Self-DNA Early Exposure in Cultivated and Weedy Setaria Triggers ROS Degradation Signaling Pathways and Root Growth Inhibition

The accumulation of fragmented extracellular DNA reduces conspecific seed germination and plantlet growth in a concentration-dependent manner. This self-DNA inhibition was repeatedly reported, but the underlying mechanisms are not fully clarified. We investigated the species-specificity of self-DNA inhibition in cultivated vs. weed congeneric species (respectively, Setaria italica and S. pumila) and carried out a targeted real-time qPCR analysis under the hypothesis that self-DNA elicits molecular pathways that are responsive to abiotic stressors. The results of a cross-factorial experiment on root elongation of seedlings exposed to self-DNA, congeneric DNA, and heterospecific DNA from Brassica napus and Salmon salar confirmed a significantly higher inhibition by self-DNA as compared to non-self-treatments, with the latter showing a magnitude of the effect consistent with the phylogenetic distance between the DNA source and the target species. Targeted gene expression analysis highlighted an early activation of genes involved in ROS degradation and management (FSD2, ALDH22A1, CSD3, MPK17), as well as deactivation of scaffolding molecules acting as negative regulators of stress signaling pathways (WD40-155). While being the first exploration of early response to self-DNA inhibition at molecular level on C4 model plants, our study highlights the need for further investigation of the relationships between DNA exposure and stress signaling pathways by discussing potential applications for species-specific weed control in agriculture

Targeted mutagenesis of the female-suppressor sygi gene in tetraploid kiwifruit by crispr/cas9

Kiwifruit belong to the genus Actinidia with 54 species apparently all functionally dioecious. The sex-determinants of the type XX/XY, with male heterogametic, operate independently of the ploidy level. Recently, the SyGI protein has been described as the suppressor of female development. In the present study, we exploited the CRISPR/Cas9 technology by targeting two different sites in the SyGI gene in order to induce a stable gene knock-out in two tetraploid male accessions of Actinidia chinensis var. chinensis. The two genotypes showed a regenerative efficiency of 58% and 73%, respectively. Despite not yet being able to verify the phenotypic effects on the flower structure, due to the long time required by tissue-cultured kiwifruit plants to flower, we obtained two regenerated lines showing near fixation of a unique modification in their genome, resulting in both cases in the onset of a premature stop codon, which induces the putative gene knock-out. Evaluation of gRNA1 locus for both regenerated plantlets resulted in co-amplification of a minor variant differing from the target region for a single nucleotide. A genomic duplication of the region in proximity of the Y genomic region could be postulated

Investigating the Role of TP53 in Peripheral T-Cell Lymphoma-GATA3 Subtype

Introduction: Non-Hodgkin Lymphoma (NHL) accounts for 4.1% of all cancers in the United States. Peripheral T-Cell Lymphoma (PTCL) consists of ~10-15% of all NHL in the Western world. 30-50% of these PTCLs are not classifiable/diagnosed and are instead designated as PTCL-Not Otherwise Specified (PTCL-NOS). The two major molecular subgroups within PTCL-NOS are PTCL-TBX21 and PTCL-GATA3, determined by their distinct T-helper (TH) transcriptional programs. GATA3 and TBX21 are the master-transcriptional regulators of TH2- and TH1-cell differentiation, respectively. The overall survival analysis of PTCL-NOS cases illustrates the clinical outcome of PTCL-GATA3 cases are significantly lower than PTCL-TBX21 cases over a broad timeframe. Thus, the need for understanding the underlying mechanism and finding therapeutic targets is at the utmost importance. Background: TP53 mutations and/or TP53 loss deletions are frequent in PTCL-GATA3 cases, compared to PTCL-TBX21. TP53 is a protein that is essential in cycle regulation but also acts as a tumor suppressor. It stops cells from dividing if they have mutated or damaged DNA. Due to the high mutation rates observed in this subtype, we believe TP53 could play a major role in this mechanism. Therefore, it was important to focus on the TP53-GATA3 interaction at the genomic level. Prior studies using chromatin immunoprecipitation (ChIP)-qPCR on the intron 3 full GATA3 region suggested there was more TP53 binding in this intron region compared to other regions. Therefore, we designed a research strategy to determine the specific binding regions of TP53-GATA3 interaction and the function of the TP53 binding.https://digitalcommons.unmc.edu/surp2023/1003/thumbnail.jp

Trunk motion analysis: a systematic review from a clinical and methodological perspective

INTRODUCTION: This systematic literature review aims to check the current state of affairs of non-gait-related optoelectronic trunk movement analysis; results have been analyzed from a clinical and a methodological perspective. EVIDENCE ACQUISITION: Extensive research was performed on all papers published until December 31st, 2015, dealing with trunk movement analysis assessed by optoelectronic systems, excluding those related to gait. The research was performed on the 14th of January 2016 on three databases: Scopus, Science Direct and Pubmed. A reference search and expert consultation were also performed. EVIDENCE SYNTHESIS: Out of a total number of 8431 papers, 45 were deemed relevant: they included 1334 participants, 57.9% healthy, with age range 8-85. Few studies considered the whole trunk, and none focused on each vertebra independently: the trunk was almost always divided into three segments. Thirteen studies included 20 or more markers. Most of the papers focused mainly on the biomechanics of various movements; the lumbar area and low back pain were the most studied region and pathology respectively. CONCLUSIONS: This study has shown the relative scarcity of current literature focusing on trunk motion analysis. In clinical terms, results were sparse. The only quite well represented group of papers focused on the lumbar spine and pathologies, but the scarcity of individuals evaluated make the results questionable. The use of optoelectronic systems in the evaluation of spine movement is a growing research area. Nevertheless, no standard protocols have been developed so far. Future research is needed to define a precise protocol in terms of number and position of markers along the spine and movements and tasks to be evaluated

Characterization of the poplar pan-genome by genome-wide identification of structural variation

Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa. We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2?Mb and 62.9?Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species.Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes.Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome

A flexible, computationally efficient method for fitting the proportional hazards model to interval-censored data: A Novel Method for Fitting the Proportional Hazards Model to Interval-Censored Data

The proportional hazards model (PH) is currently the most popular regression model for analyzing time-to-event data. Despite its popularity, the analysis of interval-censored data under the PH model can be challenging using many available techniques. This paper presents a new method for analyzing interval-censored data under the PH model. The proposed approach uses a monotone spline representation to approximate the unknown nondecreasing cumulative baseline hazard function. Formulating the PH model in this fashion results in a finite number of parameters to estimate while maintaining substantial modeling flexibility. A novel expectation-maximization (EM) algorithm is developed for finding the maximum likelihood estimates of the parameters. The derivation of the EM algorithm relies on a two-stage data augmentation involving latent Poisson random variables. The resulting algorithm is easy to implement, robust to initialization, enjoys quick convergence, and provides closed-form variance estimates. The performance of the proposed regression methodology is evaluated through a simulation study, and is further illustrated using data from a large population-based randomized trial designed and sponsored by the United States National Cancer Institute

Phenotypic plasticity, QTL mapping and genomic characterization of bud set in black poplar

<p>Abstract</p> <p>Background</p> <p>The genetic control of important adaptive traits, such as bud set, is still poorly understood in most forest trees species. Poplar is an ideal model tree to study bud set because of its indeterminate shoot growth. Thus, a full-sib family derived from an intraspecific cross of <it>P. nigra </it>with 162 clonally replicated progeny was used to assess the phenotypic plasticity and genetic variation of bud set in two sites of contrasting environmental conditions.</p> <p>Results</p> <p>Six crucial phenological stages of bud set were scored. Night length appeared to be the most important signal triggering the onset of growth cessation. Nevertheless, the effect of other environmental factors, such as temperature, increased during the process. Moreover, a considerable role of genotype × environment (G × E) interaction was found in all phenological stages with the lowest temperature appearing to influence the sensitivity of the most plastic genotypes.</p> <p>Descriptors of growth cessation and bud onset explained the largest part of phenotypic variation of the entire process. Quantitative trait loci (QTL) for these traits were detected. For the four selected traits (the onset of growth cessation (date2.5), the transition from shoot to bud (date1.5), the duration of bud formation (subproc1) and bud maturation (subproc2)) eight and sixteen QTL were mapped on the maternal and paternal map, respectively. The identified QTL, each one characterized by small or modest effect, highlighted the complex nature of traits involved in bud set process. Comparison between map location of QTL and <it>P. trichocarpa </it>genome sequence allowed the identification of 13 gene models, 67 bud set-related expressional and six functional candidate genes (CGs). These CGs are functionally related to relevant biological processes, environmental sensing, signaling, and cell growth and development. Some strong QTL had no obvious CGs, and hold great promise to identify unknown genes that affect bud set.</p> <p>Conclusions</p> <p>This study provides a better understanding of the physiological and genetic dissection of bud set in poplar. The putative QTL identified will be tested for associations in <it>P. nigra </it>natural populations. The identified QTL and CGs will also serve as useful targets for poplar breeding.</p

Specific exercises performed in the period of brace weaning can avoid loss of correction in Adolescent Idiopathic Scoliosis (AIS) patients: Winner of SOSORT's 2008 Award for Best Clinical Paper

<p>Abstract</p> <p>Background</p> <p>Exercises are frequently performed in order to improve the efficacy of bracing and avoid its collateral effects. Very frequently there is a loss of correction during brace weaning in AIS treatment.</p> <p>Aim</p> <p>To verify the efficacy of exercises in reducing correction loss during brace weaning.</p> <p>Study Design</p> <p>Retrospective controlled study.</p> <p>Population</p> <p>Sixty-eight consecutive patients (eight males), age 15 ± 1 and Cobb angle 22 ± 8° at start of brace weaning.</p> <p>Methods</p> <p>The start of brace weaning was defined as the first visit in which the wearing of brace for less than 18/24 hours was prescribed (according to our protocol, at Risser 3). Patients were divided into two groups according to whether or not exercises were performed: (1) EX (exercises), included 39 patients and was further divided into two sub-groups: SEAS (who performed exercises according to our institute's protocol, 14 patients) and OTH (other exercises, 25 patients) and (2) CON (controls, 29 patients) that was divided into two other sub-groups: DIS (discontinuous exercises, 19 patients) and NO (no exercises, 10 patients). Complete brace weaning was defined as the first visit in which the brace was no longer prescribed (ringapophysis closure or Risser 5, according to our protocol).</p> <p>ANOVA and Chi Square tests were performed.</p> <p>Results</p> <p>There was no difference between groups at baseline. However, at the end of treatment, 2.7 years after the start of the weaning process, Cobb angle increased significantly in both the DIS and NO groups (3.9° and 3.1° Cobb, respectively). The SEAS and OTH groups did not change. Comparing single groups, OTH (with respect to DIS) had a significant difference (P < 0.05).</p> <p>Conclusion</p> <p>Exercises can help reduce the correction loss in brace weaning for AIS.</p