Seasonality,habitat type and locality influenced bird assemblage structure in Nigeria

This is the first report of the avian assemblage in the study area of Dutse, Nigeria. In addition to recording bird species, the effects of season, dominant vegetation structure, locality and anthropogenic activities on bird abundance, species richness and diversity were investigated. Using the point transect method, 264 points on 48 km of transect were used to count birds between 06:30 and 11:00 from August 2015 to February 2016. A total of 122 bird species of 41 families were recorded. Highest bird species richness was recorded in Warwade, highest abundance in Model, and highest diversity in Malamawa. The dry season and woodland habitat showed higher bird species richness, abundance and diversity than the wet season and shrubland habitat. Tree density was more important in increasing bird abundance than shrub density. Small-scale anthropogenic activities and habitat modification, such as farming, grazing, wood removal and human interference did not appear to have impacted the birds; however, loss of high tree-density woodland habitats may pose a major threat to the bird community in Dutse. The presence of birds of concern in the area suggests the need for conservation efforts of avifauna and as well as the forested habitats in Dutse.     

Assessment of the functional response parameters of Coccinella septempunctata to varying densities of Acyrthosiphon pisum

The functional response of a predator describes the rate at which it kills its prey at different prey densities and is, therefore, an important tool to determine the efficiency of a predator in regulating the population dynamics of a prey. We investigated the functional response of Coccinella septempunctata L. (Coleoptera: Coccinellidae) to varying densities of Acyrthosiphon pisum (Harris) (Hemiptera: Aphididae). The results revealed that the linear coefficient, P₁ in the reduced logistic model was found significantly negative for the 4^th instar larvae and adult male and female of C. septempunctata (?0.002, ?0.004 and???0.002, respectively) indicating a type II functional response. The parameter estimates of adult male, female and 4^thinstar larvae of C. septempunctata calculated through Holling's disc model revealed that the highest attack rate (a) (1.047?±?0.014), shortest handling time (T_h) (0.0984?±?0.024?h) and largest maximum capture rate (T/T_h) (243.902) was exhibited by female. Parameter estimates calculated through Rogers’s equation also showed the same sequence where maximum attack rate (a) of 0.00256?±?0.0003 was exhibited by female followed by 4^th instar larvae (0.00251?±?0.0005). The shortest handling time (T_h) (0.210?±?0.003?h) and highest maximum capture rate (T/T_h) (114.17) was also exhibited by female. Comparison of functional response curves of adult male, female and 4^th instar larvae revealed that maximum consumption of prey at all the densities offered was shown by female followed by 4^thinstar larvae. The study manifested that C. septempunctata could be an efficient biocontrol agent of pea aphid, A. pisum.     

Genetic mapping of an autosomal recessive postaxial polydactyly type A to chromosome 13q13.3–q21.2 and screening of the candidate genes

Postaxial Polydactyly (PAP) is characterized by fifth digit duplication in hands and/or feet. Two types of PAP including PAP-A, representing the development of well-formed extra digit, and PAP-B, representing the presence of rudimentary fifth digit, have been described. Both isolated and syndromic forms of PAP have been reported. Isolated forms of PAP usually segregate as an autosomal dominant trait and to date four loci have been identified. In the present study, we have described mapping of the first locus of autosomal recessive PAP type A on chromosome 13q13.3–13q21.2 in a consanguineous Pakistani family. Using polymorphic microsatellite markers, the disease locus was mapped to a 17.87-cM (21.13 Mb) region flanked by markers D13S1288 and D13S632, on chromosome 13q13.3–13q21.2. A maximum multipoint LOD score of 3.84 was obtained with several markers along the disease interval. DNA sequence analysis of exons and splice-junction sites of ten candidate genes (CHM-I, TSC22D1, FOXO1, DIAPH3, CCDC122, CKAP2, SUGT1, RANKL, LPAR6, C13ORF31) did not reveal potentially causal variants.     

Larvicidal potential of gold and silver nanoparticles synthesized using Acalypha fruticosa leaf extracts against Culex pipiens (Culicidae: Diptera)

Plant secondary metabolites have been recently used for the synthesis of different nanoparticles. The present investigation aimed at evaluating the effect of gold (AuNPs) and silver (AgNPs) nanoparticles synthesized using Acalypha fruticosa leaf extracts to control the mosquito Culex pipiens. The A. fruticosa AuNPs and AgNPs spectra displayed their maximum absorption at 550 nm and 440 nm, respectively. The infrared spectra revealed different functional groups related to different chemical compounds. The larval mortality of aqueous leaf extract of A. fruticosa was 499.54 ppm (LC₅₀) and 1734.06 ppm (LC₉₀) after 24 h of treatment. This study revealed that AuNP (LC₅₀, 30.2 and LC₉₀, 104.83 ppm) and AgNP (LC₅₀, 52.86 and LC₉₀, 157.227 ppm) preparations were highly effective compared to the A. fruticosa extract alone and also more affordable, as a smaller amount was required. The present findings show the potential larvicidal effect of the synthesized AuNPs and AgNPs for the control of mosquito-mediated disease transmission.     

MotViz: a tool for sequence motif prediction in parallel to structural visualization and analyses

Linking similar proteins structurally is a challenging task that may help in finding the novel members of a protein family. In this respect, identification of conserved sequence can facilitate understanding and classifying the exact role of proteins. However, the exact role of these conserved elements cannot be elucidated without structural and physiochemical information. In this work, we present a novel desktop application MotViz designed for searching and analyzing the conserved sequence segments within protein structure. With MotViz, the user can extract a complete list of sequence motifs from loaded 3D structures, annotate the motifs structurally and analyze their physiochemical properties. The conservation value calculated for an individual motif can be visualized graphically. To check the efficiency, predicted motifs from the data sets of 9 protein families were analyzed and MotViz algorithm was more efficient in comparison to other online motif prediction tools. Furthermore, a database was also integrated for storing, retrieving and performing the detailed functional annotation studies. In summary, MotViz effectively predicts motifs with high sensitivity and simultaneously visualizes them into 3D strucures. Moreover, MotViz is user-friendly with optimized graphical parameters and better processing speed due to the inclusion of a database at the back end. MotViz is available at http://www.fi-pk.com/motviz.html.     

A genome-wide study of cytogenetic changes in colorectal cancer using SNP microarrays: opportunities for future personalized treatment

In colorectal cancer (CRC), chromosomal instability (CIN) is typically studied using comparative-genomic hybridization (CGH) arrays. We studied paired (tumor and surrounding healthy) fresh frozen tissue from 86 CRC patients using Illumina's Infinium-based SNP array. This method allowed us to study CIN in CRC, with simultaneous analysis of copy number (CN) and B-allele frequency (BAF)--a representation of allelic composition. These data helped us to detect mono-allelic and bi-allelic amplifications/deletion, copy neutral loss of heterozygosity, and levels of mosaicism for mixed cell populations, some of which can not be assessed with other methods that do not measure BAF. We identified associations between CN abnormalities and different CRC phenotypes (histological diagnosis, location, tumor grade, stage, MSI and presence of lymph node metastasis). We showed commonalities between regions of CN change observed in CRC and the regions reported in previous studies of other solid cancers (e.g. amplifications of 20q, 13q, 8q, 5p and deletions of 18q, 17p and 8p). From Therapeutic Target Database, we identified relevant drugs, targeted to the genes located in these regions with CN changes, approved or in trials for other cancers and common diseases. These drugs may be considered for future therapeutic trials in CRC, based on personalized cytogenetic diagnosis. We also found many regions, harboring genes, which are not currently targeted by any relevant drugs that may be considered for future drug discovery studies. Our study shows the application of high density SNP arrays for cytogenetic study in CRC and its potential utility for personalized treatment.     

Revealing the community and metabolic potential of active methanotrophs by targeted metagenomics in the Zoige wetland of the Tibetan Plateau

The Zoige wetland of the Tibetan Plateau is one of the largest alpine wetlands in the world and a major emission source of methane. Methane oxidation by methanotrophs can counteract the global warming effect of methane released in the wetlands. Understanding methanotroph activity, diversity and metabolism at the molecular level can guide the isolation of the uncultured microorganisms and inform strategy-making decisions and policies to counteract global warming in this unique ecosystem. Here we applied DNA stable isotope probing using ¹³C-labelled methane to label the genomes of active methanotrophs, examine the methane oxidation potential and recover metagenome-assembled genomes (MAGs) of active methanotrophs. We found that gammaproteobacteria of type I methanotrophs are responsible for methane oxidation in the wetland. We recovered two phylogenetically novel methanotroph MAGs distantly related to extant Methylobacter and Methylovulum. They belong to type I methanotrophs of gammaproteobacteria, contain both mxaF and xoxF types of methanol dehydrogenase coding genes, and participate in methane oxidation via H₄MPT and RuMP pathways. Overall, the community structure of active methanotrophs and their methanotrophic pathways revealed by DNA-SIP metagenomics and retrieved methanotroph MAGs highlight the importance of methanotrophs in suppressing methane emission in the wetland under the scenario of global warming.     

Bioactive aristolactams from Piper umbellatum

Four alkaloids named piperumbellactams A-D (1-4) were isolated from branches of Piper umbellatum together with known N-hydroxyaristolam II (5), N-p-coumaroyl tyramine (6), 4-nerolidylcatechol (7), N-trans-feruloyltyramine, E-3-(3,4-dihydroxyphenyl)-N-2-[4-hydroxyphenylethyl]-2-propenamide, beta-amyrin, friedelin, apigenin 8-C-neohesperidoside, acacetin 6-C-beta-d-glucopyranoside, beta-sitosterol, its 3-O-beta-d-glucopyranoside and its 3-O-beta-d-[6'-dodecanoyl]-glucopyranoside. Glycosidase inhibition, antioxidant and antifungal activities of these compounds were evaluated. Compounds 1-3 showed moderate alpha-glucosidase enzyme inhibition with IC50 values 98.07+/-0.44, 43.80+/-0.56 and 29.64+/-0.46, respectively. In DPPH radical scavenging assay, compounds 2, 3 and 6 showed potent inhibitory activity while compounds 4, 5 and 7 showed potent antifungal activity.     

Biological control of the diamondback moth, Plutella xylostella: A review

The diamondback moth (DBM), Plutella xylostella (L.) (Lepidoptera: Plutellidae), is one of the most destructive cosmopolitan insect pests of brassicaceous crops. It was the first crop insect reported to be resistant to DDT and now, in many crucifer producing regions, it has shown significant resistance to almost every synthetic insecticide applied in the field. In certain parts of the world, economical production of crucifers has become almost impossible due to insecticidal control failures. Consequently, increased efforts worldwide have been undertaken to develop integrated pest management (IPM) programs, principally based on manipulation of its natural enemies. Although over 130 parasitoid species are known to attack various life stages of DBM, most control worldwide is achieved by relatively few hymenopteran species belonging to the ichneumonid genera Diadegma and Diadromus, the braconid genera Microplitis and Cotesia, and the eulophid genus Oomyzus. DBM populations native to different regions have genetic and biological differences, and specific parasitoid strains may be associated with the specific DBM strains. Therefore, accurate identification based on genetic studies of both host and parasitoid is of crucial importance to attaining successful control of DBM through inoculative or inundative releases. Although parasitoids of DBM larvae and pupae are currently its principal regulators, bacteria-derived products (e.g., crystal toxins from Bacillus thuringiensis) and myco-insecticides principally based on Zoophthora radicans and Beauveria bassiana are increasingly being applied or investigated for biological control. Viruses, nematodes and microsporidia also have potential as biopesticides for DBM. When an insect pest is exposed to more than one mortality factor, there is the possibility of interactions that can enhance, limit, or limit and enhance the various aspects of effectiveness of a particular control tactic. This paper reviews the effectiveness of various parasitoids and entomopathogens against DBM, interactions among them, and their possible integration into modern IPM programs.