Design of a data set of qPCR primers for the early region of Human Papillomavirus oncogenic types 16 and 18.

High-Risk Human Papillomavirus (HR-HPV) types 16 and 18 are estimated to be responsible for 72.4% of all HPV-related cancers worldwide in both men and women, including cervical, anal, penile, vulval, vaginal and head and neck cancers [1]. Important efforts worldwide have devoted to the study of these genotypes, throughout epidemiology and basic science approaches. Of particular interest are the genes from the early region (E), coding non-structural proteins. Early genes E1 and E2 products are involved in replication and transcription regulation, while E6 and E7 proteins are recognised for their oncogenic potential. In this data report, we described a set of primers based on reference sequences from HPV16 and HPV18 designed to cover the early region of these oncogenic genotypes. The design was based on multiple sequences alignment to identify the less conserved regions along the open reading frames (ORFs) E6, E7, E1 and E2. The design allows a highly stringent real time PCR essay ranged from 123 to 598 bp overlapping products for HPV16 (12 products in total) and from 183 to 526 bp for HPV18 (11 products in total), both spanning the early genomic region. The high annealing temperatures (Ta) and regions selected for primer bind were intended for genotypic specificity, without compromising the qPCR amplification efficiency (≥ 90%). Evaluation of qPCR conditions for primer set was performed using DNA standards as controls, generated from the HPV16 and 18 genomes clones. This provides relevant information for further multiple quantitative real-time PCR analysis (qPCR), using the SYBR green chemistry, which is is more affordable than generating multiple fluorescently labeled probes.

[Molecular detection of human papillomavirus among patients with benign prostatic hyperplasia and prostate cáncer.] / Detección molecular del virus de papiloma humano en pacientes con hiperplasia prostática benigna y cáncer de próstata.

OBJECTIVE: To analyze the presenceof human papillomavirus in prostate and its associationwith prostate cancer. METHODS: A case-control study was conducted.Tissue samples with benign hyperplasia and prostatecancer were collected. Risk factors related to prostatecancer and human papillomavirus were assessedby a medical interview. Prostate tissue was obtainedby transrectal biopsy or transurethral resection. Theidentification of viral genome was assessed by the amplificationof 450 pb., from L1 gene. Real time PCR wasused to identified HPV genotypes 16 and 18. For dataanalysis, the χ2 test, Student's T test or Mann-WhitneyU test and OR were computed. RESULTS: Thirty and 99 with benign prostatehyperplasia were included in a 1:3 ratio, with a meanage of 69.44±9.22 years. The global prevalence of humanpapillomavirus was 15.2% being similar in bothcases (15.6%) and controls (15.1%) with no significantdifference (p = 0.572). Forty percent of the infectionswere persistent. From all positive samples, only in the40% were identified some of the genotypes analyzed(16 and 18). The group of patients with Gleason scorede > 7 had a virus prevalence of 16%. CONCLUSIONS: The results show the presence ofthe human papillomavirus genome in prostate tissuewith and without neoplasia; no association was foundbetween infection and prostate cancer.

OBJETIVOS: Analizar la presencia delvirus de papiloma humano en próstata y su asociacióncon cáncer.MATERIAL Y MÉTODOS: Se realizó un estudiode casos y controles, para lo cual se colectaronmuestras de tejido con hiperplasia benigna y concáncer de próstata. Se realizó una historia clínicapara conocer la presencia de los factores de riesgoasociados al cáncer de próstata, así como los relacionadoscon el virus. El tejido prostático fue obtenidopor biopsia transrectal o resección transuretral.La identificación del genoma viral se realizó amplificandoun fragmento de 450 del gen L1 por mediode una PCR clásica. Para la identificación de los genotipos16 y 18, se utilizó PCR tiempo real. Para elanálisis de los datos se utilizó la prueba de χ2, pruebade T de Student o U de Mann-Whitney y cálculode OR. RESULTADOS: Se incluyeron 32 pacientes concáncer de próstata y 99 con hiperplasia benigna depróstata en una relación 1:3. La media de edad fuede 69.44±9.22 años. La prevalencia global del virusde papiloma humano fue de 15.2% siendo similar en los casos y entre casos (15.6%) y controles (15.1%),no existiendo diferencia significativa (p=0.572). El40% de las infecciones eran persistentes. Del totalde las muestras positivas, solamente en el 40% seencontró alguno de los dos genotipos analizados (16y 18). Los pacientes con un puntaje de Gleason > 7tuvieron una prevalencia del virus de 16%. CONCLUSIONES: Los resultados ponen de manifiestola presencia del genoma del virus del papilomahumano en próstata con y sin neoplasia, no se encontróasociación entre la infección y el cáncer de próstata.

Detección molecular del Virus de Papiloma Humano en pacientes con hiperplasia prostática benigna y cáncer de próstata / Molecular detection of human papillomavirus among patients with benign prostatic hyperplasia and prostate cáncer

OBJETIVOS: Analizar la presencia delvirus de papiloma humano en próstata y su asociacióncon cáncer.MATERIAL Y MÉTODOS: Se realizó un estudio de casos y controles, para lo cual se colectaronmuestras de tejido con hiperplasia benigna y concáncer de próstata. Se realizó una historia clínicapara conocer la presencia de los factores de riesgoasociados al cáncer de próstata, así como los relacionados con el virus. El tejido prostático fue obtenido por biopsia transrectal o resección transuretral.La identificación del genoma viral se realizó amplificando un fragmento de 450 del gen L1 por mediode una PCR clásica. Para la identificación de los genotipos 16 y 18, se utilizó PCR tiempo real. Para elanálisis de los datos se utilizó la prueba de χ2, prueba de T de Student o U de Mann-Whitney y cálculode OR.RESULTADOS: Se incluyeron 32 pacientes concáncer de próstata y 99 con hiperplasia benigna depróstata en una relación 1:3. La media de edad fuede 69.44±9.22 años. La prevalencia global del virusde papiloma humano fue de 15.2% siendo similar en los casos y entre casos (15.6%) y controles (15.1%),no existiendo diferencia significativa (p=0.572). El40% de las infecciones eran persistentes. Del totalde las muestras positivas, solamente en el 40% seencontró alguno de los dos genotipos analizados (16y 18). Los pacientes con un puntaje de Gleason > 7tuvieron una prevalencia del virus de 16%.CONCLUSIONES: Los resultados ponen de manifiesto la presencia del genoma del virus del papilomahumano en próstata con y sin neoplasia, no se encontróasociación entre la infección y el cáncer de próstata.

OBJECTIVE: To analyze the presenceof human papillomavirus in prostate and its associationwith prostate cancer.METHODS: A case-control study was conducted.Tissue samples with benign hyperplasia and prostatecancer were collected. Risk factors related to prostate cancer and human papillomavirus were assessedby a medical interview. Prostate tissue was obtainedby transrectal biopsy or transurethral resection. Theidentification of viral genome was assessed by the amplification of 450 pb., from L1 gene. Real time PCR wasused to identified HPV genotypes 16 and 18. For dataanalysis, the χ2 test, Student’s T test or Mann-WhitneyU test and OR were computed. RESULTS: Thirty and 99 with benign prostatehyperplasia were included in a 1:3 ratio, with a meanage of 69.44±9.22 years. The global prevalence of human papillomavirus was 15.2% being similar in bothcases (15.6%) and controls (15.1%) with no significantdifference (p = 0.572). Forty percent of the infectionswere persistent. From all positive samples, only in the40% were identified some of the genotypes analyzed(16 and 18). The group of patients with Gleason scorede > 7 had a virus prevalence of 16%CONCLUSIONS: The results show the presence ofthe human papillomavirus genome in prostate tissuewith and without neoplasia; no association was foundbetween infection and prostate cancer.

Human papillomavirus type 13: Genome amplification and characterization data.

As for 2020 only two complete genomes of Human papillomavirus type 13 (HPV13) are publicly available in GenBank database. In addition, reports of partial sequences of genetic regions are very limited. Therefore, genomic research that contributes to knowledge of viral components involved in HPV13 pathogenesis, and molecular mechanisms associated to multifocal epithelial hyperplasia (MEH) disease are urged. In the accompanying paper [1], we aimed to obtain the complete genome sequence of HPV13 associated to MEH disease, obtained from a Mayan boy living in Yucatan, Mexico. Coding sequences were annotated, and viral proteins traduced and deposited in GenBank with accession number MT068446. In this data report, we present the oligonucleotide list used to amplify the complete genome, a graphical abstract of process employed for the amplification of circular HPV13 genome, a representative figure of PCR products obtained for sequencing and multiple sequence alignments with the translated coding sequences of the existing genomes: X62843 is the first HPV13 genome reported [2]; it was generated from a clone obtained from a Turkish patient; DQ344807 was originally obtained from a patient in the Amazonian region [3]. The multiple sequence alignments show the main viral proteins (predicted). This provides relevant information for future molecular analysis and epidemiological studies because HPV13 is an understudied genotype associated to a neglected disease that appears more commonly in children. Additionally, the description of the methods can help in future sequencing of HPV genomes. We hope that our solutions will help researchers who do not have next-generation sequencing (NGS) platforms. A more comprehensive analysis of this data may be obtained from "Genomic characterization of Human papillomavirus type 13, associated to Multifocal Epithelial Hyperplasia, in a Mayan community" [1].

Comparative Transcriptomes of the Body Wall of Wild and Farmed Sea Cucumber Isostichopus badionotus.

Overfishing of sea cucumber Isostichopus badionotus from Yucatan has led to a major population decline. They are being captured as an alternative to traditional species despite a paucity of information about their health-promoting properties. The transcriptome of the body wall of wild and farmed I. badionotus has now been studied for the first time by an RNA-Seq approach. The functional profile of wild I. badionotus was comparable with data in the literature for other regularly captured species. In contrast, the metabolism of first generation farmed I. badionotus was impaired. This had multiple possible causes including a sub-optimal growth environment and impaired nutrient utilization. Several key metabolic pathways that are important in effective handling and accretion of nutrients and energy, or clearance of harmful cellular metabolites, were disrupted or dysregulated. For instance, collagen mRNAs were greatly reduced and deposition of collagen proteins impaired. Wild I. badionotus is, therefore, a suitable alternative to other widely used species but, at present, the potential of farmed I. badionotus is unclear. The environmental or nutritional factors responsible for their impaired function in culture remain unknown, but the present data gives useful pointers to the underlying problems associated with their aquaculture.

Genomic characterization of human papillomavirus type 13, associated to multifocal epithelial hyperplasia, in a Mayan community.

Human papillomavirus type 13 (HPV13) is a low-risk HPV type associated with Multifocal Epithelial Hyperplasia (MEH). It is considered a rare pathology of oral mucosa, more prevalent in certain ethnical groups, such as the Maya from Yucatan in Mexico. As for 2020 only two complete genomes of HPV13 are publicly available in Genbank database (one from Turkey one from the Amazonian). We aimed to obtain the complete genome sequence of HPV13 associated to MEH, obtained from a community in the Mayan area from Mexico. A bank of oral swabs from children with MEH were used. To enrich the sample, a Rolling Cycle Amplification (RCA) method was performed followed by overlapping end-point PCR of 500 bp fragments, Sanger sequencing and assembly. Eight open reading frames (ORFs) were annotated (E1, E2, E4, E5, E6, E7, L1 and L2 genes). When compared with the other two previously reported genomes the identity at nucleotide level is high 98.9% and 99.6%, respectively. The phylogenetic tree shows that Yucatan HPV13 is more closely related to HPV13 obtained from the Amazonian. Most changes identified at amino acid level are substitutions derived from nucleotide variations or SNPs in coding regions. Amino-acid changes were observed in E2 and E1 proteins (n ≥ 8), and in L1, L2, E6 and E5 proteins (n ≤ 5). E7 protein from Yucatan has 100% identity with the reported from Amazonian and differs (94.1% identity) with the one from Turkey due to 3 substitutions and three missing amino acids. In conclusion, the genome from HPV13 (7831 bp, 49 nt missing) associated to MEH in the Mayan area from Yucatan was obtained from stored swabs; this is the first effort in Mexico, the second in Latin America, and the third of the world. More research that contributes to the knowledge of the determinants underlying this neglected pathology are urged.

A Glycosaminoglycan-Rich Fraction from Sea Cucumber Isostichopus badionotus Has Potent Anti-Inflammatory Properties In Vitro and In Vivo.

Sea cucumber body wall contains several naturally occurring bioactive components that possess health-promoting properties. Isostichopus badionotus from Yucatan, Mexico is heavily fished, but little is known about its bioactive constituents. We previously established that I. badionotus meal had potent anti-inflammatory properties in vivo. We have now screened some of its constituents for anti-inflammatory activity in vitro. Glycosaminoglycan and soluble protein preparations reduced 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced inflammatory responses in HaCaT cells while an ethanol extract had a limited effect. The primary glycosaminoglycan (fucosylated chondroitin sulfate; FCS) was purified and tested for anti-inflammatory activity in vivo. FCS modulated the expression of critical genes, including NF-ĸB, TNFα, iNOS, and COX-2, and attenuated inflammation and tissue damage caused by TPA in a mouse ear inflammation model. It also mitigated colonic colitis caused in mice by dextran sodium sulfate. FCS from I. badionotus of the Yucatan Peninsula thus had strong anti-inflammatory properties in vivo.

22-Oxocholestane oximes as potential anti-inflammatory drug candidates.

22-Oxocholestanes bearing the oxime functionality in the side chain have been synthesized from diosgenin and evaluated in vivo as anti-inflammatory agents in an acute inflammation mouse ear model, against the commercial glucocorticoid dexamethasone. The final compounds were all regioselectively obtained with an E configuration at the oxime double bond. The title compounds reduced ear-induced inflammation and edema. The most active oximes repressed the expression of proinflammatory genes TNF-α, COX-2, and IL-6; including macrophage migration inhibitory factor. Overall, our data suggest that 22-oxocholestane oximes exert a strong in vivo anti-inflammatory activity.

Genome-wide in silico identification of GPI proteins in Mycosphaerella fijiensis and transcriptional analysis of two GPI-anchored ß-1,3-glucanosyltransferases.

The hemibiotrophic fungus Mycosphaerella fijiensis is the causal agent of black Sigatoka (BS), the most devastating foliar disease in banana (Musa spp.) worldwide. Little is known about genes that are important during M. fijiensis-Musa sp. interaction. The fungal cell wall is an attractive area of study because it is essential for maintenance of cellular homeostasis and it is the most external structure in the fungal cell and therefore mediates the interaction of the pathogen with the host. In this manuscript we describe the in silico identification of glycosyl phosphatidylinositol-protein (GPI) family in M. fijiensis, and the analysis of two ß-1,3-glucanosyltrans-ferases (Gas), selected by homology with fungal pathogenicity factors. Potential roles in pathogenesis were evaluated through analyzing expression during different stages of black Sigatoka disease, comparing expression data with BS symptoms and fungal biomass inside leaves. Real-time quantitative RT-PCR showed nearly constant expression of MfGAS1 with slightly increases (about threefold) in conidia and at speck-necrotrophic stage during banana-pathogen interaction. Conversely, MfGAS2 expression was increased during biotrophy (about seven times) and reached a maximum at speck (about 23 times) followed by a progressive decrease in next stages, suggesting an active role in M. fijiensis pathogenesis.