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The aim of this study was to define the transcript expression of 12 genes, identify new polymorphisms in selected 2 genes and to estimate the association between the level of expression, gene polymorphism and litter size in sows. Two groups of sows were selected: 71 crossbred sows and 328 purebred sows. For transcript analysis endometrial tissue samples were collected, while blood was sampled for the purpose of DNA polymorphism analysis. For all animals data on litter size and weaned piglets were obtained. Transcript analysis of 12 genes was performed in the uterine endometrium of sows in the luteal and follicular phases. Eight out of 12 genes showed higher mRNA expression levels during the luteal phase (AREG, FABP3, IL1A, ITGAV, ITGB3, NMB, OPN, RBP4). In turn, higher expression levels in the follicular phase were observed for 4 genes (IL1B, PPARG, S100A8, SELL). Analysis of six new polymorphic sites within the OPN and AREG genes revealed the highest heterozygosity for OPNe6_Knoll, OPNp3_617 and AREGe2_317 polymorphisms and the lowest heterozygosity in the AREGe3_561 locus. Association analyses concerning transcript expression levels of the 12 genes and the OPN and AREG genotypes in the two groups of sows showed a significant relationship between the IL1A, ITGB3 transcript expression and the OPNe7_603 genotype also between OPNp3_617 genotype and ITGB3 transcript expression. With regard to the litter size and the number of weaned piglets a significant relation with the OPNp3_617, OPNe6_462 and AREGe2_317 genotypes was observed only in the purebred sows. Transcript expression of the genes encoding osteopontin and amphiregulin in the uterus of the sows affect reproductive traits by preparing the uterus for embryo reception.

Desmoplastic small round cell tumor (DSRCT) is an aggressive sarcoma occurring in the young, teenager, and adult populations. The aim of this study is to compare initial tumor presentation, therapeutic management and scalability between pediatric and adult DSRCT patients and investigate the possibility of specific therapeutic approaches. A multicenter retrospective study of 81 Franco-Belgian medical files with DSRCT harboring Ewing sarcoma-Wilm tumor transcript was made. Median age was 17 years (3 to 58) with 42 children (13.5 y [3;17]) and 39 adults (28 y [18;58]). No significant differences were found between the 2 groups regarding initial symptoms and metastasis at diagnosis. The therapeutic approaches were similar for both groups: use of neoadjuvant chemotherapy (78.6% vs. 79.5%, P=1), primary surgery (71.4% vs. 69.2%, P=0.73), adjuvant chemotherapy (54.8% vs. 61.5%, P=0.99), radiotherapy (23.8% and 10.3%, P=0.11) and intraperitoneal chemotherapy (14.3% vs. 2.6%; P=0.11). Median time to recurrence was 12 versus 18 months (P=0.13). Overall survival at 2 years and recurrence free were 46.4% versus 60.1% (P=0.83) and 14.3% versus 16%, respectively (P=0.16). Clinical presentation, initial therapeutics and outcome of DSRCT are equivalent suggesting that similar management should be considered for children and adults with DSRCT.

Heart failure (HF) is one of the main causes of death worldwide. Recent studies reported altered DNA methylation in failing human hearts. This may suggest a role of DNA methylation, most frequently implicated in epigenetic control, in the development of heart failure. Here, employing RT-qPCR, we characterized transcript levels for main DNA methyltransferases (DNMTs), DNMT1, DNMT3A, and DNMT3B, mediate DNA methylation, and they have different functions that complement each other during methylation. All analyzes were performed at different stages of porcine myocardial cell primary culture. In the present study we demonstrated increasing transcript expression levels for all analyzed genes during in vitro cultivation. The changes for DNMT1 and DNMT3A seem to be particularly important, where statistically significant changes were observed. Running title: DNMTs role in cardiac muscle cell culture

Background Allergic contact dermatitis (ACD) and irritant contact dermatitis (ICD) are common skin conditions with an overlapping clinical and histological appearance, but distinct underlying mechanisms. Patch testing is the gold standard for ACD diagnosis, yet the interpretation of its results may be confounded by weak and varying macroscopic reactions. Objective To examine whether gene transcript profiling of RNA sampled from patch tested patient skin by tape stripping (TS) could differentiate ACD from ICD and the baseline skin state (control) METHODS: Nine patients (seven females, two males; mean age 38.6 years, range 24-72 years) with confirmed ACD through patch testing were recruited. Total RNA was isolated from TS samples and relative transcript abundance was determined by quantitative real-time polymeraise chain reaction using 39 gene-specific primers. Results TS captured gene transcripts derived from diverse skin cell types, including not only keratinocytes, but also epidermal and dermal antigen-presenting cells. Among the genes analysed in transcript profiling, genes encoding epidermal barrier components and inflammatory mediators exhibited changes in transcript abundance in ACD skin compared to ICD or control skin. Conclusions Our findings reveal the potential of skin TS for non-invasive biopsy during patch testing and molecular marker-based ACD diagnosis.

The change in the expression of gibberellin biosynthesis (HvGA3ox2) and catabolism (HvGA2ox3) genes in the embryos of γ-irradiated barley seeds at doses of 4–50 Gy was studied over 30 hours of germination. It was shown that transcription activity of the gibberellin catabolism gene HvGA2ox3 was predominantly increased at each stage of germination, except 12 h after the beginning of the experiment. The transcriptional activity of the gibberellin biosynthesis gene HvGA3ox2 was reduced during the early stages of the observation period (after 6 and 12 hours) and increased after irradiation during the later stages (after 24 and 30 hours). The peak of the transcriptional activity of the genes studied was noted in the embryos of both control and irradiated seeds 18 hours after the onset of germination. At a dose of 20 Gy, the gibberellin biosynthesis gene transcript concentration (HvGa3ox2) was maximal and exceeded the gibberellin catabolism gene transcript concentration (HvGa2ox3) by more than an order of magnitude.

Background: Semaphorin 3F (SEMA3F) plays a substantial role in carcinogenesis, because of its role in inducing angiogenesis, and creating a microenvironment for the developing tumor. Objective: The purpose of this work was to assess the impact of cisplatin, depending on the concentration and exposure time on the expression pattern of SEMA3F in an endometrial cancer cell line. Materials and Methods: Cultures of the Ishikawa endometrial cancer cells were incubated with cisplatin with the following concentrations: 2.5μM; 5μM; and 10μM and for the following periods of time: 12; 24; and 48 hours. Cells not incubated with the drug constituted the control in the experiment. To determine the effect of cisplatin on the expression of SEMA3F, the real-time quantitative reverse transcription reaction (RtqPCR; mRNA) was used, as well as the ELISA assay (protein). The statistical analysis was done with the admission of p Results: The silencing of SEMA3F expression on the transcriptome and proteome levels in a culture unexposed to the effects of cisplatin in comparison to endometrial cancer cells under the influence of cisplatin (p Conclusions: Using cisplatin in an endometrial cancer cell culture results in an increased expression of SEMA3F, which advantageously affects the normalization of the neoplastic angiogenic process and lowers the proliferation of the cells making up the mass of the tumor.

Summary Heading date is a key agronomic trait affecting crop yield. In rice, Early heading date 1 (Ehd1) is an important B‐type response regulator in determination of heading date. Although many regulatory factors of Ehd1 expression have been functionally characterized, the direct regulators of Ehd1 largely remain to be identified. Here, we identified a new regulator of Ehd1, OsRE1, that directly binds to the A‐box motif in the Ehd1 promoter. Osre1 confers an early heading phenotype due to elevated expression levels of Ehd1. OsRE1 is a nucleus‐localized bZIP transcription factor with a diurnal rhythmic expression pattern. Furthermore, we identified an OsRE1‐interacting protein, OsRIP1, and demonstrated that OsRIP1 can repress the transcript expression of Ehd1 in an OsRE1‐dependent manner. Our genetic data showed that OsRE1 and OsRIP1 may function upstream of Ehd1 in regulating heading date. Together, our results suggest that OsRE1 functions cooperatively with OsRIP1 to regulate heading date through finely modulating the expression of Ehd1. In addition, OsRE1 and OsRIP1 are two minor heading date regulators, which are more desirable for fine‐tuning heading date to improve rice regional adaptability.

The current study uses the metabolic probe, antipyrine, and AhRR transcript expression (qRT-PCR) to examine the impact of the AhRR (565C > G or Pro185Ala, rs2292596) genetic polymorphism upon CYP1A2 inducibility in an established cohort of male firefighters with exposure to dioxin-like chemicals. The lipid adjusted concentrations of 29 dioxin and dioxin-like congeners were measured in serum. Possession of the G allele (CG and GG genotypes) was correlated with high expression AhRR transcript and lower CYP1A2 induction than found in individuals homozygous for CC. The induction of CYP1A2 was dioxin-dependent among carriers of the G allele. Multivariate models indicated that CYP1A2 activity, detected as urinary 3-hydroxymethylantipyrine, was significantly correlated with cotinine concentration and for those currently working as firefighters, dioxin body burden (β = 0.54, p = 0.041). The efficacy of the AhRR in regulating the AhR signaling pathway is influenced by the AhRR (565C > G) polymorphism. Our study of firefighters using the induction of CYP1A2 as an indicator suggest that G allele proteins have variable AhR repressor activity which is manifested in a dioxin-dependent manner. These results provide evidence of metabolic differences that may affect susceptibility to dioxin-mediated health effects.

BACKGROUND: Donor -specific HLA antibody (DSA) is present in many kidney transplant patients whose biopsies are classified as no rejection (NR). We explored whether in some NR kidneys DSA has subtle effects not currently being recognized. METHODS: We used microarrays to examine the relationship between standard-of-care DSA and rejection-related transcript increases in 1679 kidney transplant indication biopsies in the INTERCOMEX study (ClinicalTrials.gov NCT01299168), focusing on biopsies classified as NR by automatically assigned archetypal clustering. DSA testing results were available for 835 NR biopsies and were positive in 271 (32%). RESULTS: DSA positivity in NR biopsies was associated with mildly increased expression of antibody-mediated rejection (ABMR)–related transcripts, particularly IFNG-inducible and NK cell transcripts. We developed a machine learning DSA probability (DSA(Prob)) classifier based on transcript expression in biopsies from DSA-positive versus DSA-negative patients, assigning scores using 10-fold cross-validation. This DSA(Prob) classifier was very similar to a previously described “ABMR probability” classifier trained on histologic ABMR in transcript associations and prediction of molecular or histologic ABMR. Plotting the biopsies using Uniform Manifold Approximation and Projection revealed a gradient of increasing molecular ABMR-like transcript expression in NR biopsies, associated with increased DSA (P

Changes in the surrounding environment are mirrored by changes in the transcript profile of an organism. In the case of a plant pathogen, host colonization would be a challenge that triggers changes in transcript expression patterns. Determining the transcriptional profile could provide valuable clues on how an organism responds to defined stimuli, in this case, how a pathogen colonizes its host. Several robust data analysis methods and pipelines are available that can identify these differentially expressed transcripts. In this chapter we outline the steps and other caveats that are needed to run one such pipeline.

Recent advances in single-cell RNA sequencing technologies have made detection of transcripts in single cells possible. The level of resolution provided by these technologies can be used to study changes in transcript usage across cell populations and help investigate new biology. Here, we introduce RNA-Scoop, an interactive cell cluster and transcriptome visualization tool to analyze transcript usage across cell categories and clusters. The tool allows users to examine differential transcript expression across clusters and investigate how usage of specific transcript expression mechanisms varies across cell groups.

De novo transcriptome assembly from billions of RNA-seq reads is very challenging due to alternative splicing and various levels of expression, which often leads to incorrect, mis-assembled transcripts. BayesDenovo addresses this problem by using both a read-guided strategy to accurately reconstruct splicing graphs from the RNA-seq data and a Bayesian strategy to estimate, from these graphs, the probability of transcript expression without penalizing poorly expressed transcripts. Simulation and cell line benchmark studies demonstrate that BayesDenovo is very effective in reducing false positives and achieves much higher accuracy than other assemblers, especially for alternatively spliced genes and for highly or poorly expressed transcripts. Moreover, BayesDenovo is more robust on multiple replicates by assembling a larger portion of common transcripts. When applied to breast cancer data, BayesDenovo identifies phenotype-specific transcripts associated with breast cancer recurrence. National Institutes of Health (NIH)United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [CA149653, CA164384, CA149147, GM125878] Published version This work is supported by National Institutes of Health (NIH) (CA149653, CA164384, CA149147 and GM125878).

Persistent HPV infection is causative for the majority of cervical cancer cases; however, current guidelines do not require HPV testing for newly diagnosed cervical cancer. Using an institutional cohort of 88 patients with cervical cancer treated uniformly with standard-of-care chemoradiation treatment (CRT) with prospectively collected clinical outcome data, we observed that patients with cervical tumors containing HPV genotypes other than HPV 16 have worse survival outcomes after CRT compared with patients with HPV 16+ tumors, consistent with previously published studies. Using RNA sequencing analysis, we quantified viral transcription efficiency and found higher levels of E6 and the alternative transcript E6*I in cervical tumors with HPV genotypes other than HPV 16. These findings were validated using whole transcriptome data from The Cancer Genome Atlas (n = 304). For the first time to our knowledge, transcript expression level of HPV E6*I was identified as a predictive biomarker of CRT outcome in our complete institutional data set (n = 88) and within the HPV 16+ subset (n = 36). In vitro characterization of HPV E6*I and E6 overexpression revealed that both induce CRT resistance through distinct mechanisms dependent upon p53-p21. Our findings suggest that high expression of E6*I and E6 may represent novel biomarkers of CRT efficacy, and these patients may benefit from alternative treatment strategies.

Newly evolved SARS-CoV-2 variants are driving ongoing outbreaks of COVID-19 around the world. Efforts to determine why these viral variants have improved fitness are limited to mutations in the viral spike (S) protein and viral entry steps using non-SARS-CoV-2 viral particles engineered to display S. Here we show that SARS-CoV-2 virus-like particles can package and deliver exogenous transcripts, enabling analysis of mutations within all structural proteins and rapid dissection of multiple steps in the viral life cycle. Identification of an RNA packaging sequence was critical for engineered transcripts to assemble together with SARS-CoV-2 structural proteins S, nucleocapsid (N), membrane (M) and envelope (E) into non-replicative SARS-CoV-2 virus-like particles (SC2-VLPs) that deliver these transcripts to ACE2- and TMPRSS2-expressing cells. Using SC2-VLPs, we tested the effect of 30 individual mutations within the S and N proteins on particle assembly and entry. While S mutations unexpectedly did not affect these steps, SC2-VLPs bearing any one of four N mutations found universally in more-transmissible viral variants (P199L, S202R, R203M and R203K) showed increased particle production and up to 10-fold more reporter transcript expression in receiver cells. Our study provides a platform for rapid testing of viral variants outside a biosafety level 3 setting and identifies viral N mutations and viral particle assembly as mechanisms to explain the increased spread of current viral variants, including Delta (N:R203M).One-Sentence SummaryR203M substitution within SARS-CoV-2 N, found in delta variant, improves RNA packaging into virus-like particles by 10-fold.

Objective: To characterise placental gene expression at term to evaluate sex-specific genetic changes that occur in small for gestational age (SGA) infants. Design: Case control study. Setting: Australian hospitals. Samples: Twelve human placental samples from pregnancies that were either SGA or appropriate for gestational age (AGA). Methods: RNA-sequencing of term placental tissue from both SGA and AGA infants. Candidate genes associated with fetal size and fetal sex were identified using differential gene expression and weighted gene co-expression network analyses. Single-cell sequencing data was used for candidate validation and to estimate candidate transcript expression in specific placental cell populations. Main outcome measures: Functions of differentially expressed genes in the placenta of SGA infants that differed by fetal sex. Results: Differential gene expression and weighted gene co-expression network analyses identified 403 candidate transcripts associated with SGA infants. One hundred and three of these transcripts showed sex-specific expression. Sex-independent transcript expression for genes involved in protein synthesis, and sex-dependent transcript expression for genes involved in cell cycle processes in males and endoplasmic reticulum stress in females was validated (17 and 7 transcripts for females and males) in published placental RNA-sequencing datasets. Conclusions: Sexual dimorphism is an important consideration when examining placental dysfunction and poor fetal growth. This study identified activation of shared and divergent molecular mechanisms (i.e., cell cycle and endoplasmic reticulum stress), in response to an adverse environmental stressor.

Great efforts have been made on the algorithms that deal with RNA-seq data to enhance the accuracy and efficiency of differential expression (DE) analysis. However, no consensus has been reached on the proper threshold values of fold change and adjusted p-value for filtering differentially expressed genes (DEGs). It is generally believed that the more stringent the filtering threshold, the more reliable the result of a DE analysis. Nevertheless, by analyzing the impact of both adjusted p-value and fold change thresholds on DE analyses, with RNA-seq data obtained for three different cancer types from the Cancer Genome Atlas (TCGA) database, we found that, for a given sample size, the reproducibility of DE results became poorer when more stringent thresholds were applied. No matter which threshold level was applied, the overlap rates of DEGs were generally lower for small sample sizes than for large sample sizes. The raw read count analysis demonstrated that the transcript expression of the same gene in different samples, whether in tumor groups or in normal groups, showed high variations, which resulted in a drastic fluctuation in fold change values and adjustedp-values when different sets of samples were used. Overall, more stringent thresholds did not yield more reliable DEGs due to high variations in transcript expression; the reliability of DEGs obtained with small sample sizes was more susceptible to these variations. Therefore, less stringent thresholds are recommended for screening DEGs. Moreover, large sample sizes should be considered in RNA-seq experimental designs to reduce the interfering effect of variations in transcript expression on DEG identification.

Keloids are considered as favorable fibro-proliferative skin tumors developing past the site of the first dermal injury. Neural forerunner cell communicated formatively down-controlled protein 4 (NEDD4) is an E3 ubiquitin ligase catalyst that objectives proteins for ubiquitination. In this investigation, it was intended to survey Neural Precursor Cell Expressed Developmentally Down-Regulated Protein 4 Gene Transcript Variant 3(NEDD4 TV3) and Insulin-like Gross Factor - 1 (IGF-1) in patients with dynamic keloid ≤ 6months length. The examination included 40 patients of keloids and 20 subjects of coordinated age, sex and weight file (BMI). There was critical positive relationship between's NEDD4TV-3 and IGF quality articulation. This information add novel angles to the part of NEDD4 TV3 in the advancement of keloid.

Background: Molecular studies have tried to address the unmet need for prognostic biomarkers in prostate cancer (PCa). Some gene expression tests improve upon clinical factors for prediction of outcomes, but additional tools for accurate prediction of tumor aggressiveness are needed. Methods: Based on a previously published panel of 23 gene transcripts that distinguished patients with metastatic progression, we constructed a prediction model using independent training and testing datasets. Using the validated messenger RNAs and Gleason score (GS), we performed model selection in the training set to define a final locked model to classify patients who developed metastatic-lethal events from those who remained recurrence-free. In an independent testing dataset, we compared our locked model to established clinical prognostic factors and utilized Kaplan-Meier curves and receiver operating characteristic analyses to evaluate the model's performance. Results: Thirteen of 23 previously identified gene transcripts that stratified patients with aggressive PCa were validated in the training dataset. These biomarkers plus GS were used to develop a four-gene (CST2, FBLN1, TNFRSF19, and ZNF704) transcript (4GT) score that was significantly higher in patients who progressed to metastatic-lethal events compared to those without recurrence in the testing dataset (P = 5.7 × 10-11). The 4GT score provided higher prediction accuracy (area under the ROC curve [AUC] = 0.76; 95% confidence interval [CI] = 0.69-0.83; partial area under the ROC curve [pAUC] = 0.008) than GS alone (AUC = 0.63; 95% CI = 0.56-0.70; pAUC = 0.002), and it improved risk stratification in subgroups defined by a combination of clinicopathological features (ie, Cancer of the Prostate Risk Assessment-Surgery). Conclusion: Our validated 4GT score has prognostic value for metastatic-lethal progression in men treated for localized PCa and warrants further evaluation for its clinical utility.

Polyunsaturated fatty acids (PUFAs) are essential in the animal diet, notably eicosapentaenoic and docosahexaenoic acids (EPA and DHA, respectively), and in recent years, microalgae like marine diatoms are being considered as an alternative source of PUFA. Therefore, this study evaluated the effect of three nitrogen/phosphorus (N/P) ratios (21/1, 14/1 and 7/1) and two growth phases (exponential and stationary) on both EPA concentration and gene transcript levels, four front-end desaturases and two elongases, involved in EPA biosynthesis of the microalgae Phaeodactylum tricornutum Bohlin. The experiment was carried out for 12 days, and the samples were assessed for growth and nutrient intake; in addition, qPCR was performed, as well as an analysis of fatty acids. Gene transcript levels were growth phase-dependent, and only two genes, PTD6 and PTD5A, were responsive to N/P ratios. EPA levels in P. tricornutum biomass were shown to be growth phase-dependent, with higher concentrations in the exponential phase (28.64% of total fatty acids), irrespective of N/P treatments. In at least one N/P ratio (21/1), the transcription of one gene, PTD5A, could be associated with EPA levels. Data from gene transcript levels and EPA concentrations, as well as the lack of some EPA intermediates, might indicate some type of regulatory steps between gene transcription and actual EPA biosynthesis.

Alpha-lactalbumin is a protein of milk expressed by mammary epithelial cells and by some breast tumors. The alpha-lactalbumin gene has two transcripts. The expression of transcript 2 has not yet been studied. The main objective of this paper was to establish the expression profile of alpha-lactalbumin at the mRNA level and to develop a technique discriminating between the two transcripts. The study was performed on 46 fresh mammary biopsies: 17 malignant tumors, 13 benign tumors, and 16 adjacent healthy tissues. We developed an RT-nested PCR to detect LALBA gene expression without distinction between transcripts. We also designed an RT-nested PCR that detects transcript 2. Both nested PCRs avoid amplification of potentially contaminating genomic DNA. We show that benign tumors tend to appear at a young age contrarily to malignant tumors appearing later with p value = 0.002. Moreover, LALBA transcript expression varies among tissues more important in benign (69%) than in malignant (35%) tumors with significant p value = 0.041. The intensity of the bands reflected differential expression between patients with concordant data between both RT-nested PCRs. We also performed a qualitative analysis according to histopathological parameters and molecular subtypes. The expression of transcript 2 appeared associated with the HER2+ subtype, while transcript 1 was associated with the luminal A and triple-negative subtypes. In conclusion, we designed specific and sensitive methods to detect LALBA transcripts. We show for the first time a differential expression of these transcripts, but we need to confirm their potential use as markers in breast cancer.

Circular RNAs (circRNAs) are a class of endogenous non-coding RNAs (ncRNAs) with a closed-loop structure that are mainly produced by variable processing of precursor mRNAs (pre-mRNAs). They are widely present in all eukaryotes and are very stable. Currently, circRNA studies have become a hotspot in RNA research. It has been reported that circRNAs constitute a significant proportion of transcript expression, and some are significantly more abundantly expressed than other transcripts. CircRNAs have regulatory roles in gene expression and critical biological functions in the development of organisms, such as acting as microRNA sponges or as endogenous RNAs and biomarkers. As such, they may have useful functions in the diagnosis and treatment of diseases. CircRNAs have been found to play an important role in the development of several diseases, including atherosclerosis, neurological disorders, diabetes, and cancer. In this paper, we review the status of circRNA research, describe circRNA-related databases and the identification of circRNAs, discuss the role of circRNAs in human diseases such as colon cancer, atherosclerosis, and gastric cancer, and identify remaining research questions related to circRNAs.

Introduction: After ischemic stroke (IS), peripheral leukocytes infiltrate the damaged region and modulate the response to injury. We previously showed that peripheral blood cells display different gene expression profiles after IS and these transcriptional programs reflect the changes in immune processes in response to IS. Dissecting the temporal dynamics of gene expression after IS improves our understanding of the changes of molecular and cellular pathways involved in acute brain injury. Methods: We analyzed the transcriptomic profiles of 33 IS patients in isolated monocytes, neutrophils and whole blood. RNA-sequencing was performed on all the stroke samples as well as 12 controls with vascular risk factors (diabetes and/or hypertension and/or hypercholesterolemia). To identify differentially expressed genes, subjects were split into time points (TPs) from stroke onset (TP1= 0-24 h; TP2= 24-48 h; and TP3= > 48 h), and controls were assigned TP0. A linear regression model including time and the interaction of diagnosis x TP with cutoff of p|1.2| was used. Time dependent changes were analyzed using artificial neural networks to identify clusters of genes that behave in a similar way across TPs. Results: Unique patterns of temporal expression were distinguished for the three sample types. These include genes not expressed in TP0 that peak only within the first 24 h, others that peak or decrease in TP2 and TP3, and more complex patterns. Genes that peak at TP1 in monocytes and neutrophils are related to cell adhesion and leukocyte differentiation/migration, respectively. Early peaks in whole blood occur in genes related to transcriptional regulation. In monocytes, interleukin pathways are enriched across all TPs, whereas there is a trend of suppression after 24 h in neutrophils. The inflammasome pathway is enriched in the earlier TPs in neutrophils, while not enriched in monocytes until over 48 hours. Conclusion: Our analyses on gene expression dynamics and cluster patterns allow identification of key genes and pathways at different time points following ischemic injury that are valuable as IS biomarkers and may be possible treatment targets.

The analysis of mRNA transcript abundance with RNA-Seq is a central tool in molecular biology research, but often analyses fail to account for the uncertainty in these estimates, which can be significant, especially when trying to disentangle isoforms or duplicated genes. Preserving un-certainty necessitates a full probabilistic model of the all the sequencing reads, which quickly becomes intractable, as experiments can consist of billions of reads. To overcome these limitations, we propose a new method of approximating the likelihood function of a sparse mixture model, using a technique we call the Pólya tree transformation. We demonstrate that substituting this approximation for the real thing achieves most of the benefits with a fraction of the computational costs, leading to more accurate detection of differential transcript expression.AvailabilityThe method is implemented in a Julia package available from https://github.com/dcjones/poleeContactdcjones@cs.washington.edu

Transcript and gene quantification is the first step in many RNA-seq analyses. While many factors and properties of experimental RNA-seq data likely contribute to differences in accuracy between various approaches to quantification, it has been demonstrated (1) that quantification accuracy generally benefits from considering, during alignment, potential genomic origins for sequenced fragments that reside outside of the annotated transcriptome.Recently, Varabyou et al. (2) demonstrated that the presence of transcriptional noise leads to systematic errors in the ability of tools — particularly annotation-based ones — to accurately estimate transcript expression. Here, we confirm the findings of Varabyou et al. (2) using the simulation framework they have provided. Using the same data, we also examine the methodology of Srivastava et al.(1) as implemented in recent versions of salmon (3), and show that it substantially enhances the accuracy of annotation-based transcript quantification in these data.

1. The aim of the present study was to identify differentially expressed genes (DEGs) and metabolic pathways involved in this phenotype. Fibromelanosis is the most striking feature of black-bone chickens, such as the Silkie and Dongxiang indigenous breeds. Due to the accumulation of eumelanin in connective tissues, fibromelanosis manifests as black colouration of the skin, muscles, gut, and periosteum. Studies on fibromelanosis can provide useful information pertaining to human diseases and offer commercial value to the poultry industry. However, the genetic basis of fibromelanosis remains unclear. 2. Digital gene expression analysis was performed on black and white skin samples collected from the HW1 black-bone chicken line to detect differences in genome-wide expression patterns. A total of >30 billion bp were sequenced, and 2,707,926,466 bp and 2,948,782,964 bp of clean data obtained for creation of libraries for black and white skin, respectively. In total, 252 DEGs from 15,508 mapped genes were identified with 83 up-regulated in white skin and 169 up-regulated in black skin. 3. Gene ontology analysis highlighted that genes from the extracellular region and associated components were abundant among the DEGs. Pathway analysis revealed that many DEGs were linked to amino acid metabolism and the immune system. qRT-PCR validation using 14 genes showed good conformity with the sequence analysis of fibromelanosis-related genes. 4. The results showed that L-dopachrometautomerase precursor (DCT), tyrosine aminotransferase (TAT), 4-hydroxyphenylpyruvate dioxygenase (HPD) from the tyrosine metabolism pathway, coagulation factor II (F2), fibrinogen beta chain (FGB), plasminogen (PLG) and complement component 7 (C7) from the complement and coagulation cascades were important genes in the fibromelanosis process in black-bone chickens. These candidate genes require further correlation analysis and functional verification.

Chronic myeloid leukemia; BCR-ABL1 transcripts; Response to imatinib Leucemia mieloide crónica; Transcripciones de BCR-ABL1; Respuesta al imatinib Leucèmia mieloide crònica; Transcripcions BCR-ABL1; Resposta a imatinib The most frequent BCR-ABL1-p210 transcripts in chronic myeloid leukemia (CML) are e14a2 and e13a2. Imatinib (IM) is the most common first-line tyrosine–kinase inhibitor (TKI) used to treat CML. Some studies suggest that BCR-ABL1 transcript types confer different responses to IM. The objective of this study was to correlate the expression of e14a2 or e13a2 to clinical characteristics, cumulative cytogenetic and molecular responses to IM, acquisition of deep molecular response (DMR) and its duration (sDMR), progression rate (CIP), overall survival (OS), and treatment-free remission (TFR) rate. We studied 202 CML patients, 76 expressing the e13a2 and 126 the e14a2, and correlated the differential transcript expression with the above-mentioned parameters. There were no differences in the cumulative incidence of cytogenetic responses nor in the acquisition of DMR and sDMR between the two groups, but the e14a2 transcript had a positive impact on molecular response during the first 6 months, whereas the e13a2 was associated with improved long-term OS. No correlation was observed between the transcript type and TFR rate.

Summary The vrille (vri) gene encodes a transcriptional repressor required for Drosophila development as well as circadian behavior in adults. Alternate first exons produce vri transcripts predicted to produce a short VRI isoform during development and long VRI in adults. A vri mutant (vriΔ679) lacking long VRI transcripts is viable, confirming that short VRI is sufficient for developmental functions, yet behavioral rhythms in vriΔ679 flies persist, showing that short VRI is sufficient for clock output. E-box regulatory elements that drive rhythmic long VRI transcript expression are required for developmental expression of short VRI transcripts. Surprisingly, long VRI transcripts primarily produce short VRI in adults, apparently due to a poor Kozak sequence context, demonstrating that short VRI drives circadian behavior. Thus, E-box-driven long VRI transcripts primarily control circadian rhythms via short VRI, whereas the same E-boxes drive short VRI transcripts that control developmental functions using short VRI.