A data-driven genome annotation approach for cassava.

Genome annotation files play a critical role in dictating the quality of downstream analyses by providing essential predictions for gene positions and structures. These files are pivotal in decoding the complex information encoded within DNA sequences. Here, we generated experimental data resolving RNA 5'- and 3'-ends as well as full-length RNAs for cassava TME12 sticklings in ambient temperature and cold. We used these data to generate genome annotation files using the TranscriptomeReconstructoR (TR) tool. A careful comparison to high-quality genome annotations suggests that our new TR genome annotations identified additional genes, resolved the transcript boundaries more accurately and identified additional RNA isoforms. We enhanced existing cassava genome annotation files with the information from TR that maintained the different transcript models as RNA isoforms. The resultant merged annotation was subsequently utilized for comprehensive analysis. To examine the effects of genome annotation files on gene expression studies, we compared the detection of differentially expressed genes during cold using the same RNA-seq data but alternative genome annotation files. We found that our merged genome annotation that included cold-specific TR gene models identified about twice as many cold-induced genes. These data indicate that environmentally induced genes may be missing in off-the-shelf genome annotation files. In conclusion, TR offers the opportunity to enhance crop genome annotations with implications for the discovery of differentially expressed candidate genes during plant-environment interactions.

Fertility-sparing surgery vs standard surgery for early-stage cervical cancer: difference in 5-year life expectancy by tumor size.

BACKGROUND: Cervical cancer incidence among premenopausal women is rising, and fertility-sparing surgery serves as an important option for this young population. There is a lack of evidence on what tumor size cutoff should be used to define candidacy for fertility-sparing surgery. OBJECTIVE: We sought to describe how the association between fertility-sparing surgery (compared with standard surgery) and life expectancy varies by tumor size among patients with cervical cancers measuring ≤4 cm in largest diameter. Our secondary objective was to quantify the probability of undergoing adjuvant radiotherapy among patients who underwent fertility-sparing surgery as a function of tumor size. STUDY DESIGN: We identified patients in the National Cancer Database aged ≤45 years, diagnosed with stage I cervical cancer with tumors ≤4 cm between 2006 and 2018, who received no preoperative radiation or chemotherapy, and who underwent either fertility-sparing surgery (cone or trachelectomy, either simple or radical) or standard surgery (simple or radical hysterectomy) as their primary treatment. Propensity-score matching was performed to compare patients who underwent fertility-sparing surgery with those who underwent standard surgery. A flexible parametric model was employed to quantify the difference in life expectancy within 5 years of diagnosis (restricted mean survival time) based on tumor size among patients who underwent fertility-sparing and those who underwent standard surgery. In addition, among those who underwent fertility-sparing surgery, a logistic regression model was used to explore the relationship between tumor size and the probability of receiving adjuvant radiation. RESULTS: A total of 11,946 patients met the inclusion criteria of whom 904 (7.6%) underwent fertility-sparing surgery. After propensity-score matching, 897 patients who underwent fertility-sparing surgery were matched 1:1 with those who underwent standard surgery. Although the 5-year life expectancy was similar among patients who had fertility sparing surgery and those who had standard surgery regardless of tumor sizes, the estimates of life-expectancy differences associated with fertility-sparing surgery were more precise among patients with smaller tumors (1-cm tumor: restricted mean survival time difference, -0.10 months; 95% confidence interval, -0.67 to 0.47) than among those with larger tumors (4-cm tumor: restricted mean survival time difference, -0.11 months; 95% confidence interval, -3.79 to 3.57). The probability of receiving adjuvant radiation increased with tumor size, ranging from 5.6% (95% confidence interval, 3.9-7.9) for a 1-cm tumor to 37% (95% confidence interval, 24.3-51.8) for a 4-cm tumor. CONCLUSION: Within 5 years of diagnosis, young patients with stage I cancers measuring ≤4 cm had similar survival outcomes after either fertility-sparing surgery or standard surgery. However, because few patients with tumors >2 cm underwent fertility-sparing surgery, a clinically important survival difference could not be excluded in this population.

Disparities in the use of assisted reproductive technologies after breast cancer: a population-based study.

PURPOSE: Equitable access to oncofertility services is a key component of cancer survivorship care, but factors affecting access and use remain understudied. METHODS: To describe disparities in assisted reproductive technology (ART) use among women with breast cancer in California, we conducted a population-based cohort study using linked oncology, ART, and demographic data. We identified women age 18-45 years diagnosed with invasive breast cancer between 2000 and 2015. The primary outcome was ART use-including oocyte/embryo cryopreservation or embryo transfer-after cancer diagnosis. We used log-binomial regression to estimate prevalence ratios (PRs) and 95% confidence intervals (CIs) to identify factors associated with ART use. RESULTS: Among 36,468 women with invasive breast cancer, 206 (0.56%) used ART. Women significantly less likely to use ART were age 36-45 years at diagnosis (vs. 18-35 years: PR = 0.17, 95% CI 0.13-0.22); non-Hispanic Black or Hispanic (vs. non-Hispanic White: PR = 0.31, 95% CI 0.21-0.46); had at least one child (vs. no children: adjusted PR [aPR] = 0.39, 95% CI 0.25-0.60); or lived in non-urban areas (vs. urban: aPR = 0.28, 95% CI 0.10-0.75), whereas women more likely to use ART lived in high-SES areas (vs. low-/middle-SES areas: aPR = 2.93, 95% CI 2.04-4.20) or had private insurance (vs. public/other insurance: aPR = 2.95, 95% CI 1.59-5.49). CONCLUSION: Women with breast cancer who are socially or economically disadvantaged, or who already had a child, are substantially less likely to use ART after diagnosis. The implementation of policies or programs targeting more equitable access to fertility services for women with cancer is warranted.

All-cause and cancer-specific mortality after fertility-sparing surgery for stage IA and IC epithelial ovarian cancer.

OBJECTIVE: To compare all-cause and cancer-specific mortality between women who underwent fertility-sparing surgery (FSS) versus standard surgery for stage IA and IC epithelial ovarian cancer. METHODS: Reproductive aged patients (18-45) with stage IA or IC epithelial ovarian cancer diagnosed between 2000 and 2015 were identified in the California Cancer Registry. FSS was defined as retention of the contralateral ovary and the uterus, and standard surgery included at least removal of both ovaries and the uterus. The primary outcome was all-cause mortality and the secondary outcome was cancer-specific mortality. Inverse probability of treatment weighting (IPTW) was used to create two groups balanced on covariates of interest. The Kaplan-Meier method and Cox proportional hazards analysis were used to model survival outcomes. RESULTS: Among 1119 women who met inclusion criteria, 390 (34.9%) underwent FSS. IPTW yielded a balanced cohort of 394 women who underwent FSS and 723 women who underwent standard surgery. Among patients who underwent FSS, there were 45 deaths corresponding to an 85.4% (95% confidence interval [CI] 0.79-0.92) 10-year all-cause survival probability, compared to 81 deaths and 86.4% 10-year all-cause survival probability (95% CI 0.83-0.90) among patients who underwent standard surgery. FSS was not associated with increased all-cause mortality (HR 1.04, 95% CI 0.72-1.49) or cancer-specific mortality (HR 1.50, 95%CI 0.97-2.31). CONCLUSIONS: Among reproductive-aged patients with early-stage epithelial ovarian cancer fertility-sparing surgery was not associated with an increased risk of death compared to standard surgery.

Minimally invasive interval debulking surgery for advanced ovarian cancer after neoadjuvant chemotherapy.

OBJECTIVE: Assess outcomes of interval debulking surgery (IDS) after neoadjuvant chemotherapy via minimally invasive surgery (MIS) compared with laparotomy in patients with advanced epithelial ovarian cancer. METHODS: Patients diagnosed with stage IIIC or IV epithelial ovarian cancer between 2013 and 2018 who received neoadjuvant chemotherapy and IDS were identified in the National Cancer Database. Primary outcome was overall survival. Secondary outcomes were 5-year survival, 30- and 90-day postoperative mortality, extent of surgery, residual disease, hospitalization duration, surgical conversions, and unplanned readmissions. Propensity score matching was used to compare MIS and laparotomy for IDS. Association of treatment approach with overall survival was assessed using Kaplan-Meier method and Cox regression. Sensitivity analysis was conducted for effect of unmeasured confounders. RESULTS: A total of 7897 patients met inclusion criteria; 2021 (25.6%) underwent MIS. Percentage undergoing MIS increased from 20.3%-29.0% over the study period. After propensity score matching, median overall survival was 46.7 months in the MIS group versus 41.0 months in the laparotomy group [hazard ratio (HR) 0.86 (95%CI 0.79-0.94)]. Five-year survival probability was higher in MIS versus laparotomy (38.3% vs 34.8%, p < 0.01). There was lower 30- and 90-day mortality (0.3% vs 0.7% [p = 0.04] and 1.4% vs 2.5% [p = 0.01], respectively), shorter length of stay (median 3 vs 5 days, p < 0.01), lower residual disease (23.9% vs 26.7%, p < 0.01), and lower additional cytoreductive procedures (59.3% vs 70.8%, p < 0.01) in MIS compared to laparotomy, with similar rates of unplanned readmission (2.7% vs 3.1%, p = 0.39). CONCLUSIONS: Patients who undergo IDS by MIS have similar overall survival and decreased morbidity compared with laparotomy.

Diagnostic accuracy of sentinel lymph node frozen section analysis in patients with early-stage cervical cancer: A systematic review and meta-analysis.

OBJECTIVE: To assess the diagnostic accuracy of intraoperative SLN frozen section analysis compared with ultrastaging in patients with early-stage cervical cancer. METHODS: A systematic literature review was conducted following the PRISMA checklist. MEDLINE (via Ovid), Embase, and the Cochrane Central Register of Controlled Trials were searched from inception until February 2023. The inclusion criteria were patients with early-stage cervical cancer (2018 FIGO stage I-II), consisting of the histological subtype squamous cell carcinoma, adenocarcinoma, or adenosquamous carcinoma (≥90% of the patients in each study), who underwent SLN detection (with any tracer) and intraoperative frozen section followed by SLN ultrastaging. Randomized controlled trials, prospective and retrospective observational studies were considered. The detection rates and measures of diagnostic accuracy were pooled using a random effects univariate model. A preplanned subgroup meta-analysis was conducted, with isolated tumor cells excluded as positive lymph nodes. The review was registered in PROSPERO (CRD42023397147). RESULTS: The search identified 190 articles, with 153 studies considered potentially eligible after removing duplicates. Fourteen studies met the selection criteria, including a total of 1720 patients. Seven studies were retrospective, and the other seven were prospective. Frozen section analysis detected 159 of 292 (54.5%) patients with lymph node metastases. In 281 patients the type of volume metastasis was reported: 1 of 41 (2.4%) patients had isolated tumor cells, 21 of 78 (26.9%) patients had micrometastases, and 133 of 162 (82.1%) patients had macrometastases. The pooled sensitivity of intraoperative SLN frozen section analysis was 65% (95% CI, 51-77%) for macrometastases, micrometastases, and isolated tumor cells. When we excluded patients with isolated tumor cells, the pooled sensitivity increased to 72% (95% CI, 60-82%). CONCLUSION: SLN frozen section detects 65% of lymph node metastases compared with SLN ultrastaging and may prevent unnecessary radical surgery in some patients with early-stage cervical cancer.

Systematic mapping review of guidelines for BRCA1/2 genetic testing globally: investigating geographic and regional disparities in health equity for women and families at risk for hereditary ovarian cancer.

OBJECTIVE: Identification of persons at risk for hereditary syndromes through genetic testing prior to cancer diagnosis may proactively reduce the cancer burden morbidity and mortality. Using a framework of health equity, this study characterizes the global landscape of publication and reference to BRCA1/2 genetic testing guidelines (GTG). METHODS: This study used a systematic literature search supplemented by an International Gynecologic Cancer Society (IGCS) informal survey and cross referenced with Myriad Genetics records, to identify published GTG, their country of origin, and countries referencing them. RESULTS: Of 1011 identified publications, 166 met the inclusion criteria, from which 46 unique guidelines were identified, published by 18 countries and two regions (Europe and the UK). Authorship from the USA accounted for 63% of publications on GTG. Systematic mapping reviews revealed 34 countries with published and/or referenced guidelines, the IGCS survey revealed 22 additional countries, and coordination with Myriad Genetics revealed additional information for two countries and primary information for one country. Of the 57 countries evaluated, 33% published their own guidelines and reference guidelines from another country/region, 5% published their own guidelines without referencing another country/region, and 61% only referenced a guideline from another country/region. No data were available for 138 of 195 countries, disproportionately from Africa, the Middle East, Eastern Europe, and Southeast Asia. CONCLUSIONS: Global geographic disparities in the publication and referencing of GTG exist, with a large emphasis on North American and European guidelines in the published literature. These disparities highlight a need for uniform BRCA GTG to improve global health equity.

Assessing gaps in motherhood after cancer: development and psychometric testing of the Survivorship Oncofertility Barriers Scale.

OBJECTIVE: With a growing population of young cancer survivors, there is an increasing need to address the gaps in evidence regarding cancer survivors' obstetric outcomes, fertility care access, and experiences. As part of a large research program, this study engaged survivors and experts in co-developing and testing the validity, reliability, acceptability, and feasibility of a scale to assess survivor-reported barriers to motherhood after cancer. METHODS: Scale items were developed based on literature and expert review of 226 reproductive health items, and six experience and focus groups with 26 survivors of breast and gynecological cancers. We then invited 128 survivors to complete the scale twice, 48 hours apart, and assessed the scale's psychometric properties using exploratory factor analyses including reliability, known-group validity, and convergent validity. RESULTS: Item development identified three primary themes: multifaceted barriers for cancer survivors; challenging decisions about whether and how to pursue motherhood; and a timely need for evidence about obstetric outcomes. Retained items were developed into a 24-item prototype scale with four subscales. Prototype testing showed acceptable internal consistency (Cronbach's alpha=0.71) and test-retest reliability (intraclass correlation coefficient=0.70). Known-group validity was supported; the scale discriminated between groups by age (x=70.0 for patients ≥35 years old vs 54.5 for patients <35 years old, p=0.02) and years since diagnosis (x=71.5 for ≥6 years vs 54.3 for<6 years, p=0.01). The financial subscale was correlated with the Economic StraiN and Resilience in Cancer measure of financial toxicity (ρ=0.39, p<0.001). The scale was acceptable and feasibly delivered online. The final 22-item scale is organized in four subscales: personal, medical, relational, and financial barriers to motherhood. CONCLUSION: The Survivorship Oncofertility Barriers Scale demonstrated validity, reliability, and was acceptable and feasible when delivered online. Implementing the scale can gather the data needed to inform shared decision making and to address disparities in fertility care for survivors.

Survival outcomes following pregnancy or assisted reproductive technologies after breast cancer: A population-based study.

BACKGROUND: This study sought to determine the impact of pregnancy or assisted reproductive technologies (ART) on breast-cancer-specific survival among breast cancer survivors. METHODS: The authors performed a cohort study using a novel data linkage from the California Cancer Registry, the California birth cohort, and the Society for Assisted Reproductive Technology Clinic Outcome Reporting System data sets. They performed risk-set matching in women with stages I-III breast cancer diagnosed between 2000 and 2012. For each pregnant woman, comparable women who were not pregnant at that point but were otherwise similar based on observed characteristics were matched at the time of pregnancy. After matching, Cox proportional hazards models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for the association of pregnancy with breast-cancer-specific survival. We repeated these analyses for women who received ART. RESULTS: Among 30,021 women with breast cancer, 553 had a pregnancy and 189 attempted at least one cycle of ART. In Cox proportional hazards modeling, the pregnancy group had a higher 5-year disease-specific survival rate; 95.6% in the pregnancy group and 90.6% in the nonpregnant group (HR, 0.43; 95% CI, 0.24-0.77). In women with hormone receptor-positive cancer, we found similar results (HR, 0.43; 95% CI, 0.2-0.91). In the ART analysis, there was no difference in survival between groups; the 5-year disease-specific survival rate was 96.9% in the ART group and 94.1% in the non-ART group (HR, 0.44; 95% CI, 0.17-1.13). CONCLUSION: Pregnancy and ART are not associated with worse survival in women with breast cancer. LAY SUMMARY: We sought to determine the impact of pregnancy or assisted reproductive technologies (ART) among breast cancer survivors. We performed a study of 30,021 women by linking available data from California and the Society for Assisted Reproductive Technology Clinic Outcome Reporting System. For each pregnant woman, we matched at the time of pregnancy comparable women who were not pregnant at that point but were otherwise similar based on observed characteristics. We repeated these analyses for women who received ART. We found that pregnancy and ART were not associated with worse survival.

Employment disruption among women with gynecologic cancers.

BACKGROUND: Adverse employment outcomes pose significant challenges for cancer patients, though data patients with gynecologic cancers are sparse. We evaluated the decrease in employment among patients in the year following the diagnosis of a gynecologic cancer compared with population-based controls. METHODS: Patients aged 18 to 63 years old, who were diagnosed with cervical, ovarian, endometrial, or vulvar cancer between January 2009 and December 2017, were identified in Truven MarketScan, an insurance claims database of commercially insured patients in the USA. Patients working full- or part-time at diagnosis were matched to population-based controls in a 1:4 ratio via propensity score. Multivariable Cox proportional hazards models were used to evaluate the risk of employment disruption in patients versus controls. RESULTS: We identified 7446 women with gynecologic cancers (191 vulvar, 941 cervical, 1839 ovarian, and 4475 endometrial). Although most continued working following diagnosis, 1579 (21.2%) changed from full- or part-time employment to long-term disability, retirement, or work cessation. In an adjusted model, older age, the presence of comorbidities, and treatment with surgery plus adjuvant therapy versus surgery alone were associated with an increased risk of employment disruption (p<0.0003, p=0.01, and p<0.0001, respectively) among patients with gynecologic cancer. In the propensity-matched cohort, patients with gynecologic cancers had over a threefold increased risk of employment disruption relative to controls (HR 3.67, 95% CI 3.44 to 3.95). CONCLUSION: Approximately 21% of patients with gynecologic cancer experienced a decrease in employment in the year after diagnosis. These patients had over a threefold increased risk of employment disruption compared with controls.

Levosimendan or milrinone for right ventricular inotropic treatment?-A secondary analysis of a randomized trial.

BACKGROUND: The aim of the present study was to compare the effects of milrinone and levosimendan on right ventricular (RV) inotropy and lusitropy in patients after aortic valve replacement (AVR) for aortic stenosis, a procedure in which an abnormal postoperative RV function may be seen. METHODS: In a prospective, blinded trial, 31 patients were randomized to receive either milrinone (0.4 and 0.8 µg/kg/min, n = 16) or levosimendan (0.1 and 0.2 µg/kg/min, n = 15) after AVR for aortic stenosis. RV performance, afterload (pulmonary arterial elastance), RV strain, systolic (SR-S) and early diastolic (SR-E) strain rate were measured by pulmonary artery thermodilution catheterization and transoesophageal two-dimensional speckle tracking echocardiography. To circumvent the indirect effects of inodilator-induced hemodynamic changes on RV systolic and diastolic deformation, pulmonary arterial elastance, central venous pressure and heart rate were maintained constant by atrial pacing, plasma volume expansion with colloids and phenylephrine-induced vasoconstriction during treatment with the inotropes. RESULTS: A dose-dependent increase in stroke volume index and cardiac index by approximately 20% were seen with both agents at the highest doses, with no difference between groups (P = .792 and 0.744, respectively). In both groups, RV strain and SR-S dose-dependently increased by 20% and 15%-19%, respectively, at the highest doses (P = .742 and 0.259, respectively) with no difference between groups. SR-E improved by both agents 20%-24% at the highest dose with no difference between groups (P = .714). CONCLUSIONS: The direct RV inotropic and lusitropic effects of levosimendan and milrinone were comparable at clinically relevant infusion rates.

Glutathione transferases catalyze recycling of auto-toxic cyanogenic glucosides in sorghum.

Cyanogenic glucosides are nitrogen-containing specialized metabolites that provide chemical defense against herbivores and pathogens via the release of toxic hydrogen cyanide. It has been suggested that cyanogenic glucosides are also a store of nitrogen that can be remobilized for general metabolism via a previously unknown pathway. Here we reveal a recycling pathway for the cyanogenic glucoside dhurrin in sorghum (Sorghum bicolor) that avoids hydrogen cyanide formation. As demonstrated in vitro, the pathway proceeds via spontaneous formation of a dhurrin-derived glutathione conjugate, which undergoes reductive cleavage by glutathione transferases of the plant-specific lambda class (GSTLs) to produce p-hydroxyphenyl acetonitrile. This is further metabolized to p-hydroxyphenylacetic acid and free ammonia by nitrilases, and then glucosylated to form p-glucosyloxyphenylacetic acid. Two of the four GSTLs in sorghum exhibited high stereospecific catalytic activity towards the glutathione conjugate, and form a subclade in a phylogenetic tree of GSTLs in higher plants. The expression of the corresponding two GSTLs co-localized with expression of the genes encoding the p-hydroxyphenyl acetonitrile-metabolizing nitrilases at the cellular level. The elucidation of this pathway places GSTs as key players in a remarkable scheme for metabolic plasticity allowing plants to reverse the resource flow between general and specialized metabolism in actively growing tissue.

The Intracellular Localization of the Vanillin Biosynthetic Machinery in Pods of Vanilla planifolia.

Vanillin is the most important flavor compound in the vanilla pod. Vanilla planifolia vanillin synthase (VpVAN) catalyzes the conversion of ferulic acid and ferulic acid glucoside into vanillin and vanillin glucoside, respectively. Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) of vanilla pod sections demonstrates that vanillin glucoside is preferentially localized within the mesocarp and placental laminae whereas vanillin is preferentially localized within the mesocarp. VpVAN is present as the mature form (25 kDa) but, depending on the tissue and isolation procedure, small amounts of the immature unprocessed form (40 kDa) and putative oligomers (50, 75 and 100 kDa) may be observed by immunoblotting using an antibody specific to the C-terminal sequence of VpVAN. The VpVAN protein is localized within chloroplasts and re-differentiated chloroplasts termed phenyloplasts, as monitored during the process of pod development. Isolated chloroplasts were shown to convert [14C]phenylalanine and [14C]cinnamic acid into [14C]vanillin glucoside, indicating that the entire vanillin de novo biosynthetic machinery converting phenylalanine to vanillin glucoside is present in the chloroplast.

The iron-regulated transporter 1 plays an essential role in uptake, translocation and grain-loading of manganese, but not iron, in barley.

Transporters involved in manganese (Mn) uptake and intracellular Mn homeostasis in Arabidopsis and rice are well characterized, while much less is known for barley, which is particularly prone to Mn deficiency. In this study we have investigated the role of the iron-regulated transporter 1 (IRT1) for Mn uptake and translocation in barley plants. We employed an RNAi approach to reduce HvIRT1 expression to 5% of the wild-type level. This enabled characterization of the functional role of HvIRT1 by use of advanced imaging and phenotyping techniques applied to plants growing in hydroponics or soils with different Mn availability. Our results highlight the importance of HvIRT1 for the transport of Mn across the root endodermis into the stele. In the hvirt1-RNAi lines, a chlorotic phenotype with reduced shoot Mn concentration and impaired photosynthetic functionality was observed, especially under conditions with low Mn availability. We also document that HvIRT1 controlled the Mn distribution within the barley grain. Surprisingly, unlike other IRT1 orthologues, HvIRT1 played no significant role in iron uptake. We conclude that the barley IRT1 orthologue has a novel function with respect to ensuring sufficient shoot Mn concentrations. The preference of IRT1 for Mn instead of Fe is discussed in an evolutionary context.

Localization and in-Vivo Characterization of Thapsia garganica CYP76AE2 Indicates a Role in Thapsigargin Biosynthesis.

The Mediterranean plant Thapsia garganica (dicot, Apiaceae), also known as deadly carrot, produces the highly toxic compound thapsigargin. This compound is a potent inhibitor of the sarcoplasmic-endoplasmic reticulum Ca2+-ATPase calcium pump in mammals and is of industrial importance as the active moiety of the anticancer drug mipsagargin, currently in clinical trials. Knowledge of thapsigargin in planta storage and biosynthesis has been limited. Here, we present the putative second step in thapsigargin biosynthesis, by showing that the cytochrome P450 TgCYP76AE2, transiently expressed in Nicotiana benthamiana, converts epikunzeaol into epidihydrocostunolide. Furthermore, we show that thapsigargin is likely to be stored in secretory ducts in the roots. Transcripts from TgTPS2 (epikunzeaol synthase) and TgCYP76AE2 in roots were found only in the epithelial cells lining these secretory ducts. This emphasizes the involvement of these cells in the biosynthesis of thapsigargin. This study paves the way for further studies of thapsigargin biosynthesis.

The bifurcation of the cyanogenic glucoside and glucosinolate biosynthetic pathways.

The biosynthetic pathway for the cyanogenic glucoside dhurrin in sorghum has previously been shown to involve the sequential production of (E)- and (Z)-p-hydroxyphenylacetaldoxime. In this study we used microsomes prepared from wild-type and mutant sorghum or transiently transformed Nicotiana benthamiana to demonstrate that CYP79A1 catalyzes conversion of tyrosine to (E)-p-hydroxyphenylacetaldoxime whereas CYP71E1 catalyzes conversion of (E)-p-hydroxyphenylacetaldoxime into the corresponding geometrical Z-isomer as required for its dehydration into a nitrile, the next intermediate in cyanogenic glucoside synthesis. Glucosinolate biosynthesis is also initiated by the action of a CYP79 family enzyme, but the next enzyme involved belongs to the CYP83 family. We demonstrate that CYP83B1 from Arabidopsis thaliana cannot convert the (E)-p-hydroxyphenylacetaldoxime to the (Z)-isomer, which blocks the route towards cyanogenic glucoside synthesis. Instead CYP83B1 catalyzes the conversion of the (E)-p-hydroxyphenylacetaldoxime into an S-alkyl-thiohydroximate with retention of the configuration of the E-oxime intermediate in the final glucosinolate core structure. Numerous microbial plant pathogens are able to detoxify Z-oximes but not E-oximes. The CYP79-derived E-oximes may play an important role in plant defense.

A recycling pathway for cyanogenic glycosides evidenced by the comparative metabolic profiling in three cyanogenic plant species.

Cyanogenic glycosides are phytoanticipins involved in plant defence against herbivores by virtue of their ability to release toxic hydrogen cyanide (HCN) upon tissue disruption. In addition, endogenous turnover of cyanogenic glycosides without the liberation of HCN may offer plants an important source of reduced nitrogen at specific developmental stages. To investigate the presence of putative turnover products of cyanogenic glycosides, comparative metabolic profiling using LC-MS/MS and high resolution MS (HR-MS) complemented by ion-mobility MS was carried out in three cyanogenic plant species: cassava, almond and sorghum. In total, the endogenous formation of 36 different chemical structures related to the cyanogenic glucosides linamarin, lotaustralin, prunasin, amygdalin and dhurrin was discovered, including di- and tri-glycosides derived from these compounds. The relative abundance of the compounds was assessed in different tissues and developmental stages. Based on results common to the three phylogenetically unrelated species, a potential recycling endogenous turnover pathway for cyanogenic glycosides is described in which reduced nitrogen and carbon are recovered for primary metabolism without the liberation of free HCN. Glycosides of amides, carboxylic acids and 'anitriles' derived from cyanogenic glycosides appear as common intermediates in this pathway and may also have individual functions in the plant. The recycling of cyanogenic glycosides and the biological significance of the presence of the turnover products in cyanogenic plants open entirely new insights into the multiplicity of biological roles cyanogenic glycosides may play in plants.

Bioremediation strategies for removal of residual atrazine in the boreal groundwater zone.

Strategies for bioremediation of atrazine, a pesticide commonly polluting groundwater in low concentrations, were studied in two boreal nonagricultural soils. Atrazine was not mineralized in soil without bioremediation treatments. In biostimulation treatment with molasses, up to 52% of atrazine was mineralized at 10 °C, even though the degradation gene copy numbers did not increase. Incubations with radioactively labeled atrazine followed by microautoradiographic analysis revealed that bioremediation strategies increased the relative proportion of active degraders from 0.3 up to 1.9% of the total bacterial count. These results indicate that atrazine degradation might not solely be facilitated by atzA/trzN-atzB genes. In combined biostimulation treatment using citrate or molasses and augmentation with Pseudomonas citronellolis ADP or Arthrobacter aurescens strain TC1, up to 76% of atrazine was mineralized at 30 °C, and the atrazine degradation gene numbers increased up to 10(7) copies g(-1) soil. Clone libraries from passive samplers in groundwater monitoring wells revealed the presence of phylogenetic groups formerly shown to include atrazine degraders, and the presence of atrazine degradation genes atzA and atzB. These results show that the mineralization of low concentrations of atrazine in the groundwater zone at low temperatures is possible by bioremediation treatments.

Visualizing metabolite distribution and enzymatic conversion in plant tissues by desorption electrospray ionization mass spectrometry imaging.

In comparison with the technology platforms developed to localize transcripts and proteins, imaging tools for visualization of metabolite distributions in plant tissues are less well developed and lack versatility. This hampers our understanding of plant metabolism and dynamics. In this study, we demonstrate that desorption electrospray ionization mass spectrometry imaging (DESI-MSI) of tissue imprints on porous Teflon may be used to accurately image the distribution of even labile plant metabolites such as hydroxynitrile glucosides, which normally undergo enzymatic hydrolysis by specific ß-glucosidases upon cell disruption. This fast and simple sample preparation resulted in no substantial differences in the distribution and ratios of all hydroxynitrile glucosides between leaves from wild-type Lotus japonicus and a ß-glucosidase mutant plant that lacks the ability to hydrolyze certain hydroxynitrile glucosides. In wild-type, the enzymatic conversion of hydroxynitrile glucosides and the concomitant release of glucose were easily visualized when a restricted area of the leaf tissue was damaged prior to sample preparation. The gene encoding the first enzyme in hydroxynitrile glucoside biosynthesis in L. japonicus leaves, CYP79D3, was found to be highly expressed during the early stages of leaf development, and the hydroxynitrile glucoside distribution in mature leaves reflected this early expression pattern. The utility of direct DESI-MSI of plant tissue was demonstrated using cryo-sections of cassava (Manihot esculenta) tubers. The hydroxynitrile glucoside levels were highest in the outer cell layers, as verified by LC-MS analyses. The unexpected discovery of a hydroxynitrile-derived di-glycoside shows the potential of DESI-MSI to discover and guide investigations into new metabolic routes.

Analysis of peptide PSY1 responding transcripts in the two Arabidopsis plant lines: wild type and psy1r receptor mutant.

BACKGROUND: Small-secreted peptides are emerging as important components in cell-cell communication during basic developmental stages of plant cell growth and development. Plant peptide containing sulfated tyrosine 1 (PSY1) has been reported to promote cell expansion and differentiation in the elongation zone of roots. PSY1 action is dependent on a receptor PSY1R that triggers a signaling cascade leading to cell elongation. However little is known about cellular functions and the components involved in PSY1-based signaling cascade. RESULTS: Differentially expressed genes were identified in a wild type plant line and in a psy1r receptor mutant line of Arabidopsis thaliana after treatment with PSY1. Seventy-seven genes were found to be responsive to the PSY1 peptide in wild type plants while 154 genes were responsive in the receptor mutant plants. PSY1 activates the transcripts of genes involved in cell wall modification. Gene enrichment analysis revealed that PSY1-responsive genes are involved in responses to stimuli, metabolic processes and biosynthetic processes. The significant enrichment terms of PSY1-responsive genes were higher in psy1r mutant plants compared to in wild type plants. Two parallel responses to PSY1 were identified, differing in their dependency on the PSY1R receptor. Promoter analysis of the differentially expressed genes identified a light regulatory motif in some of these. CONCLUSION: PSY1-responsive genes are involved in cellular functions and stimuli responses suggesting a crosstalk between developmental cues and environmental stimuli. Possibly, two parallel responses to PSY1 exist. A motif involved in light regulation was identified in the promoter region of the differentially expressed genes. Reduced hypocotyl growth was observed in etiolated receptor mutant seedlings.