Comparative phylogenetic analysis and transcriptional profiling of MADS-box gene family identified DAM and FLC-like genes in apple (Malusx domestica)

The MADS-box transcription factors play essential roles in various processes of plant growth and development. In the present study, phylogenetic analysis of 142 apple MADS-box proteins with that of other dicotyledonous species identified six putative Dormancy-Associated MADS-box (DAM) and four putative Flowering Locus C-like (FLC-like) proteins. In order to study the expression of apple MADS-box genes, RNA-seq analysis of 3 apical and 5 spur bud stages during dormancy, 6 flower stages and 7 fruit development stages was performed. The dramatic reduction in expression of two MdDAMs, MdMADS063 and MdMADS125 and two MdFLC-like genes, MdMADS135 and MdMADS136 during dormancy release suggests their role as flowering-repressors in apple. Apple orthologs of Arabidopsis genes, FLOWERING LOCUS T, FRIGIDA, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 and LEAFY exhibit similar expression patterns as reported in Arabidopsis, suggesting functional conservation in floral signal integration and meristem determination pathways. Gene ontology enrichment analysis of predicted targets of DAM revealed their involvement in regulation of reproductive processes and meristematic activities, indicating functional conservation of SVP orthologs (DAM) in apple. This study provides valuable insights into the functions of MADS-box proteins during apple phenology, which may help in devising strategies to improve important traits in apple.

Genome-wide identification and expression analysis of NBS-encoding genes in Malus x domestica and expansion of NBS genes family in Rosaceae

Nucleotide binding site leucine-rich repeats (NBS-LRR) disease resistance proteins play an important role in plant defense against pathogen attack. A number of recent studies have been carried out to identify and characterize NBS-LRR gene families in many important plant species. In this study, we identified NBS-LRR gene family comprising of 1015 NBS-LRRs using highly stringent computational methods. These NBS-LRRs were characterized on the basis of conserved protein motifs, gene duplication events, chromosomal locations, phylogenetic relationships and digital gene expression analysis. Surprisingly, equal distribution of Toll/interleukin-1 receptor (TIR) and coiled coil (CC) (1 ∶ 1) was detected in apple while the unequal distribution was reported in majority of all other known plant genome studies. Prediction of gene duplication events intriguingly revealed that not only tandem duplication but also segmental duplication may equally be responsible for the expansion of the apple NBS-LRR gene family. Gene expression profiling using expressed sequence tags database of apple and quantitative real-time PCR (qRT-PCR) revealed the expression of these genes in wide range of tissues and disease conditions, respectively. Taken together, this study will provide a blueprint for future efforts towards improvement of disease resistance in apple.

Combinatorial chemistry toward understanding the function(s) of carbohydrates and carbohydrate conjugates

Combinatorial chemistry has contributed significantly to understanding the structure-function relationships of biologically important molecules such as proteins and nucleic acids. However, carbohydrates and carbohydrate conjugates, which have been identified as key modulators of several biological functions have not enjoyed the same measure of success. The complexity and synthetic challenges of carbohydrate conjugates have resulted in a number of conceptual approaches to rapidly access sufficient quantities of these biomolecules. This article summarizes these combinatorial approaches and also highlights fully automated library synthesis of artificial glycopeptides with the goals of understanding their biological roles.

Prospects of Understanding the Molecular Biology of Disease Resistance in Rice

Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in various crops is one of the important methods of disease management. However, identification, cloning and characterization of disease resistance genes is a very tedious effort. To increase the life span of resistant cultivars, it is important to understand the molecular basis of plant host-pathogen interaction. With the advancement in rice genetics and genomics, several rice varieties resistant to fungal, bacterial and viral pathogens have been developed. However, resistance response of these varieties break down very frequently because of the emergence of more virulent races of the pathogen in nature. To increase the durability of resistance genes under field conditions, understanding the mechanismof resistance response and its molecular basis should be well understood. Some emerging concepts like interspecies transfer of pattern recognition receptors (PRRs) and transgenerational plant immunitycan be employed to develop sustainable broad spectrum resistant varieties of rice.

Tetracladium nainitalense sp. nov., a root endophyte from Kumaun Himalaya, India

An aquatic hyphomycete, Tetracladium nainitalense sp. nov., isolated as a root endophyte from riparian plants from Nainital, Kumaun Himalaya, India, is illustrated and described. The new species is characterized by laterally applanate conidia appearing lobate, with typically four rounded apices and lacking filiform, acicular or subulate elements. An updated key to the species of Tetracladium is provided.

Design and synthesis of analogs of vitamin E: antiproliferative activity against human breast adenocarcinoma cells

Analogs of alpha-tocopherol (vitamin E; compounds 3-9) have been synthesized and tested for their antiproliferative activity using the human breast cancer cell line, MCF7. Compounds 6-9 were synthesized from a common symthom, rac-Trolox (14) and are soluble/miscible at physiological pH. Compounds 4, 8, and 9 were found to have antiproliferative activity at micromolar concentrations.

Diversity of C-linked neoglycopeptides for the exploration of subsite-assisted carbohydrate binding interactions

Diversity of alpha-galactose based C-linked neoglycopeptides (1b, 2b, 3c, 4d, and 5d) has been developed to explore the importance of subsite-assisted carbohydrate binding interactions. Deprotected C-linked neoglycopeptides (1b, 2b, 3c, 4d, and 5d) were synthesized and tested in competitive inhibition assays using a model enzyme-linked lectin (e.g., Maclura pomifera). Compound 2b, with two alpha-galactoside units on the side chain of the lysine residue of the dipeptide backbone, exhibited a remarkable effect with a 2.82-fold increase in its inhibitory properties (IC50 1.48 mM) in comparison to 1b (IC50 4.18 mM).

Natural-product-like chiral derivatives by solid-phase synthesis

In this genomics and proteomics age, highly functionalized natural products or natural-product-like compounds are likely to play important roles in understanding the functions of emerging biological targets because they serve as small-molecule chemical probes in modulating a target's specific actions (i.e. activation or deactivation). Development of stereoselective reaction-derived methods on solid phase provides a means of obtaining functionalized chiral core structures that may be used for high-throughout syntheses.

Alpha-galactose based neoglycopeptides. Inhibition of verotoxin binding to globotriosylceramide

Solution and solid phase strategies for the synthesis of alpha-galactose based neoglycopeptide derivatives 2-13 were developed. Neoglycopeptides generated were tested for the inhibition of verotoxin binding to globotriosylceramide (Gb3) using ELISA. Among all of the compounds tested, only the lipid derivatives of neoglycopeptides, 11, 12 and 13 were found to be inhibitors, IC50 = 2.0 mM (11b and 12c) and 0.2 mM (11c and 13c). All of the inhibitors (11b, 11c, 12c and 13c) have a similar branching of the two alpha-galactosyl units at the N-terminal glycine residue of a short peptide and a lipid moiety attached at the C-terminal site. Both of these factors seem to be crucial for the inhibition. It is interesting to note that the inhibitors have only a portion of the natural trisaccharide ligand. The secondary groups either may contribute in sub-site oriented interactions with the protein receptors or may mimic the internal sugar units of the cell-surface ligand, Gb3.

Prevalence of rheumatic valvular heart disease in Rwandan school children: echocardiographic evaluation using the World Heart Federation criteria

BACKGROUND

Rheumatic fever (RF) and rheumatic valvular heart disease (RHD) remain important medical, surgical and public health concerns in many parts of the world, especially in sub-Saharan Africa. However, there are no published data from Rwanda. We performed a RHD prevalence study in a randomly selected sample of Rwandan school children using the 2012 World Heart Federation (WHF) criteria.

METHODS

Echocardiographic assessment of 2 501 Rwandan school children from 10 schools in the Gasabo district near Kigali was carried out. Resulting data were evaluated by four experienced echocardiographers. Statistical analyses were carried out by statisticians.

RESULTS

RHD prevalence was 6.8/1 000 children examined (95% CI: 4.2/1 000-10.9/1 000). Seventeen met WHF criteria for RHD, 13 fulfilled criteria for 'borderline' RHD and four were 'definite' RHD. None of these 17 had been previously identified.

CONCLUSION

These data indicate a significant burden of RHD in Rwanda and support a need for defined public health RF control programmes in children there.

Plant STAND P-loop NTPases: a current perspective of genome distribution, evolution, and function : Plant STAND P-loop NTPases: genomic organization, evolution, and molecular mechanism models contribute broadly to plant pathogen defense

STAND P-loop NTPase is the common weapon used by plant and other organisms from all three kingdoms of life to defend themselves against pathogen invasion. The purpose of this study is to review comprehensively the latest finding of plant STAND P-loop NTPase related to their genomic distribution, evolution, and their mechanism of action. Earlier, the plant STAND P-loop NTPase known to be comprised of only NBS-LRRs/AP-ATPase/NB-ARC ATPase. However, recent finding suggests that genome of early green plants comprised of two types of STAND P-loop NTPases: (1) mammalian NACHT NTPases and (2) NBS-LRRs. Moreover, YchF (unconventional G protein and members of P-loop NTPase) subfamily has been reported to be exceptionally involved in biotic stress (in case of Oryza sativa), thereby a novel member of STAND P-loop NTPase in green plants. The lineage-specific expansion and genome duplication events are responsible for abundance of plant STAND P-loop NTPases; where "moderate tandem and low segmental duplication" trajectory followed in majority of plant species with few exception (equal contribution of tandem and segmental duplication). Since the past decades, systematic research is being investigated into NBS-LRR function supported the direct recognition of pathogen or pathogen effectors by the latest models proposed via 'integrated decoy' or 'sensor domains' model. Here, we integrate the recently published findings together with the previous literature on the genomic distribution, evolution, and distinct models proposed for functional molecular mechanism of plant STAND P-loop NTPases.

Pharmacological management of akathisia in combination with psychological interventions by a mental health nurse consultant

The article describes the management of akathisia by a mental health nurse (MHN) prescriber, working in partnership with the patient. A single-case design was used to evaluate this. It highlights three features: first, MHN can safely prescribe psychiatric medication in combination with concordance therapy. Second, the value base underpinning prescribing practice is partnership, honesty and choice for the patient. Finally, the pharmacological mechanism of antipsychotic medication, which contributes towards akathisia, requires further analysis.

Excess bioavailability of zinc may cause obesity in humans

The body weight or body weight/height ratio exhibits a positive linear correlation to hair zinc (Zn) concentration which is more strongly positive in men than in women. The obese of both sexes possess higher Zn concentrations in their hair than those with normal body weight/height. The degree of obesity increases with the increase in the hair Zn concentration.

Antagonism of some aquatic hyphomycetes against plant pathogenic fungi

The antagonistic activity of five aquatic hyphomycetes, viz., Heliscus lugdunensis, Tetrachaetum elegans, Tetracladium breve, T. marchalianum, and T. nainitalense, against seven plant pathogenic fungi was studied using a dual culture technique. Inhibitory activity of tested aquatic hyphomycetes was determined by measuring the radial growth of plant pathogenic fungi on dual culture plates. Tetrachaetum elegans showed antagonistic activity against Colletotrichum falcatum, Fusarium oxysporum, Pyricularia oryzae, Sclerotium sclerotiorum, and Tilletia indicaHeliscus lugdunensis showed antagonism against only two plant pathogenic fungi, Rhizoctonia solani and Colletotrichum falcatum.Tetracladium breve, T. marchalianum, and T. nainitalense showed no response towards tested plant pathogenic fungi.

Genome-Wide Analysis and Expression Profiling of Rice Hybrid Proline-Rich Proteins in Response to Biotic and Abiotic Stresses, and Hormone Treatment

Hybrid proline-rich proteins (HyPRPs) belong to the family of 8-cysteine motif (8CM) containing proteins that play important roles in plant development processes, and tolerance to biotic and abiotic stresses. To gain insight into the rice HyPRPs, we performed a systematic genome-wide analysis and identified 45 OsHyPRP genes encoding 46 OsHyPRP proteins. The phylogenetic relationships of OsHyPRP proteins with monocots (maize, sorghum, and Brachypodium) and a dicot (Arabidopsis) showed clustering of the majority of OsHyPRPs along with those from other monocots, which suggests lineage-specific evolution of monocots HyPRPs. Based on our previous RNA-Seq study, we selected differentially expressed OsHyPRPs genes and used quantitative real-time-PCR (qRT-PCR) to measure their transcriptional responses to biotic (Magnaporthe oryzae) and abiotic (heat, cold, and salt) stresses and hormone treatment (Abscisic acid; ABA, Methyl-Jasmonate; MeJA, and Salicylic acid; SA) in rice blast susceptible Pusa Basmati-1 (PB1) and blast-resistant near-isogenic line PB1+Pi9. The induction of OsHyPRP16 expression in response to the majority of stresses and hormonal treatments was highly correlated with the number of cis-regulatory elements present in its promoter region. In silico docking analysis of OsHyPRP16 showed its interaction with sterols of fungal/protozoan origin. The characterization of the OsHyPRP gene family enables us to recognize the plausible role of OsHyPRP16 in stress tolerance.

Glycomimetics: a programmed approach toward neoglycopeptide libraries

A programmed synthesis of neoglycopeptides has been developed in which two, similar or different, glycoside moieties could be attached either (i) at the N-terminal of short peptides or (ii) one at the N-internal and the other(s) at the N-terminal site, in a highly flexible and controlled manner. A stepwise branching of N-terminal peptides has been achieved by glycoside aldehyde reductive amination followed by the glycoside carboxylic acid coupling (model 1). In another approach, after N-alkylation with glycoside aldehyde, the N-glycosylated derivative is subjected to peptide synthesis. This is then followed by the attachment of the second glycoside moiety at the N-terminal using either glycoside aldehyde or glycoside carboxylic acid derivative (model 2). Alternatively, the attachment of second and third glycoside derivatives could be achieved simultaneously, by reductive amination/carboxylic acid couplings (model 3). The methodologies presented here are highly versatile and combine diversity in both peptides/pseudopeptides and glycoside moieties.

Influence of low dietary lipid content on anorexia and [14C]glucose uptake in the intestine of zinc-deficient mice

Zinc deficiency was induced in adult male mice by feeding them for 8 weeks on a purified semi-synthetic Zn-deficient diet (ZD) containing 90 g lipid/kg (60 g maize oil plus 30 g cod-liver oil). One group was then fed on a low-lipid Zn-deficient diet (ZDLR) containing 30 g cod-liver oil/kg as the sole lipid source for a further 8 weeks. At the end of the experiment the stomach clearance rate, daily food intake, body-weight gain and [14C]glucose uptake in the intestine were significantly higher in group ZDLR than in mice that continued eating the Zn-deficient lipid-adequate diet ZD, and were comparable to results for a group given a Zn-supplemented diet. These results suggest that the pathogenesis of anorexia, nutrient malabsorption and growth retardation are secondary to lipid malabsorption resulting from Zn deficiency.

Computational insights into promoter architecture of toxin-antitoxin systems of Mycobacterium tuberculosis

Toxin-antitoxin (TA) systems are two component genetic modules widespread in many bacterial genomes, including Mycobacterium tuberculosis (Mtb). The TA systems play a significant role in biofilm formation, antibiotic tolerance and persistence of pathogen inside the host cells. Deciphering regulatory motifs of Mtb TA systems is the first essential step to understand their transcriptional regulation. In this study, in silico approaches, that is, the knowledge based motif discovery and de novo motif discovery were used to identify the regulatory motifs of 79 Mtb TA systems. The knowledge based motif discovery approach was used to design a Perl based bio-tool Mtb-sig-miner available at (https://github.com/zoozeal/Mtb-sig-miner), which could successfully detect sigma (σ) factor specific regulatory motifs in the promoter region of Mtb TA modules. The manual curation of Mtb-sig-miner output hits revealed that the majority of them possessed σ^B regulatory motif in their promoter region. On the other hand, de novo approach resulted in the identification of a novel conserved motif [(T/A)(G/T)NTA(G/C)(C/A)AT(C/A)] within the promoter region of 14 Mtb TA systems. The identified conserved motif was also validated for its activity as conserved core region of operator sequence of corresponding TA system by molecular docking studies. The strong binding of respective antitoxin/toxin with the identified novel conserved motif reflected the validation of identified motif as the core region of operator sequence of respective TA systems. These findings provide computational insight to understand the transcriptional regulation of Mtb TA systems.

Computational Identification Raises a Riddle for Distribution of Putative NACHT NTPases in the Genome of Early Green Plants

NACHT NTPases and AP-ATPases belongs to STAND (signal transduction ATPases with numerous domain) P-loop NTPase class, which are known to be involved in defense signaling pathways and apoptosis regulation. The AP-ATPases (also known as NB-ARC) and NACHT NTPases are widely spread throughout all kingdoms of life except in plants, where only AP-ATPases have been extensively studied in the scenario of plant defense response against pathogen invasion and in hypersensitive response (HR). In the present study, we have employed a genome-wide survey (using stringent computational analysis) of 67 diverse organisms viz., archaebacteria, cyanobacteria, fungi, animalia and plantae to revisit the evolutionary history of these two STAND P-loop NTPases. This analysis divulged the presence of NACHT NTPases in the early green plants (green algae and the lycophyte) which had not been previously reported. These NACHT NTPases were known to be involved in diverse functional activities such as transcription regulation in addition to the defense signaling cascades depending on the domain association. In Chalmydomonas reinhardtii, a green algae, WD40 repeats found to be at the carboxyl-terminus of NACHT NTPases suggest probable role in apoptosis regulation. Moreover, the genome of Selaginella moellendorffii, an extant lycophyte, intriguingly shows the considerable number of both AP-ATPases and NACHT NTPases in contrast to a large repertoire of AP-ATPases in plants and emerge as an important node in the evolutionary tree of life. The large complement of AP-ATPases overtakes the function of NACHT NTPases and plausible reason behind the absence of the later in the plant lineages. The presence of NACHT NTPases in the early green plants and phyletic patterns results from this study raises a quandary for the distribution of this STAND P-loop NTPase with the apparent horizontal gene transfer from cyanobacteria.

Expression of immune genes in Indian major carp, Catla catla challenged with Flavobacterium columnare

Columnaris disease, caused by Flavobacterium columnare, is one of the important bacterial diseases responsible for large-scale mortalities in numerous freshwater fishes globally. This disease can cause up to 100% mortality within 24 h of infection and is considered to be a cause of concern for aquaculture industry. Despite being a serious disease, scarce information is available regarding host-pathogen interaction, particularly the modulation of different immune genes in response to F. columnare infection. Therefore, in the present study, an attempt has been made to study expression of important immune regulatory genes, namely IL-1β, iNOS, INF-γ, IL-10, TGF-β, C3, MHC-I and MHC-II in gills and kidney of Catla catla following experimental infection with F. columnare. The expression analysis of immune genes revealed that transcript levels of IL-1β, iNOS, IL-10, TGF-β, C3 and MHC-I were significantly up-regulated (p < 0.05) in both the organs of the infected catla. IFN-γ and MHC-II were up-regulated in gills of infected catla whereas, both the genes showed down-regulation in kidney. The results indicate that important immune genes of C. catla are modulated following infection with F. columnare. The knowledge thus generated will strengthen the understanding of molecular pathogenesis of F. columnare in Indian major carp C. catla.