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The increased demand for food and more sustainable agricultural practices have brought increased attention to legume crops, a family of plants that are able to carry out symbiotic nitrogen fixation which provides a reliable source of bioavailable nitrogen. [...]the cultivation of legumes can effectively reduce the reliance on the not-so-environmentally friendly synthetic nitrogen fertilizer. While comparing nodules with normal P to those with P deficiency, the most affected gene ontologies (GO) and pathways of the differentially expressed proteins (DEP) are mainly related to protein translation. Conflict of interest The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (2015).Identification of microRNAs and their mRNA targets during soybean nodule development: functional analysis of the role of miR393j-3p in soybean nodulation.New Phytol.207,748–759. doi:10.1111/nph.13365 YanZ.HossainM.

Based on these findings, they discussed the nitrogen-fixing potential of the rhizobia-sorghum interaction, and investigated the overall Bradyrhizobium diversity.Nguyen et al.worked with Bradyrhizobium species and demonstrated that the innB gene encodes a novel type III effector that controls symbiosis with Vigna radiata (mung bean). A number of approaches using molecular and functional characterization techniques were used to investigate the roles of various legume signals in nodule development.Rípodas et al.investigated transcription factors of the Nuclear Factor Y (NF-Y) family in Phaseolus vulgaris, indicating that both PvNF-YA1 and PvNF-YB7 are part of a network enabling P. vulgaris plants to discriminate and select for bacterial strains that perform better at nodule formation, possibly by forming a heterotrimeric complex with PvNF-YC1. In addition to molecular genetic studies, they used non-nodulating and super-nodulating soybean mutants to establish that early systemic redox signaling during nodule development depends on Nod factor perception and the induced tolerance response depends on the autoregulation of the nodulation mechanism.

Nitrogen fixing bacteria, collectively referred to as rhizobia, are able to trigger the organogenesis of a new organ on legumes, the nodule. The morphogenetic trigger is a Rhizobium-produced lipochitin-oligosaccharide called the Nod factor, which is necessary, and in some legumes sufficient, for triggering nodule development in the absence of the bacterium. Because plant development is substantially influenced by plant hormones, it has been hypothesized that plant hormones (mainly the classical hormones abscisic acid, auxin, cytokinins, ethylene and gibberellic acid) regulate nodule development. In recent years, evidence has shown that Nod factors might act in legumes by changing the internal plant hormone balance, thereby orchestrating the nodule developmental program. In addition, many nonclassical hormonal signals have been found to play a role in nodule development, some of them similar to signals involved in animal development. These compounds include peptide hormones, nitric oxide, reactive oxygen species, jasmonic acid, salicylic acid, uridine, flavonoids and Nod factors themselves. Environmental factors, in particular nitrate, also influence nodule development by affecting the plant hormone status. This review summarizes recent findings on the involvement of classical and nonclassical signals during nodule development with the aim of illustrating the multiple interactions existing between these compounds that have made this area so complicated to analyze.

• Gibberellin (GA) deficiency resulting from the na mutation in pea (Pisum sativum) causes a reduction in nodulation. Nodules that do form are aberrant, having poorly developed meristems and a lack of enlarged cells. Studies using additional GA-biosynthesis double mutants indicate that this results from severe GA deficiency of the roots rather than simply dwarf shoot stature. • Double mutants isolated from crosses between na and three supernodulating pea mutants exhibit a supernodulation phenotype, but the nodule structures are aberrant. This suggests that severely reduced GA concentrations are not entirely inhibitory to nodule initiation, but that higher GA concentrations are required for proper nodule development. • na mutants evolve more than double the amount of ethylene produced by wild-type plants, indicating that low GA concentrations can promote ethylene production. The excess ethylene may contribute to the reduced nodulation of na plants, as application of an ethylene biosynthesis inhibitor increased na nodule numbers. However, these nodules were still aberrant in structure. • Constitutive GA signalling mutants also form significantly fewer nodules than wild-type plants. This suggests that there is an optimum degree of GA signalling required for nodule formation and that the GA signal, and not the concentration of bioactive GA per se, is important for nodulation.

The initiation and development of legume nodules induced by compatible Rhizobium species requires a complex signal exchange involving both plant and bacterial compounds. Phytohormones have been implicated in this process, although in many cases direct evidence is lacking. Here, we characterize the root and nodulation phenotypes of various mutant lines of pea (Pisum sativum) that display alterations in their phytohormone levels and/or perception. Mutants possessing root systems deficient in gibberellins (GAs) or brassinosteroids (BRs) exhibited a reduction in nodule organogenesis. The question of whether these reductions represent direct or indirect effects of the hormone deficiency is addressed. For example, the application of GA to the roots of a GA-deficient mutant completely restored its number of nodules to that of the wild type. Grafting studies revealed that a wild-type shoot or root also restored the nodule number of a GA-deficient mutant. These findings suggest that GAs are required for nodulation. In contrast, the shoot controlled the number of nodules that formed in graft combinations of a BR-deficient mutant and its wild type. The root levels of auxin and GA were similar among these latter graft combinations. These results suggest that BRs influence a shoot mechanism that controls nodulation and that the root levels of auxin and GA are not part of this process. Interestingly, a strong correlation between nodule and lateral root numbers was observed in all lines assessed, consistent with a possible overlap in the early developmental pathways of the two organs.

Michael Talkowski and colleagues analyze balanced chromosomal abnormalities in 273 individuals by whole-genome sequencing. Their findings suggest that sequence-level resolution improves prediction of clinical outcomes for balanced rearrangements and provides insight into pathogenic mechanisms such as altered gene regulation due to changes in chromosome topology. Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C , a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. We propose that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements and provides insight into new pathogenic mechanisms, such as altered regulation due to changes in chromosome topology.

BackgroundThe prediction of a difficult cholecystectomy has traditionally been based on certain pre-operative clinical and imaging factors. Most of the previous literature reported small patient cohorts and have not used an objective measure of operative difficulty. The aim of this study was to develop a pre-operative score to predict difficult cholecystectomy, as defined by a validated intra-operative difficulty grading scale.MethodTwo cohorts from prospectively maintained databases of patients who underwent laparoscopic cholecystectomy were analysed: the CholeS Study (8755 patients) and a single surgeon series (4089 patients). Factors potentially predictive of difficulty were correlated to the Nassar intra-operative difficulty scale. A multivariable binary logistic regression analysis was then used to identify factors that were independently associated with difficult laparoscopic cholecystectomy, defined as operative difficulty grades 3 to 5. The resulting model was then converted to a risk score, and validated on both internal and external datasets.ResultIncreasing age and ASA classification, male gender, diagnosis of CBD stone or cholecystitis, thick-walled gallbladders, CBD dilation, use of pre-operative ERCP and non-elective operations were found to be significant independent predictors of difficult cases. A risk score based on these factors returned an area under the ROC curve of 0.789 (95% CI 0.773–0.806, p < 0.001) on external validation, with 11.0% versus 80.0% of patients classified as low versus high risk having difficult surgeries.ConclusionWe have developed and validated a pre-operative scoring system that uses easily available pre-operative variables to predict difficult laparoscopic cholecystectomies. This scoring system should assist in patient selection for day case surgery, optimising pre-operative surgical planning (e.g. allocation of the procedure to a suitably trained surgeon) and counselling patients during the consent process. The score could also be used to risk adjust outcomes in future research.

BackgroundA reliable system for grading operative difficulty of laparoscopic cholecystectomy would standardise description of findings and reporting of outcomes. The aim of this study was to validate a difficulty grading system (Nassar scale), testing its applicability and consistency in two large prospective datasets.MethodsPatient and disease-related variables and 30-day outcomes were identified in two prospective cholecystectomy databases: the multi-centre prospective cohort of 8820 patients from the recent CholeS Study and the single-surgeon series containing 4089 patients. Operative data and patient outcomes were correlated with Nassar operative difficultly scale, using Kendall’s tau for dichotomous variables, or Jonckheere–Terpstra tests for continuous variables. A ROC curve analysis was performed, to quantify the predictive accuracy of the scale for each outcome, with continuous outcomes dichotomised, prior to analysis.ResultsA higher operative difficulty grade was consistently associated with worse outcomes for the patients in both the reference and CholeS cohorts. The median length of stay increased from 0 to 4 days, and the 30-day complication rate from 7.6 to 24.4% as the difficulty grade increased from 1 to 4/5 (both p < 0.001). In the CholeS cohort, a higher difficulty grade was found to be most strongly associated with conversion to open and 30-day mortality (AUROC = 0.903, 0.822, respectively). On multivariable analysis, the Nassar operative difficultly scale was found to be a significant independent predictor of operative duration, conversion to open surgery, 30-day complications and 30-day reintervention (all p < 0.001).ConclusionWe have shown that an operative difficulty scale can standardise the description of operative findings by multiple grades of surgeons to facilitate audit, training assessment and research. It provides a tool for reporting operative findings, disease severity and technical difficulty and can be utilised in future research to reliably compare outcomes according to case mix and intra-operative difficulty.