Region Of Locus Research Articles

First Report of Anthracnose on Passiflora edulis Caused by Colletotrichum siamense in Guangdong Province in China.

Passion fruit (Passiflora edulis Sims) is an important tropical and subtropical species with high commercial value due to its wide uses in juice production and fresh fruit consumption. A disease affecting the leaves was observed on passion fruit vines in the South Subtropical Botanical Garden in Zhanjiang city in April and September 2020 with an incidence of 30 to 60%. Affected leaves usually developed small circular reddish-brown spots, which enlarged to oval spots and large irregular spots. The spots were brown and surrounded by a yellow halo with sunken cavities, which are typical symptoms of anthracnose. Diseased cultivars HuangjinBaiXiangGuo were collected in Zhanjiang city (21.2N110.3E), Suixi city (21.4N110.2E) and Leizhou city (20.9N110.1E) in Guangdong province. Leaf samples were disinfested with 1% NaOCl for 5 min, and cultured on potato dextrose agar (PDA) at 28 °C for one week. Eight single-spore isolates were recovered from PSA medium. Colonies developing on PSA were grayish white with a regular border. Conidia weretraight, hyaline with rounded ends, 5.3 to 6.8×15.2 to 21.3μm (n = 50 conidia of each isolate). Fungal mycelia were hyaline, septate, and branched. Conidia were born on a long conidiogenous cell, appressoria were dark, smooth-walled, oval, 15.5 to 21.3×4.0 to 5.8 μm (n=50).The isolates were morphologically identified as Colletotrichum sp. (Weir et al. 2012). Tests of pathogenicity were performed according to Koch's postulates using three isolates. Five plants with 2-3 vines were inoculated with each isolate separately and 3-4 leaves of each plant were inoculated. Fresh wounds were made with a sterile needle on the healthy surface of leaves of P. edulis HuangjinBaiXiangGuo and each leaf was covered with a piece of cotton drenched with 200 μL of conidial suspension (106 conidia/ml) from each isolate. Control seedlings were inoculated identiclly except sterile water was used to drench the cotton. Inoculated plants were placed in a moisturizing light incubator at 25℃ and 80% humidity under a 12-h light/dark cycle for 14 days and examined daily to monitor disease symptom development. Small round brown spots were observed at the inoculation sites 3 days after the inoculation and eventually became large brown lesions. There were no symptoms observed in the water-inoculated plants. A Colletotrichum sp. strain based on morphology was consistently reisolated from leaves lesions fulfilling Koch's postulates. For molecular identification, the internal transcribed spacer (ITS) region of ribosomal DNA, calmodulin (Cal), tubulin (Tub) and Apmat loci of three isolates were amplified using primer pairs of ITS4/ITS5, CL1C/CL2C, T1/T2 and AM-F/AM-R (Sharma et al. 2015). A phylogenetic tree derived from a neighbor-joining analysis of a concatenated alignment of ITS, CAL, Tub and ApMAT sequences was created. The accession numbers of three isolates BXGZJ 1-1, BXGSX 2-2 and BXGLZ 3-2 used in this study were MZ605383- MZ605385 for ITS, MZ605389- MZ605391 for CAL, MZ605392- MZ605394 for Tub and MZ605386- MZ605388 for ApMAT. The sequences of the three isolates were aligned with related species of Colletotrichum (Sharma et al. 2015). Analyses based on concatenated data sets of four genes showed that the sequences of the 3 isolates had the highest identity of 99% to those of the type strain C. siamense ICMP18578. According to both morphological and sequence analyses, the P. edulia pathogen was identified as C. siamense. There is a report of foliar diseases on P. edulia caused by C. brevisporum in Hainan province in China (Qiu et al., 2021). To our knowledge, this is the first report of anthracnose on P. edulia caused by C. siamense in China. Identification of pathogens could provide valuable information for disease diagnosis and effective chemicals to control the disease, so as to reduce yield loss and improve fruit quality.

The New Variation in the Promoter Region of FLOWERING LOCUS T Is Involved in Flowering in Brassica rapa.

Flowering time is an important agronomic trait in Brassica rapa and has a wide range of variation. The change from vegetative to reproductive development is a major transition period, especially in flowering vegetable crops. In this study, two non-heading Chinese cabbage varieties with significantly different flowering times, Pak-choi (B. rapa var. communis Tesn et Lee) and Caitai (B. rapa var. tsaitai Hort.), were used to construct segregated F2 populations. The bulk-segregant approach coupled with whole genome re-sequencing was used for QTL sequencing (QTL-seq) analysis to map flowering time traits. The candidate genes controlling flowering time in B. rapa were predicted by homologous gene alignment and function annotation. The major-effect QTL ft7.1 was detected on chromosome A07 of B. rapa, and the FT family gene BrFT was predicted as the candidate gene. Moreover, a new promoter regional difference of 1577 bp was revealed by analyzing the sequence of the BrFT gene. The promoter region activity analysis and divergent gene expression levels indicated that the difference in the promoter region may contribute to different flowering times. These findings provide insights into the mechanisms underlying the flowering time in Brassica and the candidate genes regulating flowering in production.

Pycard and BC017158 Candidate Genes of Irm1 Locus Modulate Inflammasome Activation for IL-1β Production.

We identified Pycard and BC017158 genes as putative effectors of the Quantitative Trait locus (QTL) that we mapped at distal chromosome 7 named Irm1 for Inflammatory response modulator 1, controlling acute inflammatory response (AIR) and the production of IL-1β, dependent on the activation of the NLRP3 inflammasome. We obtained the mapping through genome-wide linkage analysis of Single Nucleotide Polymorphisms (SNPs) in a cross between High (AIRmax) and Low (AIRmin) responder mouse lines that we produced by several generations of bidirectional selection for Acute Inflammatory Response. A highly significant linkage signal (LOD score peak of 72) for ex vivo IL-1β production limited a 4 Mbp interval to chromosome 7. Sequencing of the locus region revealed 14 SNPs between “High” and “Low” responders that narrowed the locus to a 420 Kb interval. Variants were detected in non-coding regions of Itgam, Rgs10 and BC017158 genes and at the first exon of Pycard gene, resulting in an E19K substitution in the protein ASC (apoptosis associated speck-like protein containing a CARD) an adaptor molecule in the inflammasome complex. Silencing of BC017158 inhibited IL1-β production by stimulated macrophages and the E19K ASC mutation carried by AIRmin mice impaired the ex vivo IL-1β response and the formation of ASC specks in stimulated cells. IL-1β and ASC specks play major roles in inflammatory reactions and in inflammation-related diseases. Our results delineate a novel genetic factor and a molecular mechanism affecting the acute inflammatory response.

Gene and lncRNA expression patterns associated with Qfhs.ndsu-3AS Fusarium head blight resistance QTL in durum wheat

To identify the transcriptional mechanisms underpinning Fusarium head blight (FHB) resistance in durum wheat, an RNA-seq comparative transcriptome analysis was conducted on spikes 72 h after inoculation of a resistant line Langdon(Dic-3A)10 and a susceptible cultivar ‘Langdon’. Previously, 14 differentially expressed genes (DEGs) were mapped in the region of the quantitative trait locus Qfhs.ndsu-3AS, associated with type II resistance to FHB. Here, we focused on the global response of durum wheat to Fusarium graminearum (Fg) infection, identifying the molecular pathways in which DEGs are involved and lncRNAs with roles in transcriptional and post-transcriptional regulation of gene expression. A set of 921 DEGs was identified using the reference genome of the cultivar ‘Svevo’. Relative to the susceptible cultivar, the resistant line Langdon(Dic-3A)10 showed 452 up-regulated genes and 469 down-regulated genes. Upregulated genes in the resistant line included fungal cell-wall degrading enzymes, transcription factors, and genes involved in kinase signalling, phytohormone pathways, calcium signalling, secondary metabolite biosynthesis and toxin sensitivity. Differentially expressed lncRNAs showed different genome locations: 12 cis intergenic (6 up-regulated in Langdon(Dic-3A)10), 4 trans intergenic (one up-regulated in Langdon(Dic-3A)10), 4 intronic (two up-regulated in Langdon(Dic-3A)10) and 2 putative miRNAs precursors. Possible target genes were predicted for 14 lncRNAs, indicating potential regulative effects on wax and lignin synthesis and ankyrines in the resistant line. In a context where resistance sources against Fg are scarce in durum germplasm, the transcriptomic characterization of a valuable genotype contributes to the understanding of the genetic basis and regulatory network involved in the resistance conferred by Qfhs.ndsu-3AS.

EWS::FLI1 and HOXD13 Control Tumor Cell Plasticity in Ewing Sarcoma.

Propagation of Ewing sarcoma requires precise regulation of EWS::FLI1 transcriptional activity. Determining the mechanisms of fusion regulation will advance our understanding of tumor progression. Here we investigated whether HOXD13, a developmental transcription factor that promotes Ewing sarcoma metastatic phenotypes, influences EWS::FLI1 transcriptional activity. Existing tumor and cell line datasets were used to define EWS::FLI1 binding sites and transcriptional targets. Chromatin immunoprecipitation and CRISPR interference were employed to identify enhancers. CUT&RUN and RNA sequencing defined binding sites and transcriptional targets of HOXD13. Transcriptional states were investigated using bulk and single-cell transcriptomic data from cell lines, patient-derived xenografts, and patient tumors. Mesenchymal phenotypes were assessed by gene set enrichment, flow cytometry, and migration assays. We found that EWS::FLI1 creates a de novo GGAA microsatellite enhancer in a developmentally conserved regulatory region of the HOXD locus. Knockdown of HOXD13 led to widespread changes in expression of developmental gene programs and EWS::FLI1 targets. HOXD13 binding was enriched at established EWS::FLI1 binding sites where it influenced expression of EWS::FLI1-activated genes. More strikingly, HOXD13 bound and activated EWS::FLI1-repressed genes, leading to adoption of mesenchymal and migratory cell states that are normally suppressed by the fusion. Single-cell analysis confirmed that direct transcriptional antagonism between HOXD13-mediated gene activation and EWS::FLI1-dependent gene repression defines the state of Ewing sarcoma cells along a mesenchymal axis. Ewing sarcoma tumors are comprised of tumor cells that exist along a mesenchymal transcriptional continuum. The identity of cells along this continuum is, in large part, determined by the competing activities of EWS::FLI1 and HOXD13. See related commentary by Weiss and Bailey, p. 4360.

A Malaria Parasite Cross Reveals Genetic Determinants of Plasmodium falciparum Growth in Different Culture Media.

What genes determine in vitro growth and nutrient utilization in asexual blood-stage malaria parasites? Competition experiments between NF54, clone 3D7, a lab-adapted African parasite, and a recently isolated Asian parasite (NHP4026) reveal contrasting outcomes in different media: 3D7 outcompetes NHP4026 in media containing human serum, while NHP4026 outcompetes 3D7 in media containing AlbuMAX, a commercial lipid-rich bovine serum formulation. To determine the basis for this polymorphism, we conducted parasite genetic crosses using humanized mice and compared genome-wide allele frequency changes in three independent progeny populations cultured in media containing human serum or AlbuMAX. This bulk segregant analysis detected three quantitative trait loci (QTL) regions [on chromosome (chr) 2 containing aspartate transaminase AST; chr 13 containing EBA-140; and chr 14 containing cysteine protease ATG4] linked with differential growth in serum or AlbuMAX in each of the three independent progeny pools. Selection driving differential growth was strong (s = 0.10 – 0.23 per 48-hour lifecycle). We conducted validation experiments for the strongest QTL on chr 13: competition experiments between ΔEBA-140 and 3D7 wildtype parasites showed fitness reversals in the two medium types as seen in the parental parasites, validating this locus as the causative gene. These results (i) demonstrate the effectiveness of bulk segregant analysis for dissecting fitness traits in P. falciparum genetic crosses, and (ii) reveal intimate links between red blood cell invasion and nutrient composition of growth media. Use of parasite crosses combined with bulk segregant analysis will allow systematic dissection of key nutrient acquisition/metabolism and red blood cell invasion pathways in P. falciparum.

Elucidating the importance and regulation of key enhancers for human MEIS1 expression

Myeloid ecotropic virus insertion site 1 (MEIS1) is essential for normal hematopoiesis and is a critical factor in the pathogenesis of a large subset of acute myeloid leukemia (AML). Despite the clinical relevance of MEIS1, its regulation is largely unknown. To understand the transcriptional regulatory mechanisms contributing to human MEIS1 expression, we created a knock-in green florescent protein (GFP) reporter system at the endogenous MEIS1 locus in a human AML cell line. Using this model, we have delineated and dissected a critical enhancer region of the MEIS1 locus for transcription factor (TF) binding through in silico prediction in combination with oligo pull-down, mass-spectrometry and knockout analysis leading to the identification of FLI1, an E-twenty-six (ETS) transcription factor, as an important regulator of MEIS1 transcription. We further show direct binding of FLI1 to the MEIS1 locus in human AML cell lines as well as enrichment of histone acetylation in MEIS1-high healthy and leukemic cells. We also observe a positive correlation between high FLI1 transcript levels and worse overall survival in AML patients. Our study expands the role of ETS factors in AML and our model constitutes a feasible tool for a more detailed understanding of transcriptional regulatory elements and their interactome.

Recent status of Genotyping by Sequencing (GBS) Technology in cucumber (Cucumis sativus L.): a review.

Current and advanced breeding tools are being used to improve economically important horticultural crops to meet the consumers' needs and preferences. Genotyping-by-sequencing (GBS) is an extremely useful tool in the investigation and analysis of the genetic diversity of different cultivars. Based on a broad range of genetic backgrounds like single nucleotide polymorphism (SNPs), GBS is known as a novel technique to facilitate the detection of quantitative trait loci (QTL) regions robustly linked with interested traits compared to genome-wide association study (GWAS) and QTL. GBS has gained popularity among breeders in recent years and it is also employed in cucumber breeding programs. Cucumbers (C. sativus L.) are monoecious, gynoecious and some of them are parthenocarpic species. Cucumber is one of the most economical and essential crops in the Cucurbitaceae family. For time immemorial, cucumber has been produced and consumed all over the world like other cucurbits. To a large extent, cultivated cucurbits are beneficial to human health for providing necessary minerals and fibers.Therefore, this review portrays the current status of advances made by using GBS and its combination with other tools in various studies of cucumber such as the use of GBS and single nucleotide polymorphism (SNP) markers, GBS and GWAS, also with QTL and marker-assisted selection (MAS) are applied to display and detect explicit genetic architecture complex traits in crops and chromosome rearrangements.Cucumber breeding programs have undoubtedly benefited from genotyping-by-sequencing. Using the GBS method, research discovered lots of new candidate genes that control various traits including spine color, fruit stalk-end color, and disease resistance in cucumber lines.

Genomic evaluation and genome-wide association studies for total number of teats in a combined American and Danish Yorkshire pig populations selected in China.

Joint genomic evaluation by combining data recordings and genomic information from different pig herds and populations is of interest for pig breeding companies because the efficiency of genomic selection (GS) could be further improved. In this work, an efficient strategy of joint genomic evaluation combining data from multiple pig populations is investigated. Total teat number (TTN), a trait that is equally recorded on 13,060 American Yorkshire (AY) populations (~14.68 teats) and 10,060 Danish Yorkshire (DY) pigs (~14.29 teats), was used to explore the feasibility and accuracy of GS combining datasets from different populations. We first estimated the genetic correlation (rg) of TTN between AY and DY pig populations (rg = 0.79, se = 0.23). Then we employed the genome-wide association study to identify quantitative trait locus (QTL) regions that are significantly associated with TTN and investigate the genetic architecture of TTN in different populations. Our results suggested that the genomic regions controlling TTN are slightly different in the two Yorkshire populations, where the candidate QTL regions were on SSC 7 and SSC 8 for the AY population and on SSC 7 for the DY population. Finally, we explored an optimal way of genomic prediction for TTN via three different genomic best linear unbiased prediction models and we concluded that when TTN across populations are regarded as different, but correlated, traits in a multitrait model, predictive abilities for both Yorkshire populations improve. As a conclusion, joint genomic evaluation for target traits in multiple pig populations is feasible in practice and more accurate, provided a proper model is used.

Identification and Clarification of VrCYCA1: A Key Genic Male Sterility-Related Gene in Mungbean by Multi-Omics Analysis

Heterosis has been utilized in crops for a long time, and although crop fertility is the basis for the utilization of heterosis, there is limited information concerning the genic male sterility (GMS) of mungbean. Therefore, based on the genic male sterile mutant, M1, obtained by EMS mutagenesis of the Weilyu cultivar, this project used multi-omics analysis to detect the male sterile site and further identify its candidate gene, and then the mechanism of the candidate gene was discussed. As a result, one locus region (Chr5: 6,835,001–6,935,000 bp) associated with GMS was identified, and nine genes were found within the 100 Kb region. The candidate gene, VrCYCA1, around the above loci had a TATA box deletion approximately 4.7 Kb upstream of the gene, and this was evidenced by comparative genomics, transcriptome analysis, and RT-qPCR analysis. The expression level of VrCYCA1 was significantly downregulated (log2FC = −2.06, p-value = 0.025) in the ms lines compared with the control group. Moreover, 6653 genes showed differential expression between the Weilyu lines and mutant lines as well as 165 metabolites with significant differences in their concentration levels. Among those differentially expresses genes, 226 were annotated with functional categories involved in flowering and endosperm development, and six genes had protein–protein interactions with VrCYCA1. Seven categories of metabolites and seven genes participated in the relationship between reproductive growth and vegetative growth, which might have caused the sterility of mungbean in the mutant plants. This study used multi-omics data to mine a mungbean GMS-related gene, VrCYCA1, and constructed a GMS genetic network to explore the molecular mechanism of VrCYCA1. The results lay a solid foundation for further molecular biology research and utilization in mungbean male sterility.

The Use of DArTseq Technology to Identify New SNP and SilicoDArT Markers Related to the Yield-Related Traits Components in Maize.

In the last decade, many scientists have used molecular biology methods in their research to locate the grain-yield-determining loci and yield structure characteristics in maize. Large-scale molecular analyses in maize do not only focus on the identification of new markers and quantitative trait locus (QTL) regions. DNA analysis in the selection of parental components for heterotic crosses is a very important tool for breeders. The aim of this research was to identify and select new markers for maize (SNP and SilicoDArT) linked to genes influencing the size of the yield components in maize. The plant material used for the research was 186 inbred maize lines. The field experiment was established in twolocations. The yield and six yield components were analyzed. For identification of SNP and SilicoDArT markers related to the yield and yield components, next-generation sequencing was used. As a result of the biometric measurements analysis, differentiation in the average elevation of the analyzed traits for the lines in both locations was found. The above-mentioned results indicate the existence of genotype–environment interactions. The analysis of variance for the observed quality between genotypes indicated a statistically significant differentiation between genotypes and a statistically significant differentiation for all the observed properties betweenlocations. A canonical variable analysis was applied to present a multi-trait assessment of the similarity of the tested maize genotypes in a lower number of dimensions with the lowest possible loss of information. No grouping of lines due to the analyzed was observed. As a result of next-generation sequencing, the molecular markers SilicoDArT (53,031) and SNP (28,571) were obtained. The genetic distance between the analyzed lines was estimated on the basis of these markers. Out of 81,602 identified SilicoDArT and SNP markers, 15,409 (1559 SilicoDArT and 13,850 SNPs) significantly related to the analyzed yield components were selected as a result of association mapping. The greatest numbers of molecular markers were associated with cob length (1203), cob diameter (1759), core length (1201) and core diameter (2326). From 15,409 markers significantly related to the analyzed traits of the yield components, 18 DArT markers were selected, which were significant for the same four traits (cob length, cob diameter, core length, core diameter) in both Kobierzyce and Smolice. These markers were used for physical mapping. As a result of the analyses, it was found that 6 out of 18 (1818; 14,506; 2317; 3233; 11,657; 12,812) identified markers are located inside genes. These markers are located on chromosomes 8, 9, 7, 3, 5, and 1, respectively.

Identifying genetic variants and pathways influencing daughter averages for twinning in North American Holstein cattle and evaluating the potential for genomic selection

Multiple birth in dairy cattle is a detrimental trait both economically for producers and for animal health. Genetics of twinning is complex and has led to several quantitative trait loci regions being associated with increased twinning. To identify variants associated with this trait, calving records from 2 time periods were used to estimate daughter averages for twinning for Holstein bulls. Multiple analyses were conducted and compared including GWAS, genomic prediction, and gene set enrichment analysis for pathway detection. Although pathway analysis did not yield many congruent pathways of interest between data sets, it did indicate two of interest. Both pathways have ties to the strong candidate region on BTA11 from the genome-wide association analysis across data sets. This region does not overlap with previously identified quantitative trait loci regions for twinning or ovulation rate in cattle. The strongest associated SNPs were upstream from 2 candidate genes LHCGR and FSHR, which are involved in folliculogenesis. Genomic prediction showed a moderate correlation accuracy (0.43) when predicting genomic breeding values for bulls with estimates from calving records from 2010 to 2016. Future analysis of the region on BTA11 and the relation of the candidate genes could improve this accuracy.

Epigenetic regulation of genes involved in fluid‐electrolyte balance in the kidney

Recent studies have identified at least 20 different kidney cell types based upon chromatin structure and gene expression. Histone deacetylases (HDACs) are epigenetic transcriptional regulators via deacetylation of histone lysines resulting in inaccessible chromatin. We reported that kidney epithelial HDAC1 and HDAC2 activity is critical for maintaining a healthy kidney and preventing fluid‐electrolyte abnormalities. However, to what extent does Hdac1/Hdac2 knockdown affect chromatin structure and subsequent transcript expression in the kidney? To answer this question, we used single nucleus Assay for Transposase‐Accessible Chromatin‐sequencing (snATAC‐seq) and snRNA‐seq to profile kidney nuclei from adult male and female, control and littermate inducible kidney epithelial‐specific Hdac1/Hdac2 knockdown mice (iKSHdac1/2KO). Compared to littermate control mice iKSHdac1/2KO mice had significant elevations in plasma sodium (male control n=17, PNa= 143.6 ± 1.5 vs KO n=8, 147.6 ± 3.5, P=0.002, female control n=6, 141.8 ± 2.5 vs KO n=8 144.6 ± 1.8, P=0.03). iKSHdac1/2KO mice also had a significant increase in the kidney to body mass ratio (males 11.5 ±1.4 mg/g vs 13.1 ±1.5 P=0.1, females 9.7 ± 1.0 vs 12.3 ± 1.4, P=0.001) but no differences in liver to body mass ratio. Kidney histological analyses determined significant interstitial fibrosis, tubular atrophy and necrosis, dilated tubules, and protein casts in the iKSHdac1/2KO regardless of sex. Kidney structure was normal in all control mice. Survival was also significantly impacted in the iKSHdac1/2KO as all of these mice died (male mice died 27‐28 days after induction of knockdown). At 2 weeks after induction of KO, kidney nuclei from control and iKSHdac1/2KO mice were isolated and snATAC‐seq and snRNA‐seq analyses completed. We identified 26 unique clusters in both datasets that represented epithelial, endothelial, immune, stromal, and podocyte cells. Hdac1/Hdac2 knockdown resulted in significant changes in the chromatin structure predominantly within the promoter region of gene loci involved in fluid‐electrolyte balance such as the aquaporins, with both increased and decreased accessibility captured. Aqp1 expressed in the proximal tubules was reduced 60% and principal cell Aqp2 was reduced 50% in the iKSHdac1/2KO mice compared to controls. However, not all aquaporins were affected as for example, principal cell Aqp4 was not significantly different between the mice (P=0.98). Moreover, sex‐specific transcriptomic and chromatin structure were apparent in the proximal tubule clusters. Hdac1/Hdac2 knockdown resulted in different gene loci being accessible with a corresponding increased transcript number in the kidney, but among all mice only 24‐30% of chromatin accessibility agreed with transcript expression (e.g. open chromatin, increased transcript). To conclude, although chromatin structure does affect transcription, ~70% of the differentially expressed genes cannot be explained by changes in chromatin accessibility and HDAC1/HDAC2 had a minimal effect on these global patterns. Yet, the genes that are targets of HDAC1 and HDAC2 are critically important for maintaining kidney function and survival.

Differential Etv2 threshold requirement for endothelial and erythropoietic development.

SUMMARYEndothelial and erythropoietic lineages arise from a common developmental progenitor. Etv2 is a master transcriptional regulator required for the development of both lineages. However, the mechanisms through which Etv2 initiates the gene-regulatory networks (GRNs) for endothelial and erythropoietic specification and how the two GRNs diverge downstream of Etv2 remain incompletely understood. Here, by analyzing a hypomorphic Etv2 mutant, we demonstrate different threshold requirements for initiation of the downstream GRNs for endothelial and erythropoietic development. We show that Etv2 functions directly in a coherent feedforward transcriptional network for vascular endothelial development, and a low level of Etv2 expression is sufficient to induce and sustain the endothelial GRN. In contrast, Etv2 induces the erythropoietic GRN indirectly via activation of Tal1, which requires a significantly higher threshold of Etv2 to initiate and sustain erythropoietic development. These results provide important mechanistic insight into the divergence of the endothelial and erythropoietic lineages.

Estrogen-Related Receptor γ Maintains Pancreatic Acinar Cell Function and Identity by Regulating Cellular Metabolism

Mitochondrial dysfunction disrupts the synthesis and secretion of digestive enzymes in pancreatic acinar cells and plays a primary role in the etiology of exocrine pancreas disorders. However, the transcriptional mechanisms that regulate mitochondrial function to support acinar cell physiology are poorly understood. Here, we aim to elucidate the function of estrogen-related receptor γ (ERRγ) in pancreatic acinar cell mitochondrial homeostasis and energy production. Two models of ERRγ inhibition, GSK5182-treated wild-type mice and ERRγ conditional knock-out (cKO) mice, were established to investigate ERRγ function in the exocrine pancreas. To identify the functional role of ERRγ in pancreatic acinar cells, we performed histologic and transcriptome analysis with the pancreas isolated from ERRγ cKO mice. To determine the relevance of these findings for human disease, we analyzed transcriptome data from multiple independent human cohorts and conducted genetic association studies for ESRRG variants in 2 distinct human pancreatitis cohorts. Blocking ERRγ function in mice by genetic deletion or inverse agonist treatment results in striking pancreatitis-like phenotypes accompanied by inflammation, fibrosis, and cell death. Mechanistically, loss of ERRγ in primary acini abrogates messenger RNA expression and protein levels of mitochondrial oxidative phosphorylation complex genes, resulting in defective acinar cell energetics. Mitochondrial dysfunction due to ERRγ deletion further triggers autophagy dysfunction, endoplasmic reticulum stress, and production of reactive oxygen species, ultimately leading to cell death. Interestingly, ERRγ-deficient acinar cells that escape cell death acquire ductal cell characteristics, indicating a role for ERRγ in acinar-to-ductal metaplasia. Consistent with our findings in ERRγ cKO mice, ERRγ expression was significantly reduced inpatients with chronic pancreatitis compared with normal subjects. Furthermore, candidate locus region genetic association studies revealed multiple single nucleotide variants for ERRγ that are associated with chronic pancreatitis. Collectively, our findings highlight an essential role for ERRγ in maintaining the transcriptional program that supports acinar cell mitochondrial function and organellar homeostasis and provide a novel molecular link between ERRγ and exocrine pancreas disorders.

Transcriptome provides insights into bovine mammary regulatory mechanisms during the lactation cycle

ABSTRACT The molecular events underlying the lactation curve of dairy animals have long been a biological conundrum for mammary biologists, and a cause of a considerable loss of income for dairy farmers. To better understand the regulatory mechanisms and developmental processes of the mammary gland during the lactation cycle, whole-genome transcriptome profiles of bovine mammary tissues at five different lactation stages were investigated using the RNA-Seq technique. The differentially expressed genes were identified by comparing different lactation stage combinations. Gene expression changes were validated using quantitative reverse-transcription polymerase chain reaction. Some differentially expressed genes were found to locate in the known quantitative trait loci regions that are associated with multiple milk production traits. Proteins of potentially important genes were confirmed to be expressed in the mammary epithelium of dairy cows. An integrated analysis of differential gene expression indicated that internal development regularities underlying the shape of the milk production curve. First, the mammary gland is enriched in similar activities during lactation onset and involution, but in opposite regulatory directions. Second, the lactation stages before and after the milk peak shared similar biological processes that were mainly involved in extracellular matrix remodelling. The discoveries of the study provide information necessary to improve milk production.

Superstructure Detection in Nucleosome Distribution Shows Common Pattern within a Chromosome and within the Genome.

Nucleosome positioning plays an important role in crucial biological processes such as replication, transcription, and gene regulation. It has been widely used to predict the genome’s function and chromatin organisation. So far, the studies of patterns in nucleosome positioning have been limited to transcription start sites, CTCFs binding sites, and some promoter and loci regions. The genome-wide organisational pattern remains unknown. We have developed a theoretical model to coarse-grain nucleosome positioning data in order to obtain patterns in their distribution. Using hierarchical clustering on the auto-correlation function of this coarse-grained nucleosome positioning data, a genome-wide clustering is obtained for Candida albicans. The clustering shows the existence beyond hetero- and eu-chromatin inside the chromosomes. These non-trivial clusterings correspond to different nucleosome distributions and gene densities governing differential gene expression patterns. Moreover, these distribution patterns inside the chromosome appeared to be conserved throughout the genome and within species. The pipeline of the coarse grain nucleosome positioning sequence to identify underlying genomic organisation used in our study is novel, and the classifications obtained are unique and consistent.

Simultaneous Detection of the HPV L1 Gene and the Human β-Globin Gene in the Blood Components of Cervical Cancer Patients Living in Yakutia

Background: To create a test for the early detection of cervical cancer (CC), we conducted exploratory studies on detecting HPV genes and genes of the human β-globin locus in plasma (Pl) and RBC suspension (RBCsus) samples from patients with newly detected CC (NDCC). Methods and Results: Smears of venous blood containing K3-EDTA from five anonymous patients aged from 45 to 55 years (residents of Yakutia), with NDCC were obtained. Three types of blood component samples were prepared – plasma (Pl), red blood cell (RBC) suspension (RBCsus), and the erythrocyte fraction treated with trypsin (RBCsus-Try). To detect circulating cell-free DNA (cfDNA) in NDCC patients, we studied the presence of genes corresponding to the HPV L1 protein region and genes of the human β-globin locus by real-time PCR (qPCR) using appropriate primers. The genes of β-globin locus and HPV L1 were detected in Pl of NDCC patients in 20% of cases, and in RBCsus in 60% of cases. The amplified gene products using primers were present in RBCsus-Try in only one patient (20% of cases). In patients with uncertain amplification, electrophoresis showed the absence of amplified products in Pl and their presence in RBCsus. Conclusion: In NDCC patients, HPV L1 and β-globin genes can be detected in both Pl and RBCsus. In addition, in RBC samples, these genes were detected more often than in plasma samples, and no absolute absence of amplification products was observed in RBC samples. The research needs to be continued.

Phenotypical and genetical characterization of the Mad allele during Drosophila wing development

Growth and patterning of Drosophila wing depends upon the sequential organizing activities of Hedgehog (Hh) and Decapentaplegic (Dpp) signaling pathways. The Hh signaling directly activates the expression of dpp through the transcription factor cubitus interruptus (Ci). Dpp itself functions as a long-range morphogen to promote cell proliferation and differentiation through an essential transcription factor encoded by Mad. Here we report that the Mad1-2 allele exhibits phenotypes distinct from classical Dpp pathway mutants in the developing wing. The activity of Dpp signaling is attenuated in Mad1-2 mutant cells. However, activation of Dpp signaling is found in a subset of cells surrounding homozygous Mad1-2 clones when the clones are located at the anterior compartment of wing disc. Further analysis reveals that Mad1-2 mutant cells display high level of Hh signaling activity and accumulate significant amount of Ci. Unexpectedly, whole genome resequencing identifies multiple mutations in the 3'UTR region of Pka-C1 genomic loci in the Mad1-2 stock. We provide genetic and molecular evidence that the Pka-C1 mutations carried by Mad1-2 likely underlies the observed Hh signaling defects. Therefore, the contribution of Pka-C1 mutation should be taken in consideration when analyzing Mad1-2 phenotypes. The isolation of independent Mad and Pka-C1 alleles from the Mad1-2 stock further supports our conclusions.

Phase variation in the glycosyltransferase genes of Pasteurella multocida associated with outbreaks of fowl cholera on free-range layer farms.

Fowl cholera caused by Pasteurella multocida has re-emerged in Australian poultry production since the increasing adoption of free-range production systems. Currently, autogenous killed whole-cell vaccines prepared from the isolates previously obtained from each farm are the main preventative measures used. In this study, we use whole-genome sequencing and phylogenomic analysis to investigate outbreak dynamics, as well as monitoring and comparing the variations in the lipopolysaccharide (LPS) outer core biosynthesis loci of the outbreak and vaccine strains. In total, 73 isolates from two different free-range layer farms were included. Our genomic analysis revealed that all investigated isolates within the two farms (layer A and layer B) carried LPS type L3, albeit with a high degree of genetic diversity between them. Additionally, the isolates belonged to five different sequence types (STs), with isolates belonging to ST9 and ST20 being the most prevalent. The isolates carried ST-specific mutations within their LPS type L3 outer core biosynthesis loci, including frameshift mutations in the outer core heptosyltransferase gene (htpE) (ST7 and ST274) or galactosyltransferase gene (gatG) (ST20). The ST9 isolates could be separated into three groups based on their LPS outer core biosynthesis loci sequences, with evidence for potential phase variation mechanisms identified. The potential phase variation mechanisms included a tandem repeat insertion in natC and a single base deletion in a homopolymer region of gatG. Importantly, our results demonstrated that two of the three ST9 groups shared identical rep-PCR (repetitive extragenic palindromic PCR) patterns, while carrying differences in their LPS outer core biosynthesis loci region. In addition, we found that ST9 isolates either with or without the natC tandem repeat insertion were both associated with a single outbreak, which would indicate the importance of screening more than one isolate within an outbreak. Our results strongly suggest the need for a metagenomics culture-independent approach, as well as a genetic typing scheme for LPS, to ensure an appropriate vaccine strain with a matching predicted LPS structure is used.