hsa-miR-29c and hsa-miR-135b differential expression aspotential biomarker of gastric carcinogenesis

AIM: To investigate the expression profiles of hsa-mi R-29 c and hsa-mi R-135 b in gastric mucosal samples and their values as gastric carcinogenesis biomarkers. METHODS: The expression levels of hsa-mi R-29 c and hsa-mi R-135 b in normal gastric mucosa, non-atrophic chronic gastritis, intestinal metaplasia and intestinaltype gastric adenocarcinoma were analysed using quantitative real-time PCR. The difference between hsa-mi R-29 c and hsa-mi R-135 b expression profiles in the grouped samples was evaluated by ANOVA and Student's t-test tests. The results were adjusted for multiple testing by using Bonferroni's correction. P values ≤ 0.05 were considered statistically significant. To evaluate hsa-mi R-29 c and hsa-mi R-135 b expressions as potential biomarkers of gastric carcinogenesis, we performed a receiver operating characteristic curve analysis and the derived area under the curve, and a Categorical Principal Components Analysis. In silico identification of the genetic targets of hsa-mi R-29 c and hsa-mi R-135 b was performed using different prediction tools, in order to identify possible genes involved in gastric carcinogenesis.RESULTS: The expression levels of hsa-mi R-29 c were higher in normal gastric mucosal samples, and decreased progressively in non-atrophic chronic gastritis samples, intestinal metaplasia samples and intestinal-type gastric adenocarcinoma samples. The expression of hsa-mi R-29 c in the gastric lesions showed that non-atrophic gastritis have an intermediate profile to gastric normal mucosa and intestinal-type gastric adenocarcinoma, and that intestinal metaplasia samples presented an expression pattern similar to that in intestinal-type gastric adenocarcinoma. This micro RNA(mi RNA) has a good discriminatory accuracy between normal gastric samples and(1) intestinal-type gastric adenocarcinoma; and(2) intestinal metaplasia, and regulates the DMNT3 A oncogene. hsa-mi R-135 b is up-regulated in non-atrophic chronic gastritis and intestinal metaplasia samples and down-regulated in normal gastric mucosa and intestinal-type gastric adenocarcinoma samples. Non-atrophic chronic gastritis and intestinal metaplasia are significantly different from normal gastric mucosa samples. hsa-mi R-135 b expression presented a greater discriminatory accuracy between normal samples and gastric lesions. This mi RNA was associated with Helicobacter pylori presence in non-atrophic chronic gastritis samples and regulates the APC and KLF4 tumour suppressor genes.CONCLUSION: Our results provide evidence of epigenetic alterations in non-atrophic chronic gastritis and intestinal metaplasia and suggest that hsa-mi R-29 c and hsa-mi R-135 b are promising biomarkers of gastric carcinogenesis.

Value of a newly sequenced bacterial genome

Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft(partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.

The Long Way from Complex Phenotypes to Genes: The Story of Rat Chromosome 4 and Its Behavioral Effects

Quantitative trait loci (QTLs) mapping has been performed during the past decades in an attempt to identify genes, gene products and mechanisms underlying numerous quantitative traits. It’s a strategy based on natural variations in genes and gene products, which facilitates translation from animal models to human clinical conditions. Our team has shown that the inbred rat strains Lewis (LEW) and Spontaneously Hypertensive Rats (SHR) differ with respect to several emotionality- related behaviors, one of which (inner locomotion in the open field) was strongly influenced by a QTL (Anxrr16) on rat chromosome 4. Since then, several other studies not only corroborated the initial description of Anxrr16, but also extrapolated its effects to a broader context (rats from both sexes and regardless of the estrous cycle phase) and suggested that this same region influences other emotionality-related behaviors as well as alcohol intake. Other QTLs affecting neurobiological traits were also found on rat chromosome 4 and several candidate genes have been pointed out as possibly influencing those phenotypes. Altogether, these studies suggest that rat chromosome 4 constitutes an interesting target for the study of the molecular bases of anxiety and other traits related to emotional reactivity.

Helicobacter pylori and its reservoirs:A correlation with the gastric infection

Helicobacter pylori(H. pylori) has long been found to cause gastric diseases such as gastritis, gastric ulcers and gastric cancer. The transmission medium of this bacterium has yet to be determined, though several studies have speculated that the oral cavity is a reservoir for H. pylori. Others have also reported that the oral cavity may be a source of both transmission and gastric reinfection; however, such results are controversial. We reviewed the literature and selected studies that report an association among H. pylori detections in the oral cavity(dental plaque, saliva, tongue, tonsil tissue, root canals, oral mucosa) in humans and in animals, as well as in the human stomach. The oral cavity may be considered the main reservoir for H. pylori. There are a correlations between H. pylori infection in the oral cavity and periodontal disease, oral tissue inflammation, H. pylori transmission, and gastric reinfection. We believe that the mouth is a reservoir and that it plays a crucial role in both H. pylori transmission and gastric infection.

Association of insertion-deletions polymorphisms with colorectal cancer risk and clinical features

AIM To investigate the association between 16 insertiondeletions(INDEL) polymorphisms, colorectal cancer(CRC) risk and clinical features in an admixed population.METHODS O n e h u n d re d a n d fo r ty p a t i e n t s w i t h C R C a n d 140 cancer-free subjects were examined. Genomic DNA was extracted from peripheral blood samples. Polymorphisms and genomic ancestry distribution were assayed by Multiplex-PCR reaction, separated by capillary electrophoresis on the ABI 3130 Genetic Analyzer instrument and analyzed on Gene Mapper ID v3.2. Clinicopathological data were obtained by consulting the patients' clinical charts, intra-operative documentation, and pathology scoring.RESULTS Logistic regression analysis showed that polymorphism variations in IL4 gene was associated with increased CRC risk, while TYMS and UCP2 genes were associated with decreased risk. Reference to anatomical localization of tumor Del allele of NFKB1 and CASP8 were associated with more colon related incidents than rectosigmoid. In relation to the INDEL association with tumor node metastasis(TNM) stage risk, the Ins alleles of ACE, HLAG and TP53(6 bp INDEL) were associated with higher TNM stage. Furthermore, regarding INDEL association with relapse risk, the Ins alleles of ACE, HLAG, and UGT1A1 were associated with early relapse risk, as well as the Del allele of TYMS. Regarding INDEL association with death risk before 10 years, the Ins allele of SGSM3 and UGT1A1 were associated with death risk.CONCLUSION The INDEL variations in ACE, UCP2, TYMS, IL4, NFKB1, CASP8, TP53, HLAG, UGT1A1, and SGSM3 were associated with CRC risk and clinical features in an admixed population. These data suggest that this cancer panel might be useful as a complementary tool for better clinical management, and more studies need to be conducted to confirm these findings.

Stability of Brazilian Seasonally Dry Forests under Climate Change: Inferences for Long-Term Conservation

We identified climatically stable areas of seasonally dry forests (SDFs) from Central Brazil through time and assessed the effectiveness of the current reserves network in representing these climatically stable areas, as well as areas of high suitability in the present or in the future only. We used an ensemble approach based on several methods for ecological niche modelling (ENMs) to obtain potential distributions 16 SDF’ species for past (last glacial maximum), present, and future (end of XXI century) climate scenarios. We then computed how many current Brazilian reserves matched both stable areas (suitable areas for all time periods), present and future geographical ranges alone for each species, in a multi-level gap analysis. We found range shifts due to climate changes for SDF’ species. Although the future geographical range and stable areas for all analyzed species matched at least with one reserve, many protected areas will lose importance in protecting suitable areas for species in the future. Moreover, the current Brazilian reserves cover only a small amount of their climatically stable areas. However, some reserves will be suitable for many SDF’ species (90%) at the same time, but climatically stable for only half of them. Our findings show that vegetation community from SDFs may persist in Brazilian territories until the end of XXI century, and challenges about long-term conservation of the SDFs may be partially reached with already existing Brazilian reserve network, however the reserves should be connected to permit habitat tracking.

Analysis of 12 variants in the development of gastric and colorectal cancers

AIM To evaluate the relation between 12 polymorphisms and the development of gastric cancer(GC) and colorectal cancer(CRC).METHODS In this study,we included 125 individuals with GC diagnosis,66 individuals with CRC diagnosis and 475 cancer-free individuals. All participants resided in the North region of Brazil and authorized the use of their samples. The 12 polymorphisms(in CASP8,CYP2 E1,CYP19 A1,IL1 A,IL4,MDM2,NFKB1,PAR1,TP53,TYMS,UGT1 A1 and XRCC1 genes) were genotyped in a single PCR for each individual,followed by fragment analysis. To avoid misinterpretation due to population substructure,we applied a previously developed set of 61 ancestryinformative markers that can also be genotyped by multiplex PCR. The statistical analyses were performed in Structure v.2.3.4,R environment and SPSS v.20.RESULTS After statistical analyses with the control of confounding factors,such as genetic ancestry,three markers(rs79071878 in IL4,rs3730485 in MDM2 and rs28362491 in NFKB1) were positively associated with the development of GC. One of these markers(rs28362491) and the marker in the UGT1 A1 gene(rs8175347) were positively associated with the development of CRC. Therefore,we investigated whether the joint presence of the deleterious alleles of each marker could affect the development of cancer and we obtained positive results in all analyses. Carriers of the combination of alleles RP1 + DEL(rs79071878 and rs28361491,respectively) are at 10-times greater risk of developing GC than carriers of other combinations. Similarly,carriers of the combination of DEL + RARE(rs283628 and rs8175347) are at about 12-times greater risk of developing CRC than carriers of other combinations.CONCLUSION These findings are important for the comprehension of gastric and CRC development,particularly in highly admixed populations,such as the Brazilian population.

An inter-laboratory study of DNA-based identity,parentage and species testing in animal forensic genetics

The probative value of animal forensic genetic evidence relies on laboratory accuracy and reliability.Inter-laboratory comparisons allow laboratories to evaluate their performance on specific tests and analyses and to continue to monitor their output.The International Society for Animal Genetics(ISAG)administered animal forensic comparison tests(AFCTs)in 2016 and 2018 to assess the limitations and capabilities of laboratories offering forensic identification,parentage and species determination services.The AFCTs revealed that analyses of low DNA template concentrations(≤300 pg/μL)constitute a significant challenge that has prevented many laboratories from reporting correct identification and parentage results.Moreover,a lack of familiarity with species testing protocols,interpretation guidelines and representative databases prevented over a quarter of the participating laboratories from submitting correct species determination results.Several laboratories showed improvement in their genotyping accuracy over time.However,the use of forensically validated standards,such as a standard forensic short tandem repeat(STR)kit,preferably with an allelic ladder,and stricter guidelines for STR typing,may have prevented some common issues from occurring,such as genotyping inaccuracies,missing data,elevated stutter products and loading errors.The AFCTs underscore the importance of conducting routine forensic comparison tests to allow laboratories to compare results from each other.Laboratories should keep improving their scientific and technical capabilities and continuously evaluate their personnel’s proficiency in critical techniques such as low copy number(LCN)analysis and species testing.Although this is the first time that the ISAG has conducted comparison tests for forensic testing,findings from these AFCTs may serve as the foundation for continuous improvements of the overall quality of animal forensic genetic testing.

Endophytic Mycobiota Characterization of the Amazonian Mistletoe Cladocolea micrantha Hosted in Cashew Tree

Endophytic fungi were identified from different parts of the medicinal parasitic mistletoe Cladocolea micrantha and from its host Anacardium occidentale, suggesting a strict host-parasite relationship. Eight fungal endophytes were isolated and morphologically characterized. The ascomycete Guignardia mangiferae and strains of Mycelia sterilia were prevalent in the isolations. The unequivocal identification of Guignardia mangiferae at a probabilistic degree close to 100% was carried out by DNA extraction followed by PCR analyses of the ITS-1 and ITS-2 regions and comparison of the genetic sequence with the NCBI database.