bluuebunny/crossref_metadata_2025_split huggingface dataset:
Research on the Influence of Different Temperature Conditions on the Microbial Community in Anearobic-Anoxic-Oxic process on the Plateau
Authors: Huang Decai , Zong Yongchen , Zhang Ning , Li Yuanwei , Hao Kaiyue 
Published: September 2020

AbstractIn order to further understand the influence of different temperature conditions in the low temperature range on the microbial community structure in the Anearobic-Anoxic-Oxic waste water treatment process on the plateau, four temperature conditions were designed in the research, including 25°C, 20°C, 15°C and 10°C. Each working condition lasted three days. Activated sludge from anaerobic tank, anoxic tank and oxic tank under each working condition was analyzed based on the 16S rRNA high-throughput sequencing technology. The result shows that the plateau temperature conditions have little influence on the level abundance of phylum. Under all conditions, Bacteroidetes, Proteobacteria and Actinobacteria are the main phyla. The abundance of nitrifying bacterium and phosphorus removal bacteria rose in the first three conditions and fell at 10 °C. The abundance of Denitrification bacteria and Nitrite oxidizing bacteria was significantly higher than that of Ammonia oxidation bacteria and Azotobacter bacteria and Phosphorus-accumulating Organisms(PAO) had an overall advantage over Glycogen-accumulating Organisms (GAO) throughout the research.
Identification of novel differentially expressed zooxanthellal genes fromAiptasia-Symbiodiniumendosymbiosis through SDS-based RNA purification
Authors: Chen Bo-Nien , Song Paching , Chen Ming-Chyuan , Hong Ming-Chang 
Published: September 2020

AbstractEndosymbiosis between dinoflagellates and cnidarian hosts first occurred more than 200 million years ago; however, symbiosis-specific genes and cellular processes involved in the establishment, maintenance, and breakdown of endosymbiosis remain unclear. Therefore, this study aimed to identify the zooxanthellal genes associated with the aforementioned biological processes during endosymbiosis inAiptasia-Symbiodiniumendosymbionts. Here, zooxanthellae isolates were treated with 0.02% SDS to decrease potential host RNA contamination and to enhance the identification of novel symbiosis/nonsymbiosis-associated differentially expressed zooxanthellal genes through suppressive subtractive hybridization (SSH) and next-generation sequencing (NGS) methods. Consequently, among 214 symbiosis-specific transcripts identified herein that displayed identity to only 5.6% of host-derived transcripts, 64% were well-known functional genes. In the nonsymbiotic stage, 181 differentially expressed transcripts were identified, of which 64.1% belonged to well-known functional genes. BLAST revealed that 8 categories of cellular processes were significantly induced in symbiotic or nonsymbiotic zooxanthellae. Together with the results of quantitative analysis, the results revealed that photosynthesis, flagellate biosynthesis and motility, stress-induced responses, cell wall biosynthesis, starch synthesis and transport, lipid biosynthesis and metabolism, host/symbiont immune response, intercellular communication, cell growth, and cell cycle regulation were the major cellular processes occurring in symbiotic/nonsymbiotic stages. The present results provide insights into the mechanisms involved in regulating the different physiological processes in symbiotic/nonsymbiotic zooxanthellae and may guide future studies.
An important role of the interplay betweenBdnftranscription and histone acetylation in epileptogenesis
Authors: Walczak Agnieszka , Czaban Iwona , Skupien Anna , Pels Katarzyna K. , Szczepankiewicz Andrzej A. , Krawczyk Katarzyna , Ruszczycki Błażej , Wilczynski Grzegorz M. , Dzwonek Joanna , Magalska Adriana 
Published: September 2020

AbstractBrain-Derived Neurotrophic Factor is one of the most important trophic proteins in the brain. The role of this growth factor in neuronal plasticity, in health and disease, has been extensively studied. However, mechanisms of epigenetic regulation ofBdnfgene expression in epilepsy are still elusive. In our previous work, using a rat model of neuronal activation upon kainate-induced seizures, we observed a repositioning ofBdnfalleles from the nuclear periphery towards the nuclear center. This change ofBdnfintranuclear position was associated with transcriptional gene activity.In the present study, using the same neuronal activation model, we analyzed the relation between the percentage of theBdnfallele at the nuclear periphery and clinical and morphological traits of epilepsy. We observed that the decrease of the percentage of theBdnfallele at the nuclear periphery correlates with stronger mossy fiber sprouting - an aberrant form of excitatory circuits formation. Moreover, usingin vitrohippocampal cultures we showed thatBdnfrepositioning is a consequence of the transcriptional activity. Inhibition of RNA polymerase II activity in primary cultured neurons with Actinomycin D completely blockedBdnfgene transcription and repositioning observed after neuronal excitation. Interestingly, we observed that histone deacetylases inhibition with Trichostatin A induced a slight increase ofBdnfgene transcription and its repositioning even in the absence of neuronal excitation. Presented results provide novel insight into the role of BDNF in epileptogenesis. Moreover, they strengthen the statement that this particular gene is a good candidate to search for a new generation of antiepileptic therapies.
Disulfiram inhibitsM. tuberculosisgrowth by altering methionine pool, redox status and host-immune response
Authors: Chaudhary Deepika , Marzuki Mardiana , Lee Andrea , Bouzeyen Rania , Singh Avantika , Gosain Tannu Priya , Kidwai Saqib , Grady Courtney , Tsotetsi Kholiswa , Chawla Kiran , Shihui Foo , Lum Josephine , Gupta Sonu Kumar , Agarwal Nisheeth , Tsenova Liana , Kumar Yashwant , Lee Bernett , Kumar Pradeep , Thakur Krishan Gopal , Singh Ramandeep , Singhal Amit 
Published: September 2020

ABSTRACTMethionine biosynthetic pathway, essential for the growth ofMycobacterium tuberculosis(Mtb) in the host, represents an attractive target for the development of novel anti-tuberculars. Here, we have biochemically characterized homoserine acetyl transferase (HSAT viz. MetA) ofMtb, which catalyses the first committed step of methionine and S-adenosylmethionine (SAM) biosynthesis. High-throughput screening of a 2300 compound library resulted in identification of thiram, an anti-fungal organosulfur compound, as the most potent MetA inhibitor. Further analysis of thiram analogs led to the identification of orally bioavailable disulfiram (DIS, an anti-alcoholism FDA approved drug) as a novel inhibitor of MetA. Both thiram and DIS restricted the growth of drug-sensitive and drug-resistantMtbstrains in a bactericidal manner. ThermoFlour assay demonstrated direct binding of DIS with MetA. Metabolomic and transcriptomic studies showed DIS mediated perturbation of methionine and redox homeostasis, respectively, inMtb. In concordance, the effect of DIS onMtbgrowth was partially rescued by supplementation with either L-methionine as well as N-acetyl cysteine, suggesting a multi-target killing mechanism. InMtb-infected mice, DIS administration restricted bacterial growth, increased efficacy of isoniazid, ameliorated lung pathology, modulated lung immune cell landscape and protective immune response. Taken together, our results demonstrate that DIS can be repurposed for designing an effective anti-tubercular therapy.
Energy-dependent protein folding: modeling how a protein folding machine may work
Authors: Sahakyan Harutyun K. , Nazaryan Karen B. , Mushegian Arcady R. , Sorokina Irina N. 
Published: September 2020

AbstractProteins fold robustly and reproducibly in vivo, but many cannot fold in vitro in isolation from cellular components. The pathways to proteins’ native conformations, either in vitro or in vivo, remain largely unknown. The slow progress in recapitulating protein folding pathways in silico may be an indication of the fundamental deficiencies in our understanding of folding as it occurs in nature. Here we consider the possibility that protein folding in living cells may not be driven solely by the decrease in Gibbs free energy and propose that protein folding in vivo should be modeled as an active energy-dependent process. The mechanism of action of such protein folding machine might include direct manipulation of the peptide backbone. To show the feasibility of a protein folding machine, we conducted molecular dynamics simulations that were augmented by the application of mechanical force to rotate the C-terminal amino acid while simultaneously limiting the N-terminal amino acid movements. Remarkably, the introduction of this simple manipulation of peptide backbones to the standard molecular dynamics simulation indeed facilitated the formation of native structures in five diverse alpha-helical peptides. Such effect may play a role during co-translational protein folding in vivo: considering the rotating motion of the tRNA 3’-end in the peptidyltransferase center of the ribosome, it is possible that this motion might introduce rotation to the nascent peptide and influence the peptide’s folding pathway in a way similar to what was observed in our simulations.
Calibration of consonant perception to room reverberation
Authors: Vlahou Eleni , Ueno Kanako , Shinn-Cunningham Barbara G. , Kopčo Norbert 
Published: September 2020

AbstractPurposeWe examined how consonant perception is affected by a preceding speech carrier simulated in the same or a different room, for a broad range of consonants. Carrier room, carrier length, and carrier length/target room uncertainty were manipulated. A phonetic feature analysis tested which phonetic categories are most influenced by the acoustic context of the carrier.MethodTwo experiments were performed, each with 9 participants. Targets consisted of vowel-consonant (VC) syllables presented in one of 2 strongly reverberant rooms, preceded by a VC carrier presented either in the same room, a different reverberant room, or an anechoic room. In Experiment 1 the carrier length and the target room randomly varied from trial to trial while in Experiment 2 they were fixed within blocks of trials.ResultsCompared to the no-carrier condition, a consistent carrier provided only a small advantage for consonant perception, whereas inconsistent carriers disrupted performance significantly. For a different-room carrier, carrier length had an effect; performance dropped significantly in the 2-VC compared to the 4-VC carrier length. The only effect of carrier uncertainty was an overall drop in performance. Phonetic analysis showed that an inconsistent carrier significantly degraded identification of the manner of articulation, especially for stop consonants, and, in one of the rooms, also of voicing.ConclusionsCalibration of consonant perception to strong reverberation is exhibited through disruptions in perception when the room is switched. The strength of calibration varies across different consonants and phonetic features, as well as across rooms and durations of exposure to a given room.
Patterns of roost site use by Asian hornbills and implications for seed dispersal
Authors: Naniwadekar Rohit , Rathore Akanksha , Shukla Ushma , Datta Aparajita 
Published: September 2020

AbstractAnimals spend a significant amount of time roosting. Therefore, understanding roosting patterns and the processes that influence roosting behaviour and roost site choice is essential. Hornbills exhibit interesting roosting patterns with some species roosting communally in large flocks. They are important seed dispersers and patterns of roost site use can have a significant influence on seed dispersal distributions and thereby on plant recruitment. We documented roost site use by four Great Hornbills (Buceros bicornis) and one Wreathed Hornbill (Rhyticeros undulatus) at a site in north-east India using GPS telemetry. We examined the influence of riverine habitats, nests and foraging range on roost selection. We determined the proportion of seeds that hornbills disperse at roosts and the dispersal distances of seeds dispersed at roosts from the source trees. Through telemetry, we found that roosts of Great Hornbills were generally in forested habitats. Our telemetry data showed that Wreathed Hornbill roosts were close to the river. These results were corroborated by observational data from roost sites where we had regular detections of relatively large flocks of Wreathed Hornbills and occasionally Great Hornbills. The roost sites were not close to the nest sites and were generally within the 95% kernel density diurnal activity ranges. Hornbills dispersed a small proportion of seeds at roost sites. Seeds dispersed at roost sites had almost twice the dispersal distances compared to those dispersed at non-roost sites. This study highlights variation in roost site pattern across individual hornbills and its implications for seed dispersal.
An Assistive Computer Vision Tool to Automatically Detect Changes in Fish Behavior In Response to Ambient Odor
Authors: Banerjee Sreya , Alvey Lauren , Brown Paula , Yue Sophie , Li Lei , Scheirer Walter J. 
Published: September 2020

AbstractThe analysis of fish behavior in response to odor stimulation is a crucial component of the general study of cross-modal sensory integration in vertebrates. In zebrafish, the centrifugal pathway runs between the olfactory bulb and the neural retina, originating at the terminalis neuron in the olfactory bulb. Any changes in the ambient odor of a fish’s environment warrants a change in visual sensitivity and can trigger mating-like behavior in males due to increased GnRH signaling in the terminalis neuron. Behavioral experiments to study this phenomenon are commonly conducted in a controlled environment where a video of the fish is recorded over time before and after the application of chemicals to the water. Given the subtleties of behavioral change, trained biologists are currently required to annotate such videos as part of a study. This process of manually analyzing the videos is time-consuming, requires multiple experts to avoid human error/bias and cannot be easily crowdsourced on the Internet. Machine learning algorithms from computer vision, on the other hand, have proven to be effective for video annotation tasks because they are fast, accurate, and, if designed properly, can be less biased than humans. In this work, we propose to automate the entire process of analyzing videos of behavior changes in zebrafish by using tools from computer vision, relying on minimal expert supervision. The overall objective of this work is to create a generalized tool to predict animal behaviors from videos using state-of-the-art deep learning models, with the dual goal of advancing understanding in biology and engineering a more robust and powerful artificial information processing system for biologists.
Root growth responses to mechanical impedance are regulated by a network of ROS, ethylene and auxin signalling in Arabidopsis
Authors: Jacobsen Amy G.R. , Xu Jian , Topping Jennifer F. , Lindsey Keith 
Published: September 2020

SummaryThe growth and development of root systems, essential for plant performance, is influenced by mechanical properties of the substrate in which the plants grow. Mechanical impedance, such as by compacted soil, can reduce root elongation and limit crop productivity.To understand better the mechanisms involved in plant root responses to mechanical impedance stress, we investigated changes in the root transcriptome and hormone signalling responses of Arabidopsis to artificial root barrier systemsin vitro.We demonstrate that upon encountering a barrier, reduced Arabidopsis root growth and the characteristic ‘step-like’ growth pattern is due to a reduction in cell elongation associated with changes in signalling gene expression. Data from RNA-sequencing combined with reporter line and mutant studies identified essential roles for reactive oxygen species, ethylene and auxin signalling during the barrier response.We propose a model in which early responses to mechanical impedance include reactive oxygen signalling that is followed by integrated auxin and ethylene responses to mediate root growth changes. Inhibition of ethylene responses allows improved growth in response to root impedance, a result that may inform future crop breeding programmes.
miR-125-chinmopathway regulates dietary restriction dependent enhancement of lifespan inDrosophila
Authors: Pandey Manish , Bansal Sakshi , Bar Sudipta , Sokol Nicholas S. , Tennessen Jason M. , Kapahi Pankaj , Chawla Geetanjali 
Published: September 2020

AbstractDietary restriction (DR) extends healthy lifespan in diverse species. Age and nutrient-related changes in the abundance of microRNAs (miRNAs) and their processing factors have been linked to organismal longevity. However, the mechanisms by which they modulate lifespan and the tissue-specific role of miRNA mediated networks in DR dependent enhancement of lifespan remains largely unexplored. We show that two neuronally enriched and highly conserved microRNAs,miR-125andlet-7mediate the DR response inDrosophila melanogaster. Functional characterization ofmiR-125demonstrates its role in neurons while its targetchinmoacts both in neurons and the fat body to modulate fat metabolism and longevity. Proteomic analysis revealed that Chinmo exerts its DR effects by regulating expression ofFATP, CG2017, CG9577, CG17554, CG5009, CG8778, CG9527andFASN1. Our findings identifymiR-125as a conserved effector of DR pathway and open up the avenue for this small RNA molecule and its downstream effectors to be considered as potential drug candidates for treatment of late-onset diseases and biomarkers for healthy aging in humans.
Many are called but few are chosen – Multiple clonal origins greatly elevate the functional heterogeneity of tumors
Authors: Chen Bingjie , Wu Xianrui , Ruan Yongsen , Zhang Yulin , Wen HJ , Lan Ping , Wu Chung-I 
Published: September 2020

AbstractEach tumor is usually accepted to be of a single origin from a progenitor cell. The shared evolutionary paths impose a limit on the nature of genetic diversity of the tumor. However, there are also numerous stem cell niches with independent proliferation potentials. To reconcile the contrasting perspectives, we propose a model whereby each tumor is of multiple clonal origins but the most proliferative one would eclipse other minor clones. The detection of the minor clones would entail an extreme scheme of large-number but small-volume sampling. In two cases of colon tumors so sampled, one indeed has 13 independent clones of disparate sizes and even the smaller clones have tens of thousands of cells dispersed non-locally. The other, much larger, tumor has only one prevailing clone that engulfs two tiny patches of minor clones. In both cases, the expanding clone spawns a hierarchy of subclones that resemble vassal states on its wake of expansion. The timing of metastasis can also be mapped to the precise stage of the clonal expansion. In conclusion, multiple independent clones, likely common but difficult to detect, can greatly elevate the non-neutral diversity within a tumor. This much-elevated diversity has many theoretical and clinical implications.
Tet2 Controls β cells Responses to Inflammation in Type 1 Diabetes
Authors: Rui Jinxiu , Deng Songyan , Ponath Gerald , Kursawe Romy , Lawlor Nathan , Sumida Tomokazu , Levine-Ritterman Maya , Perdigoto Ana Luisa , Stitzel Michael L. , Pitt David , Lu Jun , Herold Kevan C. 
Published: September 2020

Abstractβ cells may participate and contribute to their own demise during Type 1 diabetes (T1D). We identified a novel role of Tet2 in regulating immune killing of β cells. Tet2 is induced in murine and human β cells with inflammation but its expression is reduced in surviving β cells. Tet2-KO mice that receive WT bone marrow transplants develop insulitis but not diabetes and islet infiltrates do not eliminate β cells even though immune cells from the mice can transfer diabetes to NOD/scidrecipients. Tet2-KO β cells show reduced expression of inflammatory genes, associated with closed transcription factor binding sites. Tet2-KO recipients are protected from transfer of disease by diabetogenic immune cells. We conclude that Tet2 regulates pathologic interactions between β cells and immune cells and controls intrinsic protective pathways. Modulating TET2 may enable survival of β cells or their replacements in the setting of pathologic immune cells.
Phospho-islands and the evolution of phosphorylated amino acids in mammals
Authors: Moldovan Mikhail A. , Gelfand Mikhail S. 
Published: September 2020

AbstractBackgroundProtein phosphorylation is the best studied post-translational modification strongly influencing protein function. Phosphorylated amino acids not only differ in physico-chemical properties from non-phosphorylated counterparts, but also exhibit different evolutionary patterns, tending to mutate to and originate from negatively charged amino acids. The distribution of phosphosites along protein sequences is non-uniform, as phosphosites tend to cluster, forming so-called phospho-islands.MethodsHere, we have developed an HMM-based procedure for the identification of phospho-islands and studied the properties of the obtained phosphorylation clusters. To check robustness of evolutionary analysis, we consider different models for the reconstructions of ancestral phosphorylation states.ResultsClustered phosphosites differ from individual phosphosites in several functional and evolutionary aspects including underrepresentation of phosphotyrosines, higher conservation, more frequent mutations to negatively charged amino acids. The spectrum of tissues, frequencies of specific phosphorylation contexts, and mutational patterns observed near clustered sites also are different.
Rapid adaptation to malaria facilitated by admixture in the human population of Cabo Verde
Authors: Hamid Iman , Korunes Katharine , Beleza Sandra , Goldberg Amy 
Published: September 2020

AbstractHumans have undergone large migrations over the past hundreds to thousands of years, exposing ourselves to new environments and selective pressures. Yet, evidence of ongoing or recent selection in humans is difficult to detect. Many of these migrations also resulted in gene flow between previously separated populations. These recently admixed populations provide unique opportunities to study rapid evolution in humans. Developing methods based on distributions of local ancestry, we demonstrate that this sort of genetic exchange has facilitated detectable adaptation to a malaria parasite in the admixed population of Cabo Verde within the last ∼20 generations. We estimate the selection coefficient is approximately 0.08, one of the highest inferred in humans. Notably, we show that this strong selection at a single locus has likely affected patterns of ancestry genome-wide, potentially biasing demographic inference. Our study provides evidence of adaptation in a human population on historical timescales.