A complete mapping of the proteins in the small ribosomal subunit of Escherichia coli

The relative positions of the centers of mass of the 21 proteins of the 30S ribosomal subunit from Escherichia coli have been determined by triangulation using neutron scattering data. The resulting map of the quaternary structure of the small ribosomal subunit is presented, and comparisons are made with structural data from other sources.     

Visualizing tmRNA entry into a stalled ribosome

Bacterial ribosomes stalled on defective messenger RNAs (mRNAs) are rescued by tmRNA, an approximately 300-nucleotide-long molecule that functions as both transfer RNA (tRNA) and mRNA. Translation then switches from the defective message to a short open reading frame on tmRNA that tags the defective nascent peptide chain for degradation. However, the mechanism by which tmRNA can enter and move through the ribosome is unknown. We present a cryo-electron microscopy study at approximately 13 to 15 angstroms of the entry of tmRNA into the ribosome. The structure reveals how tmRNA could move through the ribosome despite its complicated topology and also suggests roles for proteins S1 and SmpB in the function of tmRNA.     

Carboxyl terminus heterogeneity of type IV fimbrial subunit protein of Pasteurella multocida isolates

Pasteurella multocida, a Gram-negative bacterial pathogen, known to affect a wide range of domestic as well as wild animal and avian species throughout the world by causing either systemic or localized infections termed as ‘pasteurellosis’. P. multocida isolates are known to possess type IV fimbriae (pili) as one of the major virulence factors based on their role in adhesion to host surfaces and subsequent pathogenesis. In the present study, ptfA gene of Indian P. multocida isolates (n?=?8) originated from different animal (buffalo, sheep, goat, pig) and avian host species (chicken, turkey, duck, quail) were amplified, cloned, sequenced and compared with available ptfA/fimbrial protein sequences in GenBank/publications (n?=?22) to understand its variability with respect to geography/host/serogroup/disease specific patterns. Multiple sequence alignment revealed highly conserved N-terminus α-1 helix region and heterogeneous C-terminus (68–137 aa) comprised of β-strand regions (β1, β2, β3, β4) with conserved two pairs of cysteine residues. Interestingly, an existence of absolute homogeneity among the P. multocida isolates that caused haemorrhagic septicaemia in bovines and septicaemic pasteurellosis in sheep and goats was noticed. Pig isolates had 99.3 % homogeneity. On contrary, more diversity (35.8 %) was observed among isolates that caused fowl cholera in avians irrespective of identical capsular/somatic serogroup and similar host species. Phylogenetic analysis based on nucleotide sequences of ptfA gene revealed formation of mixed clusters with isolates representing different disease conditions as well as serogroups irrespective of country of origin which indicated the possible role of cross-species transmission among different animal/avian species. The study indicated highly conserved and host specific fimbriae among animal species than relatively divergent fimbriae among avian species.     

Growth strategy of trees related to successional status I. Architecture and extension growth

The architecture and growth pattern of early (Alnus nepalensis and Schima khasiana) and late (Machilus kingii, Quercus dealbata and Q. griffithii) successional tree species in a sub-tropical montane, humid, evergreen forest at Upper Shillong (1900 m) in north-east India were analyzed and related to their ecological strategy for niche occupancy in the forest ecosystem. In the early successional species the architectural development pattern and growth design are geared to maximize production under high light environments. These trees have an indeterminate pattern of shoot growth, a prolonged growth period with greater extension growth and rhythmicity (except for A. nepalensis with continuous growth) and branch mainly by syllepsis. These species emphasize vertical growth at the expense of lateral spread. In contrast, the late successional species make modest growth under a determinate scheme, the growth being confined to preformed bud primordia for a brief period of the growing season. There is less rhythmicity in growth and branch productin is by prolepsis. These species emphasize lateral spread, as an adaptation to highly competitive environments. In forest situations these species have one determinate flush of shoot growth only but in open situations there were two such flushes. Bifurcation ratio values are found to vary in forest and open situations, suggesting the capacity of the species to adjust their architecture to changed light conditions.     

Characterization of a begomovirus causing horsegram yellow mosaic disease in India

The virus causing horsegram (Macrotyloma uniflorum) yellow mosaic disease has been shown to be a typical Old World bipartite begomovirus. The viral origin of the disease has been established through agroinoculation of horsegram using partial tandem repeat clones of both DNA-A and DNA-B. The DNA-A genome shows less than 89% identity with the corresponding sequences of all the begomoviruses in the databases earlier to this sequence submission (AJ627904). Therefore Horsegram yellow mosaic virus (HgYMV-[IN:Coi]) can be considered to be a new species of the genus Begomovirus (family Geminiviridae). Phylogenetic analysis shows that this virus is part of the cluster of mungbean yellow mosaic viruses of legumes from South and South East Asia.     

The major quantitative trait locus for mungbean yellow mosaic Indian virus resistance is tightly linked in repulsion phase to the major bruchid resistance locus in a cross between mungbean [Vigna radiata (L.) Wilczek] and its wild relative Vigna radiata ssp. sublobata

Mungbean yellow mosaic Indian virus (MYMIV) and bruchid infestation are severe production constraints of mungbean in South Asia, a major global mungbean production area. Marker-assisted selection for resistance against these disorders while maintaining or even improving agronomic traits is an important step toward breeding elite mungbean varieties. This study employed recombinant inbred lines (F12) derived from a cross between MYMIV-tolerant Vigna radiata NM92 and bruchid-resistant V. radiata ssp. sublobata TC1966 to identify chromosomal locations associated with disease and insect pest resistance and seed traits. A linkage map comprising 11 linkage groups was constructed with random amplified polymorphic DNA (RAPD), sequence characterized amplified regions (SCAR), cleaved amplified polymorphic DNA (CAP), amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. Quantitative trait loci (QTLs) for MYMIV and bruchid resistance, 100 seed weight and seed germination rate were identified. Three major QTLs for MYMIV and one major bruchid resistance locus were mapped on LG 9. The resistance alleles were contributed by the MYMIV tolerant parent NM92 and the bruchid resistant parent TC1966 respectively. One of the MYMIV QTLs was tightly linked in repulsion phase to the bruchid resistance locus. In addition, three minor QTLs for MYMIV resistance were found, where the resistance alleles were contributed by TC1966. Lines combining MYMV resistance alleles from both parents have greater resistance to MYMIV than the tolerant parent. Two minor bruchid resistance QTLs were identified in TC1966. Furthermore, three QTLs each for 100 seed weight and germination rate were detected. The markers defining the QTLs identified in this study will be useful in marker-assisted breeding of improved mungbean varieties in the future.     

Successional patterns and gap phase dynamics of a humid tropical forest of the Western Ghats of Kerala, India: ground vegetation, biomass, productivity and nutrient cycling

The population dynamics of the ground vegetation and its energetics such as biomass accumulation and net primary productivity, and the nutrient cycling patterns in the humid tropical forest of the Western Ghats in India are largely determined by gap age and by whether gaps are formed naturally or through selection felling. Responses of plant categories such as herbs, shrubs, tree seedlings and saplings also vary depending upon gap type and age. An exotic species such as Chromolaena odorata occurred only in selection-felled gaps ((9 ± 3)−(49 ± 4) individuals (100 m)⁻²). Nilgirianthus ciliatus, a dominant shrub, plays a key role in the gaps in determining population dynamics of others. The net primary productivity of the ground vegetation, which is about 31.17 ± 4.26 kg (100 m)⁻² year⁻¹ in an undisturbed site, increased a year after gap formation to 102.82 ± 6.46 kg (100 m)⁻² year⁻¹ in natural gaps and to 71.82 ± 2.36 kg (100 m)⁻² year⁻¹ in selection-felled gaps. Five years after gap formation, net primary productivity of the ground vegetation declined considerably, this being related to decline in fast-growing shrub and secondary tree species in the vegetation and gap closure. A similar trend was also recorded for the rates of nutrient uptake and nutrient accumulation in the vegetation.

In natural gaps the soil nutrient level increased gradually with gap age. This could be attributed to slow release of nutrients from the fallen trunks and nutrient storage in the rapidly recovering vegetation. In contrast, in selection-felled gaps, the quantities of soil nutrients such as nitrogen, phosphorus and magnesium were higher in 1-year-old gaps than in undisturbed sites, owing to the release of these nutrients from leaf litter and wood debris which were deposited in larger quantities within the gap itself, and owing to sparse ground vegetation resulting from the greater disturbance of the soil, in the first 1 or 2 years. The fractional annual turnover rates of elements of the ground vegetation and the soil were higher in 1-year-old gaps and declined with gap age. The significance of these results for forest management is discussed.     

Genetic variability and heritability estimates for hardseededness and flowering in balansa clover (Trifolium michelianum Savi) populations

Suitability of annual pasture legume species like balansa clover (Trifolium michelianum Savi) in southern Australian farming systems depends on their hardseededness and time to flowering. Late maturing varieties with increased rate of hardseed breakdown, particularly in the late summer—early autumn period are desirable to ensure reliable regeneration in permanent pastures. Two half-sib family balansa clover populations were used to estimate heritability for the rate of breakdown of hardseededness and time to flowering. High narrow-sense heritability estimates (90.5–96.1%, rate of hardseed breakdown; 85.9–94.5%, time to flowering) were obtained, and were mainly attributed to additive gene effects. There was no relationship between rate of hardseed breakdown and time to flowering in Group1 half-sib family, which indicated that selection for both traits could be undertaken independently. In half-sib family Group 2 the relationship between the two traits suggested the possibility of selecting late maturing cultivars with increased rate of hardseed breakdown. Significant differences in time to flowering and rate of hardseed breakdown both within and between the two half-sib family groups suggested that phenotypic recurrent selection would be effective in improving the traits in these populations.