bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome Analysis of xa5-mediated Resistance to Bacterial Leaf Streak in Rice (Oryza sativa L.)
Authors: Xie Xiaofang , Chen Zhiwei , Guan Huazhong , Zheng Yan , Zhang Jing , Qin Mingyue , Wu Weiren 
Published: August 2019

AbstractBacterial leaf steak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is a devastating disease in rice production. The resistance to BLS in rice is a quantitatively inherited trait, of which the molecular mechanism is still unclear. It has been proved that xa5, a recessive bacterial blast resistance gene, is the most possible candidate gene of the QTL qBlsr5a for BLS resistance. To study the molecular mechanism of xa5 function in BLS resistance, we created transgenic lines with RNAi of Xa5 (LOC_Os05g01710) and used RNA-seq to analyze the transcriptomes of a Xa5-RNAi line and the wild-type line at 9 h after inoculation with Xoc, with the mock inoculation with water as control. The results showed that Xa5-RNAi could (1) increase the resistance to BLS as expected from xa5; (2) alter (mainly up-regulate) the expression of hundreds of genes, most of which were related to disease resistance; and (3) greatly enhance the response of thousands of genes to Xoc infection, especially of the genes involved in cell death pathways, suggesting that xa5 displays BLS resistance effect probably mainly because of the enhanced response of the cell death-related genes to Xoc infection.
In silicoanalysis ofCDC73gene revealing 11 novel SNPs associated with Jaw Tumor Syndrome
Authors: Abdelmoneim Abdelrahman H. , Mohammed Alaa I. , Gadim Esraa O. , A.Mohammed Mayada , Hamza Sara H. , Mirghani Sara A. , Mahmoud Thwayba A. , Hassan Mohamed A. 
Published: August 2019

AbstractBack groundhyperparathyroidism-jaw tumor (HPT-JT) is an autosomal dominant disorder with variable expression, with an estimated prevalence of 6.7 per 1,000 population. Genetic testing for predisposing CDC73 (HRPT2) mutations has been an important clinical advance, aimed at early detection and/or treatment to prevent advanced disease. The aim of this study is to assess the effect of SNPs onCDC73structure and function using different bioinformatics tools.MethodComputational analysis using eight differentin-silicotools including SIFT, PROVEAN, PolyPhen-2, SNAP2, PhD-SNP, SNPs&GO, PMut and Imutant were used to identify the impact on the structure and/or function ofCDC73gene that might be causing jaw tumour.ResultsFrom (733) SNPs identified in theCDC73gene we found that only Eleven were deleterious to the function and structure of protein and expected to cause syndrome.ConclusionEleven substantial genetic/molecular aberrations inCDC73gene were identified that could serve as actionable targets for chemotherapeutic intervention in patients whose disease is no longer surgically curable.
Effects of dietary NFC/NDF on rumen microbiomes of Karakul sheep based on Three Generations of Full-length Amplifiers sequencing
Authors: Pu Xuanxuan , Guo Xuefeng , Jiang Chenyu , Liu Junfeng , Zhang Xiuping , Zhang Sujiang , Cheng Long , Shan Anshan 
Published: August 2019

AbstractAn study was was conducted to investigate the effects of dietary(non fibrous carbohydrate) NFC/(neutral detergent fiber)NDF on ruminal bacteria in Karakul sheep. Twelve Karakul sheep were assigned randomly to four dietary treatments of NFC/NDF (0.78, 1.23, 1.61 and 2.00 respectively) as group 1, 2, 3 to 4. The experiment lasted for four periods, period I (1~18 d), II (19~36 d), III (37~54 d) and IV (55~72 d). Ruminal digesta were collected consecutively for three days to measure pH and bacteria per period. The results indicated that the average ruminal pH and amounts of OTUs were decreased with the increase of dietary NFC/NDF for four periods. At phylum level, Bacteroidetes and Firmicutes were the predominant bacteria of four periods, Bacteroidetes were decreased, while the relative abundance of Firmicutes was increased with dietary NFC/NDF for four periods, but the difference wasn’t significant (P>0.05). At genus level, the most relative abundance genus was unidentified-Lachnospiraceae which reached the highest in group 3 for four periods, but the difference wasn’t significant (P>0.05). Conclusion: ruminal pH and bacteria were decreased with the increase of dietary NFC/NDF and the most dominant bacteria were not change with dietary NFC/NDF and periods in Karakul sheep.
Cryo-EM structure of full-length HIV-1 Env bound with the Fab of antibody PG16
Authors: Pan Junhua , Peng Hanqin , Chen Bing , Harrison Stephen C. 
Published: August 2019

AbstractThe HIV-1 envelope protein (Env) is the target of neutralizing antibodies and the template for vaccine immunogen design. The dynamic conformational equilibrium of trimeric Env influences its antigenicity and potential immunogenicity. Antibodies that bind at the trimer apex stabilize a “closed” conformation characteristic of the most difficult to neutralize isolates. A goal of vaccine development is therefore to mimic the closed conformation in a designed immunogen. A disulfide-stabilized, trimeric Env ectodomain -- the “SOSIP” construct -- has many of the relevant properties; it is also particularly suitable for structure determination. Some single-molecule studies have, however, suggested that the SOSIP trimer is not a good representation of Env on the surface of a virion or an infected cell. We isolated Env (fully cleaved to gp120 and gp41) from the surface of expressing cells using tagged, apex-binding Fab PG16 and determined the structure of the PG16-Env complex by cryo-EM to an overall resolution of 4.6 Å. Placing the only purification tag on the Fab ensured that the isolated Env was continuously stabilized in its closed, native conformation. The Env structure in this complex corresponds closely to the SOSIP structures determined by both x-ray crystallography and cryo-EM. Although the membrane-interacting elements are not resolved in our reconstruction, we can make inferences about the connection between ectodomain and membrane-proximal external region (MPER) by reference to the published cryo-tomography structure of an Env “spike” and the NMR structure of the MPER-transmembrane segment. We discuss these results in view of the conflicting interpretations in the literature.
Mapping the living mouse brain neural architecture: strain specific patterns of brain structural and functional connectivity
Authors: Karatas Meltem , Noblet Vincent , Nasseef Md Taufiq , Bienert Thomas , Reisert Marco , Hennig Jürgen , Yalcin Ipek , Kieffer Brigitte Lina , von Elverfeldt Dominik , Harsan Laura-Adela 
Published: August 2019

AbstractMapping the structural and functional brain connectivity fingerprints became an essential approach in neurology and experimental neuroscience because network properties can underlie behavioral phenotypes. In mouse models, revealing strain related patterns of brain wiring have a tremendous importance, since these animals are used to answer questions related to neurological or neuropsychiatric disorders. C57BL/6 and BALB/cJ inbred strains are primary “genetic backgrounds” for brain disease modelling and for testing therapeutic approaches. Nevertheless, extensive literature describes basal differences in the behavioral, neuroanatomical and neurochemical profiles of the two strains, which raises the question whether the observed effects are pathology specific or depend on the genetic background. Here we performed a systematic comparative exploration of brain structure and function of C57BL/6 and BALB/cJ mice via Magnetic Resonance Imaging (MRI). We combined voxel-based morphometry (VBM), diffusion MRI and high resolution fiber mapping (hrFM) and resting state functional MRI (rs-fMRI) and depicted brain-wide dissimilarities in the morphology and “connectome” features in the two strains. Particularly C57BL/6 animals show bigger and denser frontal cortical areas, cortico-striatal tracts and thalamic and midbrain pathways, and higher density of fibers in the genu and splenium of the corpus callosum. These features are fairly reflected in the functional connectograms that emphasize differences in “hubness”, frontal cortical and basal forbrain connectivity. We demonstrate strongly divergent reward-aversion circuitry patterns and some variations of the default mode network features. Inter-hemispherical functional connectivity showed flexibility and adjustment regarding the structural patterns in a strain specific manner. We further provide high-resolution tractograms illustrating also inter-individual variability across inter-hemispherical callosal pathways in the BALB/cJ strain.
Dynamic control of cortical head-direction signal by angular velocity
Authors: Finkelstein Arseny , Rouault Hervé , Romani Sandro , Ulanovsky Nachum 
Published: August 2019

AbstractThe sense of direction requires accurate tracking of head direction at different turning-velocities, yet it remains unclear how this is achieved in the mammalian brain. Here we recorded head-direction cells in bat dorsal presubiculum and found that, surprisingly, the head-direction signal in this cortical region was dynamically controlled by angular velocity. In most neurons, a sharp head-direction tuning emerged at some angular velocity, but was absent at other velocities – resulting in a 4-fold increase in head-direction cell abundance. The head-direction tuning changed as a function of angular velocity primarily via a redistribution of spikes between the neuron’s preferred and null directions – while keeping the average firing-rate constant. These results could not be explained by existing ‘ring-attractor’ models of the head-direction system. We propose a novel recurrent network model that accounts for the observed dynamics of head-direction cells. This model predicts that the new classes of cells we found can improve the sensitivity of the head-direction system to directional sensory cues, and support angular-velocity integration.
Using a novel web application for thermodynamic characterization ofTel22G-quadruplex unfolding
Authors: Prislan I. , Sajko S. , Poklar Ulrih N. , Fuerst L. 
Published: August 2019

ABSTRACTMeasuring and quantifying thermodynamic parameters that determine stability of and interactions between biological macromolecules is an essential and necessary complement to structural studies. Although several laboratories are able to obtain basic thermodynamic parameters for the observed process, the data interpretation and analysis quality of reported data can be extremely tedious. We have started to develop a web application that will help users to perform thermodynamic characterization of G-quadruplex unfolding. The application can perform global fitting of calorimetric and spectroscopic data, and it uses a three-state equilibrium model to obtain thermodynamic parameters for each transition step: the Gibbs energy, the enthalpy, and the heat capacity. As well as these, the application can define the number of K+ions and the number of water molecules being released or taken up during the unfolding. To test our application, we used UV spectroscopy, circular dichroism, and differential scanning calorimetry, to monitor folding and unfolding of a model 22-nucleotide-long sequence of human 3’-telomeric overhang, known asTel22. The obtained data was fed to the web application and global fit revealed that unfolding ofTel22involves at least one intermediate state, and that K+ions are released during the unfolding, whereas water molecules are taken up.STATEMENT OF SIGNIFICANCEThe laws of thermodynamics provide tools for the use of elegant mathematical expressions to describe stabilities and interactions of biological macromolecule. Even though thermodynamic profiles of simple transitions (e.g., two state) can be obtained in a relatively straightforward manner, performing thermodynamic analysis of complex/ multistep transitions or global analysis of several experimental data requires some experiences and skills. In the present study we are demonstrating how newly developed web application can be used to provide better understanding of driving forces responsible for the structural interconversion of G-quadruplex structures. We have tested this web application with experimental data obtained from monitoring thermal folding/ unfolding of the 5’-AG3T2AG3T2AG3T2AG3-3’ (Tel22) DNA sequence. We believe that this application can be used as a research and/or teaching tool, and it will allow comparisons of the thermodynamic parameters obtained between different laboratories.
A nutritional memory impairs survival, transcriptional and metabolic response to dietary restriction in old mice
Authors: Hahn Oliver , Drews Lisa F. , Nguyen An , Tatsuta Takashi , Gkioni Lisonia , Hendrich Oliver , Zhang Qifeng , Langer Thomas , Pletcher Scott , Wakelam Michael J. O. , Beyer Andreas , Grönke Sebastian , Partridge Linda 
Published: August 2019

AbstractDietary restriction (DR) during adulthood can greatly extend lifespan and improve metabolic health in diverse species. However, whether DR in mammals is still effective when applied for the first time at old age remains elusive. Here, we conducted a late-life DR switch experiment employing 800 mice, by switching old animals from ad libitum (AL) to DR and vice versa. Strikingly, the switch from DR-to-AL acutely increased mortality, while the switch from AL-to-DR caused only a weak and gradual increase in survival, highlighting a memory of earlier nutrition. A significant association between fat preservation and survival response pointed to the white adipose tissue (WAT) as a potential memory source. Consistently, post-switch RNA-seq profiling in liver and WAT demonstrated that the transcriptional and metabolic program of chronic DR remained largely refractory to the AL-to-DR switch specifically in adipose tissue. Integration of lipidomics confirmed impaired membrane lipogenesis and limited mitochondrial copy number increase under late-life DR as functional consequences of this memory effect. Together, our results provide evidence for a nutritional memory as a limiting factor for DR-induced longevity and metabolic remodeling of WAT in mammals.
Occurrence and stability of hetero-hexamer associations formed by β-carboxysome CcmK shell components
Authors: Garcia-Alles Luis F. , Root Katharina , Maveyraud Laurent , Aubry Nathalie , Lesniewska Eric , Mourey Lionel , Zenobi Renato , Truan Gilles 
Published: August 2019

AbstractThe carboxysome is a bacterial micro-compartment (BMC) subtype that encapsulates enzymatic activities necessary for carbon fixation. Carboxysome shells are composed of a relatively complex cocktail of proteins, their precise number and identity being species dependent. Shell components can be classified in two structural families, the most abundant class associating as hexamers (BMC-H) that are supposed to be major players for regulating shell permeability. Up to recently, these proteins were proposed to associate as homo-oligomers. Genomic data, however, demonstrated the existence of paralogs coding for multiple shell subunits. Here, we studied cross-association compatibilities among BMC-H CcmK proteins of Synechocystis sp. PCC6803. Co-expression in Escherichia coli proved a consistent formation of hetero-hexamers combining CcmK1 and CcmK2 or, remarkably, CcmK3 and CcmK4 subunits. Unlike CcmK1/K2 hetero-hexamers, the stoichiometry of incorporation of CcmK3 in associations with CcmK4 was low. Cross-interactions implicating other combinations were weak, highlighting a structural segregation of the two groups that could relate to gene organization. Sequence analysis and structural models permitted to localize interactions that would favor formation of CcmK3/K4 hetero-hexamers. Attempts to crystallize these CcmK3/K4 associations conducted to the unambiguous elucidation of a CcmK4 homo-hexamer structure. Yet, subunit exchange could not be demonstrated in vitro. Biophysical measurements showed that hetero-hexamers are thermally less stable than homo-hexamers, and impeded in forming larger assemblies. These novel findings are discussed in frame with reported data to propose a functional scenario in which minor CcmK3/K4 incorporation in shells would introduce sufficient local disorder as to allow shell remodeling necessary to adapt rapidly to environmental changes.
Metabolic Control of Viral Infection through PPAR-α Regulation of STING Signaling
Authors: Tao Lili , Lowe Alexandria , Wang Guoxun , Dozmorov Igor , Chang Tyron , Yan Nan , Reese Tiffany A. 
Published: August 2019

AbstractPeroxisomal proliferator activated receptors (PPARs) are sensors of dietary lipids and pharmacological targets in the treatment of metabolic disorders. PPAR ligands are also immunosuppressive. However, their function during infection is debated and the mechanisms that underlie their immunoregulatory properties are unclear. We investigated the consequences of PPAR activation during herpesvirus infection. We found that activation of PPAR-α increased herpesvirus replication, suppressed type I interferon production and induced reactive oxygen species (ROS). We discovered that ROS induced by PPAR-α stimulation suppressed the cytoplasmic DNA sensing pathway after direct activation of stimulator of interferon (STING), the ER adapter downstream of cytoplasmic DNA recognition. Although high ROS induces inflammasome activation and cytokine production, we found that ROS inhibited interferon production after cytoplasmic DNA recognition. Treatment of mice with a clinically relevant agonist of PPAR-α increased herpesvirus replication and pathogenesis, comparable to levels observed previously in type I interferon receptor knockout mice. These findings reveal that activation of PPAR-α regulates immunity to cytoplasmic DNA and DNA virus infection through inhibition of interferon. Moreover, these results demonstrate that STING signaling and interferon production is regulated by ROS.
Enhancement of corrosion protection of low nickel austenitic stainless steel by electroactive polyimide-CuO composites coating in chloride environment
Authors: Malav Jeetendra Kumar , Rathod Ramesh C. , Tandon Vipin , Patil Awanikumar P. 
Published: August 2019

Purpose
The purpose of this study is to improve the anticorrosion performance of low nickel stainless steel (AISI 201) in 3.5% NaCl by electroactive polyimide/copper oxide (EPI/CuO) composites coating.

Design/methodology/approach
Electroactive polyimide/copper oxide (EPI/CuO) composites were prepared by oxidative coupling polymerization followed by thermal imidization method.

Findings
The functional and structural properties of composites were characterized by X-ray diffraction, Fourier transmission infra-red and ultra violet-visible spectroscopy and the surface topography was characterized by field emission scanning electron microscope analysis and anticorrosion performance in 3.5 Wt.% NaCl was evaluated by electrochemical techniques. The obtained results of electrochemical techniques measurement indicated that the composites coated samples give better corrosion protection against attacking electrolyte.

Originality/value
The ever-increasing price of nickel (Ni) is driving the industries to use low-Ni austenitic stainless steels (ASSs). However, it exhibits relatively poor corrosion resistance as compared with conventional Cr-Ni ASSs. Nonetheless, its corrosion resistance can be enhanced by polymeric (electroactive polyimide [EPI]) coating. CuO particles exhibit the hydrophobic properties and can be used as inorganic filler to incorporate in EPI to further enhance the corrosion protection. The present research paper is beneficial for industries to use low-cost AISI 201, enhance its corrosion resistance and replace the use of costly conventional Cr-Ni ASSs.
Corrosion resistance of composite coating used for fastener protection
Authors: Lin Zhifeng , Xu Likun , Li Xiangbo , Wang Li , Guo Weimin , Wu Chuanjie , Yang Yi 
Published: August 2019

Purpose
The purpose of this paper is to examine the performance of a fastener composite coating system, sherardized (SD) coating/zinc-aluminum (ZA) coating whether it has good performance in marine environment.

Design/methodology/approach
In this paper, SD coating was fabricated on fastener surface by solid-diffusion method. ZA coating was fabricated by thermal sintering method. Corrosion behaviours of the composite coating were investigated with potentiodynamic polarization curves, open circuit potential and electrochemical impedance spectroscopy methods.

Findings
Neutral salt spray (NSS) and deep sea exposure tests revealed that the composite coating had excellent corrosion resistance. Polarization curve tests showed that corrosion current density of the sample with composite coating was significantly decreased, indicating an effective corrosion protection of the composite coating. OCP measurement of the sample in NaCl solution demonstrated that the composite coating had the best cathodic protection effect. The good corrosion resistance of the composite coating was obtained by the synergy of SD and ZA coating.

Practical implications
SD/ZA coating can be used in marine environment to prolong the life of carbon steel fastener.

Social implications
SD/ZA composite coating can reduce the risk and accident caused by failed fastener, avoid huge economic losses.

Originality/value
A new kind of composite coating was explored to protect the carbon steel fastener in marine environment. And the composite coating has the long-term anti-corrosion performance both in simulated and marine environment test.
Salt spray corrosion and electrochemical corrosion performances of Dacromet fabricated Zn–Al coating
Authors: Liu Xiaoxiao , Kong Dejun 
Published: August 2019

PurposeThis study aims to investigate the salt spray corrosion (SSC) and electrochemical corrosion of obtained Zn–Al coating, which provided a basis for comprehensive analysis of corrosion behavior of Zn–Al coating.Design/methodology/approachA Zn–Al coating was fabricated on Q235A steel using a Dacromet method. The SSC and electrochemical corrosion performances in 3.5 Wt.% NaCl solution were investigated using an SSC chamber and electrochemical workstation, respectively, and the corrosion mechanism of Zn–Al coating was discussed.FindingsThe Dacromet fabricated Zn–Al coating is primarily composed of Zn and Al phases, its residual stress of −11.1 ± 4 MPa is compressive stress, which is beneficial to improve its corrosion resistance. In the SSC process, the corrosion product of Zn5(OH)8Cl2H2O enhances the corrosion resistance of Zn–Al coating, which provides sufficient cathodic protection for the substrate. The corrosion potential of Zn–Al coating is lower than that of substrate, which provides sufficient cathodic protection to the substrate, the Zn–Al coating in the immersion periods is protected by the corrosion product and Zn–Al sheets.Originality/valueIn this study, a Zn–Al coating was first fabricated on Q235A steel using a Dacromet method.