The Molecular Information About Deadwood Bacteriomes Partly Depends on the Targeted Environmental DNA

Microbiome studies mostly rely on total DNA extracts obtained directly from environmental samples. The total DNA consists of both intra- and extracellular DNA, which differ in terms of their ecological interpretation. In the present study, we have investigated for the first time the differences among the three DNA types using microbiome sequencing of Picea abies deadwood logs (Hunter decay classes I, III, and V). While the bacterial compositions of all DNA types were comparable in terms of more abundant organisms and mainly depended on the decay class, we found substantial differences between DNA types with regard to less abundant amplicon sequence variants (ASVs). The analysis of the sequentially extracted intra- and extracellular DNA fraction, respectively, increased the ecological depth of analysis compared to the directly extracted total DNA pool. Both DNA fractions were comparable in proportions and the extracellular DNA appeared to persist in the P. abies deadwood logs, thereby causing its masking effect. Indeed, the extracellular DNA masked the compositional dynamics of intact cells in the total DNA pool. Our results provide evidence that the choice of DNA type for analysis might benefit a study’s answer to its respective ecological question. In the deadwood environment researched here, the differential analysis of the DNA types underlined the relevance of Burkholderiales, Rhizobiales and other taxa for P. abies deadwood decomposition and revealed that the role of Acidobacteriota under this scenario might be underestimated, especially compared to Actinobacteriota.

Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome

Approximately 13% of the human genome can fold into non-canonical (non-B) DNA structures (e.g. G-quadruplexes, Z-DNA, etc.), which have been implicated in vital cellular processes. Non-B DNA also hinders replication, increasing errors and facilitating mutagenesis, yet its contribution to genome-wide variation in mutation rates remains unexplored. Here, we conducted a comprehensive analysis of nucleotide substitution frequencies at non-B DNA loci within noncoding, non-repetitive genome regions, their ±2 kb flanking regions, and 1-Megabase windows, using human-orangutan divergence and human single-nucleotide polymorphisms. Functional data analysis at single-base resolution demonstrated that substitution frequencies are usually elevated at non-B DNA, with patterns specific to each non-B DNA type. Mirror, direct and inverted repeats have higher substitution frequencies in spacers than in repeat arms, whereas G-quadruplexes, particularly stable ones, have higher substitution frequencies in loops than in stems. Several non-B DNA types also affect substitution frequencies in their flanking regions. Finally, non-B DNA explains more variation than any other predictor in multiple regression models for diversity or divergence at 1-Megabase scale. Thus, non-B DNA substantially contributes to variation in substitution frequencies at small and large scales. Our results highlight the role of non-B DNA in germline mutagenesis with implications to evolution and genetic diseases.

Prevalence and Subtype Distribution of High-Risk Human Papillomavirus Among Women Presenting for Cervical Cancer Screening at Karanda Mission Hospital

PURPOSE High-risk human papillomaviruses (hrHPV) are the primary cause of cervical cancer. Human papillomavirus (HPV) vaccination is expected to prevent cervical cancers caused by the HPV types included in vaccines and possibly by cross-protection from other types. This study sought to determine the hrHPV type distribution in women at a rural Zimbabwe hospital. METHODS We implemented a cross-sectional study at the Karanda Mission Hospital. Using the Visual Inspection with Acetic Acid Cervicography technique, clinicians collected cervical swabs from 400 women presenting for screening for cervical cancer. Samples were initially analyzed by Cepheid GeneXpert; candidate hrHPV genotypes were further characterized using the Anyplex II HPV28 Detection Kit. RESULTS Twenty-one percent of the 400 women were positive for a high-risk genotype when using the GeneXpert analyzer; 17% were positive when using the multiplex analysis. Almost two thirds of the hrHPV women had a single DNA type identified, whereas one third had multiple genotypes, ranging from 2 to 5. hrHPV was observed more frequently in HIV-positive than in HIV-negative women (27% v 15%). Of the 113 isolates obtained, 77% were hrHPV genotypes not included in the bivalent or quadrivalent vaccines, and 47% represented DNA types not covered in the nonavalent vaccine. Forty-seven percent of the women with hrHPV harbored a single genotype that was not covered by the nonavalent vaccine. CONCLUSION A large fraction of hrHPV isolates from women participating in a cervical cancer screening program in northern Zimbabwe are DNA types not covered by the bivalent, quadrivalent, or nonavalent vaccines. These findings suggest the importance of characterizing the hrHPV DNA types isolated from cervical neoplasia in this population and determining whether cross-immunization against these genotypes develops after administration of the vaccines in current use.

Condyloma accuminatum of the male urethra: A case report

Condyloma acuminatum is an anogenital lesion caused by the human papillomavirus infection. It is a common, sexually transmitted disease. It usually affects the external genitalia, while urethral and bladder involvement is uncommon. Human papillomavirus types are classified into three categories depending on their oncogenic potential: low risk (type 6, 11, 42, 43, 44, 59, 66, 68, and 70), intermediate-risk (type 30, 31, 33, 34, 35, 39, 40, 49, 51, 52, 53, 57, 58, 63, and 64) and high risk (type 16, 18, 45, and 56). High-risk and intermediate-risk human papillomavirus DNA types, together with other co-factors still to be defined, account for over 90% of anogenital pre-malignant and malignant tumours. Herein, we report a unique case of condyloma acuminatum positive for human papillomavirus -6 involving the penile urethra, presents as the primary and only site of the disease in a diabetic type-2 patient.

Distribution of Human Papillomavirus Genotypes in Condylomata Acuminata: An Austrian Cohort Study

Introduction: Condylomata acuminata are caused by various genotypes of human papilloma viruses (HPV). Methods: We assessed the frequency of 33 different HPV DNA types in 49 patients with condylomata acuminata by the polymerase chain reaction technique. Results: Forty-two percent of the patients were infected with low-risk genotypes, and 21% of the patients tested positive for high-risk genotypes. Multiple infections with low- and high-risk genotypes were detectable in 36% of the patients. Conclusion: As our results are in line with previous large-scale reports, our data might serve as a basis for monitoring the efficacy of HPV vaccination in Austria.

POLYMORPHISM ARG72PRO OF THE P53 GENE AND THE RISK OF HUMAN PAPILLOMAVIRUS ASSOCIATED CERVICAL CANCER IN WOMEN FROM KYRGYZ REPUBLIC

Aim. Allele frequency and genotype distribution in the cervical cancer group were compared with those of the control group to determine whether polymorphism Arg72Pro of Р53 gene elevates the susceptibility of Kyrgyz women to cervical cancer (CC). Materials and Methods. A total of 102 women (mean age 53,5±10 years) of Kyrgyz nationality with cervical cancer were recruited into the study and 102 healthy women were used as the control group (mean age 46,5±8,5 years). The diagnosis of cervical cancer was confirmed histologically. 88 % (90/102) of women with cervical cancer were human papillomavirus (HPV) positive. 17 % (15/90) specimens were positive for HPV type 16, 48 % (43/90) were positive for HPV type 18 and 35 % (32/90) were positive both HPV - 16/18. Presence of human papillomavirus DNA types 16 and 18 was analyzed by polymerase chain reaction with hybridization-fluorescence detection. The Arg72Pro polymorphisms of the P53 gene were determined by the PCR-RFLP method. Results. No significant difference was found between genotype distributions in the cervical cancer patients and the control group (χ2=1,24; р=0,54). However, the Arg72Arg genotype and Arg72 allele was significantly more frequent in women with cervical cancers infected with HPV than in the control group (χ2=7,25; р=0,027 for для genotype, χ2=6,83; р=0,009 for allele). Women who are HIV positive and having the Arg72 allele had 1,94 fold (OR=1,94 [1,20-3,15]; р=0,009) higher risk of developing CC compared with subjects carrying neither of these alleles. HPV positive women carrying the genotype Arg72Arg had 1,85 fold (OR=1,85 [1,03-3,32]; р=0,027) higher risk of CC. Conclusion. The Arg72Arg genotype of р53 gene in HIV positive women from Kyrgyz Republic may represent a potential risk factor for the development of cervical cancer.

HPV and the Development of Colorectal Cancer

<p>Over the past two decades, many studies reported that around (20%) of the worldwide malignant tumors problem can be related to viral infections. Some publications recently have described a relationship between malignant colorectal tumors and human papilloma virus (HPV), but these findings are still debatable. The purpose of this report is to evaluate the existence of the genetic sequences and the proteins of HPV in the transformed cells of colorectal cancer in Saudi Arabia. Extracted DNA from eighty three archival colorectal tumor samples were examined for HPV DNA types 16 and 18 and their protein products using polymerase chain reaction (PCR) technique in addition to immunohistochemical staining. All colorectal cancer and control cases were found negative for both 16 and 18 HPV types by using PCR. Moreover, immunostaining did not detect any nuclear expression of HPV proteins in all examined cases. Our outcomes supports the statement that HPV is not engaged in the initiation and progression of colorectal carcinomas especially in the Western province of Saudi Arabia.</p>

Natural Transformation of Gallibacterium anatis

ABSTRACTGallibacterium anatisis a pathogen of poultry. Very little is known about its genetics and pathogenesis. To enable the study of gene function inG. anatis, we have established methods for transformation and targeted mutagenesis. The genusGallibacteriumbelongs to thePasteurellaceae, a group with several naturally transformable members, includingHaemophilus influenzae. Bioinformatics analysis identifiedG. anatishomologs of theH. influenzaecompetence genes, and natural competence was induced inG. anatisby the procedure established forH. influenzae: transfer from rich medium to the starvation medium M-IV. This procedure gave reproducibly high transformation frequencies withG. anatischromosomal DNA and with linearized plasmid DNA carryingG. anatissequences. Both DNA types integrated into theG. anatischromosome by homologous recombination. Targeted mutagenesis gave transformation frequencies of >2 × 10−4transformants CFU−1. Transformation was also efficient with circular plasmid containing noG. anatisDNA; this resulted in the establishment of a self-replicating plasmid. Nine diverseG. anatisstrains were found to be naturally transformable by this procedure, suggesting that natural competence is common and the M-IV transformation procedure widely applicable for this species. TheG. anatisgenome is only slightly enriched for the uptake signal sequences identified in other pasteurellaceaen genomes, butG. anatisdid preferentially take up its own DNA over that ofEscherichia coli. Transformation by electroporation was not effective for chromosomal integration but could be used to introduce self-replicating plasmids. The findings described here provide important tools for the genetic manipulation ofG. anatis.