Tainá Raiol

Genetic Variability and Phylogeny of the High-Risk HPV-31, -33, -35, -52, and -58 in Central Brazil

More than 100 HPV types have been described, 13 of which are classified as high‐risk due to their association with the development of cervical cancer. The intratype genomic diversity of HPV‐16 and ‐18 has been studied extensively, while little data have been generated for other less common high‐risk types. The present study explores the nucleotide variability and phylogeny of the high‐risk HPV‐31, ‐33, ‐35, ‐52, and ‐58, in samples from Central Brazil. For this purpose, the LCR and the E6 and L1 genes were sequenced. Several variants of these HPV types were detected, some of which have been detected in other parts of the world. Furthermore, new variants of all types examined were characterized in a total of 13 new variants. Based on the E6 and L1 sequences, variants were described comprising conservative and non‐conservative amino acid changes. For phylogenetic tree construction, samples characterized in this study were compared to others described and submitted to GenBank previously. The phylogenetic analysis of HPV‐31, ‐33, ‐35, and ‐58 isolates did not reveal ethnic or geographical clustering as observed previously for HPV‐16 and ‐18. HPV‐35 analysis showed a dichotomic branching characteristic of viral subtypes. Interestingly, four clusters relative to the analysis of HPV‐52 isolates were identified, two of which could be classified as Asian and European branches. The genomic characterization of HPV variants is crucial for understanding the intrinsic geographical relatedness and biological differences of these viruses and contributes further to studies on their infectivity and pathogenicity. J. Med. Virol. 81:685–692, 2009

Identification of Human Papillomavirus Type 58 Lineages and the Distribution Worldwide

BACKGROUND Human papillomavirus type 58 (HPV-58) accounts for a much higher proportion of cervical cancers in East Asia than other types. A classification system of HPV-58, which is essential for molecular epidemiological study, is lacking. METHODS AND RESULTS This study analyzed the sequences of 401 isolates collected from 15 countries and cities. The 268 unique concatenated E6-E7-E2-E5-L1-LCR sequences that comprised 57% of the whole HPV-58 genome showed 4 distinct clusters. L1 and LCR produced tree topologies that best resembled the concatenated sequences and thus are the most appropriate surrogate regions for lineage classification. Moreover, short fragments from L1 (nucleotides 6014-6539) and LCR (nucleotides 7257-7429 and 7540-52) were found to contain sequence signatures informative for lineage identification. Lineage A was the most prevalent lineage across all regions. Lineage C was more frequent in Africa than elsewhere, whereas lineage D was more prevalent in Africa than in Asia. Among lineage A variants, sublineage A2 dominated in Africa, the Americas, and Europe, but not in Asia. Sublineage A1, which represents the prototype that originated from a patient with cancer, was rare worldwide except in Asia. CONCLUSIONS HPV-58 can be classified into 4 lineages that show some degree of ethnogeographic predilection in distribution. The evolutionary, epidemiological, and pathological characteristics of these lineages warrant further study.

Geographical distribution and oncogenic risk association of human papillomavirus type 58 E6 and E7 sequence variations.

Human papillomavirus (HPV) 58 accounts for a notable proportion of cervical cancers in East Asia and parts of Latin America, but it is uncommon elsewhere. The reason for such ethnogeographical predilection is unknown. In our study, nucleotide sequences of E6 and E7 genes of 401 HPV58 isolates collected from 15 countries/cities across four continents were examined. Phylogenetic relationship, geographical distribution and risk association of nucleotide sequence variations were analyzed. We found that the E6 genes of HPV58 variants were more conserved than E7. Thus, E6 is a more appropriate target for type‐specific detection, whereas E7 is more appropriate for strain differentiation. The frequency of sequence variation varied geographically. Africa had significantly more isolates with E6‐367A (D86E) but significantly less isolates with E6‐203G, ‐245G, ‐367C (prototype‐like) than other regions (p ≤ 0.003). E7‐632T, ‐760A (T20I, G63S) was more frequently found in Asia, and E7‐793G (T74A) was more frequent in Africa (p < 0.001). Variants with T20I and G63S substitutions at E7 conferred a significantly higher risk for cervical intraepithelial neoplasia grade III and invasive cervical cancer compared to other HPV58 variants (odds ratio = 4.44, p = 0.007). In conclusion, T20I and/or G63S substitution(s) at E7 of HPV58 is/are associated with a higher risk for cervical neoplasia. These substitutions are more commonly found in Asia and the Americas, which may account for the higher disease attribution of HPV58 in these areas.

Complete genome sequence of Mycobacterium massiliense.

Mycobacterium massiliense is a rapidly growing bacterium associated with opportunistic infections. The genome of a representative isolate (strain GO 06) recovered from wound samples from patients who underwent arthroscopic or laparoscopic surgery was sequenced. To the best of our knowledge, this is the first announcement of the complete genome sequence of an M. massiliense strain.

New variants of human papillomavirus type 18 identified in central Brazil

HPV-18 is the second most prevalent human papillomavirus genotype found in cervical cancer. Nucleotide variations in HPV-18 sequence can interfere with the viral oncogenic potential. However, the knowledge about HPV-18 variants in Brazil is still limited. The present study aims to determine the LCR, E6, and L1 genetic variability of HPV-18 variants found in women co-infected with HIV-1 in Central Brazil. Four HPV-18 samples were identified and had the LCR, E6, and L1 genomic regions sequenced. It was possible to characterize three European variants and one African variant of HPV-18. All of them are new variants, showing nucleotide substitutions not previously reported. Nucleotide variations in binding sites for transcriptional factors were observed. Phylogenetic analysis was also performed, evidencing the three clusters related to the Asian-American, African, and European variants. The characterization of HPV genetic variability is of pivotal importance to the understanding of the viral pathogenicity.

A Deep Insight into the Sialome of Rhodnius neglectus, a vector of chagas disease

Background Triatomines are hematophagous insects that act as vectors of Chagas disease. Rhodnius neglectus is one of these kissing bugs found, contributing to the transmission of this American trypanosomiasis. The saliva of hematophagous arthropods contains bioactive molecules responsible for counteracting host haemostatic, inflammatory, and immune responses. Methods/Principal Findings Next generation sequencing and mass spectrometry-based protein identification were performed to investigate the content of triatomine R. neglectus saliva. We deposited 4,230 coding DNA sequences (CDS) in GenBank. A set of 636 CDS of proteins of putative secretory nature was extracted from the assembled reads, 73 of them confirmed by proteomic analysis. The sialome of R. neglectus was characterized and serine protease transcripts detected. The presence of ubiquitous protein families was revealed, including lipocalins, serine protease inhibitors, and antigen-5. Metalloproteases, disintegrins, and odorant binding protein families were less abundant. Conclusions/Significance The data presented improve our understanding of hematophagous arthropod sialomes, and aid in understanding hematophagy and the complex interplay among vectors and their vertebrate hosts.

Phylogeny and polymorphism in the long control region, E6, and L1 of human papillomavirus types 53, 56, and 66 in central Brazil.

Introduction: Several studies related that different human papillomavirus (HPV) types and intratype variants can present different oncogenic potential. In opposite to HPVs 16 and 18 variants, information about variants of other carcinogenic HPV types is still scarce. The aim of this study was to investigate the genetic variability of HPVs 53, 56, and 66 from Central Brazil isolates. Methods: The long control region (LCR), E6, and L1 genomic regions were amplified and sequenced. We evaluate for nucleotide variations in relation to the reference sequence of each HPV type and also the conservation of physicochemical properties of the deduced amino acid substitutions. In silico analysis was performed to locate binding sites for transcriptional factors within the LCR. Moreover, we performed a phylogenetic analysis with the Central Brazilian and worldwide sequences available at genomic databases. Results: Gathering LCR, E6, and L1 genomic regions, the highest genetic variability was found among HPV-53 isolates with 52 nucleotide variations, followed by HPVs 56 and 66 with 24 and 16 nucleotide substitutions, respectively. The genetic analysis revealed 11 new molecular variants of all HPV types analyzed, totalizing 31 new nucleotide and 3 new amino acid variations. Eight nonconservative amino acid substitutions were detected, which may indicate a biological and pathogenic diversity among HPV types. Furthermore, 8 nucleotide substitutions were localized at putative binding sites for transcription factors in the LCR with a potential implication on viral oncogene expression. The HPVs 53, 56, and 66 phylogenetic analysis confirmed a dichotomic division only described to HPV subtypes and different from the patterns described for HPVs 16 and 18 variants. Conclusions: The high genetic variability observed emphasizes the importance of investigating polymorphisms in types other than HPVs 16 or 18 to better understand the molecular genomic profile of viral infection by different HPV types.

Excalibur: an autonomic cloud architecture for executing parallel applications

IaaS providers often allow the users to specify many requirements for their applications. However, users without advanced technical knowledge usually do not provide a good specification of the cloud environment, leading to low performance and/or high monetary cost. In this context, the users face the challenges of how to scale cloud-unaware applications without re-engineering them. Therefore, in this paper, we propose and evaluate a cloud architecture, namely Excalibur, to execute applications in the cloud. In our architecture, the users provide the applications and the architecture sets up the whole environment and adjusts it at run-time accordingly. We executed a genomics workflow in our architecture, which was deployed in Amazon EC2. The experiments show that the proposed architecture dynamically scales this cloud-unaware application up to 10 instances, reducing the execution time by 73% and the cost by 84% when compared to the execution in the configuration specified by the user.

A Mouse Variable Gene Fragment Binds to DNA Independently of the BCR Context: A Possible Role for Immature B-Cell Repertoire Establishment

B-cell maturation occurs in several steps and requires constant stimulus for its continuing development. From the emergence of the pre-B-cell receptor, signal transduction stimulates and supports B-cell development. Current viewpoints indicate that both positive selection pressure for autoantigens and tonic signaling constitutively stimulate B-cell maturation. In this work, we tested for the presence of a putative DNA binding site in a variable gene segment in a germline configuration, independently of VDJ recombination. After a survey of the public antibody databases, we chose a single mouse heavy variable gene segment that is highly represented in anti-nucleic acid antibodies and tested it for ssDNA binding. A phage display approach was used to search for intrinsic binding to oligo deoxythymidine. The results revealed that binding to an antigen can be influenced by the use of a specific DNA binding V gene segment. Our data support the idea that some variable genes have intrinsic reactivity towards specific types of endogenous autoantigens, and this property may contribute to the establishment of the immature B-cell repertoire.

Genome-Wide Identification of Non-coding RNAs in Komagatella pastoris str. GS115

The methylotrophic yeast Komagatella pastoris is a relevant bioengineering platform for protein synthesis. Even though non-coding RNAs are well known to be key players in the control of gene expression no comprehensive annotation of non-coding RNAs has been reported for this species. We combine here published RNA-seq data with a wide array of homology based annotation tools and de novo gene predictions to compile the non-coding RNAs in K. pastoris.