Biallelic inheritance in a single Pakistani family with intellectual disability implicates new candidate gene RDH14

In a multi-branch family from Pakistan, individuals presenting with palmoplantar keratoderma segregate in autosomal dominant fashion, and individuals with intellectual disability (ID) segregate in apparent autosomal recessive fashion. Initial attempts to identify the ID locus using homozygosity-by-descent (HBD) mapping were unsuccessful. However, following an assumption of locus heterogeneity, a reiterative HBD approach in concert with whole exome sequencing (WES) was employed. We identified a known disease-linked mutation in the polymicrogyria gene, ADGRG1, in two affected members. In the remaining two (living) affected members, HBD mapping cross-referenced with WES data identified a single biallelic frameshifting variant in the gene encoding retinol dehydrogenase 14 (RDH14). Transcription data indicate that RDH14 is expressed in brain, but not in retina. Magnetic resonance imaging for the individuals with this RDH14 mutation show no signs of polymicrogyria, however cerebellar atrophy was a notable feature. RDH14 in HEK293 cells localized mainly in the nucleoplasm. Co-immunoprecipitation studies confirmed binding to the proton-activated chloride channel 1 (PACC1/TMEM206), which is greatly diminished by the mutation. Our studies suggest RDH14 as a candidate for autosomal recessive ID and cerebellar atrophy, implicating either disrupted retinoic acid signaling, or, through PACC1, disrupted chloride ion homeostasis in the brain as a putative disease mechanism.

Transcriptome sequencing and global analysis of blue light-responsive genes provide clues for high carotenoid yields in Blakeslea trispora

Blakeslea trispora has great potential uses in industrial production because of the excellent capability of producing a large quantity of carotenoids. However, the mechanism of light induced carotenoid biosynthesis even the structural and regulatory genes in pathways remain unclear. In this paper, we reported the first transcriptome study in B. trispora in which we have carried out global survey of expression changes of genes participated in blue light response. We verified that the yield of β-carotene reaching to 3-fold when transferred from darkness to blue light for 24 h and the enhancement of transcription levels of carRA and carB presented a positive correlation with the increase in carotenoid production. RNA-seq analysis revealed that 1124 genes were upregulated and 740 genes were downregulated respectively after blue light exposure. Annotation through GO, KEGG, Swissprot and COG databases showed 11119 unigenes compared well with known gene sequences, 5514 unigenes were classified into Gene Ontology, and 4675 unigenes were involved in distinct pathways. Among the blue light responsive genes, 4 genes (carG1, carG3, carRA and carB) identified to function in carotenoid metabolic pathways were dominantly upregulated. We also discovered that 142 TF genes belonging to 45 different superfamilies showed significant differential expression (p≤ 0.05), 62 of which were obviously repressed by blue light. The detailed profile of transcription data will not only allow us to conduct further functional genomics study in B. trispora, but also enhance our understanding of potential metabolic pathway and regulatory network involved in light regulated carotenoid synthesis.

Framework estimation of stochastic gene activation using transcription average level

Gene activation is usually a non-Markovian process that has been modeled as various frameworks that consist of multiple rate-limiting steps. Understanding the exact activation framework for a gene of interest is a central problem for single-cell studies. In this paper, we focus on the dynamical data of the average transcription level M(t), which is typically neglected when deciphering gene activation. Firstly, the smooth trend lines of M(t) data present rich, visually dynamic features. Secondly, tractable analysis of M(t) allows the establishment of bijections between M(t) dynamics and system parameter regions. Because of these two clear advantages, we can rule out frameworks that fail to capture M(t) features and we can further test potential competent frameworks by fitting M(t) data. We implemented this procedure to determine an exact activation framework for a large number of mouse fibroblast genes under tumor necrosis factor induction; the cross-talk between the signaling and basal pathways is crucial to trigger the first peak of M(t), while the following damped gentle M(t) oscillation is regulated by the multi-step basal pathway. Moreover, the fitted parameters for the mouse genes tested revealed two distinct regulation scenarios for transcription dynamics. Taken together, we were able to develop an efficient procedure for using traditional M(t) data to estimate the gene activation frameworks and system parameters. This procedure, together with sophisticated single-cell transcription data, may facilitate a more accurate understanding of stochastic gene activation.

Multiple shifts in gene network interactions shape phenotypes of Drosophila melanogaster selected for long and short night sleep duration

All but the simplest phenotypes are believed to result from interactions between two or more genes forming complex networks of gene regulation. Sleep is a complex trait known to depend on the system of feedback loops of the circadian clock, and on many other genes; however, the main components regulating the phenotype and how they interact remain an unsolved puzzle. Genomic and transcriptomic data may well provide part of the answer, but a full account requires a suitable quantitative framework. Here we conducted an artificial selection experiment for sleep duration with RNA-seq data acquired each generation. The phenotypic results are robust across replicates and previous experiments, and the transcription data provides a high-resolution, time-course data set for the evolution of sleep-related gene expression. In addition to a Hierarchical Generalized Linear Model analysis of differential expression that accounts for experimental replicates we develop a flexible Gaussian Process model that estimates interactions between genes. 145 gene pairs are found to have interactions that are different from controls. Our method not only is considerably more specific than standard correlation metrics but also more sensitive, finding correlations not significant by other methods. Statistical predictions were compared to experimental data from public databases on gene interactions.

Union, Employer, and compensation system gaps and failures: Workers with injuries perceptions

BACKGROUND: Workers who suffered a workplace injury and submitted a claim with the compensation board in Ontario often faced economic and non-economic costs that provoked depressive feelings, family strain, financial strain, and feelings of diminished self-worth. OBJECTIVE: This qualitative descriptive study aimed to understand the perceived gaps and failures associated with the support systems (e.g., union, compensation and employer) that were in place to assist some male underground workers in Sudbury, Ontario, Canada who had suffered a workplace injury and had a compensation claim. METHODS: Twelve in-depth, in-person, individual, semi-structured interviews were conducted and data were transcribed verbatim and anonymized at the time of transcription. Data analysis followed Braun and Clarke’s guidelines for thematic analysis. RESULTS: Themes that emerged include: unfair and inadequate recognition of an injury; limited communication with stakeholders involved with their claim, including claim adjudicators, challenges when returning to work, and compensation claim system barriers. CONCLUSIONS: Cooperation, collaboration, knowledge transfer, and decreased power imbalances could help to reduce the economic and non-economic strain felt by a worker with an injury. Additionally, a government-funded third-party advocate who knows the medical system, union contracts, the workers’ compensation system, and employer policies and practices could act on behalf of an injured worker.

Development of an Efficient Preparation and Verifying System for Rice Gametophytic Male Sterility using RNAi on Candidate Gene and OsMYB86R as a Reporter

Background: Gametophytic male sterility plays an important role in the study of pollen development mechanism and the breeding of three-generation hybrid rice. Because of the inherent phenotypic and genetic characteristics of gametophytic male sterility, it is very hard to find and identify gametophytic male sterility, which makes the related research lay behind the sporophytic male sterility. On the other hand, with the abundance of gene transcription data, a large number of pollen-specific genes have been found, and most of them are possibly associated with gametophytic male sterility. In order to promote the research of these genes in pollen development and heterosis utilization, it is necessary to construct an efficient, economical and accurate method to test these genes and identify if they are gametophytic male sterility related genes.Results: In this study, at first, the OsC1/OsMYB86 gene involved in anthocyanin synthesis in rice was modified and identified, and the function of revised OsMYB86R gene was created as the same as OsMYB86, and OsMYB86R is more convenient to be used as a reporter gene because the restriction site is removed. Then, an ascorbic acid oxidase gene OsPTD1 was downregulated using RNAi driven by its own promoter, which resulted in abnormal pollen tube growth; Lastly, the RNAi elements were linked with OsMYB86R and together-transferred into an osmyb86 mutant, and the purple color segregation of T1 and F1 derived from positive plants were distorted, which showed that the OsPTD1 related gametogenic male sterility was successfully prepared and determined.Conclusion: In this study, an easy and efficient method to prepare and identify gametophyte male sterility was established by using the strategy of RNAi and OsMYB86R as reporter. Comparing with the current methods, the advantages of this method are: (1) in material preparation, save time, a generation less comparing with conventional method, also a lot of mutation screening maybe avoided; (2) in identification, less cost, no PCR, electrophoresis, and other processes needed, and no expensive chemicals and instruments required; (3) in the results, more accurate, much less background affection, no damage on the plant. As a result, it is an easy, efficient, low-cost, accurate method to prepare and identify gametophytic male sterility genes. It is very important in elucidating the mechanism of pollen development and promoting the utilization of heterosis.

The seasonal dynamics of bud dormancy in grapevine suggest a regulated checkpoint prior to acclimation

ABSTRACTGrapevine (Vitis vinifera L.) displays wide plasticity to climate and seasonality, ranging from strongly deciduous to evergreen. Understanding the physiology of decisions to grow or quiesce is critical for improved crop management, prediction, and the adaptability of production to alternative climate scenarios. The perenniating bud (N+2) is a major economic unit and focus of study. Here we investigated the physiology and transcriptome of cv. Merlot buds grown in a temperate maritime climate from summer to spring in two consecutive years. The changes in bud respiration, hydration and internal tissue oxygen data were consistent with the transcriptome data. ABA-responsive gene processes prevailed upon the transition to a deep metabolic and cellular quiescence in the bud during autumn. Light, together with hypoxia and redox signalling presided over the resumption of nuclear and cellular growth in the transition to spring. Comparisons with transcriptome data from bud burst studies revealed a number of regulatory candidates for the orderly resumption of growth in spring, including components that may integrate light and temperature signalling. Importantly however, the bud burst forcing data, which is widely used as a measure of bud dormancy, were not consistent with the physiological and transcription data. We hypothesise the existence of a physiological checkpoint following bud set in summer, which if not met results in extreme quiescence. Collectively this is the most integrated developmental dataset of the latent bud of cultivated grapevine, and establishes a platform for systems approaches to study seasonal plasticity.One sentence summaryPhysiology and transcriptome data provide strong evidence of a regulatory checkpoint prior to acclimation and dormancy in latent grapevine buds.

Variation in Expression of Reference Genes across Life Stages of a Bee, Megachile rotundata

The alfalfa leafcutting bee, Megachile rotundata is widely used in the western United States as a pollinator for alfalfa seed production. Unfortunately, immatures experience high mortality in agriculturally managed populations. Quantified gene expression could be used to identify how this bee responds during different life stages to pathogens, environmental toxins, and other stresses, but stably expressed reference genes are needed to normalize transcription data. We evaluated twelve candidate genes for their transcription stability across different life stages, including during and after diapause. RPS18 and RPL8 were the two most stably expressed genes, followed by RPS5 and RPL27A. These genes were also very stable even during and after diapause, while the most variable genes being APN, PMIIM, NPC2, and Cr-PII had increased expression levels during larval growth and were also variable during and after diapause. The four reference genes we identified in M. rotundata may prove useful for transcriptomic studies in other bees as well, such as honey bees.

Code-Crossing in Indonesian EFL Classroom Interaction

The phenomena of language use in the class still become the object of study ever since the languages are essential aspects in classroom interaction. It cannot be denied that in the classroom interaction, the communicative styles of the lecturers and students will be influenced by many aspects. One of them is the social status differences which lead to the occurrence of code-crossing in the class. For that purpose, the study in this paper is directed to explore the occurrence of code-crossing in the class and the factors influencing it. This research applied a qualitative research design taking two English classes and their students at one university in Makassar as the subject. The data of this research were collected by employing classroom observation and audio recording. The data were analyzed descriptively by adopting Discourse Analysis approach which relies on data recording, data transcription, data selection, and data interpretation. The result of the research shows that the lecturers and the students employed code-crossing in EFL classroom interaction which can be seen from the use of low and high code. This study also found that the use of that high and low code in the form of code-crossing of the lecturers and the students is influenced by the power of social status, age differences, the social distance or familiarity, and intimacy between the lecturers and the students. Findings from this study are worthy of reading for English language teaching practitioners in their effort to create effective classroom interaction.