AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses

Background  

Large multigene sequence alignments have over recent years been increasingly employed for phylogenomic reconstruction of the eukaryote tree of life. Such supermatrices of sequence data are preferred over single gene alignments as they contain vastly more information about ancient sequence characteristics, and are thus more suitable for resolving deeply diverging relationships. However, as alignments are expanded, increasingly numbers of sites with misleading phylogenetic information are also added. Therefore, a major goal in phylogenomic analyses is to maximize the ratio of information to noise; this can be achieved by the reduction of fast evolving sites.     

Growth and survival potentials of immobilized diazotrophic cyanobacterial isolates exposed to common ricefield herbicides

Summary The effect of graded concentrations of four common ricefield herbicides (Arozin, Butachlor, Alachlor, 2,4-D) on diazotrophic growth, macromolecular contents, heterocyst frequency and tolerance potentials of Ca-alginate immobilized diazotrophic cyanobacterial isolates Nostoc punctiforme, N. calcicola, Anabaena variabilis, Gloeocapsasp., Aphanocapsa sp. and laboratory strain N. muscorum ISU (Anabaena ATCC 27893) was studied and compared with free-living cultures. Cyanobacterial isolates showed progressive inhibition of growth with increasing dosage of herbicides in both free and immobilized states. There were significant differences in the relative toxicity of the four herbicides. Arozin proved to be more growth toxic in comparison to Alachlor, Butachlor and 2,4-D. Growth performance of the immobilized cyanobacterial isolates under herbicide stress showed a similar diazotrophic growth pattern to free cells with no difference in lethal and sub-lethal dosages. However, at lethal concentrations of herbicides, the immobilized cells exhibited prolonged survivability of 14–16 days as compared to their free-living counterparts (8–12 days). The decline in growth, macromolecular contents and heterocyst frequency was found to be similar in both the states in graded dosages of herbicides. Of the test organisms, A. variabilis showed maximum natural tolerance towards all the four herbicides tested. Evidently immobilization by Ca-alginate seems to provide protection to the diazotrophic cyanobacterial inoculants to a certain extent against the growth-toxic action of herbicides.     

Integration of Leprosy Elimination into Primary Health Care in Orissa,India

Background

Leprosy was eliminated as a public health problem (<1 case per 10,000) in India by December 2005. With this target in sight the need for a separate vertical programme was diminished. The second phase of the National Leprosy Eradication Programme was therefore initiated: decentralisation of the vertical programme, integration of leprosy services into the primary health care (PHC) system and development of a surveillance system to monitor programme performance.

Methodology/Principal Findings

To study the process of integration a qualitative analysis of issues and perceptions of patients and providers, and a review of leprosy records and registers to evaluate programme performance was carried out in the state of Orissa, India. Program performance indicators such as a low mean defaulter rate of 3.83% and a low-misdiagnosis rate of 4.45% demonstrated no detrimental effect of integration on program success. PHC staff were generally found to be highly knowledgeable of diagnosis and management of leprosy cases due to frequent training and a support network of leprosy experts. However in urban hospitals district-level leprosy experts had assumed leprosy activities. The aim was to aid busy PHC staff but it also compromised their leprosy knowledge and management capacity. Inadequate monitoring of a policy of ‘new case validation,’ in which MDT was not initiated until primary diagnosis had been verified by a leprosy expert, may have led to approximately 26% of suspect cases awaiting confirmation of diagnosis 1–8 months after their initial PHC visit.

Conclusions/Significance

This study highlights the need for effective monitoring and evaluation of the integration process. Inadequate monitoring could lead to a reduction in early diagnosis, a delay in initiation of MDT and an increase in disability rates. This in turn could reverse some of the programme''s achievements. These findings may help Andhra Pradesh and other states in India to improve their integration process and may also have implications for other disease elimination programmes such as polio and guinea worm (dracunculiasis) as they move closer to their elimination goals.     

Draft genome sequence of the nitrophenol-degrading actinomycete Rhodococcus imtechensis RKJ300

We report the 8.231-Mb genome sequence of Rhodococcus imtechensis RKJ300, isolated from pesticide-contaminated soil in Punjab, India. The genome sequence of the strain RKJ300 will be helpful in exploring the molecular pathways involved in the degradation of nitrophenols.     

Membrane Fusion Triggering: THREE MODULES WITH DIFFERENT STRUCTURE AND FUNCTION IN THE UPPER HALF OF THE MEASLES VIRUS ATTACHMENT PROTEIN STALK*

The measles virus (MV) fusion apparatus consists of a fusion protein and an attachment protein named hemagglutinin (H). After receptor-binding through its cuboidal head, the H-protein transmits the fusion-triggering signal through its stalk to the fusion protein. However, the structural basis of signal transmission is unclear because only structures of H-heads without their stalk have been solved. On the other hand, the entire ectodomain structure of the hemagglutinin-neuraminidase protein of another Paramyxovirus revealed a four-helix bundle stalk. To probe the structure of the 95-residue MV H-stalk we individually substituted head-proximal residues (positions 103–153) with cysteine, and biochemically and functionally characterized the resultant proteins. Our results indicate that most residues in the central segment (positions 103–117) can be cross-linked by engineered disulfide bonds, and thus may be engaged in a tetrameric structure. While covalent tetramerization disrupts fusion triggering function, disulfide bond reduction restores it in most positions except Asp-113. The next stalk segment (residues 123–138) also has high propensity to form covalent tetramers, but since these cross-links have little or no effect on function, it can conduct the fusion-triggering signal while remaining in a stabilized tetrameric configuration. This segment may act as a spacer, maintaining H-heads at an optimal height. Finally, the head-proximal segment (residues 139–154) has very limited propensity to trap tetramers, suggesting bifurcation into two flexible linkers clamped by inter-subunit covalent links formed by natural Cys-139 and Cys-154. We discuss the modular structure of the MV H-stalk in the context of membrane fusion triggering and cell entry by Paramyxoviruses.     

Effect of alloxan-diabetes and subsequent treatment with insulin on kinetic properties of succinate oxidase activity from rat liver mitochondria

We evaluated early and late effects of alloxan-diabetes and subsequent insulin treatment on the kinetic properties of succinate oxidase (SO) in rat liver mitochondria. Diabetic state lowered the SO activity; insulin treatment was effective in restoring the activity only in one-week diabetic rats. The energies of activation in low and high temperature ranges (EH and EL) decreased significantly in diabetic animals; once again insulin treatment was partially effective only in the one-week diabetic group. The total phospholipids (TPL) and cholesterol (CHL) contents did not change in one-week groups. In one-month diabetic animals TPL decreased while CHL increased; insulin treatment induced further changes without restoring normality. The lysophospholipid (Lyso), sphingomyelin (SPM), phosphatidylinositol (PI) and phosphatidylserine (PS) content increased in the diabetic state while phosphatidylcholine (PC) and phosphatidylethanolamine (PE) decreased. Insulin treatment had a partial restorative effect. The changes in EH correlated negatively with SPM. The phase transition temperature, Tt, decreased in diabetic and insulin-treated groups. These changes correlated positively with the ratios of TPL/PI and TPL/PS. The membrane fluidity decreased in the diabetic state; insulin had a restorative effect only in the one-week group.     

Effect of gamma irradiation on microbial load,aflatoxins and phytochemicals present in Trigonella foenum-graecum

The effects of gamma irradiation on microbial load, total aflatoxins and phytoconstituents content of Trigonella foenum-graecum have been studied. Gamma irradiation at a dose of 2.5 kGy resulted in 2 log reduction of the total aerobic microbial count. A complete sterilization was, however, observed at 10 kGy. The total aflatoxin level decreased gradually with increase in gamma irradiation dose as compared to its un-irradiated counterparts, whereas the high performance liquid chromatography (HPLC) profile showed no change in the levels of phytochemicals up to the gamma irradiation dose of 10 kGy. HPLC profiles, however, differed in peak areas, and retention times of the components. These results suggest that gamma irradiation at a dose of 5.0 kGy was very effective for microbial decontamination because it did not adversely affect the active components of T. foenum-graecum.     

NaCl induced metabolic changes in the diazotrophic cyanobacterium <Emphasis Type="Italic">Anabaena cylindrica</Emphasis>

NaCl induced changes in fatty acid composition and nitrogenase, glutamine synthetase (GS) and nitrate reductase (NR) activities have been studied in a diazotrophic cyanobacterium Anabaena cylindrica. GC-MS analysis revealed that the cellular fatty acid composition of NaCl untreated cells of A. cylindrica contained saturated and unsaturated fatty acids in high (85.15%) and low (13.17%) proportions, respectively. In contrast, NaCl adapted cells of A. cylindrica had reduced and increased levels of saturated (45.2%) and unsaturated (40%) fatty acids, respectively. It had a higher overall level of fatty acid unsaturation under NaCl stress mainly due to increase in C12:4, C10:1, C16:1 and C18:2 constituents. The activities of nitrogenase, GS and NR were reduced significantly in NaCl adapted cells as compared to its NaCl untreated counterparts.