HOCTAR database: a unique resource for microRNA target prediction

An Antarctic strain (NJ-7) of Chlorella vulgaris possesses the same 18S rRNA sequence as that of a temperate strain (UTEX259), but shows significantly higher freezing tolerance than the latter. Suppression subtractive hybridization (SSH) was performed to identify genes of intensified expression in NJ-7 relative to UTEX259. Among the genes identified, Ccor1 and Ccor2, co-organized in the same gene cluster Ccor1-Ccor2-Ccor1-Ccor2, showed much higher expression levels in NJ-7 than in UTEX259 at both 20°C and 4°C. As detected by Northern blot and Western blot analyses, the two genes were cold-inducible in NJ-7 but almost not expressed in UTEX259. Their encoded products are predicted to share 55.7% identity to each other and possess physicochemical characteristics similar to that of late embryogenesis abundant (LEA) proteins in plants. The purified recombinant Ccor1 and Ccor2 showed high heat-stability and could act as cryoprotectants to lactate dehydrogenase in vitro. Based on their expression patterns and protein characteristics, we propose that Ccor1 and Ccor2 are two novel LEA proteins and are related to the greatly enhanced freezing tolerance in the Antarctic strain.     

Mitigation of stress: new treatment alternatives

Complaints of stress are common in modern life. Psychological stress is a major cause of lifestyle-related issues, contributing to poor quality of life. Chronic stress impedes brain function, causing impairment of many executive functions, including working memory, decision making and attentional control. The current study sought to describe newly developed stress mitigation techniques, and their influence on autonomic and endocrine functions. The literature search revealed that the most frequently studied technique for stress mitigation was biofeedback (BFB). However, evidence suggests that neurofeedback (NFB) and noninvasive brain stimulation (NIBS) could potentially provide appropriate approaches. We found that recent studies of BFB methods have typically used measures of heart rate variability, respiration and skin conductance. In contrast, studies of NFB methods have typically utilized neurocomputation techniques employing electroencephalography, functional magnetic resonance imaging and near infrared spectroscopy. NIBS studies have typically utilized transcranial direct current stimulation methods. Mitigation of stress is a challenging but important research target for improving quality of life.     

Induction of the inhibitor of RecBCD enzyme inEscherichia coli is alexA-independent SOS response

Exonuclease V (ExoV), an enzyme involved in the RecBCD pathway of recombination, was inhibited in cells induced for SOS functions. In vitro experiments showed that an ExoV inhibitor (Exi) induced after SOS induction was responsible for the inhibition of ExoV. Unlike other SOS functions, Exi protein was induced even inlexA(Ind^–) mutants. Phage Mud(amp^r,lac) was fused to the promoter of theexi gene in alexA(Ind^–) strain, and in these fusion strains-galactosidase was inducible five- to six-fold after DNA damage. The Exi protein, in addition to the inhibition of ATP-dependent DNase activity of ExoV, appeared to repress the synthesis of polypeptide subunits of ExoV as well. Further, Exi protein appeared to be an inducible repressor of a number of other genes in SOS-induced cells.     

Restriction in vivo

Summary Degradation products of restricted T4 DNA induced filamentation, mutagenesis, and to a lesser extent, synthesis of recA protein in wild type cells but not in recA, lexA or recBC mutants of Escherichia coli. We conclude that the structural damage to the DNA caused by restriction cleavage and exonuclease V degradation can induce SOS functions. Degradation of restricted nonglucosylated T4 DNA by exonuclease V delayed cell division and induced filament formation and mutagenesis in lexA ⁺ but not in lexA ^- cells. Delay of cell division was also dependent upon recA and recBC funtions. Such degradation of DNA also dramatically increased mutagenesis in tif ^- Sfi^- cells at 42°C. The synthesis of recA protein continued in the restricting host after infection by the nonglucosylated T4 phage, but enhanced synthesis is not induced to the extent seen in SOS induced tif ^- cells grown at 42°. We also found that restriction of nonglucosylated T4 was alleviated in UV irradiated cells. The UV induced alleviation of rgl and r _K restriction depended upon post irradiation protein synthesis and was not observed in recA, lexA or recBC mutants.     

Heat shock-induced relaxation of restriction enzyme specificity inEscherichia coli

Methylated and hydroxymethylated cytosine containing DNA was restricted by proteins encoded by themcrBC (rglB) loci ofE. coli. In vivo, RglB proteins recognize and cleave hmCT2 and hmCT4 DNAs at 30°C and 42°C but hmCT6 DNA was unaffected at both temperatures, However, cells carrying therglB genes cloned on pBR322 (pDSS17) did not restrict hmCT6 at 30°C, but hmCT6 DNA was cleaved efficiently at 42°C. Heat shock treatment for five minutes was enough to induce this promiscuity in recognition specificity. We call this activity RglB star. A single copy ofrglB located on the chromosome or cloned on a low copy vector pMU575 failed to show RglB star activity.De novo protein synthesis was not required for the manifestation of RglB star activity.     

Nomenclature relating to restriction of modified DNA in Escherichia coli.

At least three restriction systems that attack DNA containing naturally modified bases have been found in common Escherichia coli K-12 strains. These systems are McrA, McrBC, and Mrr. A brief summary of the genetic and phenotypic properties so far observed in laboratory strains is set forth, together with a proposed nomenclature for describing these properties.     

Serum proteome of leprosy patients undergoing erythema nodosum leprosum reaction: regulation of expression of the isoforms of haptoglobin

Validated proteome profile allows better understanding of disease progression, subtype classification, susceptibility patterns, and disease prognosis. Leprosy is a spectral disease, with clinically, histologically, immunologically, and bacteriologically distinguishable subtypes. In addition, a significant fraction of patients undergo immune mediated reactions even after multidrug therapy (MDT). Erythema nodosum leprosum (ENL) is an immune complex mediated reactional condition in leprosy, characterized by a systemic inflammatory condition afflicting borderline lepromatous (BL) and lepromatous leprosy patients (LL). In this study, we have analyzed serum proteome of leprosy patients undergoing ENL reactions and compared it with that of healthy noncontact controls. Depletion of albumin and immunoglobulin G (IgG) was optimized using Aurum serum protein mini kit (Bio-Rad), and then two-dimensional gel electrophoresis (2-DE) of these serum samples was performed. Differentially expressed proteins were identified by MALDI-TOF and MALDI-TOF MS/MS mass spectrometry. Significant increase in one of the isoforms of alpha2 chain of haptoglobin was observed in ENL condition. In addition, haptoglobin phenotype was determined for healthy controls and leprosy patients. Hp 0-0 phenotype was detected in 21.4% of the ENL patients undergoing treatment, which on follow up examination showed typable phenotype, thus showing a condition of acquired anhaptoglobinemia. Since ENL still remains a threat to leprosy disease management, the above findings may provide new insights in understanding the development and progression of this inflammatory condition.     

Discerning non-disjunction in Down syndrome patients by means of GluK1-(AGAT)n and D21S2055-(GATA)n microsatellites on chromosome 21

INTRODUCTION:

Down syndrome (DS), the leading genetic cause of mental retardation, stems from non-disjunction of chromosome 21.

AIM:

Our aim was to discern non-disjunction in DS patients by genotyping GluK1-(AGAT)_n and D21S2055-(GATA)_n microsatellites on chromosome 21 using a family-based study design.

MATERIALS AND METHODS:

We have used a PCR and automated DNA sequencing followed by appropriate statistical analysis of genotype data for the present study

RESULTS AND DISCUSSION:

We show that a high power of discrimination and a low probability of matching indicate that both markers may be used to distinguish between two unrelated individuals. That the D21S2055-(GATA)_n allele distribution is evenly balanced, is indicated by a high power of exclusion [PE=0.280]. The estimated values of observed heterozygosity and polymorphism information content reveal that relative to GluK1-(AGAT)_n[H_obs=0.286], the D21S2055- (GATA)_n[H_obs=0.791] marker, is more informative. Though allele frequencies for both polymorphisms do not conform to Hardy-Weinberg equilibrium proportions, we were able to discern the parental origin of non-disjunction and also garnered evidence for triallelic (1:1:1) inheritance. The estimated proportion of meiosis-I to meiosis-II errors is 2:1 in maternal and 4:1 in paternal cases for GluK1-(AGAT)_n, whereas for D21S2055-(GATA)_n, the ratio is 2:1 in both maternal and paternal cases. Results underscore a need to systematically evaluate additional chromosome 21-specific markers in the context of non-disjunction DS.     

Recombinant E. coli expressing Vitreoscilla haemoglobin prefers aerobic metabolism under microaerobic conditions: A proteome-level study

Vitreoscilla haemoglobin (VHb) expression in heterologous host was shown to enhance growth and oxygen utilization capabilities under oxygen-limited conditions. The exact mechanism by which VHb enhances the oxygen utilization under oxygen-limiting conditions is still unknown. In order to understand the role of VHb in promoting oxygen utilization, changes in the total protein profile of E. coli expressing the vgb gene under its native promoter was analysed. Two-dimensional difference gel electrophoresis (2D DIGE) was employed to quantify the differentially expressed proteins under oxygen-limiting conditions. Overexpression of proteins involved in aerobic metabolic pathways and suppression of proteins involved in non-oxidative metabolic pathways shown in this study indicates that the cells expressing VHb prefer aerobic metabolic pathways even under oxygen limitation. Under these conditions, the expression levels of proteins involved in central metabolic pathways, cellular adaptation and cell division were also found to be altered. These results imply that Vitreoscilla haemoglobin expression alters aerobic metabolism specifically, in addition to altering proteins involved in other pathways, the significance of which is not clear as of now.