Geodermatophilus nigrescens sp. nov., isolated from a dry-hot valley

A novel actinomycete, designated as strain YIM 75980^T, was isolated from a soil sample collected from a dry-hot river valley in Dongchuan county, Yunnan province, south-west China and was subjected to polyphasic taxonomic characterization. The organism produced circular, smooth, red to black coloured colonies comprising coccoid-shaped cells. Colonies on agar medium lacked mycelia and cells adhered to the agar. Strain YIM 75980^T contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan and contained galactose, arabinose and glucosamine as the main sugars in the whole-cell hydrolysates. The predominant menaquinone was MK-9 (H₄) and the major fatty acids were iso-C_15:0, iso-C_16:0 and C_16:0. The DNA G + C content of strain YIM 75980^T was 73.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences clearly showed that strain YIM 75980^T formed a distinct clade within the genus Geodermatophilus and was closely related to Geodermatophilus obscurus DSM 43160^T (level of similarity, 97.9%). Furthermore, the result of DNA–DNA hybridization between strain YIM 75980^T and G. obscurus 43160^T demonstrated that this isolate represented a different genomic species in the genus Geodermatophilus. Moreover, the physiological and biochemical data showed the differentiation of strain YIM 75980^T from its closest phylogenetic neighbour. Therefore, it is proposed that strain YIM 75980^T represents a novel species of the genus Geodermatophilus, for which the name Geodermatophilus nigrescens sp. nov. is proposed. The type strain is YIM 75980^T (=CCTCC AA 2011015^T =JCM 18056^T).     

CD38 is a key enzyme for the survival of mouse microglial BV2 cells

CD38 is a multifunctional enzyme that can not only generate cyclic adenosine diphosphate-ribose (cADPR) - a key Ca(2+) -mobilizing second messenger - by consuming NAD(+), but also hydrolyze extracellular NAD(+). There have been only a small number of studies on the functions of CD38 in the CNS. Brain inflammation plays critical roles in ischemic brain injury and multiple other neurological diseases, in which microglia activation is a key event. In this study we determined the roles of CD38 in the basal survival of mouse BV2 microglia cells by applying CD38 siRNA. Our study found that silencing of CD38 led to significantly decreased survival of the cells. We also found that decreased CD38 levels can lead to apoptosis of the microglial cells, as assessed by flow cytometry-based Annexin V/7-AAD assay, caspase-3 immunostaining and Hoechst staining assays. Our study has further indicated that the CD38 silencing-induced apoptosis is mainly caspase 3-dependent. Collectively, our study has provided the first evidence suggesting that CD38 plays a critical role in the basal survival of microglia, and decreased CD38 can lead to caspase 3-dependent apoptosis of the cells. These results suggest that CD38 may become a therapeutic target for modulating microglial survival in neurological diseases.     

Properties and functions of KATP during mouse perinatal development

BackgroundPrevailing data suggest that ATP-sensitive potassium channels (K_ATP) contribute to a surprising resistance to hypoxia in mammalian embryos, thus we aimed to characterize the developmental changes of K_ATP channels in murine fetal ventricular cardiomyocytes.MethodsPatch clamp was applied to investigate the functions of K_ATP. RT-PCR, Western blot were used to further characterize the molecular properties of K_ATP channels.ResultsSimilar K_ATP current density was detected in ventricular cardiomyocytes of late development stage (LDS) and early development stage (EDS). Molecular–biological study revealed the upregulation of Kir6.1/SUR2A in membrane and Kir6.2 remained constant during development. Kir6.1, Kir6.2, and SUR1 were detectable in the mitochondria without marked difference between EDS and LDS. Acute hypoxia–ischemia led to cessation of APs in 62.5% of tested EDS cells and no APs cessation was observed in LDS cells. SarcK_ATP blocker glibenclamide rescued 47% of EDS cells but converted 42.8% of LDS cells to APs cessations under hypoxia-ischemic condition. MitoK_ATP blocker 5-HD did not significantly influence the response to acute hypoxia–ischemia at either EDS or LDS. In summary, sarcK_ATP played distinct functional roles under acute hypoxia-ischemic condition in EDS and LDS fetal ventricular cardiomyocytes, with developmental changes in sarcK_ATP subunits. MitoK_ATP were not significantly involved in the response of fetal cardiomyocytes to acute hypoxia–ischemia and no developmental changes of K_ATP subunits were found in mitochondria.     

Dual Recruitment of Cdc48 (p97)-Ufd1-Npl4 Ubiquitin-selective Segregase by Small Ubiquitin-like Modifier Protein (SUMO) and Ubiquitin in SUMO-targeted Ubiquitin Ligase-mediated Genome Stability Functions

Protein modification by SUMO and ubiquitin critically impacts genome stability via effectors that "read" their signals using SUMO interaction motifs or ubiquitin binding domains, respectively. A novel mixed SUMO and ubiquitin signal is generated by the SUMO-targeted ubiquitin ligase (STUbL), which ubiquitylates SUMO conjugates. Herein, we determine that the "ubiquitin-selective" segregase Cdc48-Ufd1-Npl4 also binds SUMO via a SUMO interaction motif in Ufd1 and can thus act as a selective receptor for STUbL targets. Indeed, we define key cooperative DNA repair functions for Cdc48-Ufd1-Npl4 and STUbL, thereby revealing a new signaling mechanism involving dual recruitment by SUMO and ubiquitin for Cdc48-Ufd1-Npl4 functions in maintaining genome stability.     

Rearrangement of Actin Cytoskeleton by Zika Virus Infection Facilitates Blood–Testis Barrier Hyperpermeability

In recent years, various serious diseases caused by Zika virus (ZIKV) have made it impossible to be ignored. Confirmed existence of ZIKV in semen and sexually transmission of ZIKV suggested that it can break the blood–testis barrier (BTB), or Sertoli cell barrier (SCB). However, little is known about the underlying mechanism. In this study, interaction between actin, an important component of the SCB, and ZIKV envelope (E) protein domain III (EDIII) was inferred from co-immunoprecipitation (Co-IP) liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis. Confocal microscopy confirmed the role of actin filaments (F-actin) in ZIKV infection, during which part of the stress fibers, the bundles that constituted by paralleled actin filaments, were disrupted and presented in the cell periphery. Colocalization of E and reorganized actin filaments in the cell periphery of transfected Sertoli cells suggests a participation of ZIKV E protein in ZIKV-induced F-actin rearrangement. Perturbation of F-actin by cytochalasin D (CytoD) or Jasplakinolide (Jas) enhanced the infection of ZIKV. More importantly, the transepithelial electrical resistance (TEER) of an in vitro mouse SCB (mSCB) model declined with the progression of ZIKV infection or overexpression of E protein. Co-IP and confocal microscopy analyses revealed that the interaction between F-actin and tight junction protein ZO-1 was reduced after ZIKV infection or E protein overexpression, highlighting the role of E protein in ZIKV-induced disruption of the BTB. We conclude that the interaction between ZIKV E and F-actin leads to the reorganization of F-actin network, thereby compromising BTB integrity.     

Selection for the compactness of highly expressed genes in <Emphasis Type="Italic">Gallus gallus</Emphasis>

Background  

Coding sequence (CDS) length, gene size, and intron length vary within a genome and among genomes. Previous studies in diverse organisms, including human, D. Melanogaster, C. elegans, S. cerevisiae, and Arabidopsis thaliana, indicated that there are negative relationships between expression level and gene size, CDS length as well as intron length. Different models such as selection for economy model, genomic design model, and mutational bias hypotheses have been proposed to explain such observation. The debate of which model is a superior one to explain the observation has not been settled down. The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates. As D. Melanogaster, chicken has a larger effective population size, selection for chicken genome is expected to be more effective in increasing protein synthesis efficiency. Therefore, in this study the chicken was used as a model organism to elucidate the interaction between gene features and expression pattern upon selection pressure.     

Ultrasensitive Responses and Specificity in Cell Signaling

Background  

Interconnected cell signaling pathways are able to efficiently and accurately transmit a multitude of different signals, despite an inherent potential for undesirable levels of cross-talk. To ensure that an appropriate response is produced, biological systems have evolved network-level mechanisms that insulate pathways from crosstalk and prevent 'leaking' or 'spillover' between pathways. Many signaling pathways have been shown to respond in an ultrasensitive (switch-like) fashion to graded input, and this behavior may influence specificity. The relationship of ultrasensitivity to signaling specificity has not been extensively explored.     

Smad Ubiquitylation Regulatory Factor 1/2 (Smurf1/2) Promotes p53 Degradation by Stabilizing the E3 Ligase MDM2

The tumor suppressor p53 protein is tightly regulated by a ubiquitin-proteasomal degradation mechanism. Several E3 ubiquitin ligases, including MDM2 (mouse double minute 2), have been reported to play an essential role in the regulation of p53 stability. However, it remains unclear how the activity of these E3 ligases is regulated. Here, we show that the HECT-type E3 ligase Smurf1/2 (Smad ubiquitylation regulatory factor 1/2) promotes p53 degradation by enhancing the activity of the E3 ligase MDM2. We provide evidence that the role of Smurf1/2 on the p53 stability is not dependent on the E3 activity of Smurf1/2 but rather is dependent on the activity of MDM2. We find that Smurf1/2 stabilizes MDM2 by enhancing the heterodimerization of MDM2 with MDMX, during which Smurf1/2 interacts with MDM2 and MDMX. We finally provide evidence that Smurf1/2 regulates apoptosis through p53. To our knowledge, this is the first report to demonstrate that Smurf1/2 functions as a factor to stabilize MDM2 protein rather than as a direct E3 ligase in regulation of p53 degradation.     

Synergistic effects in the designs of neuraminidase ligands: Analysis from docking and molecular dynamics studies

Docking and molecular dynamics were used to study the nine ligands (see Scheme 1) at the neuraminidase (NA) active sites. Their binding modes are structurally and energetically different, with details given in the text. Compared with 1A (oseltamivir carboxylate), the changes of core template or/and functional groups in the other ligands cause the reductions of interaction energies and numbers of H-bonds with the NA proteins. Nonetheless, all these ligands occupy the proximity space at the NA active sites and share some commonness in their binding modes. The fragment approach was then used to analyze and understand the binding specificities of the nine ligands. The contributions of each core template and functional group were evaluated. It was found that the core templates rather than functional groups play a larger role during the binding processes; in addition, the binding qualities are determined by the synergistic effects of the core templates and functional groups. Among the nine ligands, 1A (oseltamivir carboxylate) has the largest synergistic energy and its functional groups fit perfectly with the NA active site, consistent with the largest interaction energy, numerous H-bonds with the NA active-site residues as well as experimentally lowest IC₅₀ value. Owing to the poorer metabolizability than oseltamivir, large contribution of the benzene core template and fine synergistic effects of the functional groups, the 4-(N-acetylamino)-5-guanidino-3-(3-pentyloxy)benzoic acid should be an ideal lead compound for optimizing NA drugs.     

Associations of <Emphasis Type="Italic">GHSR</Emphasis> gene polymorphisms with chicken growth and carcass traits

Ghrelin receptor (GHSR), or growth hormone secretagogue receptor, modulates many physiological effects by binding to its ligand and therefore is a candidate gene for chicken production performance. In this study, five polymorphisms (four SNP and a ‘GGTACA’ indel) of GHSR gene were genotyped in a F₂ full sib chicken population to investigate their associations with production traits. Results showed that c.739 + 726T > C (M2) was significantly associated with body weight (BW) at 28 days (BW28), BW90, dressed weight, eviscerated weight, eviscerated weight with giblet, breast muscle weight and leg muscle weight (P < 0.05). Meanwhile, T allele rather than C was positive for chicken body weight gain as individuals with CC had the lowest value of all traits. Otherwise, no significant association of c.264G > A (M1), c.3211-196_3211-181delGGTACA (M3), c.3211 + 75C > T (M4), and c.3211 + 150C > T (M5) with any growth and carcass traits was found. Haplotypes based on five polymorphisms were significantly associated with hatch weight, BW7, BW14, BW21 and breast angle (P < 0.05), as well as BW28 (P < 0.01). Therefore, it was concluded that M2 of the GHSR gene and the analyzed haplotypes were associated with some chicken growth and carcass traits.