Search

Background: \ud The SARS-CoV-2 delta (B.1.617.2) variant was first detected in England in March, 2021. It has since rapidly become the predominant lineage, owing to high transmissibility. It is suspected that the delta variant is associated with more severe disease than the previously dominant alpha (B.1.1.7) variant. We aimed to characterise the severity of the delta variant compared with the alpha variant by determining the relative risk of hospital attendance outcomes.\ud \ud Methods: \ud This cohort study was done among all patients with COVID-19 in England between March 29 and May 23, 2021, who were identified as being infected with either the alpha or delta SARS-CoV-2 variant through whole-genome sequencing. Individual-level data on these patients were linked to routine health-care datasets on vaccination, emergency care attendance, hospital admission, and mortality (data from Public Health England's Second Generation Surveillance System and COVID-19-associated deaths dataset; the National Immunisation Management System; and NHS Digital Secondary Uses Services and Emergency Care Data Set). The risk for hospital admission and emergency care attendance were compared between patients with sequencing-confirmed delta and alpha variants for the whole cohort and by vaccination status subgroups. Stratified Cox regression was used to adjust for age, sex, ethnicity, deprivation, recent international travel, area of residence, calendar week, and vaccination status.\ud \ud Findings: \ud Individual-level data on 43 338 COVID-19-positive patients (8682 with the delta variant, 34 656 with the alpha variant; median age 31 years [IQR 17–43]) were included in our analysis. 196 (2·3%) patients with the delta variant versus 764 (2·2%) patients with the alpha variant were admitted to hospital within 14 days after the specimen was taken (adjusted hazard ratio [HR] 2·26 [95% CI 1·32–3·89]). 498 (5·7%) patients with the delta variant versus 1448 (4·2%) patients with the alpha variant were admitted to hospital or attended emergency care within 14 days (adjusted HR 1·45 [1·08–1·95]). Most patients were unvaccinated (32 078 [74·0%] across both groups). The HRs for vaccinated patients with the delta variant versus the alpha variant (adjusted HR for hospital admission 1·94 [95% CI 0·47–8·05] and for hospital admission or emergency care attendance 1·58 [0·69–3·61]) were similar to the HRs for unvaccinated patients (2·32 [1·29–4·16] and 1·43 [1·04–1·97]; p=0·82 for both) but the precision for the vaccinated subgroup was low.\ud \ud Interpretation: \ud This large national study found a higher hospital admission or emergency care attendance risk for patients with COVID-19 infected with the delta variant compared with the alpha variant. Results suggest that outbreaks of the delta variant in unvaccinated populations might lead to a greater burden on health-care services than the alpha variant.\ud \ud Funding: \ud Medical Research Council; UK Research and Innovation; Department of Health and Social Care; and National Institute for Health Research.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were rising during early summer 2021 in many countries as a result of the Delta variant. We assessed reverse transcription polymerase chain reaction swab positivity in the Real-time Assessment of Community Transmission–1 (REACT-1) study in England. During June and July 2021, we observed sustained exponential growth with an average doubling time of 25 days, driven by complete replacement of the Alpha variant by Delta and by high prevalence at younger, less-vaccinated ages. Prevalence among unvaccinated people [1.21% (95% credible interval 1.03%, 1.41%)] was three times that among double-vaccinated people [0.40% (95% credible interval 0.34%, 0.48%)]. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.

Gene expression changes resulting from social interactions may give rise to long term behavioral change, or simply reflect the activity of neural circuitry associated with behavioral expression. In honey bees, social cues broadly modulate aggressive behavior and brain gene expression. Previous studies suggest that expression changes are limited to contexts in which social cues give rise to stable, relatively long-term changes in behavior. Here we use a traditional beekeeping approach that inhibits aggression, smoke exposure, to deprive individuals of aggression-inducing olfactory cues and evaluate whether behavioral changes occur in absence of expression variation in a set of four biomarker genes (drat, cyp6g1/2, GB53860, inos) associated with aggression in previous studies. We also evaluate two markers of a brain hypoxic response (hif1α, hsf) to determine whether smoke induces molecular changes at all. We find that bees with blocked sensory perception as a result of smoke exposure show a strong, temporary inhibition of aggression relative to bees allowed to perceive normal social cues. However, blocking sensory perception had minimal impacts on aggression-relevant gene expression, althought it did induce a hypoxic molecular response in the brain. Results suggest that certain genes differentiate social cue-induced changes in aggression from long-term modulation of this phenotype.

ObjectiveDiverticular disease is a common complex disorder characterised by mucosal outpouchings of the colonic wall that manifests through complications such as diverticulitis, perforation and bleeding. We report the to date largest genome-wide association study (GWAS) to identify genetic risk factors for diverticular disease.DesignDiscovery GWAS analysis was performed on UK Biobank imputed genotypes using 31 964 cases and 419 135 controls of European descent. Associations were replicated in a European sample of 3893 cases and 2829 diverticula-free controls and evaluated for risk contribution to diverticulitis and uncomplicated diverticulosis. Transcripts at top 20 replicating loci were analysed by real-time quatitative PCR in preparations of the mucosal, submucosal and muscular layer of colon. The localisation of expressed protein at selected loci was investigated by immunohistochemistry.ResultsWe discovered 48 risk loci, of which 12 are novel, with genome-wide significance and consistent OR in the replication sample. Nominal replication (pCTAGE1 with a p value of 2.3×10−10 and 0.002 (ORallelic=1.14 (95% CI 1.05 to 1.24)) in the replication analysis. Four loci showed stronger effects for diverticulitis, PHGR1 (OR 1.32, 95% CI 1.12 to 1.56), FAM155A-2 (OR 1.21, 95% CI 1.04 to 1.42), CALCB (OR 1.17, 95% CI 1.03 to 1.33) and S100A10 (OR 1.17, 95% CI 1.03 to 1.33).ConclusionIn silico analyses point to diverticulosis primarily as a disorder of intestinal neuromuscular function and of impaired connective fibre support, while an additional diverticulitis risk might be conferred by epithelial dysfunction.

OBJECTIVE Previously generated genetic risk scores (GRSs) for type 1 diabetes (T1D) have not captured all known information at non-HLA loci or, particularly, at HLA risk loci. We aimed to more completely incorporate HLA alleles, their interactions, and recently discovered non-HLA loci into an improved T1D GRS (termed the “T1D GRS2”) to better discriminate diabetes subtypes and to predict T1D in newborn screening studies. RESEARCH DESIGN AND METHODS In 6,481 case and 9,247 control subjects from the Type 1 Diabetes Genetics Consortium, we analyzed variants associated with T1D both in the HLA region and across the genome. We modeled interactions between variants marking strongly associated HLA haplotypes and generated odds ratios to create the improved GRS, the T1D GRS2. We validated our findings in UK Biobank. We assessed the impact of the T1D GRS2 in newborn screening and diabetes classification and sought to provide a framework for comparison with previous scores. RESULTS The T1D GRS2 used 67 single nucleotide polymorphisms (SNPs) and accounted for interactions between 18 HLA DR-DQ haplotype combinations. The T1D GRS2 was highly discriminative for all T1D (area under the curve [AUC] 0.92; P < 0.0001 vs. older scores) and even more discriminative for early-onset T1D (AUC 0.96). In simulated newborn screening, the T1D GRS2 was nearly twice as efficient as HLA genotyping alone and 50% better than current genetic scores in general population T1D prediction. CONCLUSIONS An improved T1D GRS, the T1D GRS2, is highly useful for classifying adult incident diabetes type and improving newborn screening. Given the cost-effectiveness of SNP genotyping, this approach has great clinical and research potential in T1D.

Background: The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods: We did an ecological study to examine the association between the regional proportion of infections with the SARS-CoV-2 B.1.1.7 variant and reported symptoms, disease course, rates of reinfection, and transmissibility. Data on types and duration of symptoms were obtained from longitudinal reports from users of the COVID Symptom Study app who reported a positive test for COVID-19 between Sept 28 and Dec 27, 2020 (during which the prevalence of B.1.1.7 increased most notably in parts of the UK). From this dataset, we also estimated the frequency of possible reinfection, defined as the presence of two reported positive tests separated by more than 90 days with a period of reporting no symptoms for more than 7 days before the second positive test. The proportion of SARS-CoV-2 infections with the B.1.1.7 variant across the UK was estimated with use of genomic data from the COVID-19 Genomics UK Consortium and data from Public Health England on spike-gene target failure (a non-specific indicator of the B.1.1.7 variant) in community cases in England. We used linear regression to examine the association between reported symptoms and proportion of B.1.1.7. We assessed the Spearman correlation between the proportion of B.1.1.7 cases and number of reinfections over time, and between the number of positive tests and reinfections. We estimated incidence for B.1.1.7 and previous variants, and compared the effective reproduction number, R t, for the two incidence estimates. Findings: From Sept 28 to Dec 27, 2020, positive COVID-19 tests were reported by 36 920 COVID Symptom Study app users whose region was known and who reported as healthy on app sign-up. We found no changes in reported symptoms or disease duration associated with B.1.1.7. For the same period, possible reinfections were identified in 249 (0·7% [95% CI 0·6–0·8]) of 36 509 app users who reported a positive swab test before Oct 1, 2020, but there was no evidence that the frequency of reinfections was higher for the B.1.1.7 variant than for pre-existing variants. Reinfection occurrences were more positively correlated with the overall regional rise in cases (Spearman correlation 0·56–0·69 for South East, London, and East of England) than with the regional increase in the proportion of infections with the B.1.1.7 variant (Spearman correlation 0·38–0·56 in the same regions), suggesting B.1.1.7 does not substantially alter the risk of reinfection. We found a multiplicative increase in the R t of B.1.1.7 by a factor of 1·35 (95% CI 1·02–1·69) relative to pre-existing variants. However, R t fell below 1 during regional and national lockdowns, even in regions with high proportions of infections with the B.1.1.7 variant. Interpretation: The lack of change in symptoms identified in this study indicates that existing testing and surveillance infrastructure do not need to change specifically for the B.1.1.7 variant. In addition, given that there was no apparent increase in the reinfection rate, vaccines are likely to remain effective against the B.1.1.7 variant. Funding: Zoe Global, Department of Health (UK), Wellcome Trust, Engineering and Physical Sciences Research Council (UK), National Institute for Health Research (UK), Medical Research Council (UK), Alzheimer's Society.

BackgroundWe have successfully used whole-genome sequencing to provide additional information for transmission pathways in infectious spread. We report and interpret genomic sequencing results in clinical context from a large outbreak of COVID-19 with 46 cases across staff and patients in a community hospital in the UK.MethodsFollowing multiple symptomatic cases within a two-week period, all staff and patients were screened by RT-PCR and staff subsequently had serology tests.ResultsThirty staff (25%) and 16 patients (62%) tested positive for COVID-19. Genomic sequencing data showed significant overlap of viral haplotypes in staff who had overlapping shift patterns. Patient haplotypes were more distinct from each other but had overlap with staff haplotypes.ConclusionsThis study includes clinical and genomic epidemiological detail that demonstrates the value of a combined approach. Viral genetic sequencing has identified that staff transmission of COVID-19 was important in this community hospital outbreak.Key pointsDetailed analysis of a large community hospital outbreak in older adults and staff with concurrent clinical and genomic data, including working patterns.Staff transmission was important in this community hospital outbreak.We found plausible associations between staff and patient cases.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant., Graphical Abstract, Highlights • Increasing frequency of SARS-CoV-2 D614G is consistent with a selective advantage • Phylodynamic analyses do not show significantly different growth of D614G clusters • There is no association of D614G replacement with greater severity of infection • The D614G replacement is associated with higher viral loads and younger patient age, Analysis of the spread and frequency of SARS-CoV-2 D614G in the United Kingdom suggests a selective advantage for this strain that is associated with higher viral loads in younger patients but not higher COVID-19 clinical severity or mortality.

We performed shotgun genome sequencing on a total of 19 different Musa genotypes including representatives of wild banana species Musa acuminata and M. balibisiana, allopolyploid bananas and plantains, Fe'i banana, pink banana (also known as hairy banana) and abacá (also known as hemp banana). We aligned sequence reads against a previously sequenced reference genome and assessed ploidy and, in the case of allopolyploids, the contributions of the A and B genomes; this provides important quality-assurance data about the taxonomic identities of the sequenced plant material. These data will be useful for phylogenetics, crop improvement, studies of the complex story of intergenomic recombination in AAB and ABB allotriploid bananas and plantains and can be integrated into resources such as the Banana Genome Hub.

Type 1 diabetes (T1D) is a significant problem in Indians and misclassification of T1D and type 2 diabetes (T2D) is a particular problem in young adults in this population due to the high prevalence of early onset T2D at lower BMI. We have previously shown a genetic risk score (GRS) can be used to discriminate T1D from T2D in Europeans. We aimed to test the ability of a T1D GRS to discriminate T1D from T2D and controls in Indians. We studied subjects from Pune, India of Indo-European ancestry; T1D (n = 262 clinically defined, 200 autoantibody positive), T2D (n = 345) and controls (n = 324). We used the 9 SNP T1D GRS generated in Europeans and assessed its ability to discriminate T1D from T2D and controls in Indians. We compared Indians with Europeans from the Wellcome Trust Case Control Consortium study; T1D (n = 1963), T2D (n = 1924) and controls (n = 2938). The T1D GRS was discriminative of T1D from T2D in Indians but slightly less than in Europeans (ROC AUC 0.84 v 0.87, p

International audience; AbstractMaternal stress is a common source of heritable health and behavioral variation. This type of maternal effect could be particularly important for honey bees (Apis mellifera), as a single queen is responsible for many generations of workers who perform all colony functions including raising subsequent worker generations. Multiple factors work synergistically to cause colony loss, but a role for maternal stress effects is unstudied. We used an artificial cold temperature treatment as a proof-of-concept approach to investigate whether acute queen stress causes changes in worker phenotypes, including egg hatching rate, development time, and adult behavior and immune function. We found that queen stress impacts early-life phenotypes (egg hatching and development time), with more limited impacts on adult phenotypes (behavior and immune function). Thus, if maternal stress impacts colony health, it is likely through cumulative impacts on worker population numbers, not through phenotypic effects that impact individual adult worker behavior or health resilience. This study addresses an important and overlooked question, and provides a baseline understanding of the likely impacts of queen stress on worker phenotypes.

ObjectivesTo determine the analytical validity of SNP-chips for genotyping very rare genetic variants.DesignRetrospective study using data from two publicly available resources, the UK Biobank and the Personal Genome Project.SettingResearch biobanks and direct-to-consumer genetic testing in the UK and USA.Participants49,908 individuals recruited to UK Biobank, and 21 individuals who purchased consumer genetic tests and shared their data online via the Personal Genomes Project.Main outcome measuresWe assessed the analytical validity of genotypes from SNP-chips (index test) with sequencing data (reference standard). We evaluated the genotyping accuracy of the SNP-chips and split the results by variant frequency. We went on to select rare pathogenic variants in the BRCA1 and BRCA2 genes as an exemplar for detailed analysis of clinically-actionable variants in UK Biobank, and assessed BRCA-related cancers (breast, ovarian, prostate and pancreatic) in participants using cancer registry data.ResultsSNP-chip genotype accuracy is high overall; sensitivity, specificity and precision are all >99% for 108,574 common variants directly genotyped by the UK Biobank SNP-chips. However, the likelihood of a true positive result reduces dramatically with decreasing variant frequency; for variants with a frequency BRCA1 and BRCA2 genes, the overall performance metrics of the SNP-chips in UK Biobank are sensitivity 34.6%, specificity 98.3% and precision 4.2%. Rates of BRCA-related cancers in individuals in UK Biobank with a positive SNP-chip result are similar to age-matched controls (OR 1.28, P=0.07, 95% CI: 0.98 to 1.67), while sequence-positive individuals have a significantly increased risk (OR 3.73, P=3.5×10−12, 95% CI: 2.57 to 5.40).ConclusionSNP-chips are extremely unreliable for genotyping very rare pathogenic variants and should not be used to guide health decisions without validation.SUMMARY BOXSection 1: What is already known on this topicSNP-chips are an accurate and affordable method for genotyping common genetic variants across the genome. They are often used by direct-to-consumer (DTC) genetic testing companies and research studies, but there several case reports suggesting they perform poorly for genotyping rare genetic variants when compared with sequencing.Section 2: What this study addsOur study confirms that SNP-chips are highly inaccurate for genotyping rare, clinically-actionable variants. Using large-scale SNP-chip and sequencing data from UK Biobank, we show that SNP-chips have a very low precision of

Sleep is an essential human function but its regulation is poorly understood. Identifying genetic variants associated with quality, quantity and timing of sleep will provide biological insights into the regulation of sleep and potential links with disease. Using accelerometer data from 85,670 individuals in the UK Biobank, we performed a genome-wide association study of 8 accelerometer-derived sleep traits, 5 of which are not accessible through self-report alone. We identified 47 genetic associations across the sleep traits (P-8) and replicated our findings in 5,819 individuals from 3 independent studies. These included 26 novel associations for sleep quality and 10 for nocturnal sleep duration. The majority of newly identified variants were associated with a single sleep trait, except for variants previously associated with restless legs syndrome that were associated with multiple sleep traits. Of the new associated and replicated sleep duration loci, we were able to fine-map a missense variant (p.Tyr727Cys) in PDE11A, a dual-specificity 3’,5’-cyclic nucleotide phosphodiesterase expressed in the hippocampus, as the likely causal variant. As a group, sleep quality loci were enriched for serotonin processing genes and all sleep traits were enriched for cerebellar-expressed genes. These findings provide new biological insights into sleep characteristics.

The Oxford Nanopore Technologies (ONT) MinION is a new sequencing technology that potentially offers read lengths of tens of kilobases (kb) limited only by the length of DNA molecules presented to it. The device has a low capital cost, is by far the most portable DNA sequencer available, and can produce data in real-time. It has numerous prospective applications including improving genome sequence assemblies and resolution of repeat-rich regions. Before such a technology is widely adopted, it is important to assess its performance and limitations in respect of throughput and accuracy. In this study we assessed the performance of the MinION by re-sequencing three bacterial genomes, with very different nucleotide compositions ranging from 28.6% to 70.7%; the high G+C strain was underrepresented in the sequencing reads. We estimate the error rate of the MinION (after base calling) to be 38.2%. Mean and median read lengths were 2kb and 1kb respectively, while the longest single read was 98kb. The whole length of a 5kb rRNA operon was covered by a single read. As the first nanopore-based single molecule sequencer available to researchers, the MinION is an exciting prospect; however, the current error rate limits its ability to compete with existing sequencing technologies, though we do show that MinION sequence reads can enhance contiguity of de novo assembly when used in conjunction with Illumina MiSeq data.

We announce the genome sequence for Xanthomonas species strain Nyagatare, isolated from beans showing unusual disease symptoms in Rwanda. This strain represents the first sequenced genome belonging to an as-yet undescribed Xanthomonas species known as species-level clade 1. It has at least 100 kb of genomic sequence that shows little or no sequence similarity to other xanthomonads, including a unique lipopolysaccharide synthesis gene cluster. At least one genomic region appears to have been acquired from relatives of Agrobacterium or Rhizobium species. The genome encodes homologues of only three known type-three secretion system effectors: AvrBs2, XopF1 and AvrXv4. Availability of the genome sequence will facilitate development of molecular tools for detection and diagnostics for this newly discovered pathogen of beans and facilitate epidemiological investigations of a potential causal link between this pathogen and the disease outbreak.

SummaryFibroblast Growth Factor 21 (FGF21) is a hormone that induces weight loss in model organisms. These findings have led to trials in humans of FGF21 analogues with some showing weight loss and lipid lowering effects. Recent genetic studies have shown that a common allele in the FGF21 gene alters the balance of macronutrients consumed but there was little evidence of an effect on metabolic traits. We studied a common FGF21 allele (A:rs838133) in 451,099 people from the UK Biobank study. We replicated the association between the A allele and higher percentage carbohydrate intake. We then showed that this allele is more strongly associated with body fat distribution, with less fat in the lower body, and higher blood pressure, than it is with BMI, where there is only nominal evidence of an effect. These human phenotypes of naturally occurring variation in the FGF21 gene will inform decisions about FGF21’s therapeutic potential.

Xanthomonas axonopodis pathovar vasculorum strain NCPPB 900 was isolated from sugarcane on Reunion island in 1960. Consistent with its belonging to fatty-acid type D, multi-locus sequence analysis confirmed that NCPPB 900 falls within the species X. axonopodis . This genome harbours sequences similar to plasmids pXCV183 from X. campestris pv. vesicatoria 85-10 and pPHB194 from Burkholderia pseudomallei . Its repertoire of predicted effectors includes homologues of XopAA, XopAD, XopAE, XopB, XopD, XopV, XopZ, XopC and XopI and transcriptional activator-like effectors and it is predicted to encode a novel phosphonate natural product also encoded by the genome of the phylogenetically distant X. vasicola pv. vasculorum . Availability of this novel genome sequence may facilitate the study of interactions between xanthomonads and sugarcane, a host-pathogen system that appears to have evolved several times independently within the genus Xanthomonas and may also provide a source of target sequences for molecular detection and diagnostics.

Many readers of this journal will need no introduction to the bacterial genus Streptomyces, which includes several hundred species, many of which produce biotechnologically useful secondary metabolites. The last 2 years have seen numerous publications describing Streptomyces genome sequences (Table ​(Table1),1), mostly as short genome announcements restricted to just 500 words and therefore allowing little description and analysis. Our aim in this current manuscript is to survey these recent publications and to dig a little deeper where appropriate. The genus Streptomyces is now one of the most highly sequenced, with 19 finished genomic sequences (Table ​(Table2)2) and a further 125 draft assemblies available in the GenBank database as of 3rd of May 2014; by the time this is published, no doubt there will be more. The reasons given for sequencing this latest crop of Streptomyces include production of industrially important enzymes, degradation of lignin, antibiotic production, rapid growth and halo-tolerance and an endophytic lifestyle (Table ​(Table11). Table 1 Recent genome publications (2013 and 2014) for Streptomyces species Table 2 Completely sequenced Streptomyces species genome sequences available in GenBank as of 29 April 2014 Mining genomes for secondary metabolism gene clusters Given the strong emphasis on secondary metabolism in Streptomyces genomics research, it is timely that version 2.0 of antiSMASH has been released and published (Blin et al., 2013). This computational tool has become a de facto standard for mining secondary metabolism gene clusters in genome sequences. Version 2.0 is completely revamped and, significantly, can now be used with highly fragmented draft-quality genome sequences whereas the previous version only worked well with finished genomes. Clearly, this is of immense importance to the discovery of novel metabolites in the ever-expanding database of streptomycete draft-quality genome sequences. For example, antiSMASH 2.0 analysis of the Streptomyces roseochromogenes subsp. oscitans DS 12.976 genome sequence revealed 43 new gene clusters in addition to recovering the already known clorobiocin gene cluster (Ruckert et al., 2014). The genome sequence of Streptomyces gancidicus strain BKS 13–15 was published before antiSMASH 2.0 became available. The authors state that seven genes mapped on to the streptomycin biosynthesis pathway based on gene-by-gene sequence similarities (Kumar et al., 2013) against homologues of genes in KEGG pathways (Kanehisa et al., 2012). However, we found no bioinformatic evidence for a streptomycin biosynthesis pathway encoded in this genome, although our antiSMASH 2.0 search did find 38 putative gene clusters. In common with many other pathways for secondary metabolism, genes for production of the aminoglycoside streptomycin are organized into a cluster of contiguous genes. The nucleotide sequences of at least two such clusters are available (GenBank accessions {"type":"entrez-nucleotide","attrs":{"text":"GU384160","term_id":"288549237","term_text":"GU384160"}}GU384160 and {"type":"entrez-nucleotide","attrs":{"text":"AJ862840","term_id":"62896300","term_text":"AJ862840"}}AJ862840 from Streptomyces platensis and Streptomyces griseus respectively). Our blastn searches (using these two cluster sequences as queries) failed to detect a complete streptomycin gene cluster in the S. gancidicus genome, but there were some regions of sequence similarity on a 111 kb contig (GenBank: {"type":"entrez-nucleotide","attrs":{"text":"AOHP01000057","term_id":"455649599","term_text":"AOHP01000057"}}AOHP01000057). An antiSMASH 2.0 search failed to find any aminoglycoside biosynthetic cluster in this genome. We are not aware of any experimental evidence that this strain produces the aminoglycoside streptomycin and conclude that these seven genes highlighted by the authors (Kumar et al., 2013) most probably encode components of another, perhaps novel, pathway. This illustrates the value of the antiSMASH 2.0 tool, which has the potential to discover new pathways, rather than relying on similarity to the pathways already represented in the KEGG database (and therefore, by definition, not novel). The case of Streptomyces species strain Mg1 (Hoefler et al., 2013) illustrates another consideration when mining bacterial genome sequences for secondary metabolism gene clusters. Many of the recently published Streptomyces genome sequences are assembled from massively parallel sequencing platforms such as 454 GS-FLX and Illumina HiSeq. The short sequence reads (typically less than 450 bp) and relatively high error rates associated with these platforms can lead to rather fragmented and/or incomplete genome assemblies. The situation is not helped by the biased sequence composition (approximately 70% G + C) of Streptomyces DNA. Furthermore, non-ribosomal peptide synthases (NRPS) and polyketide synthetases (PK) are long, modular proteins made up of many repeated domain units. This means that the genes encoding these key enzymes can be particularly difficult to assemble accurately from short sequence reads. To overcome this issue, the authors of the Mg1 genome project (Hoefler et al., 2013) exploited the PacBio SMRT sequencing technology, which provides sequences reads of several Kb in length, meaning that an entire PK or NRPS gene could be represented on a single sequence read, thus avoiding the difficulties of assembling repetitive sequence from short fragments. They also generated an assembly of the same genome based on 454 GS-FLX and Illumina HiSeq. The results were striking: more than 90% of the genome was represented in a single contig of 7.8 Mb in the PacBio-based assembly and the PacBio-based assembly was 19.9% longer than the 454/Illumina-based one (8 705 754 versus 7 260 368 bp). As the authors point out, this implies that more than 1 Mb of sequence in the PacBio-based assembly is missing from the 454/Illumina-based one, as can be seen in Fig. ​Fig.1A.1A. However, the 454/Illumina-based assembly is not simply a subset of the PacBio-based one; as illustrated in Fig. ​Fig.1B,1B, a substantial portion of the 454/Illumina-based assembly is missing from the PacBio assembly. Although it is by no means certain which assembly is more ‘correct’, it might be possible to generate a more complete genome assembly by reconciling the two different assemblies. Figure 1 Comparison of two different genome assemblies for Streptomyces strain Mg1, one based on PacBio sequence data and the other based on 454 and Illumina sequence data. A illustrates alignment of both the assemblies against the PacBio-based assembly. B illustrates ... Fragmentation and incompleteness of a genome assembly has implications for discovery of secondary metabolism gene clusters. In Fig. ​Fig.1C,1C, we show a putative NRPS gene cluster detected apparently intact in a single contig of the PacBio-based sequence assembly identified by antiSMASH 2.0. Searching the 454/Illumina-based assembly reveals two incomplete fragments of the gene cluster, lying on two different contigs, and with part of the cluster apparently absent. Although we should be cautious about extrapolating too much from this single anecdotal example, the evidence suggests that longer read lengths can be very valuable in genome mining for secondary metabolism clusters.

We present a draft genome sequence for enset (Ensete ventricosum) available via the Sequence Read Archive (accession number SRX202265) and GenBank (accession number AMZH01. Enset feeds 15 million people in Ethiopia, but is arguably the least studied African crop. Our sequence data suggest a genome size of approximately 547 megabases, similar to the 523-megabase genome of the closely related banana (Musa acuminata). At least 1.8% of the annotated M. acuminata genes are not conserved in E. ventricosum. Furthermore, enset contains genes not present in banana, including reverse transcriptases and virus-like sequences as well as a homolog of the RPP8-like resistance gene. We hope that availability of genome-wide sequence data will stimulate and accelerate research on this important but neglected crop.

We report here the annotated draft genome sequences of strains Xanthomonas arboricola pv. celebensis NCPPB 1832 and NCPPB 1630 (NCPPB, National Collection of Plant Pathogenic Bacteria), both isolated from Musa species in New Zealand. This will allow the comparison of genomes between phylogenetically distant xanthomonads that have independently converged with the ability to colonize banana plants.

We report here the annotated draft genome sequence of Pseudomonas syringae pv. syringae strain ALF3, isolated in Wyoming. A comparison of this genome sequence with those of closely related strains of P. syringae adapted to other hosts will facilitate research into interactions between this pathogen and alfalfa.

The use of molecular methods is altering our understanding of the microbial biosphere and the complexity of the tree of life. Here, we report a newly discovered uncultured plastid-bearing eukaryotic lineage named the rappemonads. Phylogenies using near-complete plastid ribosomal DNA (rDNA) operons demonstrate that this group represents an evolutionarily distinct lineage branching with haptophyte and cryptophyte algae. Environmental DNA sequencing revealed extensive diversity at North Atlantic, North Pacific, and European freshwater sites, suggesting a broad ecophysiology and wide habitat distribution. Quantitative PCR analyses demonstrate that the rappemonads are often rare but can form transient blooms in the Sargasso Sea, where high 16S rRNA gene copies mL −1 were detected in late winter. This pattern is consistent with these microbes being a member of the rare biosphere, whose constituents have been proposed to play important roles under ecosystem change. Fluorescence in situ hybridization revealed that cells from this unique lineage were 6.6 ± 1.2 × 5.7 ± 1.0 μm, larger than numerically dominant open-ocean phytoplankton, and appear to contain two to four plastids. The rappemonads are unique, widespread, putatively photosynthetic algae that are absent from present-day ecosystem models and current versions of the tree of life.

Introduction Thiopurines are commonly used in the maintenance treatment of inflammatory bowel disease (IBD) but this is limited by myelosuppression in 7% of patients.1 Thiopurine S-methyltransferase (TPMT) variants only explain 20% of thiopurine-induced myelosuppression (TIM) in Europeans suggesting the presence of other genetic determinants.2 We aimed to identify the clinical features of TIM and to identify novel variants associated with TIM through a genome wide association study and whole exome sequencing. Method We recruited 491 IBD patients with TIM from 82 hospitals. Inclusion criteria included drug exposure in the 7 days prior to TIM, white blood cell count ≤2.5 ×109/L, or neutrophil count ≤1.0 ×109/L and that TIM necessitated dose reduction/drug withdrawal. After expert adjudication, 329 cases assigned a high likelihood of causality were genotyped and exome sequenced with 635 thiopurine-tolerant IBD controls for use in the final analyses. Results We first confirmed an association of TIM with TPMT in an initial GWAS. We then, using exome sequencing, discovered a novel 6 bp in-frame deletion (rs746071566; AGGAGTC/A,p.Gly17_Val18del) at position 48611918 of chromosome 13 in exon 1 of NUDT15 (5.8% cases, 0.2% controls, OR=38.2,p=1.33×10-8). This deletion was replicated in an independent cohort (3/75 [4%] cases vs. 2/785 [0.3%] thiopurine-tolerant IBD controls; OR=16.2, p=0.006). All NUDT15 coding variants were confirmed with complete concordance by Sanger sequencing. Multivariable logistic regression demonstrated that adjusted dose (OR 2.2,p=9.4×10-11), NUDT15 genotype (OR 21.7,p=2.0×10-8) and TPMT genotype (OR 2.2,p=2.6×10-4 for MUT/WT and OR 51.2,p=1.8×10-4 for MUT/MUT) were independently associated with TIM. Conclusion These are the largest ever clinical and genetic analyses of thiopurine-induced myelosuppression. We identified NUDT15 coding variants, including a novel 6 bp deletion; carriage of any coding variant confers a 22-fold increase in the odds of TIM, independent of TMPT genotype and thiopurine dose. Although NUDT15 variants are less common than TPMT variants, their effect size for heterozygotes is greater. The number of patients needed to genotype to prevent TIM due to NUDT15 coding variant heterozygosity is 100. The estimated absolute risk of TIM in NUDT15 heterozygotes is 59%. A future clinical decision tool incorporating NUDT15 and TPMT genotypes will offer personalised thiopurine therapy and prevent the considerable morbidity and costs associated with severe bone marrow toxicity. Reference . Gisbert JP & Gomollon F.doi10.1111/j.1572-0241.2008.01848.x (2008) . Yang SK et al. doi10.1038/ng.3060 (2014) Disclosure of Interest None Declared

Background Childhood hematogenous chronic osteomyelitis remains a serious cause of morbidity throughout the developing world. The aim of our study was to develop a reliable and clinically useful classification system for this condition in children. Methods The case notes and radiographs of 87 children with chronic hematogenous osteomyelitis of one or more long bone were reviewed to devise a classification system. We undertook reliability studies of the proposed classification system. Five observers classified the selected radiographs of 32 patients on two separate occasions. Results The classification divides the condition into 3 main types: type A--Brodie's abscess, type B--sequestrum involucrum, and type C--sclerotic. Type B has four subtypes. Intraobserver agreement was 95% for the main types and 77% (kappa coefficient 0.7) with the subtypes. Interobserver agreement was 95% to 97% for the main types and 78% (multirater kappa=0.54) for the subtypes. Conclusions The results suggest that our classification system for chronic hematogenous osteomyelitis in children is reliable.

We aimed to determine if a modified Dunn osteotomy could be safely performed without surgical dislocation and consequent preservation of the ligamentum teres. All patients undergoing a modified Dunn osteotomy for a slipped capital femoral epiphysis over an 8-year period were included in this study, and all had a severe slip with an open physis. The modified Dunn procedure was performed on 34 hips in 34 patients. The mean age was 13.1 years (range, 11 to 16 y) with a mean follow-up time of 54 months (range, 15 to 102 mo). All slips were severe (grade 3) with a mean slip angle of 73.2 degrees (range, 60 to 90 degrees). Nineteen slips were stable and 15 were unstable. Of the unstable slips, the average time from initial presentation to the emergency department until surgery was 9.4 days (range, 2 to 42 d). Excluding 1 patient who developed complete collapse of the femoral head (NAHS 56), the average Nonarthritic Hip score was 98 (range, 93.7 to 100). Four (11.8%) patients developed avascular necrosis of the femoral head, of which 3 were unstable slips. A modified Dunn osteotomy with preservation of the ligamentum teres allows an excellent restoration of the anatomic alignment of the femoral head and neck. Rates of AVN are not increased compared with other techniques of subcapital osteotomy but this complication cannot be eliminated particularly in patients with unstable slips. Level III.

Common bacterial blight is a devastating seed-borne disease of common beans that also occurs on other legume species including lablab and Lima beans. We sequenced and analysed the genomes of 26 isolates of Xanthomonas axonopodis pv. phaseoli and X. fuscans subsp. fuscans, the causative agents of this disease, collected over four decades and six continents. This revealed considerable genetic variation within both taxa, encompassing both single-nucleotide variants and differences in gene content, that could be exploited for tracking pathogen spread. The bacterial isolate from Lima bean fell within the previously described Genetic Lineage 1, along with the pathovar type isolate (NCPPB 3035). The isolates from lablab represent a new, previously unknown genetic lineage closely related to strains of X. axonopodis pv. glycines. Finally, we identified more than 100 genes that appear to have been recently acquired by Xanthomonas axonopodis pv. phaseoli from X. fuscans subsp. fuscans.

A novel protein translocation system, the type-6 secretion system (T6SS), may play a role in virulence of Campylobacter jejuni. We investigated 181 C. jejuni isolates from humans, chickens, and environmental sources in Vietnam, Thailand, Pakistan, and the United Kingdom for T6SS. The marker was most prevalent in human and chicken isolates from Vietnam.

1. Secondary production was estimated for Plecoptera, Odonata and Megaloptera (mostly large predators) occurring on the snag habitat of a subtropical blackwater river in the southeastern U.S.A. Coastal Plain for 2 years. Production estimates and gut analyses were used in estimating species-specific ingestion to construct a quantitative food web of the predator portion of the invertebrate assemblage. Neither basal resources (e.g. detritus) nor predaceous vertebrates (e.g. fishes) were considered in this analysis. A discharge-specific model of snag-habitat availability was used to convert values per m2 of snag surface to values per m2 of river bed. 2. These three orders included the major large predators on the snag habitat, as well as two detritivorous stoneflies. The major predators were the hellgrammite (Corydaluscornutus), five perlid stoneflies (Paragnetinakansensis, Perlestaplacida, Neoperlaclymene, Acroneuriaevoluta and Acroneuriaabnormis) and two dragonflies (Neurocorduliamolesta and Boyeriavinosa). The detritivores were Pteronarcysdorsata and Taeniopteryxlita. 3. Total predator production was high, but varied from only 7.1 to 7.4 g dry mass (DM) m−2 y−1 of snag surface (2.4–2.7 g DM m−2 y−1 of river bed) over two years. Corydalus was the largest predator and had the highest production (2.8–3.1 g DM m−2 of snag surface). The most productive stoneflies were Perlesta (0.7–1.0 g DM m−2 of snag surface) and Paragnetina (1.0–1.3 g DM m−2 of snag surface). The most productive dragonfly was Neurocordulia (0.7–1.9 g DM m−2 of snag surface). Production of the non-predaceous stoneflies was 1.0–2.3 g DM m−2 of snag surface. Production values per m2 of river bed were 2–3.5 times lower than the values per m2 snag surface. 4. Measurement of ingestion fluxes within the predator portion of the food web showed that predaceous invertebrates were primarily supported by chironomid and mayfly prey. However, the greatest consumption of chironomids and mayflies was by omnivorous hydropsychid caddisflies, which had a considerably higher production than the larger predators. There was a hierarchy of feeding with Corydalus as top predator consuming all other groups, followed in order by dragonflies, stoneflies and hydropsychids. Although the feeding hierarchy suggested the presence of four predatory trophic levels within the invertebrate assemblage, calculations of trophic position indicated there were less than two. With primary consumers (e.g. midges) having a trophic position of 2, Corydalus had a trophic position of only 3.5. 5. A relatively high fraction of invertebrate production was consumed by predaceous invertebrates, ranging from 9 to >100% for various primary consumer groups, with total consumption representing 52% of total production. Because these estimates do not include vertebrate consumption or emergence, it means that a high fraction of larval mortality is due to predation.

Nutrient limitation of periphyton and phytoplankton was assessed in the Upper Guadalupe River, Texas USA. Nutrient-diffusing substrates with added nitrogen (N) and phosphorus (P) were used to identify the limiting nutrient for lotic algae at three river sites in summer, fall, and winter. Pots enriched with P had significantly higher chlorophyll a concentrations for 7 of 9 trials. Added N alone did not significantly increase algal standing crops, although it was found to be secondarily limiting on one (and possibly two) occasions. Flow-through enrichment experiments were conducted in order to quantify the concentration of P needed to significantly increase algal standing crops. Response to enrichment was rapid when ambient P concentration was low (< 0.010 mg L−1), but more moderate when ambient P levels were higher (0.015–0.025 mg L−1). Nutrient limitation of phytoplankton in small surface-release reservoirs varied throughout the study, but N was either primarily or secondarily limiting in 6 of 8 trials; shifts in the limiting nutrient were correlated with fluctuations in flow into the reservoirs. Our enrichment studies show that algal response to nutrient addition was unpredictable as phytoplankton tended to be N-limited while periphyton was mainly P-limited. Further, while discharge apparently dictated the nutrient-biomass relationship for phytoplankton in reservoirs, ambient nutrient level is an important determinant of lotic periphyton response to enrichment.

The present study indicates that most semiconductor components are fabricated such that they are not affected by operation in a dielectric oil environment. A quantitative estimate of the conditions under which oil-soluble ions will invert semiconductor surfaces and interfere with proper device operation is developed. The results are discussed in terms of pressure-tolerant electronic systems—solid-state components operated immersed in chemically inert dielectric oils when these components are subject to, and experience, ambient hydrostatic pressures of the ocean depths. The feasibility of pressure-tolerant electronic systems is demonstrated.

Estimates of annual production for the predaceous aquatic insect Corydalus cornutus (Megaloptera) revealed considerable variation among four Texas streams with similar water quality characteristics but differing in size, flow, and temperature. Values of production varied from 1.62 g dry mass m-2 yr-~ to 13.19 g dry mass m-2 yr-l. This variation was largely due to differences in growth and development which occurred as a result of differences in thermal regime. At three of the streams, C. cornutus appeared to be univoltine with a cohort production interval (CPI) of 333 days. At a fourth site with higher summer temperatures, development from egg to mature larva occurred in 6-7 months or less, leading to a CPI of 210 days and suggesting bivoltinism (not previously reported for this group). Of the factors thought to control secondary production, in- cluding habitat, temperature, food quality and quantity, and biological interactions, temperature seems to be the most important. In addition, a direct relationship was found between production and stream width. This effect could result from limited primary production in canopied, narrow streams which might reduce prey species production and thus lower prey availability to C. cornutus. Permanency of flow appeared not to strongly influence production because the highest production was found in an intermittent stream. Our estimates of production for C. cornutus are among the highest yet reported for a predaceous species and approach the values obtained for primary consumer species in desert streams.