Fragment DNA Sequencing Research Articles

Two single nucleotide polymorphisms in the caprine GnIH gene are associated with litter size

Gonadotropin-inhibitory hormone (GnIH) can decrease luteinizing hormone and/or follicle-stimulating hormone levels in rat, mouse, sheep, and cattle by the direct suppression of gonadotropin-releasing hormone (GnRH). The present study investigated polymorphisms in the GnIH genes of two dairy goat breeds and their association with litter size. Single nucleotide polymorphisms (SNPs) g.1837C>G and g.3195G>A (GenBank Accession Nos. KR778885 and KR819142) were detected in the GnIH genes of Xinong Saanen and Guanzhong dairy goat breeds using DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Furthermore, the g.1837C>G and g.3195G>A loci were closely linked in both breeds (r<sup>2</sup> > 0.33). Association analysis showed that these SNPs had significant effects on the litter size of goats (P < 0.05). In both breeds, individuals with the CC/GG (g.1837C>G/g.3195G>A) genotype showed larger litter sizes in the second and average parities than individuals with the GG/AA genotype (P < 0.05). Known biochemical and physiological functions, along with our results, indicate that the CC/GG genotype may be used in marker-assisted selection to choose individuals with a larger litter size from both breeds.

Whole-genome sequencing of eukaryotes: From sequencing of DNA fragments to a genome assembly

Rapid advances in sequencing technologies of second- and even third-generation made the whole genome sequencing a routine procedure. However, the methods for assembling of the obtained sequences and its results require special consideration. Modern assemblers are based on heuristic algorithms, which lead to fragmented genome assembly composed of scaffolds and contigs of different lengths, the order of which along the chromosome and belonging to a particular chromosome often remain unknown. In this regard, the resulting genome sequence can only be considered as a draft assembly. The principal improvement in the quality and reliability of a draft assembly can be achieved by targeted sequencing of the genome elements of different size, e.g., chromosomes, chromosomal regions, and DNA fragments cloned in different vectors, as well as using reference genome, optical mapping, and Hi-C technology. This approach, in addition to simplifying the assembly of the genome draft, will more accurately identify numerical and structural chromosomal variations and abnormalities of the genomes of the studied species. In this review, we discuss the key technologies for the genome sequencing and the de novo assembly, as well as different approaches to improve the quality of existing drafts of genome sequences.

Gene Encoding Nitrilase from Soil Sample of Lombok Gold Mine Industry using Metagenomics Approach

<p class="Els-body-text">This paper describes a efficient screening gene nitrilase from contaminated soil from Lombok gold mine industry. DNA was extracted directly from soil using the soil DNA isolation kit based on enzymatic, chemical and mechanical lysis. The existence of nitrilase gene in soil sample can be identified by nitrilase gene amplification using H1F˗H1R primer. BLASTN analysis result revealed that the nitrilase gene fragment which was amplified by H1F˗H1R primer has a high homology with <em>Rhodococcus rhodochrous </em>strain<em> tg1˗A6 nitrilase gene</em>. These amplification and DNA fragment sequencing results indicated that nitrilase gene existence on soil sample can be identified by metagenomic approach</p><p class="Els-Abstract-text"> </p><div><p class="Els-keywords"><strong>Keywords:</strong> Metagenomics; nitrilase gene; <em>Rhodococcus rhodochrous</em>; soil.</p></div>

Isolation of Rickettsia rickettsii from the tick Amblyomma sculptum from a Brazilian spotted fever-endemic area in the Pampulha Lake region, southeastern Brazil

Brazilian spotted fever (BSF) is a tick-borne disease caused by the bacterium Rickettsia rickettsii, the deadliest spotted fever of the world, transmitted in southeastern Brazil mainly by the tick Amblyomma sculptum, a member of the Amblyomma cajennense species complex. In the present study, over 5000 adults of A. sculptum ticks were collected by dry ice traps in the Municipal Ecological Park, alongside the Pampulha Lake region, a BSF-endemic area of Belo Horizonte city, state of Minas Gerais, southeastern Brazil. Ticks were taken alive to the laboratory, where a sample of 2100 specimens was processed for isolation of R. rickettsii. For this purpose, ticks were macerated and intraperitoneally inoculated into guinea pigs. Only one out of 21 inoculated guinea pigs presented high fever within 21days post inoculation with tick homogenates. This febrile animal was euthanized and its internal organs were macerated and inoculated into additional guinea pigs (guinea pig passage). A spleen sample from a febrile guinea pig was used to inoculate Vero cells, resulting in a successful isolation and in vitro establishment of rickettsiae. Rickettsia-infected Vero cells were used for molecular characterization of the rickettsial isolate through PCR and DNA sequencing of fragments of three rickettsial genes (gltA, ompA, and ompB), which were all 100% identical to corresponding sequences of R. rickettsii from GenBank. The present R. rickettsii isolate was designated as strain Pampulha. A minimal infection rate of 0.05% R. rickettsii-infected ticks was estimated for A. sculptum population of the Pampulha Lake region. Our results, coupled with epidemiological evidences, suggest that R. rickettsii strain Pampulha, isolated from A. sculptum ticks in the present study, is the strain responsible for human clinical cases of BSF in the Pampulha Lake region of Belo Horizonte city.

Визначення поліморфних варіантів фрагментів ДНК збудників хламідійних інфекцій сільськогосподарських тварин

Under the currently existing classification, adopted at the Second European Symposium «Animal Chlamydioses and Zoonotic Implications (EMAC-2)», Chlamydia pathogens of animals and humans are intracellular gram-negative bacteria belonging to Chlamydiales order, Chlamydiaseae family, Chlamydia genus. The above mentioned genus includes 11 species: C. abortus, C. avium, C. caviae, C. felis, C. gallinacea, S. muridarum, C. pecorum, C. pneumoniae, C. psittaci, C. suis and C. trachomatis, 10 of them being pathogenic for animals and Chlamydia trachomatis being exclusively human Chlamydiosis agent. Development of highly sensitive and specific molecular genetic test systems for indication and species differentiation of the said Chlamydia genus bacteria will permit to reliably study various aspects of chlamydial infection. Aim of the study was to perform bioinformatiс alignment of different genes’ nucleotide sequences to determine polymorphic DNA regions of Chlamydia genus bacteria, which are the basis for designing oligonucleotide primers for molecular genetic test systems capable of differentiating pathogens, causing disease in cattle and small ruminants, horses and pigs, by species. Bioinformatic study has been performed in 411 primary nucleotide DNA sequences of genes encoding 16S rRNA, RNase P RNA and MOMP of four chlamydial infections agents of farm animals (C. abortus, C. pecorum, C. pneumoniea, C. suis) obtained from the international electronic databases «GenBank» and «PubMed». Meanwhile, it was determined that the gene encoding the main outer membrane protein (MOMP) of Chlamydia possesses the highest variability level, making 97.1%. Using the method of aligning the primary sequences of the said gene, by means of «MEGA4» and «MEGA7» software, polymorphic fragments of nucleotide DNA sequences have been determined for C. abortus, C. pecorum, C. pneumoniea and C. suis. Specificity testing of polymorphic fragments, determined for each of the four chlamydia species with nucleotide sequences of microorganisms, both opportunistic and other infections pathogens, was carried out using «Blast» online software applications. Polymorphic fragments of the gene encoding MOMP of the above Chlamydia genus bacteria will be used to design oligonucleotide primers of test systems for indication and specific differentiation of farm animals’ chlamydial infections agents in polymerase chain reaction.

Genome-Wide Analysis of Chromatin Accessibility in Arabidopsis Infected with Pseudomonas syringae.

Changes in chromatin accessibility are an important aspect of the molecular changes that occur in eukaryotic cells responding to stress, and they appear to play a critical role in stress-induced transcriptional activation/reprogramming and epigenetic changes. In plants, pathogen infection has been shown to induce rapid and drastic transcriptional reprogramming; growing evidence suggests that chromatin remodeling plays an essential role in this phenomenon. The recent development of genomic tools to assess chromatin accessibility presents a significant opportunity to investigate the relationship between chromatin dynamicity and gene expression. In this protocol, we have adopted a popular chromatin accessibility assay, DNase-seq, to measure chromatin accessibility in Arabidopsis infected with the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). DNase-seq provides information on chromatin accessibility through the sequencing of DNA fragments generated by DNase I digestion of open chromatin, followed by mapping these sequences on a reference genome. Of the two popular DNase-seq approaches, we based our method on the Stamatoyannopoulos protocol, which involves two DNase cleavages rather than a single cleavage, followed by size fractionation. Please note that this two-cleavage approach is widely accepted and has been used extensively by ENCODE (Encyclopedia of DNA Elements) project, a public research consortium investigating cis- and trans-elements in the transcriptional regulation in animal cells. To enhance the quality of the chromatin accessibility assay, we modified this protocol by including two centrifugation steps for nuclear enrichment and size fractionation and an extra washing step for removal of chloroplasts and Pst. The outcomes obtained by this approach are also discussed.

POSSIBILITIES OF DE NOVO TRANSCRIPTOME SEQUENCING IN PYLOGENETIC RESEARCH ON AN EXAMPLE OF TARAXACUM OFFICINALE (ASTERACEAE)

<p class="Default"> </p><p>As a result of the research we obtained a cDNA library, sequences and carried out <em>de novo </em>assembly and functional annotation of the transcriptome of systematically complex, almost cosmopolitan <em>Taraxacum officinale</em>. Systematics of the species is complicated because of separation of many microspecies and intraspecific taxa, which may be explained by the presence of ploidy races, the phenomenon of apomixis and significant polymorphism. Attempts of separation of microspecies and closely related species based on sequencing of chloroplast and nuclear DNA fragments, did not give acceptable results. We have made the first attempt to analyze the transcriptome for understanding the genome evolution of agamospermous-sexual complex of the species. A total of 84440 reads were obtained with a total 31,540,710 bp. As a result of the <em>de novo </em>assembly, we obtained 13902 contigs, with an average GC content equal to 38.1% and a maximum length of 5255 bp. In total, we received 3798 annotated genes. According to the functional annotation based on sequence homology, 2687 contigs were attributed to biological processes (19.32%), 3299 – to molecular functions (23.7%), 2157 – to the cellular component (15.51%) and 7497 contigs – with unknown functions. In the first category “single-organism cellular process”, “response to stimulus”, “photosynthesis-light reaction”, “oxidation-reduction” and “translation” have dominated. In the category of molecular function “nucleic acid binding”, “hydrolase activity”, “transferase” and “oxidoreductase” activities have dominated. In the cellular component category “integral component of membrane”, “chloroplast thylakoid membrane”, “photosystems” and “nucleus” have dominated.</p>

Towards the Development of a Noninvasive Prenatal Test for Beta-Thalassemia: Utilization of Probe Capture Enrichment and Next Generation Sequencing

β-thalassemia causes significant morbidity and mortality worldwide. Currently, the diagnosis can be made prenatally for couples at risk using invasive procedures such as chorionic villus sampling and amniocentesis. Noninvasive prenatal testing (NIPT) on maternal blood samples would enable earlier fetal diagnosis and eliminate risks associated with these procedures.The discovery of cell-free fetal DNA (cfFDNA) in maternal plasma and advances in next generation sequencing (NGS) have made NIPT a clinical reality for aneuploidies. Diagnosing autosomal recessive (AR) disorders is more challenging as it requires determination of both the paternally and maternally inherited alleles and can be particularly difficult when both parents carry the same mutation. Previous studies used methods to identify the paternally inherited allele in maternal plasma through the detection of a DNA sequence variant present in the father and absent in the mother. Our method expands the target region beyond the β-globin gene into highly polymorphic regions to increase the likelihood of identifying unique paternal sequences. Unlike the detection of the paternal allele, there is no direct qualitative approach for determining the maternally inherited allele. Our solution is an indirect quantitative method that compares the ratio of allelic sequence reads to infer which maternal allele was inherited by the fetus.We have developed a novel NGS assay which utilizes probe capture enrichment, a method employing thousands of short overlapping oligonucleotide probes complementary to a target sequence region. This design makes it uniquely applicable to short, fragmented DNA, such as cell-free DNA (~150 base pairs). Our probe assay targets a contiguous 900 bp region which spans a portion of the β-globin gene (part of exon 2 as well as the entirety of IVS-1 and exon 1) and extends 579 bp into the highly polymorphic 5' UTR region to identify linked sequence variations. Additionally, the assay targets 451 single nucleotide polymorphisms (SNPs) throughout the genome. SNPs that are "informative" (i.e. an allele present in the fetus and absent in the mother) are used to calculate the fraction of cfDNA from the fetus.We have evaluated our assay’s performance in a set of experiments designed to simulate the challenging aspects of cfFDNA: very low quantity and short fragment size. The assay’s sensitivity was tested by preparing libraries containing amounts of DNA ranging from 50 to 0.05 ngs. At DNA amounts as low as 5 ng (5-fold lower than that expected in plasma), 100% coverage was achieved for the targeted β-globin region and SNPs. The probe/NGS system successfully captured and sequenced DNA fragments as short as 35 bps and as little as 0.5 ng of DNA with >95% coverage. To test the ability of the probe/NGS system to resolve mixtures, DNA samples from patients with known β-globin mutations were combined in ratios ranging from 2.5:97.5 to 20:80 in 25 ng total DNA to mimic the maternal/fetal cfDNA mixture. Our assay was able to detect minority heterozygous mutant alleles at proportions as low as 1.25% and 0.3 ng of DNA. In a mixture designed to simulate a case with a shared parental mutation (CD41/42(-TTCT)), we identified a linked SNP (rs713040) allele, which was within 250 bp of the mutation and unique to the minor fraction. We used this SNP to distinguish the CD41/42 (-TTCT) mutation contributed by the minor fraction.Based on 6 mixtures, we observed 24.3% (110/451) of SNPs to be informative, allowing for a precise estimate of the minor fraction. We estimated the minor fraction to be 11.88% and 5.98% compared to the expected 10% and 5%, respectively. To show proof of concept for inferring the minor ("fetal") genotype when the major ("maternal") genotype was heterozygous mutant (IVS1-5 (G>C)), the estimated minor fraction (10.4% based on 104 informative SNPs) was used to calculate the expected allelic ratios of the 3 different possible minor ("fetal") genotypes. The minor genotype was correctly inferred as wt/wt based on the observed mixture ratio (42.56/57.41 mut/wt) compared to the expected (44.93/55.07).These data show that our probe capture/NGS system can overcome the challenges implicit in the analysis of cfFDNA for NIPT: low DNA amount (<5 ng) and short fragments (<150 bp). We expect that our approach using the fetal fraction estimate will allow us to successfully infer the fetal genotype when applied to maternal plasma. DisclosuresErlich:Allen and Overy, Law Office: Consultancy.

6 ANEUPLOIDY TOLERANCE IN RHESUS MACAQUE PRE-IMPLANTATION EMBRYOS VIA MICRONUCLEI FORMATION, CELLULAR FRAGMENTATION, AND BLASTOMERE EXCLUSION

A primary contributor to in vitro fertilization (IVF) failure is the presence of unbalanced chromosomes in pre-implantation embryos. Previous array-based and next-generation sequencing (NGS) studies determined that ~50 to 80% of human embryos are aneuploid at the cleavage stage. During early mitotic divisions, many human embryos also sequester mis-segregated chromosomes into micronuclei and concurrently undergo cellular fragmentation. We hypothesised that cellular fragmentation represents a response to mis-segregated chromosomes that are encapsulated into micronuclei. Here, we utilised the rhesus macaque pre-implantation embryo as a model to study human embryonic aneuploidy using a combination of EevaTM time-lapse imaging for evaluating cell divisions, single-cell/-fragment DNA-Sequencing (DNA-Seq), and confocal microscopy of nuclear structures. Results from our time-lapse image analysis demonstrated that there are considerable differences in the timing of the first and third mitotic divisions between rhesus blastocysts and those that arrested before this stage in development (P &lt; 0.01; ANOVA). By examining the chromosome content of each blastomere from cleavage stage embryos via DNA-Seq, we determined that rhesus embryos have an aneuploidy frequency up to ~62% (N = 26) with several embryos exhibiting chromosomal mosaicism between blastomeres (N = 6). Certain blastomeres also exhibited reciprocal whole chromosomal gains or losses, indicating that these embryos had undergone mitotic non-disjunction early in development. In addition, findings of reciprocal sub-chromosomal deletions/duplications among blastomeres suggest that chromosomal breakage had occurred in some embryos as well. Embryo immunostaining for the nuclear envelope protein, LAMIN-B1, demonstrated that fragmented cleavage-stage rhesus embryos often contain micronuclei and that cellular fragments can enclose DNA. Our DNA-Seq analysis confirmed that cellular fragments might encapsulate whole and/or partial chromosomes lost from blastomeres. When embryos were immunostained with gamma-H2AX, a marker of chromatin fragility, we observed distinct foci solely in micronuclei and DNA-containing cellular fragments. This suggests that micronuclei may be ejected from blastomeres through the process of cellular fragmentation and, once sequestered, these mis-segregated chromosomes become highly unstable and undergo DNA degradation. Finally, we also observed that ~10% of embryos prevented cellular fragments or large blastomeres from incorporating into the inner cell mass or trophectoderm at the blastocyst stage (n = 5). Upon confocal imaging, multiple nuclei and intense gamma-H2AX foci were found in a large unincorporated blastomere in one of the blastocysts. Altogether, our findings demonstrate that the rhesus embryo responds to segregation errors by eliminating chromosome-containing micronuclei via cellular fragmentation and/or selecting against aneuploid blastomeres that fail to divide during pre-implantation development with significant implications for human IVF.

Diet assessment of the Atlantic Sea Nettle Chrysaora quinquecirrha in Barnegat Bay, New Jersey, using next-generation sequencing.

Next-generation sequencing (NGS) methodologies have proven useful in deciphering the food items of generalist predators, but have yet to be applied to gelatinous animal gut and tentacle content. NGS can potentially supplement traditional methods of visual identification. Chrysaora quinquecirrha (Atlantic sea nettle) has progressively become more abundant in Mid-Atlantic United States' estuaries including Barnegat Bay (New Jersey), potentially having detrimental effects on both marine organisms and human enterprises. Full characterization of this predator's diet is essential for a comprehensive understanding of its impact on the food web and its management. Here, we tested the efficacy of NGS for prey item determination in the Atlantic sea nettle. We implemented a NGS 'shotgun' approach to randomly sequence DNA fragments isolated from gut lavages and gastric pouch/tentacle picks of eight and 84 sea nettles, respectively. These results were verified by visual identification and co-occurring plankton tows. Over 550000 contigs were assembled from ~110million paired-end reads. Of these, 100 contigs were confidently assigned to 23 different taxa, including soft-bodied organisms previously undocumented as prey species, including copepods, fish, ctenophores, anemones, amphipods, barnacles, shrimp, polychaete worms, flukes, flatworms, echinoderms, gastropods, bivalves and hemichordates. Our results not only indicate that a 'shotgun' NGS approach can supplement visual identification methods, but targeted enrichment of a specific amplicon/gene is not a prerequisite for identifying Atlantic sea nettle prey items.

Impact of TNF-α and LTα gene polymorphisms on genetic susceptibility in Indian SLE patients

The promoter polymorphisms of tumour necrosis factor-α (TNF-α) and intronic Lymphotoxin-α (LTα) have been implicated as genetic risk factors for systemic lupus erythematosus (SLE) in various ethnic groups. The aim of this study was to investigate an impact of TNF-α (−308G/A; 238G/A) and LTα (+252A/G) gene polymorphisms in disease susceptibility among Indian 200 SLE patients along with 201 healthy controls. The gene polymorphisms were studied by using direct DNA sequencing and Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) methods. Serum levels were measured by multiplex assay. Allelic frequencies of TNF-α −308A (OR=2.3, p=0.0001, Pc=0.0003) and LTα +252G (OR=2.1, p<0.0001, Pc<0.001) were significantly higher in SLE patients. Frequency of haplotype-AGG was found to be higher in patients than controls (OR=12.2, p=0.0050). Serum levels of TNF-α and LTα also were found to be significantly higher in patients showing variant alleles. TNF-α −308G/A+A/A genotypes (p<0.01) and LTα +252 A/G+G/G genotypes (p<0.02) were significantly associated with renal disorders and haematological manifestations. SLE patients with −308G/A+A/A genotypes showed higher prevalence of anti-dsDNA antibodies (OR=3.9, p=0.0014, Pc=0.0098) and anti-Sm antibodies (OR=4.1, p=0.0002, Pc=0.0014). The present study suggests TNF-α −308A and LTα +252G as risk alleles for disease susceptibility associated with higher serum levels of TNF-α and LTα and concomitant discrete clinical features among Indian SLE patients.

Misconceptions on Missing Data in RAD-seq Phylogenetics with a Deep-scale Example from Flowering Plants.

Restriction-site associated DNA (RAD) sequencing and related methods rely on the conservation of enzyme recognition sites to isolate homologous DNA fragments for sequencing, with the consequence that mutations disrupting these sites lead to missing information. There is thus a clear expectation for how missing data should be distributed, with fewer loci recovered between more distantly related samples. This observation has led to a related expectation: that RAD-seq data are insufficiently informative for resolving deeper scale phylogenetic relationships. Here we investigate the relationship between missing information among samples at the tips of a tree and information at edges within it. We re-analyze and review the distribution of missing data across ten RAD-seq data sets and carry out simulations to determine expected patterns of missing information. We also present new empirical results for the angiosperm clade Viburnum (Adoxaceae, with a crown age >50 Ma) for which we examine phylogenetic information at different depths in the tree and with varied sequencing effort. The total number of loci, the proportion that are shared, and phylogenetic informativeness varied dramatically across the examined RAD-seq data sets. Insufficient or uneven sequencing coverage accounted for similar proportions of missing data as dropout from mutation-disruption. Simulations reveal that mutation-disruption, which results in phylogenetically distributed missing data, can be distinguished from the more stochastic patterns of missing data caused by low sequencing coverage. In Viburnum, doubling sequencing coverage nearly doubled the number of parsimony informative sites, and increased by >10X the number of loci with data shared across >40 taxa. Our analysis leads to a set of practical recommendations for maximizing phylogenetic information in RAD-seq studies. [hierarchical redundancy; phylogenetic informativeness; quartet informativeness; Restriction-site associated DNA (RAD) sequencing; sequencing coverage; Viburnum.].

Polymorphisms of Flanking Region of the ASB15 Gene and Their Associations with Performance Traits in Chicken

ABSTRACTResearch on the identity of genes and their relationship with traits of economic importance in chickens could assist in the selection of poultry. In this study, an F2 resource population of Gushi chickens crossed with Anka broilers was used to detect single-nucleotide polymorphisms (SNPs) in the flanking region of the ASB15 gene by DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). One SNP of −1271 C>T in 5′ flanking region of the chicken ASB15 gene and two SNPs of the 10618 A>G and 10716 G>A in 3′ flanking region were identified. Furthermore, the 10618 A>G and 10716 G>A in 3′ flanking region were in complete linkage. Association analysis results showed that −1271 C>T was not associated with performance traits, while the 10618 A>G and 10716 G>A were significantly associated with BW2, 4, 6, 8, 10, 12, SL12, CD8, CW4, 8, 12, BSL4, 8, 12, and SEW, EW, WW, BMW, LW, CW, SFT. Our results suggest that the ASB15 gene profoundly affects chicken performance traits.

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers.

BackgroundThe yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes (known sequences of fixed length) primarily encode the sample identity of sequenced DNA fragments, barcodes made of random sequences (Unique Molecular Identifier or UMIs) are often used to distinguish between PCR duplicates and transcript abundance in, for example, single-cell RNA sequencing (scRNA-seq). In paired-end sequencing, different barcodes can be inserted at each fragment end to either increase the number of multiplexed samples in the library or to use one of the barcodes as UMI. Alternatively, UMIs can be combined with the sample barcodes into composite barcodes, or with standard Illumina® indexing. Subsequent analysis must take read duplicates and sample identity into account, by identifying UMIs.ResultsExisting tools do not support these complex barcoding configurations and custom code development is frequently required. Here, we present Je, a suite of tools that accommodates complex barcoding strategies, extracts UMIs and filters read duplicates taking UMIs into account. Using Je on publicly available scRNA-seq and iCLIP data containing UMIs, the number of unique reads increased by up to 36 %, compared to when UMIs are ignored.ConclusionsJe is implemented in JAVA and uses the Picard API. Code, executables and documentation are freely available at http://gbcs.embl.de/Je. Je can also be easily installed in Galaxy through the Galaxy toolshed.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1284-2) contains supplementary material, which is available to authorized users.

Discriminating coding from non-coding regions based on codon structure and methylation-mediated substitution: An application in rice and cattle

Coding regions are the fragments of DNA sequence that codes for protein through the process of transcription and translation respectively. On the other hand, the non coding regions do not give rise to any protein. Discrimination of coding regions from the non coding regions is essential for genome annotation. In this study, an attempt has been made to develop a random forest based computational approach for discriminating coding regions (CDS) from non-coding regions (introns). The features based on codon structure and methylation mediated substitutions were used in this approach. The developed approach achieved high classification accuracy, while tested on two agriculturally important species i.e., rice and cattle. The proposed approach is believed to complement the other prediction methods. Based on the proposed approach, an online prediction server ‘DCDNC’ has also been developed for easy prediction by the users. The prediction server is freely available at http://cabgrid.res.in:8080/DCDNC.

Enrichment by hybridisation of long DNA fragments for Nanopore sequencing.

Enrichment of DNA by hybridisation is an important tool which enables users to gather target-focused next-generation sequence data in an economical fashion. Current in-solution methods capture short fragments of around 200–300 nt, potentially missing key structural information such as recombination or translocations often found in viral or bacterial pathogens. The increasing use of long-read third-generation sequencers requires methods and protocols to be adapted for their specific requirements. Here, we present a variation of the traditional bait–capture approach which can selectively enrich large fragments of DNA or cDNA from specific bacterial and viral pathogens, for sequencing on long-read sequencers. We enriched cDNA from cultured influenza virus A, human cytomegalovirus (HCMV) and genomic DNA from two strains of Mycobacterium tuberculosis (M. tb) from a background of cell line or spiked human DNA. We sequenced the enriched samples on the Oxford Nanopore MinION™ and the Illumina MiSeq platform and present an evaluation of the method, together with analysis of the sequence data. We found that unenriched influenza A and HCMV samples had no reads matching the target organism due to the high background of DNA from the cell line used to culture the pathogen. In contrast, enriched samples sequenced on the MinION™ platform had 57 % and 99 % best-quality on-target reads respectively.

Rickettsial infection in ticks infesting wild birds from two eco-regions of Argentina.

Several tick-borne Rickettsia species are recognized human pathogens in Argentina. Here we evaluated rickettsial infection in ticks collected on passerine birds during 2011-2012 in two eco-regions of Argentina. The ticks were processed by molecular analysis through polymerase chain reaction (PCR) detection and DNA sequencing of fragments of two rickettsial genes, gltA and ompA. A total of 594 tick specimens (532 larvae and 62 nymphs), representing at least 4 species (Amblyomma tigrinum, Ixodes pararicinus, Haemaphysalis juxtakochi, Haemaphysalis leporispalustris), were evaluated. At least one A. tigrinum larva, collected on Coryphospingus cucullatus in Chaco Seco, was infected with Rickettsia parkeri, whereas at least 12 larvae and 1 nymph of I. pararicinus, collected from Troglodytes aedon, Turdus amaurochalinus, Turdus rufiventris, C. cucullatus and Zonotrichia capensis, were infected with an undescribed Rickettsia agent, genetically related to several rickettsial endosymbionts of ticks of the Ixodes ricinus complex. R. parkeri is a recognized human pathogen in several American countries including Argentina, where a recent study incriminated A. tigrinum as the potential vector of R. parkeri to humans. Birds could play an important role in dispersing R. parkeri-infected A. tigrinum ticks. Additionally, we report for the first time a rickettsial agent infecting I. pararicinus ticks.

Comparison of antimicrobial resistant genes in chicken gut microbiome grown on organic and conventional diet

Antibiotics are widely used in chicken production for therapeutic purposes, disease prevention and growth promotion, and this may select for drug resistant microorganisms known to spread to humans through consumption of contaminated food. Raising chickens on an organic feed regimen, without the use of antibiotics, is increasingly popular with the consumers. In order to determine the effects of diet regimen on antibiotic resistant genes in the gut microbiome, we analyzed the phylotypes and identified the antimicrobial resistant genes in chicken, grown under conventional and organic dietary regimens. Phylotypes were analyzed from DNA extracted from fecal samples from chickens grown under these dietary conditions. While gut microbiota of chicken raised in both conventional and organic diet exhibited the presence of DNA from members of Proteobacteria and Bacteroidetes, organic diet favored the growth of members of Fusobacteria. Antimicrobial resistance genes were identified from metagenomic libraries following cloning and sequencing of DNA fragments from fecal samples and selecting for the resistant clones (n=340) on media containing different concentrations of eight antibiotics. The antimicrobial resistant genes exhibited diversity in their host distribution among the microbial population and expressed more in samples from chicken grown on a conventional diet at higher concentrations of certain antimicrobials than samples from chicken grown on organic diet. Further studies will elucidate if this phenomena is widespread and whether the antimicrobial resistance is indeed modulated by diet. This may potentially assist in defining strategies for intervention to reduce the prevalence and dissemination of antibiotic resistance genes in the production environment.

Combination effect of cytochrome P450 1A1 gene polymorphisms on uterine leiomyoma: A case-control study.

Uterine leiomyoma (UL) is an estrogen-dependent neoplasm of the uterus, and estrogen metabolizing enzymes affect its progression. This study aimed to evaluate the association between two single-nucleotide polymorphisms of cytochrome P450 1A1 (CYP1A1) gene and UL risk. The study consisted of 105 patients with UL and 112 healthy women as controls. Ile462Val (A/G) and Asp449Asp (T/C) polymorphisms of CYP1A1 gene were analyzed by DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism methods, respectively. The findings indicated no association between Ile462Val (A/G) and Asp449Asp (T/C) polymorphisms of CYP1A1 gene and UL (p < 0.05). However, the combination effect of TT/AG genotypes of the Asp449Asp (T/C) and Ile462Val (A/G) polymorphisms was associated with 4.3-fold higher risk of UL. In addition, haplotype analysis revealed that TG haplotype of the Asp449Asp (T/C) and Ile462Val (A/G) polymorphisms could increase the UL risk nearly 4.9-fold. Asp449Asp (T/C) and Ile462Val (A/G) polymorphisms of CYP1A1 gene were not associated with UL susceptibility; however, the combination of the TT/AG genotypes and TG haplotype could increase the UL risk.

Cigarette smoking has a differential effect on the plasma level of clozapine in Taiwanese schizophrenic patients associated with the CYP1A2 gene -163A/C single nucleotide polymorphism.

The efficacy of clozapine clearance has been shown to be associated with smoking and genetic polymorphism of CYP1A2. This study aims to investigate the effect of smoking on the plasma level of clozapine in Taiwanese schizophrenic patients and its relevance to the CYP1A2 gene -163A/C single nucleotide polymorphism. A total of 143 hospitalized schizophrenic patients who had received clozapine therapy for at least 14 days were enrolled in this study. The trough plasma concentration of clozapine was measured with LC/MS/MS. The -163A/C variant in the CYP1A2 gene was identified by DNA sequencing and restriction fragment length polymorphism analysis. The effect of smoking on the clozapine level was examined by multiple linear regression analysis and its relation to the -163A/C variant of the CYP1A2 gene was analyzed using a general linear model with Bonferroni correction. Patients with smoking habits showed a significantly lower plasma level of clozapine than those without smoking habits (P=0.022) and the difference in clozapine levels between smokers and nonsmokers appeared to be significant in the individuals carrying the homozygous -163A allele (P=0.02). It was also found that nonsmokers carrying the -163A allele tended to have higher plasma levels of clozapine. This tendency was not found in the individuals with smoking habits. Cigarette smoking has a significant impact on the plasma level of clozapine in Taiwanese schizophrenic patients carrying the homozygous -163A allele in the CYP1A2 gene. Cigarette smoking may increase the clearance of clozapine in these patients.