Origins Of Heterospory And The Seed Habit: The Role Of Heterochrony

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149713/1/tax04577.pd

De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum

<p>Abstract</p> <p>Background</p> <p>Because of their phylogenetic position and unique characteristics of their biology and life cycle, ferns represent an important lineage for studying the evolution of land plants. Large and complex genomes in ferns combined with the absence of economically important species have been a barrier to the development of genomic resources. However, high throughput sequencing technologies are now being widely applied to non-model species. We leveraged the Roche 454 GS-FLX Titanium pyrosequencing platform in sequencing the gametophyte transcriptome of bracken fern (<it>Pteridium aquilinum</it>) to develop genomic resources for evolutionary studies.</p> <p>Results</p> <p>681,722 quality and adapter trimmed reads totaling 254 Mbp were assembled <it>de novo </it>into 56,256 unique sequences (i.e. unigenes) with a mean length of 547.2 bp and a total assembly size of 30.8 Mbp with an average read-depth coverage of 7.0×. We estimate that 87% of the complete transcriptome has been sequenced and that all transcripts have been tagged. 61.8% of the unigenes had blastx hits in the NCBI nr protein database, representing 22,596 unique best hits. The longest open reading frame in 52.2% of the unigenes had positive domain matches in InterProScan searches. We assigned 46.2% of the unigenes with a GO functional annotation and 16.0% with an enzyme code annotation. Enzyme codes were used to retrieve and color KEGG pathway maps. A comparative genomics approach revealed a substantial proportion of genes expressed in bracken gametophytes to be shared across the genomes of <it>Arabidopsis</it>, <it>Selaginella </it>and <it>Physcomitrella</it>, and identified a substantial number of potentially novel fern genes. By comparing the list of <it>Arabidopsis </it>genes identified by blast with a list of gametophyte-specific <it>Arabidopsis </it>genes taken from the literature, we identified a set of potentially conserved gametophyte specific genes. We screened unigenes for repetitive sequences to identify 548 potentially-amplifiable simple sequence repeat loci and 689 expressed transposable elements.</p> <p>Conclusions</p> <p>This study is the first comprehensive transcriptome analysis for a fern and represents an important scientific resource for comparative evolutionary and functional genomics studies in land plants. We demonstrate the utility of high-throughput sequencing of a normalized cDNA library for <it>de novo </it>transcriptome characterization and gene discovery in a non-model plant.</p

Inadequate perioperative prophylaxis and postsurgical complications after graft implantation are important risk factors for subsequent vascular graft infections – prospective results from the VASGRA Cohort Study

Introduction Reconstructive vascular surgery has become increasingly common. Vascular graft infections (VGI) are serious complications leading to increased morbidity and mortality. Previously described risk factors for VGI include groin incision, wound infections, and comorbidities. We aimed to identify modifiable predictors for VGI as targets for infection prevention strategies. Methods Participants of the prospective Vascular Graft Infection Cohort (VASGRA) with surgery between 2013 and 2017 were included. Observation time was calculated from surgery until confirmed VGI or last follow-up. Variables were assessed by infection status using non-parametric tests. Uni- and multivariable Cox proportional hazard regression models, adjusted for demographic factors, were applied to assess risk factors for a VGI. Results A total of 438, predominantly male (83.1%) patients with a median age of 71 years (IQR 63–76) contributed to 554 person-years (PY) of follow-up. Thereof, 39 (8.9%) developed a vascular graft infection, amounting to an incidence rate of 7.0/100 PY. We found incisional surgical site infections (aHR 10.09 [2.88–35.34]), hemorrhage (aHR 4.92 [1.28–18.94]), renal insufficiency (aHR 4.85 [1.20–19.61]), inadequate perioperative prophylaxis in patients with an established antibiotic treatment compared to additional application of perioperative prophylaxis (aHR 2.87 [95%CI 1.17–7.05]), and procedure time per 1-hour increase (aHR 1.22 [95% CI 1.08–1.39]) to be risk factors for VGI. Conclusions We identified procedure time, inadequate perioperative prophylaxis, especially among patients with an established antibiotic treatment, and several postsurgical infectious and non-infectious complications as modifiable predictive factors for VGI and therefore key to improved surveillance programs and prevention strategies