Heterotrophic nitrification and aerobic denitrification by a novel Halomonas campisalis

A novel halophilic strain that could carry out heterotrophic nitrification and aerobic denitrification was isolated and named as Halomonas campisalis ha3. It removed inorganic nitrogen compounds (e.g. NO₃ ^?, NO₂ ^? and NH₄ ⁺) simultaneously, and grew well in the medium containing up to 20 % (w/v) NaCl. PCR revealed four genes in the genome of ha3 related to aerobic denitrification: napA, nirS, norB and nosZ. The optimal conditions for aerobic denitrification were pH 9.0, at 37 °C, with 4 % (w/v) NaCl and sodium succinate as carbon source. The nitrogen removal rate was 87.5 mg NO₃ ^?–N l^?1 h^?1. Therefore, this strain is a potential aerobic denitrifier for the treatment of saline wastewater.     

Isolation and characterization of two cDNAs encoding translation initiation factor 1A from rice(Oryza sativa L.).

The eukaryotic initiation factor 1A(eIF1A) is essential for transferring of the initiator Met-tRNA to 40S ribosomal subunits to form the 40S pre-initiation complex. In present study, we describe the cloning and characterization of two eIF1A genes from rice, which were designated as Oryza sativa eukaryotic initiation factor 1A genes OseIF1A-1, OseIF1A-2, respectively. Both rice elF1As shared high identities in amino acids with eIF1A proteins from other eukaryotes. The mRNA expression analysis revealed that OseIF1A-2 mRNA was much more accumulated than OseIF1A-1 in all tissues but each gene is expressed in root, stem, leaf and flowering spike in high and nearly equal level, and in immature spike in lower level. These results, together with their different location in unrooted phylogenetic tree inferred from amino acid sequences of all known eIF1As, suggested that there are two types of eIF1A genes with different function or different regulation in rice.     

FLAGS: A Flexible and Adaptive Association Test for Gene Sets Using Summary Statistics

Genome-wide association studies (GWAS) have been widely used for identifying common variants associated with complex diseases. Despite remarkable success in uncovering many risk variants and providing novel insights into disease biology, genetic variants identified to date fail to explain the vast majority of the heritability for most complex diseases. One explanation is that there are still a large number of common variants that remain to be discovered, but their effect sizes are generally too small to be detected individually. Accordingly, gene set analysis of GWAS, which examines a group of functionally related genes, has been proposed as a complementary approach to single-marker analysis. Here, we propose a flexible and adaptive test for gene sets (FLAGS), using summary statistics. Extensive simulations showed that this method has an appropriate type I error rate and outperforms existing methods with increased power. As a proof of principle, through real data analyses of Crohn’s disease GWAS data and bipolar disorder GWAS meta-analysis results, we demonstrated the superior performance of FLAGS over several state-of-the-art association tests for gene sets. Our method allows for the more powerful application of gene set analysis to complex diseases, which will have broad use given that GWAS summary results are increasingly publicly available.     

The hierarchy of structural transitions induced in cytochrome c by anionic phospholipids determines its peroxidase activation and selective peroxidation during apoptosis in cells

Activation of peroxidase catalytic function of cytochrome c (cyt c) by anionic lipids is associated with destabilization of its tertiary structure. We studied effects of several anionic phospholipids on the protein structure by monitoring (1) Trp59 fluorescence, (2) Fe-S(Met80) absorbance at 695 nm, and (3) EPR of heme nitrosylation. Peroxidase activity was probed using several substrates and protein-derived radicals. Peroxidase activation of cyt c did not require complete protein unfolding or breakage of the Fe-S(Met80) bond. The activation energy of cyt c peroxidase changed in parallel with stability energies of structural regions of the protein probed spectroscopically. Cardiolipin (CL) and phosphatidic acid (PA) were most effective in inducing cyt c peroxidase activity. Phosphatidylserine (PS) and phosphatidylinositol bisphosphate (PIP2) displayed a significant but much weaker capacity to destabilize the protein and induce peroxidase activity. Phosphatidylinositol trisphosphate (PIP3) appeared to be a stronger inducer of cyt c structural changes than PIP2, indicating a role for the negatively charged extra phosphate group. Comparison of cyt c-deficient HeLa cells and mouse embryonic cells with those expressing a full complement of cyt c demonstrated the involvement of cyt c peroxidase activity in selective catalysis of peroxidation of CL, PS, and PI, which corresponded to the potency of these lipids in inducing cyt c's structural destabilization.     

Image Recognition of Breast Tumor Proliferation Level Based on Convolution Neural Network

Pathological slide is increasingly applied in the diagnosis of breast tumors despite the issues of large amount of data, slow viewing and high subjectivity. To overcome these problems, a micrograph recognition method based on convolutional neural network is proposed for pathological slide of breast tumor. Combined with multi-channel threshold and watershed segmentation, a sample database including single cell, adhesive cell and invalid cell was established. Then, the convolution neural network with six layers is constructed, which has ability to classify the stained breast tumor cells with accuracy of more than 90%, and evaluate the proliferation level with relative error of less than 5%. The experimental result indicates the effectiveness of this approach, and is useful for providing an objective basis for evaluating the malignancy of breast tumors.     

Cytochrome c/cardiolipin relations in mitochondria: a kiss of death

Recently, phospholipid peroxidation products gained a reputation as key regulatory molecules and participants in oxidative signaling pathways. During apoptosis, a mitochondria-specific phospholipid, cardiolipin (CL), interacts with cytochrome c (cyt c) to form a peroxidase complex that catalyzes CL oxidation; this process plays a pivotal role in the mitochondrial stage of the execution of the cell death program. This review is focused on redox mechanisms and essential structural features of cyt c’s conversion into a CL-specific peroxidase that represent an interesting and maybe still unique example of a functionally significant ligand change in hemoproteins. Furthermore, specific characteristics of CL in mitochondria—its asymmetric transmembrane distribution and mechanisms of collapse, the regulation of its synthesis, remodeling, and fatty acid composition—are given significant consideration. Finally, new concepts in drug discovery based on the design of mitochondria-targeted inhibitors of cyt c/CL peroxidase and CL peroxidation with antiapoptotic effects are presented.     

Protein Microarray Characterization of the S-Nitrosoproteome

Nitric oxide (NO) mediates a substantial part of its physiologic functions via S-nitrosylation, however the cellular substrates for NO-mediated S-nitrosylation are largely unknown. Here we describe the S-nitrosoproteome using a high-density protein microarray chip containing 16,368 unique human proteins. We identified 834 potentially S-nitrosylated human proteins. Using a unique and highly specific labeling and affinity capture of S-nitrosylated proteins, 138 cysteine residues on 131 peptides in 95 proteins were determined, defining critical sites of NO''s actions. Of these cysteine residues 113 are novel sites of S-nitrosylation. A consensus sequence motif from these 834 proteins for S-nitrosylation was identified, suggesting that the residues flanking the S-nitrosylated cysteine are likely to be the critical determinant of whether the cysteine is S-nitrosylated. We identify eight ubiquitin E3 ligases, RNF10, RNF11, RNF41, RNF141, RNF181, RNF208, WWP2, and UBE3A, whose activities are modulated by S-nitrosylation, providing a unique regulatory mechanism of the ubiquitin proteasome system. These results define a new and extensive set of proteins that are susceptible to NO regulation via S-nitrosylation. Similar approaches could be used to identify other post-translational modification proteomes.It is known that NO regulates the majority of its physiologic function through S-nitrosylation (1). Protein-assisted or small molecule, S-nitrosoglutathione (GSNO)¹ trans-nitrosylation, oxidative S-nitrosation, and metalloprotein-catalyzed S-nitrosylation are the prominent cellular mechanisms that are utilized to S-nitrosylate proteins (2). A number of proteins are known to be S-nitrosylated and this post-translational modification can either activate or inactivate a protein''s biologic activity (1, 3). A number of attempts at probing tissue-specific S-nitrosoproteomes have been made, but the results of these are limited to proteins that are S-nitrosylated to a great degree and which are present at high concentrations (2, 4–6). Recently, to investigate determinants of S-nitrosylation, yeast and human target protein microarrays have been studied. However, these assay were limited because of the small number of proteins present on the chip (7). In addition, many proteins that are known to be S-nitrosylated have been studied through a targeted and biased approach (8). To overcome these shortcomings, we report the use of a 16,368 human protein microarray chip to better define the human S-nitrosoproteome.Ubiquitin is a 76-amino-acid long polypeptide that can be covalently added to lysine residues on targeted proteins either as single monomers or in chains. Ubiquitination of proteins can dramatically alter their function or localization depending on the number of ubiquitin attached and the nature of their linkages. The most well characterized ubiquitin-mediated process is targeting of the protein for degradation by the 26S proteasome, which occurs via poly-ubiquitination linked together through lysine 48 on the ubiquitin monomers. Ubiquitination occurs in a three-step enzymatic process in which the third enzyme, the ubiquitin protein ligase (E3) determines protein target specificity (9). NO S-nitrosylates the RING finger E3 ligases, parkin and XIAP, modifying their function (10, 11). In the case of parkin, S-nitrosylation transiently activates its E3 ligase activity, but ultimately inhibits its activity (12). In contrast, XIAP''s E3 ligase activity is unaffected by S-nitrosylation, but its anti-apoptotic function is compromised (11). Using the 16,368 human protein microarray, we identify a number of NO-regulated E3 ligases, the majority of which are activated by NO-dependent S-nitrosylation.     

Aerobic and anaerobic methanotrophic communities in urban landscape wetland

Applied Microbiology and Biotechnology - Both aerobic methane-oxidizing bacteria (MOB) and nitrite-dependent anaerobic methane oxidation (n-damo) organisms can be important methane sinks in a...     

Genome sequence and annotation of <Emphasis Type="Italic">Sporolactobacillus pectinivorans</Emphasis> GD201205 <Superscript>T</Superscript>, a lactic acid-producing bacterium

The novel species Sporolactobacillus pectinivorans GD201205^T can produce lactic acid and aromatic compounds such as isoamyl acetate and phenethyl acetate. To characterize this strain, we sequenced the whole genome of S. pectinivorans GD201205^T and determined that it contains a 3,926,837-bp chromosome with a GC content of 44.27%, 4320 genes, 64 tRNAs, 14 rRNAs, and four sRNAs. The identification of the gene sequence of S. pectinivorans GD201205^T provides a basis for understanding its molecular genetics and features, which in turn will facilitate its potential application as a starter culture in the food processing industry.     

Identification of the avian infectious bronchitis coronaviruses with mutations in gene 3

The sequence of a 6.0-kb fragment was compared in the 3'-encoding region of the genome in 27 infectious bronchitis virus (IBV) strains. All these strains have the same S-3-M-5-N gene order, as is the case for other IBVs. However, the sizes of the corresponding open reading frames (ORFs) of some genes varied among the virus strains. Phylogenetic analysis and sequence alignments demonstrated that recombination events had occurred in the origin and evolution of the strains CK/CH/LSD/03I and CK/CH/LLN/98I and the possible recombinant junction sites might be located at the 3c and M genes, respectively. The normal product of ORF 3a is 57 amino acids long, whereas a 43-bp deletion at the 3'-end of the CK/CH/LSD/03I 3a gene was detected, resulting in a frameshift event and C-terminally truncated protein with 47 amino acids. Comparison of the growth ability in embryos and replication and pathogenicity in chickens with IBV carrying the normal 3a gene indicated that this deleted sequence in the 3a gene of CK/CH/LSD/03I was not necessary for viral pathogenesis and replication either in vitro or in vivo. Occurrence of a mutation at the corresponding position of the CK/CH/LLN/98I start codon in the 3a gene led to the absence of ORF 3a in this virus, resulting in a novel genomic organization at the 3'-encoding regions: S-3b, 3c-M-5a, 5b-N. Comparison with other viruses carrying the normal 3a gene revealed that CK/CH/LLN/98I had replication and pathogenicity abilities in vivo similar to those of other IBVs; however, its growth ability in embryos was lower, although the relationship between the lower growth ability and the ORF 3a defect requires further confirmation.