Bioinformatic analysis of multi-drug resistant class 1 integron-coded protein of Citrobacter freundii

Background: The understanding of the secondary structure of the class 1 integron coded protein is necessary to decipher potential drug target and also to infer evolutionary ancestry at the proteomic level. This study was therefore aimed at determining the secondary structure of class 1 integron-coded protein and also to provide information on their evolutionary ancestry. Methodology: Five different sequences of Citrobacter freundii with the following accession numbers; KP902625.1, KP902624.1, KP902623.1, KP901093.1 and KP902609.1 were obtained using nucleotide BLAST (http://blast. ncbi.nlm.nih.gov/Blast.cgi) and subjected to evolutionary analysis, pairwise distance calculation, secondary structure and neutrality test using MEGA explorer, Kimura 2 parameter, SOPMA tool and Tajima’s test respectively. Results: Results of the NCBI queries revealed significant identity with class 1 integron of the studied Citrobacter freundii. The nucleotide sequence alignment depicted several conserved regions with varying degree of transitions, transversions, insertions, and deletions while the amino acid sequences of the nucleotides showed 42 conserved sites among all the sequences. The secondary structure of the class 1 integron coded protein depicted significant representation of the random coil (43.74±3.24), alpha helix (25.69±6.29) and the extended strands (22.42±2.41) than the beta turns (8.15±1.12). The Tajima’s Neutrality test of five nucleotide sequences of Citrobacter freundii analyzed by considering the first, second and third codons as well as the non-coding regions revealed a total of 127 positions in the final datasets while the Tajima’s Neutrality test was estimated to be -0.1038. Conclusion: The study confirmed common evolutionary ancestor for the class 1 integron coded protein found in Citrobacter freundii. Our study also documents the higher representation of random coil, alpha helix and extended strands than the beta turns. The negative value of the Tajima’s neutrality test suggests higher levels of both low and high frequency polymorphisms thus indicating a decrease in the class 1 integron population size and balancing selection Keywords: Evolutionary, Protein structure, Class 1 integrons, Citrobacter freundi

Transcriptional factor influence on OTA production and the quelling attribute of Sirna on the OTA producing strains of Aspergillus section Nigri

This study determined the influence of some transcriptional factors on ochratoxin A production as well as investigates the quelling attributes of some designed siRNA on the OTA producing Aspergillus section Nigri using standard recommended techniques. Results obtained following comparison of the pks gene promoter sequences from 15 isolates depicts differences in length and homology with the pks gene ranging from 218bp in a strain of the Aspergillus niger to 700bp in Aspergillus carbonarius. The alignment of the pks gene promoter region revealed that six and two of the aligned genes have Aba A binding site corresponding to CATTCT and CATTCC respectively while Brl A binding site was absent in all the isolates. Pac C binding site corresponding to CCTGGC and GCCAAG was also found in two and three of the pks gene promoter region respectively. The three designed siRNA shows significant impact on OTA inhibitions with no significant statistical differences (80.9, 74.4 and 75.3% for pks_Ia, pks_Ib and pks_Ic respectively) (F= 3.830, p>0.05). It can be concluded that Are A and Aba A are potential enhancers for ochratoxin A biosynthesis and none of the investigated transcriptional factors is enough for the activation of ochratoxin A production. However, pks gene was seen as a good target gene for inactivation in order to develop efficient means for ochratoxin A control using RNA silencing technology.Key words: Transcriptional factors, Ochratoxin A, siRNA, Quelling , Aspergillus section Nigr

Genetic diversity of ochratoxigenic Aspergillus section Nigri, using RAPD and VCG techniques

This study evaluates the genetic diversity of ochratoxigenic Aspergillus section Nigri using RAPD and VCG techniques. Results obtained revealed OPX 07 as the most informative of the tested RAPD markers generating 12 polymorphic bands while the least bands were generated by OPR 19. Of the 40 Aspergillus section Nigri (20 each of Aspergillus niger and Aspergillus carbonarius), 22 VCGs and 27 RAPD haplotypes were delineated. The two techniques demonstrated similar resolution except in few cases where the RAPD technique further sub divided some VCGs into simpler haplotypes. The average percentage of variable VCG and RAPD reactions were 25 and 50% in that order of sequence while 75 and 50% of the isolates were resolved as same isolates by these techniques respectively. It was also found that the Simpson index of genetic diversity approached one for the isolates from the four geopolitical zones of Ogun State, Nigeria with the mean genetic diversity within isolates (GL) contributing significantly approximately 89% of the total diversity observed within the isolates (F=22.23, p<0.05). The remaining 11% of variation could only be allotted to diversity among isolates (GS). On the whole, the total genetic diversity (HT) was found to be approximately 48%. In conclusion, RAPD markers provided better resolution than the classical VCG typing technique.Keywords; Genetic Diversity, Ochratoxigenic Aspergillus, RAPD and VC

Biochemical and bacteriological profiles of asymptomatic bacteriuria among school children in Ago-Iwoye, Nigeria

Background: Asymptomatic bacteriuria (ASB) in children is a predisposing factor to symptomatic urinary tract infection (UTI) that may be complicated by blood stream infections if not appropriately treated with resultant mortality or morbidity. The objectives of this study are to determine the prevalence of ASB, and evaluate both biochemical and bacteriological characteristics of urine samples of primary school pupils in Ago-Iwoye, Ijebu North Local Government Area (LGA), Ogun State, Nigeria.Methodology: Three hundred and seventy-two (186 males and 186 females) apparently healthy (asymptomatic) pupils aged 2-16 years from four randomly selected primary schools in the LGA were screened for ASB. Clean catch specimen of midstream urine was collected from each subject. Biochemical analysis of the urine was performed with Combi 10 reagent strip. MacConkey and Cysteine Lactose Electrolyte Deficient (CLED) agar plates were inoculated with calibrated wireloop delivering 0.01 ml of urine for aerobic culture at 37oC for 24 hours. Identification of significant bacteria on culture plates was done using conventional biochemical tests.Results: The frequency of clear, slightly turbid and turbid urine were 31 (8.3%), 99 (26.6%) and 56 (15.1%) respectively. All analyzed urine samples were alkaline and negative for ketone, glucose and blood, but contained protein in 230 (61.8%), bilirubin in 184 (49.5%), nitrites in 64 (17.2%) and urobilinogen in 14 (3.7%) subjects. The prevalence of significant bacteriuria was 11.8% (44 of 372) with 7.0% in males and 16.7% in females (p = 0.0063). The frequency of bacteria isolated in descending order were Escherichia coli 61.4%, Staphylococcus saprophyticus 61.4%, Staphylococcus aureus 45.5%, Bacillus subtilis 45.5%, Enterococcus faecalis 43.2%, Enterobacter spp 36.4%, Serratia marscencen 31.8%, Klebsiella pneumoniae 22.7%, Proteus mirabilis 22.7% and Pseudomonas aeruginosa 20.5%.Conclusion: This result highlights the presence of significant bacteriuria among apparently healthy pupils in the study area, with higher prevalence in the female pupils. The apparent risk of developing symptomatic UTI with the attendant complications in these pupils should spur preventive education of parents/guardians and the general populace about this entity.Keywords: Asymptomatic bacteriuria, S. saprophyticus, morbidity, prevalence, primary school pupil

The Future of Data Analysis in the Neurosciences

Neuroscience is undergoing faster changes than ever before. Over 100 years our field qualitatively described and invasively manipulated single or few organisms to gain anatomical, physiological, and pharmacological insights. In the last 10 years neuroscience spawned quantitative big-sample datasets on microanatomy, synaptic connections, optogenetic brain-behavior assays, and high-level cognition. While growing data availability and information granularity have been amply discussed, we direct attention to a routinely neglected question: How will the unprecedented data richness shape data analysis practices? Statistical reasoning is becoming more central to distill neurobiological knowledge from healthy and pathological brain recordings. We believe that large-scale data analysis will use more models that are non-parametric, generative, mixing frequentist and Bayesian aspects, and grounded in different statistical inferences

Biological Resolution of Virulence Genes of Salmonella Species from different Microbiomes

The pathogenic promiscuity of virulence associated macromolecules in Salmonella infection is a key driver to their wide epidemiology and curtailing  such distribution is contingent upon proper clarification of these virulence genes. This study was therefore aimed at determining the virulence  genes of Salmonella species from different microbiomes. To achieve this, a total of three hundred (300) biological specimens were aseptically  collected and processed for Salmonella presence using the BAM USFDA technique prior to their genotypic characterization while virulence gene  detection was carried out in a primer specific polymerase chain reaction. Results obtained depict the distribution of the following Salmonella species  viz; Salmonella gallinarum 19(26.39%), Salmonella heidelberg 19(26.39%), Salmonella enteritidis 18(25%) and Salmonella typhimurium  16(22.22%) while the occurrence of the virulence genes (InvA, SopE, AgfA and SpvC) were Salmonella enteritidis ( 7(38.8), 6(33.3), 9(50), 3(16.7),  Salmonella typhimurium ( 5(26.3), 3(15.8), 2(10.5), 7(36.8)), Salmonella heidelberg (0(0), 8(50), 4(25), 4(25), and Salmonella gallinarum (12(63.2),  6(31.6), 2(10.5), 7(36.8)) respectively. It was however found that the different microbiomes analyzed were ubiquitously rich in virulence genes  associated Salmonella species.   La promiscuité pathogène des macromolécules associées à la virulence dans l’infection à Salmonella est un facteur clé de leur large épidémiologie  et la réduction de cette distribution dépend de la clarification appropriée de ces gènes de virulence. Cette étude visait donc à déterminer les gènes  de virulence des espèces de Salmonella de différents microbiomes. Pour ce faire, un total de trois cents (300) échantillons biologiques ont été  collectés et traités de manière aseptique pour la présence de Salmonella à l’aide de la technique BAM USFDA avant leur caractérisation génotypique  tandis que la détection du gène de virulence a été effectuée dans une réaction en chaîne par polymérase spécifique à l’amorce. Les résultats  obtenus décrivent la distribution des espèces de Salmonella suivantes, à savoir ; Salmonella gallinarum 19(26,39%), Salmonella heidelberg  19(26,39%), Salmonella enteritidis 18(25%) et Salmonella typhimurium 16(22,22%) alors que la présence des gènes de virulence (InvA, SopE, AgfA et  SpvC) était Salmonella enteritidis ( 7(38,8), 6(33,3), 9(50), 3(16,7), Salmonella typhimurium ( 5(26,3), 3(15,8), 2(10,5), 7(36,8)), Salmonella heidelberg (0(  0), 8(50), 4(25), 4(25) et Salmonella gallinarum (12(63.2), 6(31.6), 2(10.5), 7(36.8)) respectivement. différents microbiomes analysés étaient  ubiquitairement riches en gènes de virulence associés aux espèces de Salmonella  &nbsp

First hint for CP violation in neutrino oscillations from upcoming superbeam and reactor experiments

We compare the physics potential of the upcoming neutrino oscillation experiments Daya Bay, Double Chooz, NOvA, RENO, and T2K based on their anticipated nominal luminosities and schedules. After discussing the sensitivity to theta_{13} and the leading atmospheric parameters, we demonstrate that leptonic CP violation will hardly be measurable without upgrades of the T2K and NOvA proton drivers, even if theta_{13} is large. In the presence of the proton drivers, the fast track to hints for CP violation requires communication between the T2K and NOvA collaborations in terms of a mutual synchronization of their neutrino-antineutrino run plans. Even in that case, upgrades will only discover CP violation in a relatively small part of the parameter space at the 3 sigma confidence level, while 90% confidence level hints will most likely be obtained. Therefore, we conclude that a new facility will be required if the goal is to obtain a significant result with high probability.Comment: 27 pages, 12 figure

Impact of high conductivity on particle transport to liquid droplets for liquid marble formation

This study investigates the influence of particle conductivity on the promotion of particle extraction and transport to a pendent liquid droplet in the presence of an electric field by applying a thin metal shell of nickel or gold onto polystyrene core particles. Despite significantly increasing the conductivity of the material, the addition of a metal shell to the core particles did not have a concomitant significant impact on initial particle extraction and transport behaviour. For the same applied potential, gold coated particles were extracted from a smaller separation distance than core polystyrene particles, while nickel coated particles were extracted from a slightly increased separation distance. Small separation distances correspond to a stronger electrostatic force required for extraction, so coating the polystyrene particles with gold made them more difficult to extract. Furthermore, these metal-coated particles were extracted from significantly smaller separation distances when compared to the same polystyrene core particles with conductive polymer shells. This is attributed more to increased inter-particle cohesion than from the increased particle mass as a result of the metal coating. In addition, the nickel and gold metal shell coated particles had differing particle hydrophobicity, impacting the final stability of the resultant liquid marble. Comparison is also made with glass core particles, to observe the impact of constant particle mass and changing conductivity and interparticle cohesion, highlighting that increasing conductivity is less significant than the opposing effect of cohesion. Herein, we conclude that the ability to form liquid marbles using an electrostatic extraction method is dependent on a complex interplay of fundamental particle properties of conductivity, density, and cohesion

The identification of poultry processing in archaeological ceramic vessels using in-situ isotope references for organic residue analysis.

Poultry products are rarely considered when reconstructing pottery use through organic residue analysis, impinging upon our understanding of the changing role of these animals in the past. Here we evaluate an isotopic approach for distinguishing chicken fats from other animal products. We compare the carbon isotopes of fatty acids extracted from modern tissues and archaeological bones and demonstrate that archaeological bones from contexts associated with pottery provide suitable reference ranges for distinguishing omnivorous animal products (e.g. pigs vs. chickens) in pots. When applied to pottery from the Anglo-Saxon site of Flixborough, England, we succeeded in identifying residues derived from chicken fats that otherwise could not be distinguished from other monogastric and ruminant animals using modern reference values only. This provides the first direct evidence for the processing of poultry or their products in pottery. The results highlight the utility of ‘in-situ’ archaeological bone lipids to identify omnivorous animal-derived lipids in archaeological ceramic vessels

Best practices in data analysis and sharing in neuroimaging using MRI

Given concerns about the reproducibility of scientific findings, neuroimaging must define best practices for data analysis, results reporting, and algorithm and data sharing to promote transparency, reliability and collaboration. We describe insights from developing a set of recommendations on behalf of the Organization for Human Brain Mapping, and identify barriers that impede these practices, including how the discipline must change to fully exploit the potential of the world’s neuroimaging data