Computational and experimental analysis reveals a novel Src family kinase in the C. elegans genome

MOTIVATION: The complete genomes of a number of organisms have already been sequenced. However, the vast majority of annotated genes are derived by gene prediction methods. It is important to not only validate the predicted coding regions but also to identify genes that may have been missed by these programs. METHODS: We searched the entire C.elegans genomic sequence database maintained by the Sanger Center using human c-Src sequence in a TBLASN search. We have confirmed one of the predicted regions by isolation of a cDNA and carried out a phylogenetic analysis of Src kinase family members in the worm, fly and several vertebrate species. RESULTS: Our analysis identified a novel tyrosine kinase in the C.elegans genome that contains functional features typical of the Src family kinases that we have designated as Src-1. The open reading frame contains a conserved N-terminal myristoylation site and a tyrosine residue within the C-terminus that is crucial for regulating the activity of Src kinases. Our phylogenetic analysis of Src family members from C. elegans, Drosophila and other higher organisms revealed a relationship among Src kinases from C. elegans and Drosophila.     

Immobilization Results in Sustained Calcium Transport in Nostoc calcicola Bréb

The uptake pattern of Ca²⁺ by the cyanobacterium Nostoc calcicola Bréb in its freely suspended and immobilized form is comprised of two distinct phages; (a) rapid uptake for 1^st 10 min followed by (b) slower transport at least up to 60 min. Entrapment of cyanobacterial cells in polyvinyl foam always maintained a higher Ca²⁺ profile over freely suspended cells. Also, the intracellular Ca²⁺ concentration was three times more in the former under similar experimental conditions. Whereas, illumination supported maximum Ca²⁺ transport in all the sets, darkness resulted in drastic reduction (90%) of Ca²⁺ uptake in freely suspended cells and least (15%) in polyvinyl entrapped cyanobacterial cells. Exogenously added ATP (10 μM) on the other hand, enhanced Ca²⁺ uptake in dark incubated freely suspended cells; ATP at the same concentration failed to bring out any significant enhancement in cation uptake in immobilized cells facing dark exposure. It was observed that these cells were still able to sustain sufficient ATP preserves to drive active transport of Ca²⁺ even in the dark. Furthermore, the immobilized cells exhibited remarkable Ca²⁺ transport rate even at the age of 20 and 50 days at which its free living counterpart took up insignificant Ca²⁺. These findings suggest the improved metabolic efficiency of polyvinyl foam entrapped cells over freely suspended cells in terms of Ca²⁺ accumulation and its possible use as a bioreactor for metal accumulation/removal in repetitive cycles without any measurable loss in cell biomass. Received: 21 May 2001 / Accepted: 27 June 2001     

Vitamin K uptake in hepatocytes and hepatoma cells

Hepatocellular carcinoma (HCC) or hepatoma cells have impaired ability to perform vitamin K-dependent carboxylation reactions. Vitamin K can also inhibit growth of HCC cells in vitro. Both carboxylation and growth inhibition are vitamin K dose dependent. We used rat hepatocytes, a vitamin K-growth sensitive (MH7777) and a vitamin K-growth resistant (H4IIE) rat hepatoma cell line to examine vitamin K uptake and vitamin K-mediated microsomal carboxylation. We found that vitamin K is taken up by normal rat hepatocytes against a saturable concentration gradient. The relative rates of uptake by rat hepatocytes and the two rat cell lines MH7777 and H4IIE correlated with their sensitivity to vitamin K-mediated cell growth inhibition. Pooled hepatocytes from liver nodules from rats treated with the hepatocarcinogen diethylnitrosamine (DEN) also had a reduced rate of vitamin K uptake. However, using a cell-free system, microsomes from both normal rat hepatocytes and the two rat hepatoma cell lines had a similar ability to support carboxylation mediated by exogenously added vitamin K. The results support the hypothesis that different sensitivity of hepatoma cells to vitamin K may be due to differences in vitamin K uptake and may be unrelated to the actions of vitamin K on carboxylation.     

Microbial metabolites as eco-friendly agrochemicals for the next millennium

As a result of the increasing environmental and health-related problems caused by the synthetic agrochemicals currently used, suitable and non-hazardous innovative alternatives are being sought. Antagonism and allelopathy, both in nature and in agro-ecosystems, have attracted these researchers' attention, with the main goal of using these phenomena in the biological control of weeds. This article presents a review on the use and efficacy of microbial secondary metabolites which have potential as natural herbicides, either directly or as templates for bio-rational eco-friendly agrochemicals (allelochemicals). Their merits as alternatives to synthetic chemicals and biological control agents have been highlighted for an holistic approach in integrated pest/weed management.     

Evidence for the nitrate assimilation-dependent nitrite excretion in cyanobacterium Nostoc MAC

Nitrate uptake and nitrite efflux patterns in Nostoc MAC showed a rapid phase followed by their saturation. Nitrite efflux was maximum in nitrate medium whereas the cells incubated in N₂ and NH ₄ ⁺ media exhibited a decreased nitrite efflux activity. The simultaneous presence of NH ₄ ⁺ and nitrate significantly decreased nitrite efflux. L-Methionine-Dl-sulphoximine (MSX) prevented inhibition of nitrite efflux by NH ₄ ⁺ . In the dark there was negligible nitrite efflux, whereas illumination increased the rate of nitrite efflux significantly. The nitrite efflux system was maximally operative at pH 8.0, 30°C and a photon fluence rate of 50 mol m^-2. s^-1. These results confirm that (i) the nitrite efflux system in Nostoc MAC is dependent upon nitrate uptake and assimilation and is repressible by NH ₄ ⁺ ; (ii) NH ₄ ⁺ itself is not the actual repressor of nitrite efflux; a product of NH ₄ ⁺ assimilation via glutamine synthetase (GS) is required for repression to occur; (iii) the catalytic function of GS does not appear to be involved in nitrate assimilation-dependent nitrite efflux, and (iv) the optimum pH, temperature and illumination for maximum nitrite efflux were found to be 8.0, 30°C and 50mol m^-2. s respectively.B.B. Singh, P.K. Pandey and P.S. Bisen are with the Department of Microbiology, Barkatullah University. Bhopal 462026, India. S.Singh is with the Department of Microbiology, School of Life Sciences, North Maharashtra University, Jalgaon, India     

Bio-ethanol from water hyacinth biomass: An evaluation of enzymatic saccharification strategy

Biomass feedstock having less competition with food crops are desirable for bio-ethanol production and such resources may not be localized geographically. A distributed production strategy is therefore more suitable for feedstock like water hyacinth with a decentralized availability. In this study, we have demonstrated the suitability of this feedstock for production of fermentable sugars using cellulases produced on site. Testing of acid and alkali pretreatment methods indicated that alkali pretreatment was more efficient in making the sample susceptible to enzyme hydrolysis. Cellulase and β-glucosidase loading and the effect of surfactants were studied and optimized to improve saccharification. Redesigning of enzyme blends resulted in an improvement of saccharification from 57% to 71%. A crude trial on fermentation of the enzymatic hydrolysate using the common baker’s yeast Saccharomyces cerevisiae yielded an ethanol concentration of 4.4 g/L.     

On the roles of Notch, Delta, kuzbanian, and inscuteable during the development of Drosophila embryonic neuroblast lineages

The generation of cellular diversity in the nervous system involves the mechanism of asymmetric cell division. Besides an array of molecules, including the Par protein cassette, a heterotrimeric G protein signalling complex, Inscuteable plays a major role in controlling asymmetric cell division, which ultimately leads to differential activation of the Notch signalling pathway and correct specification of the two daughter cells. In this context, Notch is required to be active in one sibling and inactive in the other. Here, we investigated the requirement of genes previously known to play key roles in sibling cell fate specification such as members of the Notch signalling pathway, e.g., Notch (N), Delta (Dl), and kuzbanian (kuz) and a crucial regulator of asymmetric cell division, inscuteable (insc) throughout lineage progression of 4 neuroblasts (NB1-1, MP2, NB4-2, and NB7-1). Notch-mediated cell fate specification defects were cell-autonomous and were observed in all neuroblast lineages even in cells born from late ganglion mother cells (GMC) within the lineages. We also show that Dl functions non-autonomously during NB lineage progression and clonal cells do not require Dl from within the clone. This suggests that within a NB lineage Dl is dispensable for sibling cell fate specification. Furthermore, we provide evidence that kuz is involved in sibling cell fate specification in the central nervous system. It is cell-autonomously required in the same postmitotic cells which also depend on Notch function. This indicates that KUZ is required to facilitate a functional Notch signal in the Notch-dependent cell for correct cell fate specification. Finally, we show that three neuroblast lineages (NB1-1, NB4-2, and NB7-1) require insc function for sibling cell fate specification in cells born from early GMCs whereas insc is not required in cells born from later GMCs of the same lineages. Thus, there is differential requirement for insc for cell fate specification depending on the stage of lineage progression of NBs.     

Bioactivity of the compounds in genus Dysoxylum

The diets of the wolf Canis lupus, red fox Vulpes vulpes and raccoon dog Nyctereutes ussurienusis Matschie were studied in the grassland of eastern Inner Mongolia from August to October in 2007 and from March to July in 2008. Feces were collected from dens and latrines. The frequency of occurrence and the dry weight of the remains of each food item in the feces were calculated. Livestock (50.65% frequency of occurrence) constituted the bulk of the wolf diet, while small rodents (76.31% frequency of occurrence) were most frequently eaten by the foxes. Small rodents (22.69% frequency of occurrence) were important to the raccoon dogs but they also frequently consumed birds (39.81% frequency of occurrence) and insects (26.39% frequency of occurrence). The wolf was the most omnivorous and the red fox was the least omnivorous of these three kinds of canidae according to the diversity index. The food niches of the wolf and the red fox overlapped more than that of the raccoon dog and other species. These three kinds of canidae shared many resources and consequently competition occurred to them. However, their diets also differed to some extent which helped them to avoid competition. Furthermore, raccoon dogs were dormant in winter when food was scarce, which may be the reason why all these species could coexist in a rather unproductive grassland.     

Analysis of Genetic Diversity of Persea bombycina “Som” Using RAPD-Based Molecular Markers

The utility of RAPD markers in assessing genetic diversity and phenetic relationships in Persea bombycina, a major tree species for golden silk (muga) production, was investigated using 48 genotypes from northeast India. Thirteen RAPD primer combinations generated 93 bands. On average, seven RAPD fragments were amplified per reaction. In a UPGMA phenetic dendrogram based on Jaccard’s coefficient, the P. bombycina accessions showed a high level of genetic variation, as indicated by genetic similarity. The grouping in the phenogram was highly consistent, as indicated by high values of cophenetic correlation and high bootstrap values at the key nodes. The accessions were scattered on a plot derived from principal correspondence analysis. The study concluded that the high level of genetic diversity in the P. bombycina accessions may be attributed to the species’ outcrossing nature. This study may be useful in identifying diverse genetic stocks of P. bombycina, which may then be conserved on a priority basis.