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Purpose: N6-methyladenosine (m6A) methylation was the most abundant internal modification on messenger RNAs in eukaryotes. This study intended to explore the role of m6A methylation in endometrial cancer (EC). Materials and Methods: The m6A-sequencing data "GSE93911" of human EC were downloaded from Gene Expression Omnibus database. Hisat2 software and MACS2 were used to perform the alignment of reads and m6A methylation peak calling, and the peaks were annotated using Chipseeker. Then, differential m6A methylation peaks between normal and tumor samples were analyzed, followed by the functional enrichment analysis of the differentially methylated genes in promoter and 3' untranslated region (UTR) using Clusterprofiler. Based on the 450K methylated chip data, gene expression and clinical data in The Cancer Genome Atlas, the differentially methylated genes were verified, followed by Cox univariate/multivariate regression analysis and survival analysis. Finally, a risk prognosis model was constructed. Results: The m6A peak number was decreased in EC. The distribution of m6A peaks was highly enriched near transcriptional start site, in promoter, UTR, intron and exon, followed by distal intergenic. A total of 581 differentially methylated genes (361 hyper- and 220 hypomethylated genes) were identified in promoter and UTR regions that were enriched in insulin resistance (IR) and extracellular matrix (ECM). A total of 181 genes with significant differential expressions and differential methylation site in EC were selected. Of which, 31 genes were correlated with survival, and an 11-gene risk prognosis model was identified, including GDF7, BNC2, SLC8A1, B4GALNT3, DHCR24, ESRP1, HOXB9, IGSF9, KIAA1324, MSnX1, and PHGDH. Conclusion: The m6A methylation regulated EC progression by targeting the genes related to IR and ECM. A 11-gene risk prognosis model was identified to predict survival of patients with EC.

Reproductive phenology is well known to be a key feature of crop adaptation to diverse ecogeographic variation and management practices. Lentil is one of the founder pulse crops of middle-eastern Neolithic agriculture, and the modern-day domesticated lentil germplasm is generally considered to form three broad adaptation groups: Mediterranean, South Asian and northern temperate, which correspond approximately to the major global production environments. Understanding the molecular basis of these adaptations is crucial to maximise efficiency of breeding programs. Here, we use a QTL approach to dissect the earliness that is characteristic of the South Asian pilosae ecotype, and that suits it to the typically short winter cropping season. We identified two loci, DTF6a and DTF6b, at which dominant alleles confer early flowering. We show that, although these loci can interact in an additive manner, DTF6a alone is sufficient to confer early flowering even in extremely short photoperiods. Comparisons with closely related legume species confirmed the presence of a conserved cluster of three FT orthologs among potential candidate genes in the region, and expression analysis in near-isogenic material showed that the early dtf6a allele is associated with a strong derepression of the FTa1 gene in particular. Analysis of sequence variation revealed the presence of a 7.4 kb deletion in the FTa1-FTa2 intergenic region in the pilosae parent, and a wide survey of over 400 accessions with diverse origin showed that the dtf6a allele is dominant in South Asia material. Collectively, these results contribute to understanding the molecular basis of global adaptation in lentil, and further emphasize the importance of this conserved genomic region for adaptation in temperate legumes generally.

Blood disease in bananas caused by Ralstonia syzygii subsp. celebesensis is a bacterial wilt disease that causes major yield losses of banana in Indonesia and peninsular Malaysia. The disease has significantly increased its geographic distribution in the past decade. Diagnostic methods are an important component of disease management in vegetatively propagated crops such as banana to constrain incursions of plant pathogens. Therefore, the objectives of this study were (i) to design and rigorously validate a novel banana Blood disease (BBD) real-time PCR assay with a high level of specificity and sensitivity of detection and (ii) to validate published PCR-based diagnostic methods targeting the intergenic region in the megaplasmid (“121 assay” with primer set 121) or the phage tail protein-coding sequence in the bacterial chromosome (“Kubota assay” and “BDB2400 assay” with primer set BDB2400). Assay validation included 339 samples (174 Blood disease bacteria, 51 bacteria associated with banana plants, 51 members of the Ralstonia solanacearum species complex, and 63 samples from symptomatic and healthy plant material). Validation parameters were analytical specificity (inclusivity and exclusivity), selectivity, limit of detection, accuracy, and ruggedness. The 121 assay and our newly developed BBD real-time PCR assay detected all R. syzygii subsp. celebesensis strains with no cross-specificity during validation. Two different PCR assays using the primer set BDB2400 lacked specificity and selectivity. This study reveals that our novel BBD real-time PCR assay and the conventional PCR 121 assay are reliable methods for Blood disease diagnostics, as they comply with all tested validation parameters.

Severe leaf spot disease was observed on Aloe vera plants in the winters of 2011 and 2012 during a survey of various nurseries of Gwalior, India. Irregular, sunken, dark creamish brown spots having reddish brown margin were noticed on both surfaces of the leaves. The causal organism was consistently isolated from symptomatic leaves on potato dextrose agar media (PDA). A total 59 isolates of fungi were recovered from diseased A. vera leaves, and 37 isolates were identified as belonging to the genus Fusarium. On the basis of morphological characteristics and internal transcribed spacer (ITS) region of rDNA amplified using the primers ITS4/ITS5 the pathogen was identified as Fusarium proliferatum (Matsushima) Nirenberg and pathogenicity of the isolate was confirmed by using Koch’s postulates. To the best of our knowledge, this is the first report of leaf spot disease caused by Fusarium proliferatum on A. vera plants in India.

This work was carried out during two successive seasons (2016 and 2017) on cucumber fruits from a plastic greenhouse and from open field cultivation in El Gharbeia and El Giza Governorates, Egypt. Isolation trials from spoilage fruit samples of plastic greenhouse cultivation recorded high frequency of Alternaria tenusinium, Fusarium spp. and Pleospora alli. The most common fungi of rotten cucumber fruits from an open field were Galactomyces spp. and Fusarium spp. Pathogenicity tests proved that, Fusarium solani from El-Gharbeia followed by A. tenusinium from El-Giza were the most frequent isolates responsible for rot of cucumber fruits from plastic greenhouse cultivation. Moreover, the most frequent isolates causing postharvest disease of cucumber fruits of the open field were Galactomyces candidium from El-Giza followed by Geotrichum sp. and F. fujikuroi from El-Gharbeia Governorates, respectively. This is the first report of several fungi causing postharvest fruit rot disease of cucumber i.e., G. candidium, Geotrichum sp., A. tenusinium, P. alli and Fusarium spp. (F. fujikuroi, F. verticiolides, F. solani, F. geraminearium and Fusarium incarnatum). Fungal isolates were identified according to cultural, morphological and molecular characterization based on sequencing of internal transcribed spacer1 (ITS1). All the ITS nucleotide sequences of fungi were applied and conserved in GenBank.

Baihuasheshecao (Hedyotis diffusa), a Chinese herb for cancer treatment, is frequently adulterated by a related species Hedyotis corymbosa. DNA sequencing of the complete internal transcribed spacer region was applied to differentiate H. diffusa from H. corymbosa and other closely related species. The molecular data showed that four out of seven herb samples of Baihuasheshecao were adulterants. Chemical analyses by TLC and HPLC were used to authenticate H. diffusa and H. corymbosa. Two marker compounds were identified exclusively in H. diffusa: 6-O-(E)-p-coumaroyl scandoside methyl ester (compound 1) and 10(S)-hydroxypheophytin a (compound 2). Both compounds showed moderate anti-proliferation effect on PC3 human androgen-independent prostate cancer cells, while compound 2 also showed strong anti-proliferation effect on LNCaP human androgen-sensitive prostate cancer cells. Accordingly, these bioactive marker compounds could be applied to verify the authenticity and assess the quality of Baihuasheshecao.

This study provides the frst comprehensive report on the molecular characteristics of African swine fever virus (ASFV) variants in Serbia between 2019 and 2022. Since its frst observation in July 2019, the disease has been found in wild boar and domestic swine. The study involved the analysis of 95 ASFV-positive samples collected from 12 infected administrative districts in Serbia. Partial four genomic regions were genetically characterized, including B646L, E183L, B602L, and the intergenic region (IGR) between the I73R-I329L genes. The results of the study suggest that multiple ASFV strains belonging to genotype II are circulating in Serbia, as evidenced by the analysis of the IGR between I73R-I329L genes that showed the most diferences. Furthermore, the phylogenetic analysis of the B602L gene showed three diferent clades within the CVR I group of ASFV strains. Regarding the IGR, 98.4% were grouped into IGR II, with only one positive sample grouped into the IGR III group. These fndings provide essential insights into the molecular characteristics of ASFV variants in Serbia and contribute to the knowledge of circulating strains of ASFV in Europe. However, further research is necessary to gain a better understanding of ASFV spread and evolution

Objective To investigate the prevalence of multidrug-resistant (MDR) Pseudomonas aeruginosa (PA) producing extended-spectrum beta-lactamases (ESBLs) and metallo-beta-lactamases (MBLs) in burn patients in Algeria. Methods Between April 2016 and October 2019, 47 non-redundant isolates of PA were collected from 47 burn patients admitted to the Department of Burns at the Military Hospital of Algiers in Algeria. Antibiotic susceptibility testing was performed by agar diffusion and the Phoenix automated method. Resistance genes were identified by PCR, and molecular typing of isolates was carried out by enterobacterial repetitive intergenic consensus (ERIC) sequences-polymerase chain reaction (PCR). Results Among the 47 non-redundant MDR PA strains isolated, 59.57% were phenotypically ESBLs-positive, and 100% were phenotypically MBL-positive. The ESBL-positive isolates were subsequently screened for six groups of bla genes encoding ESBL-type enzymes, namely blaCTX-M2, blaPER, blaTEM, blaSHV, blaVEB, and blaGES. Out of the 28 ESBL-producing strains, 23 (82.14%) were blaCTX-M2 positive; 18 (38.29%) were blaPER positive, and 16 (34.04%) were blaTEM positive, while 5 (17.9%) were co-harboring blaCTX-M2, blaTEM, and blaPER genes. The blaSHV, blaVEB, and blaGES genes were not detected in any of the ESBL positive isolates. Since all isolates were MBL-positive, all 47 strains were screened for the blaNDM-1, blaIMP, blaVIM genes that produce MBLs; however, none of these genes were detected. Additional screening for the oprD gene demonstrated that 45 (95.74%) of the isolates were positive for this gene. Finally, ERIC PCR revealed 11 distinct PA clones among the blaCTX-M2 positive strains. Conclusion This is the first study to report the presence of CTX-M2-producing PA in the North Africa region and the first to detect blaCTX-M2-positive and blaPER-positive PA clinical isolates in Algeria, therefore demonstrating the spread of such MDR strains to this part of the world. Identification of bacterial genotypic alterations that confer antibiotic resistance is critical in determining the most effective antimicrobial strategies to be employed. Therefore, our findings could potentially facilitate clinical decision making regarding the antibiotics of choice for the treatment of burn patients that suffer from PA infections in Algeria.

Puerariae lobatae radix (Ge‐Gen in Chinese) and Puerariae thomsonii radix (Fen‐Ge) are widely used as medicine and health products, particularly in Chinese medicine. Puerarin and daidzein are the primary bioactive compounds in Puerariae radix. These isoflavones have been used to treat cardiovascular and cerebrovascular diseases, hypertension, diabetes, and osteoporosis. The content of puerarin in Ge‐Gen is about six times higher than that in Fen‐Ge, so its use has a higher pharmacological effect. It is therefore of great importance to effectively distinguish between these two species. However, because their basal plants, P. lobata (Willd.) Ohwi and P. thomsonii Benth., possess an extremely similar appearance, and detecting the level of chemical constituents is just a rough distinction, it is necessary to develop more efficient identification approaches. Here the complete chloroplast genomes of P. lobata and P. thomsonii were deciphered, including sequencing, assembly, comparative analysis, and molecular marker development. The results showed that they are 153,393 and 153,442 bp in length, respectively; both contain 124 annotated genes, including eight encoding rRNA, 29 encoding tRNA, and 87 encoding proteins. Phylogenetic analysis showed that they form a clade, indicating that they originate from the same ancestor. After obtaining 10 intergenic/intronic regions with a genetic distance greater than 0.5 cm, primers were designed to amplify regions of high variability in P. lobata and P. thomsonii. Finally, a 60‐bp differential base fragment, located in the intron of rpl16, was developed as a molecular marker to efficiently distinguish between these two species., The content of the medicinal isoflavone puerarin in the root of Puerariae lobatae (Ge‐Gen) is about six times higher than that in Puerariae thomsonii (Fen‐Ge), but these two plants are visually indistinguishable. By deciphering the complete chloroplast genome of these two plants, the authors developed a molecular marker to efficiently distinguish between them.

Enterotoxigenic Escherichia coli (ETEC) is a leading cause of diarrheal disease in developing nations where it accounts for a significant disease burden in children between the ages of 0 to 59 months. It is also the number one bacterial causative agent of traveler's diarrhea. ETEC infects hosts through the fecal-oral route and utilizes colonization factors (CF) to adhere within the small intestine. Over 25 CFs have been identified; 7 are considered major CFs and a vaccine targeting these is predicted to provide protection against up to 66% of ETEC associated disease. Coli Surface Antigen 6 (CS6) is a major CF and is associated with disease-causing ETEC isolates. Analysis of the CS6 operon sequence led to the identification of two regions of variability among clinical isolates which we predicted exert effects on CS6 transcript and protein expression. A total of 7 recombinant E. coli strains were engineered to encode the CS6 operon in wild-type, hybrid, and mutant configurations. Western blot analysis and RT-qPCR provided evidence to support the importance of an intergenic hairpin structure on CS6 expression. Our results reveal the significance of CS6 sequence selection regarding ETEC vaccine development and present novel information regarding CS6 sequence variation in WT ETEC strains.

Background As a popular and valuable technique, grafting is widely used to protect against soil-borne diseases and nematodes in vegetable production. Growing evidences have revealed that long intergenic ncRNAs (lincRNAs) are strictly regulated and play essential roles in plants development and stress responses. Nevertheless, genome-wide identification and function deciphering of pepper lincRNAs, especially for their roles in improving grafting pepper resistance to Phytophthora capsici is largely unknown. Results In this study, RNA-seq data of grafting and control pepper plants with or without P. capsici inoculation were used to identify lincRNAs. In total, 2,388 reliable lincRNAs were identified. They were relatively longer and contained few exons than protein-coding genes. Similar to coding genes, lincRNAs had higher densities in euchromatin regions; and longer chromosome transcribed more lincRNAs. Expression pattern profiling suggested that lincRNAs commonly had lower expression than mRNAs. Totally, 607 differentially expressed lincRNAs (DE-lincRANs) were identified, of which 172 were found between P. capsici resistance grafting pepper sample GR and susceptible sample LDS. The neighboring genes of DE-lincRNAs and miRNAs competitively sponged by DE-lincRNAs were identified. Subsequently, the expression level of DE-lincRNAs was further confirmed by qRT-PCR and regulation patterns between DE-lincRNAs and neighboring mRNAs were also validated. Function annotation revealed that DE-lincRNAs increased the resistance of grafting prepper to P. capsici by modulating the expression of disease-defense related genes through cis-regulating and/or lincRNA-miRNA-mRNA interaction networks. Conclusions This study identified pepper lincRNAs and suggested their potential roles in increasing the resistance level of grafting pepper to P. capsici.

Emmer wheat (Triticum turgidum ssp. dicoccum) is an important gene source for wheat improvement but less studied in crosses with its descendant species durum (Triticum turgidum ssp. durum), especially in respect to the type of genetic components, intergenic interactions and the genetic mechanisms governing responses to drought. In this study, generation means analysis was performed using F1, F2, BC1P1 and BC1P2 from two different crosses of emmer × durum. Seeds were planted in a RCBD design with three replications under two water regimes. Results showed that there was a highly considerable difference between generations for all studied traits. The presence of significant mean parameter for all the traits, indicated the quantitative inheritance of the traits. Estimating the number of effective genes, polygenic control of the traits were confirmed. In moisture stress condition, epistatic effect for grain yield and yield-related traits illustrated the importance of epistasis in plant adaptation and performance stability. The additive × additive effect, which is fixable, was remarkable in both crosses. Under both water regimes, narrow-sense heritability was relatively high and estimates of gain from selection were positive for most of the traits. Among generations studied, the backcrosses were superior for drought tolerant indices. Based on the results, emmer wheat seems to have genetic potential for durum improvement.

Accumulating evidence indicates that specific strains of mucosa-associated Escherichia coli (E. coli) can influence the development of colorectal carcinoma. This study aimed to investigate the prevalence and characterization of mucosa-associated E. coli obtained from the colorectal cancer (CRC) patients and control group. At two referral university-affiliated hospitals in northwest Iran, 100 patients, 50 with CRC and 50 without, were studied over the course of a year. Fresh biopsy specimens were used to identify mucosa-associated E. coli isolates after dithiothreitol mucolysis. To classify the E. coli strains, ten colonies per sample were typed using enterobacterial repetitive intergenic consensus-based PCR (ERIC-PCR). The strains were classified into phylogroups using the quadruplex PCR method. The PCR method was used to examine for the presence of cyclomodulin, bfp, stx1, stx2, and eae-encoding genes. The strains were tested for biofilm formation using the microtiter plate assay. CRC patients had more mucosa-associated E. coli than the control group ( p < 0.05 ). Enteropathogenic Escherichia coli (EPEC) was also found in 23% of CRC strains and 7.1% of control strains ( p < 0.05 ). Phylogroup A was predominant in control group specimens, while E. coli isolates from CRC patients belonged most frequently to phylogroups D and B2. Furthermore, the frequency of cyclomodulin-encoding genes in the CRC patients was significantly higher than the control group. Around 36.9% of E. coli strains from CRC samples were able to form biofilms, compared to 16.6% E. coli strains from the control group ( p < 0.05 ). Noticeably, cyclomodulin-positive strains were more likely to form biofilm in comparison to cyclomodulin-negative strains ( p < 0.05 ). In conclusion, mucosa-associated E. coli especially cyclomodulin-positive isolates from B2 and D phylogroups possessing biofilm-producing capacity colonize the gut mucosa of CRC patients.

Algal symbiont shuffling in favour of more thermotolerant species has been shown to enhance coral resistance to heat-stress. Yet, the mechanistic underpinnings and long-term implications of these changes are poorly understood. This work studied the modifications in coral DNA methylation, an epigenetic mechanism involved in coral acclimatization, in response to symbiont manipulation and subsequent heat stress exposure. Symbiont composition was manipulated in the great star coral Montastraea cavernosa through controlled thermal bleaching and recovery, producing paired ramets of three genets dominated by either their native symbionts (genus Cladocopium) or the thermotolerant species (Durusdinium trenchi). Single-base genome-wide analyses showed significant modifications in DNA methylation concentrated in intergenic regions, introns and transposable elements. Remarkably, DNA methylation changes in response to heat stress were dependent on the dominant symbiont, with twice as many differentially methylated regions found in heat-stressed corals hosting different symbionts (Cladocopium vs. D. trenchii) compared to all other comparisons. Interestingly, while differential gene body methylation was not correlated with gene expression, an enrichment in differentially methylated regions was evident in repetitive genome regions. Overall, these results suggest that changes in algal symbionts favouring heat tolerant associations are accompanied by changes in DNA methylation in the coral host. The implications of these results for coral adaptation, along with future avenues of research based on current knowledge gaps, are discussed in the present work.

Long non-coding RNAs (lncRNAs) play pivot roles in regulating mRNA expression in eukaryotic organisms without coding any proteins. In the current study, a comprehensive analysis of 260 published RNA-Seq datasets collected from different tissues (fruits, leaves, stems, and roots) of Coffea arabica L. was performed to discover potential lncRNAs. A total of 10,564 unique lncRNAs were identified. Our results showed that 77.14% of the lncRNAs were intergenic and 60.39% of them are located within 5 Kbp from the partner gene. In general, all the identified lncRNAs showed shorter lengths, fewer number of exons, and lower expression levels as compared to mRNAs in different studied tissues. Several lncRNAs were determined as differentially expressed (DE) in fruits as compared to leaves, stems, or roots. The functional characterization of the DE lncRNAs revealed their roles in regulating significant biological processes in different tissues of C. arabica. The current study provides a comprehensive analysis and dataset of lncRNAs in C. arabica that could be utilized in further studies concerning the roles of these molecules in plant cells.

Rice production and quality are seriously affected by the lepidopteran pest, striped stem borer (SSB), in Northeast China. In this study, a synthetic cry1C gene encoding Bacillus thuringiensis (Bt) δ-endotoxin, which is toxic to lepidopteran pest, was transformed into a japonica rice variety (Jigeng 88) in Northeast China by Agrobacterium-mediated transformation. Through molecular detection and the Basta resistance germination assay, a total of 16 single-copy homozygous transgenic lines were obtained from 126 independent transformants expressing cry1C. Finally, four cry1C-transgenic lines (JL16, JL23, JL41, and JL42) were selected by evaluation of the Cry1C protein level, insect-resistance and agronomic traits. The cry1C-transgenic lines had higher resistance to SSB and higher yield compared with non-transgenic (NT) control plants. T-DNA flanking sequence analysis of the transgenic line JL42 showed that the cry1C gene was inserted into the intergenic region of chromosome 11, indicating that its insertion may not interfere with the genes near insertion site. In summary, this study developed four cry1C-transgenic japonica rice lines with high insect resistance and high yield. They can be used as insect-resistant germplasm materials to overcome the problem of rice yield reduction caused by SSB and reduce the use of pesticides in Northeast China.

Background Mosquitoes are important vectors of disease-causing organisms such as filarial worms, malaria parasites, and arboviruses endemic to sub-Saharan Africa including Nigeria. Malaria is a disease caused by a plasmodium parasite, transmitted by the bite of infected mosquitoes and is no doubt a public health concern. There is limited information on the genetic diversity of mosquitoes in Nigeria. This is necessary because information about the genetic diversity of mosquitoes is a very important step towards vector control and management with the aim to mitigate or eliminate burden resulting from malaria and other diseases caused by mosquitoes. In the present study, we investigated the genetic variability and relatedness of mosquitoes based on the DNA sequences of the mitochondrial cytochrome oxidase subunit I (COI) and ribosomal intergenic non-coding spacer gene regions (IGS). Mosquitoes were collected from five different states in Northcentral Nigeria, they were morphologically identified using standard keys and genomic DNA was extracted. The specific regions of interests were amplified, and the PCR products were then sequenced. Results PCR was able to successfully amplify the expected amplicon sizes of COI and IGS sequences (710 and 169) base pairs, respectively. For COI sequence, pairwise genetic distance between mosquito species ranged from 0.00 to 0.17 in the COI sequences. The pairwise genetic distance among Culex, Aedes and Anopheles species in the IGS sequences ranged from 0.000 to 0.118. Phylogenetic analysis of the sequences of the mitochondrial cytochrome oxidase subunit showed that there was genetic diversity amongst the different mosquito species sampled. It effectively showed marked differences between Culicine and Anopheline mosquitoes. Conclusions The ribosomal IGS primers used for this study only amplified Anopheles spp. However, it revealed that there is diversity among the Anopheles gambiae and Anopheles arabiensis samples collected. This study concludes that the mitochondrial COI and ribosomal IGS gene regions are reliable markers for mosquito genetic diversity study and will surely yield a reliable result for molecular diversity assessment of mosquito species.

Genome Rearrangements are events that affect large stretches of genomes during evolution. Many mathematical models have been used to estimate the evolutionary distance between two genomes based on genome rearrangements. However, most of them focused on the (order of the) genes of a genome, disregarding other important elements in it. Recently, researchers have shown that considering regions between each pair of genes, called intergenic regions, can enhance distance estimation in realistic data. Two of the most studied genome rearrangements are the reversal, which inverts a sequence of genes, and the transposition, which occurs when two adjacent gene sequences swap their positions inside the genome. In this work, we study the transposition distance between two genomes, but we also consider intergenic regions, a problem we name Sorting by Intergenic Transpositions. We show that this problem is NP-hard and propose two approximation algorithms, with factors 3.5 and 2.5, considering two distinct definitions for the problem. We also investigate the signed reversal and transposition distance between two genomes considering their intergenic regions. This second problem is called Sorting by Signed Intergenic Reversals and Intergenic Transpositions. We show that this problem is NP-hard and develop two approximation algorithms, with factors 3 and 2.5. We check how these algorithms behave when assigning weights for genome rearrangements. Finally, we implemented all these algorithms and tested them on real and simulated data.

This study investigated the role and molecular mechanisms of the long intergenic non-protein coding RNA 472 (LINC00472) in neuropathic pain using a chronic constrictive injury (CCI) rat model.CCI rat model was established and PC12 cells were induced by LPS to simulate neuropathological injury in vivo and in vitro. The levels of LINC00472, miR-300, and high mobility group box protein 1 (HMGB1) in the spinal cord tissue of CCI rats and PC12 pheochromocytoma cells were assessed by qRT-PCR and western blot. The effects of LINC00472 on neuropathic pain in the CCI rats were observed by their pain behavior. ELISA was used to detect the levels of inflammatory cytokines in rat tissues and cells. The molecular mechanisms of LINC00472 were verified by luciferase experiments, RNA immunoprecipitation, and RNA pull down assays.The expression of LINC00472 and HMGB1 were upregulated, and the expression of miR-300 was downregulated in the spinal cord tissues of CCI rats and in PC12 cells. The upregulation of LINC00472 in CCI rats significantly induced the occurrence of neuropathic pain. In addition, downregulation of LINC00472 inhibited the inflammatory response of CCI rats and PC12 cells. This study identified miR-300 as a target gene of LINC00472, and HMGB1 as the target gene of miR-300. Further experiments confirmed that the expression of anti-miR-300 could partially reverse the anti-inflammatory effects and the reduction of neuropathic pain induced by low expression of LINC00472.LINC00472 promotes the progression of neuropathic pain by reducing miR-300 expression and increasing HMGB1 expression. The LINC00472/miR-300/HMGB1 axis may be a novel therapeutic target for neuropathic pain.

Loss of the awn in some cereals, including sorghum, is a key transition during cereal domestication or improvement that has facilitated grain harvest and storage. The genetic basis of awn loss in sorghum during domestication or improvement remains unknown. Here, we identified the awn1 gene encoding a transcription factor with the ALOG domain that is responsible for awn loss during sorghum domestication or improvement. awn1 arose from a gene duplication on chromosome 10 that translocated to chromosome 3, recruiting a new promoter from the neighboring intergenic region filled with “noncoding DNA” and recreating the first exon and intron. awn1 acquired high expression after duplication and represses the elongation of awns in domesticated sorghum. Comparative mapping revealed high collinearity at the awn1 paralog locus on chromosome 10 across cereals, and awn growth and development were successfully reactivated on the rice spikelet by inactivating the rice awn1 ortholog. RNA-seq and DAP-seq revealed that as a transcriptional repressor, AWN1 bound directly to a motif in the regulatory regions of three MADS genes related to flower development and two genes, DL and LKS2, involved in awn development. AWN1 downregulates the expression of these genes, thereby repressing awn elongation. The preexistence of regulatory elements in the neighboring intergenic region of awn1 before domestication implicates that noncoding DNA may serve as a treasure trove for evolution during sorghum adaptation to a changing world. Taken together, our results suggest that gene duplication can rapidly drive the evolution of gene regulatory networks in plants.

Long intergenic non-coding RNAs (lincRNAs) belong to the category of long non-coding RNAs (lncRNAs), originated from intergenic regions, which do not code for proteins. LincRNAs perform prominent role in regulation of gene expression during plant development and stress response by directly interacting with DNA, RNA, or proteins, or triggering production of small RNA regulatory molecules. Here, we identified 2973 lincRNAs and investigated their expression dynamics during peduncle elongation in two Indian rice cultivars, Pokkali and Swarna, at the time of heading. Differential expression analysis revealed common and cultivar-specific expression patterns, which we utilized to infer the lincRNA candidates with potential involvement in peduncle elongation and panicle exsertion. Their putative targets were identified using in silico prediction methods followed by pathway mapping and literature-survey based functional analysis. Further, to infer the mechanism of action, we identified the lincRNAs which potentially act as miRNA precursors or target mimics. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01059-2.

The analysis of variability of four intergenic spacers of chloroplast DNA in the endangered closely related species of junipers — Juniperus excelsa, J. polycarpos, and J. foetidissima in the northern limits of their distribution—. Caucasus and Crimea was performed. Analysis of molecular variance (AMOVA) showed a high degree of differentiation of the three taxa (GCT = 0.9905, P < 0.0001). Seven haplotypes have been identified in total. The population of J. foetidissima from Armenia is characterized by high genetic diversity (H = 0.442); the genetic diversity was smaller in J. excelsa (H = 0.200); the J. polycarpos populations were found to be monomorphic. The studied samples, together with those included in the analysis from GenBank from the main part of the range, formed three clades corresponding to three taxa, with high statistical support.

The great importance in the development of acute intestinal obstruction (AIO) is the change in intestinal kinetics during pregnancy. In pregnant women, the rhythmic function of the intestine slows down due to an increase in the threshold of excitability of its receptors to biologically active substances. The article provides an overview of modern literary sources on the problem of acute intestinal obstruction in pregnant women. According to foreign literature sources, the incidence of intestinal obstruction in pregnant women is 1:3600–1:66000, and complications of diseases of the digestive system rank 4th among the causes of maternal mortality during pregnancy — 9%. According to domestic scientific sources, the frequency with which intestinal obstruction occurs in pregnant women is 1:40000–1:50000 births, mortality reaches 35–50%, stillbirth — 60–75%. The development of the disease is caused by physiological changes in the body of a pregnant woman. With increasing gestational age there are changes in the anatomical arrangement of the abdominal organs. From the second trimester of pregnancy, the uterus extends beyond the pelvis and gradually occupies the entire abdominal cavity. The increase in the size of the uterus due to hypertrophy and hyperplasia of muscle fibers, amniotic fluid, fetal growth, leads to increased intraabdominal pressure, displacement of the small intestine and lumbar colon up, thereby creating conditions for compression of intestinal loops, nodules, development. The modern classification, clinic, diagnostics and methods of treatment of this surgical pathology are presented. The author presents his own clinical case of acute intestinal obstruction in a 51-year-old pregnant woman with the sixth desired pregnancy, which occurred as a result of assisted reproductive technologies and a large intergenetic interval. Both surgeon and obstetrician-gynecologist treat intestinal obstruction in pregnant women. Conservative treatment is carried out simultaneously with diagnostic procedures. No effect of conservative therapy for 2 hours is an indication for surgery. The main purpose of surgery is to eliminate the causes of intestinal obstruction and restore bowel function. The scope of surgery is determined in each case individually and depends on the type of AIO and the age of the disease. The chosen tactics of the preoperative period, the volume of surgery, anesthesia and adequate management of the postoperative period can cure acute surgical pathology, maintain the desired pregnancy, avoid the development of obstetric and surgical purulent-septic complications. The research was carried out in accordance with the principles of the Helsinki declaration. The informed consent of the patient was obtained for conducting the studies. No conflict of interest was declared by the authors. Key words: sharp bowel obstruction, pregnancy, extracorporal impregnation, large intergenic interval.

The simple sequence repeats (SSRs) of plant chloroplasts show considerable genetic variation and have been widely used in species identification and phylogenetic relationship determination. Whether chloroplast genome SSRs can be used to classify Cyatheaceae species has not yet been studied. Therefore, the chloroplast genomes of eight Cyatheaceae species were sequenced, and their SSR characteristics were compared and statistically analyzed. The results showed that the chloroplast genome structure was highly conserved (genome size: 154,046–166,151 bp), and the gene content (117 genes) and gene order were highly consistent. The distribution characteristics of SSRs (number, relative abundance, relative density, GC content) showed taxon specificity. The primary results were the total numbers of SSRs and mononucleotides: Gymnosphaera (61–67 and 40–47, respectively), Alsophila (121–122 and 95–96), and Sphaeropteris (102–103 and 77–80). Statistical and clustering analyses of SSR characteristics showed that their distribution was consistent with the recent classification of Cyatheaceae, which divided the eight Cyatheaceae species into three genera. This study indicates that the distribution characteristics of Cyatheaceae chloroplast SSRs can provide useful phylogenic information at the genus level., Whether chloroplast genome SSRs can be used to classify Cyatheaceae species has not yet been studied. Therefore, the chloroplast genomes of eight Cyatheaceae species were sequenced by our team, and their SSR characteristics were compared and statistically analyzed. Statistical and clustering analyses of SSR characteristics showed that their distribution was consistent with the recent classification of Cyatheaceae, which divided the eight Cyatheaceae species into three genera.

On the basis of the analysis of the nucleotide polymorphism of the intergenic spacers psbA–trnH, trnL–trnF, and trnS–trnG of chloroplast DNA of the Oxytropis species from Asian Russia, O. tragacanthoides section Hystrix subgenus Tragacanthoxytropis, O. coerulea, O. filiformis, and O. mandshurica sect. Janthina, and O. deflexa and O. glabra sect. Mesogaea subg. Phacoxytropis, it was found that all populations are characterized by high haplotype diversity (h varies from 0.676 to 1.000), except for species of the sect. Mesogaea (h varies from 0 to 0.333). Species-specific markers were found for O. tragacanthoides, O. deflexa, O. glabra, and O. mandshurica, as well as specific markers for the sect. Mesogaea. Reconstruction of the phylogenetic relationships of the chlorotypes of the species of the subg. Phacoxytropis, Tragacanthoxytropis, and Oxytropis showed that the species of the sect. Janthina are combined into one well-supported clade with the species of the subg. Tragacanthoxytropis and Oxytropis, but their relationships remained unresolved. An analysis of the genealogical relationships of the ribotypes of the ITS of nuclear DNA revealed a common ribotype for the species O. tragacanthoides, O. coerulea, O. lanata, O. chankaensis, O. oxyphylla, and O. triphylla, belonging to three subgenera. The revealed genetic affinity with clear morphological differences is characteristic of taxa with a common origin that have experienced relatively recent rapid adaptive radiation. The obtained data on the variability of markers of the nuclear and chloroplast genomes confirm the status of O. coerulea, O. filiformis, and O. mandshurica as three separate species.

Thiopurines (e.g., 6-mercaptopurine [6MP]) are essential for the cure of acute lymphoblastic leukemia (ALL) but can cause dose-limiting hematopoietic toxicity. Germline variants in drug-metabolizing enzyme genes TPMT and NUDT15 have been linked to the risk of thiopurine toxicity. However, the full spectrum of genetic polymorphism in these genes and their impact on the pharmacological effects of thiopurines remain unclear. Herein, we comprehensively sequenced the TPMT and NUDT15 genes in 685 children with ALL from the Children’s Oncology Group AALL03N1 trial and evaluated their association with 6MP dose intensity. We identified 6 and 5 coding variants in TPMT and NUDT15 respectively, confirming the association at known pharmacogenetic variants. Importantly, we discovered a novel gain-of-function non-coding variants in TPMT associated with increased 6MP tolerance (rs12199316), with independent validation in 380 patients from the St. Jude Total Therapy XV protocol. Located adjacent to a regulatory DNA element, this inter-genic variant was strongly associated TPMT transcription, with the variant allele linked to higher expression (P = 2.6 × 10(−9)). For NUDT15, one non-coding common variant, rs73189762, was identified as potentially related to 6MP intolerance. Collectively, we described pharmacogenetic variants in TPMT and NUDT15 associated with thiopurine sensitivity, providing further insights for implementing pharmacogenetics-based thiopurine individualization.

While generally referred to as "non-integrating" vectors, adenovirus vectors have the potential to integrate into host DNA via random, illegitimate (nonhomologous) recombination. The present study provides a quantitative assessment of the potential integration frequency of adenovirus 5 (Ad5)-based vectors following intravenous injection in mice, a common route of administration in gene therapy applications particularly for transgene expression in liver. We examined the uptake level and persistence in liver of first generation (FG) and helper-dependent (HD) Ad5 vectors containing the mouse leptin transgene. As expected, the persistence of the HD vector was markedly higher than that of the FG vector. For both vectors, the majority of the vector DNA remained extrachromosomal and predominantly in the form of episomal monomers. However, using a quantitative gel-purification-based integration assay, a portion of the detectable vector was found to be associated with high molecular weight (HMW) genomic DNA, indicating potential integration with a frequency of up to ~44 and 7000 integration events per μg cellular genomic DNA (or ~0.0003 and 0.05 integrations per cell, respectively) for the FG and HD Ad5 vectors, respectively, following intravenous injection of 1 × 1011 virus particles. To confirm integration occurred (versus residual episomal vector DNA co-purifying with genomic DNA), we characterized nine independent integration events using Repeat-Anchored Integration Capture (RAIC) PCR. Sequencing of the insertion sites suggests that both of the vectors integrate randomly, but within short segments of homology between the vector breakpoint and the insertion site. Eight of the nine integrations were in intergenic DNA and one was within an intron. These findings represent the first quantitative assessment and characterization of Ad5 vector integration following intravenous administration in vivo in wild-type mice.