Display omitted
•Modified RADseq protocol yields strongly reduced number of length extended loci.•Evaluation of assembly metrics eases clustering threshold selection using ipyrad.•Locus filtering by ...length facilitates detection of biased data.•Dataset reduction improves overall data quality.•Informative RADseq loci support coalescent-based phylogenetic inference with ASTRAL.
Analysing multiple genomic regions while incorporating detection and qualification of discordance among regions has become standard for understanding phylogenetic relationships. In plants, which usually have comparatively large genomes, this is feasible by the combination of reduced-representation library (RRL) methods and high-throughput sequencing enabling the cost effective acquisition of genomic data for thousands of loci from hundreds of samples. One popular RRL method is RADseq. A major disadvantage of established RADseq approaches is the rather short fragment and sequencing range, leading to loci of little individual phylogenetic information. This issue hampers the application of coalescent-based species tree inference. The modified RADseq protocol presented here targets ca. 5,000 loci of 300-600nt length, sequenced with the latest short-read-sequencing (SRS) technology, has the potential to overcome this drawback. To illustrate the advantages of this approach we use the study group Aichryson Webb & Berthelott (Crassulaceae), a plant genus that diversified on the Canary Islands. The data analysis approach used here aims at a careful quality control of the long loci dataset. It involves an informed selection of thresholds for accurate clustering, a thorough exploration of locus properties, such as locus length, coverage and variability, to identify potential biased data and a comparative phylogenetic inference of filtered datasets, accompanied by an evaluation of resulting BS support, gene and site concordance factor values, to improve overall resolution of the resulting phylogenetic trees. The final dataset contains variable loci with an average length of 373nt and facilitates species tree estimation using a coalescent-based summary approach. Additional improvements brought by the approach are critically discussed.
Two regioisomeric lactams, which are derived from terpenoid ketone (−)-menthone in two steps, are oligomerized in an easy acid-induced procedure to obtain oligoamides that contain alkyl groups and ...stereocenters; for this, a nucleophilic oligomerization via a non-ionic propagating site (neutral conditions) and a polycondensation are also possible. Furthermore, a regioselective synthesis is demonstrated where (−)-menthone is transformed into one of these lactams in a one-step procedure via Beckmann rearrangement without isolation of any oxime intermediate using the reagent hydroxylamine- O -sulfonic acid (HOSA). These concise oligoamide syntheses smooth the way to novel sustainable long-chain polyamides with highly interesting structures.
Plants have evolved signaling mechanisms such as the multi-step phosphorelay (MSP) to respond to different internal and external stimuli. MSP responses often result in gene transcription regulation ...that is modulated through transcription factors such as B-type Arabidopsis response regulator (ARR) proteins. Among these proteins, ARR2 is a key component that is expressed ubiquitously and is involved in many aspects of plant development. Although it has been noted that B-type ARRs bind to their cognate genes through a DNA-binding domain termed the GARP domain, little is known about the structure and function of this type of DNA-binding domain; thus, how ARRs bind to DNA at a structural level is still poorly understood. In order to understand how the MSP functions in planta, it is crucial to unravel both the kinetics as well as the structural identity of the components involved in such interactions. For this reason, this work focusses on resolving how the GARP domain of ARR2 (GARP2) binds to the promoter region of ARR5, one of its native target genes in cytokinin signaling. We have established that GARP2 specifically binds to the ARR5 promoter with three different bi-molecular interaction systems—qDPI-ELISA, FCS, and MST—and we also determined the KD of this interaction. In addition, structural modeling of the GARP2 domain confirms that GARP2 entails a HTH motif, and that protein–DNA interaction most likely occurs via the α3-helix and the N-terminal arm of this domain since mutations in this region hinder ARR2’s ability to activate transcription.
Infections with the human malaria parasite Plasmodium falciparum during pregnancy can lead to severe complications for both mother and child, resulting from the cytoadhesion of parasitized ...erythrocytes in the intervillous space of the placenta. Cytoadherence is conferred by the specific interaction of the parasite-encoded adhesin VAR2CSA with chondroitin-4-sulfate (CSA) present on placental proteoglycans. CSA presented elsewhere in the microvasculature does not afford VAR2CSA-mediated cytoadhesion of parasitized erythrocytes. To address the placenta-specific binding tropism, we investigated the effect of the receptor/ligand arrangement on cytoadhesion, using artificial membranes with different CSA spacing intervals. We found that cytoadhesion is strongly dependent on the CSA distance, with half-maximal adhesion occurring at a CSA distance of 9 ± 1 nm at all hydrodynamic conditions. Moreover, binding to CSA was cooperative and shear stress induced. These findings suggest that the CSA density, together with allosteric effects in VAR2CSA, aid in discriminating between different CSA milieus.
•Cytoadhesion of parasitized erythrocytes depends on the intermolecular distance between neighboring chondroitin-4-sulfate molecules.•VAR2CSA is an allosteric adhesin that binds chondroitin-4-sulfate in a cooperative and shear stress–induced manner.
Objective:
Advanced tongue cancer is a devastating diagnosis with potential for significant morbidity after treatment. This is especially true for patients undergoing total glossectomy with laryngeal ...preservation (TGLP), free flap reconstruction and adjuvant radiotherapy. The goals of this study were to: 1) determine long‐term objective functional and quality of life outcomes, 2) investigate the influence of rehabilitation on functional recovery and 3) determine swallowing ability in patients with TGLP.
Study Design:
Prospective cohort study and systematic review of the literature.
Methods:
Functional outcomes data were collected from 2000–2010. Outcomes were measured pre‐ and 12 months post‐surgery and included: gastrostomy‐tube (G‐Tube) rates, swallowing transit times on video fluoroscopic swallowing studies, speech intelligibility and EORTC‐H&N 35 quality of life scores. A systematic review of the literature was conducted to determine comprehensive long term G‐Tube rates.
Results:
Twelve patients were included and eight were still living at 12 months post‐surgery. Fifty percent of patients in this study and 24% with systematic review used G‐Tubes at 1 year post‐surgery. Patients who could swallow did not aspirate, but more than doubled swallowing transit times. Spoken sentence intelligibility averaged 66% and mean quality of life scores improved 8.9 points 12 months post‐surgery. Patients who attended >80% of swallowing and speech rehabilitation sessions demonstrated superior swallowing and speech functional outcomes.
Conclusions:
Although a potentially morbid treatment, TGLP and free flap reconstruction can provide good swallowing and speech outcomes as well as meaningful long‐term quality of life. Regular attendance of rehabilitation sessions is imperative to optimize functional outcomes. Laryngoscope, 2013
Background
Laparoscopic surgery (LS) induces physical stress to the surgeon that is associated with an increased prevalence of musculoskeletal pain and injury in the shoulder–neck region. The aim of ...this research project is to develop an arm support system (ASsyst) that reduces physical stress and is applicable to various laparoscopic interventions and operation room settings.
Methods
A systematic approach to develop an ASsyst started in October 2012 consisting of five consecutive steps. In step 1, 14 laparoscopic interventions were observed using subjective and objective measures to determine key indicators for the conception of an ASsyst in LS. In step 2, an expert workshop was held to find and evaluate solutions to generate concepts for a support system based on the results of step 1 and general methods. During the third step, prototypes of ASsyst were tested in an experimental setting. Steps 4 and 5 are currently in process and include the final development of the ASsyst using the most promising concept for the evaluation during simulated LS.
Results
Increased levels of physical stress were found in LS. Asymmetric strains were common. Three prototypes of ASsyst emerged from step 1 and 2. These prototypes were a cable construction with a noose for the lower arm, a support from below the elbow and a pneumatic vest supporting the upper arm. The experimental testing of these prototypes demonstrated reduced physical stress when compared to the unsupported environment. The support from below the elbow seemed to be the most practical in terms of implementation in various operation room settings and acceptance by surgeons. Step 4 and 5 are still in process.
Conclusions
Ergonomic problems have been identified in LS that could be addressed by an ASsyst. The concept of supporting the elbow from below has been found to be the most promising approach.
The bone marrow microenvironment is physiologically hypoxic with areas being as low as 1% O2, e.g. the stem cell niche. Acute myeloid leukaemia (AML) blasts misuse these bone marrow niches for ...protection by the local microenvironment, but also might create their own microenvironment. Here we identify IL-8 as a hypoxia-regulated cytokine in both AML cell lines and primary AML samples that is induced within 48 hours of severe hypoxia (1% O2). IL-8 lacked effects on AML cells but induced migration in mesenchymal stromal cells (MSC), an integral part of the bone marrow. Accordingly, MSC were significantly increased in AML bone marrow as compared to healthy bone marrow. Interestingly, mononuclear cells obtained from healthy bone marrow displayed both significantly lower endogenous and hypoxia-induced production of IL-8. IL-8 mRNA expression in AML blasts from 533 patients differed between genetic subgroups with significantly lower expression of IL-8 in acute promyelocytic leukaemia (APL), while in non APL-AML patients with FLT ITD had the highest IL-8 expression. In this subgroup, high IL-8 expression was also prognostically unfavourable. In conclusion, hypoxia as encountered in the bone marrow specifically increases IL-8 expression of AML, which in turn impacts niche formation. High IL-8 expression might be correlated with poor prognosis in certain AML subsets.
PDF
