Dataset of potential targets for Mycobacterium tuberculosis H37Rv through comparative genome analysis

Mycobacterium tuberculosis is the causative agent of the disease, tuberculosis and H37Rv is the most studied clinical strain. We use comparative genome analysis of Mycobacterium tuberculosis H37Rv and human for the identification of potential targets dataset. We used DEG (Database of Essential Genes) to identify essential genes in the H37Rv strain. The analysis shows that 628 of the 3989 genes in Mycobacterium tuberculosis H37Rv were found to be essential of which 324 genes lack similarity to the human genome. Subsequently hypothetical proteins were removed through manual curation. This further resulted in a dataset of 135 proteins with essential function and no homology to human.     

Glucagon-like peptide-1 protects mesenteric endothelium from injury during inflammation

Glucagon-like peptide-1 (GLP-1) is a proglucagon-derived hormone with cellular protective actions. We hypothesized that GLP-1 would protect the endothelium from injury during inflammation. Our aims were to determine the: (1) effect of GLP-1 on basal microvascular permeability, (2) effect of GLP-1 on increased microvascular permeability induced by lipopolysaccaride (LPS), (3) involvement of the GLP-1 receptor in GLP-1 activity, and (4) involvement of the cAMP/PKA pathway in GLP-1 activity. Microvascular permeability (L_p) of rat mesenteric post-capillary venules was measured in vivo. First, the effect of GLP-1 on basal L_p was measured. Second, after systemic LPS injection, L_p was measured after subsequent perfusion with GLP-1. Thirdly, L_p was measured after LPS injection and perfusion with GLP-1 + GLP-1 receptor antagonist. Lastly, L_p was measured after LPS injection and perfusion with GLP-1 + inhibitors of the cAMP/PKA pathway. Results are presented as mean area under the curve (AUC) ± SEM. GLP-1 had no effect on L_p (AUC: baseline = 27 ± 1.4, GLP-1 = 1 ± 0.4, p = 0.08). LPS increased L_p two-fold (AUC: LPS = 54 ± 1.7, p < 0.0001). GLP-1 reduced the LPS increase in L_p by 75% (AUC: LPS + GLP-1 = 34 ± 1.5, p < 0.0001). GLP-1 antagonism reduced the effects of GLP-1 by 60% (AUC: LPS + GLP-1 + antagonist = 46 ± 2.0, p < 0.001). The cAMP synthesis inhibitor reduced the effects of GLP-1 by 60% (AUC: LPS + GLP-1 + cAMP inhibitor = 46 ± 1.5, p < 0.0001). The PKA inhibitor reduced the effects of GLP-1 by 100% (AUC: LPS + GLP-1 + PKA inhibitor = 56 ± 1.5, p < 0.0001). GLP-1 attenuates the increase in microvascular permeability induced by LPS. GLP-1 may protect the endothelium during inflammation, thus decreasing third-space fluid loss.     

Living with urea stress

Intracellular organic osmolytes are present in certain organisms adapted to harsh environments. These osmolytes protect intracellular macromolecules against denaturing environmental stress. In contrast to the usually benign effects of most organic osmolytes, the waste product urea is a well-known perturbant of macromolecules. Although urea is a perturbing solute which inhibits enzyme activity and stability, it is employed by some species as a major osmolyte. The answer to this paradox was believed to be the discovery of protective osmolytes (methylamines). We review the current state of knowledge on the various ways of counteracting the harmful effects of urea in nature and the mechanisms for this. This review ends with the mechanistic idea that cellular salt (KCl/NaCl) plays a crucial role in counteracting the effects of urea, either by inducing required chaperones or methylamines, or by thermodynamic interactions with urea-destabilised proteins. We also propose future opportunities and challenges in the field.     

Molecular epidemiology of clinical and carrier strains of methicillin resistant Staphylococcus aureus (MRSA) in the hospital settings of north India

Background

The study was conducted between 2000 and 2003 on 750 human subjects, yielding 850 strains of staphylococci from clinical specimens (575), nasal cultures of hospitalized patients (100) and eye & nasal sources of hospital workers (50 & 125 respectively) in order to determine their epidemiology, acquisition and dissemination of resistance genes.

Methods

Organisms from clinical samples were isolated, cultured and identified as per the standard routine procedures. Susceptibility was measured by the agar diffusion method, as recommended by the Nat ional Committee for Clinical Laboratory Standards (NCCLS). The modified method of Birnboin and Takahashi was used for isolation of plasmids from staphylococci. Pulsed-field gel electrophoresis (PFGE) typing of clinical and carrier Methicillin resistant Staphylococcus aureus (MRSA) strains isolated during our study was performed as described previously.

Results

It was shown that 35.1% of Staphylococcus aureus and 22.5% of coagulase-negative staphylococcal isolates were resistant to methicillin. Highest percentage of MRSA (35.5%) was found in pus specimens (n = 151). The multiple drug resistance of all MRSA (n = 180) and Methicillin resistant Coagulase-negative Staphylococcus aureus (MRCNS) (n = 76) isolates was detected. In case of both methicillin-resistant as well as methicillin-sensitive Saphylococcal isolates zero resistance was found to vancomycin where as highest resistance was found to penicillin G followed by ampicillin. It was shown that the major reservoir of methicillin resistant staphylococci in hospitals are colonized/infected inpatients and colonized hospital workers, with carriers at risk for developing endogenous infection or transmitting infection to health care workers and patients. The results were confirmed by molecular typing using PFGE by SmaI-digestion. It was shown that the resistant markers G and T got transferred from clinical S. aureus (JS-105) to carrier S. aureus (JN-49) and the ciprofloxacin (Cf) and erythromycin (E) resistance seemed to be chromosomal mediated. In one of the experiments, plasmid pJMR1O from Staphylococcus aureus coding for ampicillin (A), gentamicin (G) and amikacin (Ak) resistance was transformed into Escherichia coli. The minimal inhibitory concentrations (MICs) for A and G were lower in E. coli than in S. aureus. However, the MIC for Ak was higher in E. coli transformants than in S. aureus.

Conclusion

There is a progressive increase in MRSA prevalence and multi-drug resistance in staphylococci. Vancomycin is still the drug of choice for MRSA infections. The major reservoir of methicillin resistant staphylococci in hospitals is colonized/infected inpatients and colonized hospital workers. Resistance transfer from staphylococci to E. coli as well as from clinical to carrier staphylococci due to antibiotic stress seemed to be an alarming threat to antimicrobial chemotherapy.     

Acidic pH enhances structure and structural stability of the capsid protein of hepatitis E virus

Hepatitis E virus (HEV) is enterically transmitted and endemic to tropical areas of the world. The major capsid protein of HEV is pORF2 ( approximately 74 kDa), encoded by open reading frame 2 (ORF2). When expressed in insect cells, it is processed into a approximately 55 kDa form (n-pORF2). We also generated a mutant, m-pORF2, lacking a C-terminal hydrophobic region shown earlier to be required for its homo-oligomerization. Circular dichroism was used to measure the secondary structure and stability of these proteins as a function of pH and temperature. With decreasing pH both proteins acquired increasing alpha-helicity and thermal stability in terms of midpoint of denaturation and the Gibbs energy change.     

Diverse effects of mutations in exon II of the von Hippel-Lindau (VHL) tumor suppressor gene on the interaction of pVHL with the cytosolic chaperonin and pVHL-dependent ubiquitin ligase activity

We examined the biogenesis of the von Hippel-Lindau (VHL) tumor suppressor protein (pVHL) in vitro and in vivo. pVHL formed a complex with the cytosolic chaperonin containing TCP-1 (CCT or TRiC) en route to assembly with elongin B/C and the subsequent formation of the VCB-Cul2 ubiquitin ligase. Blocking the interaction of pVHL with elongin B/C resulted in accumulation of pVHL within the CCT complex. pVHL present in purified VHL-CCT complexes, when added to rabbit reticulocyte lysate, proceeded to form VCB and VCB-Cul2. Thus, CCT likely functions, at least in part, by retaining VHL chains pending the availability of elongin B/C for final folding and/or assembly. Tumor-associated mutations within exon II of the VHL syndrome had diverse effects upon the stability and/or function of pVHL-containing complexes. First, a pVHL mutant lacking the entire region encoded by exon II did not bind to CCT and yet could still assemble into complexes with elongin B/C and elongin B/C-Cul2. Second, a number of tumor-derived missense mutations in exon II did not decrease CCT binding, and most had no detectable effect upon VCB-Cul2 assembly. Many exon II mutants, however, were found to be defective in the binding to and subsequent ubiquitination of hypoxia-inducible factor 1alpha (HIF-1alpha), a substrate of the VCB-Cul2 ubiquitin ligase. We conclude that the selection pressure to mutate VHL exon II during tumorigenesis does not relate to loss of CCT binding but may reflect quantitative or qualitative defects in HIF binding and/or in pVHL-dependent ubiquitin ligase activity.     

Apc deficiency is associated with increased Egfr activity in the intestinal enterocytes and adenomas of C57BL/6J-Min/+ mice

Overexpression of the epidermal growth factor receptor (EGFR) and its increased tyrosine kinase activity are implicated in colorectal cancer (CRC) development and malignant progression. The C57BL/6J-Min/+ (Min/+) mouse is a model for CRC and develops numerous intestinal adenomas. We analyzed the normal mucosa of Min/+ and Apc+/+ (WT) littermate mice together with Apc-null adenomas to gain insight into the roles of Egfr in these intestinal tissues. Protein analyses showed that Egfr activity was highest in the tumors, and also up-regulated in Min/+ relative to WT enterocytes. Expression of ubiquitylated Egfr (Egfr-Ub) was increased in Min/+ enterocytes and tumors. Tumors exhibited increased association of Egfr with clathrin heavy chain (CHC), Gab1, and p85alpha, the regulatory subunit of phosphoinositide 3-kinase (PI3K), and tumors also overexpressed c-Src, PDK1, and Akt. Immunohistochemistry for Akt-p-Ser473 revealed a low level of this active kinase in Min/+ and WT enterocytes and its strong presence in tumors. Prostaglandin E2 (PGE2) is a product of cyclooxygenase-2 (Cox-2) activity that is up-regulated in Min/+ tumors and transactivates Egfr. PGE2 expression was significantly higher in untreated Min/+ tumors and reduced by treatment with the Cox-2 inhibitor, celecoxib. Dietary administration of this NSAID also inhibited Egfr activity in tumors. Increased activation of the EGFR-PI3K-Akt signaling pathway in tumors relative to Apc+/+ and ApcMin/+ enterocytes provides potential opportunities for therapeutic interventions to differentially suppress tumor formation, promotion, progression, and/or recurrence.     

Microtubule Affinity-Regulating Kinase 4: Structure, Function, and Regulation

MAP/Microtubule affinity-regulating kinase 4 (MARK4) belongs to the family of serine/threonine kinases that phosphorylate the microtubule-associated proteins (MAP) causing their detachment from the microtubules thereby increasing microtubule dynamics and facilitating cell division, cell cycle control, cell polarity determination, cell shape alterations, etc. The MARK4 gene encodes two alternatively spliced isoforms, L and S that differ in their C-terminal region. These isoforms are differentially regulated in human tissues including central nervous system. MARK4L is a 752-residue-long polypeptide that is divided into three distinct domains: (1) protein kinase domain (59–314), (2) ubiquitin-associated domain (322–369), and (3) kinase-associated domain (703–752) plus 54 residues (649–703) involved in the proper folding and function of the enzyme. In addition, residues 65–73 are considered to be the ATP-binding domain and Lys88 is considered as ATP-binding site. Asp181 has been proposed to be the active site of MARK4 that is activated by phosphorylation of Thr214 side chain. The isoform MARK4S is highly expressed in the normal brain and is presumably involved in neuronal differentiation. On the other hand, the isoform MARK4L is upregulated in hepatocarcinoma cells and gliomas suggesting its involvement in cell cycle. Several biological functions are also associated with MARK4 including microtubule bundle formation, nervous system development, and positive regulation of programmed cell death. Therefore, MARK4 is considered as the most suitable target for structure-based rational drug design. Our sequence, structure- and function-based analysis should be helpful for better understanding of mechanisms of regulation of microtubule dynamics and MARK4 associated diseases.     

Effectiveness of phytase pre-treatment on growth performance,nutrient digestibility and mineral status of common carp (Cyprinus carpio) juveniles fed Moringa by-product based diet

Several anti-nutritional substances are found in plant derivatives for example phytate, that make the nutrients and minerals unavailable to fish, hence leading to poor growth performance. Presence of the anti-nutrient factor such as phytate is a chelated compound and need enzyme for its breakdown and availability of nutrients to improve fish growth. This research work was performed to check the improvement of overall performance of Cyprinus carpio fingerlings by the help of phytase addition in Moringa oleifera by- products based diet. Combination of Moringa seed meal and Moringa leaf meal was utilized as test ingredient to formulate seven test feeds, containing graded levels of phytase (0, 500, 650, 800, 950, 1100 and 1250 FTU kg⁻¹). In feeding trial of 70 days, fingerlings were given feed two times in a day at the rate of 4% of wet weight of their bodies and faeces were collected. According to current results, it was found that growth performance parameters i.e. weight gain; 25 g, specific growth rate; 1.67 and feed conversion ratio; 1.10 were improved to maximum at 950 FTU kg⁻¹. Digestibility of nutrients (crude protein; 73%, crude fat; 71% and gross energy; 67%) and minerals absorption was also maximum (Ca; 70%, Zn; 66%, K; 74%, Mn; 66% and P; 71%) at 950 FTU kg⁻¹. Lowest growth efficiency, nutrient digestibility and mineral absorption were observed in fingerlings fed at control diet (0 FTU kg⁻¹). Results of the current study, proved that 950 FTU kg⁻¹ is the most optimum level of phytase to formulate economical and ecofriendly feed for improved growth of C. carpio fingerlings as it decreases the discharge of minerals and nutrients in water bodies.     

Quantifying the potential impact of alien plants of Iran using the Generic Impact Scoring System (GISS) and Environmental Impact Classification for Alien Taxa (EICAT)

Biological Invasions - Assessing the impacts of alien plant species is scientifically important and critical for supporting invasion-related policies. Generic Impact Scoring System (GISS) and...