Mitochondrial Genome Analysis of Wild Rice (Oryza minuta) and Its Comparison with Other Related Species

Oryza minuta (Poaceae family) is a tetraploid wild relative of cultivated rice with a BBCC genome. O. minuta has the potential to resist against various pathogenic diseases such as bacterial blight (BB), white backed planthopper (WBPH) and brown plant hopper (BPH). Here, we sequenced and annotated the complete mitochondrial genome of O. minuta. The mtDNA genome is 515,022 bp, containing 60 protein coding genes, 31 tRNA genes and two rRNA genes. The mitochondrial genome organization and the gene content at the nucleotide level are highly similar (89%) to that of O. rufipogon. Comparison with other related species revealed that most of the genes with known function are conserved among the Poaceae members. Similarly, O. minuta mt genome shared 24 protein-coding genes, 15 tRNA genes and 1 ribosomal RNA gene with other rice species (indica and japonica). The evolutionary relationship and phylogenetic analysis revealed that O. minuta is more closely related to O. rufipogon than to any other related species. Such studies are essential to understand the evolutionary divergence among species and analyze common gene pools to combat risks in the current scenario of a changing environment.     

Isolation of enterotoxigenic, hemolytic, and antibiotic-resistant Aeromonas hydrophila strains from infected fish in Bangladesh

Strains of Aeromonas hydrophila isolated from skin infections of common freshwater fish in Bangladesh were tested for enterotoxin production, hemolysin production, and any correlation between these two activities. We also tested the resistance patterns of A. hydrophila to different drugs, especially in relation to ampicillin. The A. hydrophila strains produced an enterotoxin that was related to their beta-hemolytic activities. Production of beta-hemolysin may thus be an indicator of enterotoxicity. As 50% of the strains of A. hydrophila were found to be susceptible to 12.5 micrograms of ampicillin per ml, media containing this antibiotic may not be suitable for their isolation.     

Overexpression and optimization of glutamate decarboxylase in Lactobacillus plantarum Taj‐Apis362 for high gamma‐aminobutyric acid production

Gamma‐aminobutyric acid (GABA) is an important bioactive compound biosynthesized by microorganisms through decarboxylation of glutamate by glutamate decarboxylase (GAD). In this study, a full‐length GAD gene was obtained by cloning the template deoxyribonucleic acid to pTZ57R/T vector. The open reading frame of the GAD gene showed the cloned gene was composed of 1410 nucleotides and encoded a 469 amino acids protein. To improve the GABA‐production, the GAD gene was cloned into pMG36e‐LbGAD, and then expressed in Lactobacillus plantarum Taj‐Apis362 cells. The overexpression was confirmed by SDS‐PAGE and GAD activity, showing a 53 KDa protein with the enzyme activity increased by sevenfold compared with the original GAD activity. The optimal fermentation conditions for GABA production established using response surface methodology were at glutamic acid concentration of 497.973 mM, temperature 36°C, pH 5.31 and time 60 h. Under the conditions, maximum GABA concentration obtained (11.09 mM) was comparable with the predicted value by the model at 11.23 mM. To our knowledge, this is the first report of successful cloning (clone‐back) and overexpression of the LbGAD gene from L. plantarum to L. plantarum cells. The recombinant Lactobacillus could be used as a starter culture for direct incorporation into a food system during fermentation for production of GABA‐rich products.     

Pinpointing phosphotyrosine-dependent interactions downstream of the collagen receptor DDR1

Activation of the receptor tyrosine kinase DDR1 by collagen results in robust and sustained phosphorylation, however little is known about its downstream mediators. Using phosphopeptide mapping and site-directed mutagenesis, we here identified multiple tyrosine phosphorylation sites within DDR1. We found that Nck2 and Shp-2, two SH2 domain-containing proteins, bind to DDR1 in a collagen-dependent manner. The binding site of Shp-2 was mapped to tyrosine-740 of DDR1 within an ITIM-consensus sequence. Lastly, ablation of DDR1 in the mouse mammary gland resulted in delocalized expression of Nck2, suggesting that defects observed during alveologenesis are caused by the lack of the DDR1-Nck2 interaction.     

In situ release of coral mucus by <Emphasis Type="Italic">Acropora</Emphasis> and its influence on the heterotrophic bacteria

In situ mucus release by Acropora nobilis and degradation of mucus from A. nobilis and Acropora formosa, by heterotrophic bacteria were investigated at Bidong and Tioman Island, Malaysia. Mucus release rate for A. nobilis was on average 38.7 ± 35.2 mg C m⁻² h⁻¹, of which ca. 70% consisted of dissolved organic carbon (DOC) and 30% particulate organic carbon (POC). In the mucus degradation experiment, seawater-mucus mixtures were incubated and compared with control runs for 24 h. Bacterial abundance in the seawater-mucus mixture increased significantly and coincided with a decline in DOC concentration. In controls, bacteria and DOC did not significantly change. The coral mucus had a high content of inorganic phosphate. It is suggested that the coral mucus rich in DOC and phosphate can induce the high bacterial growth.