bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation, screening, degradation characteristics of a quinclorac-degrading bacteria D and its potential of bioremediation for rice field environment polluted by quinclorac
Authors: Huang Siqi , Pan Jiuyue , Tuwang Mancuo , Li Hongyan , Ma Chenyi , Chen Mingxue , Lin Xiaoyan 
Published: April 2021

AbstractQuinclorac (QNC) is a highly selective, hormonal, and low-toxic herbicide with a long duration. And the growth and development of subsequent crops are easily affected by QNC accumulated in the soil. In this paper, a QNC-degrading strain D was isolated and screened from the rice paddy soil. Through morphology, physiological and biochemical tests and 16Sr DNA gene analysis, strain D was identified asCellulosimicrobium cellulanssp. And the QNC degradation characteristics of strain D were studied. Under the optimal culture conditions, the QNC-degrading rate was 45.9% after culturing for 21 days. The QNC-degrading efficiency of strain D in the field was evaluated by a simulated pot experiment. The results show that strain D can promote the growth of rice and QNC-degrading effectively. This research could provide a new bacterial species for microbial degradation of QNC and lay a theoretical foundation for further research on QNC remediation.ImportanceAt present, some QNC-degrading bacteria have been isolated from different environments, but there are no reports ofCellulosimicrobium cellulanssp. bacterial that could degrade QNC. In this study, a new QNC-degradation strain was selected from the paddy soil. The degradation characteristics of strain D were studied in detail. The results shown that strain D had a satisfactory quinclorac-degrading efficiency. Two degradation products of QNC by strain D were identified by HPLC-Q-TOF/MS: 3-pyridylacetic acid (138.0548 m/z) and 3-ethylpyridine (108.0805 m/z), which have not been reported before. The strain D had a potential ability of quinclorac-degrading effectively in the quinclorac-polluted paddy field environment.
Clp protease and antisense RNA jointly regulate the global regulator CarD to mediate mycobacterial starvation response
Authors: Li Xinfeng , Chen Fang , Liu Xiaoyu , Xiao Jinfeng , Andongma Binda T. , Tang Qing , Cao Xiaojian , Chou Shan-Ho , Galperin Michael Y. , He Jin 
Published: April 2021

AbstractUnder starvation conditions, bacteria tend to slow down their translation rate by reducing rRNA synthesis, but the way they accomplish that may vary in different bacteria. InMycobacteriumspecies, transcription of rRNA is activated by the RNA polymerase (RNAP) accessory transcription factor CarD, which interacts directly with RNAP to stabilize the RNAP-promoter open complex formed on rRNA genes. The functions of CarD have been extensively studied, but the mechanisms that control its expression remain obscure. Here, we report that the level of CarD was tightly regulated when mycobacterial cells switched from nutrient-rich to nutrient-deprived conditions. At the translational level, an antisense RNA ofcarD(AscarD) was induced in a SigF-dependent manner to bind withcarDmRNA and inhibit CarD translation, while at the post-translational level, the residual intracellular CarD was quickly degraded by the Clp protease. AscarD thus worked synergistically with Clp protease to decrease the CarD level to help mycobacterial cells cope with the nutritional stress. Altogether, our work elucidates the regulation mode of CarD and delineates a new mechanism for the mycobacterial starvation response, which is important for the adaptation and persistence of mycobacterial pathogens in the host environment.
Loss of adipocyte phospholipase genePLAAT3causes lipodystrophy and insulin resistance due to inactivated arachidonic acid-mediated PPARγsignaling
Authors: Schuermans Nika , Chehadeh Salima El , Hemelsoet Dimitri , Bogaert Elke , Debackere Elke , Hilbert Pascale , Van Doninck Nike , Taquet Marie-Caroline , Rosseel Toon , De Clercq Griet , Van Haverbeke Carole , Chanson Jean-Baptiste , Funalot Benoit , Authier François-Jérôme , Kaya Sabine , Terryn Wim , Callens Steven , Depypere Bernard , Van Dorpe Jo ,   Program for Undiagnosed Diseases (UD-PrOZA), Poppe Bruce , Depienne Christel , Dermaut Bart 
Published: April 2021

SummaryPLAAT3 is a phospholipid modifying enzyme predominantly expressed in white adipose tissue (WAT). It is a candidate drug target as Plaat3 deficiency in mice protects against picornavirus infection and diet-induced obesity. We identified four patients with homozygous loss-of-function mutations inPLAAT3, presenting with partial lipodystrophy, severe insulin resistance and dyslipidemia. PLAAT3-deficient WAT showed a failure to liberate arachidonic acid (AA) from membrane phospholipids resulting in an inactive gene network downstream of adipogenesis master regulator and anti-diabetic drug target PPARG. These findings establish PLAAT3 deficiency in humans as a novel type of partial lipodystrophy due to an AA- and PPARG-dependent defect in WAT differentiation and function.
Human myelin protein P2: From crystallography to time-lapse membrane imaging and neuropathy-associated variants
Authors: Uusitalo Maiju , Berg Klenow Martin , Laulumaa Saara , Blakeley Matthew P. , Simonsen Adam Cohen , Ruskamo Salla , Kursula Petri 
Published: April 2021

AbstractPeripheral myelin protein 2 (P2) is a fatty acid-binding protein expressed in vertebrate peripheral nervous system myelin, as well as in human astrocytes. Suggested functions of P2 include membrane stacking and lipid transport. Mutations in the PMP2 gene, encoding P2, are associated with Charcot-Marie-Tooth disease (CMT). Recent studies have revealed three novel PMP2 mutations in CMT patient families. To shed light on the structure and function of the corresponding P2 variants, we used X-ray and neutron crystallography, small-angle X-ray scattering, circular dichroism spectroscopy, computer simulations, and lipid binding assays. The crystal and solution structures of the I50del, M114T, and V115A variants of P2 showed only minor differences to the wild-type protein, whereas the thermal stability of the disease variants was reduced. Lipid vesicle aggregation assays revealed no change in membrane stacking characteristics, while the variants showed slightly altered fatty acid binding. Time-lapse imaging of lipid bilayers indicated membrane blebbing induced by P2, which could be related to its function in stacking of two curved membrane surfaces in myelin in vivo. All variants caused blebbing of membranes on similar timescales. In order to better understand the links between structure, dynamics, and function, the crystal structure of perdeuterated P2 was refined from room temperature data collected using both neutrons and X-rays, and the results were compared to molecular dynamics simulations and cryocooled crystal structures. Taken together, our data indicate similar properties of all known CMT variants of human P2; while crystal structures are nearly identical, stability and function of the disease variants are impaired compared to the wild-type protein. Our data provide new insights into the structure-function relationships and dynamics of P2 in health and disease.
Subjective understanding of actions and emotions requires interaction of the semantic and action observation networks
Authors: Zhan Minye , Goebel Rainer , de Gelder Beatrice 
Published: April 2021

AbstractPrevious studies have investigated the neural basis of action and emotion perception conveyed by whole body postures and movements. However, subjective understanding of other people’s bodily actions and emotions, raises different issues that are currently not well understood and have so far seldom been investigated. In this 7T fMRI study, we proceeded beyond conventional univariate/multivariate analyses with predefined categories, and examined the representational geometry of subjective action- and emotion-understanding by mapping individual subjective reports with word embeddings. Dimensionality reduction revealed that the representations for perceived action and emotion were high dimensional, each correlated to but were not reducible to the predefined action and emotion categories. Searchlight representational similarity analysis showed that the representations in the left middle superior temporal sulcus and left dorsal premotor cortex corresponded to the subjective action and emotion understanding of the participants. Furthermore, using task-residual functional connectivity and hierarchical clustering, we found that areas in the action observation network and the semantic/default-mode network were functionally connected to these two seed regions, and showed similar representations. Our study provides direct evidence that both networks were concurrently involved in subjective action and emotion understanding. Our approach shows how subjective understanding of action and emotion stimuli can be reliably studied and complement insights based on from predefined stimulus categories.
FAN1 nuclease processes and pauses on disease-associated slipped-DNA repeats: Mechanism against repeat expansions
Authors: Deshmukh Amit Laxmikant , Caron Marie-Christine , Mohiuddin Mohiuddin , Lanni Stella , Panigrahi Gagan B. , Khan Mahreen , Engchuan Worrawat , Shum Natalie , Faruqui Aisha , Wang Peixiang , Yuen Ryan K.C. , Nakamori Masayuki , Nakatani Kazuhiko , Masson Jean-Yves , Pearson Christopher E. 
Published: April 2021

SummaryFAN1 nuclease is a modifier of repeat expansion diseases, including Huntington’s disease (HD), fragile X syndrome, and autism. The age of HD onset correlates with ongoing ‘inchworm-like’ repeat expansions (1-3 CAG units/event) in HD brains, and is regulated by three modifiers: The first two, repeat tract length and purity exert their effects by enhancing and slowing CAG expansions, respectively, by affecting the formation of slipped-DNAs — mutagenic intermediates of instability; which are processed to expansions by the third modifiers, DNA repair proteins. FAN1 protects against hyper-expansions of repeats, by unknown mechanisms. We show FAN1, through iterative cycles bound, dimerized and cleaved slipped-DNAs, yielding striking patterns of distinctexo-nucleasepausesalong slip-outs; 5′-C↓A↓GC↓A↓G-3′ and 5′-C↓T↓G↓C↓T↓G-3′. The transcriptionally-displaced CAG strand was excised slower than its complementary CTG strand, required A•A and T•T mismatches, as fully-paired hairpinsarrestedexcision progression, while disease-delayingCAAinterruptions further slowed FAN1 excision. In contrast,endo-nucleolytic cleavage was insensitive to slip-outs. Rare FAN1 variants were found in autism individuals with CGG/CCG repeat expansions. Excision of CGG/CCG slip-outs were similarly excised, with CGG being slower than CCG. The slip-out specific ligand, Naphthyridine-Azaquinolone, shown to induce contractions of expanded repeats in cells, required FAN1 for its effect, and protected slip-outs from FAN1’sexo- but notendo-nucleolytic digestion. FAN1’s ‘inchworm’ pausing of slip-out excision is suited to minimize incremental expansions and modulating disease onset.
Analyzing Brain Morphology in Alzheimer’s Disease Using Discriminative and Generative Spiral Networks
Authors: Azcona Emanuel A. , Besson Pierre , Wu Yunan , Kurani Ajay S. , Bandt S. Kathleen , Parrish Todd B. , Katsaggelos Aggelos K. ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: April 2021

AbstractSeveral patterns of atrophy have been identified and strongly related to Alzheimer’s disease (AD) pathology and its progression. Morphological changes in brainshapehave been identified up to ten years before clinical diagnoses of AD, making its early detection more relevant. We propose novel geometric deep learning frameworks for the analysis of brain shape in the context of neurodegeneration caused by AD. Our deep neural networks learn low-dimensional shape descriptors of multiple neuroanatomical structures, instead of handcrafted features for each structure. A discriminative network using spiral convolution on 3D meshes is constructed for thein-vivobinary classification of AD from healthy controls (HCs) using a fast and efficient “spiral” convolution operator on 3D triangular mesh surfaces of human brain subcortical structures extracted from T1-weighted magnetic resonance imaging (MRI). Our network architecture consists of modular learning blocks using residual connections to improve overall classifier performance.In this work: (1) a discriminative network is used to analyze the efficacy of disease classification using input data from multiple brain structures and compared to using a single hemisphere or a single structure. It also outperforms prior work using spectral graph convolution on the same the same tasks, as well as alternative methods that operate on intermediate point cloud representations of 3D shapes. (2) Additionally, visual interpretations for regions on the surface of brain structures that are associated to true positive AD predictions are generated and fall in accordance with the current reports on the structural localization of pathological changes associated to AD. (3) A conditional generative network is also implemented to analyze the effects of phenotypic priors given to the model (i.e. AD diagnosis) in generating subcortical structures. The generated surface meshes by our model indicate learned morphological differences in the presence of AD that agrees with the current literature on patterns of atrophy associated to the disease. In particular, our inference results demonstrate an overall reduction in subcortical mesh volume and surface area in the presence of AD, especially in the hippocampus. The low-dimensional shape descriptors obtained by our generative model are also evaluated in our discriminative baseline comparisons versus our discriminative network and the alternative shape-based approaches.
TAZ/TEAD complex regulates TGF-β1-mediated fibrosis in iPSC-derived renal organoids
Authors: Yang Xiaoping , Delsante Marco , Daneshpajouhnejad Parnaz , Fenaroli Paride , Mandell Kira Perzel , Wang Xiaoxin , Takahashi Shogo , Halushka Marc K. , Kopp Jeffrey B. , Levi Moshe , Rosenberg Avi Z. 
Published: April 2021

AbstractChronic kidney disease (CKD) progresses by replacement of functional tissue compartments with fibrosis, representing a maladaptive repair process. Shifting kidney repair towards a physiologically-intact architecture, rather than fibrosis, is key to blocking CKD progression. In this study, we developed a fibrosis model that uses human induced pluripotent stem cell (iPSC)-based three-dimensional renal organoids, in which exogenous TGF-β1 induces production of extracellular matrix. In these organoids, TGF- β1 increased transcription factor tafazzin (TAZ) expression. Further, in human kidney biopsies, nuclear TAZ expression was markedly increased in mild and moderate fibrosis. In cultured renal tubular cells expressing a fibrogenic program, TAZ formed a trimeric complex with phosphorylated mothers against decapentaplegic homolog 3 (p-SMAD3) and TEA domain protein (TEAD)-4. Overexpression of TEAD4 protein suppressed collagen-1α1 (COL1A1) promoter activity, and expression of TAZ attenuated this inhibition. INT-767, a dual bile acid receptor agonist binding farnesoid X receptor (FXR) and the Takeda G protein-coupled receptor 5 (TGR5), decreased the TGF-β1-induced increase in p-SMAD3 and TAZ, and preserved renal organoid architecture. These data demonstrate, in an iPSC-derived renal organoid fibrosis model, that INT767 prevents fibrosis programs early in the course of tubular injury through modulation of the TEAD4/TAZ pathway.
Gas flow permeability and gas pressures in stilt roots of Red Mangrove (Rhizophora mangleL.)
Authors: Searcy Dennis G. 
Published: April 2021

AbstractThe Red Mangrove (Rhizophora mangle) is typically rooted in anoxic mud conditions that require special adaptations for root oxygenation. Each plant has multiple “stilt roots” that descend from upper branches and end in roots buried the mud. In cross section each stilt root consists of a core of porous aerenchyma surrounded by an impermeable layer of xylem, and outside the xylem there is a second layer aerenchyma. Oxygen must be provided to the mud roots through the aerenchyma either by diffusion or by gas flow, where the separate layers could provide up- and down-flow pathways. To test whether the stilt root’s properties were consistent with gas flow, conductivities were measured. A technique was developed that measured flow conductivities in S.I. scientific units without using a flow meter and a calibrated pressure gauge. The core aerenchyma was more permeable to gas flow than any other plant tissue, except for those stems that are hollow tubes. Because there was little lateral leakage from the core aerenchyma, it had pipe-like properties. In the outer aerenchyma gas conductivity was high, and gas flowed easily through large lenticels on the surface of the stilt root. To complete the calculations, gas pressures in the stilt roots were measured. The calculated gas flow rates through mud roots was not sufficient to supply O2for root respiration, suggesting that diffusion may be the more important mechanism for these plants.
The genome of the poecilogonous annelidStreblospio benedicti
Authors: Zakas Christina , Harry Nathan D. , Scholl Elizabeth H. , Rockman Matthew V. 
Published: April 2021

AbstractStreblospio benedictiis a common marine annelid that has become an important model for developmental evolution. It is the only known example of poecilogony, where two distinct developmental modes occur within a single species, that is due to a heritable difference in egg size. The dimorphic developmental programs and life-histories exhibited in this species depend on differences within the genome, making it an optimal model for understanding the genomic basis of developmental divergence. Studies usingS. benedictihave begun to uncover the genetic and genomic principles that underlie developmental uncoupling, but until now they have been limited by the lack of availability of genomic tools. Here we present an annotated chromosomal-level genome assembly ofS. benedictigenerated from a combination of Illumina reads, Nanopore long reads, Chicago and Hi-C chromatin interaction sequencing, and a genetic map from experimental crosses. At 701.4 Mb, theS. benedictigenome is the largest annelid genome to date that has been assembled to chromosomal scaffolds, yet it does not show evidence of extensive gene family expansion, but rather longer intergenic regions. The complete genome ofS. benedictiis valuable for functional genomic analyses of development and evolution, as well as phylogenetic comparison within the Annelida and the Lophotrochozoa. Despite having two developmental modes, there is no evidence of genome duplication or substantial gene number expansions. Instead, lineage specific repeats account for much of the expansion of this genome compared to other annelids.
Targeting circPTPN12/miR-21-5p/ΔNp63α pathway as a therapeutic strategy for human endometrial fibrosis
Authors: Song Minmin , Zhao Guangfeng , Sun Haixiang , Yao Simin , Zhou Zhenhua , Jiang Peipei , Wu Qianwen , Zhu Hui , Wang Huiyan , Dai Chenyan , Wang Jingmei , Li Ruotian , Cao Yun , lv Haining , Liu Dan , Dai Jianwu , Zhou Yan , Hu Yali 
Published: April 2021

AbstractEmerging evidence demonstrates the important role of circular RNAs (circRNAs) in regulating pathological processes in various diseases including organ fibrosis. Endometrium fibrosis is the leading cause of uterine infertility, but the role of circRNAs in its pathogenesis is largely unknown. Here, we provide the evidence that upregulation of circPTPN12 in endometrial epithelial cells (EECs) of fibrotic endometrium functions as endogenous sponge of miR-21-5p to inhibit miR-21-5p expression and activity, which in turn results in upregulation of ΔNp63α to induce the epithelial mesenchymal transition (EMT) of EECs (EEC-EMT). In a mouse model of endometrium fibrosis, circPTPN12 appears to be a cofactor of driving EEC-EMT. Our findings reveal the novel mechanism in the pathogenesis of endometrium fibrosis and the potential therapeutic strategy for endometrium fibrosis via targeting circPTPN12/miR-21-5p/ΔNp63α pathway.
The CADM2 gene and behavior: A phenome-wide scan in UK-Biobank
Authors: A. Pasman Joëlle , Chen Zeli , Vink Jacqueline M. , Van Den Oever Michel C. , Pattij Tommy , Vries Taco J. De , Abdellaoui Abdel , Verweij Karin J.H. 
Published: April 2021

AbstractThis phenome-wide association study examined SNP and gene–based associations of the CADM2 gene with 242 psycho-behavioral traits (N=12,211–453,349). We found significant associations with 51 traits, many more than for other genes. We replicated previously reported associations with substance use, risk-taking, and health behavior, and uncovered novel associations with sleep and dietary traits. Accordingly, CADM2 is involved in many psycho-behavioral traits, suggesting a common denominator in their biology.
Changes in eating habits and sedentary behavior during the COVID-19 pandemic in adolescents with chronic conditions
Authors: Mazzolani Bruna Caruso , Smaira Fabiana Infante , Astley Camilla , Iraha Amanda Yuri , Pinto Ana Jessica , Marques Isabela Gouveia , Amarante Milla Cordeiro , Rezende Nathalia Saffioti , Sieczkowska Sofia Mendes , Franco Tathiane Christine , do Amaral Miranda Luana Cristina , Lindoso Lívia , Helito Alberto Carame , Oba Jane , Queiroz Ligia Bruni , R Pereira Rosa Maria , Roschel Hamilton , Silva Clovis Artur , Gualano Bruno 
Published: April 2021

ABSTRACTPurposeTo report on the impact of the COVID-19 outbreak on eating habits and sedentary behavior among adolescents with multiple chronic conditions (n=347) from a tertiary, referral hospitalvs. healthy peers.MethodsThis observational study was conducted in Sao Paulo (Brazil) between July and October 2020, period in which a set of social distancing measures to contain the pandemic.ResultsThe main findings of this study were that adolescents with chronic conditions showed important changes in eating habits (e.g., less often consumption of convenience foods and more often eating in front of television than before quarantine). Also, 86.8% of adolescents with chronic conditions reported increasing screen time during pandemic. No major differences were observed between patients and controls.ConclusionsAdolescents with chronic conditions exposed to pandemic showed substantial changes in lifestyle, stressing the need for specific care to mitigate poor eating habits and excessive sedentary behavior in this group.