BMC Molecular Biology最新文献

{"title":"HexA is required for growth, aflatoxin biosynthesis and virulence in Aspergillus flavus","authors":"Jun Yuan,&nbsp;Ding Li,&nbsp;Ling Qin,&nbsp;Jiaojiao Shen,&nbsp;Xiaodong Guo,&nbsp;Elisabeth Tumukunde,&nbsp;Mingzhu Li,&nbsp;Shihua Wang","doi":"10.1186/s12867-019-0121-3","DOIUrl":"https://doi.org/10.1186/s12867-019-0121-3","url":null,"abstract":"<p>Woronin bodies are fungal-specific organelles whose formation is derived from peroxisomes. The former are believed to be involved in the regulation of mycotoxins biosynthesis, but not in their damage repair function. The hexagonal peroxisome protein (HexA or Hex1) encoded by <i>hexA</i> gene in <i>Aspergillus</i> is the main and the essential component of the Woronin body. However, little is known about HexA in <i>Aspergillus flavus</i>.</p><p>In this study, <i>hexA</i> knock-out mutant (Δ<i>hexA</i>) and complementation strain (Δ<i>hexA</i>^C) were produced using homologous recombination. The results showed that, Δ<i>hexA</i> and Δ<i>hexA</i>^C were successfully constructed. And the data analysis indicated that the colony diameter, stress sensitivity and the sclerotia formation of <i>A. flavu</i>s were nearly not affected by the absence of HexA. Yet, the deletion of <i>hexA</i> gene reduced the production of asexual spores and lessened virulence on peanuts and maize seeds markedly. In addition, it was also found that there was a significant decrease of Aflatoxin B1 production in deletion mutant, when compared to wild type.</p><p>Therefore, it suggested that the <i>hexA</i> gene has an essential function in conidia production and secondary metabolism in <i>A. flavus</i>. The gene is also believed to be playing an important role in the invasion of <i>A. flavus</i> to the host.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"20 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2019-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-019-0121-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4453750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification of brain miRNAs in response to high-intensity intermittent swimming training in Rattus norvegicus by deep sequencing","authors":"Yanhong Zhao,&nbsp;Anmin Zhang,&nbsp;Yanfang Wang,&nbsp;Shuping Hu,&nbsp;Ruiping Zhang,&nbsp;Shuaiwei Qian","doi":"10.1186/s12867-019-0120-4","DOIUrl":"https://doi.org/10.1186/s12867-019-0120-4","url":null,"abstract":"<p>Physical exercise can improve brain function by altering brain gene expression. The expression mechanisms underlying the brain’s response to exercise still remain unknown. miRNAs as vital regulators of gene expression may be involved in regulation of brain genes in response to exercise. However, as yet, very little is known about exercise-responsive miRNAs in brain.</p><p>We constructed two comparative small RNA libraries of rat brain from a high-intensity intermittent swimming training (HIST) group and a normal control (NC) group. Using deep sequencing and bioinformatics analysis, we identified 2109 (1700 from HIST, 1691 from NC) known and 55 (50 from HIST, 28 from NC) novel candidate miRNAs. Among them, 34 miRNAs were identified as significantly differentially expressed in response to HIST, 16 were up-regulated and 18 were down-regulated. The results showed that all members of mir-200 family were strongly up-regulated, implying mir-200 family may play very important roles in HIST response mechanisms of rat brain. A total of 955 potential target genes of these 34 exercise-responsive miRNAs were identified from rat genes. Most of them are directly involved in the development and regulatory function of brain or nerve. Many acknowledged exercise-responsive brain genes such as <i>Bdnf</i>, <i>Igf</i>-<i>1</i>, <i>Vgf</i>, <i>Ngf c</i>-<i>Fos,</i> and <i>Ntf3</i> etc. could be targeted by exercise-responsive miRNAs. Moreover, qRT-PCR and SABC immunohistochemical analysis further confirm the reliability of the expression of miRNAs and their targets.</p><p>This study demonstrated that physical exercise could induce differential expression of rat brain miRNAs and 34 exercise-responsive miRNAs were identified in rat brain. Our results suggested that exercise-responsive miRNAs could play important roles in regulating gene expression of rat brain in response to exercise.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"20 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2019-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-019-0120-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4608335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MiRNAs differentially expressed in skeletal muscle of animals with divergent estimated breeding values for beef tenderness","authors":"Berna I. G. Kappeler,&nbsp;Luciana C. A. Regitano,&nbsp;Mirele D. Poleti,&nbsp;Aline S. M. Cesar,&nbsp;Gabriel C. M. Moreira,&nbsp;Gustavo Gasparin,&nbsp;Luiz L. Coutinho","doi":"10.1186/s12867-018-0118-3","DOIUrl":"https://doi.org/10.1186/s12867-018-0118-3","url":null,"abstract":"<p>MicroRNAs (miRNAs) are small noncoding RNAs of approximately 22 nucleotides, highly conserved among species, which modulate gene expression by cleaving messenger RNA target or inhibiting translation. MiRNAs are involved in the regulation of many processes including cell proliferation, differentiation, neurogenesis, angiogenesis, and apoptosis. Beef tenderness is an organoleptic characteristic of great influence in the acceptance of meat by consumers. Previous studies have shown that collagen level, marbling, apoptosis and proteolysis are among the many factors that affect beef tenderness. Considering that miRNAs can modulate gene expression, this study was designed to identify differentially expressed miRNAs that could be modulating biological processes involved with beef tenderness.</p><p>Deep sequence analysis of miRNA libraries from <i>longissimus thoracis</i> muscle allowed the identification of 42 novel and 308 known miRNAs. Among the known miRNAs, seven were specifically expressed in skeletal muscle. Differential expression analysis between animals with high (H) and low (L) estimated breeding values for shear force (EBVSF) revealed bta-mir-182 and bta-mir-183 are up-regulated (q value?&lt;?0.05) in animals with L EBVSF, and bta-mir-338 is up-regulated in animals with H EBVSF. The number of bovine predicted targets for bta-mir-182, bta-mir-183 and bta-mir-338 were 811, 281 and 222, respectively, which correspond to 1204 unique target genes. Among these, four of them, <i>MEF2C</i>, <i>MAP3K2</i>, <i>MTDH</i> and <i>TNRC6B</i> were common targets of the three differentially expressed miRNAs. The functional analysis identified important pathways related to tenderness such as apoptosis and the calpain–calpastatin system.</p><p>The results obtained indicate the importance of miRNAs in the regulatory mechanisms that influence muscle proteolysis and meat tenderness and contribute to our better understanding of the role of miRNAs in biological processes associated with beef tenderness.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"20 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2019-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-018-0118-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4119594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Graphene oxide down-regulates genes of the oxidative phosphorylation complexes in a glioblastoma","authors":"Maciej Szmidt,&nbsp;Adrian Stankiewicz,&nbsp;Kaja Urbańska,&nbsp;Sławomir Jaworski,&nbsp;Marta Kutwin,&nbsp;Mateusz Wierzbicki,&nbsp;Marta Grodzik,&nbsp;Beata Burzyńska,&nbsp;Monika Góra,&nbsp;André Chwalibog,&nbsp;Ewa Sawosz","doi":"10.1186/s12867-018-0119-2","DOIUrl":"https://doi.org/10.1186/s12867-018-0119-2","url":null,"abstract":"<p>Recently different forms of nanographene were proposed as the material with high anticancer potential. However, the mechanism of the suppressive activity of the graphene on cancer development remains unclear. We examined the effect of oxygenated, reduced and pristine graphene on the gene expression in glioblastoma U87 cell line.</p><p>Conducting microarrays and RT-qPCR analysis we explored that graphene oxide (rather than reduced graphene oxide and pristine graphene) down-regulates the mRNA expression of mitochondrial oxidative phosphorylation (OXPHOS) nuclear genes of complexes I, III, IV and V. The presented results provide first evidence for the hypothesis that the suppressed growth of GBM can be the consequence of down-regulation of OXPHOS protein expression and decreased ATP level.</p><p>We suggest that changes in the expression of OXPHOS genes identified in our study may mediate the anti-proliferative and anti-migratory effects of graphene oxide in glioblastoma cells. However, further investigations with different cell lines, regarding expression, regulation and activity of OXPHOS genes identified in our study is necessary to elucidate the mechanism mediating the anti-proliferative and anti-migratory effects of graphene oxide in glioblastoma cells.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"20 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2019-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-018-0119-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4119593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Dictyostelium discoideum homologue of Twinkle, Twm1, is a mitochondrial DNA helicase, an active primase and promotes mitochondrial DNA replication","authors":"Ashley Harman,&nbsp;Christian Barth","doi":"10.1186/s12867-018-0114-7","DOIUrl":"https://doi.org/10.1186/s12867-018-0114-7","url":null,"abstract":"<p>DNA replication requires contributions from various proteins, such as DNA helicases; in mitochondria Twinkle is important for maintaining and replicating mitochondrial DNA. Twinkle helicases are predicted to also possess primase activity, as has been shown in plants; however this activity appears to have been lost in metazoans. Given this, the study of Twinkle in other organisms is required to better understand the evolution of this family and the roles it performs within mitochondria.</p><p>Here we describe the characterization of a Twinkle homologue, Twm1, in the amoeba <i>Dictyostelium discoideum</i>, a model organism for mitochondrial genetics and disease. We show that Twm1 is important for mitochondrial function as it maintains mitochondrial DNA copy number in vivo. Twm1 is a helicase which unwinds DNA resembling open forks, although it can act upon substrates with a single 3′ overhang, albeit less efficiently. Furthermore, unlike human Twinkle, Twm1 has primase activity in vitro. Finally, using a novel in bacterio approach, we demonstrated that Twm1 promotes DNA replication.</p><p>We conclude that Twm1 is a replicative mitochondrial DNA helicase which is capable of priming DNA for replication. Our results also suggest that non-metazoan Twinkle could function in the initiation of mitochondrial DNA replication. While further work is required, this study has illuminated several alternative processes of mitochondrial DNA maintenance which might also be performed by the Twinkle family of helicases.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"19 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2018-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-018-0114-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4742815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Matrix association region/scaffold attachment region (MAR/SAR) sequence: its vital role in mediating chromosome breakages in nasopharyngeal epithelial cells via oxidative stress-induced apoptosis","authors":"Sang-Nee Tan,&nbsp;Sai-Peng Sim,&nbsp;Alan S. B. Khoo","doi":"10.1186/s12867-018-0116-5","DOIUrl":"https://doi.org/10.1186/s12867-018-0116-5","url":null,"abstract":"<p>Oxidative stress is known to be involved in most of the aetiological factors of nasopharyngeal carcinoma (NPC). Cells that are under oxidative stress may undergo apoptosis. We have previously demonstrated that oxidative stress-induced apoptosis could be a potential mechanism mediating chromosome breakages in nasopharyngeal epithelial cells. Additionally, caspase-activated DNase (CAD) may be the vital player in mediating the chromosomal breakages during oxidative stress-induced apoptosis. Chromosomal breakage occurs during apoptosis and chromosome rearrangement. Chromosomal breakages tend to cluster in certain regions, such as matrix association region/scaffold attachment region (MAR/SAR). We hypothesised that oxidative stress-induced apoptosis may result in chromosome breaks preferentially at the MAR/SAR sites. The <i>AF9</i> gene at 9p22 was targeted in this study because 9p22 is a deletion site commonly found in NPC.</p><p>By using MAR/SAR recognition signature (MRS), potential MAR/SAR sites were predicted in the <i>AF9</i> gene. The predicted MAR/SAR sites precisely match to the experimentally determined MAR/SARs. Hydrogen peroxide (H₂O₂) was used to induce apoptosis in normal nasopharyngeal epithelial cells (NP69) and NPC cells (HK1). Nested inverse polymerase chain reaction was employed to identify the <i>AF9</i> gene cleavages. In the SAR region, the gene cleavage frequency of H₂O₂-treated cells was significantly higher than that of the non-treated cells. A few chromosomal breakages were detected within the <i>AF9</i> region which was previously found to be involved in the mixed lineage leukaemia?(<i>MLL</i>)-<i>AF9</i> translocation in an acute lymphoblastic leukaemia patient. As for the non-SAR region, no significant difference in the gene cleavage frequency was found between the untreated control and H₂O₂-treated cells. Furthermore, H₂O₂-induced cleavages within the SAR region were reduced by caspase-3 inhibitor, which indirectly inhibits CAD.</p><p>These results reaffirm our previous findings that oxidative stress-induced apoptosis could be one of the potential mechanisms underlying chromosome breakages in nasopharyngeal epithelial cells. MAR/SAR may play a vital role in defining the location of chromosomal breakages mediated by oxidative stress-induced apoptosis, where CAD is the major nuclease.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"19 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2018-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-018-0116-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4495156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular analysis of NPAS3 functional domains and variants","authors":"Leiah M. Luoma,&nbsp;Fred B. Berry","doi":"10.1186/s12867-018-0117-4","DOIUrl":"https://doi.org/10.1186/s12867-018-0117-4","url":null,"abstract":"<p><i>NPAS3</i> encodes a transcription factor which has been associated with multiple human psychiatric and neurodevelopmental disorders. In mice, deletion of <i>Npas3</i> was found to cause alterations in neurodevelopment, as well as a marked reduction in neurogenesis in the adult mouse hippocampus. This neurogenic deficit, alongside the reduction in cortical interneuron number, likely contributes to the behavioral and cognitive alterations observed in <i>Npas3</i> knockout mice. Although loss of Npas3 has been found to affect proliferation and apoptosis, the molecular function of NPAS3 is largely uncharacterized outside of predictions based on its high homology to bHLH–PAS transcription factors. Here we set out to characterize NPAS3 as a transcription factor, and to confirm whether NPAS3 acts as predicted for a Class 1 bHLH–PAS family member.</p><p>Through these studies we have experimentally demonstrated that NPAS3 behaves as a true transcription factor, capable of gene regulation through direct association with DNA. NPAS3 and ARNT are confirmed to directly interact in human cells through both bHLH and PAS dimerization domains. The C-terminus of NPAS3 was found to contain a functional transactivation domain. Further, the NPAS3::ARNT heterodimer was shown to directly regulate the expression of <i>VGF</i> and <i>TXNIP</i> through binding of their proximal promoters. Finally, we assessed the effects of three human variants of NPAS3 on gene regulatory function and do not observe significant deficits.</p><p>NPAS3 is a true transcription factor capable of regulating expression of target genes through their promoters by directly cooperating with ARNT. The tested human variants of NPAS3 require further characterization to identify their effects on NPAS3 expression and function in the individuals that carry them. These data enhance our understanding of the molecular function of NPAS3 and the mechanism by which it contributes to normal and abnormal neurodevelopment and neural function.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"19 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2018-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-018-0117-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4113270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integration of transcriptome and proteome profiles in glioblastoma: looking for the missing link","authors":"Jean-Michel Lemée,&nbsp;Anne Clavreul,&nbsp;Marc Aubry,&nbsp;Emmanuelle Com,&nbsp;Marie de Tayrac,&nbsp;Jean Mosser,&nbsp;Philippe Menei","doi":"10.1186/s12867-018-0115-6","DOIUrl":"https://doi.org/10.1186/s12867-018-0115-6","url":null,"abstract":"<p>Glioblastoma (GB) is the most common and aggressive tumor of the brain. Genotype-based approaches and independent analyses of the transcriptome or the proteome have led to progress in understanding the underlying biology of GB. Joint transcriptome and proteome profiling may reveal new biological insights, and identify pathogenic mechanisms or therapeutic targets for GB therapy. We present a comparison of transcriptome and proteome data from five GB biopsies (TZ) vs their corresponding peritumoral brain zone (PBZ). Omic analyses were performed using RNA microarray chips and the isotope-coded protein label method (ICPL).</p><p>As described in other cancers, we found a poor correlation between transcriptome and proteome data in GB. We observed only two commonly deregulated mRNAs/proteins (neurofilament light polypeptide and synapsin 1) and 12 altered biological processes; they are related to cell communication, synaptic transmission and nervous system processes. This poor correlation may be a consequence of the techniques used to produce the omic profiles, the intrinsic properties of mRNA and proteins and/or of cancer- or GB-specific phenomena. Of interest, the analysis of the transcription factor binding sites present upstream from the open reading frames of all altered proteins identified by ICPL method shows a common binding site for the topoisomerase I and p53-binding protein TOPORS. Its expression was observed in 7/11 TZ samples and not in PBZ. Some findings suggest that TOPORS may function as a tumor suppressor; its implication in gliomagenesis should be examined in future studies.</p><p>In this study, we showed a low correlation between transcriptome and proteome data for GB samples as described in other cancer tissues. We observed that NEFL, SYN1 and 12 biological processes were deregulated in both the transcriptome and proteome data. It will be important to analyze more specifically these processes and these two proteins to allow the identification of new theranostic markers or potential therapeutic targets for GB.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"19 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2018-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-018-0115-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4835952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analyses of changes in myocardial long non-coding RNA and mRNA profiles after severe hemorrhagic shock and resuscitation via RNA sequencing in a rat model","authors":"Lin Lin,&nbsp;Zhengfei Yang,&nbsp;Guanghui Zheng,&nbsp;Yongxun Zhuansun,&nbsp;Yue Wang,&nbsp;Jianguo Li,&nbsp;Rui Chen,&nbsp;Wanchun Tang","doi":"10.1186/s12867-018-0113-8","DOIUrl":"https://doi.org/10.1186/s12867-018-0113-8","url":null,"abstract":"<p>Ischemia–reperfusion injury has been proven to induce organ dysfunction and death, although the mechanism is not fully understood. Long non-coding RNAs (lncRNAs) have drawn wide attention with their important roles in the gene expression of some biological processes and diseases, including myocardial ischemia–reperfusion (I/R) injury. In this paper, a total of 26 Sprague–Dawley (SD) rats were randomized into two groups: sham and ischemia–reperfusion (I/R) injury. Hemorrhagic shock was induced by removing 45% of the estimated total blood volume followed by reinfusion of shed blood. High-throughput RNA sequencing was used to analyze differentially expressed (DE) lncRNAs and messenger RNAs (mRNAs) in the heart tissue 4?h after reperfusion. Myocardial function was also evaluated.</p><p>After resuscitation, the decline of myocardial function of shocked animals, expressed by cardiac output, ejection fraction, and myocardial performance index (MPI), was significant (p?&lt;?0.05). DE lncRNAs and mRNAs were identified by absolute value of fold change?≥?2 and the false discovery rate ≤?0.001. In rats from the I/R injury group, 851 lncRNAs and 1015 mRNAs were significantly up-regulated while 1533 lncRNAs and 1702?m RNAs were significantly down-regulated when compared to the sham group. Among the DE lncRNAs, we found 12 location-associated with some known apoptosis-related protein-coding genes which were up-regulated or down-regulated accordingly, including STAT3 and Il1r1. Real time PCR assays confirmed that the expression levels of five location-associated lncRNAs (NONRATT006032.2, NONRATT006033.2, NONRATT006034.2, NONRATT006035.2 and NONRATT029969.2) and their location-associated mRNAs (STAT3 and Il1r1) in the rats from the I/R injury group were all significantly up-regulated versus the sham group.</p><p>The DE lncRNAs (NONRATT006032.2, NONRATT006033.2, NONRATT006034.2 and NONRATT006035.2) could be compatible with their role in myocardial protection by stimulating their co-located gene (STAT3) after hemorrhagic shock and resuscitation. The final prognosis of I/R injury might be regulated by different genes, which is regarded as a complex network.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"19 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2018-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-018-0113-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4051770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis","authors":"Paola M. Boggiatto,&nbsp;Daniel Fitzsimmons,&nbsp;Darrell O. Bayles,&nbsp;David Alt,&nbsp;Catherine E. Vrentas,&nbsp;Steven C. Olsen","doi":"10.1186/s12867-018-0111-x","DOIUrl":"https://doi.org/10.1186/s12867-018-0111-x","url":null,"abstract":"<p><i>Brucella melitensis</i> bacteria cause persistent, intracellular infections in small ruminants as well as in humans, leading to significant morbidity and economic loss worldwide. The majority of experiments on the transcriptional responses of <i>Brucella</i> to conditions inside the host have been performed following invasion of cultured mammalian cells, and do not address gene expression patterns during long-term infection.</p><p>Here, we examine the application of the previously developed coincidence cloning methodology to recover and characterize <i>B. melitensis</i> RNA from the supramammary lymph node of experimentally-infected goats. Using coincidence cloning, we successfully recovered <i>Brucella</i> RNA from supramammary lymph nodes of <i>B. melitensis</i>-infected goats at both short-term (4?weeks) and long-term (38?weeks) infection time points. Amplified nucleic acid levels were sufficient for analysis of <i>Brucella</i> gene expression patterns by RNA-sequencing, providing evidence of metabolic activity in both the short-term and the long-term samples. We developed a workflow for the use of sequence polymorphism analysis to confirm recovery of the inoculated strain in the recovered reads, and utilized clustering analysis to demonstrate a distinct transcriptional profile present in samples recovered in long-term infection. In this first look at <i>B. melitensis</i> gene expression patterns in vivo, the subset of <i>Brucella</i> genes that was highly upregulated in long-term as compared to short-term infection included genes linked to roles in murine infection, such as genes involved in proline utilization and signal transduction. Finally, we demonstrated the challenges of qPCR validation of samples with very low ratios of pathogen:host RNA, as is the case during in vivo brucellosis, and alternatively characterized intermediate products of the coincidence cloning reaction.</p><p>Overall, this study provides the first example of recovery plus characterization of <i>B. melitensis</i> RNA from in vivo lymph node infection, and demonstrates that the coincidence cloning technique is a useful tool for characterizing in vivo transcriptional changes in <i>Brucella</i> species. Genes upregulated in long-term infection in this data set, including many genes not previously demonstrated to be virulence factors in mice or macrophage experiments, are candidates of future interest for potential roles in <i>Brucella</i> persistence in natural host systems.</p>","PeriodicalId":497,"journal":{"name":"BMC Molecular Biology","volume":"19 1","pages":""},"PeriodicalIF":2.946,"publicationDate":"2018-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12867-018-0111-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4006827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}