Prediction of GTP interacting residues,dipeptides and tripeptides in a protein from its evolutionary information

Background  

Guanosine triphosphate (GTP)-binding proteins play an important role in regulation of G-protein. Thus prediction of GTP interacting residues in a protein is one of the major challenges in the field of the computational biology. In this study, an attempt has been made to develop a computational method for predicting GTP interacting residues in a protein with high accuracy (Acc), precision (Prec) and recall (Rc).     

Identification of NAD interacting residues in proteins

Background  

Small molecular cofactors or ligands play a crucial role in the proper functioning of cells. Accurate annotation of their target proteins and binding sites is required for the complete understanding of reaction mechanisms. Nicotinamide adenine dinucleotide (NAD⁺ or NAD) is one of the most commonly used organic cofactors in living cells, which plays a critical role in cellular metabolism, storage and regulatory processes. In the past, several NAD binding proteins (NADBP) have been reported in the literature, which are responsible for a wide-range of activities in the cell. Attempts have been made to derive a rule for the binding of NAD⁺ to its target proteins. However, so far an efficient model could not be derived due to the time consuming process of structure determination, and limitations of similarity based approaches. Thus a sequence and non-similarity based method is needed to characterize the NAD binding sites to help in the annotation. In this study attempts have been made to predict NAD binding proteins and their interacting residues (NIRs) from amino acid sequence using bioinformatics tools.     

Effects of neonatal neural progenitor cell implantation on adult neuroanatomy and cognition in the Ts65Dn model of Down syndrome

As much of the aberrant neural development in Down syndrome (DS) occurs postnatally, an early opportunity exists to intervene and influence life-long cognitive development. Recent success using neural progenitor cells (NPC) in models of adult neurodegeneration indicate such therapy may be a viable option in diseases such as DS. Murine NPC (mNPC, C17.2 cell line) or saline were implanted bilaterally into the dorsal hippocampus of postnatal day 2 (PND 2) Ts65Dn pups to explore the feasibility of early postnatal treatment in this mouse model of DS. Disomic littermates provided karyotype controls for trisomic pups. Pups were monitored for developmental milestone achievement, and then underwent adult behavior testing at 14 weeks of age. We found that implanted mNPC survived into adulthood and migrated beyond the implant site in both karyotypes. The implantation of mNPC resulted in a significant increase in the density of dentate granule cells. However, mNPC implantation did not elicit cognitive changes in trisomic mice either neonatally or in adulthood. To the best of our knowledge, these results constitute the first assessment of mNPC as an early intervention on cognitive ability in a DS model.     

Improving the genetic representation of rare taxa within complex microbial communities using DNA normalization methods

Complex microbial communities typically contain a large number of low abundance species, which collectively, comprise a considerable proportion of the community. This ‘rare biosphere’ has been speculated to contain keystone species and act as a repository of genomic diversity to facilitate community adaptation. Many environmental microbes are currently resistant to cultivation, and can only be accessed via culture‐independent approaches. To enhance our understanding of the role of the rare biosphere, we aimed to improve their metagenomic representation using DNA normalization methods, and assess normalization success via shotgun DNA sequencing. A synthetic metagenome was constructed from the genomic DNA of five bacterial species, pooled in a defined ratio spanning three orders of magnitude. The synthetic metagenome was fractionated and thermally renatured, allowing the most abundant sequences to hybridize. Double‐stranded DNA was removed either by hydroxyapatite chromatography, or by a duplex‐specific nuclease (DSN). The chromatographic method failed to enrich for the genomes present in low starting abundance, whereas the DSN method resulted in all genomes reaching near equimolar abundance. The representation of the rarest member was increased by approximately 450‐fold. De novo assembly of the normalized metagenome enabled up to 18.0% of genes from the rarest organism to be assembled, in contrast to the un‐normalized sample, where genes were not able to be assembled at the same sequencing depth. This study has demonstrated that the application of normalization methods to metagenomic samples is a powerful tool to enrich for sequences from rare taxa, which will shed further light on their ecological niches.     

Myc-mediated proliferation and lymphomagenesis,but not apoptosis,are compromised by E2f1 loss

Myc and E2f1 promote cell cycle progression, but overexpression of either can trigger p53-dependent apoptosis. Mice expressing an Emu-Myc transgene in B lymphocytes develop lymphomas, the majority of which sustain mutations of either the Arf or p53 tumor suppressors. Emu-Myc transgenic mice lacking one or both E2f1 alleles exhibited a slower onset of lymphoma development associated with increased expression of the cyclin-dependent kinase inhibitor p27(Kip1) and a reduced S phase fraction in precancerous B cells. In contrast, Myc-induced apoptosis and the frequency of Arf and p53 mutations in lymphomas were unaffected by E2f1 loss. Therefore, Myc does not require E2f1 to induce Arf, p53, or apoptosis in B cells, but depends upon E2f1 to accelerate cell cycle progression and downregulate p27(Kip1).     

Hemicellulases and auxiliary enzymes for improved conversion of lignocellulosic biomass to monosaccharides

Background  

High enzyme loading is a major economic bottleneck for the commercial processing of pretreated lignocellulosic biomass to produce fermentable sugars. Optimizing the enzyme cocktail for specific types of pretreated biomass allows for a significant reduction in enzyme loading without sacrificing hydrolysis yield. This is especially important for alkaline pretreatments such as Ammonia fiber expansion (AFEX) pretreated corn stover. Hence, a diverse set of hemicellulases supplemented along with cellulases is necessary for high recovery of monosaccharides.     

Molecular evidence for a recent founder event in the UK populations of the Adonis blue butterfly (<Emphasis Type="Italic">Polyommatus bellargus</Emphasis>)

Contrary to accepted theories of post-glacial colonisation of the UK approximately 10,000 year BP (yBP), historical population data for Polyommatus bellargus suggests the butterfly was either extremely rare or not present before 1775. We examined the phylogeography of the species by sequencing the ‘hypervariable’ mitochondrial control region of UK and French butterflies. Overall, 22 polymorphic nucleotide sites were identified within the control region. French specimens were highly variable, with 17 polymorphic sites, whereas most UK specimens were monomorphic. Average nucleotide diversity was 0.026 (SD 0.016, n = 8) in France, whilst the UK values ranged from 0.00 (n = 6) (for every UK population outside Dorset, n = 43) to 0.01 (SD 0.008, n = 7) (Dorset). The mean number of pairwise differences among the French samples was 7.42, whilst the UK values ranged from 0.00 (all populations except Dorset) to 0.295 (Dorset). One French haplotype differed from the predominant UK version by just a single nucleotide substitution. It seems implausible that the species can have been resident in the UK for 10,000 years without accumulating variation at this mitochondrial region. Thus, the results suggest that either a severe genetic bottleneck or founder event has occurred recently in the UK.     

An investigation of the differential performance of clones of the aphid Sitobion avenae on two host species

Individuals of the grain aphid Sitobion avenae were collected from wheat and cocksfoot stands around Hampshire, UK, during March and April 1994. Eight wheat and eight cocksfoot aphid clones were chosen on the basis of readily distinguishable RAPD-PCR fingerprint profiles. The performances (weight, fecundity and survival) of successive generations of each of these clones were then carefully monitored in the laboratory as new generations of aphids were transferred either to winter wheat or to cocksfoot in planned sequences. Even those clones that were originally caught on the same host showed significant variability in performance. Clones generally performed better on their host of origin than they did on the alternate host, and they performed less well on the alternate host compared to the clones that had originated there. A comparison of the performance of third generation aphids with first generation aphids showed that the experience of the mother in the second generation often influences the subsequent performance of their offspring. As the sequence of host transfers had more effect on the performance of wheat clones than cocksfoot clones, it is likely that wheat clones are more specialised, such that wheat is a satisfactory host for cocksfoot clones but not vice versa. The study provides evidence of genetic variation in performance on host and evidence for clonal adaptation to particular host species. This adaptation may well be a major cause of the observed consistent genetic differentiability of populations of S. avenae found on wheat and roadside grasses in early spring in southern England.