GenBank Data Research Articles

Detection and Characterization of Circovirus in Canary Flocks.

Circovirus infections have been documented in adult and nestling canaries (Fringillidae) but the distribution of the virus in the world is not yet known. In captive canary flocks, Circovirus infections have been reported based on the clinical observations. In this study, the presence of both canary circovirus (CaCV) and chicken anemia virus (CAV) in canary flocks was investigated. Virus strains were detected by PCR and direct sequencing of amplified products. Nucleotide sequences were aligned and compared with existing data in GenBank. PCR identified CaCV-positive birds, giving an overall positivity rate of 25%, but all samples were negative for CAV. According to the sequencing data, three distinct strains were identified. Our results indicated a relationship between genetic variation in the replicase gene ( rep) and the geographic regions as well as the feasibility of using the rep gene for virus detection and molecular epidemiology investigations. We are reporting detection and characterization of canary circovirus based on the rep gene. Sequencing results and sequence identity analysis revealed that the rep gene could be used for detecting and discriminating the members of family Circoviridae. This manuscript is the first report of canary circovirus in Iran and of three new strains in the world.

Genetic Variability in the Yellow-Necked Field Mouse (Sylvaemus flavicollis Melch., 1834, Muridae, Rodentia) at the Eastern Border of the Range

The first characterization of the genetic variability in populations of S. flavicollis on the eastern border of the range is presented. Seven individuals from the most northeastern habitat of the species (Middle Urals) were karotyped. No deviations from the standard chromosome set, either by the chromosome number or morphology, were revealed. Analysis of the mtDNA cytochrome b gene sequences (1133 bp) in 44 individuals from five populations on the eastern border of the species range (Middle and Southern Urals) resulted in identification of 17 haplotypes. All haplotypes were new and not found earlier in other parts of the species range. The genetic diversity indices and analysis of the demographic and genetic structure indicate a relatively recent origin of the populations under study as a result of rapid expansion. Phylogenetic analysis (97 haplotypes, including the GenBank data) showed that all haplotypes described at the eastern border of the range belonged to the same phylogroup distributed in the Balkan region, Northern and Eastern Europe, and Russia (Samara oblast). Close relationships between the examined populations and the populations from the northern part of the species range in Eastern Europe was demonstrated.

A Challenge to Integrate Bioinformatics and Biodiversity Informatics Data as Museomics

Museum-preserved samples are attracting attention as a rich resource for DNA studies. Museomics aims to link DNA sequence data back to the museum collection. Molecular biologists are interested in morphological information including body size, pattern, and colors, and sequence data have also become essential for biodiversity research as evidence for species identification and phylogenetic analysis. For more than 30 years, molecular data, such as DNA and protein sequences, have been captured by the DNA Data Bank of Japan (DDBJ), the European Bioinformatics Institute (EBI, UK), and the National Center for Biotechnology Information (NCBI, US) under the International Nucleotide Sequence Database Collaboration (INSDC). INSDC provides collected molecular data to researchers as public databases including GenBank for DNA sequences and Gene Expression Omnibus (GEO) for gene expression. These three institutes synchronize archived data and publish all data on an FTP (File Transfer Protocol) site so that it is available for big data analysis. In recent years, high-throughput sequencing technology, also called next-generation sequencing (NGS) technology, has been widely utilized for molecular biology including genomics, transcriptomics, and metagenomics. Biodiversity researchers also focus on NGS data for DNA barcoding and phylogenetic analysis as well as molecular biology. Additionally, a portable NGS platform, MinION (Oxford Nanopore Technologies), has been launched, enabling biodiversity researchers to perform DNA sequencing in the field. Along with GenBank and GEO data, INSDC accepts NGS data and provides a public primary database, called the Sequence Read Archive (SRA). As of March 2018, 6.4 Peta Bases of NGS data is freely available under more than 130,000 projects in SRA. The Database Center for Life Science (DBCLS) provides a search engine for public NGS data, called DBCLS SRA (http://sra.dbcls.jp/) in collaboration with DDBJ. SRA contains not only raw sequence reads or processed data mapped to genome, but also information on the experimental design, including project types, sequencing platforms, and sample species. Researchers can use this data to refine their search results. We also linked publications referring to NGS data to the corresponding SRA entries. The mission of DBCLS is to accelerate the accessibility of life science data. Collected data used to be described in the Excel-readable tabular format, but these formats are difficult to merge with other databases because of the ambiguity of labels. To overcome this difficulty, we recently integrated life science data with Semantic Web technology. We held annual meetings to integrate life science data, called BioHackathons, in which researchers from all over the world participated. UniProt and Ensembl databases currently provide an RDF (Resource Description Framework) version of curated genome and protein data, respectively. In the biodiversity domain, there are many databases such as GBIF (The Global Biodiversity Information Facility) for species occurrence records, EoL (The Encyclopedia of Life) as a knowledge base of all species, and BoL (The Barcode of Life) for DNA barcoding data. RDF is utilized to describe Darwin Core based data so that bioinformatics and biodiversity informatics researchers can technically merge both types of data. Currently, specimen data and DNA sequence data are not linked. Museomics starts with cross-referencing specimen and sequence IDs and by making data sources comply with an existing standard.

Occurrence of Glaucus atlanticus in the Midriff Islands Region, Gulf of California, Mexico

A recent molecular study on pelagic nudibranchs showed that Glaucus marginatus (Reinhardt and Bergh, 1864) is a complex of three cryptic species, whereas the congener G. atlanticus (Forster, 1777) remain as one species. The objective of the present study was to determine the identity of pelagic nudibranchs collected in the Gulf of California using both molecular and traditional taxonomy. New DNA sequences (COI) and GenBank data were used to confirm the specimens' identity as G. atlanticus. Records from G. atlanticus were obtained from databases to determine the species geographic range. Present results increase that range northwards by approximately 150 km in the Gulf of California. Molecular data indicate that G. atlanticus from the Gulf has a wide infl uence from populations from the North and South Pacific and Indian Oceans. There is no current evidence of other cryptic species.

Molecular characterization of keratin degrading fungi isolated from semi-arid soil by PCR using ITS4 and ITS5 primers

This study was aimed to explore molecular characters of fungal isolates and analyze the phylogenic relationship between isolates. Soil samples collected from different habitats of Jaipur, were analyzed for the prevalence of keratinophilic fungi using the hair baiting technique. The physiological conditions of soil samples were analyzed to study the effect of environmental factors on the growth and occurrence of fungi. Keratinophilic fungi were isolated and then identified on the basis of their macro and micro morphological characteristics. The identification of fungi was confirmed by DNA sequencing by PCR amplification using ITS4 and ITS5 gene primers. The fungal species were identified by the nBLAST using fungal DNA sequences against the data available in NCBI/GenBank. The isolated keratinophilic fungal species were identified as Chaetomium seminis-citrulli and Penicillium guttulosum. These two fungi were reported first time from Rajasthan, India using hair baiting technique. Phylogenic trees were constructed using MEGA7 software with the help of keratinophilic fungi reference data retrieved from NCBI GenBank data, to study the phylogenic relationship between the isolated fungi.

Analysis of MAPK and MAPKK gene families in wheat and related Triticeae species

BackgroundThe mitogen-activated protein kinase (MAPK) family is involved in signal transduction networks that underpin many different biological processes in plants, ranging from development to biotic and abiotic stress responses. To date this class of enzymes has received little attention in Triticeae species, which include important cereal crops (wheat, barley, rye and triticale) that represent over 20% of the total protein food-source worldwide.ResultsThe work presented here focuses on two subfamilies of Triticeae MAPKs, the MAP kinases (MPKs), and the MAPK kinases (MKKs) whose members phosphorylate the MPKs. In silico analysis of multiple Triticeae sequence databases led to the identification of 152 MAPKs belonging to these two sub-families. Some previously identified MAPKs were renamed to reflect the literature consensus on MAPK nomenclature. Two novel MPKs, MPK24 and MPK25, have been identified, including the first example of a plant MPK carrying the TGY activation loop sequence common to mammalian p38 MPKs. An EF-hand calcium-binding domain was found in members of the Triticeae MPK17 clade, a feature that appears to be specific to Triticeae species. New insights into the novel MEY activation loop identified in MPK11s are offered. When the exon-intron patterns for some MPKs and MKKs of wheat, barley and ancestors of wheat were assembled based on transcript data in GenBank, they showed deviations from the same sequence predicted in Ensembl. The functional relevance of MAPKs as derived from patterns of gene expression, MPK activation and MKK-MPK interaction is discussed.ConclusionsA comprehensive resource of accurately annotated and curated Triticeae MPK and MKK sequences has been created for wheat, barley, rye, triticale, and two ancestral wheat species, goat grass and red wild einkorn. The work we present here offers a central information resource that will resolve existing confusion in the literature and sustain expansion of MAPK research in the crucial Triticeae grains.

Can we build it? Yes we can, but should we use it? Assessing the quality and value of a very large phylogeny of campanulid angiosperms

The study of very large and very old clades holds the promise of greater insights into evolution across the tree of life. However, there has been a fair amount of criticism regarding the interpretations and quality of studies to date, with some suggesting that detailed studies carried out on smaller, tractable scales should be preferred over the increasingly grand syntheses of these data. We provided in detail our trials and tribulations of compiling a large, sparsely sampled matrix from GenBank data and inferring a well-supported, time-calibrated phylogeny of Campanulidae. We also used a simulation approach to assess tree quality and to study the value of using very large, comprehensive phylogenies in a comparative context. A robust and well-supported phylogeny can be produced as long as automated procedures are supplemented with some human intervention. In the case of campanulids, the overall topology may be driven not only by particular genes, but also particular sequences for a gene. We also determined that estimates of divergence times should be fairly robust to issues related to clade-specific heterogeneity. Finally, we demonstrated how relying on results from smaller, younger clades are prone to produce biased interpretations oftropical to temperate evolution across campanulids as a whole. While we were both surprised and encouraged by the robust and fairly well-resolved, comprehensive phylogeny of campanulids, challenges still remain. Nevertheless, large phylogenies are inherently valuable in a comparative context if only toattenuate the issue of ascertainment bias.

DNA Barcoding of Swamp Sediment Bacterial Isolates for Swamp Aquaculture Probiotic

Bacteria derived from swamp sediments and aquaculture ponds potential to be probiotics. The study aims to determine the sequence of 16S r RNA gene of isolate of probiotics candidate bacteria from sediment of swamp, to determine the phylogenetic tree between the bacterial species from isolates and Gene Bank data central for their potential as probiotic. The samples of bacteria resulted from pure isolation selected from the sediment of pond cultivation and swamp waters at Lebung Karangan Reservation, Ogan Ilir Regency, Indralaya, South Sumatra. This study was started from cultivating bacteria, extracting DNA of bacteria, amplification 16S r RNA genes by PCR, running electrophoresis, and sequencing the amplicon for determining DNA barcodes of bacteria from sediment of swamp and rearing pond. The result of BLAST analysis showed that KA isolate had the highest similarity 97% withStreptomyces sp.Hjorring101 from Denmark and RA isolate had the highest similarity 98% withStreptomyces sp. BD99 from Pakistan. KE isolate had the highest similarity 99% withBacillus subtilisCESi5 from Japan and RE isolate had the highest similarity 93% withBacillus sp.2bFR from Manado. All of isolates were bacteria potentially as swamp aquaculture probiotics.

New myxosporeans parasitizing Phractocephalus hemioliopterus from Brazil: morphology, ultrastructure and SSU-rDNA sequencing.

Myxozoans are a diverse group of parasitic cnidarians, with some species recognized as serious pathogens to their hosts. The present study describes 2 new myxobolid species (Myxobolus figueirae sp. nov. and Henneguya santarenensis sp. nov.) infecting skin and gill filaments of the Amazonian pimelodid fish Phractocephalus hemioliopterus, based on ultrastructural, histology and phylogenetic analysis. The fish were caught in the Amazon River, Pará, Brazil. The plasmodial development of M. figueirae sp. nov. was in the dermis and those of H. santarenensis sp. nov. were of the intralamellar type. For both species, the plasmodia were surrounded by a connective tissue layer, but there was no inflammatory infiltrate. For M. figueirae sp. nov., mature spores were ovoid measuring 9.1 to 10 (9.5 ± 0.3) µm in length, 5.8 to 6.9 (6.4 ± 0.3) µm in width and 4.4 to 4.5 (4.5 ± 0.1) µm in thickness. Two polar capsules were elongated and of unequal size. For H. santarenensis sp. nov., mature spores were ellipsoidal in the frontal view, measuring 26.3 to 36.1 (31.9 ± 3) µm in total length, 9.6 to 11.9 (10.8 ± 0.5) µm in body length, 3.7 to 4.9 (4.3 ± 0.3) µm in width and 16.6 to 25.6 (21 ± 3.1) µm in caudal process. The polar capsules were elongated and of equal size. Phylogenetic analysis, based on partial small subunit ribosomal DNA (SSU rDNA) sequences and using the closest myxozoan sequences to each one of the species studied here based on previous GenBank data, showed M. figueirae sp. nov. and H. santarenensis sp. nov. clustering in distinct lineages. While H. santarenensis sp. nov. clustered in a well-supported subclade composed of Henneguya species that infect gills of South American pimelodid hosts, M. figueirae sp. nov. clustered in a weakly supported subclade containing parasite species of bryconid hosts.

Vittaria graminifolia(Pteridaceae) andDidymoglossum petersii(Hymenophyllaceae) in Broxton Rocks, GA

We report on the occurrence of independent gametophytes of Didymoglossum petersii and both gametophytes and sporophytes of Vittaria graminifolia in the Broxton Rocks Preserve of southern Georgia. This is the first time sporophytes of V. graminifolia have been observed in the United States. In order to unambiguously identify both taxa, we extracted DNA for each. In the case of V. graminifolia, we used BLAST to compare our results to sequences in GenBank for two plastid loci (rbcL and rpoA) to determine its affinities. Because there are no GenBank data for D. petersii, it was necessary to collect an additional specimen of this species for comparison in a phylogenetic analysis. Results confirm the identity of each specimen and provide insight into the biogeographic history of D. petersii.

Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey.

Diversity-generating retroelements (DGRs) are novel genetic elements that use reverse transcription to generate vast numbers of sequence variants in specific target genes. Here, we present a detailed comparative bioinformatic analysis that depicts the landscape of DGR sequences in nature as represented by data in GenBank. Over 350 unique DGRs are identified, which together form a curated reference set of putatively functional DGRs. We classify target genes, variable repeats and DGR cassette architectures, and identify two new accessory genes. The great variability of target genes implies roles of DGRs in many undiscovered biological processes. There is much evidence for horizontal transfers of DGRs, and we identify lineages of DGRs that appear to have specialized properties. Because GenBank contains data from only 10% of described species, the compilation may not be wholly representative of DGRs present in nature. Indeed, many DGR subtypes are present only once in the set and DGRs of the candidate phylum radiation bacteria, and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea archaea, are exceptionally diverse in sequence, with little information available about functions of their target genes. Nonetheless, this study provides a detailed framework for classifying and studying DGRs as they are uncovered and studied in the future.

First Report of Gladiolus Rust Caused by Uromyces transversalis in Merida, Venezuela

In December of 2016, rust sori were observed on leaves of gladiolus plants (Gladiolus sp.) in a garden located in the National Forest Products Laboratory, Faculty of Forestry and Environmental Sciences, University of Los Andes, Merida, Venezuela. All gladiolus plants in the garden were infected. The uredinia were bright orange, variable in shape from globose to ovoid, coalescing transversely across the leaf. The urediniospores were hyaline to yellow gold, ovate to oblong, echinulate, and measured 15 to 26 × 15 to 20 μm with a wall 1.5 to 2.5 μm thick. Telia were not observed. Based on uredinial morphology, the pathogen was identified as Uromyces transversalis (Thum.) G. Winter (Hernandez 2004). Molecular analyses were performed to confirm identification of the rust. Genomic DNA was extracted from symptomatic gladiolus leaves, and the first 680 bp of the nuclear ribosomal large subunit (28S) were amplified and sequenced following protocols described in Aime (2006). The Venezuelan isolate shared 100% identity with U. transversalis BRIP56045 (GenBank accession no. KM249863; McTaggart et al. 2016) in BLAST analyses. A voucher specimen has been deposited in the Arthur Fungarium, Purdue University (PUR N16743) and sequence data in GenBank (MF374730). Gladiolus rust is capable of causing severe disease on up to 100% of plants being grown for flower production (Blomquist et al. 2007; Rodriguez-Alvarado et al. 2006). U. transversalis has been reported on Gladiolus sp. in parts of Africa and Europe, Australia, New Zealand, Argentina, Brazil, Martinique, and Mexico (Blomquist et al. 2007; Hernandez 2004). To our knowledge, this is the first report of U. transversalis causing gladiolus rust in Venezuela. The country must take quarantine control measures as well as eradication programs for this pathogen before it is spread throughout the national territory.

Molecular epidemiology of goat pox viruses.

Goat pox disease outbreaks were observed in different places affecting Black Bengal Goats in West Bengal (WB) and Tellicherry, Vembur and non-descriptive breeds in Tamil Nadu (TN) causing severe lesions and mortality up to 30%. Clinical specimens from all the outbreaks were screened by polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) and confirmed the diseases as Goat Pox. Virus isolation in Vero cell line was done with randomly selected ten samples, cytopathic effects (CPE) characterized by syncytia and intracytoplasmic inclusion bodies were observed after several blind passages. Nucleotide sequence of complete p32 gene using randomly selected two isolates and three clinical specimens revealed presence of Goat pox virus (GTPV)-specific signature residues in all the sequences. Phylogenetic analysis using the present five sequences along with GenBank data of GTPV complete p32 gene sequences showed all the GTPV sequences cluster together except Pellor strain (NC004003) and FZ Chinese strain (KC951854). The five sequences either from WB or TN cluster more closely with GTPV isolates of Maharashtra state that were responsible for cross species outbreak of pox disease in both sheep (KF468759) and goats (KF468762) in India during the year 2010. All the Indian goat pox viruses, including the Mukteswar strain, isolated in 1946 and sequence reported in 2004 clustered together with the GTPVs causing the recent outbreaks. It was observed that GTPVs caused similar clinical manifestation irrespective of their geographical locations and breed characteristics, no variation observed among the Indian isolates based on p32 gene over the period of seventy years and disease outbreaks could not be observed or reported in vaccinated goats.

Abstract A15: The relationship between cervical cancer associated genes and human papilloma viruses in rural Africans in Zaria

Abstract Cervical cancer is a major public health problem and one of the leading gynecological cancers in developing nations. Reports from Nigeria, the largest black nation in the world by population, show that the national incidence of cervical cancer is 250/100,000. We sought to evaluate the relationship between cervical cancer associated genes and human papilloma viruses from rural Africans in Zaria, Nigeria using immunohistochemistry and molecular phylogenetics. Selected cervical cancer associated genes sequences which include Ki-67 (NM_002417.4), p53 (AB082923.1), EGFR (NM_005228.3), MYC (M25803.1), KRAS (EF471957.1), TGF-B (AF254794.1) and RB (AH002963.2) genes and HPV 16 (KJ869425.1 E6 and E7 variants), HPV 18 (KJ869426.1), HPV 45 (S40261.1), HPV 6 (A25369.1), HPV 11 (J04351.1), HPV 31 (KJ869427.1) and HPV 33 (KJ869428.1) sequences were retrieved from the gene bank data base. The sequences were aligned and bootstrap at 2000 bp to create a molecular phylogenetic tree. Haematoxylin and Eosin together with immunohistochemistry were performed on fifty formalin-fixed paraffin-embedded (FFPE) tissue blocks using Anti- Ki-67, p53, EGFR, MYC, KRAS, TGF-B and RB monoclonal antibodies. Result from the phylogenetic analysis reveals trichotomized tree showing apparent significant evolutionary relationship between cladogram of HPV16 and MYC; HPV18, HPV6 and KRAS genes; EGFR gene and HPV45. Immunohistochemistry results show multivariate expression of Ki-67, p53, EGFR, MYC, KRAS, TGF-B and RB of proteins from the cervical cancer tissue blocks used. Combination of Ki-67 biomarker and other cervical cancer associated genes together with HPV subtypes-genotyping can serve as useful instruments in proper management of the disease. Citation Format: John Idoko, Mohammed Faruk, Jigo Dangude Yaro, James Oluwa Enemari, Peter Akpulu. The relationship between cervical cancer associated genes and human papilloma viruses in rural Africans in Zaria [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr A15.

How many species and under what names? Using DNA barcoding and GenBank data for west Central African amphibian conservation.

Development projects in west Central Africa are proceeding at an unprecedented rate, often with little concern for their effects on biodiversity. In an attempt to better understand potential impacts of a road development project on the anuran amphibian community, we conducted a biodiversity assessment employing multiple methodologies (visual encounter transects, auditory surveys, leaf litter plots and pitfall traps) to inventory species prior to construction of a new road within the buffer zone of Moukalaba-Doudou National Park, Gabon. Because of difficulties in morphological identification and taxonomic uncertainty of amphibian species observed in the area, we integrated a DNA barcoding analysis into the project to improve the overall quality and accuracy of the species inventory. Based on morphology alone, 48 species were recognized in the field and voucher specimens of each were collected. We used tissue samples from specimens collected at our field site, material available from amphibians collected in other parts of Gabon and the Republic of Congo to initiate a DNA barcode library for west Central African amphibians. We then compared our sequences with material in GenBank for the genera recorded at the study site to assist in identifications. The resulting COI and 16S barcode library allowed us to update the number of species documented at the study site to 28, thereby providing a more accurate assessment of diversity and distributions. We caution that because sequence data maintained in GenBank are often poorly curated by the original submitters and cannot be amended by third-parties, these data have limited utility for identification purposes. Nevertheless, the use of DNA barcoding is likely to benefit biodiversity inventories and long-term monitoring, particularly for taxa that can be difficult to identify based on morphology alone; likewise, inventory and monitoring programs can contribute invaluable data to the DNA barcode library and the taxonomy of complex groups. Our methods provide an example of how non-taxonomists and parataxonomists working in understudied parts of the world with limited geographic sampling and comparative morphological material can use DNA barcoding and publicly available sequence data (GenBank) to rapidly identify the number of species and assign tentative names to aid in urgent conservation management actions and contribute to taxonomic resolution.

Unexpected High Diversity of Terrestrial Cyanobacteria from the Campus of the University of the Ryukyus, Okinawa, Japan.

Terrestrial cyanobacterial strains were isolated from the Nishihara campus of the University of the Ryukyus, Okinawa, Japan. The 13 sampling sites were distributed in a 200 m radius and appeared as dry, blackened stains. From these small areas, 143 cyanobacterial strains were established. The strains were divided into five morphotypes, including unicells, unicells with baeocytes, non-branching filaments, false-branching filaments, and heterocystous strains. From the strains, 105 partial 16S rRNA gene sequences were obtained and could be classified into 30 generic types. Among them, 22 unique strains and over 1100 bps of data were selected for further phylogenetic analyses. These sequences were positioned into six main clades corresponding to cyanobacterial orders: Nostocales, Chroococidiopsidales, Chroococcales, Oscillatoriales, Pleurocapsales, and Synechococcales. Almost all sequences had no identical matching data in GenBank and many of them had no closely related data. These data suggest that the terrestrial cyanobacteria are very divese even within close sampling areas, such as within the campus of the University of the Ryukyus. The established strains are not only important for classification of terrestrial cyanobacteria but also for possible application studies in the future.

Performance evaluation of isoproturon-degrading indigenous bacterial isolates in soil microcosm

ABSTRACTIsoproturon (IPU)-degrading soil bacteria were isolated from herbicide-applied wheat fields. These isolates were identified using cultural, morphological, biochemical and 16S rRNA sequencing methods. 16S rRNA sequences of both the bacterial isolates were compared with NCBI GenBank data base and identified as Bacillus pumilus and Pseudoxanthomonas sp. A soil microcosm study was carried out for 40 days in six different treatments. Experimental results revealed maximum 95.98% IPU degradation in treatment 6 where bacterial consortia were augmented in natural soil, followed by 91.53% in treatment 5 enriched with organic manure as an additional carbon source. However, only 14.03% IPU was degraded in treatment 1 (control) after 40 days. In treatments (2–4), 75.59%, 70.92% and 77.32% IPU degradation was recorded, respectively. IPU degradation in all the treatments varied significantly over the control. 4-Isopropylaniline was detected as IPU degradation by-product in the medium. The study confirmed that B. pumilus and Pseudoxanthomonas sp. performed effectively in soil microcosms and could be employed profitably for field-scale bioremediation experiments.

Genetic population structure and phylogeny of the common octopus Octopus vulgaris Cuvier, 1797 in the western Mediterranean Sea through nuclear and mitochondrial markers

Genetic information is crucial for the proper exploitation of Octopus vulgaris, the most commercially valuable octopus species worldwide. The main aim of the present study was to investigate genetic structure, with the intent to inform effective management of the common octopus in Sardinia (western Mediterranean Sea), one of the most productive areas within Italian waters. Patterns of population structure were assessed in 246 specimens from seven population samples. Variation in five nuclear-encoded microsatellites and sequences of two mitochondrial genes (COI and COIII) highlighted high variability and low but significant genetic differentiation among populations, which clustered into four groups corresponding to the north, northwest, south, and east coasts of Sardinia. Secondarily, the sequence data from Sardinia were compared with GenBank data from other areas. AMOVA and Bayesian analyses supported the occurrence of significant differences within the Mediterranean Sea, and between Eastern Atlantic and Mediterranean samples. The described genetic differentiation at a regional geographical scale could be determined by a combination of historical and/or current events restricting gene flow. The occurrence of significant genetic structuring at different spatial scales is an important piece of information to define the most appropriate conservation strategies in the area, both at the local and regional level.

Bacterial and fungal biodeterioration of discolored building paints in Lagos, Nigeria.

Microbial induced discolorations are an unsightly feature occurring on painted walls in Lagos, the commercial hub of Nigeria. Very few studies have been carried out conventionally about the microbial community structure of discolored painted walls in Nigeria therefore, knowledge of the true microbial diversity is elusive. To further our understanding of the phylogenetic diversity of representative microbial community on 40 discolored and three clean-looking buildings, a comparative DNA sequence analysis of 16S rDNA genes was undertaken. Following DNA extraction, portions of the rDNA genes were amplified by PCR and sequenced. Resulting sequences were compared with GenBank data base sequences. Fifteen unique fungal sequences and one bacterial sequence were obtained. Majority (37.50%) of rDNA sequences analyzed, represent the genus Meyerozyma of which the novel fungus Meyerozyma guilliermondii, which to our knowledge, has not yet been implicated in painted walls was detected. Clones from the discolored painted wall isolates also produced a data set in which 31.25% of sequences were related to Fusarium proliferatum and 6.25% were Pseudomonas aeruginosa. The remaining sequences clustered with members of the genera Candida (6.25%), Aspergillus (12.5%) and Cerrena (6.25%). The study provides reliable data on microbial communities on painted walls and information for paint biocide formulation.

A new and updated resource for codon usage tables

BackgroundDue to the degeneracy of the genetic code, most amino acids can be encoded by multiple synonymous codons. Synonymous codons naturally occur with different frequencies in different organisms. The choice of codons may affect protein expression, structure, and function. Recombinant gene technologies commonly take advantage of the former effect by implementing a technique termed codon optimization, in which codons are replaced with synonymous ones in order to increase protein expression. This technique relies on the accurate knowledge of codon usage frequencies. Accurately quantifying codon usage bias for different organisms is useful not only for codon optimization, but also for evolutionary and translation studies: phylogenetic relations of organisms, and host-pathogen co-evolution relationships, may be explored through their codon usage similarities. Furthermore, codon usage has been shown to affect protein structure and function through interfering with translation kinetics, and cotranslational protein folding.ResultsDespite the obvious need for accurate codon usage tables, currently available resources are either limited in scope, encompassing only organisms from specific domains of life, or greatly outdated. Taking advantage of the exponential growth of GenBank and the creation of NCBI’s RefSeq database, we have developed a new database, the High-performance Integrated Virtual Environment-Codon Usage Tables (HIVE-CUTs), to present and analyse codon usage tables for every organism with publicly available sequencing data. Compared to existing databases, this new database is more comprehensive, addresses concerns that limited the accuracy of earlier databases, and provides several new functionalities, such as the ability to view and compare codon usage between individual organisms and across taxonomical clades, through graphical representation or through commonly used indices. In addition, it is being routinely updated to keep up with the continuous flow of new data in GenBank and RefSeq.ConclusionGiven the impact of codon usage bias on recombinant gene technologies, this database will facilitate effective development and review of recombinant drug products and will be instrumental in a wide area of biological research. The database is available at hive.biochemistry.gwu.edu/review/codon.