Characteristics of rapidly formed hydrogen-producing granules and biofilms

The physicochemical and microbiological characteristics of rapidly formed hydrogen-producing granules and biofilms were evaluated in the present study. Microbial species composition was examined using the 16S rDNA-based separation and sequencing techniques, and spatial distribution and internal structure of microbial components were evaluated by examining the confocal laser scanning microscope (CLSM) images. Phylogenetic analysis indicated that a pure culture of Clostridium pasteurianum-like bacterium (98% similarity) was found in microbial community of granules and biofilms. It is postulated that containing such a species favored the rapid immobilization of hydrogen-producing culture. Manure granules and biofilms secreted 24-35 mg extracellulous proteins and 142-175 mg extracellulous polysaccharides in each gram of culture (in VSS). Such a high productivity of extracellulous polymers (ECP), a bio-glue to facilitate cell-to-cell and/or cell-to-substratum interaction, may work as the driving forces for the immobilization of C. pasteurianum. As abundant proteins were noted in the granule cores, it can be derived that rapid formation of the hydrogen-producing granules could be due to the establishment of precursor protein-rich microbial nuclei.     

Testicular expression and distribution of the rat bcl2 modifying factor in response to reduced intratesticular testosterone

The Bcl2 modifying factor (Bmf) is a pro-apoptotic member of the Bcl2 family of apoptosis-related proteins that has been shown to initiate apoptosis in response to the loss of attachment of cells from their basal lamina (anoikis). Experimental reduction in intratesticular testosterone concentration brings about the death of spermatids as a consequence of their sloughing from Sertoli cells. Given the role of Bmf in anoikis in other systems, we hypothesized that Bmf would be expressed in germ cells and that its expression and normal distribution might be altered under conditions that induce widespread germ cell loss. To test these hypotheses, we demonstrated that Bmf indeed is expressed in the testis and cloned the full-length rat Bmf cDNA. Immunohistochemistry revealed that Bmf is present in the subacrosomal space of postmeiotic spermatids from step 4 to 16 of spermiogenesis. To test the hypothesis that Bmf expression and distribution are altered by conditions that elicit anoikis, intratesticular testosterone was reduced by implanting Silastic capsules containing testosterone and estradiol into adult rats for 8 weeks. As hypothesized, this resulted in a significant change in Bmf distribution relative to untreated animals. In particular, Bmf exhibited a loss of its normal subacrosomal distribution, becoming redistributed throughout the cytoplasm and nucleus, and appeared in cells in which it is not normally expressed (e.g., pachytene spermatocytes). Additionally, Bmf mRNA expression increased in response to lowered testosterone. These results suggest that Bmf may well be involved in germ cell apoptosis and/or anoikis in response to decreased intratesticular testosterone concentration.     

Multipattern Consensus Regions in Multiple Aligned Protein Sequences and Their Segmentation

Decomposing a biological sequence into its functional regions is an important prerequisite to understand the molecule. Using the multiple alignments of the sequences, we evaluate a segmentation based on the type of statistical variation pattern from each of the aligned sites. To describe such a more general pattern, we introduce multipattern consensus regions as segmented regions based on conserved as well as interdependent patterns. Thus the proposed consensus region considers patterns that are statistically significant and extends a local neighborhood. To show its relevance in protein sequence analysis, a cancer suppressor gene called p53 is examined. The results show significant associations between the detected regions and tendency of mutations, location on the 3D structure, and cancer hereditable factors that can be inferred from human twin studies.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27]     

Multiplex polymerase chain reaction to detect toxigenic Vibrio cholerae and to biotype Vibrio cholerae O1

A multiplex polymerase chain reaction (PCR) was developed to identify cholera toxin-producing Vibrio cholerae and to biotype V. cholerae O1. Enterotoxin-producing V. cholerae strains were identified with a primer pair that amplified a fragment of the ctxA2-B gene. Vibrio cholerae O1 strains were simultaneously differentiated into biotypes with three primers specified for the hlyA gene in the same reaction. The hlyA amplicon in the multiplex PCR serves as an internal control when testing toxin-producing strains, as hlyA gene sequences exist in all tested V. cholerae strains. Enrichment of V. cholerae present on oysters for 6 h in alkaline peptone water before detection by a nested PCR with internal primers for ctxA2-B gene yielded a detection limit lower than 3 colony-forming units (cfu) per gram of food.     

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring

Background

Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families.

Results

The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function.

Conclusions

Our results demonstrate that the method we present here using a k- modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family.

     

Integrated analysis of hydrothermal flowthroughpretreatment

ABSTRACT: BACKGROUND: The impact of hydrothermal flowthrough (FT) pretreatment severity on pretreatment and solubilization performance metrics was evaluated for three milled feedstocks (corn stover, bagasse, and poplar) and two conversion systems (simultaneous saccharification and fermentation using yeast and fungal cellulase, and fermentation by Clostridium thermocellum). RESULTS: Compared to batch pretreatment, FT pretreatment consistently resulted in higher xylan recovery, higher removal of non-carbohydrate components and higher glucan solubilization by simultaneous saccharification and fermentation (SSF). Xylan recovery was above 90% for FT pretreatment below 4.1 severity but decreased at higher severities, particularly for bagasse. Removal of non-carbohydrate components during FT pretreatment increased from 65% at low severity to 80% at high severity for corn stover, and from 40% to 70% for bagasse and poplar. Solids obtained by FT pretreatment were amenable to high conversion for all of the feedstocks and conversion systems examined. The optimal time and temperature for FT pretreatment on poplar were found to be 16 minutes and 210 oC. At these conditions, SSF glucan conversion was about 85%, 94% of the xylan was removed, and 62% of the non carbohydrate mass was solubilized. Solubilization of FT-pretreated poplar was compared for C. thermocellum fermentation (10% inoculum), and for yeast-fungal cellulase SSF (5% inoculum, cellulase loading of 5 and 10 FPU/g glucan supplemented with beta-glucosidase at 15 and 30 U/g glucan). Under the conditions tested, which featured low solids concentration, C. thermocellum fermentation achieved faster rates and more complete conversion of FT-pretreated poplar than did SSF. Compared to SSF, solubilization by C. thermocellum was 30% higher after 4 days, and was over twice as fast on ball-milled FT-pretreated poplar. CONCLUSIONS: Xylan removal trends were similar between feedstocks whereas glucan conversion trends were significantly different, suggesting that factors in addition to xylan removal impact amenability of glucan to enzymatic attack. Corn stover exhibited higher hydrolysis yields than bagasse or poplar, which could be due to higher removal of non-carbohydrate components. Xylan in bagasse is more easily degraded than xylan in corn stover and poplar. Conversion of FT-pretreated substrates at low concentration was faster and more complete for C.thermocellum than for SSF.     

Proteomic analysis for the anti‐apoptotic effects of cystamine on apoptosis‐prone macrophage

Increased macrophage vulnerability is associated with progression of systemic lupus erythematosus. Our previous studies have shown that cystamine, an inhibitor of transglutaminase 2 (TG2), alleviated the apoptosis of hepatocyte and brain cell in lupus‐prone mice NZB/W‐F1. In present study, we further investigated the effects of cystamine on apoptosis‐prone macrophages (APMs) in the lupus mice. Using two‐dimensional gel electrophoresis (2‐DE) analysis, we found that cystamine induced a differential protein expression pattern of APM as comparing to the PBS control. The protein spots presenting differential level between cystamine and PBS treatment were then identified by peptide‐mass fingerprinting (PMF). After bioinformatic analysis, these identified proteins were found involved in mitochondrial apoptotic pathway, oxidative stress, and mitogen‐activated protein (MAP) kinase‐mediated pathway. Further investigation revealed that cystamine significantly decreased the levels of apoptotic Bax and Apaf‐1 and the activity of caspase‐3, and increased the levels of anti‐apoptotic Bcl‐2 in APM. We also found that these apoptotic mediators were up‐regulated in a correlation with the progression of lupus severity in NZB/W‐F1, which were little affected in BALB/c mice. We also found that the reduced serum glutathione was restored by cystamine in NZB/W‐F1. Interestingly, the phosphorylation of extracellular signal‐regulated kinase 1/2 (ERK1/2) in APM and the phagocytic ability was diminished in presence of cystamine. In conclusion, our findings indicate that cystamine significantly inhibited mitochondrial pathway, induced antioxidant proteins, and diminished phosphorylation of extracellular ERK1/2, which may alleviate the apoptosis and the phagocytic ability of APM. J. Cell. Biochem. 110: 660–670, 2010. © 2010 Wiley‐Liss, Inc.