bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small-scale soil microbial community heterogeneity linked to landforms on King George Island, maritime Antarctica
Authors: Zhang Yumin , Lu Lu , xChang Xulu , Jiang Fan , Gao Xiangdong , Peng Fang 
Published: April 2018

ABSTRACTWe analysed soil-borne microbial (bacterial, archaeal, and fungal) communities around the Fildes Region of King George Island, maritime Antarctica, which were divided into two groups according to soil elemental compositions and environmental attributes (soil chemical parameters and vegetation conditions) located in Holocene raised beach and Tertiary volcanic stratigraphy. Prokaryotic communities of the two groups were well separated; they predominantly correlated with soil elemental compositions, and were secondly correlated with environmental attributes (e.g., soil pH, total organic carbon,, and vegetation coverage; Pearson test,r= 0.59 vs. 0.52, bothP< 0.01). The relatively high abundance of P, S, Cl, and Br in Group 1 was likely due to landform uplift. Lithophile-elements (Si, Al, Ca, Sr, Ti, V, and Fe) correlated with prokaryotic communities in Group 2 may originate from weathering of Tertiary volcanic rock. The elements and nutrients accumulated during formation of different landforms influenced the development of soils, plant growth, and microbial communities, and resulted in small-scale spatially heterogeneous biological distributions. We propose that the geological evolution of the Fildes Region was crucial to its microbial community development.IMPORTANCEThis current study analyzed soil-borne microbial communities around the Fildes Region of King George Island, maritime Antarctica, which were divided into two groups according to soil elemental compositions and environmental attributes. We provide new evidence for the crucial influence of landforms on small-scale structures and spatial heterogeneity of soil microbial communities.
Bacillus cereusHS24 Suppresses Conidia Germination ofMagnaporthe oryzaeby Inhibiting the Ca2+Signaling Pathway
Authors: Huang Wenxiang , Liu Xingyu , Zhou Xiaosi , Chen Yu , Li Ye , Liu Hongxia 
Published: April 2018

AbstractRice yield is greatly reduced due to rice blast, a worldwide multi-cycle fungal disease caused by the ascomyceteMagnaporthe oryzae.Previously,Bacillus cereusHS24 was isolated from rice growing area, which showed a strong bio-control effect onM. oryzae.In order to better exploit it as a bio-control agent, HS24 has been studied for its mechanism of controlling rice blast. Our results showed that conidial germination ofM. oryzaewas significantly inhibited by HS24 suspension,nand the inhibition rate reached to 97.83% at the concentration of 10 CFU/ml. The transcriptional level ofCAMKII, PMC1andCCH1,which are key genes involved in Ca2+signaling pathway, were significantly decreased in HS24-treated conidia. The treatment ofM. oryzaewith Ca2+signaling pathway inhibitors KN-93, Verapamil, and cyclopiazonic acid (CPA) significantly reduced conidial germination rate and inhibited germ tube elongation. This inhibition effect was found to be concentration-dependent, similar to the HS24 treatment. By quantifying free Ca2+inM. oryzaeconidia, a significant reduction of intracellular free Ca2+concentration in HS24-treated conidia in comparison to sterile water-treated conidia was found. The addition of exogenous Ca2+did not abolish the inhibitory effect of HS24 on the reduction of intracellular free Ca2+concentration and conidial germination. In conclusion,B. cereusHS24 can inhibit conidial germination by suppressing Ca2+signaling inM. oryzae,and thus offers a great potential as a bio-control agent in rice blast management.ImportanceIn the bio-control of rice blast, most of researches focused on the inhibitory effect of bio-control agents on development ofM. oryzae, including inhibition of conidia germination, germ tube deformity, mycelium growth inhibition, etc, while little work has elucidated the molecular mechanisms underlying the various phenotypic change inM. oryzae.In order to better exploit HS24 as a potential bio-control agent, we studied the molecular mechanisms underlying the suppression ofB. cereusHS24 onM. oryzaeGuy11, and draw the conclusion that HS24 may inhibit conidia germination and germ tube elongation through inhibiting the Ca2+signaling pathway. In this study, we characterized the morphological and physiological changes ofM. oryzaewhen interacting withB. cereusHS24, and further investgated the responses ofM. oryzaeCa2+signallig pathway to HS24 treatment. Thus we have provided one more piece for theB. cereus/M. oryzaesupression puzzle at the molecular level.
Structural basis for relief of the sarcoplasmic reticulum Ca2+-ATPase inhibition by phospholamban at saturating Ca2+conditions
Authors: Gortari Eli Fernández-de , Michel Espinoza-Fonseca L. 
Published: April 2018

AbstractWe have performed extensive atomistic molecular dynamics simulations to probe the structural mechanism for relief of sarcoplasmic reticulum Ca2+-ATPase (SERCA) inhibition by phospholamban (PLB) at saturating Ca2+conditions. Reversal of SERCA-PLB inhibition by saturating Ca2+operates as a physiological rheostat to reactivate SERCA function in the absence of PLB phosphorylation. Simulation of the inhibitory complex at super-physiological Ca2+concentrations ([Ca2+]=10 mM) revealed that calcium ions interact primarily with SERCA and the lipid headgroups, but not with the cytosolic domain of PLB or the cytosolic side of the SERCA-PLB interface. At this [Ca2+], a single Ca2+ion is translocated from the cytosol to the transmembrane transport sites. We used this Ca2+-bound complex as an initial structure to simulate the effects of saturating Ca2+at physiological conditions ([Ca2+]total≈400 μM). At these conditions, ~30% of the Ca2+-bound complexes exhibit structural features that correspond to an inhibited state. However, in ~70% of the Ca2+-bound complexes, Ca2+moves to transport site I, recruits Glu771 and Asp800, and disrupts key inhibitory contacts involving conserved PLB residue Asn34. Structural analysis showed that Ca2+induces only local changes in interresidue inhibitory interactions, but does not induce dissociation, repositioning or changes in the structural dynamics of PLB. Upon relief of SERCA inhibition, Ca2+binding produces a productive site I configuration that is sufficient for subsequent SERCA activation. We propose that at saturating [Ca2+] and in the absence of PLB phosphorylation, binding of a single Ca2+ion in the transport sites rapidly shifts the equilibrium toward a non-inhibited SERCA-PLB complex.
CAGEfightR: Cap Analysis of Gene Expression (CAGE) in R/Bioconductor
Authors: Thodberg Malte , Thieffry Axel , Vitting-Seerup Kristoffer , Andersson Robin , Sandelin Albin 
Published: April 2018

AbstractWe developed the CAGEfightR R/Biconductor-package for analyzing CAGE data. CAGEfightR allows for fast and memory efficient identification of transcription start sites (TSSs) and predicted enhancers. Downstream analysis, including annotation, quantification, visualization and TSS shape statistics are implemented in easy-to-use functions. The package is freely available at https://bioconductor.org/packages/CAGEfightR
Lymphoid origin of intrinsically activated plasmacytoid dendritic cells in mice
Authors: Araujo Alessandra M. , Dekker Joseph D. , Garrison Kendra , Su Zhe , Rhee Catherine , Hu Zicheng , Lee Bum-Kyu , Osorio Hurtado Daniel , Lee Jiwon , Iyer Vishwanath R. , Ehrlich Lauren I. R. , Georgiou George , Ippolito Gregory C. , Yi S. Stephen , Tucker Haley O. 
Published: April 2018

AbstractWe identified a novel mouse plasmacytoid dendritic cell (pDC) lineage derived from the common lymphoid progenitors (CLPs) that is dependent on expression ofBcl11a. These CLP-derived pDCs, which we refer to as “B-pDCs”, have a unique gene expression profile that includes hallmark B cell genes, normally not expressed in conventional pDCs. Despite expressing most classical pDC markers such as SIGLEC-H and PDCA1, B-pDCs lack IFN-α secretion, exhibiting a distinct inflammatory profile. Functionally, B-pDCs induce T cell proliferation more robustly than canonical pDCs following Toll-like receptor 9 (TLR9) engagement. B-pDCs, along with another homogeneous subpopulation of myeloid derived pDCs, display elevated levels of the cell-surface receptor tyrosine kinase AXL, mirroring human AXL+transitional DCs in function and transcriptional profile. Murine B-pDCs therefore represent a phenotypically and functionally distinct CLP-derived DC lineage specialized in T cell activation and previously not described in mice.
Protective immunity induced by an intranasal multivalent vaccine comprising 10 Lactococcus lactis strains expressing highly prevalent M‐protein antigens derived from Group A Streptococcus
Authors: Wozniak Aniela , Scioscia Natalia , García Patricia C. , Dale James B. , Paillavil Braulio A. , Legarraga Paulette , Salazar‐Echegarai Francisco J. , Bueno Susan M. , Kalergis Alexis M. 
Published: April 2018

ABSTRACTStreptococcus pyogenes (group A Streptococcus) causes diseases ranging from mild pharyngitis to severe invasive infections. The N‐terminal fragment of streptococcal M protein elicits protective antibodies and is an attractive vaccine target. However, this N‐ terminal fragment is hypervariable: there are more than 200 different M types. In this study, an intranasal live bacterial vaccine comprising 10 strains of Lactococcus lactis, each expressing one N‐terminal fragment of M protein, has been developed. Live bacterial‐vectored vaccines cost less to manufacture because the processes involved are less complex than those required for production of protein subunit vaccines. Moreover, intranasal administration does not require syringes or specialized personnel. Evaluation of individual vaccine types (M1, M2, M3, M4, M6, M9, M12, M22, M28 and M77) showed that most of them protected mice against challenge with virulent S. pyogenes. All 10 strains combined in a 10‐valent vaccine (M×10) induced serum and bronchoalveolar lavage IgG titers that ranged from three‐ to 10‐fold those of unimmunized mice. After intranasal challenge with M28 streptococci, survival of M×10‐immunized mice was significantly higher than that of unimmunized mice. In contrast, when mice were challenged with M75 streptococci, survival of M×10‐immunized mice did not differ significantly from that of unimmunized mice. Mx‐10 immunized mice had significantly less S. pyogenes in oropharyngeal washes and developed less severe disease symptoms after challenge than did unimmunized mice. Our L. lactis‐based vaccine may provide an alternative solution to development of broadly protective group A streptococcal vaccines.
Association of the hypha‐related protein Pra1 and zinc transporter Zrt1 with biofilm formation by the pathogenic yeast Candida albicans
Authors: Kurakado Sanae , Arai Rika , Sugita Takashi 
Published: April 2018

ABSTRACTBloodstream infection by the pathogenic fungus Candida albicans is a major health problem. Candidemia is often associated with medical devices, which can act as substrates for biofilm development. Biofilm‐related infections are relatively difficult to treat because of their resistance to antimicrobial agents. It is therefore important to explore the mechanisms of biofilm formation. Dimorphism is a major contributor to biofilm formation in C. albicans. To determine whether the hypha‐related proteins Pra1 (pH‐regulated antigen) and Zrt1 (zinc transporter) are responsible for biofilm formation, the ability of pra1 and zrt1 deletion mutants to form biofilms was investigated. Biofilm formation by both deletion mutants was less than that of the wild‐type strain. Because Pra1 and Zrt1 are also related to the zinc homeostasis system, the effects of adding zinc on biofilm formation were also examined. Biofilm formation was increased in the presence of zinc. These data suggest that Pra1 and Zrt1 regulate biofilm formation through zinc homeostasis.
Transcytosis of Junonia coenia densovirus VP4 across the gut epithelium of Spodoptera frugiperda (Lepidoptera: Noctuidae)
Authors: Kemmerer Mariah , Bonning Bryony C. 
Published: April 2018

AbstractThe Junonia coenia densovirus rapidly traverses the gut epithelium of the host lepidopteran without replicating in the gut cells. The ability of this virus to transcytose across the gut epithelium is of interest for the potential use of virus structural proteins as delivery vehicles for insecticidal peptides that act within the insect hemocoel, rather than in the gut. In this study, we used fall armyworm, Spodoptera frugiperda to examine the binding of the virus to brush border membrane vesicle proteins by two‐dimensional ligand blot analysis. We also assessed the rate of flux of the primary viral structural protein, VP4 fused to eGFP with a proline‐rich linker (VP4‐P‐eGFP) through the gut epithelium ex vivo in an Ussing chamber. The mechanisms involved with transcytosis of VP4‐P‐eGFP were assessed by use of inhibitors. Bovine serum albumin (BSA) and eGFP were used as positive and negative control proteins, respectively. In contrast to BSA, which binds to multiple proteins on the brush border membrane, VP4‐P‐eGFP binding was specific to a protein of high molecular mass. Protein flux was significantly higher for VP4‐P‐eGFP after 2 h than for albumin or eGFP, with rapid transcytosis of VP4‐P‐eGFP within the first 30 min. In contrast to BSA which transcytosed following clathrin‐mediated endocytosis, the movement of VP4‐P‐eGFP was vesicle‐mediated but clathrin‐independent. The specificity of binding combined with the efficiency of transport across the gut epithelium suggest that VP4 will provide a useful carrier for insecticidal peptides active within the hemocoel of key lepidopteran pests including S. frugiperda.
dispRity: A modular R package for measuring disparity
Authors: Guillerme Thomas 
Published: April 2018

Abstract

Biological data is multivariate in essence: many traits in organisms covary with each other in space and time. This causes biologists to either reduce these to a manageable number of variables or, increasingly, to use multivariate toolkits. One such toolkit is based on creating a multidimensional space where the variables are the axes. It is then possible to measure diverse aspects of the distribution of some observation (e.g. species) in this space. For example, if studying morphology, one can create a morphospace for two groups of species, measure the volume occupied by each of these groups and then test whether these two volumes are significantly different or not.

There are as many definitions of these multidimensional spaces, metrics and tests as there are questions that can be tackled with such methods. Many of these methods are implemented in specific software or r packages. However, the definition of the space, metric and test is often dependent on the software/package and authors points of view or specific questions. This can unfortunately hamper researchers’ ability to apply different methods that best suits their specific questions.

Here I present the dispRity package, a flexible R package for performing multidimensional analysis. It allows users to define each step of the analysis (whether it is the space, the metric or the test) through a highly modular architecture where each definition can be passed as a function. It also provides a tidy interface through the dispRity object, allowing users to easily run reproducible multivariate analysis.

The dispRity package also comes with an extend manual regularly updated following users’ questions or suggestions. Furthermore, the package contains some simulation tools (e.g to simulate complex multidimensional space or morphological data). Finally, it also contains a suite of utility functions to work with dispRity objects aimed at helping users to develop their own multidimensional metrics and/or tests.
Physiological role of Kvβ2 (AKR6) in murine skeletal muscle growth and regulation
Authors: Chapalamadugu K. C. , Tur J. , Badole S. L. , Kukreja R. C. , Brotto M. , Tipparaju S. M. 
Published: April 2018

AbstractAimPotassium channel accessory subunits (Kvβ) play a key role in cardiac electrical activity through ion channel modulation. In this study, we hypothesize that Kvβ2 regulates skeletal muscle growth and fibre phenotype via protein‐protein interactions.MethodsKvβ2 knockout mouse model was used for morphometric, immunohistochemical and biochemical analysis to evaluate the role of Kvβ2 in skeletal muscle physiology.ResultsDeletion of Kvβ2 gene in mice (Kvβ2 knockout, KO) leads to significant decrease in body weight along with skeletal muscle size. Key hindlimb muscles such as biceps, soleus and gastrocnemius were significantly smaller in size in KO mice compared to that of wild type. Morphometric measurements and histological analysis clearly point that the fibre size is decreased in each of the muscle type in KO compared with wild‐type mice. In addition, Kvβ2 deletion contributes to fibre‐type switching from fast to slow fibre as indicated by more abundant MHCI‐expressing fibres in gastrocnemius and soleus muscles, which may underscore the smaller muscle size alongside increase in U3 ubiquitin ligase; NEDD4 expression. Using targeted siRNA knockdown approach, we identified that Kvβ2 knockdown does not affect the myoblasts proliferation. However, Pax7 expression was significantly decreased in 4‐week‐old gastrocnemius muscle, suggesting that cellular reserve for growth may be deficient in KO mice. This is further supported by decreased migratory capacity of C2C12 cells upon siRNA‐targeted Kvβ2 knockdown.ConclusionOverall, this is the first report identifying that genetic deletion of Kvβ2 leads to decreased skeletal muscle size along with isotype switching.
Genotype‐guided warfarin dosing vs. conventional dosing strategies: a systematic review and meta‐analysis of randomized controlled trials
Authors: Tse Gary , Gong Mengqi , Li Guangping , Wong Sunny Hei , Wu William K. K. , Wong Wing Tak , Roever Leonardo , Lee Alex Pui Wai , Lip Gregory Y. H. , Wong Martin C. S. , Liu Tong ,   International Health Informatics Study (IHIS) Network
Published: April 2018

AimsPrevious trials on the effectiveness of genotype‐guided warfarin dosing vs. conventional dosing have been inconclusive. We conducted a systematic review and meta‐analysis of randomized trials comparing genotype‐guided to conventional dosing strategies.MethodsPubMed and the Cochrane Library were searched up to 23 October 2017.ResultsA total of 76 and 94 entries were retrieved were retrieved from PubMed and the Cochrane Library, respectively. A total of 2626 subjects in the genotype‐guided dosing (mean age 63.3 ± 5.8 years; 46% male) and 2604 subjects in the conventional dosing (mean age 64.7 ± 6.1 years; 46% male) groups (mean follow‐up duration 64 days) from 18 trials were included. Compared with conventional dosing, genotype‐guided dosing significantly shortened the time to first therapeutic international normalized ratio (INR) (mean difference 2.6 days, standard error 0.3 days; P < 0.0001; I2 0%) and time to first stable INR (mean difference 5.9 days, standard error 2.0 days; P < 0.01; I2 94%). Genotype‐guided dosing also increased the time in therapeutic range (mean difference 3.1%, standard error 1.2%; P < 0.01; I2 80%) and reduced the risks of both excessive anticoagulation, defined as INR ≥4 [risk ratio (RR) 0.87; 95% confidence interval (CI) 0.78, 0.98; P < 0.05; I2: 0%), and bleeding (RR 0.82; 95% CI 0.69, 0.98; P < 0.05; I2 31%). No difference in thromboembolism (RR 0.84; 95% CI 0.56, 1.26; P = 0.40; I2 0%) or mortality (RR 1.16; 95% CI 0.46, 2.91; P = 0.76; I2 0%) was observed between the two groups.ConclusionsGenotype‐guided warfarin dosing offers better safety with less bleeding compared with conventional dosing strategies. No significant benefit on thromboembolism or mortality was evident.
New insights on the functional role of URG7 in the cellular response to ER stress
Authors: Armentano Maria Francesca , Caterino Marianna , Miglionico Rocchina , Ostuni Angela , Pace Maria Carmela , Cozzolino Flora , Monti Maria , Milella Luigi , Carmosino Monica , Pucci Piero , Bisaccia Faustino 
Published: April 2018

Background informationUp‐regulated Gene clone 7 (URG7) is an ER resident protein, whose expression is up‐regulated in the presence of hepatitis B virus X antigen (HBxAg) during HBV infection. In virus‐infected hepatocytes, URG7 shows an anti‐apoptotic activity due to the PI3K/AKT signalling activation, does not seem to have tumorigenic properties, but it appears to promote the development and progression of fibrosis. However, the molecular mechanisms underlying URG7 activity remain largely unknown.ResultsTo shed light on URG7 activity, we first analysed its interactome in HepG2 transfected cells: this analysis suggests that URG7 could have a role in affecting protein synthesis, folding and promoting proteins degradation. Moreover, keeping into account its subcellular localisation in the ER and that several viral infections give rise to ER stress, a panel of experiments was performed to evaluate a putative role of URG7 in ER stress. Our main results demonstrate that in ER‐stressed cells URG7 is able to modulate the expression of Unfolded Protein Response (UPR) markers towards survival outcomes, up‐regulating GRP78 protein and down‐regulating the pro‐apoptotic protein CHOP. Furthermore, URG7 reduces the ER stress by decreasing the amount of unfolded proteins, by increasing both the total protein ubiquitination and the AKT activation and reducing Caspase 3 activation.ConclusionsAll together these data suggest that URG7 plays a pivotal role as a reliever of ER stress‐induced apoptosis.SignificanceThis is the first characterisation of URG7 activity under ER stress conditions. The results presented here will help to hypothesise new strategies to counteract the antiapoptotic activity of URG7 in the context of the viral infection.
GM-CSF and IL-4 are not involved in IVIG-mediated amelioration of ITP in mice: a role for IL-11 cannot be ruled out
Authors: Lewis B J B , Leontyev D , Neschadim A , Blacquiere M , Branch D R 
Published: April 2018

SummaryPreviously, we have reported that interleukin (IL)-4, granulocyte–macrophage colony-stimulating factor (GM-CSF), and IL-11, but not IL-33, are up-regulated in two strains of mice with immune thrombocytopenia (ITP) that are responsive to intravenous immunoglobulin (IVIg) treatment. Previously, IL-4 was ruled out in the mechanism of IVIg; however, other publications have suggested this cytokine as a major player in the mechanism of IVIg action. Thus, we sought to further investigate a role for IL-4 and, in addition, GM-CSF and IL-11 in the mechanism of action of IVIg using a murine model of ITP. A passive platelet antibody model was used to generate ITP in IL-4 receptor knock-out (IL-4R–/–), IL-11 receptor knock-out (IL-11Rα–/–) and GM-CSF knock-out (Csf2–/–) mice. We also used a neutralizing antibody to IL-11 and recombinant human IL-11 (rhIL-11) in addition to depleting basophils in vivo to study the effect of IVIg to ameliorate ITP. Our results showed that basophils, IL-4 and GM-CSF were unimportant in both ITP induction and its amelioration by IVIg. The role of IL-11 in these processes was less clear. Even though IL-11Rα–/– mice with ITP responded to IVIg similarly to wild-type (WT) mice, treatment of ITP WT mice with rhIL-11 instead of IVIg showed an increase in platelet numbers and WT mice administered anti-IL-11 showed a significant reduction in the ability of IVIg to ameliorate the ITP. Our findings indicate that neither IL-4, basophils or GM-CSF have roles in IVIg amelioration of ITP; however, a role for IL-11 requires further study.