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Numerous activities within honey bee (Apis mellifera L.) colonies rely on feedback loops for organization at the group level. Classic examples of these self-organizing behaviors occur during foraging and swarm nest site selection. The waggle dance provides positive feedback, promoting foraging at a specific location or increased scouting at a potential nest site. Rather less well known than the waggle dance, the stop signal, a short vibration often delivered while butting against a dancing bee, is currently best understood as a counter to the waggle dance, offering negative feedback towards the advertised foraging location or nest site. When the stop signal is received by a waggle dancer she is more likely to terminate her dance early and retire from the dance floor. Bees that experienced danger or overcrowding at a food source are more likely to perform the stop signal upon their return to the colony, resulting in an inhibition of foraging at that location. During a swarm’s nest site selection process, scout bees that visited a different site than the one being advertised are more likely to stop-signal the waggle dancer than are scouts that had visited the same site. Over time, the scout bees build recruitment to a single site until a quorum is reached and the swarm can move to it. The balance between the positive feedback from the waggle dance and the negative feedback from the stop signal allows for a more sensitive adjustment of response from the colony as a unit. Many of the processes associated with the feedback loops organizing a honey bee colony’s activities are in striking parallel to other systems, such as intercellular interactions involved in motor neuron function.

Abstract Background The photorespiratory nitrogen cycle in C3 plants involves an extensive diversion of carbon and nitrogen away from the direct pathways of assimilation. The liberated ammonia is re-assimilated, but up to 25% of the carbon may be released into the atmosphere as CO2. Because of the loss of CO2 and high energy costs, there has been considerable interest in attempts to decrease the flux through the cycle in C3 plants. Transgenic tobacco plants were generated that contained the genes gcl and hyi from E. coli encoding glyoxylate carboligase (EC 4.1.1.47) and hydroxypyruvate isomerase (EC 5.3.1.22) respectively, targeted to the peroxisomes. It was presumed that the two enzymes could work together and compete with the aminotransferases that convert glyoxylate to glycine, thus avoiding ammonia production in the photorespiratory nitrogen cycle. Results When grown in ambient air, but not in elevated CO2, the transgenic tobacco lines had a distinctive phenotype of necrotic lesions on the leaves. Three of the six lines chosen for a detailed study contained single copies of the gcl gene, two contained single copies of both the gcl and hyi genes and one line contained multiple copies of both gcl and hyi genes. The gcl protein was detected in the five transgenic lines containing single copies of the gcl gene but hyi protein was not detected in any of the transgenic lines. The content of soluble amino acids including glycine and serine, was generally increased in the transgenic lines growing in air, when compared to the wild type. The content of soluble sugars, glucose, fructose and sucrose in the shoot was decreased in transgenic lines growing in air, consistent with decreased carbon assimilation. Conclusions Tobacco plants have been generated that produce bacterial glyoxylate carboligase but not hydroxypyruvate isomerase. The transgenic plants exhibit a stress response when exposed to air, suggesting that some glyoxylate is diverted away from conversion to glycine in a deleterious short-circuit of the photorespiratory nitrogen cycle. This diversion in metabolism gave rise to increased concentrations of amino acids, in particular glutamine and asparagine in the leaves and a decrease of soluble sugars.

Background: Lupus nephritis (LN) is a serious manifestation of systemic lupus erythematosus (SLE) and failure to respond to traditional immunosuppression increases morbidity and mortality. Rituximab has been considered a novel therapeutic option for the management of SLE., Materials and Methods: We conducted a single-center, prospective, observational study from July 2018 to June 2019 to evaluate the effectiveness of rituximab in patients with resistant LN. Resistant LN was defined as the failure to respond to conventional immunosuppressive therapy including both cyclophosphamide and mycophenolate mofetil. All adult patients (> 18 years) with biopsy-proven class III/IV LN were included in the study. Four doses of intravenous rituximab (375 mg/m 2 ) on 0, 1, 2, 3 weeks were administered. Patients were followed for 6 months, and the rates of complete renal response (CRR), partial renal response (PRR), or no renal response (NRR) were measured. The change in baseline 24-hour urine protein, mean serum creatinine levels, and mean serum CD-19 levels at 24 weeks were also measured., Results: Six months after rituximab therapy, total sustained renal response (CRR+PRR) was observed in 52% cases of resistant LN (CRR was achieved in 24% of patients and PRR in 28%, respectively). Rituximab was associated with a significant decline in the 24-hour urine protein, even in non-responders. However, the improvement in eGFR and serum creatinine was not statistically significant. The mean absolute CD-19 count was significantly low in responders compared to the non-responder group., Conclusion: Rituximab is a safe and effective therapeutic strategy for patients with resistant LN.

Patients with end-stage renal disease (ESRD) are at an increased risk of hepatitis C virus (HCV) infection. This study evaluated the prevalence of HCV infection in patients with ESRD on maintenance hemodialysis (MHD) and studied the effectiveness of sofosbuvir-velpatasvir and sofosbuvir-daclatasvir regimens in these patients. This study included patients with ESRD on MHD between January 2019 and December 2021 who were screened for HCV serology status. HCV-positive patients received sofosbuvir-velpatasvir or sofosbuvir-daclatasvir. Efficacy was assessed by the sustained virological response (SVR), and safety assessments included monitoring adverse events and laboratory parameters. Out of 1330 patients, 188 patients (14.1%) were positive for anti-HCV, with Genotype 1 being the most common genotype. Of these, 106 patients were included. The majority were males (61.3%), and the mean age was 48.4 years. Hypertension (45.3%) was the most common cause of renal failure, followed by diabetes (31.1%). Most patients (63.2%) were positive for HCV in the first 2 years of their dialysis treatment. Out of 106 patients, only 54 had received blood transfusions. Ninety-four (88.7%) patients received sofosbuvir-velpatasvir, whereas 12 (11.3%) received sofosbuvir-daclatasvir. SVR at 12 and 24 weeks after stopping treatment was seen in all (100%) patients. Asthenia and fatigue were the most common adverse events (11.2%). No patients reported on-treatment virologic failure or discontinuation of treatment because of adverse events. The prevalence of HCV infection in this population was 14.1%, and treatment of HCV infection using sofosbuvir-velpatasvir or sofosbuvir-daclatasvir regimens was well tolerated and effective., (Copyright © 2023 Copyright: © 2023 Saudi Journal of Kidney Diseases and Transplantation.)

Background: Rupture of the Achilles tendon is a considerable cause of morbidity with reduced function following injury. Randomized studies have so far failed to show a difference in outcome between operative and nonoperative management of Achilles tendon rupture, provided that no re-rupture occurs. Percutaneous Achilles repair has been suggested to result in superior patient satisfaction compared with open repair in patients with an acute Achilles tendon rupture., Aim and Objectives: To assess and evaluate the functional outcome after percutaneous repair in patients of the acute and closed Achilles tendon ruptures., Materials and Methods: It was a prospective study conducted on patients diagnosed as having rupture of the Achilles tendon. A total of 25 patients with mean age of 44.4 (range 19-65) years were taken, who underwent percutaneous Achilles tendon repair., Results: The number of patients who reported excellent or good scores (ATRS > 80) at 3, 6 and 12 months were 0%, 16% and 100%, respectively. The mean AOFAS hind foot score at 3-, 6- and 12-month follow-ups was 77.9 ± 4.3, 92.04 ± 2.4 and 96.16.32 ± 1.1, respectively. The number of patients who reported excellent or good scores (AOFAS > 74) at 3, 6 and 12 months were 76%, 100% and 100%, respectively. Most of the patients in our study showed no complications, and only 2 (8%) of patients had the features of sural nerve injury which was resolved in the subsequent follow-ups., Conclusion: Percutaneous repair of the Achilles tendon is an effective procedure which gives excellent functional outcome with very few complications. The percutaneous technique gives an additional advantage of less operative time, no wound complications, less damage to the soft tissues, and improved cosmesis as compared to the open repair., Competing Interests: Conflict of InterestNone., (© Indian Orthopaedics Association 2023, Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Full-house pattern on immunofluorescence (IF) on kidney biopsy in a patient without systemic lupus erythematosus is termed as nonlupus full-house nephropathy (FHN). In this study, we retrospectively compiled patients with nonlupus FHN and compared them with lupus FHN for clinicopathological presentation. We included patients with full-house IF patterns in renal biopsies collected from March 2007 to August 2018, clinical and histopathological data at the time of presentation were studied retrospectively. Treatment received and outcome at the end of follow-up was studied. Patients with nonlupus FHN who did not show any systemic disease (idiopathic group) were compared with a group of lupus nephritis patients. Of 178 patients, 34 had nonlupus FHN with 21 having idiopathic nonlupus FHN and 13 patients having secondary nonlupus FHN (membranous nephropathy, IgA nephropathy, postinfection glomerulonephritis). Males were more often in idiopathic nonlupus FHN patients than lupus FHN patients (P = 0.005). Kidney biopsies more often showed a mesangial (P = 0.0006) and less proliferative pattern of injury (P = 0.0002) and less intense C1q staining (P = 0.0001) in idiopathic nonlupus than lupus FHN. Clinically, idiopathic nonlupus FHN presented with more proteinuria (P = 0.0059) and less complement consumption (P = 0.001) than lupus FHN patients. Compared to lupus FHN, nonlupus has mainly nephrotic syndrome as clinical presentation. There was no difference in the clinical outcome between lupus FHN and idiopathic nonlupus FHN. Nonlupus FHN is not a very common condition and has less female involvement than in lupus FHN. Idiopathic nonlupus FHN has certain histopathological features with less C1q staining by IF, less frequent proliferative lesions and higher mesangial or membranous lesions by light microscopy compared to lupus FHN. Regarding outcomes, there is no significant difference between lupus FHN and idiopathic nonlupus FHN., Competing Interests: None

This study was conducted to retrospectively investigate the indications for renal biopsy in the native kidneys of children and to analyze the pathological findings in a single tertiary care hospital in North-East India for the past 12 years. All children (≤18 years) who underwent renal biopsy at our hospital from March 2007 to April 2018 were included. Renal tissue specimens were studied under light and immunofluorescence microscopy. The study group included 254 patients (female 57%). The median age was 15 years (range 6-18 years). The most frequent indications for renal biopsy were nephrotic syndrome (NS) (53.9%), urinary abnormality in systemic disease (22.1%), nephritic syndrome (15.4%), asymptomatic hematuria (4.7%), significant proteinuria (3.1%), and unexplained renal failure (0.8%). On histopathological examination, primary glomerular diseases were the most frequent (68.9%) followed by secondary glomerular diseases (30.3%) and tubulointerstitial diseases (0.8%). The most common primary glomerular diseases were minimal change disease (26.8%), focal segmental glomerular sclerosis (12.2%), diffuse proliferative glomerulonephritis (9.1%), membranous nephropathy (8.7%), IgA nephropathy (8.3%), membranoproliferative glomerulonephritis (2%), and mesangioproliferative glomerulonephritis (2%). Lupus nephritis (LN) (29.5%) was the most common secondary glomerular disease. NS was the most common indication of renal biopsy, and LN was the most common histopathological diagnosis in children ≤18 years.

Introduction: To avoid temporary hemodialysis, urgent initiated PD (UIPD) has been designed. In these patients, PD is initiated within 3 days after PD catheter placement. In this study, we evaluated the outcomes of UIPD in end-stage renal disease patients compared with the conventional start of PD., Methods: This is a single-center observational study, comparing outcomes of UIPD to conventional initiation of PD. All patients diagnosed with ESRD from March 2013 to February 2019 and were willing for CAPD were recruited. In UIPD group treatment was initiated at day 2 of catheter insertion with a dialysate volume of 1000 mL per dwell for 2 hours gradually increased to 2000 mL per dwell volume by 8 to 10 days., Results: During the study period, 98 patients were started on peritoneal dialysis in our hospital: 35 UIPD, 63 conventional PD. The mean age was 60.81 ± 13.04 years. 67% of patients were males with diabetes mellitus (32%) being the most common cause of CKD. Among the patients in UIPD, the mean age was 58.49 ± 16.1 years, while as in conventional group mean age was 62.10 ± 10.9 years. The Median follow-up time was 381 days. Technique survival was seen in 95 patients (96.9%). There was no difference in technique failure between UIPD vs conventional group. Total complications in our study occurred in 16 patients out of 98 patients during this period. There was no significant difference in the complication rates between the UIPD group and the conventional group., Conclusion: Our study showed that catheter patency, technique survival, and catheter-related complications were comparable between UIPD and conventional start peritoneal dialysis.

Purpose: The STAMPEDE trial recruits men with newly diagnosed, high-risk, hormone-sensitive prostate cancer. To ascertain the feasibility of targeted next-generation sequencing (tNGS) and the prevalence of baseline genomic aberrations, we sequenced tumor and germline DNA from patients with metastatic prostate cancer (mPCa) starting long-term androgen-deprivation therapy (ADT)., Methods: In a 2-stage approach, archival, formalin-fixed, paraffin-embedded (FFPE) prostate tumor core biopsy samples were retrospectively subjected to 2 tNGS assays. Prospective enrollment enabled validation using tNGS in tumor and germline DNA., Results: In stage 1, tNGS data were obtained from 185 tumors from 287 patients (65%); 98% had de novo mPCa. We observed PI3K pathway aberrations in 43%, due to PTEN copy-number loss (34%) and/or activating mutations in PIK3 genes or AKT (18%) and TP53 mutation or loss in 33%. No androgen receptor ( AR ) aberrations were detected; RB1 loss was observed in < 1%. In stage 2, 93 (92%) of 101 FFPE tumors (biopsy obtained within 8 months) were successfully sequenced prospectively. The prevalence of DNA damage repair (DDR) deficiency was 14% (somatic) and 5% (germline). BRCA2 mutations and mismatch repair gene mutations were exclusive to high-volume disease. Aberrant DDR (22% v 15%), Wnt pathway (16% v 4%), and chromatin remodeling (16% v 8%) were all more common in high-volume compared with low-volume disease, but the small numbers limited statistical comparisons., Conclusion: Prospective genomic characterization is feasible using residual diagnostic tumor samples and reveals that the genomic landscapes of de novo high-volume mPCa and advanced metastatic prostate cancer have notable similarities (PI3K pathway, DDR, Wnt, chromatin remodeling) and differences ( AR , RB1 ). These results will inform the design and conduct of biomarker-directed trials in men with metastatic hormone-sensitive prostate cancer.

Diabetes mellitus is the most common cause of chronic kidney disease worldwide. The prevalence of nondiabetic renal disease (NDRD) among patients with type 2 diabetes mellitus (T2DM) varies widely. This study aimed to evaluate the renal biopsies performed on type 2 diabetic patients for suspicion of NDRD and to correlate clinicopathological findings. All T2DM patients aged > 18 years were included in this study, who had renal biopsy performed for the following reasons: recent-onset nephrotic syndrome, unexplained rapid deterioration of renal function, proteinuria not accompanied by retinopathy, and unexplained hematuria. Renal biopsy was analyzed by light microscopy and immunofluorescence. Based on biopsy findings, the patients were grouped into three: (i) isolated NDRD, (ii) NDRD ± diabetic nephropathy (DN), and (iii) isolated DN. A total of 140 patients were enrolled in this study. Recent-onset nephrotic syndrome was the most common indication for biopsy, followed by the presence of active urine sediment. Forty-two percent of the patients had isolated DN, while NDRD was seen in 34% and DN ± NDRD in 24%. Focal segmental glomerulosclerosis (FSGS) and IgA nephropathy were the most common causes of isolated NDRD, while chronic tubulointerstitial nephritis (CTIN) was common in NDRD plus DN. Short duration of diabetes, absence of diabetic retinopathy, and lower glycated hemoglobin were predictive of NDRD. NDRD was seen in 58% of the patients with atypical presentations. FSGS and CTIN were common in NDRD diseases. Judicious use of biopsy in diabetic patients with atypical presentation may help in the diagnosis of NDRD.

Context: Multiparametric magnetic resonance imaging (mpMRI) detects most, but not all, clinically significant prostate cancer. The genetic basis of prostate cancer visibility and invisibility on mpMRI remains uncertain., Objective: To systematically review the literature on differential gene expression between mpMRI-visible and mpMRI-invisible prostate cancer, and to use bioinformatic analysis to identify enriched processes or cellular components in genes validated in more than one study., Evidence Acquisition: We performed a systematic literature search of the Medline, EMBASE, PubMed, and Cochrane databases up to January 2020 in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) statement. The primary endpoint was differential genetic features between mpMRI-visible and mpMRI-invisible tumours. Secondary endpoints were explanatory links between gene function and mpMRI conspicuity, and the prognostic value of differential gene enrichment., Evidence Synthesis: We retrieved 445 articles, of which 32 met the criteria for inclusion. Thematic synthesis from the included studies showed that mpMRI-visible cancer tended towards enrichment of molecular features associated with increased disease aggressivity, including phosphatase and tensin homologue ( PTEN ) loss and higher genomic classifier scores, such as Oncotype and Decipher. Three of the included studies had accompanying publicly available data suitable for further bioinformatic analysis. An over-representation analysis of these datasets revealed increased expression of genes associated with extracellular matrix components in mpMRI-visible tumours., Conclusions: Prostate cancer that is visible on mpMRI is generally enriched with molecular features of tumour development and aggressivity, including activation of proliferative signalling, DNA damage, and inflammatory processes. Additionally, there appears to be concordant cellular components and biological processes associated with mpMRI conspicuity, as highlighted by bioinformatic analysis of large genetic datasets., Patient Summary: Prostate cancer that is detected by magnetic resonance imaging (MRI) tends to have genetic features that are associated with more aggressive disease. This suggests that MRI can be used to assess the likelihood of aggressive prostate cancer, based on tumour visibility., (© 2020 The Author(s).)

Introduction: The introduction of multiparametric MRI (mpMRI) has enabled enhanced risk stratification for men at risk of prostate cancer, through accurate prebiopsy identification of clinically significant disease. However, approximately 10%-20% of significant prostate cancer may be missed on mpMRI. It appears that the genomic basis of lesion visibility or invisibility on mpMRI may have key implications for prognosis and treatment. Here, we describe a protocol for the first systematic review and novel bioinformatic analysis of the genomic basis of prostate cancer conspicuity on mpMRI., Methods and Analysis: A systematic search of MEDLINE, PubMed, EMBASE and Cochrane databases will be conducted. Screening, data extraction, statistical analysis and reporting will be performed in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Included papers will be full text articles, written between January 1980 and December 2019, comparing molecular characteristics of mpMRI-visible lesions and mpMRI-invisible lesions at the DNA, DNA-methylation, RNA or protein level. Study bias and quality will be assessed using a modified Newcastle-Ottawa score. Additionally, we will conduct a novel bioinformatic analysis of supplementary material and publicly available data, to combine transcriptomic data and reveal common pathways highlighted across studies. To ensure methodological rigour, this protocol is written in accordance with the PRISMA Protocol 2015 checklist., Ethics and Dissemination: Ethical approval will not be required, as this is an academic review of published literature. Findings will be disseminated through publications in peer-reviewed journals, and presentations at national and international conferences., Prospero Registration Number: CRD42019147423., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY. Published by BMJ.)

Background: The prostate cancer (PCa) diagnostic pathway is undergoing a radical change with the introduction of multiparametric magnetic resonance imaging (mpMRI), genomic testing, and different prostate biopsy techniques. It has been proposed that these tests should be used in a sequential manner to optimise risk stratification., Objective: To characterise the genomic, epigenomic, and transcriptomic features of mpMRI-visible and -nonvisible PCa in clinically localised disease., Design, Setting, and Participants: Multicore analysis of fresh prostate tissue sampled immediately after radical prostatectomy was performed for intermediate- to high-risk PCa., Intervention: Low-pass whole-genome, exome, methylation, and transcriptome profiling of patient tissue cores taken from microscopically benign and cancerous areas in the same prostate. Circulating free and germline DNA was assessed from the blood of five patients., Outcome Measurement and Statistical Analysis: Correlations between preoperative mpMRI and genomic characteristics of tumour and benign prostate samples were assessed. Gene profiles for individual tumour cores were correlated with existing genomic classifiers currently used for prognostication., Results and Limitations: A total of 43 prostate cores (22 tumour and 21 benign) were profiled from six whole prostate glands. Of the 22 tumour cores, 16 were tumours visible and six were tumours nonvisible on mpMRI. Intratumour genomic, epigenomic, and transcriptomic heterogeneity was found within mpMRI-visible lesions. This could potentially lead to misclassification of patients using signatures based on copy number or RNA expression. Moreover, three of the six cores obtained from mpMRI-nonvisible tumours harboured one or more genetic alterations commonly observed in metastatic castration-resistant PCa. No circulating free DNA alterations were found. Limitations include the small cohort size and lack of follow-up., Conclusions: Our study supports the continued use of systematic prostate sampling in addition to mpMRI, as avoidance of systematic biopsies in patients with negative mpMRI may mean that clinically significant tumours harbouring genetic alterations commonly seen in metastatic PCa are missed. Furthermore, there is inconsistency in individual genomics when genomic classifiers are applied., Patient Summary: Our study shows that tumour heterogeneity within prostate tumours visible on multiparametric magnetic resonance imaging (mpMRI) can lead to misclassification of patients if only one core is used for genomic analysis. In addition, some cancers that were missed by mpMRI had genomic aberrations that are commonly seen in advanced metastatic prostate cancer. Avoiding biopsies in mpMRI-negative cases may mean that such potentially lethal cancers are missed., (Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.)

Background: Cytokines have been found to be the important mediators during renal graft outcome. Therefore, we designed this study to investigate the role of recipients' IL-1 β promoter (-511) and IL-1 β exon-5 (+3954) polymorphisms with the risk of graft outcome., Methodology: We enrolled one hundred recipients of living-related renal transplants together with the age and sex matched controls from the healthy population not having any renal abnormality for this study. Genotype frequencies of the IL-1 β promoter (-511) and IL-1 β exon-5 (+3954) were analyzed using PCR-RFLP technique., Results: Our results revealed significant differences in the healthy control group and patient group in IL 1β +3954 (p < 0.001). The frequency of variant type TT genotype was higher in RE group as compared to SGF and showed 4 fold risk of rejection (OR = 4.54, p < 0.069) although p value was not significant. The frequency of wild type CC genotype and CT was not significant (p value 0.89 and 0.74 respectively)., Conclusion: Our findings suggest that there is a prevalence of mutated allele of IL-1 gene cluster in our population, which may be responsible for renal dysfunction.

The threat to global food security of stagnating yields and population growth makes increasing crop productivity a critical goal over the coming decades. One key target for improving crop productivity and yields is increasing the efficiency of photosynthesis. Central to photosynthesis is Rubisco, which is a critical but often rate-limiting component. Here, we present full Rubisco catalytic properties measured at three temperatures for 75 plants species representing both crops and undomesticated plants from diverse climates. Some newly characterized Rubiscos were naturally "better" compared to crop enzymes and have the potential to improve crop photosynthetic efficiency. The temperature response of the various catalytic parameters was largely consistent across the diverse range of species, though absolute values showed significant variation in Rubisco catalysis, even between closely related species. An analysis of residue differences among the species characterized identified a number of candidate amino acid substitutions that will aid in advancing engineering of improved Rubisco in crop systems. This study provides new insights on the range of Rubisco catalysis and temperature response present in nature, and provides new information to include in models from leaf to canopy and ecosystem scale., (© 2016 American Society of Plant Biologists. All Rights Reserved.)

Photosynthesis in C3 plants is limited by features of the carbon-fixing enzyme Rubisco, which exhibits a low turnover rate and can react with O2 instead of CO2 , leading to photorespiration. In cyanobacteria, bacterial microcompartments, known as carboxysomes, improve the efficiency of photosynthesis by concentrating CO2 near the enzyme Rubisco. Cyanobacterial Rubisco enzymes are faster than those of C3 plants, though they have lower specificity toward CO2 than the land plant enzyme. Replacement of land plant Rubisco by faster bacterial variants with lower CO2 specificity will improve photosynthesis only if a microcompartment capable of concentrating CO2 can also be installed into the chloroplast. We review current information about cyanobacterial microcompartments and carbon-concentrating mechanisms, plant transformation strategies, replacement of Rubisco in a model C3 plant with cyanobacterial Rubisco and progress toward synthesizing a carboxysome in chloroplasts., (© 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.)

Recycling of the 2-phosphoglycolate generated by the oxygenase reaction of Rubisco requires a complex and energy-consuming set of reactions collectively known as the photorespiratory cycle. Several approaches aimed at reducing the rates of photorespiratory energy or carbon loss have been proposed, based either on screening for natural variation or by means of genetic engineering. Recent work indicates that plant yield can be substantially improved by the alteration of photorespiratory fluxes or by engineering artificial bypasses to photorespiration. However, there is also evidence indicating that, under certain environmental and/or nutritional conditions, reduced photorespiratory capacity may be detrimental to plant performance. Here we summarize recent advances obtained in photorespiratory engineering and discuss prospects for these advances to be transferred to major crops to help address the globally increasing demand for food and biomass production., (© The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

The findings from genome-wide association studies hold enormous potential for novel insight into disease mechanisms. A major challenge in the field is to map these low-risk association signals to their underlying functional sequence variants (FSV). Simple sequence study designs are insufficient, as the vast numbers of statistically comparable variants and a limited knowledge of noncoding regulatory elements complicate prioritization. Furthermore, large sample sizes are typically required for adequate power to identify the initial association signals. One important question is whether similar sample sizes need to be sequenced to identify the FSVs. Here, we present a proof-of-principle example of an extreme discordant design to map FSVs within the 2q33 low-risk breast cancer locus. Our approach employed DNA sequencing of a small number of discordant haplotypes to efficiently identify candidate FSVs. Our results were consistent with those from a 2,000-fold larger, traditional imputation-based fine-mapping study. To prioritize further, we used expression-quantitative trait locus analysis of RNA sequencing from breast tissues, gene regulation annotations from the ENCODE consortium, and functional assays for differential enhancer activities. Notably, we implicate three regulatory variants at 2q33 that target CASP8 (rs3769823, rs3769821 in CASP8, and rs10197246 in ALS2CR12) as functionally relevant. We conclude that nested discordant haplotype sequencing is a promising approach to aid mapping of low-risk association loci. The ability to include more efficient sequencing designs into mapping efforts presents an opportunity for the field to capitalize on the potential of association loci and accelerate translation of association signals to their underlying FSVs. Cancer Res; 76(7); 1916-25. ©2016 AACR., (©2016 American Association for Cancer Research.)

Aim: Increased incidence of CVD has been observed in recent years in the Kashmir valley (North India). Since the risk factor development of the cardiovascular diseases (CVD) takes place during childhood, we undertook an epidemiological survey to assess the prevalence of dyslipidemia in the school children of Kashmir valley., Materials and Methods: 1131 children of 5-19 years of age were selected and evaluated for BMI, cholesterol, TGs, LDL and HDL levels from different areas of Srinagar city (urban) region of the Kashmir valley from June 2011-June 2014., Results: The frequency of dyslipidemia in Kashmiri children varied along the subjects. Hypertriglyceridemia was seen in 82.6% of the males and 47.6% of females in the age group of 5-9 years, 38.5% of males and 51.1% of females in the age group of 10-14 years and 24.7% of males and 35.9% of the females in the age group of 15-19 years. Low levels of HDL than normal were seen in 34.7% of males and 19% of females in the age group of 5-9 years. Similarly low HDL levels were seen in 17.9% of males and 15.5% of females in the age group of 10-14 years. The incidence of low HDL was also seen in 4.9% of males and 10.8% of females in the age group of 15-19 years., Conclusions: In the present study dyslipidemia was more common in centrally obese children and the most common component was high triglycerides and low HDL's. Female school children were at higher risk of developing CVD than males., (Copyright © 2016 Diabetes India. Published by Elsevier Ltd. All rights reserved.)

Rubisco is a major target for improving crop photosynthesis and yield, yet natural diversity in catalytic properties of this enzyme is poorly understood. Rubisco from 25 genotypes of the Triticeae tribe, including wild relatives of bread wheat (Triticum aestivum), were surveyed to identify superior enzymes for improving photosynthesis in this crop. In vitro Rubisco carboxylation velocity (V c), Michaelis-Menten constants for CO2 (K c) and O2 (K o) and specificity factor (S c/o) were measured at 25 and 35 °C. V c and K c correlated positively, while V c and S c/o were inversely related. Rubisco large subunit genes (rbcL) were sequenced, and predicted corresponding amino acid differences analysed in relation to the corresponding catalytic properties. The effect of replacing native wheat Rubisco with counterparts from closely related species was analysed by modelling the response of photosynthesis to varying CO2 concentrations. The model predicted that two Rubisco enzymes would increase photosynthetic performance at 25 °C while only one of these also increased photosynthesis at 35 °C. Thus, under otherwise identical conditions, catalytic variation in the Rubiscos analysed is predicted to improve photosynthetic rates at physiological CO2 concentrations. Naturally occurring Rubiscos with superior properties amongst the Triticeae tribe can be exploited to improve wheat photosynthesis and crop productivity., (© The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

Improving canopy photosynthetic light use efficiency instead of leaf photosynthesis holds great potential to catalyze the next "green revolution". However, leaves in a canopy experience different biochemical limitations due to the heterogeneities of microclimates and also physiological parameters. Mechanistic dynamic systems models of canopy photosynthesis are now available which can be used to design the optimal canopy architectural and physiological parameters to maximize CO 2 uptake. Rapid development of modern crop genetics research now makes it possible to link such canopy models with genetic variations of crops to develop genetics-based dynamic systems models of canopy photosynthesis. Such models can guide marker-assisted breeding or genomic selection or engineering of crops to enhance light and nitrogen use efficiencies for different regions under future climate change scenarios.

The antiquity and global abundance of the enzyme, RuBisCO, attests to the crucial and longstanding role it has played in the biogeochemical cycles of Earth over billions of years. The counterproductive oxygenase activity of RuBisCO has persisted over billions of years of evolution, despite its competition with the carboxylase activity necessary for carbon fixation, yet hypotheses regarding the selective pressures governing RuBisCO evolution have been limited to speculation. Here we report the resurrection and biochemical characterization of ancestral RuBisCOs, dating back to over one billion years ago (Gyr ago). Our findings provide an ancient point of reference revealing divergent evolutionary paths taken by eukaryotic homologues towards improved specificity for CO2, versus the evolutionary emphasis on increased rates of carboxylation observed in bacterial homologues. Consistent with these distinctions, in vivo analysis reveals the propensity of ancestral RuBisCO to be encapsulated into modern-day carboxysomes, bacterial organelles central to the cyanobacterial CO2 concentrating mechanism.

Introducing a carbon-concentrating mechanism and a faster Rubisco enzyme from cyanobacteria into higher plant chloroplasts may improve photosynthetic performance by increasing the rate of CO2 fixation while decreasing losses caused by photorespiration. We previously demonstrated that tobacco plants grow photoautotrophically using Rubisco from Synechococcus elongatus, although the plants exhibited considerably slower growth than wild-type and required supplementary CO2 . Because of concerns that vascular plant assembly factors may not be adequate for assembly of a cyanobacterial Rubisco, prior transgenic plants included the cyanobacterial chaperone RbcX or the carboxysomal protein CcmM35. Here we show that neither RbcX nor CcmM35 is needed for assembly of active cyanobacterial Rubisco. Furthermore, by altering the gene regulatory sequences on the Rubisco transgenes, cyanobacterial Rubisco expression was enhanced and the transgenic plants grew at near wild-type growth rates, although still requiring elevated CO2 . We performed detailed kinetic characterization of the enzymes produced with and without the RbcX and CcmM35 cyanobacterial proteins. These transgenic plants exhibit photosynthetic characteristics that confirm the predicted benefits of introduction of non-native forms of Rubisco with higher carboxylation rate constants in vascular plants and the potential nitrogen-use efficiency that may be achieved provided that adequate CO2 is available near the enzyme., (© 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.)

Rubisco catalyses the carboxylation of ribulose-1,5-bisphosphate (RuBP), enabling net CO2 assimilation in photosynthesis. The properties and regulation of Rubisco are not optimal for biomass production in current and projected future environments. Rubisco is relatively inefficient, and large amounts of the enzyme are needed to support photosynthesis, requiring large investments in nitrogen. The competing oxygenation of RuBP by Rubisco decreases photosynthetic efficiency. Additionally, Rubisco is inhibited by some sugar phosphates and depends upon interaction with Rubisco activase (Rca) to be reactivated. Rca activity is modulated by the chloroplast redox status and ADP/ATP ratios, thereby mediating Rubisco activation and photosynthetic induction in response to irradiance. The extreme thermal sensitivity of Rca compromises net CO2 assimilation at moderately high temperatures. Given its central role in carbon assimilation, the improvement of Rubisco function and regulation is tightly linked with irradiance, nitrogen and water use efficiencies. Although past attempts have had limited success, novel technologies and an expanding knowledge base make the challenge of improving Rubisco activity in crops an achievable goal. Strategies to optimize Rubisco and its regulation are addressed in relation to their potential to improve crop resource use efficiency and climate resilience of photosynthesis., (© 2014 Rothamsted Research Ltd. Plant, Cell & Environment published by John Wiley & Sons Ltd.)

The world's crop productivity is stagnating whereas population growth, rising affluence, and mandates for biofuels put increasing demands on agriculture. Meanwhile, demand for increasing cropland competes with equally crucial global sustainability and environmental protection needs. Addressing this looming agricultural crisis will be one of our greatest scientific challenges in the coming decades, and success will require substantial improvements at many levels. We assert that increasing the efficiency and productivity of photosynthesis in crop plants will be essential if this grand challenge is to be met. Here, we explore an array of prospective redesigns of plant systems at various scales, all aimed at increasing crop yields through improved photosynthetic efficiency and performance. Prospects range from straightforward alterations, already supported by preliminary evidence of feasibility, to substantial redesigns that are currently only conceptual, but that may be enabled by new developments in synthetic biology. Although some proposed redesigns are certain to face obstacles that will require alternate routes, the efforts should lead to new discoveries and technical advances with important impacts on the global problem of crop productivity and bioenergy production.

ERECTA encodes a receptor-like kinase and is proposed as a candidate for determining transpiration efficiency of plants. Two genes homologous to ERECTA in Arabidopsis were identified on chromosomes 6 (TaER2) and 7 (TaER1) of bread wheat (Triticum aestivum L.), with copies of each gene on the A, B and D genomes of wheat. Similar expression patterns were observed for TaER1 and TaER2 with relatively higher expression of TaER1 in flag leaves of wheat at heading (Z55) and grain-filling (Z73) stages. Significant variations were found in the expression levels of both TaER1 and TaER2 in the flag leaves at both growth stages among 48 diverse bread wheat varieties. Based on the expression of TaER1 and TaER2, the 48 wheat varieties could be classified into three groups having high (5 varieties), medium (27 varieties) and low (16 varieties) levels of TaER expression. Significant differences were also observed between the three groups varying for TaER expression for several transpiration efficiency (TE)- related traits, including stomatal density (SD), transpiration rate, photosynthetic rate (A), instant water use efficiency (WUEi) and carbon isotope discrimination (CID), and yield traits of biomass production plant-1 (BYPP) and grain yield plant-1 (GYPP). Correlation analysis revealed that the expression of TaER1 and TaER2 at the two growth stages was significantly and negatively associated with SD (P<0.01), transpiration rate (P<0.05) and CID (P<0.01), while significantly and positively correlated with flag leaf area (FLA, P<0.01), A (P<0.05), WUEi (P<0.05), BYPP (P<0.01) and GYPP (P<0.01), with stronger correlations for TaER1 than TaER2 and at grain-filling stage than at heading stage. These combined results suggested that TaER involved in development of transpiration efficiency -related traits and yield in bread wheat, implying a function for TaER in regulating leaf development of bread wheat and contributing to expression of these traits. Moreover, the results indicate that TaER could be exploitable for manipulating important agronomical traits in wheat improvement.

Background and Aims: We were interested in the effect of impedance to root growth on root and shoot architecture of wheat. It is known that Rht-1 semi-dwarfing alleles decrease the degree of leaf stunting due to root impedance. We compared commercial wheat cultivars containing different Rht-1 alleles to determine whether leaf stunting caused by root impedance differed between cultivars. We investigated effects of impedance to root growth on the angular spread of roots., Methods: The wheat cultivars Avalon, Robigus and Battalion, carrying semi-dwarfing alleles of Rht-1 , and cv. Cadenza, carrying the tall, wild-type allele, were grown under two levels of soil strength in a sand culture system designed to allow the mechanical impedance of the root growth environment to be adjusted independently of water and nutrient availability., Results: Impeded roots grew more steeply than non-impeded roots: the angular spread of roots decreased from 55° to 43° from the vertical, but the genotypic effects were weak. Root impedance reduced leaf elongation and the number of tillers. Leaf area and total root length provided a common relationship across all genotype x treatment combinations. Leaf stunting in Cadenza was more severe., Conclusion: Our data support the hypothesis that the severity of leaf stunting due to root impedance is related to the Rht allele. Impeded roots had a smaller angular spread.

In photosynthetic organisms, D-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the major enzyme assimilating atmospheric CO2 into the biosphere. Owing to the wasteful oxygenase activity and slow turnover of Rubisco, the enzyme is among the most important targets for improving the photosynthetic efficiency of vascular plants. It has been anticipated that introducing the CO2-concentrating mechanism (CCM) from cyanobacteria into plants could enhance crop yield. However, the complex nature of Rubisco's assembly has made manipulation of the enzyme extremely challenging, and attempts to replace it in plants with the enzymes from cyanobacteria and red algae have not been successful. Here we report two transplastomic tobacco lines with functional Rubisco from the cyanobacterium Synechococcus elongatus PCC7942 (Se7942). We knocked out the native tobacco gene encoding the large subunit of Rubisco by inserting the large and small subunit genes of the Se7942 enzyme, in combination with either the corresponding Se7942 assembly chaperone, RbcX, or an internal carboxysomal protein, CcmM35, which incorporates three small subunit-like domains. Se7942 Rubisco and CcmM35 formed macromolecular complexes within the chloroplast stroma, mirroring an early step in the biogenesis of cyanobacterial β-carboxysomes. Both transformed lines were photosynthetically competent, supporting autotrophic growth, and their respective forms of Rubisco had higher rates of CO2 fixation per unit of enzyme than the tobacco control. These transplastomic tobacco lines represent an important step towards improved photosynthesis in plants and will be valuable hosts for future addition of the remaining components of the cyanobacterial CCM, such as inorganic carbon transporters and the β-carboxysome shell proteins.

Increasing photosynthesis in wheat has been identified as an approach to enhance crop yield, with manipulation of key genes involved in electron transport and the Calvin cycle as one avenue currently being explored. However, natural variation in photosynthetic capacity is a currently unexploited genetic resource for potential crop improvement. Using gas-exchange analysis and protein analysis, the existing natural variation in photosynthetic capacity in a diverse panel of 64 elite wheat cultivars grown in the field was examined relative to growth traits, including biomass and harvest index. Significant variations in photosynthetic capacity, biomass, and yield were observed, although no consistent correlation was found between photosynthetic capacity of the flag leaf and grain yield when all cultivars were compared. The majority of the variation in photosynthesis could be explained by components related to maximum capacity and operational rates of CO2 assimilation, and to CO2 diffusion. Cluster analysis revealed that cultivars may have been bred unintentionally for desirable traits at the expense of photosynthetic capacity. These findings suggest that there is significant underutilized photosynthetic capacity among existing wheat varieties. Our observations are discussed in the context of exploiting existing natural variation in physiological processes for the improvement of photosynthesis in wheat., (© The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

The present study characterizes the kinetic properties of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from 28 terrestrial plant species, representing different phylogenetic lineages, environmental adaptations and photosynthetic mechanisms. Our findings confirm that past atmospheric CO(2)/O(2) ratio changes and present environmental pressures have influenced Rubisco kinetics. One evolutionary adaptation to a decreasing atmospheric CO(2)/O(2) ratio has been an increase in the affinity of Rubisco for CO(2) (Kc falling), and a consequent decrease in the velocity of carboxylation (kcat (c)), which in turn has been ameliorated by an increase in the proportion of leaf protein accounted by Rubisco. The trade-off between K(c) and k(cat)(c) was not universal among the species studied and deviations from this relationship occur in extant forms of Rubisco. In species adapted to particular environments, including carnivorous plants, crassulacean acid metabolism species and C(3) plants from aquatic and arid habitats, Rubisco has evolved towards increased efficiency, as demonstrated by a higher k(cat)(c)/K(c) ratio. This variability in kinetics was related to the amino acid sequence of the Rubisco large subunit. Phylogenetic analysis identified 13 residues under positive selection during evolution towards specific Rubisco kinetic parameters. This crucial information provides candidate amino acid replacements, which could be implemented to optimize crop photosynthesis under a range of environmental conditions., (© 2014 John Wiley & Sons Ltd.)

Carbon assimilation by most ecosystems requires ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Its kinetic parameters are likely to have evolved in parallel with intracellular CO2 availability, with the result that faster forms of Rubisco occur in species with CO2 -concentrating mechanisms. The Rubisco catalytic properties were determined and evaluated in relation to growth and carbon assimilation capacity in Mediterranean Limonium species, inhabiting severe stress environments. Significant kinetic differences between closely related species depended on two amino acid substitutions at functionally important residues 309 and 328 within the Rubisco large subunit. The Rubisco of species facing the largest CO2 restrictions during drought had relatively high affinity for CO2 (low Michaelis-Menten constant for CO2 Kc) but low maximum rates of carboxylation (kcatc), while the opposite was found for species that maintained higher CO2 concentrations under similar conditions. Rubisco kinetic characteristics were correlated with photosynthetic rate in both well-watered and drought-stressed plants. Moreover, the drought-mediated decrease in plant biomass accumulation was consistently lower in species with higher Rubisco carboxylase catalytic efficiency (kcatc/Kc). The present study is the first demonstration of Rubisco adaptation during species diversification within closely related C3 plants, revealing a direct relationship between Rubisco molecular evolution and the biomass accumulation of closely related species subjected to unfavourable conditions., (© 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.)

The photosynthetic efficiency of C3 plants suffers from the reaction of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) with O2 instead of CO2 , leading to the costly process of photorespiration. Increasing the concentration of CO2 around Rubisco is a strategy used by photosynthetic prokaryotes such as cyanobacteria for more efficient incorporation of inorganic carbon. Engineering the cyanobacterial CO2 -concentrating mechanism, the carboxysome, into chloroplasts is an approach to enhance photosynthesis or to compartmentalize other biochemical reactions to confer new capabilities on transgenic plants. We have chosen to explore the possibility of producing β-carboxysomes from Synechococcus elongatus PCC7942, a model freshwater cyanobacterium. Using the agroinfiltration technique, we have transiently expressed multiple β-carboxysomal proteins (CcmK2, CcmM, CcmL, CcmO and CcmN) in Nicotiana benthamiana with fusions that target these proteins into chloroplasts, and that provide fluorescent labels for visualizing the resultant structures. By confocal and electron microscopic analysis, we have observed that the shell proteins of the β-carboxysome are able to assemble in plant chloroplasts into highly organized assemblies resembling empty microcompartments. We demonstrate that a foreign protein can be targeted with a 17-amino-acid CcmN peptide to the shell proteins inside chloroplasts. Our experiments establish the feasibility of introducing carboxysomes into chloroplasts for the potential compartmentalization of Rubisco or other proteins., (© 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.)

Food security is a global concern and substantial yield increases in crops are required to feed the growing world population. Mutagenesis is an important tool in crop improvement and is free of the regulatory restrictions imposed on genetically modified organisms. Targeting Induced Local Lesions in Genomes (TILLING), which combines traditional chemical mutagenesis with high-throughput genome-wide screening for point mutations in desired genes, offers a powerful way to create novel mutant alleles for both functional genomics and improvement of crops. TILLING is generally applicable to genomes whether small or large, diploid or even allohexaploid, and shows great potential to address the major challenge of linking sequence information to the function of genes and to modulate key traits for plant breeding. TILLING has been successfully applied in many crop species and recent progress in TILLING is summarized below, especially on the developments in mutation detection technology, application of TILLING in gene functional studies and crop breeding. The potential of TILLING/EcoTILLING for functional genetics and crop improvement is also discussed. Furthermore, a small-scale forward strategy including backcross and selfing was conducted to release the potential mutant phenotypes masked in M2 (or M3) plants., (© 2014 Institute of Botany, Chinese Academy of Sciences.)

Rationale: Research is needed on initial smoking abstinence and relapse risk., Objective: This study aims to investigate the effects of different durations of initial abstinence on sensitivity to smoking-related stimuli and response inhibition in the context of a larger battery of outcome measures., Methods: Smokers were randomly assigned to receive payment contingent on smoking abstinence across all 15 study days (15C) or just the final 2 days (2C). Smoking status and subject ratings were assessed daily. Participants completed fMRI sessions at baseline and day 14 during which they completed craving ratings after exposure to smoking-related and neutral stimuli and performed a response inhibition task. On day 15, participants completed a smoking preference session involving 20 exclusive choices between smoking and money., Results: The payment contingencies were effective in producing greater smoking abstinence in the 15C vs. 2C conditions. Ratings of withdrawal decreased, while ratings of ease and confidence in abstaining increased in the 15C vs. 2C conditions across the 15-day study. 15C participants were less likely to choose the smoking option in the preference session. 15C participants reported greater reductions in craving compared to the 2C participants in the presence of smoking-related and neutral stimuli (i.e., decreases in generalized craving), but no differences were noted in cue reactivity per se or in response inhibition., Conclusions: Results systematically replicate prior observations that a period 2 weeks of initial abstinence decreases the relative reinforcing effects of smoking and improves other outcomes associated with relapse risk compared to the initial day or two of a cessation effort, and extends them by underscoring the importance of generalized rather than cue-induced craving in relation to relapse risk during the initial weeks of smoking cessation.

Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyzes carboxylation of ribulose-1,5-bisphosphate, the first in a series of reactions leading to the incorporation of atmospheric CO₂ into biomass. Rubisco requires Rubisco activase (RCA), an AAA+ ATPase that reactivates Rubisco by remodelling the conformation of inhibitor-bound sites. RCA is regulated by the ratio of ADP:ATP, with the precise response potentiated by redox regulation of the alpha-isoform. Measuring the effects of ADP on the activation of Rubisco by RCA using the well-established photometric assay is problematic because of the adenine nucleotide requirement of 3-phosphoglycerate (3-PGA) kinase. Described here is a novel assay for measuring RCA activity in the presence of variable ratios of ADP:ATP. The assay couples the formation of 3-PGA from ribulose 1,5-bisphosphate and CO₂ to NADH oxidation through cofactor-dependent phosphoglycerate mutase, enolase, PEP carboxylase and malate dehydrogenase. The assay was used to determine the effects of Rubisco and RCA concentration and ADP:ATP ratio on RCA activity, and to measure the activation of a modified Rubisco by RCA. Variations of the basic assay were used to measure the activation state of Rubisco in leaf extracts and the activity of purified Rubisco. The assay can be automated for high-throughput processing by conducting the reactions in two stages.

Asparagine is the predominant free amino acid in potato tubers and the present study aimed to establish whether it is imported from the leaves or synthesised in situ. Free amino acid concentrations are important quality determinants for potato tubers because they react with reducing sugars at high temperatures in the Maillard reaction. This reaction produces melanoidin pigments and a host of aroma and flavour volatiles, but if free asparagine participates in the final stages, it results in the production of acrylamide, an undesirable contaminant. ¹⁴CO₂ was supplied to a leaf or leaves of potato plants (cv. Saturna) in the light and radioactivity incorporated into amino acids was determined in the leaves, stems, stolons and tubers. Radioactivity was found in free amino acids, including asparagine, in all tissues, but the amount incorporated in asparagine transported to the tubers and stolons was much less than that in glutamate, glutamine, serine and alanine. The study showed that free asparagine does not play an important role in the transport of nitrogen from leaf to tuber in potato, and that the high concentrations of free asparagine that accumulate in potato tubers arise from synthesis in situ. This indicates that genetic interventions to reduce free asparagine concentration in potato tubers will have to target asparagine metabolism in the tuber.

In this review, we examine how roots penetrate a structured soil. We first examine the relationship between soil water status and its mechanical strength, as well as the ability of the soil to supply water to the root. We identify these as critical soil factors, because it is primarily in drying soil that mechanical constraints limit root elongation. Water supply to the root is important because root water status affects growth pressures and root stiffness. To simplify the bewildering complexity of soil-root interactions, the discussion is focused around the special cases of root elongation in soil with pores much smaller than the root diameter and the penetration of roots at interfaces within the soil. While it is often assumed that the former case is well understood, many unanswered questions remain. While low soil-root friction is often viewed as a trait conferring better penetration of strong soils, it may also increase the axial pressure on the root tip and in so doing reduce the rate of cell division and/or expansion. The precise trade-off between various root traits involved in root elongation in homogeneous soil remains to be determined. There is consensus that the most important factors determining root penetration at an interface are the angle at which the root attempts to penetrate the soil, root stiffness, and the strength of the soil to be penetrated. The effect of growth angle on root penetration implicates gravitropic responses in improved root penetration ability. Although there is no work that has explored the effect of the strength of the gravitropic responses on penetration of hard layers, we attempt to outline possible interactions. Impacts of soil drying and strength on phytohormone concentrations in roots, and consequent root-to-shoot signalling, are also considered.

Opportunities exist for replacing reduced height (Rht) genes Rht-B1b and Rht-D1b with alternative dwarfing genes, such as the gibberellin-responsive gene Rht12, for bread wheat improvement. However, a comprehensive understanding of the effects and mode of action of Rht12 is lacking. In the present study, the effects of Rht12 were characterized by analyzing its effects on seeding vigour, seedling roots, leaf and stem morphology, spike development and carbohydrate assimilation and distribution. This was carried out in the four genotypes of F2:3 lines derived from a cross between Ningchun45 and Karcagi (12) in two experiments of autumn sowing and spring sowing. Rht12 significantly decreased stem length (43%∼48% for peduncle) and leaf length (25%∼30% for flag leaf) while the thickness of the internode walls and width of the leaves were increased. Though the final plant stature was shortened (40%) by Rht12, the seedling vigour, especially coleoptile length and root traits at the seedling stage, were not affected adversely. Rht12 elongated the duration of the spike development phase, improved the proportion of spike dry weight at anthesis and significantly increased floret fertility (14%) in the autumn sowing experiment. However, Rht12 delayed anthesis date by around 5 days and even the dominant Vrn-B1 allele could not compensate this negative effect. Additionally, grain size was reduced with the ability to support spike development after anthesis decreased in Rht12 lines. Finally, grain yield was similar between the dwarf and tall lines in the autumn sowing experiment. Thus, Rht12 could substantially reduce plant height without altering seeding vigour and significantly increase spikelet fertility in the favourable autumn sowing environment. The successful utilization of Rht12 in breeding programs will require careful selection since it might delay ear emergence. Nonetheless, the potential exists for wheat improvement by using Rht12.

Rubisco (ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase) enables net carbon fixation through the carboxylation of RuBP. However, some characteristics of Rubisco make it surprisingly inefficient and compromise photosynthetic productivity. For example, Rubisco catalyses a wasteful reaction with oxygen that leads to the release of previously fixed CO(2) and NH(3) and the consumption of energy during photorespiration. Furthermore, Rubisco is slow and large amounts are needed to support adequate photosynthetic rates. Consequently, Rubisco has been studied intensively as a prime target for manipulations to 'supercharge' photosynthesis and improve both productivity and resource use efficiency. The catalytic properties of Rubiscos from diverse sources vary considerably, suggesting that changes in turnover rate, affinity, or specificity for CO(2) can be introduced to improve Rubisco performance in specific crops and environments. While attempts to manipulate plant Rubisco by nuclear transformation have had limited success, modifying its catalysis by targeted changes to its catalytic large subunit via chloroplast transformation have been much more successful. However, this technique is still in need of development for most major food crops including maize, wheat, and rice. Other bioengineering approaches for improving Rubisco performance include improving the activity of its ancillary protein, Rubisco activase, in addition to modulating the synthesis and degradation of Rubisco's inhibitory sugar phosphate ligands. As the rate-limiting step in carbon assimilation, even modest improvements in the overall performance of Rubisco pose a viable pathway for obtaining significant gains in plant yield, particularly under stressful environmental conditions.

The balance between the supply and demand of the major food crops is fragile, fueling concerns for long-term global food security. The rising population, increasing wealth and a proliferation of non-food uses (e.g. bioenergy) has led to growing demands on agriculture, while increased production is limited by greater urbanization, and the degradation of land. Furthermore, global climate change with increasing temperatures and lower, more erratic rainfall is projected to decrease agricultural yields. There is a predicted need to increase food production by at least 70% by 2050 and therefore an urgent need to develop novel and integrated approaches, incorporating high-throughput phenotyping that will both increase production per unit area and simultaneously improve the resource use efficiency of crops. Yield potential, yield stability, nutrient and water use are all complex multigenic traits and while there is genetic variability, their complexity makes such traits difficult to breed for directly. Nevertheless molecular plant breeding has the potential to deliver substantial improvements, once the component traits and the genes underlying these traits have been identified. In addition, interactions between the individual traits must also be taken into account, a demand that is difficult to fulfill with traditional screening approaches. Identified traits will be incorporated into new cultivars using conventional or biotechnological tools. In order to better understand the relationship between genotype, component traits, and environment over time, a multidisciplinary approach must be adopted to both understand the underlying processes and identify candidate genes, QTLs and traits that can be used to develop improved crops., (© 2012 Institute of Botany, Chinese Academy of Sciences.)

The genes for CA1Pase (2-carboxy-D-arabinitol-1-bisphosphate phosphatase) from French bean, wheat, Arabidopsis and tobacco were identified and cloned. The deduced protein sequence included an N-terminal motif identical with the PGM (phosphoglycerate mutase) active site sequence [LIVM]-x-R-H-G-[EQ]-x-x-[WN]. The corresponding gene from wheat coded for an enzyme with the properties published for CA1Pase. The expressed protein lacked PGM activity but rapidly dephosphorylated 2,3-DPG (2,3-diphosphoglycerate) to 2-phosphoglycerate. DTT (dithiothreitol) activation and GSSG inactivation of this enzyme was pH-sensitive, the greatest difference being apparent at pH 8. The presence of the expressed protein during in vitro measurement of Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) activity prevented a progressive decline in Rubisco turnover. This was due to the removal of an inhibitory bisphosphate that was present in the RuBP (ribulose-1,5-bisphosphate) preparation, and was found to be PDBP (D-glycero-2,3-pentodiulose-1,5-bisphosphate). The substrate specificity of the expressed protein indicates a role for CA1Pase in the removal of 'misfire' products of Rubisco.

Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) form a major family of signalling proteins in plants and have been associated with metabolic regulation and stress responses. They comprise three subfamilies: SnRK1, SnRK2, and SnRK3. SnRK1 plays a major role in the regulation of carbon metabolism and energy status, while SnRKs 2 and 3 have been implicated in stress and abscisic acid (ABA)-mediated signalling pathways. The burgeoning and divergence of this family of protein kinases in plants may have occurred to enable cross-talk between metabolic and stress signalling, and ABA-response-element-binding proteins (AREBPs), a family of transcription factors, have been shown to be substrates for members of all three subfamilies. In this study, levels of SnRK1 protein were shown to decline dramatically in wheat roots in response to ABA treatment, although the amount of phosphorylated (active) SnRK1 remained constant. Multiple SnRK2-type protein kinases were detectable in the root extracts and showed differential responses to ABA treatment. They included a 42 kDa protein that appeared to reduce in response to 3 h of ABA treatment but to recover after longer treatment. There was a clear increase in phosphorylation of this SnRK2 in response to the ABA treatment. Fractions containing this 42 kDa SnRK2 were shown to phosphorylate synthetic peptides with amino acid sequences based on those of conserved phosphorylation sites in AREBPs. The activity increased 8-fold with the addition of calcium chloride, indicating that it is calcium-dependent. The activity assigned to the 42 kDa SnRK2 also phosphorylated a heterologously expressed wheat AREBP.