bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA methylation dynamics during stress-response in woodland strawberry (Fragaria vesca)
Authors: López María-Estefanía , Roquis David , Becker Claude , Denoyes Béatrice , Bucher Etienne 
Published: March 2022

SummaryEnvironmental stresses can result in a wide range of physiological and molecular responses in plants. These responses can also impact epigenetic information in genomes especially at the level of DNA methylation. DNA methylation is the hallmark heritable epigenetic modification and plays a key role in silencing transposable elements (TEs). Although DNA methylation is an essential epigenetic mechanism, fundamental aspects of its contribution to stress responses and adaptation remain obscure.We investigated epigenome dynamics of wild strawberry (Fragaria vesca) in response to variable environmental conditions at DNA methylation level. F. vesca methylome responded with great plasticity to ecologically relevant abiotic and hormonal stresses. Thermal stress resulted in substantial genome-wide loss of DNA methylation. Notably, all tested stress conditions resulted in marked hot spots of differential DNA methylation near centromeric or pericentromeric regions, particularly in non-symmetrical DNA methylation context. Additionally, we identified differentially methylated regions (DMRs) within promoter regions of transcription factor (TF) superfamilies involved in plant stress-response and assessed the effects of these changes on gene expression.These findings improve our understanding on stress-response at the epigenome level by highlighting the correlation between DNA methylation, TEs and gene expression regulation in plants subjected to a broad range of environmental stresses.
Rapid in vivo multiplexed editing (RIME) of the adult mouse liver
Authors: Katsuda Takeshi , Cure Hector , Simeonov Kamen P. , Arany Zoltan , Grompe Markus , Stanger Ben Z. 
Published: March 2022

AbstractBackground & AimsAssessing mammalian gene function in vivo has traditionally relied on manipulation of the mouse genome in embryonic stem cells or peri-zygotic embryos. These approaches are time consuming and require extensive breeding when simultaneous mutations in multiple genes is desired. The aim of this study is to introduce a Rapid In vivoMultiplexed Editing (RIME), and to provide a proof-of-concept of this system.Approach & ResultsRIME, a system wherein CRISPR/Cas9 technology, paired with adeno-associated viruses (AAVs), permits the inactivation of one or more genes in the adult mouse liver. The method is quick, requiring as little as 1 month from conceptualization to knockout (KO), and highly efficient, enabling editing in >95% of target cells. To highlight its utility, we used this system to inactivate, alone or in combination, genes with functions spanning metabolism, mitosis, mitochondrial maintenance, and cell proliferation.ConclusionRIME enables the rapid, efficient, and inexpensive analysis of multiple genes in the mouse liver in vivo.
Introduction of a condensed, reverse tricarboxylic acid cycle for additional CO2 fixation in plants
Authors: Wilson Nathan J. , Smith-Moore Caroline M. , Xu Yuan , Edwards Brianne , Hovary Christophe La , Barampuram Swathi , Li Kai , Aslett Denise , Ji Mikyoung , Lin Xuli , Vintila Simina , Kleiner Manuel , Xie Deyu , Shachar-Hill Yair , Grunden Amy , Sederoff Heike 
Published: March 2022

AbstractPlants employ the Calvin-Benson cycle (CBC) to fix atmospheric CO2 for the production of biomass. The flux of carbon through the CBC is limited by the activity and selectivity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Alternative pathways that do not use RuBisCO to fix CO2 exist but occur only in anaerobic microorganisms. Rather than modifying existing routes of carbon metabolism in plants, we have developed a synthetic carbon fixation cycle that does not exist in nature, but is inspired by metabolisms of bacterial autotrophs. This synthetic cycle uses endogenous plant metabolites to fix CO2 and yield glyoxylate as a product. In this work, we build and characterize a condensed, reverse tricarboxylic acid (crTCA) cycle in vitro and in planta. We demonstrate that a simple, synthetic cycle can be used to fix carbon in vitro under aerobic and mesophilic conditions and that these enzymes retain activity when expressed transiently in planta. We then evaluate stable transgenic lines of Camelina sativa that have both phenotypic and physiologic changes. Transgenic C. sativa are shorter than controls with increased rates of photosynthetic CO2 assimilation and changes in photorespiratory metabolism. This first iteration of a build-test-learn phase of the crTCA cycle provides promising evidence that this pathway can be used to increase photosynthetic capacity in plants.
Seed Germination, Post-fire Plant Growth and Conservation of the Rare Endemic and Endangered Chamaecrista glandulosa var. mirabilis (Fabaceae)
Authors: Vilá Terrada Fernando J. , López Colón Jonathan A. 
Published: March 2022

AbstractConservation has been challenged by biodiversity loss drivers. Also, fire disturbance can temporarily change ecosystems. Fire effects in soil nutrients and pH, plant abundance, reproduction, seed weight, seed germination, and plant growth were assessed. Four seed starting systems were used for germination and growth under laboratory conditions. We found significant differences in the means of iron, manganese, nickel, soil pH, and plant height, and a significant positive linear relationship between seed weight and plant height. Results indicate that fires increase soil pH and cause changes in micronutrients that can increase plant growth. Large size plants are produced from high weight seeds. Finally, ex situ conservation and species reintroduction were feasible conservation strategies that should be integrated with in situ conservation.
Nuclear translocation triggered at the onset of hearing in cochlear inner hair cells of rats
Authors: Iyer Megana R. , Kalluri Radha 
Published: March 2022

AbstractNuclear position is precisely orchestrated during cell division, migration, and maturation of cells and tissues. Here we report a previously unrecognized, programmed movement of the nucleus in rat cochlear inner hair cells. This cell-type specific nuclear movement among hair cells of the inner ear offers a new glimpse into the cellular mechanisms involved in the functional maturation of inner hair cells. In early post-natal days, the nucleus sits at the very basal pole of the hair cell, far from the apically located mechano-transducing stereocilia, but close to where synapses with primary afferent and efferent neurons are forming. By maturity, the nucleus moves to occupy a new position half-way along the length of the cell. Remarkably, nuclear translocation happens quickly over the course of 1-2 post-natal days, coinciding with the onset of hearing. The movement of the nucleus likely signals the closing of a critical period correlated with the forming and refining of synapses at the onset of hearing.Significance StatementThe misplacement of a cell’s nucleus has been implicated in hearing, vision, and muscular pathologies. In this study, we report a remarkably abrupt change in nuclear position in cochlear inner hair cells that coincides with the onset of hearing in rats, when hair cells switch from producing sensory-independent action potentials to sensory-dependent graded potentials. This work suggests that post-mitotic nuclear migration may be critical to the final phase of post-natal development in mammalian hearing.
Design of the mammalian cone photoreceptor to Off bipolar cell synapse
Authors: Grabner Chad P. , Futagi Daiki , Shi Jun , Bindokas Vytas , Kitano Katsunori , Schwartz Eric , DeVries Steven H. 
Published: March 2022

AbstractGraded synapses in sensory systems reliably transmit small signals in the presence of continuous quantal noise. To understand how signaling is optimized during graded transmission, we counted the number of vesicles released by a mammalian cone terminal and compared it to the simultaneous responses in each Off bipolar cell type. Off bipolar cells contacting the terminal base comprised two groups depending on how they sampled transmitter release. In both groups, responses initially grew non-linearly with the number of released vesicles implicating a role for cooperativity during sparse release. One group sampled release from most of a cone’s ∼20 ribbons and can exploit averaging to improve signal reliability. The other, less-sensitive group made 1-3 contacts at the terminal center and responded to pooled transmitter, a consequence of membrane depolarization, using an insensitive kainate receptor. Off bipolar cells use different strategies to minimize transmission noise and encode cone output over different ranges.
Medial prefrontal cortex Notch1 signalling mediates methamphetamine-induced psychosis via Hes1-dependent suppression of GABAB1 receptor expression
Authors: Ni Tong , Zhu Li , Wang Shuai , Zhu Weili , Xue Yanxue , Zhu Yingjie , Ma Dongliang , Wang Hongyan , Guan Fanglin , Chen Teng 
Published: March 2022

AbstractMethamphetamine (METH), a widely abused stimulant drug, induces psychosis in approximately half of abusers; this effect is becoming a major concern for society. Although the Notch1 signalling pathway has been shown to play a part in the pathogenesis of some psychiatric disorders, its role in METH-induced psychosis (MIP) is still unknown. Here, we showed that Notch1 signalling was downregulated in the medial prefrontal cortex (mPFC) in a MIP mouse model. Direct genetic and pharmacological manipulations of Notch1 signalling bidirectionally altered MIP-related behaviours and governed neuronal activity in the mPFC. Moreover, Notch1 signalling negatively regulated GABAB1 receptor expression in the mPFC of MIP mice through Hes1, a transcriptional repressor in Notch1 signalling. Further, we show that Hes1 can directly bind to the GABAB1 receptor promoter. Notably, pharmacological regulation of the GABAB receptor in the mPFC reversed the changes in MIP-related behaviours caused by the dysfunction of Notch1 signalling. Together, our findings uncover a previously unrecognised Notch1-Hes1-GABAB1 receptor-dependent mechanism involved in regulating mPFC neuronal activity and behavioural phenotypes in MIP. Our work provides mechanistic insight into the aetiology and pathophysiology of MIP.
Genomic and Transcriptomic Profiling of Phoenix Colonies
Authors: Sindeldecker Devin , Dunn Matthew , Zimmer Aubree , Anderson Matthew , Alfonzo Juan , Stoodley Paul 
Published: March 2022

AbstractPseudomonas aeruginosa is a Gram-negative bacterium responsible for numerous human infections. Previously, novel antibiotic tolerant variants known as phoenix colonies as well as variants similar to viable but non-culturable (VBNC) colonies were identified in response to high concentrations of aminoglycosides. In this study, the mechanisms behind phoenix colony and VBNC-like colony emergence were further explored using both whole genome sequencing and RNA sequencing. Phoenix colonies were found to have a single nucleotide polymorphism (SNP) in the PA4673 gene, which is predicted to encode a GTP-binding protein. No SNPs were identified within VBNC-like colonies compared to the founder population. RNA sequencing did not detect change in expression of PA4673 but revealed multiple differentially expressed genes that may play a role in phoenix colony emergence. One of these differentially expressed genes, PA3626, encodes for a tRNA pseudouridine synthase which when knocked out led to a complete lack of phoenix colonies. Although not immediately clear whether the identified genes in this study may have interactions which have not yet been recognized, they may contribute to the understanding of how phoenix colonies are able to emerge and survive in the presence of antibiotic exposure.
Moving Yeasts: Resolving the Mystery
Authors: Puri Gulab , Chaudhari Sulbha , Inamdar Areeb , Kohli Manish , Sangawe Vishal , Jadhav Chandrakant , Teja Lakshman , Adhapure Nitin 
Published: March 2022

AbstractWe have recently discovered a novel dimorphic yeastAureobasidium tremulumsp.nov. The species name tremulum indicates its trembling movement. With keen microscopic observations and various experimentation, we concluded that the movement is of two types, trembling movement, and actual displacement. The movement is because of two reasons; 1. Due to the dynamic movement of intracellular lipid granules, and; 2. Due to the movement of an intracellular bacterial population which is present as an endosymbiont. The mechanism of displacement has been hypothesized. The presence of both lipid granules and bacteria has been confirmed using microscopic analysis (Bright field, Phase contrast, confocal, Cryo-SEM, and HR-TEM). The bacterial presence was confirmed using whole-genome metagenomic analysis. Endosymbiotic bacteria have also been isolated and identified by 16s rRNA gene sequencing. Interestingly, some of them possibly are novel species. Also, the whole genome ofA.tremulumhas been announced. We also report on, restriction of the mode of bacterial mycophagy in presence of an antibiotic.
Predicting the pathogenicity of missense variants using features derived from AlphaFold2
Authors: Schmidt Axel , Röner Sebastian , Mai Karola , Klinkhammer Hannah , Kircher Martin , Ludwig Kerstin U. 
Published: March 2022

ABSTRACTEach individual genome harbors multiple missense variants, which can be systematically identified via genome or exome sequencing. This class of genetic variation can alter the functional properties of the respective protein, and thereby lead to clinically relevant phenotypes, such as cancer or Mendelian diseases. Despite advances in computational prediction scores, the classification of missense variants as clinically significant or benign remains a major challenge. Recently, the structure of the human proteome was derived with unprecedented accuracy using the artificial intelligence system AlphaFold2. However, the question of whether AlphaFold2 structures can improve the accuracy of computational pathogenicity prediction for missense variants remains unclear. To address this, we first engineered a set of features for each amino acid from these structures. We then trained a random forest to distinguish between proxy-benign and proxy-pathogenic missense variants derived from gnomAD. This yielded a novel AlphaFold2-based pathogenicity prediction score, termed AlphScore. Important feature classes used by AlphScore are solvent accessibility, amino acid network related features, features describing the physicochemical environment, and AlphaFold2’s quality parameter (pLDDT). AlphScore alone showed lower performance than existing scores, such as CADD or REVEL. However, when AlphScore was added to those scores, the performance always increased, as measured by the approximation of deep mutational scan data, as well as the prediction of expert-curated missense variants from the ClinVar database. Overall, our data indicate that the integration of AlphaFold2 predicted structures can improve pathogenicity prediction of missense variants.
Phenethylamine-producing gut bacteria induces diarrhea-predominant irritable bowel syndrome by increasing serotonin biosynthesis
Authors: Zhai Lixiang , Huang Chunhua , Ning Ziwan , Zhang Yijing , Zhuang Min , Yang Wei , Wang Xiaolei , Wang Jingjing , Zhang Eric Lu , Xiao Haitao , Zhao Ling , Lam Yan Y. , Chow Chi Fung Willis , Huang Jiandong , Yuan Shuofeng , Chan Kui Ming , Wong Hoi Leong Xavier , Bian Zhao-xiang 
Published: March 2022

SummaryDespite the strong association between gut microbial dysbiosis, serotonin (5-HT) dysregulation and diarrhea-predominant irritable bowel syndrome (IBS-D), the mechanism by which changes in the gut microbiota contribute to the pathogenesis of IBS-D, particularly the role of dysregulated 5-HT production, remains unclear. The present study identifiedRuminococcus gnavusin the human gut microbiota as a key risk factor of IBS-D.R. gnavuswas significantly enriched in IBS-D patients and exhibited positive correlation with serum 5- HT level and severity of diarrhea symptoms. We showed thatR. gnavusinduced diarrhea-like symptoms in mice by promoting microbial shunting of essential aromatic amino acids to aromatic trace amines including phenethylamine and tryptamine, thereby stimulating the biosynthesis of peripheral 5-HT, a potent stimulator for gastrointestinal transit. This study identify gut-microbial metabolism of dietary amino acids as a cause of IBS-D and lays a foundation for developing novel therapeutic target for the treatment of IBS-D.Graphical abstract
Gut microbiota-derived tryptamine impairs insulin sensitivity
Authors: Zhai Lixiang , Xiao Haitao , Lin Chengyuan , Lam Yan Y. , Wong Hoi Leong Xavier , Gong Mengxue , Wu Guojun , Deng Yusheng , Ning Ziwan , Huang Chunhua , Zhang Yijing , Zhuang Min , Yang Chao , Zhang Eric Lu , Zhao Ling , Zhang Chenhong , Fang Xiaodong , Jia Wei , Zhao Liping , Bian Zhao-xiang 
Published: March 2022

SummaryGut-microbiota plays a pivotal role in development of type 2 diabetes (T2D), yet the molecular mechanism remains elusive. Here, we show that tryptamine, a microbial metabolite of tryptophan, impairs glucose tolerance and insulin sensitivity. Tryptamine presents a higher level in monkeys with spontaneous diabetes and human with T2D and positively correlated with the glucose tolerance. In parallel, tryptamine level was suppressed by dietary fibers intervention in T2D subjects and negatively correlated with improvement of glucose tolerance. The inhibitory effect of tryptamine on insulin signaling as shown was dependent on a trace amine-associated receptor 1 (TAAR1)-extracellular signal-regulated kinase (ERK) signaling axis. Monoassociation of T2D-associated tryptamine-producing bacteriaRuminococcus gnavusimpairs insulin sensitivity in pseudo germ-free mice. Our findings indicate gut microbiota-derived tryptamine contributes to the development of insulin resistance in T2D and may serve as a new target for intervention.Graphical Abstract
The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns
Authors: Bishola Tshitenge Tania , Clayton Christine 
Published: March 2022

AbstractThe parasite Trypanosoma brucei grows as bloodstream forms in mammals, and as procyclic forms in tsetse flies. Transcription is polycistronic, all mRNAs are trans spliced, and polyadenylation sites are defined by downstream splicing signals. Expression regulation therefore depends heavily on post-transcriptional mechanisms. The RNA-binding protein DRBD18 was previously implicated in the export of some mRNAs from the nucleus in procyclic forms. It copurifies the outer ring of the nuclear pore, mRNA export factors and exon-junction-complex proteins. We show that for >200 mRNAs, DRBD18 depletion caused preferential accumulation of versions with shortened 3’-untranslated regions, arising from use of polyadenylation sites that were either undetectable or rarely seen in non-depleted cells. The shortened mRNAs were often, but not always, more abundant in depleted cells than the corresponding longer versions in normal cells. Their appearance was linked to the appearance of trans spliced, polyadenylated RNAs containing only downstream 3’-untranslated-region-derived sequences. Experiments with one mRNA suggested that nuclear retention alone, through depletion of MEX67, did not affect mRNA length, suggesting a specific effect of DRBD18 on processing. Since DRBD18-bound mRNAs were enriched in polypyrimidine tract motifs, and it is found in both the nucleus and the cytoplasm, we suggest that DRBD18 acts in the nucleus by binding to polypyrimidine tracts in 3’-UTRs. DRBD18 binding might both prevent polypyrimidine tract recognition by splicing factors, and promote export of the bound RNAs to the cytosol.
Protein Optimization Evolving Tool (POET) based on Genetic Programming
Authors: Bricco Alexander R. , Miralavy Iliya , Bo Shaowei , Perlman Or , Farrar Christian T. , McMahon Michael T. , Banzhaf Wolfgang , Gilad Assaf A. 
Published: March 2022

ABSTRACTProteins are used by scientists to serve a variety of purposes in clinical practice and laboratory research. To optimize proteins for greater function, a variety of techniques have been developed. For the development of reporter genes used in Magnetic Resonance Imaging (MRI) based on Chemical Exchange Saturation Transfer (CEST), these techniques have encountered a variety of challenges. Here we develop a mechanism of protein optimization using a computational approach known as “genetic programming”. We developed an algorithm called Protein Optimization Evolving Tool (POET). Starting from a small library of literature values, use of this tool allowed us to develop proteins which produce four times more MRI contrast than what was previously state-of-the-art. Next, we used POET to evolve peptides that produced CEST-MRI contrast at large chemical shifts where no other known peptides have previously demonstrated contrast. This demonstrated the ability of POET to evolve new functions in proteins. Interestingly, many of the peptides produced using POET were dramatically different with respect to their sequence and chemical environment than existing CEST producing peptides, and challenge prior understandings of how those peptides function. This suggests that unlike existing algorithms for protein engineering that rely on divergent evolution, POET relies on convergent evolution.
Differential effects of group III metabotropic glutamate receptors on spontaneous inhibitory synaptic currents in spine-innervating double bouquet and parvalbumin-expressing dendrite-targeting GABAergic interneurons in human neocortex
Authors: Lukacs Istvan P. , Francavilla Ruggiero , Field Martin , Hunter Emily , Howarth Michael , Horie Sawa , Plaha Puneet , Stacey Richard , Livermore Laurent , Ansorge Olaf , Tamas Gabor , Somogyi Peter 
Published: March 2022

AbstractDiverse neocortical GABAergic neurons specialise in synaptic targeting and their effects are modulated by presynaptic metabotropic glutamate receptors (mGluRs) suppressing neurotransmitter release in rodents, but their effects in human neocortex are unknown. We tested whether activation of group III mGluRs by L-AP4 changes GABAA receptor-mediated spontaneous inhibitory postsynaptic currents (sIPSCs) in two distinct dendritic spine-innervating GABAergic interneurons recorded in vitro in human neocortex. Calbindin-positive double bouquet cells (DBC) had columnar “horsetail” axons descending through layers II-V innervating dendritic spines (48%) and shafts, but not somata of pyramidal and non-pyramidal neurons. Parvalbumin-expressing dendrite-targeting cell (PV-DTC) axons extended in all directions innervating dendritic spines (22%), shafts (65%) and somata (13%). As measured, 20% of GABAergic neuropil synapses innervate spines, hence DBCs, but not PV-DTCs, preferentially select spine targets. Group III mGluR activation paradoxically increased the frequency of sIPSCs in DBCs (to median 137% of baseline), but suppressed it in PV-DTCs (median 92%), leaving the amplitude unchanged. The facilitation of sIPSCs in DBCs may result from their unique GABAergic input being disinhibited via network effect. We conclude that dendritic spines receive specialised, diverse GABAergic inputs, and group III mGluRs differentially regulate GABAergic synaptic transmission to distinct GABAergic cell types in human cortex.