New vistas in GPCR 3D structure prediction

Human G-protein coupled receptors (hGPCRs) comprise the most prominent family of validated drug targets. More than 50% of approved drugs reveal their therapeutic effects by targeting this family. Accurate models would greatly facilitate the process of drug discovery and development. However, 3-D structure prediction of GPCRs remains a challenge due to limited availability of resolved structure. The X-ray structures have been solved for only four such proteins. The identity between hGPCRs and the potential templates is mostly less than 30%, well below the level at which sequence alignment can be done regularly. In this study, we analyze a large database of human G-protein coupled receptors that are members of family A in order to optimize usage of the available crystal structures for molecular modeling of hGPCRs. On the basis of our findings in this study, we propose to regard specific parts from the trans-membrane domains of the reference receptor helices as appropriate template for constructing models of other GPCRs, while other residues require other techniques for their remodeling and refinement. The proposed hypothesis in the current study has been tested by modeling human β2-adrenergic receptor based on crystal structures of bovine rhodopsin (1F88) and human A2A adenosine receptor (3EML). The results have shown some improvement in the quality of the predicted models compared to Modeller software.     

Complement 3 is involved in changing the phenotype of human glomerular mesangial cells

Complement activation contributes to tissue injury in various forms of glomerulopathy and is characterized by deposition of complement components, which accelerates the progression of chronic renal damage. We recently reported that complement 3 (C3), a critical component of the complement system, is associated with the synthetic phenotype of vascular smooth muscle cells. It is possible that C3 stimulates mesangial cells to assume the synthetic phenotype to, in turn, induce glomerular injury and sclerosis. We investigated the role of C3 in the growth and phenotype of mesangial cells. Cultured human mesangial cells (HMCs) expressed C3 mRNA and protein, and levels were increased in response to IFN-gamma and TNF-alpha. HMCs also expressed C3a receptor mRNA and protein. Exogenous C3a stimulated DNA synthesis in HMCs in a dose-dependent manner. C3a decreased expression h-caldesmon mRNA, a marker of the contractile phenotype, and increased the expression of osteopontin, matrix Gla, and collagen type1 alpha1 (collagen IV) mRNAs, which are markers of the synthetic phenotype. C3a decreased expression of alpha-smooth muscle actin in HMCs. Small interfering RNA (siRNA) targeting C3 reduced the DNA synthesis and proliferation of HMCs, increased expression of h-caldesmon mRNA, and decreased expression of osteopontin, matrix Gla, and collagen IV mRNAs in HMCs. These results indicate that C3 causes HMCs to convert to the synthetic phenotype and stimulates growth of mesangial cells, suggesting that C3 may play an important role in phenotypic regulation of mesangial cells in renal diseases.     

Genetic and epigenetic alteration among three homoeologous genes of a class E MADS box gene in hexaploid wheat

Bread wheat (Triticum aestivum) is a hexaploid species with A, B, and D ancestral genomes. Most bread wheat genes are present in the genome as triplicated homoeologous genes (homoeologs) derived from the ancestral species. Here, we report that both genetic and epigenetic alterations have occurred in the homoeologs of a wheat class E MADS box gene. Two class E genes are identified in wheat, wheat SEPALLATA (WSEP) and wheat LEAFY HULL STERILE1 (WLHS1), which are homologs of Os MADS45 and Os MADS1 in rice (Oryza sativa), respectively. The three wheat homoeologs of WSEP showed similar genomic structures and expression profiles. By contrast, the three homoeologs of WLHS1 showed genetic and epigenetic alterations. The A genome WLHS1 homoeolog (WLHS1-A) had a structural alteration that contained a large novel sequence in place of the K domain sequence. A yeast two-hybrid analysis and a transgenic experiment indicated that the WLHS1-A protein had no apparent function. The B and D genome homoeologs, WLHS1-B and WLHS1-D, respectively, had an intact MADS box gene structure, but WLHS1-B was predominantly silenced by cytosine methylation. Consequently, of the three WLHS1 homoeologs, only WLHS1-D functions in hexaploid wheat. This is a situation where three homoeologs are differentially regulated by genetic and epigenetic mechanisms.     

Stability of entomopathogenic bacteria, <Emphasis Type="Italic">Xenorhabdus nematophila</Emphasis> and <Emphasis Type="Italic">Photorhabdus luminescens</Emphasis>, during in vitro culture

The entomopathogenic nematode–bacteria complexes Heterorhabditis bacteriophora/Photorhabdus luminescens and Steinernema carpocapsae/Xenorhabdus nematophila are mass produced for use as biological insecticides. Stability of the bacterial partner in culture is essential for maintaining traits important for both biological control and production. Two geographically distinct strains of each bacterial species were isolated from their nematode partners and serially subcultured on in vitro media to assess trait stability. Subculturing resulted in a shift to secondary cell production in one P. luminescens strain and both X. nematophila strains within ten in vitro culture cycles. However, when cell phenotypic variation was controlled in X. nematophila strains by regular selection for primary variants, no trait change was detected in the primary variant after prolonged subculture. When P. luminescens cell phenotypic variation was controlled by selection for primary variants, changes in the primary variant of both strains were noted including reductions in cell and inclusion body size and inclusion body prevalence. Bacterial ability to cause lethal infections following injection into the hemocoel of Tenebrio molitor larvae declined by more than half in primary variants of one P. luminescens strain. Conversely, yield was enhanced, with the subcultured P. luminescens strains showing 53.5 and 75.8% increases in primary cell density. Field adapted traits of primary variant P. luminescens strains tend to deteriorate during in vitro culture as tradeoffs for gains in yield. In vitro producers of the P. luminescens/H. bacteriophora complex must weigh the need for superior bacterial yield against the need to preserve traits important for biological control.     

Breeding Potential of Some Exotic Tomato Lines: A Combined Study of Morphological Variability,Genetic Divergence,and Association of Traits

Tomato (Solanum lycopersicum L.) is called ‘the poor man’s orange’ due to its low price and improved nutritional values. An experiment was conducted to study the breeding potential of some exotic tomato lines by assessing various qualitative and quantitative traits conferring yield and quality attributes. Among the qualitative traits, greater variability was observed for growth type, stem hairiness, and fruit shape and size. A determinate growth habit was observed in the genotype AVTO9802 while the genotype AVTO0102 produced yellow color fruits. A significant (p ≤ 0.01) variation was also observed for the studied quantitative traits. Based on yield and traits attributed to yield, the genotypes AVTO0314, GPB0107, GPB0120 and AVTO9802 were selected as promising genotypes. The differences between the genotypic and phenotypic coefficients of variation (GCV and PCV) of the studied quantitative traits were very low. This suggests that the apparent variation was mainly due to the genotypes. The higher GCV and PCV values were observed for the number of primary branches plant⁻¹ (NPB), number of fruits cluster⁻¹ (NFC), individual fruit weight (IFW) and total soluble solids (TSS). High heritability was recorded for all quantitative traits in a broad sense. However, the individual fruit diameter showed the highest heritability (99.56). The highest (102.75) genetic advance (GA) was observed for the number of fruits plant⁻¹ (NFP). High heritability coupled with high GA as percentage of mean were recorded for the traits NFP, NFC, fruit yield plant⁻¹ (FYP) and IFW. FYP showed a significant positive correlation with NFC (0.714***) and a negative correlation with days to the first harvest (−0.539***) and plant height (−0.492**). Principal component analysis revealed that the first four components explained 78.5% of the total variation among the genotypes. Thus, the promising genotypes (AVTO0314, GPB0107, GPB0120, AVTO9802 and AVTO0102) isolated from this study can be used for developing high-yielding and high-quality tomato varieties.     

Identification of QTLs for Yield and Associated Traits in F₂ Population of Rice

Identification of quantitative trait loci (QTLs) controlling yield and yield-related traits in rice was performed in the F₂ mapping population derived from parental rice genotypes DHMAS and K343. A total of 30 QTLs governing nine different traits were identified using the composite interval mapping (CIM) method. Four QTLs were mapped for number of tillers per plant on chromosomes 1 (2 QTLs), 2 and 3; three QTLs for panicle number per plant on chromosomes 1 (2 QTLs) and 3; four QTLs for plant height on chromosomes 2, 4, 5 and 6; one QTL for spikelet density on chromosome 5; four QTLs for spikelet fertility percentage (SFP) on chromosomes 2, 3 and 5 (2 QTLs); two QTLs for grain length on chromosomes 1 and 8; three QTLs for grain width on chromosomes1, 3 and 8; three QTLs for 1000-grain weight (TGW) on chromosomes 1, 4 and 8 and six QTLs for yield per plant (YPP) on chromosomes 2 (3 QTLs), 4, 6 and 8. Most of the QTLs were detected on chromosome 2, so further studies on chromosome 2 could help unlock some new chapters of QTL for this cross of rice variety. Identified QTLs elucidating high phenotypic variance can be used for marker-assisted selection (MAS) breeding. Further, the exploitation of information regarding molecular markers tightly linked to QTLs governing these traits will facilitate future crop improvement strategies in rice.     

Determination of carbohydrates in medicinal plants--comparison between TLC, mf-MELDI-MS and GC-MS

Introduction – Quality control in the pharmaceutical and phytopharmaceutical industries requires fast and reliable methods for the analysis of raw materials and final products. Objective – This study evaluates different analytical approaches in order to recognise the most suitable technique for the analysis of carbohydrates in herbal drug preparations. Methodology – The specific focus of the study is on thin‐layer chromatography (TLC), gas chromatography (GC), and a newly developed mass spectrometric method, i.e. matrix free material enhanced laser desorption/ionisation time of flight mass spectrometry (mf‐MELDI‐MS). Samples employed in the study were standards and microwave‐assisted water extracts from Quercus. Results – TLC analysis proved the presence of mono‐, di‐ and trisaccharides within the biological sample and hinted at the existence of an unknown carbohydrate of higher oligomerisation degree. After evaluation of different derivatisation techniques, GC‐MS confirmed data obtained via TLC for mono‐ to trisaccharides, delivering additionally quantified values under a considerable amount of time. A carbohydrate of higher oligomerisation degree could not be found. The application of mf‐MELDI‐MS further confirmed the presence of carbohydrates up to trisaccharides, also hinting at the presence of a form of tetrasaccharide. Besides this information, mf‐MELDI‐MS delivered further data about other substances present in the extract. Quantitative determination resulted in 1.750, 1.736 and 0.336 mg/mL for glucose, sucrose and raffinose respectively. Conclusion – Evaluation of all three techniques employed, clearly proved the heightened performance of mf‐MELDI‐MS for the qualitative analysis of complex mixtures, as targets do not need modification and analysis requires only a few minutes. In addition, GC‐MS is suitable for quantitative analysis. Copyright © 2011 John Wiley & Sons, Ltd.     

Fear-conditioning mechanisms associated with trait vulnerability to anxiety in humans

Investigations of fear conditioning in rodents and humans have illuminated the neural mechanisms underlying cued and contextual fear. A critical question is how personality dimensions such as trait anxiety act through these mechanisms to confer vulnerability to anxiety disorders, and whether humans' ability to overcome acquired fears depends on regulatory skills not characterized in animal models. In a neuroimaging study of fear conditioning in humans, we found evidence for two independent dimensions of neurocognitive function associated with trait vulnerability to anxiety. The first entailed increased amygdala responsivity to phasic fear cues. The second involved impoverished ventral prefrontal cortical (vPFC) recruitment to downregulate both cued and contextual fear prior to omission (extinction) of the aversive unconditioned stimulus. These two dimensions may contribute to symptomatology differences across anxiety disorders; the amygdala mechanism affecting the development of phobic fear and the frontal mechanism influencing the maintenance of both specific fears and generalized anxiety.     

Evidences of lateral gene transfer between archaea and pathogenic bacteria

Acquisition of new genetic material through horizontal gene transfer has been shown to be an important feature in the evolution of many pathogenic bacteria. Changes in the genetic repertoire, occurring through gene acquisition and deletion, are the major events underlying the emergence and evolution of bacterial pathogens. However, horizontal gene transfer across the domains i.e. archaea and bacteria is not so common. In this context, we explore events of horizontal gene transfer between archaea and bacteria. In order to determine whether the acquisition of archaeal genes by lateral gene transfer is an important feature in the evolutionary history of the pathogenic bacteria, we have developed a scheme of stepwise eliminations that identifies archaeal-like genes in various bacterial genomes. We report the presence of 9 genes of archaeal origin in the genomes of various bacteria, a subset of which is also unique to the pathogenic members and are not found in respective non-pathogenic counterparts. We believe that these genes, having been retained in the respective genomes through selective advantage, have key functions in the organism’s biology and may play a role in pathogenesis.