The microbial community in the plant rhizosphere is vital to plant productivity and disease resistance. Alterations in the composition and diversity of species within this community could be ...detrimental if microbes suppressing the activity of pathogens are removed. Species of the insect-pathogenic fungus, Metarhizium, commonly employed as biological control agents against crop pests, have recently been identified as plant root colonizers and provide a variety of benefits (e.g. growth promotion, drought resistance, nitrogen acquisition). However, the impact of Metarhizium amendment on the rhizosphere microbiome has yet to be elucidated. Using Illumina sequencing, we examined the community profiles (bacteria and fungi) of common bean (Phaseolus vulgaris) rhizosphere (loose soil and plant root) after amendment with M. robertsii conidia, in the presence and absence of an insect host. Although alpha diversity was not significantly affected overall, there were numerous examples of plant growth-promoting organisms that significantly increased with Metarhizium amendment (Bradyrhizobium, Flavobacterium, Chaetomium, Trichoderma). Specifically, the abundance of Bradyrhizobium, a group of nitrogen-fixing bacteria, was confirmed to be increased using a qPCR assay with genus-specific primers. In addition, the ability of the microbiome to suppress the activity of a known bean root pathogen was assessed. The development of disease symptoms after application with Fusarium solani f. sp. phaseoli was visible in the hypocotyl and upper root of plants grown in sterilized soil but was suppressed during growth in microbiome soil and soil treated with M. robertsii. Successful amendment of agricultural soils with biocontrol agents such as Metarhizium necessitates a comprehensive understanding of the effects on the diversity of the rhizosphere microbiome. Such research is fundamentally important towards sustainable agricultural practices to improve overall plant health and productivity.
Due to the complexity of the protocols and a limited knowledge of the nature of microbial communities, simulating metagenomic sequences plays an important role in testing the performance of existing ...tools and data analysis methods with metagenomic data. We developed metagenomic read simulators with platform-specific (Sanger, pyrosequencing, Illumina) base-error models, and simulated metagenomes of differing community complexities. We first evaluated the effect of rigorous quality control on Illumina data. Although quality filtering removed a large proportion of the data, it greatly improved the accuracy and contig lengths of resulting assemblies. We then compared the quality-trimmed Illumina assemblies to those from Sanger and pyrosequencing. For the simple community (10 genomes) all sequencing technologies assembled a similar amount and accurately represented the expected functional composition. For the more complex community (100 genomes) Illumina produced the best assemblies and more correctly resembled the expected functional composition. For the most complex community (400 genomes) there was very little assembly of reads from any sequencing technology. However, due to the longer read length the Sanger reads still represented the overall functional composition reasonably well. We further examined the effect of scaffolding of contigs using paired-end Illumina reads. It dramatically increased contig lengths of the simple community and yielded minor improvements to the more complex communities. Although the increase in contig length was accompanied by increased chimericity, it resulted in more complete genes and a better characterization of the functional repertoire. The metagenomic simulators developed for this research are freely available.
2019 CHOICE Outstanding Academic Title and shortlisted for the ESSE book awards 2020, for Literatures in the English Language Childhood books play a special role in reading histories, providing ...touchstones for our future tastes and giving shape to our ongoing identities. Bringing the latest work in Memory Studies to bear on writers' memoirs, autobiographical accounts of reading, and interviews with readers, Rereading Childhood Books explores how adults remember, revisit, and sometimes forget, these significant books. Asking what it means to return to familiar works by well-known authors such as Lewis Carroll, C. S. Lewis and Enid Blyton, as well as popular and ephemeral material not often considered as part of the canon, Alison Waller develops a poetics of rereading and presents a new model for understanding lifelong reading. As such she reconceives the history of children's literature through the shared and individual experiences of the readers who carry these books with them throughout their lives.
Young adult novels are full of ordinary things and everyday actions, and these “reality effects”, to use Roland Barthes’ term, can help to build the meaningful connective tissue against which textual ...adolescents exist. This article examines contemporary British realist YA in order to understand the cultural work it does in creating ordinary worlds its readers can recognise. It shows how narratives produce a shared backdrop of lived experience that can nonetheless reveal certain socio-economic and ethnic differences. Paying attention to the mundane and routine is also posited as a method for locating YA fiction within a much broader literary and cultural context than usual. Existing YA scholarship has tended to focus on ontological questions about extraordinary fictional teenagers and how they are constructed according to universal frameworks of ‘normal’. This article instead demonstrates how textual teenagers are also situated by the common realities of everyday life in ways that need to be understood as specifically inflected by national conditions. It examines two tropes of ‘ordinariness’ – cups of tea and bus journeys – in a range of British YA standalone novels from the last decade, including work by Holly Bourne, Ally Kennen, Muhammad Khan, Patrice Lawrence, Nikesh Shukla, and Lisa Williamson. In doing so, it unpacks the rich cultural meanings and functions that are at play via these apparently non-symbolic textual features, and argues that, although tea and buses often act as reassuring markers of the ordinary, in some cases they represent a narrative mode that can actually question the status quo.
Background:
The current body of literature surrounding anterior cruciate ligament (ACL) survival and the variables contributing to further ACL injuries after primary ACL reconstruction in children ...and adolescents is limited, with no long-term evidence examining the incidence and contributing factors of further ACL injuries in this younger patient population.
Purpose:
To determine the long-term survival of the ACL graft and the contralateral ACL (CACL) after primary reconstruction in patients aged ≤18 years and to identify the factors that increase the odds of subsequent ACL injuries.
Study Design:
Case series; Level of evidence, 4.
Methods:
Patients having undergone primary ACL reconstruction at age ≤18 years between 1993 and 1998 who were included in a prospective database by a single surgeon were considered for this study. Single-incision endoscopic ACL reconstruction was performed with either an autologous bone–patellar tendon–bone graft or a hamstring tendon graft. At a minimum of 15 years after ACL reconstruction, patients completed a subjective survey involving the International Knee Documentation Committee (IKDC) questionnaire in addition to questions regarding current symptoms, further ACL injuries, family history of ACL injury, and current level of activity.
Results:
A total of 288 adolescents (age range, 13-18 years) met the inclusion criteria, of whom 242 (84%) were reviewed at a mean of 16 years and 6 months after ACL reconstruction. Of these patients, 75 (31%) sustained a further ACL injury: 27 (11.2%) suffered an ACL graft rupture, 33 suffered a CACL injury (13.6%), and 15 sustained both an ACL graft rupture and a CACL injury (6.2%) over 15 years. Survival of the ACL graft was 95%, 92%, 88%, 85%, and 83% at 1, 2, 5, 10, and 15 years, respectively, and survival of the CACL was 99%, 98%, 90%, 83%, and 81%, respectively. Survival of the ACL graft was less favorable in those with a family history of ACL injury than in those without a family history (69% vs 90%, respectively; hazard ratio HR, 3.6; P = .001). Survival of the CACL was less favorable in male patients than in female patients (75% vs 88%, respectively; HR, 2.1; P = .03) and in those who returned to competitive team ball sports than in those who did not (78% vs 89%, respectively; HR, 2.3; P = .05).
Conclusion:
After ACL reconstruction in patients aged ≤18 years, a further ACL injury occurred in 1 in 3 patients over 15 years. The 15-year survival rate of the ACL graft was 83%, and the 15-year survival rate of the CACL was 81%. The ACL graft and CACL were most vulnerable within the first 5 years after index surgery. A family history of ACL rupture significantly increased the risk for ACL graft ruptures, and a CACL injury was more common in male patients and those who returned to team ball sports. High IKDC scores and continued participation in sports were maintained over the long term after ACL reconstruction in the adolescent population.
Role for urea in nitrification by polar marine Archaea Alonso-Sáez, Laura; Waller, Alison S; Mende, Daniel R ...
Proceedings of the National Academy of Sciences - PNAS,
10/2012, Letnik:
109, Številka:
44
Journal Article
Recenzirano
Odprti dostop
Despite the high abundance of Archaea in the global ocean, their metabolism and biogeochemical roles remain largely unresolved. We investigated the population dynamics and metabolic activity of ...Thaumarchaeota in polar environments, where these microorganisms are particularly abundant and exhibit seasonal growth. Thaumarchaeota were more abundant in deep Arctic and Antarctic waters and grew throughout the winter at surface and deeper Arctic halocline waters. However, in situ single-cell activity measurements revealed a low activity of this group in the uptake of both leucine and bicarbonate (<5% Thaumarchaeota cells active), which is inconsistent with known heterotrophic and autotrophic thaumarchaeal lifestyles. These results suggested the existence of alternative sources of carbon and energy. Our analysis of an environmental metagenome from the Arctic winter revealed that Thaumarchaeota had pathways for ammonia oxidation and, unexpectedly, an abundance of genes involved in urea transport and degradation. Quantitative PCR analysis confirmed that most polar Thaumarchaeota had the potential to oxidize ammonia, and a large fraction of them had urease genes, enabling the use of urea to fuel nitrification. Thaumarchaeota from Arctic deep waters had a higher abundance of urease genes than those near the surface suggesting genetic differences between closely related archaeal populations. In situ measurements of urea uptake and concentration in Arctic waters showed that small-sized prokaryotes incorporated the carbon from urea, and the availability of urea was often higher than that of ammonium. Therefore, the degradation of urea may be a relevant pathway for Thaumarchaeota and other microorganisms exposed to the low-energy conditions of dark polar waters.
Whereas large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the practical impact of variation is largely unexplored in the human microbiome. ...We therefore developed a framework for metagenomic variation analysis and applied it to 252 faecal metagenomes of 207 individuals from Europe and North America. Using 7.4 billion reads aligned to 101 reference species, we detected 10.3 million single nucleotide polymorphisms (SNPs), 107,991 short insertions/deletions, and 1,051 structural variants. The average ratio of non-synonymous to synonymous polymorphism rates of 0.11 was more variable between gut microbial species than across human hosts. Subjects sampled at varying time intervals exhibited individuality and temporal stability of SNP variation patterns, despite considerable composition changes of their gut microbiota. This indicates that individual-specific strains are not easily replaced and that an individual might have a unique metagenomic genotype, which may be exploitable for personalized diet or drug intake.
Bacteriophages have key roles in microbial communities, to a large extent shaping the taxonomic and functional composition of the microbiome, but data on the connections between phage diversity and ...the composition of communities are scarce. Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. On average, five phage taxa were identified in each sample, with up to three of these being highly abundant. The abundances of most phage taxa vary by up to four orders of magnitude between the samples, and several taxa that are highly abundant in some samples are absent in others. Significant correlations exist between the abundances of some phage taxa and human host metadata: for example, 'Group 936 lactococcal phages' are more prevalent and abundant in Danish samples than in samples from Spain or the United States of America. Quantification of phages that exist as integrated prophages revealed that the abundance profiles of prophages are highly individual-specific and remain unique to an individual over a 1-year time period, and prediction of prophage lysis across the samples identified hundreds of prophages that are apparently active in the gut and vary across the samples, in terms of presence and lytic state. Finally, a prophage-host network of the human gut was established and includes numerous novel host-phage associations.
Background:
The risks for primary anterior cruciate ligament (ACL) rupture have been established. What is less well known is the risk of graft rupture after reconstruction and also the risk of a ...primary ACL rupture in the contralateral knee.
Purpose:
To determine the long-term survival of the ACL graft and the contralateral ACL (CACL) after reconstruction and to identify factors that increase the odds of subsequent ACL injury.
Study Design:
Case series; Level of evidence, 4.
Methods:
All patients having undergone primary ACL reconstruction in 1993 or 1994 by a single surgeon in a single unit were considered. Patients were contacted to complete a subjective interview by telephone or e-mail questionnaire at a minimum of 15 years after surgery.
Results:
A total of 755 patients met the inclusion criteria, and ACL reconstruction was performed using a single-incision endoscopic technique with either autologous bone–patellar tendon–bone graft (BPTB; n = 314) or hamstring tendon graft (HT; n = 359) and metal interference screw fixation. Of these patients, 673 (89%) completed the questionnaire; 23% had sustained either a graft rupture or CACL rupture. Expected survival of the ACL graft was 95%, 93%, 91%, and 89% at a respective 2, 5, 10, and 15 years after reconstruction. Expected survival of the CACL was 97%, 93%, 90%, and 87%, respectively. Survival of the ACL graft was less favorable in men than in women (P = .007); ACL graft survival was not significantly different between the HT (88%) or BPTB (91%) groups (P = .149). Rupture of the CACL occurred twice as frequently as graft rupture in the BPTB group (graft survival, 84% vs 89%; P = .003). A positive family history of ACL rupture doubled the odds of both ACL graft and CACL rupture. The mean International Knee Documentation Committee subjective score at 15 years was 85. Return to preinjury sport levels was reported in 73% of patients, and 51% were still participating in strenuous or very strenuous activities at 15 years.
Conclusion:
Fifteen years after ACL reconstruction, expected survival of the ACL graft was 89% and expected survival of the CACL was 86%. Graft choice did not affect ACL graft rupture, but using BPTB increased the risk of CACL rupture compared with HT. Men had a less favorable survival rate of the ACL graft than did women, and a family history of ACL rupture increased the risk of both ACL graft and CACL rupture.
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