Sequence and Structural Features of Subsite Residues in GH10 and GH11 Xylanases

Xylanases are the enzymes that breakdown complex plant cell wall polysaccharide xylan into xylose by hydrolysing the β-(1→4) glycosidic linkage between xylosides. They mainly belong to the families GH10 and GH11 of the glycoside hydrolase claβs of enzymes. GH10 xylanases have (α/β)₈-barrel type of fold whereas GH11 xylanases have β-jelly roll type of fold. Both enzymes have several substrate binding subsites. This study analysed in detail the sequence and structural conservation of subsites residues by examining their 3D structures crystallized with homoxylan or its non-hydrolysable form as substrate. A total of 19 structures from GH10 and 6 structures from GH11 were analysed. It was found that in GH10 the subsites -3 to -1 consisted of conserved residues, whereas in GH11 subsites -1, -3 and +1 were found to be conserved. The substrate and subsite interaction analysed based on the presence of h-bonds and CH-π interactions showed that Face-to-Face or Edge-to-Face CH-π interactions are formed in the subsites of GH10, whereas such specific CH-π interactions were no at all observed in case of GH11 xylanases. The spatial conservation of subsite residues was also analysed using a distance matrix based approach. It was found that in GH10 xylanases conserved residues have conserved spatial position of those residues as opposed to GH11 enzymes where in subsites -2 and +2 conserved residues showed non-conservation in their spatial positions. The results presented in this study can be used in discovering new xylanases and in the engineering highly efficient xylanases.     

Evaluation of adaptability to different seasons in goat breeds of semi-arid region in India through differential expression pattern of heat shock protein genes

The present study was conducted to examine differential expression pattern of HSP genes and adaptability in Indian goat breeds of semi-arid region. The study was conducted in five animals from each breed viz. Barbari, Sirohi, and Jhakrana during winter, thermo-neutral and summer seasons. The respiratory rate (RR) and rectal temperature (RT) of the goats were recorded at 09:00 h during the study period. The blood samples were collected for RNA isolation, cDNA synthesis, and quantitative analysis of HSP genes expression by quantitative RT-PCR. The RR increased significantly (p < 0.01) during summer as compared to winter and thermo-neutral season however, RT did not change (p > 0.05) during different seasons. The expression of HSP genes was significantly (p < 0.01) increased during summer (high THI) as compared to thermo-neutral season in all the goat breeds. Among HSPs, only HSP90 was upregulated (p < 0.01) in Jhakrana goats during winter as compared to thermo-neutral season. The deviation in expression of HSP genes during summer and winter with respect to thermo-neutral season was minimum in Barbari goats. Therefore, it can be concluded that Barbari goats possessed better adaptability during summer and winter as compared to Sirohi and Jhakrana goats in semi-arid climatic conditions of India.     

Seed traits,fatty acid profile and genetic diversity assessment in <Emphasis Type="Italic">Pongamia pinnata</Emphasis> (L.) Pierre germplasm

Phenotypic variation of important seed traits like seed length, seed breadth, seed thickness, 100 seed weight and seed oil content were recorded in a total of 157 collected accessions of Pongamia. Out of these, fatty acid profiles of 38 accessions selected based on their high and low oil content was analyzed. Fatty acid profile revealed high variability in stearic, oleic and linoleic acid which varied from 0.42 to 10.61 %, 34.34 to 74.58 %, and 7.00 to 31.28 % respectively. Variations in palmitic and linolenic acid were small. Iodine value, saponification number and cetane number (CN) of fatty acid methyl esters (FAME) of seed oil ranges from 186.99 to 201.25, 81.13 to 108.19 and 46.16 to 56.47 respectively. Fatty acid compositions, degree of unsaturation and CN are the important parameters, which are used to determine quality of FAME were used as biodiesel. Some of the Pongamia accessions identified were higher in oil content while some accessions showed higher degree of unsaturation and a few of them had CN values higher than 55. Genetic diversity analysis with six TE-AFLP primers generated a total of 334 bands out of which 174 (52.10 %) were polymorphic. The genetic similarity ranged from 0.11 to 0.47. These findings clearly showed high level of genetic diversity and all economically desirable traits were not present in a single genotype of Pongamia. All these traits could be selected from these CPTs and transfer to a single elite variety through selection and breeding programme and could be utilized for large scale multiplication and plantation to produce high quantity and quality biodiesel in future.     

Analysis of genetic diversity and population structure in <Emphasis Type="Italic">Capsicum</Emphasis> landraces from North Eastern India using TE-AFLP markers

North eastern (NE) India harbours a precious germplasm repository of Capsicum in the form of various landraces. The present study was undertaken to characterise the extent of genetic variation present in different Capsicum landraces from north eastern India. A set of 171 Capsicum accessions were characterised using three-endonuclease amplified fragment length polymorphism (AFLP) markers. Out of 416 bands obtained from six primer combinations, 254 (61 %) were polymorphic. The pairwise genetic dissimilarity among accessions ranged from 0.03 to 0.97. Cluster analysis based on neighbour joining showed two major clusters. Cluster I contained most of the bhut jolokia accessions whereas cluster II contained all of the Capsicum annuum genotypes. Similar grouping was observed with population STRUCTURE analysis as well as principle coordinate analysis. Analysis of molecular variance (AMOVA) revealed 45 and 54 % variation among and within populations, respectively. This information on population structure analysis and molecular characterisation will be helpful for effective utilisation of this germplasm in Capsicum improvement programs.     

A review of survival estimates for raptors and owls

This paper reviews the literature on survival estimates for different species of raptors and owls, examines the methods used to obtain the estimates, and draws out some general patterns arising. Estimating survival usually involves the marking of birds so that they can be recognized as individuals on subsequent encounters. Annual survival can then be estimated from: (1) birds ringed at known age (usually as nestlings) and subsequently reported by members of the public (usually as found dead), the ratio of recoveries at different ages being used to calculate annual survival; (2) marked breeding adults, trapped or re‐sighted in subsequent years in particular study areas, with the proportion re‐trapped (or re‐sighted) in each year being taken as the minimum annual survival; (3) live encounter (trapped or re‐sighted) of birds marked either as nestlings or breeding adults analysed using the capture–mark–recapture (or re‐sighting) methods to estimate annual survival; (4) a combination of reports of known‐age dead birds and re‐trapping/re‐sighting of live birds; (5) use of radio‐ or satellite‐tracking to follow the fates of individuals; and (6) the integration of these methods with other information, such as change in numbers between years, to derive estimates of survival and other demographic parameters. Studies confined to particular areas usually give estimates of ‘apparent annual survival’, because they take no account of birds that leave the area. However, radio‐ or satellite‐tracking makes it possible to estimate true survival, including survival of prebreeders that have low natal‐site fidelity (this usually requires satellite telemetry). As in other birds, the preferred method for estimating survival has changed over time, as new and more robust methods of estimation have been developed. Methods 1 and 2 were the first to be developed, but without statistical underpinning, while methods 3–6 were developed later on the basis of formal statistical models. This difference has to be borne in mind in comparing older with newer estimates for particular species. Published survival estimates were found for three species of Cathartidae, one of Pandionidae, 29 of Accipitridae, 12 of Falconidae, one of Tytonidae and nine of Strigidae, almost all from temperate Northern Hemisphere species. In most of these species more than one estimate was available, and in some separate estimates for different age or sex groups. The main patterns to emerge included: (1) a significant tendency for annual adult survival to increase with body weight, smaller species having annual survival rates mainly of 60–70%, medium‐sized species having rates mainly in the range 70–90% and the largest having rates of > 90%, in the absence of obvious human‐caused losses; (2) a lower survival in the first or prebreeding years of life than in subsequent years; (3) a lack of obvious or consistent differences in survival between the sexes, where these could be distinguished; and (4) in the few species for which enough data were available, a decline in annual survival rates in the later years of life.     

Network-based approaches for linking metabolism with environment

Progress in the reconstruction of genome-wide metabolic maps has led to the development of network-based computational approaches for linking an organism with its biochemical habitat.     

TDZ-induced direct shoot organogenesis and somatic embryogenesis on cotyledonary node explants of lentil (Lens culinaris Medik.)

An efficient and simple procedure for inducing high frequency direct shoot organogenesis and somatic embryogenesis in lentil from cotyledonary node explants (without both the cotyledons) in response to TDZ alone is reported. TDZ at concentration lower than 2.0 μM induced shoot organogenesis whereas at higher concentration (2.5–15 μM) it caused a shift in regeneration from shoot organogenesis to somatic embryogenesis. The cotyledonary node and seedling cultures developed only shoots even at high concentrations of BAP and TDZ, respectively. TDZ at 0.5 and 5.0 μM was found to be optimal for inducing an average of 4–5 shoots per cotyledonary node in 93 % of the cultures and 55 somatic embryos in 68 % of the cultures, respectively. The somatic embryos were germinated when transferred to lower TDZ concentration (0.5–1.0 μM). The shoots were rooted on MS basal medium containing 2.5 μM IBA. The plantlets were obtained within 8 weeks from initiation of culture and were morphologically similar to seed-raised plants. The possible role of stress in thidiazuron induced somatic embryogenesis is discussed.Key words: Thidiazuron, Lens culinaris, Somatic embryogenesis, Organogenesis     

Iridoid glycosides from Gmelina arborea

Three iridoid glycosides 6-O-(3'-O-benzoyl)-alpha-l-rhamnopyranosylcatalpol (1a), 6-O-(3'-O-trans-cinnamoyl)-alpha-l-rhamnopyranosylcatalpol (2a) and 6-O-(3'-O-cis-cinnamoyl)-alpha-l-rhamnopyranosylcatalpol (3a) were isolated from aerial parts of Gmelina arborea and structures were elucidated by spectral analysis. Additionally a known iridoid 6-O-(3', 4'-O-dibenzoyl)-alpha-l-rhamnopyranosylcatalpol (4) was also isolated and identified.