Genetic Environments Research Articles

Co-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer

Ampicillin resistance has greatly contributed to the recent dramatic increase of a cluster of human adapted Enterococcus faecium lineages (ST17, ST18, and ST78) in hospital-based infections. Changes in the chromosomal pbp5 gene have been associated with different levels of ampicillin susceptibility, leading to protein variants (designated as PBP5 C-types to keep the nomenclature used in previous works) with diverse degrees of reduction in penicillin affinity. Our goal was to use a comparative genomics approach to evaluate the relationship between the diversity of PBP5 among E. faecium isolates of different phylogenomic groups as well as to assess the pbp5 transferability among isolates of disparate clonal lineages. The analyses of 78 selected E. faecium strains as well as published E. faecium genomes, suggested that the diversity of pbp5 mirrors the phylogenomic diversification of E. faecium. The presence of identical PBP5 C-types as well as similar pbp5 genetic environments in different E. faecium lineages and clones from quite different geographical and environmental origin was also documented and would indicate their horizontal gene transfer among E. faecium populations. This was supported by experimental assays showing transfer of large (≈180–280 kb) chromosomal genetic platforms containing pbp5 alleles, ponA (transglycosilase) and other metabolic and adaptive features, from E. faecium donor isolates to suitable E. faecium recipient strains. Mutation profile analysis of PBP5 from available genomes and strains from this study suggests that the spread of PBP5 C-types might have occurred even in the absence of a significant ampicillin resistance phenotype. In summary, genetic platforms containing pbp5 sequences were stably maintained in particular E. faecium lineages, but were also able to be transferred among E. faecium clones of different origins, emphasizing the growing risk of further spread of ampicillin resistance in this nosocomial pathogen.

Presence of the optrA Gene in Methicillin-Resistant Staphylococcus sciuri of Porcine Origin.

A total of 57 methicillin-resistant Staphylococcus aureus (MRSA) isolates and 475 methicillin-resistant coagulase-negative staphylococci (MRCoNS) collected from pigs in the Guangdong province of China in 2014 were investigated for the presence of the novel oxazolidinone-phenicol resistance gene optrA The optrA gene was detected in 6.9% (n = 33) of the MRCoNS, all of which were Staphylococcus sciuri isolates, but in none of the MRSA isolates. Five optrA-carrying methicillin-resistant (MR) S. sciuri isolates also harbored the multiresistance gene cfr Pulsed-field gel electrophoresis (PFGE) and dru typing of the 33 optrA-carrying MR S. sciuri isolates revealed 25 patterns and 5 sequence types, respectively. S1 nuclease PFGE and Southern blotting confirmed that optrA was located in the chromosomal DNAs of 29 isolates, including 1 cfr-positive isolate. The remaining four isolates harbored a ∼35-kb pWo28-3-like plasmid on which optrA and cfr were located together with other resistance genes, as confirmed by sequence analysis. Six different types of genetic environments (types I to VI) of the chromosome-borne optrA genes were identified; these types had the optrA gene and its transcriptional regulator araC in common. Tn558 was found to be associated with araC-optrA in types II to VI. The optrA gene in types II and III was found in close proximity to the ccr gene complex of the respective staphylococcal cassette chromosome mec element (SCCmec). Since oxazolidinones are last-resort antimicrobial agents for the control of serious infections caused by methicillin-resistant staphylococci in humans, the location of the optrA gene close to the ccr complex is an alarming observation.

QTLs for oil yield components in an elite oil palm (Elaeis guineensis) cross

AbstractIncreased modern farming of superior types of the oil palm, Elaeis guineensis Jacq., which has naturally efficient oil biosynthesis, has made it the world’s foremost edible oil crop. Breeding improvement is, however, circumscribed by time and costs associated with the tree’s long reproductive cycle, large size and 10–15 years of field testing. Marker-assisted breeding has considerable potential for improving this crop. Towards this, quantitative trait loci (QTL) linked to oil yield component traits were mapped in a high-yield population. In total, 164 QTLs associated with 21 oil yield component traits were discovered, with cumulative QTL effects increasing in tandem with the number of QTL markers and matching the QT+ alleles for each trait. The QTLs confirmed all traits to be polygenic, with many genes of individual small effects on independent loci, but epistatic interactions are not ruled out. Furthermore, several QTLs maybe pleiotropic as suggested by QTL clustering of inter-related traits on almost all linkage groups. Certain regions of the chromosomes seem richer in the genes affecting a particular yield component trait and likely encompass pleiotropic, epistatic and heterotic effects. A large proportion of the identified additive effects from QTLs may actually arise from genic interactions between loci. Comparisons with previous mapping studies show that most of the QTLs were for similar traits and shared similar marker intervals on the same linkage groups. Practical applications for such QTLs in marker-assisted breeding will require seeking them out in different genetic backgrounds and environments.

Greater intensity and frequency of Cryptosporidium and Giardia oocyst shedding beyond the neonatal period is associated with reductions in growth, carcase weight and dressing efficiency in sheep

Associations between intensity and frequency of Cryptosporidium and Giardia shedding with growth, carcase weight and dressing% were investigated using a longitudinal study of 1182 lambs on eight Australian farms. Live weight was recorded and faecal samples were collected on three sampling occasions; weaning (approximately 12 weeks of age), post-weaning (approximately 19 weeks) and pre-slaughter (approximately 29 weeks). Hot standard carcase weight (HSCW) and dressing% were measured at slaughter. Faecal samples were screened for presence and concentration of Cryptosporidium, Giardia and Haemonchus oocysts using a quantitative PCR. Trichostrongylid eggs were quantified with modified McMaster faecal worm egg count (WEC). Protozoan shedding intensity was categorised as high (above median oocyst concentration in positive sheep), low (below median oocyst concentration in positive sheep) or not detected. Shedding was also categorised for shedding type (no shedding, single Giardia infection, single Cryptosporidium infection, concurrent Giardia and Cryptosporidium infection) and lambs were categorised for frequency of shedding (shedding identified on 0, 1, 2 or 3 occasions). Associations of parasite shedding intensity category, shedding type, shedding frequency, WEC and Haemonchus status (positive or negative) with lamb production were assessed using general linear models (HSCW and dressing%) and linear mixed effects models (live weight). High Cryptosporidium parvum shedding was associated with lower live weight, ranging 2.31–4.52kg over the 3 sampling occasions. Cryptosporidium parvum shedding was associated with less HSCW in high (3.22kg less) and low (3.22kg less) shedding lambs post-weaning, and high (2.21kg less) and low (2.60kg less) shedding lambs pre-slaughter as well as lower dressing% (2.7% lower in high shedding lambs post-weaning). Cryptosporidium (all species) shedding pre-slaughter was associated with reduced dressing% in both high (1.25% lower) and low (1.21% lower) shedding lambs. Giardia shedding pre-slaughter was associated with 0.59kg less HSCW in high shedding lambs. Increased frequency of C. parvum and Giardia shedding in a specific animal (repeated detection) were associated with reduced HSCW and dressing%. Concurrent Giardia and Cryptosporidium shedding pre-slaughter was associated with reduced dressing%. No statistically significant main effects for either WEC (P>0.05) or Haemonchus status (P>0.05) were identified for any of the sheep meat productivity measures (live weight, HSCW and dressing%). The findings suggest naturally acquired Cryptosporidium and Giardia infections in grazing sheep are associated with depressed growth, carcase weight and dressing efficiency beyond the neonatal period in sheep representing a range of genetic backgrounds and different sheep production environments.

Electrochemical detection of neurotransmitters: Toward synapse-based neural interfaces

A synapse is an intercellular junction specialized for an electrochemical information process between presynaptic and postsynaptic neurons. At the chemical synapses, chemical neurotransmitters released from presynaptic membrane bind to receptors on the membrane of opposed postsynaptic neurons. The act of neurotransmitters not only instantly determines the types of neuronal signal, excitatory and inhibitory, but alters the genetic environments for long-term memory construction. As such, studies on neurotransmitters and the event of their release are essential to the understanding of neural function and plasticity in the brain. Electrochemical tools are powerful and suitable for the investigation of neural systems. Two major branches of electrochemical method, amperometry and fast-scan cyclic voltammetry (FSCV), are actively evolving for the detection of neurotransmitters in extreme conditions. Consequently, novel electrode materials and geometrical designs have been developed to overcome the limitations of selectivity and lifetime of the electrodes. Wireless and implantable systems have been developed for in vivo experiments. This review will focus on electroanalytical approaches for the direct measurement of the electrooxidizable neurotransmitters, while envisaging possibilities of synapse-based neural interfaces.

Characterisation of class 3 integrons with oxacillinase gene cassettes in hospital sewage and sludge samples from France and Luxembourg

In this study, antibiotic resistance class 3 integrons in Gram-negative bacteria isolated from hospital sewage and sludge and their genetic contents were characterised. Two samples of hospital effluent from France and Luxembourg and one sample of sludge from a wastewater treatment plant in France were collected in 2010 and 2011. Bacteria were cultured on selective agar plates and integrons were detected in colonies by quantitative PCR. Integron gene cassette arrays and their genetic environments were analysed by next-generation sequencing. Three class 3 integron-positive isolates were detected, including Acinetobacter johnsonii LIM75 (French hospital effluent), Aeromonas allosaccharophila LIM82 (sludge) and Citrobacter freundii LIM86 (Luxembourg hospital effluent). The gene cassettes were all implicated in antibiotic (aminoglycoside and β-lactam) or antiseptic resistance. An oxacillinase gene cassette (blaOXA-10, blaOXA-368 or blaOXA-2) was found in each integron. All of the class 3 integrons were located on small mobilisable plasmids. This study highlights the role of class 3 integrons in the dissemination of clinically relevant antibiotic resistance genes, notably oxacillinase genes, in hospital effluent.

Abstract 4510: KIT melanomas are developmentally racially biased

Abstract KIT is a critical pathway for melanocytic homeostasis and it is often down-regulated in cutaneous melanoma. However, KIT activation plays a critical role in a subpopulation of melanomas especially those in acral locations and melanomas on chronically sun damaged skin. We analyzed exome and RNAseq data from The Cancer Genome Atlas (TCGA) Network (321 cutaneous melanomas in the data set) to identify patterns unique to KIT activation. The melanomas were divided based on known mutually exclusive mutations (BRAF, NRAS and KIT) vs those without (WT). We compared RNA data between each group. KIT group had significantly higher expression of KIT than BRAF, NRAS and WT (p<0.01, FDR<0.01) and isoform 2 expression was higher than 1. KIT melanomas were found to overexpress Wnt pathway, pigmentation and genes involved epithelial-mesenchymal transition. From the exome data, germline SNPs with incidence in ethnic groups (Caucasian, Asian and African) and more likely to be present in a specific melanoma groups were selected. Comparing the 3 ethnicity groups across the 4 tumor groups Asian SNPs were significantly enhanced in KIT tumors, African in WT and Caucasian in BRAF and NRAS melanomas. We evaluated the tumors for the primary type of genetic damage. The three signatures that appeared most divergent were CC>TT for UV, (G/A)C(G)>(G/A)T(G) for deamination, and G>T for oxidative damage. UV and deamination appeared inversely proportional, while oxidative damage appeared to be independent of those other two features. KIT and WT had a greater% of non UV high deamination tumoral environments. A fraction of these tumors also had very high oxidative signatures. We then compared 2 KIT subgroups UV vs non UV (absence of CC>TT mutations) for germline ethnicity differences. Asian SNPs were highly increased in non UV subgroup whereas Caucasian SNPs were in UV subgroup. Further, we divided KIT non UV subgroup into deamination and oxidative damage subgroups and compared ethnicity differences. Deamination was significantly higher in Asians whereas oxidative damage was higher in Caucasians. A similar analysis was done to the WT group, where African SNPs were significantly increased in the non UV subgroup and were primarily associated with oxidative damage. This data implies that KIT mutant melanomas develop in a unique genetic and mutational environments and makes this an ideal system to in which study racial disparities at the molecular level. Citation Format: Margaret I. Sanchez, James M. Grichnik. KIT melanomas are developmentally racially biased. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4510.

What is the biological reality of gene-environment interaction estimates? An assessment of bias in developmental models.

Standard models used to test gene-environment interaction (G×E) hypotheses make the causal assumption that there are no unobserved variables that could be biasing the interaction estimate. Whether this assumption can be met in nonexperimental studies is unclear because the interactive biological pathways from genetic polymorphisms and environments to behavior, and the confounders that can be introduced along these pathways, are often not delineated. This is problematic in the context of studies focused on caregiver-child dyads, in which common genes and environments induce gene-environment correlation. To address the impact of sources of bias in G×E models specifically assessing the interaction between child genotype and caregiver behavior, we provide a causal framework that integrates biological and statistical concepts of G×E, and assess the magnitude of bias introduced by various confounding pathways in different causal circumstances. A simulation assessed the magnitude of bias introduced by four types of confounding pathways in different causal models. Unadjusted and adjusted statistical models were then applied to the simulated data to assess the efficacy of these procedures to capture unbiased G×E estimates. Finally, the simulation was run under null effects of the genotype to assess the impact of biasing sources on the false-positive rate. Common environmental pathways between caregiver and child inflated G×E estimates and raised the false-positive rate. Evocative effects of the child also inflated G×E estimates. Gene-environment interaction studies should be approached with consideration to the causal pathways at play and the confounding opportunities along these pathways to facilitate the inclusion of adequate statistical controls and correct inferences from study findings. Bridging biological and statistical concepts of G×E can significantly improve research design and the communication of how a G×E process fits into a broader developmental framework.

Fruit metabolite networks in engineered and non-engineered tomato genotypes reveal fluidity in a hormone and agroecosystem specific manner.

IntroductionMetabolomics provides a view of endogenous metabolic patterns not only during plant growth, development and senescence but also in response to genetic events, environment and disease. The effects of the field environment on plant hormone-specific metabolite profiles are largely unknown. Few studies have analyzed useful phenotypes generated by introducing single or multiple gene events alongside the non-engineered wild type control at field scale to determine the robustness of the genetic trait and its modulation in the metabolome as a function of specific agroecosystem environments.ObjectivesWe evaluated the influence of genetic background (high polyamine lines; low methyl jasmonate line; low ethylene line; and isogenic genotypes carrying double transgenic events) and environments (hairy vetch, rye, plastic black mulch and bare soil mulching systems) on the metabolomic profile of isogenic reverse genetic mutations and selected mulch based cropping systems in tomato fruit. Net photosynthesis and fruit yield were also determined.MethodsNMR spectroscopy was used for quantifying metabolites that are central to primary metabolism. We analyzed both the first moment (means) of metabolic response to genotypes and agroecosystems by traditional univariate/multivariate methods, and the second moment (covariances) of responses by creating networks that depicted changes in correlations of paired metabolites. This particular approach is novel and was necessary because our experimental material yielded highly variable metabolic responses that could not be easily understood using the traditional analytical approaches for first moment statistics.ResultsHigh endogenous spermidine and spermine content exhibited strong effects on amino acids, Krebs cycle intermediates and energy molecules (ADP + ATP) in ripening fruits of plants grown under different agroecosystem environments. The metabolic response to high polyamine genotypes was similar to the response to hairy vetch cover crop mulch; supported by the pattern of changes in correlation between metabolites. Changes in primary metabolites of genotypes mutated for the deficiency of ethylene or methyl jasmonate were unique under all growth conditions and opposite of high polyamine genotype results. The high polyamine trait was found to dominate the low ethylene and low jasmonate mutations under field conditions. For several metabolites low ethylene and low methyl jasmonate genotypes had an inverse relationship. Collectively, these results affirm that interactions between metabolite pathways and growth environments are affected by genotype, and influence the metabolite quality of a crop.ConclusionThis study portrays how metabolite relationships change, both in mean and in correlation, under different genotypic and environmental conditions. Although these networks are surprisingly dynamic, we also find examples of selectively conserved associations.Electronic supplementary materialThe online version of this article (doi:10.1007/s11306-016-1037-2) contains supplementary material, which is available to authorized users.

Characterization of Fosfomycin Resistance Gene, fosB, in Methicillin-Resistant Staphylococcus aureus Isolates.

To investigate the prevalence, location and genetic environments of fosfomycin-resistance (fos) genes in methicillin-resistant Staphylococcus aureus (MRSA) clinical strains, 67 fosfomycin-resistant MRSA strains were isolated from the blood and cerebrospinal fluid samples at a teaching hospital in Shanghai. The presence of fos genes in these clinical strains was detected by PCR and sequencing. The locations of fos genes were determined by Southern blotting and genetic environments were analyzed by primer walking sequencing. Multiple locus sequence typing (MLST) was used to characterize genetic diversity. Conjugation was performed to evaluate the transferability of fos genes. Among 67 fosfomycin-resistant MRSA strains, nine high level fosfomycin resistant strains (≥128 μg/ml) were fosB-positive. Three new subtypes of fosB, designated as fosB4, fosB5, and fosB6, were identified. fosB1, fosB4 or fosB6 genes were located on small plasmids (ca. 2.5 kb) and flanked by an analogous replication gene (rep). Differently, the fosB5 gene was surrounded by a shorter rep gene and two copies of a transposon gene (tnp) that shared high identity with the IS257-like transposon. Four MLST types were found among the nine fosB-positive strains. Transconjugants with the fosB genes were resistant to fosfomycin with MIC 64 or 128 μg/ml. In conclusion, different subtypes and genetic environment of fosB genes indicate that gene heterogeneity for fosfomycin resistance in MRSA isolates.

630 Cutaneous melanomas with KIT mutations may be ethnically predisposed

KIT is crucial for melanocytes development and activating mutations have shown to drive melanomagenesis particularly in acral and chronically sun damaged skin locations. Exome and RNAseq data was analyzed from 321 cutaneous melanoma from The Cancer Genome Atlas network to identify KIT specific mutational patterns. Melanomas were divided into BRAF, NRAS, KIT and those without any of those 3 driving mutations (WT). We compared Caucasian, African and Asian germline SNPs across the 4 groups. Asian SNPs were significantly higher in KIT, African in WT and Caucasian in BRAF and NRAS. The melanomas were evaluated by the type of mutations. We used CC>TT for UV, G>T for oxidative damage and (G/A)C (G) > (G/A)T(G) for deamination. UV and deamination were inversely proportional, while oxidative damage appeared to be independent. KIT mutant tumors had a greater percentage of non-UV high deamination mutations while WT had non-UV high oxidative damage. UV and non UV (based on CC>TT) KIT subgroups were compared for germline racial differences. Asian SNPs were greatly increased in non UV subgroup whereas Caucasian SNPs were increased in UV subgroup. Further, we divided non UV KIT subgroup into deamination and oxidative damage subgroups to compare racial differences. Deamination was significantly increased in Asians whereas oxidative damage was higher in Caucasians. We did a similar analysis to the WT group, and found African SNPs were significantly higher in the non UV subgroup and were primarily correlated with oxidative damage. From the RNA data, a differentially expressed gene (DEG) analysis between each group was done. We found that KIT expression was significantly more increased in KIT group than the others (p < 0.01, FDR < 0.01) and KIT isoform 2 expression was higher than 1. Our findings suggest that KIT melanomas develop in a distinctive mutational and genetic environments and may be racially predisposed.

Detection of the plasmid-mediated mcr-1 gene conferring colistin resistance in human and food isolates of Salmonella enterica and Escherichia coli in England and Wales.

In response to the first report of transmissible colistin resistance mediated by the mcr-1 gene in Escherichia coli and Klebsiella spp. from animals and humans in China, we sought to determine its presence in Enterobacteriaceae isolated in the UK. The PHE archive of whole-genome sequences of isolates from surveillance collections, submissions to reference services and research projects was retrospectively analysed for the presence of mcr-1 using Genefinder. The genetic environment of the gene was also analysed. Rapid screening of the genomes of ∼24 000 Salmonella enterica, E. coli, Klebsiella spp., Enterobacter spp., Campylobacter spp. and Shigella spp. isolated from food or humans identified 15 mcr-1-positive isolates. These comprised: 10 human S. enterica isolates submitted between 2012 and 2015 (8 Salmonella Typhimurium, 1 Salmonella Paratyphi B var Java and 1 Salmonella Virchow) from 10 patients; 3 isolates of E. coli from 2 patients; and 2 isolates of Salmonella Paratyphi B var Java from poultry meat imported from the EU. The mcr-1 gene was located on diverse plasmids belonging to the IncHI2, IncI2 and IncX4 replicon types and its association with ISApl1 varied. Six mcr-1-positive S. enterica isolates were from patients who had recently travelled to Asia. Analysis of WGS data allowed rapid confirmation of the presence of the plasmid-mediated colistin resistance gene mcr-1 in diverse genetic environments and plasmids. It has been present in E. coli and Salmonella spp. harboured by humans in England and Wales since at least 2012.

Play matters: the surprising relationship between juvenile playfulness and anxiety in later life

Besides being recognized as a potential welfare indicator, play behaviour has long been considered to have immediate and/or long-term benefits. In particular, it has been suggested that in play animals learn to cope physically and emotionally with unexpected events. Given that the propensity to play varies greatly between conspecific individuals, such interindividual variability in playfulness may be associated with differences in the animals' future behaviour, a prediction that has rarely been tested. To investigate whether different levels of playfulness in juvenility indeed coincide with behavioural differences in later life, 30 female C57BL/6J mice were subjected to the following series of behavioural observations and tests: (1) quantification of juvenile play behaviour; (2) behavioural testing in paradigms that assess anxiety-like behaviour and exploratory locomotion in an unfamiliar environment; and (3) observation of spontaneous behaviour in the familiar home cage environment. Surprisingly, a high level of juvenile playfulness was predictive of high levels of state anxiety and low levels of exploratory locomotion in later life. While this relationship existed already in adolescence, it became even more prominent in adulthood. By contrast, no substantial differences between playful and less playful mice were found with respect to home cage behaviour. While these findings may reflect better coping abilities in novel and dangerous environments in those mice that played the most during juvenility, they may also argue for the existence of different types of mice. Thus, despite genetic homogeneity and identical housing environments, preferences for either local or global use of space were observed that indicate the emergence of individuality. Concerning animal welfare, our findings suggest that play may constitute a plausible welfare indicator at the population level, but is probably less meaningful for the individual.

First report of extended-spectrum β-lactamases among clinical isolates of Escherichia coli in Gaza Strip, Palestine.

This study aimed to assess the occurrence of extended-spectrum β-lactamases (ESBLs) in clinical Escherichia coli isolates from Palestine and to characterise their type, genetic environments and associated resistance genes. Twenty-seven broad-spectrum-cephalosporin-resistant E. coli isolates were recovered between April and June 2013 in Gaza Strip hospitals. Characterisation of ESBL genes and their genetic environments, detection of associated resistance genes, and the presence and characterisation of integrons were performed by PCR and sequencing. The clonal relationship among ESBL-positive E. coli strains was determined by pulsed-field gel electrophoresis (PFGE) using the restriction enzyme XbaI. Phylogroup typing and virulence factors were studied by PCR. The following ESBL genes were identified: blaCTX-M-15 (21 isolates); blaCTX-M-14a (2 isolates); blaCTX-M-1 (2 isolates); blaCTX-M-3 (1 isolate); and blaCTX-M-27 (1 isolate). The blaTEM-1 gene was also detected in eight CTX-M-producing strains. The ISEcp1 sequence was found upstream of blaCTX-M in 23 isolates, and orf477 was found downstream of this gene in 24 isolates. IS903 was also detected downstream in three isolates. Six isolates carried class 1 integrons with the gene cassette arrangement dfrA17-aadA5. High clonal diversity was observed among the studied isolates by PFGE (24 unrelated profiles). The virulence gene fimA was detected in 23 isolates, the aer gene in 8 isolates and the papC gene in 7 isolates. The studied isolates belonged to phylogroups B2 (12 isolates), D (12 isolates) and A (3 isolates). This is the first report of the detection of CTX-M class β-lactamases in E. coli of clinical origin in Gaza Strip hospitals.

Genetic dissection of neural circuits underlying sexually dimorphic social behaviours.

The unique hormonal, genetic and epigenetic environments of males and females during development and adulthood shape the neural circuitry of the brain. These differences in neural circuitry result in sex-typical displays of social behaviours such as mating and aggression. Like other neural circuits, those underlying sex-typical social behaviours weave through complex brain regions that control a variety of diverse behaviours. For this reason, the functional dissection of neural circuits underlying sex-typical social behaviours has proved to be difficult. However, molecularly discrete neuronal subpopulations can be identified in the heterogeneous brain regions that control sex-typical social behaviours. In addition, the actions of oestrogens and androgens produce sex differences in gene expression within these brain regions, thereby highlighting the neuronal subpopulations most likely to control sexually dimorphic social behaviours. These conditions permit the implementation of innovative genetic approaches that, in mammals, are most highly advanced in the laboratory mouse. Such approaches have greatly advanced our understanding of the functional significance of sexually dimorphic neural circuits in the brain. In this review, we discuss the neural circuitry of sex-typical social behaviours in mice while highlighting the genetic technical innovations that have advanced the field.

Atypical epidemiology of CTX-M-15 among Enterobacteriaceae from a high diversity of non-clinical niches in Angola.

The objective of this study was to investigate the distribution and molecular epidemiology of ESBLs, acquired AmpCs and carbapenemases in Enterobacteriaceae from non-clinical niches in Angola, an under-researched sub-Saharan country. Eighty-one samples were recovered from healthy persons (n = 18), healthy animals (n = 33) and their environments (n = 10) or aquatic settings (n = 20) in south Angola (2013). Samples were plated onto CHROMagar™ Orientation with/without antibiotics. Standard methods were used for bacterial identification, characterization of bla genes, antibiotic susceptibility testing and conjugation assays. Clonal analysis (XbaI-PFGE, MLSTand Escherichia coli phylogroups), location of bla and plasmid characterization (S1-PFGE, I-CeuI-PFGE, replicon typingand hybridization) were also performed. ESBLs (almost exclusively CTX-M-15, 98%) were detected in 21% (45/216) of the isolates, recovered from diverse non-clinical niches and belonging to different Enterobacteriaceae species (mainly E. coli). Acquired AmpCs or carbapenemases were not found. The pandemic B2-ST131 E. coli clone was not identified, but some widespread clonal complexes (CCs) from A (CC10 and CC168), B1 (CC156) or D (CC38) phylogroups were detected. blaCTX-M-15 was variably identified on typeable (29%; 100-335 kb; IncFII, IncFIIK6, IncHI2 and IncY) or non-typeable (16%; 70-330 kb) plasmids or on the chromosome (14%), while for 41% of the isolates its specific location was not determined. This study reports, for the first time in Angola, an unexpected high occurrence of CTX-M-15 in diverse non-clinical niches and Enterobacteriaceae species, and uncovers novel plasmid replicons in under-researched geographical regions. The diffusion of blaCTX-M-15 through such a high diversity of genetic backgrounds (clones, typeable/non-typeable plasmids and genetic environments) unveils an extraordinary ability for blaCTX-M-15 acquisition and mobilization favoured by unrecognized ecological factors.

Colistin-Nonsusceptible Pseudomonas aeruginosa Sequence Type 654 with blaNDM-1 Arrives in North America.

This study describes 3 different blaNDM-1 genetic platforms in 3 different species obtained from the same patient who was directly transferred to an institution in Calgary, Alberta, Canada, following a prolonged hospital stay in India. The blaNDM-1 in the Escherichia coli isolate was located on a 176-kb IncA/C plasmid contained within an ISCR1 region. The blaNDM-1 in the Providencia rettgeri isolate was located on a 117-kb IncT plasmid contained within Tn3000, while the blaNDM-1 in the Pseudomonas aeruginosa isolate was located on the chromosome within an ISCR3 region. This report highlights the plasticity of the genetic regions and environments associated with blaNDM-1. To the best of our knowledge, this is the first report of P. aeruginosa with blaNDM-1 identified in North America and the first report of blaOXA-181 in P. rettgeri. The P. aeruginosa isolate belonged to the international high-risk sequence type 654 clone and was nonsusceptible to colistin. This case emphasizes the need for the use of appropriate infection prevention and control measures and vigilant screening for carbapenem-resistant Gram-negative bacteria in patients with a history of travel to areas of endemicity, such as the Indian subcontinent.

Impact of perinatal environmental tobacco smoke on the development of childhood allergic diseases.

Allergic diseases such as asthma, allergic rhinitis, atopic dermatitis, and food allergy, are most common chronic, noncommunicable diseases in childhood. In the past few decades, the prevalence has increased abruptly worldwide. There are 2 possible explanations for the rising prevalence of allergic diseases worldwide, that an increased disease-awareness of physician, patient, or caregivers, and an abrupt exposure to unknown hazards. Unfortunately, the underlying mechanisms remain largely unknown. Despite the continuing efforts worldwide, the etiologies and rising prevalence remain unclear. Thus, it is important to identify and control risk factors in the susceptible individual for the best prevention and management. Genetic susceptibility or environments may be a potential background for the development of allergic disease, however they alone cannot explain the rising prevalence worldwide. There is growing evidence that epigenetic change depends on the gene, environment, and their interactions, may induce a long-lasting altered gene expression and the consequent development of allergic diseases. In epigenetic mechanisms, environmental tobacco smoke (ETS) exposure during critical period (i.e., during pregnancy and early life) are considered as a potential cause of the development of childhood allergic diseases. However, the causal relationship is still unclear. This review aimed to highlight the impact of ETS exposure during the perinatal period on the development of childhood allergic diseases and to propose a future research direction.

New real-time-PCR method to identify single point mutations in hepatitis C virus.

AIMTo develop a fast, low-cost diagnostic strategy to identify single point mutations in highly variable genomes such as hepatitis C virus (HCV).METHODSIn patients with HCV infection, resistance-associated amino acid substitutions within the viral quasispecies prior to therapy can confer decreased susceptibility to direct-acting antiviral agents and lead to treatment failure and virological relapse. One such naturally occurring mutation is the Q80K substitution in the HCV-NS3 protease gene, which confers resistance to PI inhibitors, particularly simeprevir. Low-cost, highly sensitive techniques enabling routine detection of these single point mutations would be useful to identify patients at a risk of treatment failure. LightCycler methods, based on real-time PCR with sequence-specific probe hybridization, have been implemented in most diagnostic laboratories. However, this technique cannot identify single point mutations in highly variable genetic environments, such as the HCV genome. To circumvent this problem, we developed a new method to homogenize all nucleotides present in a region except the point mutation of interest.RESULTSUsing nucleotide-specific probes Q, K, and R substitutions at position 80 were clearly identified at a sensitivity of 10% (mutations present at a frequency of at least 10% were detected). The technique was successfully applied to identify the Q80K substitution in 240 HCV G1 serum samples, with performance comparable to that of direct Sanger sequencing, the current standard procedure for this purpose. The new method was then validated in a Catalonian population of 202 HCV G1-infected individuals. Q80K was detected in 14.6% of G1a patients and 0% of G1b in our setting.CONCLUSIONA fast, low-cost diagnostic strategy based on real-time PCR and fluorescence resonance energy transfer probe melting curve analysis has been successfully developed to identify single point mutations in highly variable genomes such as hepatitis C virus. This technique can be adapted to detect any single point mutation in highly variable genomes.

The blueberry (iron nodule) from the Shark Bay area, Western Australia and its implication to the genetic environments of iron nodules on Mars

Fist-sized iron nodules, extensively found on the ground of Western Australia, were investigated by element analysis (XRF, ICP-MS and ICP-AES), electron microscopes, X-ray diffraction and Mossbauser spectroscopy. Loosely-packed pisoidic structures of a few to >10 mm in size were observed in the cross-section of nodules. Chemically, the nodules are majorly made of O, Si, Fe and Al, and share similar REE pattern with the loess sourced Greatford concretions from New Zealand. Angular quartz particles, nano-sized goethite and hematite are found to be the major mineral phases. Other minerals, such as detrital zircon, barite and Ce-containing particles can also be observed but of very low abundance. No detectable carbonate or amorphous silica implies that these nodules have experienced little underground fluid alteration. The quartz particles showing particularly three sections of fractal size-distributions, together with their extensive broken features and conchoidal fractures, strongly suggest in situ fragmentation of the host rock with minimum later dynamic sorting. These observations indicate the genetic environment of those nodules is always close to the surface of the tectonically stable ground since their formation. Because of the similarity of climatic and geological features, the genesis and preservation environment of these nodules in Western Australia may provide clues on the formation of Martian iron concretions