Candidate genes for alcohol preference identified by expression profiling in alcohol-preferring and -nonpreferring reciprocal congenic rats

Background

Selectively bred alcohol-preferring (P) and alcohol-nonpreferring (NP) rats differ greatly in alcohol preference, in part due to a highly significant quantitative trait locus (QTL) on chromosome 4. Alcohol consumption scores of reciprocal chromosome 4 congenic strains NP.P and P.NP correlated with the introgressed interval. The goal of this study was to identify candidate genes that may influence alcohol consumption by comparing gene expression in five brain regions of alcohol-naïve inbred alcohol-preferring and P.NP congenic rats: amygdala, nucleus accumbens, hippocampus, caudate putamen, and frontal cortex.

Results

Within the QTL region, 104 cis-regulated probe sets were differentially expressed in more than one region, and an additional 53 were differentially expressed in a single region. Fewer trans-regulated probe sets were detected, and most differed in only one region. Analysis of the average expression values across the 5 brain regions yielded 141 differentially expressed cis-regulated probe sets and 206 trans-regulated probe sets. Comparing the present results from inbred alcohol-preferring vs. congenic P.NP rats to earlier results from the reciprocal congenic NP.P vs. inbred alcohol-nonpreferring rats demonstrated that 74 cis-regulated probe sets were differentially expressed in the same direction and with a consistent magnitude of difference in at least one brain region.

Conclusions

Cis-regulated candidate genes for alcohol consumption that lie within the chromosome 4 QTL were identified and confirmed by consistent results in two independent experiments with reciprocal congenic rats. These genes are strong candidates for affecting alcohol preference in the inbred alcohol-preferring and inbred alcohol-nonpreferring rats.

     

Automatic non-proliferative diabetic retinopathy screening system based on color fundus image

Background

Non-proliferative diabetic retinopathy is the early stage of diabetic retinopathy. Automatic detection of non-proliferative diabetic retinopathy is significant for clinical diagnosis, early screening and course progression of patients.

Methods

This paper introduces the design and implementation of an automatic system for screening non-proliferative diabetic retinopathy based on color fundus images. Firstly, the fundus structures, including blood vessels, optic disc and macula, are extracted and located, respectively. In particular, a new optic disc localization method using parabolic fitting is proposed based on the physiological structure characteristics of optic disc and blood vessels. Then, early lesions, such as microaneurysms, hemorrhages and hard exudates, are detected based on their respective characteristics. An equivalent optical model simulating human eyes is designed based on the anatomical structure of retina. Main structures and early lesions are reconstructed in the 3D space for better visualization. Finally, the severity of each image is evaluated based on the international criteria of diabetic retinopathy.

Results

The system has been tested on public databases and images from hospitals. Experimental results demonstrate that the proposed system achieves high accuracy for main structures and early lesions detection. The results of severity classification for non-proliferative diabetic retinopathy are also accurate and suitable.

Conclusions

Our system can assist ophthalmologists for clinical diagnosis, automatic screening and course progression of patients.

     

Genetic mutations in influenza H3N2 viruses from a 2012 epidemic in Southern China

Background

An influenza H3N2 epidemic occurred throughout Southern China in 2012.

Methods

We analyzed the hemagglutinin (HA) and neuraminidase (NA) genes of influenza H3N2 strains isolated between 2011–2012 from Guangdong. Mutation sites, evolutionary selection, antigenic sites, and N-glycosylation within these strains were analyzed.

Results

The 2011–2012 Guangdong strains contained the HA-A214S, HA-V239I, HA-N328S, NA-L81P, and NA-D93G mutations, similar to those seen in the A/ Perth/16/2009 influenza strain. The HA-NSS_061–063 and NNS_160–162 glycosylation sites were prevalent among the 2011–2012 Guangdong strains but the NA-NRS_402–404 site was deleted. Antigenically, there was a four-fold difference between A/Perth/16/2009 -like strains and the 2011–2012 Guangdong strains.

Conclusion

Antigenic drift of the H3N2 subtype contributed to the occurrence of the Southern China influenza epidemic of 2012.

     

A set of highly informative rat simple sequence length polymorphism (SSLP) markers and genetically defined rat strains

Background

The National Bio Resource Project for the Rat in Japan (NBRP-Rat) is focusing on collecting, preserving and distributing various rat strains, including spontaneous mutant, transgenic, congenic, and recombinant inbred (RI) strains. To evaluate their value as models of human diseases, we are characterizing them using 109 phenotypic parameters, such as clinical measurements, internal anatomy, metabolic parameters, and behavioral tests, as part of the Rat Phenome Project. Here, we report on a set of 357 simple sequence length polymorphism (SSLP) markers and 122 rat strains, which were genotyped by the marker set.

Results

The SSLP markers were selected according to their distribution patterns throughout the whole rat genome with an average spacing of 7.59 Mb. The average number of informative markers between all possible pairs of strains was 259 (72.5% of 357 markers), showing their high degree of polymorphism. From the genetic profile of these rat inbred strains, we constructed a rat family tree to clarify their genetic background.

Conclusion

These highly informative SSLP markers as well as genetically and phenotypically defined rat strains are useful for designing experiments for quantitative trait loci (QTL) analysis and to choose strategies for developing new genetic resources. The data and resources are freely available at the NBRP-Rat web site [1].

     

Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

Background

Thanks to the large amount of signal contained in genome-wide sequence alignments, phylogenomic analyses are converging towards highly supported trees. However, high statistical support does not imply that the tree is accurate. Systematic errors, such as the Long Branch Attraction (LBA) artefact, can be misleading, in particular when the taxon sampling is poor, or the outgroup is distant. In an otherwise consistent probabilistic framework, systematic errors in genome-wide analyses can be traced back to model mis-specification problems, which suggests that better models of sequence evolution should be devised, that would be more robust to tree reconstruction artefacts, even under the most challenging conditions.

Methods

We focus on a well characterized LBA artefact analyzed in a previous phylogenomic study of the metazoan tree, in which two fast-evolving animal phyla, nematodes and platyhelminths, emerge either at the base of all other Bilateria, or within protostomes, depending on the outgroup. We use this artefactual result as a case study for comparing the robustness of two alternative models: a standard, site-homogeneous model, based on an empirical matrix of amino-acid replacement (WAG), and a site-heterogeneous mixture model (CAT). In parallel, we propose a posterior predictive test, allowing one to measure how well a model acknowledges sequence saturation.

Results

Adopting a Bayesian framework, we show that the LBA artefact observed under WAG disappears when the site-heterogeneous model CAT is used. Using cross-validation, we further demonstrate that CAT has a better statistical fit than WAG on this data set. Finally, using our statistical goodness-of-fit test, we show that CAT, but not WAG, correctly accounts for the overall level of saturation, and that this is due to a better estimation of site-specific amino-acid preferences.

Conclusion

The CAT model appears to be more robust than WAG against LBA artefacts, essentially because it correctly anticipates the high probability of convergences and reversions implied by the small effective size of the amino-acid alphabet at each site of the alignment. More generally, our results provide strong evidence that site-specificities in the substitution process need be accounted for in order to obtain more reliable phylogenetic trees.

     

Outer membrane protein C (OmpC) of <Emphasis Type="Italic">Escherichia coli</Emphasis> induces neurodegeneration in mice by acting as an amyloid

Objectives

Involvement of the outer membrane protein C (OmpC) of Escherichia coli in neurodegeneration was investigated using a mouse model.

Results

OmpC formed protease-resistant fibres that exhibited the diagnostic features of an amyloid. The spectral shift in the Congo Red and the thioflavin T assays produced features similar to neurotoxic peptides. Intramuscular administration of OmpC in mice resulted in spongiform neurodegeneration of the brain through calcium-dependent apoptosis and also showed upregulation of apoptosis related genes. Immunolocalization of OmpC in brain demonstrated the direct involvement of the porin in neurodegeneration and formation of spongiform encephalopathy.

Conclusion

We have demonstrated the ability of OmpC of E. coli to induce neurodegeneration in mice.

     

Exome sequencing identifies novel and recurrent mutations in <Emphasis Type="Italic">GJA8</Emphasis> and <Emphasis Type="Italic">CRYGD</Emphasis>associated with inherited cataract

Background

Inherited cataract is a clinically important and genetically heterogeneous cause of visual impairment. Typically, it presents at an early age with or without other ocular/systemic signs and lacks clear phenotype-genotype correlation rendering both clinical classification and molecular diagnosis challenging. Here we have utilized trio-based whole exome sequencing to discover mutations in candidate genes underlying autosomal dominant cataract segregating in three nuclear families.

Results

In family A, we identified a recurrent heterozygous mutation in exon-2 of the gene encoding γD-crystallin (CRYGD; c.70C > A, p.Pro24Thr) that co-segregated with `coralliform' lens opacities. Families B and C were found to harbor different novel variants in exon-2 of the gene coding for gap-junction protein α8 (GJA8; c.20T > C, p.Leu7Pro and c.293A > C, p.His98Pro). Each novel variant co-segregated with disease and was predicted in silico to have damaging effects on protein function.

Conclusions

Exome sequencing facilitates concurrent mutation-profiling of the burgeoning list of candidate genes for inherited cataract, and the results can provide enhanced clinical diagnosis and genetic counseling for affected families.

     

The Association Between Depression,Suicidal Ideation and Psychological Strains in College Students: A Cross-National Study

Objective

This study examined the differences of psychological strains between Chinese and American college students and discussed how strains may influence individuals’ suicidal ideation and depression.

Participants/methods

A total of 539 college students (298 from China and 241 from the U.S.) were recruited in March 2016 to complete the survey study. Multiple linear regressions were used in data analysis.

Results

Students in America had higher scores on depression and stress than students in China, while students in China rated higher on suicidal ideation than students in America. In contrast of students in America facing more coping strains, students in China were confronting more value strains in their life.

Conclusion

The cross-cultural variations in the effect of psychological strains have been substantiated in current study, indicating that understanding the psychological strains in different cultural contexts is necessary for the early intervention and prevention in college aged populations.

     

Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice

Background

The next big challenge in human genetics is understanding the 98% of the genome that comprises non-coding DNA. Hidden in this DNA are sequences critical for gene regulation, and new experimental strategies are needed to understand the functional role of gene-regulation sequences in health and disease. In this study, we build upon our HuGX ('high-throughput human genes on the X chromosome’) strategy to expand our understanding of human gene regulation in vivo.

Results

In all, ten human genes known to express in therapeutically important brain regions were chosen for study. For eight of these genes, human bacterial artificial chromosome clones were identified, retrofitted with a reporter, knocked single-copy into the Hprt locus in mouse embryonic stem cells, and mouse strains derived. Five of these human genes expressed in mouse, and all expressed in the adult brain region for which they were chosen. This defined the boundaries of the genomic DNA sufficient for brain expression, and refined our knowledge regarding the complexity of gene regulation. We also characterized for the first time the expression of human MAOA and NR2F2, two genes for which the mouse homologs have been extensively studied in the central nervous system (CNS), and AMOTL1 and NOV, for which roles in CNS have been unclear.

Conclusions

We have demonstrated the use of the HuGX strategy to functionally delineate non-coding-regulatory regions of therapeutically important human brain genes. Our results also show that a careful investigation, using publicly available resources and bioinformatics, can lead to accurate predictions of gene expression.

     

Stress amplifies sex differences in primate prefrontal profiles of gene expression

Background

Stress is a recognized risk factor for mood and anxiety disorders that occur more often in women than men. Prefrontal brain regions mediate stress coping, cognitive control, and emotion. Here, we investigate sex differences and stress effects on prefrontal cortical profiles of gene expression in squirrel monkey adults.

Methods

Dorsolateral, ventrolateral, and ventromedial prefrontal cortical regions from 18 females and 12 males were collected after stress or no-stress treatment conditions. Gene expression profiles were acquired using HumanHT-12v4.0 Expression BeadChip arrays adapted for squirrel monkeys.

Results

Extensive variation between prefrontal cortical regions was discerned in the expression of numerous autosomal and sex chromosome genes. Robust sex differences were also identified across prefrontal cortical regions in the expression of mostly autosomal genes. Genes with increased expression in females compared to males were overrepresented in mitogen-activated protein kinase and neurotrophin signaling pathways. Many fewer genes with increased expression in males compared to females were discerned, and no molecular pathways were identified. Effect sizes for sex differences were greater in stress compared to no-stress conditions for ventromedial and ventrolateral prefrontal cortical regions but not dorsolateral prefrontal cortex.

Conclusions

Stress amplifies sex differences in gene expression profiles for prefrontal cortical regions involved in stress coping and emotion regulation. Results suggest molecular targets for new treatments of stress disorders in human mental health.

     

Adherent/invasive <Emphasis Type="Italic">Escherichia coli</Emphasis> (AIEC) isolates from asymptomatic people: new <Emphasis Type="Italic">E. coli</Emphasis> ST131 O25:H4/H30-Rx virotypes

Background

The widespread Escherichia coli clone ST131 implicated in multidrug-resistant infections has been recently reported, the majority belonging to O25:H4 serotype and classified into five main virotypes in accordance with the virulence genes carried.

Methods

Pathogenicity Islands I and II (PAI-I and PAI-II) were determined using conventional PCR protocols from a set of four E. coli CTX^R ST131 O25:H4/H30-Rx strains collected from healthy donors’ stool. The virulence genes patterns were also analyzed and compared them with the virotypes reported previously; then adherence, invasion, macrophage survival and biofilm formation assays were evaluated and AIEC pathotype genetic determinants were investigated.

Findings

Non-reported virulence patterns were found in our isolates, two of them carried satA, papA, papGII genes and the two-remaining isolates carried cnfI, iroN, satA, papA, papGII genes, and none of them belonged to classical ST131 virotypes, suggesting an endemic distribution of virulence genes and two new virotypes. The presence of PAI-I and PAI-II of Uropathogenic E. coli was determined in three of the four strains, furthermore adherence and invasion assays demonstrated higher degrees of attachment/invasion compared with the control strains. We also amplified intI1, insA and insB genes in all four samples.

Interpretation

The results indicate that these strains own non-reported virotypes suggesting endemic distribution of virulence genes, our four strains also belong to an AIEC pathotype, being this the first report of AIEC in México and the association of AIEC with healthy donors.

     

Single nucleotide polymorphism analysis for the production of valuable steroid intermediates in <Emphasis Type="Italic">Mycobacterium neoaurum</Emphasis>

Objectives

To investigate single nucleotide polymorphism (SNP) in the transformation process of phytosterol to valuable steroid intermediates in three steroid-producing Mycobacterium neoaurum strains using deep sequencing and bioinformation analysis.

Results

The assembled contig sequences from RNA sequencing of strains producing 9α-hydroxy-4-androstene-3,17-dione (9OHAD), 1,4-androstadiene-3,17-dione (ADD), and 22-hydroxy-23, 24-bisnorchola-1,4-dien-3-one (1,4-BNA) were analyzed for the presence of putative SNPs for steroid catabolism. 413, 375, and 491 SNPs were detected in the coding domain sequences and non-coding domain sequences of RNA sequencing reads of M. neoaurum strains producing 9OHAD, ADD, and BNA, respectively. Special attention was focused on SNPs associated with genes showing differential expression at proteome level, including the genes for sterol catabolism, glycerol catabolic process, signal transduction systems, transport system and energy metabolism.

Conclusions

The work facilitates the understanding of underlying genetic changes that may be responsible for steroid accumulation in M. neoaurum and is useful for its targeted genetic engineering.

     

Identifying functional relationships within sets of co-expressed genes by combining upstream regulatory motif analysis and gene expression information

Background

Existing clustering approaches for microarray data do not adequately differentiate between subsets of co-expressed genes. We devised a novel approach that integrates expression and sequence data in order to generate functionally coherent and biologically meaningful subclusters of genes. Specifically, the approach clusters co-expressed genes on the basis of similar content and distributions of predicted statistically significant sequence motifs in their upstream regions.

Results

We applied our method to several sets of co-expressed genes and were able to define subsets with enrichment in particular biological processes and specific upstream regulatory motifs.

Conclusions

These results show the potential of our technique for functional prediction and regulatory motif identification from microarray data.

     

The role of laterally transferred genes in adaptive evolution

Background

Bacterial genomes develop new mechanisms to tide them over the imposing conditions they encounter during the course of their evolution. Acquisition of new genes by lateral gene transfer may be one of the dominant ways of adaptation in bacterial genome evolution. Lateral gene transfer provides the bacterial genome with a new set of genes that help it to explore and adapt to new ecological niches.

Methods

A maximum likelihood analysis was done on the five sequenced corynebacterial genomes to model the rates of gene insertions/deletions at various depths of the phylogeny.

Results

The study shows that most of the laterally acquired genes are transient and the inferred rates of gene movement are higher on the external branches of the phylogeny and decrease as the phylogenetic depth increases. The newly acquired genes are under relaxed selection and evolve faster than their older counterparts. Analysis of some of the functionally characterised LGTs in each species has indicated that they may have a possible adaptive role.

Conclusion

The five Corynebacterial genomes sequenced to date have evolved by acquiring between 8 – 14% of their genomes by LGT and some of these genes may have a role in adaptation.

     

Resazurin-based 96-well plate microdilution method for the determination of minimum inhibitory concentration of biosurfactants

Objectives

To develop and validate a microdilution method for measuring the minimum inhibitory concentration (MIC) of biosurfactants.

Results

A standardized microdilution method including resazurin dye has been developed for measuring the MIC of biosurfactants and its validity was established through the replication of tetracycline and gentamicin MIC determination with standard bacterial strains.

Conclusion

This new method allows the generation of accurate MIC measurements, whilst overcoming critical issues related to colour and solubility which may interfere with growth measurements for many types of biosurfactant extracts.

     

Fine mapping of a quantitative resistance gene for gray leaf spot of maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) derived from teosinte (<Emphasis Type="Italic">Z. mays</Emphasis> ssp. <Emphasis Type="Italic">parviglumis</Emphasis>)

Key message

In this study we mapped the QTL Qgls8 for gray leaf spot (GLS) resistance in maize to a ~130 kb region on chromosome 8 including five predicted genes.

Abstract

In previous work, using near isogenic line (NIL) populations in which segments of the teosinte (Zea mays ssp. parviglumis) genome had been introgressed into the background of the maize line B73, we had identified a QTL on chromosome 8, here called Qgls8, for gray leaf spot (GLS) resistance. We identified alternate teosinte alleles at this QTL, one conferring increased GLS resistance and one increased susceptibility relative to the B73 allele. Using segregating populations derived from NIL parents carrying these contrasting alleles, we were able to delimit the QTL region to a ~130 kb (based on the B73 genome) which encompassed five predicted genes.

     

Citrate usage in the leading causes of blindness: new possibilities for the old metabolite

Introduction

Citrate is an old metabolite which is best known for the role in the Krebs cycle. Citrate is widely used in many branches of medicine. In ophthalmology citrate is considered as a therapeutic agent and an useful diagnostic tool—biomarker.

Objectives

To summarize the published literature on citrate usage in the leading causes of blindness and highlight the new possibilities for this old metabolite.

Methods

We conducted a systematic search of the scientific literature about citrate usage in ophthalmology up to January 2018. The reference lists of identified articles were searched for providing in-depth information.

Results

This systematic review included 30 articles. The role of citrate in the leading causes of blindness is presented.

Conclusions

Citrate might help inhibit cataract progression, in case of questions confirm glaucoma diagnosis or improve cornea repair treatment as adjuvant agent (therapy of ulcerating cornea after alkali injury, crosslinking procedure). However, the knowledge about possible citrate usage in ophthalmology is not widely known. Promoting recent scientific knowledge about citrate usage in ophthalmology may not only benefit of medical improvement but may also limit economic costs caused by leading causes of blindness. Further studies on citrate usage in ophthalmology should continuously be the field of scientific interest.