Exploring the tertiary gene pool of bread wheat: sequence assembly and analysis of chromosome 5Mg of Aegilops geniculata

Next‐generation sequencing (NGS) provides a powerful tool for the discovery of important genes and alleles in crop plants and their wild relatives. Despite great advances in NGS technologies, whole‐genome shotgun sequencing is cost‐prohibitive for species with complex genomes. An attractive option is to reduce genome complexity to a single chromosome prior to sequencing. This work describes a strategy for studying the genomes of distant wild relatives of wheat by isolating single chromosomes from addition or substitution lines, followed by chromosome sorting using flow cytometry and sequencing of chromosomal DNA by NGS technology. We flow‐sorted chromosome 5M^g from a wheat/Aegilops geniculata disomic substitution line [DS5M^g (5D)] and sequenced it using an Illumina HiSeq 2000 system at approximately 50 × coverage. Paired‐end sequences were assembled and used for structural and functional annotation. A total of 4236 genes were annotated on 5M^g, in close agreement with the predicted number of genes on wheat chromosome 5D (4286). Single‐gene FISH indicated no major chromosomal rearrangements between chromosomes 5M^g and 5D. Comparing chromosome 5M^g with model grass genomes identified synteny blocks in Brachypodium distachyon, rice (Oryza sativa), sorghum (Sorghum bicolor) and barley (Hordeum vulgare). Chromosome 5M^g‐specific SNPs and cytogenetic probe‐based resources were developed and validated. Deletion bin‐mapped and ordered 5M^g SNP markers will be useful to track 5M‐specific introgressions and translocations. This study provides a detailed sequence‐based analysis of the composition of a chromosome from a distant wild relative of bread wheat, and opens up opportunities to develop genomic resources for wild germplasm to facilitate crop improvement.     

Exploration of the antioxidative defense system to characterize chickpea genotypes showing differential response towards water deficit conditions

The present investigation was carried out to characterize genotypic variability in chickpea for water deficit tolerance by exploring the antioxidative defense system and seedling growth. Twenty nine chickpea genotypes including cultivars and advanced lines were grown under control and water deficit conditions induced by adding 3 % mannitol. The genotypes showed differential response in seedling growth under water deficit conditions. The activities of catalase (CAT) and superoxide dismutase (SOD) were observed to be differentially expressed in the roots of various genotypes, under control and water deficit conditions. The contents of H₂O₂, malondialdehyde (MDA) and proline were also observed to be variable in the roots of all the genotypes, under control and water deficit conditions. Stress tolerance index for the various parameters, viz, CAT and SOD activity, H₂O₂, MDA and proline content, root length, shoot length and their biomass was determined and the level of stress resistance calculated. The genotypes which showed increased activities of CAT and SOD, decreased contents of H₂O₂ and MDA together with least affected seedling growth under water deficit conditions exhibited higher stress resistance capacity. Multivariate principal component analysis for all the parameters affected under water deficit conditions, grouped the genotypes into three clusters having different (high, moderate and low) levels of stress resistance. Complete linkage clustering grouped these genotypes into two major clusters-I and II. The genotypes present in sub–sub cluster ‘A1’ and sub cluster ‘B’ of major cluster-I have been observed to possess high stress resistance levels for respective parameters. It can thus be concluded that chickpea genotypes exhibiting increased stress resistance levels in relation to SOD and CAT activities, H₂O₂ and MDA contents and seedling growth would have higher stress tolerance under water deficit conditions.     

Characterization of Phlebotomus papatasi Peritrophins,and the Role of PpPer1 in Leishmania major Survival in its Natural Vector

The peritrophic matrix (PM) plays a key role in compartmentalization of the blood meal and as barrier to pathogens in many disease vectors. To establish an infection in sand flies, Leishmania must escape from the endoperitrophic space to prevent excretion with remnants of the blood meal digestion. In spite of the role played regarding Leishmania survival, little is known about sand fly PM molecular components and structural organization. We characterized three peritrophins (PpPer1, PpPer2, and PpPer3) from Phlebotomus papatasi. PpPer1 and PpPer2 display, respectively, four and one chitin-binding domains (CBDs). PpPer3 on the other hand has two CBDs, one mucin-like domain, and a putative domain with hallmarks of a CBD, but with changes in key amino acids. Temporal and spatial expression analyses show that PpPer1 is expressed specifically in the female midgut after blood feeding. PpPer2 and PpPer3 mRNAs were constitutively expressed in midgut and hindgut, with PpPer3 also being expressed in Malpighian tubules. PpPer2 was the only gene expressed in developmental stages. Interestingly, PpPer1 and PpPer3 expression are regulated by Le. major infection. Recombinant PpPer1, PpPer2 and PpPer3 were obtained and shown to display similar biochemical profiles as the native; we also show that PpPer1 and PpPer2 are able to bind chitin. Knockdown of PpPer1 led to a 44% reduction in protein, which in spite of producing an effect on the percentage of infected sand flies, resulted in a 39% increase of parasite load at 48 h. Our data suggest that PpPer1 is a component for the P. papatasi PM and likely involved in the PM role as barrier against Le. major infection.     

Unusual transformation of substituted-3-formylchromones to pyrimidine analogues: Synthesis and antimicrobial activities of 5-(o-hydroxyaroyl)pyrimidines

Substituted-3-formylchromones (4a–e) on reaction with 1,3-bis-dimethylaminomethylene-thiourea (5) in refluxing toluene solution give novel substituted 5-(o-hydroxyaroyl)pyrimidines (6a–e) in high yields. A mechanistic rationalization of the formation of products (6a–e) is proffered. Antimicrobial activities of all the synthesized compounds (6a–e) were evaluated against various fungal and bacterial strains. Compound 6d display significant antifungal activity (MIC 15) against Geotrichum candidum in comparison fluconazole used as positive control. Some of the compounds also display good antibacterial activity. Cytotoxic profile of compound 6d against HeLa cells indicates that at concentration (20 μM) no significant cell death (～2%) was observed.     

Chemotaxis of <Emphasis Type="Italic">Burkholderia</Emphasis> sp. Strain SJ98 towards chloronitroaromatic compounds that it can metabolise

Background  

Burkholderia sp. strain SJ98 is known for its chemotaxis towards nitroaromatic compounds (NACs) that are either utilized as sole sources of carbon and energy or co-metabolized in the presence of alternative carbon sources. Here we test for the chemotaxis of this strain towards six chloro-nitroaromatic compounds (CNACs), namely 2-chloro-4-nitrophenol (2C4NP), 2-chloro-3-nitrophenol (2C3NP), 4-chloro-2-nitrophenol (4C2NP), 2-chloro-4-nitrobenzoate (2C4NB), 4-chloro-2-nitrobenzoate (4C2NB) and 5-chloro-2-nitrobenzoate (5C2NB), and examine its relationship to the degradation of such compounds.     

Investigation of Need of Natural Bioenhancer for a Metabolism Susceptible Drug—Raloxifene,in a Designed Self-Emulsifying Drug Delivery System

Bioenhancers can increase the bioavailability of metabolism susceptible drugs. The present study was designed to understand the impact of bioenhancer on permeability and bioavailability of a biopharmaceutical drug disposition classification system (BDDCS) class II drug raloxifene (RLX). RLX undergoes extensive first pass metabolism by UGT enzymes in gastrointestinal tract (GIT) and has an oral bioavailability of about 2%. Self-emulsifying drug delivery system (SEDDS) of RLX was developed using a designed approach and this formulation was loaded with reported bioenhancers: quercetin and piperine. These formulations were tested for improvement in permeability and bioavailability of the RLX. The apparent permeability using everted gut sac (P _app) for SEDDS (5.26?±?1.10?×?10^?8 cm/s) was found to be similar to that of SEDDS with bioenhancers (5.11?±?1.05?×?10^?8 cm/s). In oral bioavailability study in rat, SEDDS demonstrated a 4-fold and 2.5-fold higher AUC_0–∞ than RLX suspension (control) and marketed product, respectively. No additional improvement in permeability and bioavailability was offered by inclusion of piperine and quercetin (bioenhancers) in the SEDDS.     

Ecological niche modelling and population genetic analysis of Indian temperate bamboo Drepanostachyum falcatum in the western Himalayas

Journal of Plant Research - The present study was conducted to understand the key ecological and biological questions of conservation importance in Drepanostachyum falcatum which aimed to map...     

Guggulsterone enhances glycosylated low density lipoprotein binding in rat liver

Modification of low density lipoprotein by nonenzymic glycosylation resulted in decreased receptor-mediated lipoprotein catabolism. Guggulsterone treatment caused significant increase in binding of [¹²⁵I] low density lipoprotein as well as [¹²⁵I] glycosylated low density lipoprotein. Scatchard plot analysis of the binding activity revealed that under the influence of guggulsterone, the liver membrane contains increased amounts of a functional lipoprotein receptor that binds more low density lipoprotein particles.     

Intra-articular patient-controlled analgesia improves early rehabilitation after knee surgery

The influence of patient-controlled intra-articular analgesia with ropivacaine, morphine and ketorolac (RMK) on postoperative pain relief and early rehabilitation after anterior cruciate ligament reconstruction was studied. Twenty six patients, randomized into two groups, were enrolled in a placebo-controlled, double-blind study. At the end of surgery a catheter was placed intra-articularly and connected to a patient-controlled pump, programmed to deliver 10 mL bolus and 60 min lockout interval. RMK group received 0.25% ropivacaine, morphine 0.2 mg/mL and ketorolac 1 mg/mL; P group saline. Pain was measured with 10 cm visual analog scale. At pain scores > 3 cm, all patients were instructed to self-administer morphine intravenously using a patient-controlled pump. Daily rescue morphine consumption was noted and 48 h rehabilitation programme was evaluated. Daily morphine consumption was significantly lower in the RMK group (p < 0.001). At 24h after surgery, the patients in the RMK group experienced significantly less pain (p < 0.05). The patients in the RMK group achieved higher maximum degree of knee flexion in supine (p < 0.001) and in prone position (p < 0.05) compared to placebo group and better pain free flexion with assistance on day 1 (p < 0.05) and 2 (p > 0.05). The results show that patient-controlled intra-articular analgesia with RMK combination provides effective pain relief following anterior cruciate ligament reconstruction and improves early physical rehabilitation.     

Linkage disequilibrium pattern and age-at-diagnosis are critical for replicating genetic associations across ethnic groups in leprosy

One of the persistent challenges of genetic association studies is the replication of genetic marker-disease associations across ethnic groups. Here, we conducted high-density association mapping of PARK2/PACRG SNPs with leprosy and identified 69 SNPs significantly associated with leprosy in 198 single-case Vietnamese leprosy families. A total of 56 associated SNPs localized to the overlapping promoter regions of PARK2/PACRG. For this region, multivariate analysis identified four SNPs belonging to two major SNP bins (rs1333955, rs7744433) and two single SNP bins (rs2023004, rs6936895) that capture the combined statistical evidence (P = 1.1 × 10^?5) for association among Vietnamese patients. Next, we enrolled a case–control sample of 364 leprosy cases and 370 controls from Northern India. We genotyped all subjects for 149 SNPs that capture >80 % of the genetic variation in the Vietnamese sample and found 24 SNPs significantly associated with leprosy. Multivariate analysis identified three SNPs (rs1333955, rs9356058 and rs2023004) that capture the association with leprosy (P < 10^?8). Hence, two SNPs (rs1333955 and rs2023004) were replicated by multivariate analysis between both ethnic groups. Marked differences in the linkage disequilibrium pattern explained some of the differences in univariate analysis between the two ethnic groups. In addition, the strength of association for two promoter region SNP bins was significantly stronger among young leprosy patients in the Vietnamese sample. The same trend was observed in the Indian sample, but due to the higher age-at-diagnosis of the patients the age effect was less pronounced.