Statistical Evaluation of Trace Metals,TSH and T<Subscript>4</Subscript> in Blood Serum of Thyroid Disease Patients in Comparison with Controls

The present study is based on the measurement of concentrations of selected trace metals (Fe, Zn, Cu, Co, Mn, Ni, Cr, Cd and Pb) and thyroid hormones (TSH and T₄) in blood serum of hypothyroid and hyperthyroid patients in comparison with healthy donors/controls in order to establish the imbalances of the trace metals in diseased subjects. The serum samples were digested in HNO₃-HClO₄ mixture and quantification of the metals was performed by flame atomic absorption spectrometry. Average levels of Fe, Ni, Cu, Cr, Pb and TSH were found to be significantly higher (p < 0.05) in the serum of hypothyroid patients compared with other donor categories, while mean concentrations of Mn, Cd and T₄ were significantly elevated in the serum of hyperthyroid patients compared with other donor groups (p < 0.05). The correlation pattern of trace metals in the serum of patient groups revealed significantly different mutual associations compared with the controls. PCA and CA pointed out the interferences of the toxic metals with essential metals in the serum of both patient groups compared with the controls. Most of the metals exhibited noticeable disparities in their concentrations based on gender, food habits and tobacco use for all donor groups. Thus, the pathogenesis of thyroid diseases is significantly affecting the essential trace and toxic metals balance in both patients groups.     

A ′Fragment Fitting Approach′ to Model Disulfide Loops by Utilizing Homologous Peptide Fragments from Unrelated Proteins of Known Structures: Application to the V3 Loop of the HIV-1 Envelope Glycoprotein gp120

The V3 loop of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp120 has gained considerable attention for developing subunit vaccines against HIV-1 and also as a target to develop anti-HIV-1 drugs. These endeavors would be significantly enhanced by understanding the structural aspects of this loop. The structure of the full-length V3 loop has not been defined yet. Therefore, a novel modeling technique, termed `Fragment Fitting Approach′ (FFA), was developed to model the V3 loop. This technique utilizes fragments (³ 6 residue long) with local sequence and secondary structure similarity from unrelated proteins with known x-ray crystallographic structure and concatenating the fragments to build the model. A systematic search method was devised to identify the fragments using the combined criteria of sequence and secondary structure identity and/or similarity, predicted by a combination of methods. FFA requires partial three-dimensional coordinates of the target sequence to be modelled to get the overall coordinate path correct. The method was validated with nine disulfide-bonded loops from the Protein data bank. The modelled structures conform well with the corresponding x-ray crystallographic structures. As the models were built using the x-ray coordinates with reasonable resolution (£ 3 Å), they are expected to have stereochemically correct structures. The modelled V3 loop structure might assist in structure-based drug design of anti-HIV-1 agents targeted to this loop.     

Expression of maize prolamins in Escherichia coli

We have constructed a cDNA expression library of developing corn (Zea mays L.) endosperm using plasmid pUC8 as vector and Escherichia coli strain DH1 as host. The expression library was screened with non-radioactive immunological probes to detect the expression of gamma-zein and alpha-zein. When anti-gamma-zein antibody was used as the probe, 23 colonies gave positive reactions. The lengths of cDNA inserts of the 23 colonies were found to be 250–900 base pairs. When anti-alpha zein antibody was used, however, fewer colonies gave positive reactions. The library was also screened by colony-hybridization with ³²P-labeled DNA probes. Based on immunological and hybridization screening of the library and other evidence, we conclude that alpha-zein was either toxic to E. coli cells or rapidly degraded whereas gamma-zein and its fragments were readily expressed.     

TLR Agonist Augments Prophylactic Potential of Acid Inducible Antigen Rv3203 against Mycobacterium tuberculosis H37Rv in Experimental Animals

In general, the members of Lip gene family of Mycobacterium tuberculosis evoke strong immune response in the host. Keeping this fact into consideration, we investigated role of Rv3203, a cell wall associated protein with lipolytic activity, in imparting protection against experimental murine tuberculosis. The data of the present study suggested that archaeosome encapsulated Rv3203 induce strong lymphocyte proliferation, up-regulated Th-1 biased cytokines profile, increased expression of co-stimulatory markers on both antigen presenting cells and T lymphocytes. The immuno-prophylactic response was further modulated by exposure of the animals to zymosan, a TLR2/6 agonist, prior to immunization with archaeosome encapsulated Rv3203. Interestingly, pre-treatment of experimental animals with zymosan boosted strong immunological memory as compared to archaeosome encapsulated Rv3203 as well as BCG vaccine. We conclude that priming of immunized animal with TLR agonist followed by immunization with archaeosomes encapsulated Rv3203 offer substantial protection against tuberculosis infection and could be a potential subunit vaccine based prophylactic strategy.     

DISTRIBUTION OF ENZYMATIC BROWNING OF YOUNG SHOOT HOMOGENATES IN THE AURANTIOIDEAE

Distribution of polyphenol oxidase-catalyzed browning of young shoot homogenates was studied in 428 accessions of the orange subfamily Aurantioideae. Browning and nonbrowning phenotypes were found in both tribes, namely Clauseneae and Citreae. The browning taxa had sufficient polyphenol oxidase activity and a presently unknown phenolic substrate, while the nonbrowning taxa were devoid of both. A third group of taxa contained the substrate only and they too were designated as browning since their homogenates turned brown when the enzyme from a known source was added. The color of homogenates was taxon-specific in most browning and nonbrowning taxa. Within the genus Citrus, 4 out of the 16 species recognized by Swingle were browning and 2 were nonbrowning. Exceptions noted within either group of taxa were presumably hybrids or mutants. The significance of enzymatic browning as an additional taxonomic criterion in studying species relationships and as a genetic marker in identificaton of hybrid taxa was discussed.     

The effect of various dietary zinc concentrations on the biological interactions of zinc,copper, and iron in rats

Three groups (14 rats each) were fed one of the following diets for 8 wks: a control purified basal diet containing 12 ppm zinc, 5 ppm copper, and 35 ppm iron; the basal diet with less than 2 ppm zinc; or the basal diet supplemented with 1000 ppm zinc. Rats fed the zinc-deficient diet had decreased weight gain, moderate polydipsia, and intermittent mild diarrhea. The zinc-supplemented rats had a cyclical pattern of food intake and weight loss from weeks 5 to 8. Tissue concentrations suggest that zinc and copper were not mutually antagonistic with chronic dietary imbalances. If tissue element concentrations reflected intestinal uptake, then competition and/or inhibition of intestinal uptake occurred between zinc and iron. The fluctuations in tissue element concentrations that occurred with increased duration of the study were at variance with previous studies of shorter time periods. The dietary proportions of zinc, copper, and iron appear to influence zinc, copper, and iron metabolism at the intestinal and cellular transport levels over a given period of time.     

DISTRIBUTION OF COAGULATION OF YOUNG SHOOT HOMOGENATES IN THE AURANTIOIDEAE

Distribution of coagulation of young shoot homogenates was surveyed in 430 accessions from the orange subfamily Aurantioideae. Representatives of four genera available for study (Clausena, Glycosmis, Aegle, Feronia) were coagulating taxa. The genus Citrus included both coagulating and noncoagulating taxa. Nineteen genera (Murraya, Merillia, Pamburus, Paramignya, Triphasia, Aeglopsis, Afraegle, Balsamocitrus, Feroniella, Swinglea, Atalantia, Citropsis, Hesperethusa, Pleiospermium, Severinia, Clymenia, Eremocitrus, Poncirus, Fortunella) were noncoagulating. The status of eight genera (Micromelum, Wenzelia, Monanthocitrus, Oxanthera, Merope, Luvunga, Burkillanthus, Limnocitrus) is not known. Homogenized tissue from coagulating taxa turned into a paste while tissue from noncoagulating taxa was thin and juicy. Coagulation did not take place when the pH of the grinding medium was 11 or higher but it would occur if the pH was lowered. Homogenates of noncoagulating taxa become coagulated below pH 5.2–5.3, but remained noncoagulating above this. Noncoagulating taxa contained an unidentified substance which inhibited coagulation of tissue from coagulating taxa. The mechanism of coagulation and noncoagulaton is not presently known. The significance of coagulation and its absence as a taxonomic and genetic marker is discussed.     

Universality of Citation Distributions for Academic Institutions and Journals

Citations measure the importance of a publication, and may serve as a proxy for its popularity and quality of its contents. Here we study the distributions of citations to publications from individual academic institutions for a single year. The average number of citations have large variations between different institutions across the world, but the probability distributions of citations for individual institutions can be rescaled to a common form by scaling the citations by the average number of citations for that institution. We find this feature seems to be universal for a broad selection of institutions irrespective of the average number of citations per article. A similar analysis for citations to publications in a particular journal in a single year reveals similar results. We find high absolute inequality for both these sets, Gini coefficients being around 0.66 and 0.58 for institutions and journals respectively. We also find that the top 25% of the articles hold about 75% of the total citations for institutions and the top 29% of the articles hold about 71% of the total citations for journals.     

The nonreceptor tyrosine kinase SRMS inhibits autophagy and promotes tumor growth by phosphorylating the scaffolding protein FKBP51

Nutrient-responsive protein kinases control the balance between anabolic growth and catabolic processes such as autophagy. Aberrant regulation of these kinases is a major cause of human disease. We report here that the vertebrate nonreceptor tyrosine kinase Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites (SRMS) inhibits autophagy and promotes growth in a nutrient-responsive manner. Under nutrient-replete conditions, SRMS phosphorylates the PHLPP scaffold FK506-binding protein 51 (FKBP51), disrupts the FKBP51-PHLPP complex, and promotes FKBP51 degradation through the ubiquitin-proteasome pathway. This prevents PHLPP-mediated dephosphorylation of AKT, causing sustained AKT activation that promotes growth and inhibits autophagy. SRMS is amplified and overexpressed in human cancers where it drives unrestrained AKT signaling in a kinase-dependent manner. SRMS kinase inhibition activates autophagy, inhibits cancer growth, and can be accomplished using the FDA-approved tyrosine kinase inhibitor ibrutinib. This illuminates SRMS as a targetable vulnerability in human cancers and as a new target for pharmacological induction of autophagy in vertebrates.

This study describes the discovery and characterization of a nutrient-sensitive signaling pathway that drives growth and inhibits autophagy in mammalian cells. This pathway, which involves the non-receptor tyrosine kinase SRMS and the PHLPP scaffold protein FKBP51, promotes tumor growth and is amenable to pharmacological inhibition.     

Analysis of codon usage patterns and predicted highly expressed genes for six phytopathogenic Xanthomonas genomes shows a high degree of conservation

Members of the genus Xanthomonas are significant phytopathogens, which cause diseases in several economically important crops including rice, canola, tomato, citrus, etc. We have analyzed the genomes of six recently sequenced Xanthomonas strains for their synonymous codon usage patterns for all of protein coding genes and specific genes associated with pathogenesis, and determined the predicted highly expressed (PHX) genes by the use of the codon adaptation index (CAI). Our results show considerable heterogeneity among the genes of these moderately G+C rich genomes. Most of the genes were moderate to highly biased in their codon usage. However, unlike ribosomal protein genes, which were governed by translational selection, those genes associated with pathogenesis (GAP) were affected by mutational pressure and were predicted to have moderate to low expression levels. Only two out of 339 GAP genes were in the PHX category. PHX genes present in clusters of orthologous groups of proteins (COGs) were identified. Genes in the plasmids present in two strains showed moderate to low expression level and only a couple of genes featured in the PHX list. Common genes present in the top-20 PHX gene-list were identified and their possible functions are discussed. Correspondence analysis showed that genes are highly confined to a core in the plot.