the symbiosis of soil bacterial communities.
Neural markers for Musical Creativity in Jazz Improvisation and Classical Interpretation
Authors: Rahman Shama Sarwat , Christensen Kim , Jensen Henrik Jeldtoft , Vuust Peter , Bhattacharya Joydeep 
Published: February 2021

AbstractTwo main types of musical creativity in the western canon are improvisation and interpretation. With improvisation, the fundamental structure of the melody, chords, rhythm and tempo of a piece can be modified, while with interpretation, the focus is on the emotional dynamics. Here we characterise electrical brain activity from professional jazz and classical pianists, whilst they were engaged in these different creative tasks with musical excerpts from both genres. Multivariate EEG was recorded during two phases of each task, mental planning and actual performance. Subsequently neuronal activity patterns were source localised with standardised low resolution electromagnetic tomography (sLORETA). For each musical performance, we obtained both subjective (self-rated) and objective (blind, expert-rated) measures of musical creativity. Across both tasks and genre backgrounds, within the first and middle 4 second segments of the performance phase, for musical performances that were judged highly creative objectively by external expert music assessors, we observed an increased activation in the anterior cingulate and medial prefrontal cortex (Brodmann area, BA32), suggesting a maintenance of executive control, and integrating motoric and emotional communication during creativity. Across genre backgrounds, within the performance phase for the interpretation task compared to the improvisation task, there was an increased activity in the insula (BA 13), suggesting a convergent creative task from the linked goal-orientated conscious error-monitoring and audio-visual integration functions. Genre profession also gave rise to differences across phases; jazz pianists presented a decreased parietal (BA7) activity during improvisation tasks suggesting a role for defocussed attention and for classical pianists, both tasks were associated with occipitotemporal (BA 37) activity which is involved in semantic/ metaphorical processing suggesting a close adherence to the visual score. These 3 areas relate the cognitive demands of the creative musical task to the demands of the corresponding genre of music.HighlightsEEG activity associated to musical creativity types: Improvisation and InterpretationIncreased activity in Insula (BA 13) for Interpretation suggest convergent creativityDecreased Precuneus (BA7) activity for Improvisation suggest defocussed attentionIncreased activity in medial prefrontal cortex (BA32) in highly creative performance
Extensive N4 Cytosine Methylation is Essential forMarchantiaSperm Function
Authors: Walker James , Zhang Jingyi , Liu Yalin , Vickers Martin , Dolan Liam , Nakajima Keiji , Feng Xiaoqi 
Published: February 2021

Abstract4-methylcytosine (4mC) is an important DNA modification in prokaryotes, but its relevance, and even presence in eukaryotes have been mysterious. Here we show that spermatogenesis in the liverwortMarchantia polymorphainvolves two waves of extensive DNA methylation reprogramming. First, 5-methylcytosine (5mC), a well-known eukaryotic DNA modification, expands from transposons to the entire genome. Notably, the second wave installs 4mC throughout genic regions, covering over 50% of CG sites in sperm. 4mC is catalyzed by two novel methyltransferases (MpDN4MT1a and MpDN4MT1b) specifically expressed during late spermiogenesis. Deletion of MpDN4MT1seliminates 4mC, alters the sperm transcriptome, and produces sperm with swimming defects. Our results reveal extensive 4mC in a eukaryote and define a new family of eukaryotic methyltransferases, thereby expanding the repertoire of functional eukaryotic DNA modifications.
Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion
Authors: Serna-Pujol Núria , Salinas-Pena Mónica , Mugianesi Francesca , Le Dily François , Marti-Renom Marc A. , Jordan Albert 
Published: February 2021

AbstractUp to seven members of the histone H1 family may contribute to chromatin compaction and its regulation in human somatic cells. In breast cancer cells, knock-down of multiple H1 variants deregulates many genes, promotes the appearance of genome-wide accessibility sites and triggers an interferon response via activation of heterochromatic repeats. However, how these changes in the expression profile relate to the re-distribution of H1 variants as well as to genome conformational changes have not been yet studied. Here, we combined ChIP-seq of five endogenous H1 variants with Chromosome Conformation Capture analysis in wild-type and H1 knock-down T47D cells. The results indicate that H1 variants coexist in the genome in two large groups depending on the local DNA GC content and that their distribution is robust with respect to multiple H1 depletion. Despite the small changes in H1 variants distribution, knock-down of H1 translated into more isolated but de-compacted chromatin structures at the scale of Topologically Associating Domains or TADs. Such changes in TAD structure correlated with a coordinated gene expression response of their resident genes. This is the first report describing simultaneous profiling of five endogenous H1 variants within a cell line and giving functional evidence of genome topology alterations upon H1 depletion in human cancer cells.
Dopamine modulates visual threat processing in the superior colliculus via D2 receptors
Authors: Montardy Quentin , Zhou Zheng , Li Lei , Yang Qingning , Lei Zhuogui , Feng Xiaolong , Chen Shanping , Shi Qianqian , Zhang Huiqi , Chen Shuran , Zhang Zhijian , Zhao Binghao , Xu Fuqiang , Lu Zhonghua , Wang Liping 
Published: February 2021

AbstractDopamine (DA) system is intriguing in the aspect that distinct, typically opposing physiological functions are mediated by D1 dopamine receptors (Drd1) and D2 dopamine receptors (Drd2). Both Drd1+ and Drd2+ neurons were identified in superior colliculus (SC), a visuomotor integration center known for its role in defensive behaviors to visual threats. We hypothesized that Drd1+ and Drd2+ neurons in the SC may play a role in promoting instinctive defensive responses.Optogenetic activation of Drd2+ neurons, but not Drd1+ neurons, in the SC triggered strong defensive behaviors. Chemogenetic inhibition of SC Drd2+ neurons decreased looming-induced defensive behavior, suggesting involvement of SC Drd2+ neurons in defensive responses. To further confirm this functional role of Drd2 receptors, pretreatment with the Drd2+ agonist quinpirole in the SC impaired looming-evoked defensive responses, suggesting an essential role of Drd2 receptors in the regulation of innate defensive behavior. Inputs and outputs of SC Drd2+ neurons were investigated using viral tracing: SC Drd2+ neurons mainly receive moderate inputs from the Locus Coeruleus (LC), whilst we did not find any incoming projections from other dopaminergic structures. Our results suggest a sophisticated regulatory role of DA and its receptor system in innate defensive behavior.
Sterile Inflammation Alters Neutrophil Kinetics in Mice
Authors: Singh Alakesh , Jothiprakasam Thiruvickraman , Raghavan Jayashree V. , Jhunjhunwala Siddharth 
Published: February 2021

ABSTRACTNeutrophils play a crucial role in establishing inflammation in response to an infection or injury, but their production rates, as well as blood and tissue residence times, remain poorly characterized under these conditions. Herein, using a biomaterial implant model to establish inflammation followed byin vivotracking of newly formed neutrophils, we determine neutrophil kinetics under inflammatory conditions. To obtain quantifiable information from our experimental observations, we develop an ordinary differential equation-based mathematical model to extract kinetic parameters. Our data show that in the presence of inflammation resulting in emergency granulopoiesis-like conditions, neutrophil maturation time in the bone marrow and half-life in the blood reduces by about 40%, compared to non-inflammatory conditions. Additionally, neutrophil residence time at the inflammatory site increases by two-fold. Together, these data improve our understanding of neutrophil kinetics under inflammatory conditions, which could pave the way for therapies that focus on modulating in vivo neutrophil dynamics.
Life histories as mosaics: plastic and genetic components differ among traits that underpin life-history strategies
Authors: Felmy Anja , Reznick David N. , Travis Joseph , Potter Tomos , Coulson Tim 
Published: February 2021

AbstractLife-history variation reflects phenotypic variation across suites of traits. Differences among life-history strategies result from genetic differentiation, phenotypic plasticity, and genotype-by-environment interactions. If the relative strength and direction of these components differed among traits underlying a strategy, life histories might not evolve as a cohesive unit.We tested this hypothesis on the high- and low-predation ecotypes of Trinidadian guppies, defined by distinct life-history strategies. Using common garden experiments, we assessed how strongly 36 traits were determined by ancestral habitat (i.e., ecotype) or food availability, a key environmental difference between ecotypes. Our dataset was large (1178 individuals) and included six putatively independent origins of the derived ecotype.Traits could be confidently assigned to four groups, defined by highly significant effects of only food (13 traits), only habitat (6), both (6), or neither (11), revealing substantial variation among traits in levels of genetic and environmental control. Ecotype-food (i.e., genotype-by-environment) interactions were negligible. The directions of plastic and genetic effects were usually aligned.This suggests that life histories are mosaics with unequal rates of phenotypic and evolutionary change. Broadly speaking of “life-history evolution” masks a complex interplay of genes and environment on the multiple traits that underpin life-history strategies.
Kinetics and topology of DNA associated with circulating extracellular vesicles released during exercise
Authors: Neuberger Elmo W. I. , Hillen Barlo , Mayr Katharina , Simon Perikles , Krämer-Albers Eva-Maria , Brahmer Alexandra 
Published: February 2021

AbstractAlthough it is widely accepted that cancer derived extracellular vesicles (EVs) carry DNA cargo, the association of cell-free circulating DNA (cfDNA) and EVs in plasma of healthy humans remains elusive. Using a physiological exercise model, where EVs and cfDNA are synchronously released, we aimed to characterize the kinetics and localization of DNA associated with EVs. EVs were separated from human plasma using size exclusion chromatography or immuno-affinity capture for CD9+, CD63+, and CD81+EVs. DNA was quantified with an ultra-sensitive qPCR assay targeting repetitive LINE elements, with or without DNase digestion. This model shows that a minute part of circulating cell-free DNA is associated with EVs. During rest and following exercise, only 0.12 % of the total cfDNA occurs in association with CD9+/CD63+/CD81+EVs. DNase digestion experiments indicate that the largest part of EV associated DNA is sensitive to DNase digestion and only ~20 % are protected within the lumen of the separated EVs. A single bout of running or cycling exercise increases the levels of EVs, cfDNA, and EV associated DNA. While EV surface DNA is increasing, DNAse-resistant DNA remains at resting levels, indicating that EVs released during exercise (ExerVs) do not contain DNA. Consequently, DNA is largely associated with the outer surface of circulating EVs. ExerVs recruit cfDNA to their corona, but do not carry DNA in their lumen.
Sexually antagonistic evolution of mitochondrial and nuclear linkage
Authors: Radzvilavicius Arunas , Layh Sean , Hall Matthew D. , Dowling Damian K. , Johnston Iain G. 
Published: February 2021

AbstractAcross eukaryotes, genes encoding bioenergetic machinery are located in both mitochondrial and nuclear DNA, and incompatibilities between the two genomes can be devastating. Mitochondria are often inherited maternally, and theory predicts sex-specific fitness effects of mitochondrial mutational diversity. Yet how evolution acts on linkage patterns between mitochondrial and nuclear genomes is poorly understood. Using novel mito-nuclear population genetic models, we show that the interplay between nuclear and mitochondrial genes maintains mitochondrial haplotype diversity within populations, and it selects both for sex-independent segregation of mitochondrion-interacting genes and for paternal leakage. These effects of genetic linkage evolution can eliminate male-harming fitness effects of mtDNA mutational diversity. With maternal mitochondrial inheritance, females maintain a tight mitochondrial-nuclear match, but males accumulate mismatch mutations because of the weak statistical associations between the two genomic components. Sex-independent segregation of mitochondria-interacting loci improves the mito-nuclear match. In a sexually antagonistic evolutionary process, male nuclear alleles evolve to increase the rate of recombination, while females evolve to suppress it. Paternal leakage of mitochondria can evolve as an alternative mechanism to improve the mito-nuclear linkage. Our modelling framework provides an evolutionary explanation for the observed paucity of mitochondrion-interacting genes on mammalian sex chromosomes and for paternal leakage in protists, plants, fungi, and some animals.
Fighting over defence chemicals disrupts mating behaviour
Authors: Paul Sarah Catherine , Müller Caroline 
Published: February 2021

AbstractStudies on intraspecific contest behaviour predominantly focus on contests between individuals of the same sex, however contest behaviour is also expected to occur between individuals of the opposite sex including possible mates. Here we investigate potential trade-offs between mating and fighting behaviour in the turnip sawfly (Athalia rosae). Adults of this species collect chemical defence compounds (clerodanoids) directly from plants but also indirectly by nibbling on conspecifics that have already obtained clerodanoids themselves, a highly aggressive behavioural interaction. An A. rosae individual without clerodanoids may therefore be the potential mate or attacker of an individual of the opposite sex that has gained clerodanoids. We paired males and females with or without clerodanoid access and manipulated body mass differences between the sexes via the early life starvation of females. We show that asymmetrical clerodanoid acquisition between male-female pairs causes an increase in agonistic nibbling behaviour, irrespective of sex. Moreover, fighting over clerodanoids disrupted mating behaviour, and the frequency of aggressive nibbling behaviour in these pairs was determined by the comparative body mass of the attacking individual. Our study highlights the vital importance of investigating agonistic intersex interactions not only over mating but also over resources.
StrainFLAIR: Strain-level profiling of metagenomic samples using variation graphs
Authors: Da Silva Kévin , Pons Nicolas , Berland Magali , Oñate Florian Plaza , Almeida Mathieu , Peterlongo Pierre 
Published: February 2021

ABSTRACTCurrent studies are shifting from the use of single linear references to representation of multiple genomes organised in pangenome graphs or variation graphs. Meanwhile, in metagenomic samples, resolving strain-level abundances is a major step in microbiome studies, as associations between strain variants and phenotype are of great interest for diagnostic and therapeutic purposes.We developedStrainFLAIRwith the aim of showing the feasibility of using variation graphs for indexing highly similar genomic sequences up to the strain level, and for characterizing a set of unknown sequenced genomes by querying this graph.On simulated data composed of mixtures of strains from the same bacterial speciesEscherichia coli, results show thatStrainFLAIRwas able to distinguish and estimate the abundances of close strains, as well as to highlight the presence of a new strain close to a referenced one and to estimate its abundance. On a real dataset composed of a mix of several bacterial species and several strains for the same species, results show that in a more complex configurationStrainFLAIRcorrectly estimates the abundance of each strain. Hence, results demonstrated how graph representation of multiple close genomes can be used as a reference to characterize a sample at the strain level.Availabilityhttp://github.com/kevsilva/StrainFLAIR
Programmed ER fragmentation drives selective ER inheritance and degradation in budding yeast meiosis
Authors: Otto George M. , Cheunkarndee Tia , Leslie Jessica M. , Brar Gloria A. 
Published: February 2021

AbstractThe endoplasmic reticulum (ER) is a membrane-bound organelle with diverse, essential functions that rely on the maintenance of membrane shape and distribution within cells. ER structure and function are remodeled in response to changes in cellular demand, such as the presence of external stressors or the onset of cell differentiation, but mechanisms controlling ER remodeling during cell differentiation are not well understood. Here, we describe a series of developmentally regulated changes in ER morphology and composition during budding yeast meiosis, a conserved differentiation program that gives rise to gametes. During meiosis, the cortical ER undergoes fragmentation before collapsing away from the plasma membrane at anaphase II. This programmed collapse depends on the meiotic transcription factor Ndt80, conserved ER membrane structuring proteins Lnp1 and reticulons, and the actin cytoskeleton. A subset of ER is retained at the mother cell plasma membrane and excluded from gamete cells via the action of ER-plasma membrane tethering proteins. ER remodeling is coupled to ER degradation by selective autophagy, which is regulated by the developmentally timed expression of the autophagy receptor Atg40. Autophagy relies on ER collapse, as artificially targeting ER proteins to the cortically retained ER pool prevents their degradation. Thus, developmentally programmed changes in ER morphology determine the selective degradation or inheritance of ER subdomains by gametes.