Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses.

Jeotgalibacillus malaysiensis, a moderate halophilic bacterium isolated from a pelagic area, can endure higher concentrations of sodium chloride (NaCl) than other Jeotgalibacillus type strains. In this study, we therefore chose to sequence and assemble the entire J. malaysiensis genome. This is the first report to provide a detailed analysis of the genomic features of J. malaysiensis, and to perform genetic comparisons between this microorganism and other halophiles. J. malaysiensis encodes a native megaplasmid (pJeoMA), which is greater than 600 kilobases in size, that is absent from other sequenced species of Jeotgalibacillus. Subsequently, RNA-Seq-based transcriptome analysis was utilised to examine adaptations of J. malaysiensis to osmotic stress. Specifically, the eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) and KEGG (Kyoto Encyclopaedia of Genes and Genomes) databases were used to elucidate the overall effects of osmotic stress on the organism. Generally, saline stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. Our findings also indicate that J. malaysiensis adopted a combination of approaches, including the uptake or synthesis of osmoprotectants, for surviving salt stress. Among these, proline synthesis appeared to be the preferred method for withstanding prolonged osmotic stress in J. malaysiensis.

Complete genome sequencing of Pandoraea pnomenusa RB38 and Molecular Characterization of Its N-acyl homoserine lactone synthase gene ppnI.

In this study, we sequenced the genome of Pandoraea pnomenusa RB38 using Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. A pair of cognate luxI/R homologs was identified where the luxI homolog, ppnI, was found adjacent to a luxR homolog, ppnR1. An additional orphan luxR homolog, ppnR2, was also discovered. Multiple sequence alignment and phylogenetic analysis revealed that ppnI is an N-acyl homoserine lactone (AHL) synthase gene that is distinct from those of the nearest phylogenetic neighbor viz. Burkholderia spp. High resolution tandem mass spectrometry (LC-MS/MS) analysis showed that Escherichia coli BL21 harboring ppnI produced a similar AHL profile (N-octanoylhomoserine lactone, C8-HSL) as P. pnomenusa RB38, the wild-type donor strain, confirming that PpnI directed the synthesis of AHL in P. pnomenusa RB38. To our knowledge, this is the first documentation of the luxI/R homologs of the genus Pandoraea.

Lack of clinical manifestations in asymptomatic dengue infection is attributed to broad down-regulation and selective up-regulation of host defence response genes.

OBJECTIVES: Dengue represents one of the most serious life-threatening vector-borne infectious diseases that afflicts approximately 50 million people across the globe annually. Whilst symptomatic infections are frequently reported, asymptomatic dengue remains largely unnoticed. Therefore, we sought to investigate the immune correlates conferring protection to individuals that remain clinically asymptomatic. METHODS: We determined the levels of neutralizing antibodies (nAbs) and gene expression profiles of host immune factors in individuals with asymptomatic infections, and whose cognate household members showed symptoms consistent to clinical dengue infection. RESULTS: We observed broad down-regulation of host defense response (innate, adaptive and matrix metalloprotease) genes in asymptomatic individuals as against symptomatic patients, with selective up-regulation of distinct genes that have been associated with protection. Selected down-regulated genes include: TNF α (TNF), IL8, C1S, factor B (CFB), IL2, IL3, IL4, IL5, IL8, IL9, IL10 and IL13, CD80, CD28, and IL18, MMP8, MMP10, MMP12, MMP15, MMP16, and MMP24. Selected up-regulated genes include: RANTES (CCL5), MIP-1α (CCL3L1/CCL3L3), MIP-1ß (CCL4L1), TGFß (TGFB), and TIMP1. CONCLUSION: Our findings highlight the potential association of certain host genes conferring protection against clinical dengue. These data are valuable to better explore the mysteries behind the hitherto poorly understood immunopathogenesis of subclinical dengue infection.

Rennet-induced aggregation of heated pH-adjusted skim milk.

Heated (20-100 °C/0-30 min) skim milks (pH 6.5-7.1) were diluted in buffer (pH 7.0). Rennet was added, and the particle size with time was measured. For all samples, the size initially decreased (lag phase) and then increased (aggregation phase). Milks heated at ≤60 °C had short lag phases and rapid aggregation phases regardless of pH. Milks heated at >60 °C at pH 6.5 had long lag phases and slow aggregation phases. As the pH increased, the lag phase shortened and the aggregation phase accelerated. The aggregation time was correlated with the level of whey protein associated with the casein micelles and with the level of κ-casein dissociated from the micelles. Heated milks formed weak gels when renneted. It is proposed that the milks heated at low pH have whey proteins associated with the casein micelles and that these denatured whey proteins stabilize the micelles to aggregation by rennet and therefore inhibit gelation. In the milks heated at higher pH, the whey proteins associate with κ-casein in the serum and, on rennet treatment, the κ-casein-depleted micelles and the serum-phase whey protein/κ-casein complexes aggregate; however, the denatured whey proteins stabilize the aggregates so that gelation is still inhibited.

Effect of heat treatments and homogenisation pressure on the acid gelation properties of recombined whole milk.

The homogenisation pressure and the order of heating and homogenisation were varied in the preparation of recombined whole milks. The fat globule sizes decreased from ∼2 to 0.2µm as the homogenisation pressure increased from 50 to 850bar for samples heated before (HEHO) or after (HOHE) homogenisation. For acid gels prepared from the milks, small increases in elastic modulus of the set gels were observed with decreasing fat globule size. The yield strain of the acid gels increased linearly with decreasing fat globule size, and HOHE gels had higher yield strains than HEHO gels. The yield stress of the set gels increased with decreasing fat globule size, and the yield stress for HOHE gels were higher than the HEHO gels. Confocal micrographs of the gels revealed an almost continuous protein network structure without pores for gels from milks treated at low homogenisation pressures, and the large fat globules did not actively interact with the strands in the gel network. In contrast, a porous protein network structure with distinct strands was observed for the samples treated at high homogenisation pressures, and the small fat globules were intimately involved in the strands in the network structure. The HOHE gels had a more porous protein network with thicker strands than the HEHO gels. The size of the fat globules and their incorporation in the protein network during acidification is proposed to affect the acid gel structure and properties.

Effect of protein, nonprotein-soluble components, and lactose concentrations on the irreversible thermal denaturation of beta-lactoglobulin and alpha-lactalbumin in skim milk.

The effect of protein, nonprotein-soluble components, and lactose concentrations on the irreversible denaturation of beta-lactoglobulin (beta-LG) and alpha-lactalbumin (alpha-LA) in reconstituted skim milk samples was studied over a wide temperature range (75-100 degrees C). The irreversible thermal denaturation of beta-LG had a reaction order of 1.5 and that of alpha-LA had a reaction order of 1.0 in all systems and under all conditions. The rates of irreversible denaturation of beta-LG and alpha-LA were markedly dependent upon the composition of the milk. At all temperatures, the irreversible denaturations of beta-LG and alpha-LA were enhanced at a higher protein concentration and were retarded when the nonprotein-soluble components and lactose concentrations were increased. The effects of increasing the concentrations of lactose and nonprotein-soluble components were interpreted using the preferential hydration theory and allowed for the interpretation of the changes in the denaturations of beta-LG and alpha-LA when the milk total solids concentration was increased.

Rheological properties of acid gels prepared from heated pH-adjusted skim milk.

Reconstituted skim milk was adjusted to pH values between 6.5 and 7.1 and heated (90 degrees C) for up to 30 min. The skim milk samples were then readjusted to pH 6.7. Acid gels prepared from heated milk had markedly higher G ' values, a reduced gelation time, and an increased gelation pH than those prepared from unheated milk. An increased pH at heating decreased the gelation time, increased the gelation pH, and increased the final G ' of acid set gels prepared from the heated milk samples. There were only small differences in the level of whey protein denaturation in the samples at different pH values, and these differences could not account for the differences in the G ' of the acid gels. The levels of denatured whey protein associated with the casein micelles decreased and the levels of soluble denatured whey proteins increased as the pH at heating was increased. The results indicated that the soluble denatured whey proteins had a greater effect on the final G ' of the acid gels than the denatured whey proteins associated with the casein micelles.