A prospective evaluation of the prostate microbiome in malignant and benign tissue using transperineal biopsy.

BACKGROUND: The link between the prostate microbiome and prostate cancer remains unclear. Few studies have analyzed the microbiota of prostate tissue, and these have been limited by potential contamination by transrectal biopsy. Transperineal prostate biopsy offers an alternative and avoids fecal cross-contamination. We aim to characterize the prostate microbiome using transperineal biopsy. METHODS: Patients with clinical suspicion for prostate cancer who were to undergo transperineal prostate biopsy with magnetic resonance imaging (MRI) fusion guidance were prospectively enrolled from 2022 to 2023. Patients were excluded if they had Prostate Imaging Reporting and Data System lesions with scores ≤ 3, a history of prostate biopsy within 1 year, a history of prostate cancer, or antibiotic use within 30 days of biopsy. Tissue was collected from the MRI target lesions and nonneoplastic transitional zone. Bacteria were identified using 16S ribosomal RNA gene sequencing. RESULTS: Across the 42 patients, 76% were found to have prostate cancer. Beta diversity indices differed significantly between the perineum, voided urine, and prostate tissue. There were no beta diversity differences between cancerous or benign tissue, or between pre- and postbiopsy urines. There appear to be unique genera more abundant in cancerous versus benign tissue. There were no differences in alpha diversity indices relative to clinical findings including cancer status, grade, and risk group. CONCLUSIONS: We demonstrate a rigorous method to better characterize the prostate microbiome using transperineal biopsy and to limit contamination. These findings provide a framework for future large-scale studies of the microbiome of prostate cancer.

Preoperative optimization of the radical cystectomy patient: Current state and future directions.

Radical cystectomy (RC) is associated with high rates of morbidity and mortality despite adoption of robotics and implementation of enhanced recovery after surgery protocols. There have been increased efforts to investigate preoperative optimization through comprehensive nutritional evaluation, preoperative supplementation, and prehabilitation outside of previously described enhanced recovery after surgery protocols to reduce mortality and morbidity from RC. In this review, we summarize and evaluate the current literature on preoperative assessment and optimization in RC.

Home versus outpatient hospital intravenous immunoglobulin infusion and health care resource utilization.

BACKGROUND: Home health care delivery is projected to increase. Intravenous immunoglobulin (IVIG) therapy has high potential to move from the outpatient hospital (OPH) setting to home delivery. OBJECTIVE: This study examined the relationship between home and OPH IVIG infusions and health care utilization. METHODS: We used a retrospective cohort study design and the Humana Research Database to identify patients with 1 or more medical or pharmacy claims for an IVIG infusion agent from January 1, 2017, to December 31, 2018. Eligible patients were enrolled in a Medicare Advantage Prescription Drug (MAPD) or commercial health plan, with at least 12 months of continuous enrollment before and after their first infusion (i.e., index date) received in the home or OPH setting. We measured the odds of experiencing an inpatient (IP) stay or emergency department (ED) visit, adjusted for baseline differences in age, sex, race, region, population density, low-income, and dual eligibility status, MAPD or commercial health plan, plan type, treatment-naïve status, home health use, RxRisk-V comorbidity burden score, and indications for IVIG use. RESULTS: A total of 208 and 1079 patients received IVIG infusions in the home and OPH setting, respectively. The odds for an IP stay (odds ratio [OR] 0.56 [95% CI 0.38-0.82]) and ED visit (OR 0.62 [95% CI 0.41-0.93]) were significantly lower in patients who received IVIG infusion in the home than patients receiving infusion in the OPH setting. CONCLUSIONS: Our findings suggest there may be value to increasing referrals for IVIG home infusion. Decreased health care utilization provides value to the system in cost savings and to patients and families owing to less disruption and improved clinical outcomes. Further study can help inform health policy designed to maximize the benefits of IVIG home infusion while minimizing potential risks.

Pain Management Strategies in Contemporary Penile Implant Recipients.

PURPOSE OF REVIEW: To review the most recent literature citing opioid-sparing multimodal analgesic strategies used to manage perioperative pain in patients who underwent inflatable penile prosthesis (IPP) surgery and to provide the penile implant surgeon a variety of non-opioid-based pain management strategies for IPP management. RECENT FINDINGS: Interventions performed in the pre-operative, intraoperative, and post-operative arenas have all been shown to effectively lower pain scores and reduce opioid consumption. Certain surgical techniques performed during IPP surgery have helped with post-operative discomfort patients may feel after surgery. Multimodal analgesia (MMA) protocols adopted from other surgical fields and other urologic subspecialties that are implemented in IPP surgery have promising results with regard to post-operative pain control and opioid consumption. Protocols that implement a combination of refined surgical technique and multimodal analgesia offer substantial benefit to patients undergoing IPP surgery. Further work is needed to assess long-term pain control and opioid use in patients that undergo IPP surgery using these innovative strategies.

One-Year Outcomes After MitraClip for Functional Mitral Regurgitation.

BACKGROUND: Secondary mitral regurgitation (SMR) occurs in the absence of organic mitral valve disease and may develop as the left ventricle dilates or remodels or as a result of leaflet tethering with impaired coaptation, most commonly from apical and lateral distraction of the subvalvular apparatus, with late annular dilatation. The optimal therapy for SMR is unclear. This study sought to evaluate the 1-year adjudicated outcomes of all patients with SMR undergoing the MitraClip procedure in the EVEREST II (Endovascular Valve Edge-to-Edge Repair Study) Investigational Device Exemption program, which is comprised of the randomized clinical trial, the prospective High-Risk Registry, and the REALISM Continued Access Registry (Multicenter Study of the MitraClip System). METHODS: Patients with 3+/4+ SMR enrolled in EVEREST II were stratified by non-high surgical risk (non-HR) and high surgical risk (HR) status (defined as Society of Thoracic Surgeons risk of mortality ≥12% or predefined risk factors). Clinical, echocardiographic, and functional outcomes at 1 year were evaluated. RESULTS: A total of 616 patients (482 HR, 134 non-HR; mean age, 73.3±10.5 years; Society of Thoracic Surgeons risk, 10.2±6.9%) with SMR underwent the MitraClip procedure. At baseline, 80.5% of patients were in New York Heart Association class III/IV. Major adverse events at 30 days included death (3.6%), stroke (2.3%), and renal failure (1.5%). At discharge, 88.8% had MR ≤2+. At 1 year, there were 139 deaths, and the Kaplan-Meier estimate of freedom from mortality was 76.8%. The majority of surviving patients (84.7%) remained with MR ≤2+ and New York Heart Association class I/II (83.0%). Kaplan-Meier survival at 1 year was 74.1% in HR patients and 86.4% in non-HR patients ( P=0.0175). At 1 year, both groups achieved comparable MR reduction (MR ≤2+, 84.0% versus 87.0%) and improvement in left ventricular end-diastolic volume (-8.0 mL versus -12.7 mL), whereas New York Heart Association class I/II was found in 80.1% versus 91.8% ( P=0.008) of HR and non-HR patients, respectively. In HR patients, the annualized rate of heart failure hospitalizations decreased from 0.68 to 0.46 in the 12 months before to 12 months after the procedure ( P<0.0001). CONCLUSIONS: Transcatheter mitral valve repair with the MitraClip in patients with secondary MR is associated with acceptable safety, reduction of MR severity, symptom improvement, and positive ventricular remodeling. CLINICAL TRIAL REGISTRATION: https://www.clinicaltrials.gov . Unique identifiers: NCT00209274, NCT01940120, and NCT01931956.

Comparative Analysis of the Flax Immune Receptors L6 and L7 Suggests an Equilibrium-Based Switch Activation Model.

NOD-like receptors (NLRs) are central components of the plant immune system. L6 is a Toll/interleukin-1 receptor (TIR) domain-containing NLR from flax (Linum usitatissimum) conferring immunity to the flax rust fungus. Comparison of L6 to the weaker allele L7 identified two polymorphic regions in the TIR and the nucleotide binding (NB) domains that regulate both effector ligand-dependent and -independent cell death signaling as well as nucleotide binding to the receptor. This suggests that a negative functional interaction between the TIR and NB domains holds L7 in an inactive/ADP-bound state more tightly than L6, hence decreasing its capacity to adopt the active/ATP-bound state and explaining its weaker activity in planta. L6 and L7 variants with a more stable ADP-bound state failed to bind to AvrL567 in yeast two-hybrid assays, while binding was detected to the signaling active variants. This contrasts with current models predicting that effectors bind to inactive receptors to trigger activation. Based on the correlation between nucleotide binding, effector interaction, and immune signaling properties of L6/L7 variants, we propose that NLRs exist in an equilibrium between ON and OFF states and that effector binding to the ON state stabilizes this conformation, thereby shifting the equilibrium toward the active form of the receptor to trigger defense signaling.

Cardiovascular Outcomes Assessment of the MitraClip in Patients with Heart Failure and Secondary Mitral Regurgitation: Design and rationale of the COAPT trial.

BACKGROUND: Patients with heart failure (HF) and symptomatic secondary mitral regurgitation (SMR) have a poor prognosis, with morbidity and mortality directly correlated with MR severity. Correction of isolated SMR with surgery is not well established in this population, and medical management remains the preferred approach in most patients. The Cardiovascular Outcomes Assessment of the MitraClip Percutaneous Therapy for Heart Failure Patients with Functional Mitral Regurgitation (COAPT) trial was designed to determine whether transcatheter mitral valve (MV) repair with the MitraClip device is safe and effective in patients with symptomatic HF and clinically significant SMR. STUDY DESIGN: The COAPT trial is a prospective, randomized, parallel-controlled, open-label multicenter study of the MitraClip device for the treatment of moderate-to-severe (3+) or severe (4+) SMR (as verified by an independent echocardiographic core laboratory) in patients with New York Heart Association class II-IVa HF despite treatment with maximally tolerated guideline-directed medical therapy (GDMT) who have been determined by the site's local heart team as not appropriate for MV surgery. A total of 614 eligible subjects were randomized in a 1:1 ratio to MV repair with the MitraClip plus GDMT versus GDMT alone. The primary effectiveness end point is recurrent HF hospitalizations through 24 months, analyzed when the last subject completes 12-month follow-up, powered to demonstrate superiority of MitraClip therapy. The primary safety end point is a composite of device-related complications at 12 months compared to a performance goal. Follow-up is ongoing, and the principal results are expected in late 2018. CONCLUSIONS: HF patients with clinically significant SMR who continue to be symptomatic despite optimal GDMT have limited treatment options and a poor prognosis. The randomized COAPT trial was designed to determine the safety and effectiveness of transcatheter MV repair with the MitraClip in symptomatic HF patients with moderate-to-severe or severe SMR.

Defining Novel and Practical Metrics to Assess the Deliverables of Multiparametric Magnetic Resonance Imaging/Ultrasound Fusion Prostate Biopsy.

PURPOSE: Multiparametric magnetic resonance/ultrasound targeted prostate biopsy is touted as a tool to improve prostate cancer care and yet its true clinical usefulness over transrectal ultrasound guided prostate biopsy has not been systematically analyzed. We introduce 2 metrics to better quantify and report the deliverables of targeted biopsy. MATERIALS AND METHODS: We reviewed our prospective database of patients who underwent simultaneous multiparametric magnetic resonance/ultrasound targeted prostate biopsy and transrectal ultrasound guided prostate biopsy. Actionable intelligence metric was defined as the proportion of patients in whom targeted biopsy provided actionable information over transrectal ultrasound guided prostate biopsy. Reduction metric was defined as the proportion of men in whom transrectal ultrasound guided prostate biopsy could have been omitted. We compared metrics in our cohort with those in prior reports. RESULTS: A total of 371 men were included in study. The actionable intelligence and reduction metrics were 22.2% and 83.6% in biopsy naïve cases, 26.7% and 84.2% in prior negative transrectal ultrasound guided prostate biopsy cases, and 24% and 77.5%, respectively, in active surveillance cases. No significant differences were observed among the groups in the actionable intelligence metric and the reduction metric (p = 0.89 and 0.27, respectively). The actionable intelligence metric was 25.0% for PI-RADS™ (Prostate Imaging Reporting and Data System) 3, 27.5% for PI-RADS 4 and 21.7% for PI-RADS 5 lesions (p = 0.73). Transrectal ultrasound guided prostate biopsy could have been avoided in more patients with PI-RADS 3 compared to PI-RADS 4/5 lesions (reduction metric 92.0% vs 76.7%, p <0.01). Our results compare favorably to those of other reported series. CONCLUSIONS: The actionable intelligence metric and the reduction metric are novel, clinically relevant quantification metrics to standardize the reporting of multiparametric magnetic resonance/ultrasound targeted prostate biopsy deliverables. Targeted biopsy provides actionable information in about 25% of men. Reduction metric assessment highlights that transrectal ultrasound guided prostate biopsy may only be omitted after carefully considering the risk of missing clinically significant cancers.

Endoscopic Management of Ureteral Strictures: an Update.

PURPOSE OF REVIEW: This review focuses on the role of endoscopic treatment of ureteral stricture disease (USD) in the era of minimally invasive surgery. RECENT FINDINGS: There is a relative paucity of recent literature regarding the endoscopic treatment of USD. Laser endopyelotomy and balloon dilation are associated with good outcomes in treatment-naïve patients with short (< 2 cm), non-ischemic, benign ureteral strictures with a functional renal unit. If stricture recurs, repetitive dilation and laser endopyleotomy is not recommended, as success rates are low in this scenario. Patients with low-complexity ureteroenteric strictures and transplant strictures may benefit from endoscopic treatment options, although formal reconstruction offers higher rates of success. Formal ureteral reconstruction remains the gold-standard treatment for ureteral stricture disease as it is associated with higher rates of complete resolution. However, in carefully selected patients, endoscopic treatment modalities provide a low-cost, low-morbidity alternative.

The impact of real-world cardiovascular-related pharmacogenetic testing in an insured population.

BACKGROUND: Pharmacogenomics is intended to help clinicians provide the right drug to the right patient at an appropriate dose. However, limited evidence of clinical utility has slowed uptake of pharmacogenomic testing (PGT). OBJECTIVE: To evaluate the impact of real-world cardiovascular (CV)-related PGT on clinical outcomes, healthcare resource utilisation (HCRU) and cost in a large, heterogeneous population. METHODS: Individuals with Medicare Advantage Prescription Drug, Medicaid, or commercial coverage between 1/1/2011 and 9/30/2015 and ≥1 atherosclerotic CV-related diagnosis were identified. Those with ≥1 claim for CV-related PGT were included in the test group (index date = 1st PGT claim) and matched 1:2 to controls without PGT. Individuals aged <22 or ≥90 years old on the index date, with <12 months continuous enrollment before and after the index date, or without an ASCVD-related diagnosis in the 12-month pre-index period were excluded. The primary outcome was occurrence of a major CV event during the 12-month post-index period. RESULTS: After adjustment, the PGT group was significantly more likely to experience ischaemic stroke, pulmonary embolism, deep vein thrombosis or a composite event compared with controls. Adjusting for baseline characteristics, HCRU was significantly higher for the test group across all measured outcomes except all-cause and ASCVD-related inpatient admissions. Median all-cause and ASCVD-related healthcare costs were significantly higher for the test group. CONCLUSIONS: Real world PGT in a large population did not improve outcomes. Tailoring medication therapy to each patient holds great promise for providing quality care but a deeper understanding of how widespread utilisation of PGT might impact objective health outcomes is needed.

Can Plant Microbiome Studies Lead to Effective Biocontrol of Plant Diseases?

In this review, the wisdom and efficacy of studies seeking disease attenuating microbes and microbiomes only in healthy plant communities is questioned and an alternative view is posited, namely that success in biocontrol of crop diseases may also come from studies of microbiota, or at least individual species isolates, associated with diseased plants. In support of this view, I summarize the current extensive knowledge of the biology behind what is probably the most successful biocontrol of a plant disease, namely the biocontrol of crown gall of stone fruit using non-pathogenic Rhizobium rhizogenes K84, in which the biocontrol agent itself came from a diseased plant.

Integrated decoys and effector traps: how to catch a plant pathogen.

Plant immune receptors involved in disease resistance and crop protection are related to the animal Nod-like receptor (NLR) class, and recognise the virulence effectors of plant pathogens, whereby they arm the plant's defensive response. Although plant NLRs mainly contain three protein domains, about 10% of these receptors identified by extensive cross-plant species data base searches have now been shown to include novel and highly variable integrated domains, some of which have been shown to detect pathogen effectors by direct interaction. Sarris et al. have identified a large number of integrated domains that can be used to detect effector targets in host plant proteomes and identify unknown pathogen effectors.Please see related Research article: Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens, http://dx.doi.org/10.1186/s12915-016-0228-7 Since the time of writing, a closely related paper has been released: Kroj T, Chanclud E, Michel-Romiti C, Grand X, Morel J-B. Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread. New Phytol. 2016 (ahead of print).

Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini.

BACKGROUND: Rust fungi are an important group of plant pathogens that cause devastating losses in agricultural, silvicultural and natural ecosystems. Plants can be protected from rust disease by resistance genes encoding receptors that trigger a highly effective defence response upon recognition of specific pathogen avirulence proteins. Identifying avirulence genes is crucial for understanding how virulence evolves in the field. RESULTS: To facilitate avirulence gene cloning in the flax rust fungus, Melampsora lini, we constructed a high-density genetic linkage map using single nucleotide polymorphisms detected in restriction site-associated DNA sequencing (RADseq) data. The map comprises 13,412 RADseq markers in 27 linkage groups that together span 5860 cM and contain 2756 recombination bins. The marker sequences were used to anchor 68.9 % of the M. lini genome assembly onto the genetic map. The map and anchored assembly were then used to: 1) show that M. lini has a high overall meiotic recombination rate, but recombination distribution is uneven and large coldspots exist; 2) show that substantial genome rearrangements have occurred in spontaneous loss-of-avirulence mutants; and 3) identify the AvrL2 and AvrM14 avirulence genes by map-based cloning. AvrM14 is a dual-specificity avirulence gene that encodes a predicted nudix hydrolase. AvrL2 is located in the region of the M. lini genome with the lowest recombination rate and encodes a small, highly-charged proline-rich protein. CONCLUSIONS: The M. lini high-density linkage map has greatly advanced our understanding of virulence mechanisms in this pathogen by providing novel insights into genome variability and enabling identification of two new avirulence genes.

Structures of the flax-rust effector AvrM reveal insights into the molecular basis of plant-cell entry and effector-triggered immunity.

Fungal and oomycete pathogens cause some of the most devastating diseases in crop plants, and facilitate infection by delivering a large number of effector molecules into the plant cell. AvrM is a secreted effector protein from flax rust (Melampsora lini) that can internalize into plant cells in the absence of the pathogen, binds to phosphoinositides (PIPs), and is recognized directly by the resistance protein M in flax (Linum usitatissimum), resulting in effector-triggered immunity. We determined the crystal structures of two naturally occurring variants of AvrM, AvrM-A and avrM, and both reveal an L-shaped fold consisting of a tandem duplicated four-helix motif, which displays similarity to the WY domain core in oomycete effectors. In the crystals, both AvrM variants form a dimer with an unusual nonglobular shape. Our functional analysis of AvrM reveals that a hydrophobic surface patch conserved between both variants is required for internalization into plant cells, whereas the C-terminal coiled-coil domain mediates interaction with M. AvrM binding to PIPs is dependent on positive surface charges, and mutations that abrogate PIP binding have no significant effect on internalization, suggesting that AvrM binding to PIPs is not essential for transport of AvrM across the plant membrane. The structure of AvrM and the identification of functionally important surface regions advance our understanding of the molecular mechanisms underlying how effectors enter plant cells and how they are detected by the plant immune system.

Long-term, open-label, safety study of once-daily ropinirole extended/prolonged release in early and advanced Parkinson's disease.

Long-term safety of once-daily ropinirole extended/prolonged release (ropinirole XL/PR) was evaluated in subjects with early and advanced Parkinson's disease (PD) in this study, 101468/248. Subjects (n = 419) who completed one of three prior studies evaluating ropinirole XL/PR for the treatment of PD were enrolled in this open-label, multicenter, extension study, and were to be followed for up to 73 months. Ropinirole XL/PR was titrated/continued, and adjusted as appropriate during the maintenance phase (maximum 24 mg/d). Levodopa (L-dopa) and other nondopamine agonist PD medications were permitted. Safety outcomes that were investigated included frequency of adverse events (AEs). Subjects' preference regarding once daily versus three times daily study medication regimens was also investigated in a subset of the study population. The median duration of ropinirole XL/PR exposure was 1275 d. Most subjects (87%) reported at least one AE, with the most common (≥ 10%) AEs being, back pain (14%), hallucinations (13%), somnolence (11%) and peripheral edema (11%). Twenty-five percent of subjects discontinued the study prematurely due to an AE during the treatment period. Long-term treatment with ropinirole XL/PR was not associated with any new or unexpected safety concerns in patients with early and advanced PD, and a majority of subjects preferred the once-daily dosing regimen.

A retrospective, matched cohort study of potential drug-drug interaction prevalence and opioid utilization in a diabetic peripheral neuropathy population initiated on pregabalin or duloxetine.

BACKGROUND: Anticipating and controlling drug-drug interactions (DDIs) in older patients with painful diabetic peripheral neuropaty (pDPN) presents a significant challenge to providers. The purpose of this study was to examine the impact of newly initiated pregabalin or duloxetine treatment on Medicare Advantage Prescription Drug (MAPD) plan pDPN patients' encounters with potential drug-drug interactions, the healthcare cost and utilization consequences of those interactions, and opioid utilization. METHODS: Study subjects required a pregabalin or duloxetine pharmacy claim between 07/01/2008-06/30/2012 (index event), ≥1 inpatient or ≥2 outpatient medical claims with pDPN diagnosis between 01/01/2008-12/31/2012, and ≥12 months pre- and ≥6 post-index enrollment. Propensity score matching was used to balance the pregabalin and duloxetine cohorts on pre-index demographics and comorbidities. Potential DDIs were defined by Micromedex 2.0 and identified by prescription claims. Six-month post-index healthcare utilization (HCU) and costs were calculated using pharmacy and medical claims. RESULTS: No significant differences in pre-index demographics or comorbidities were found between pregabalin subjects (n = 446) and duloxetine subjects (n = 446). Potential DDI prevalence was significantly greater (p < 0.0001) among duoxetine subjects (56.7%) than among pregabalin subjects (2.9%). There were no significant differences in HCU or costs between pregablin subjects with and without a potential DDI. By contrast, duloxetine subjects with a potential DDI had higher mean all-cause costs ($13,908 vs. $9,830; p = 0.001), more subjects with ≥1 inpatient visits (35.6% vs 25.4%; p = 0.02), and more subjects with ≥1 emergency room visits (32.8% vs. 20.7%; p = 0.005) in comparison to duloxetine subjects without a potential DDI. There was a trend toward a difference between pregabalin and duloxetine subjects in their respective pre-versus-post differences in milligrams (mg) of morphine equivalents/30 days used (60.2 mg and 176.9 mg, respectively; p = 0.058). CONCLUSION: The significantly higher prevalence of potential DDIs and potential cost impact found in pDPN duloxetine users, relative to pregabalin users, underscore the importance of considering DDIs when selecting a treatment.

A bacterial type III secretion assay for delivery of fungal effector proteins into wheat.

Large numbers of candidate effectors from fungal pathogens are being identified through whole-genome sequencing and in planta expression studies. Although Agrobacterium-mediated transient expression has enabled high-throughput functional analysis of effectors in dicot plants, this assay is not effective in cereal leaves. Here, we show that a nonpathogenic Pseudomonas fluorescens engineered to express the type III secretion system (T3SS) of P. syringae and the wheat pathogen Xanthomonas translucens can deliver fusion proteins containing T3SS signals from P. syringae (AvrRpm1) and X. campestris (AvrBs2) avirulence (Avr) proteins, respectively, into wheat leaf cells. A calmodulin-dependent adenylate cyclase reporter protein was delivered effectively into wheat and barley by both bacteria. Absence of any disease symptoms with P. fluorescens makes it more suitable than X. translucens for detecting a hypersensitive response (HR) induced by an effector protein with avirulence activity. We further modified the delivery system by removal of the myristoylation site from the AvrRpm1 fusion to prevent its localization to the plasma membrane which could inhibit recognition of an Avr protein. Delivery of the flax rust AvrM protein by the modified delivery system into transgenic tobacco leaves expressing the corresponding M resistance protein induced a strong HR, indicating that the system is capable of delivering a functional rust Avr protein. In a preliminary screen of effectors from the stem rust fungus Puccinia graminis f. sp. tritici, we identified one effector that induced a host genotype-specific HR in wheat. Thus, the modified AvrRpm1:effector-Pseudomonas fluorescens system is an effective tool for large-scale screening of pathogen effectors for recognition in wheat.

Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus.

BACKGROUND: The adult plant stem rust resistance gene Sr2 was introgressed into hexaploid wheat cultivar (cv) Marquis from tetraploid emmer wheat cv Yaroslav, to generate stem rust resistant cv Hope in the 1920s. Subsequently, Sr2 has been widely deployed and has provided durable partial resistance to all known races of Puccinia graminis f. sp. tritici. This report describes the physical map of the Sr2-carrying region on the short arm of chromosome 3B of cv Hope and compares the Hope haplotype with non-Sr2 wheat cv Chinese Spring. RESULTS: Sr2 was located to a region of 867 kb on chromosome 3B in Hope, which corresponded to a region of 567 kb in Chinese Spring. The Hope Sr2 region carried 34 putative genes but only 17 were annotated in the comparable region of Chinese Spring. The two haplotypes differed by extensive DNA sequence polymorphisms between flanking markers as well as by a major insertion/deletion event including ten Germin-Like Protein (GLP) genes in Hope that were absent in Chinese Spring. Haplotype analysis of a limited number of wheat genotypes of interest showed that all wheat genotypes carrying Sr2 possessed the GLP cluster; while, of those lacking Sr2, some, including Marquis, possessed the cluster, while some lacked it. Thus, this region represents a common presence-absence polymorphism in wheat, with presence of the cluster not correlated with presence of Sr2. Comparison of Hope and Marquis GLP genes on 3BS found no polymorphisms in the coding regions of the ten genes but several SNPs in the shared promoter of one divergently transcribed GLP gene pair and a single SNP downstream of the transcribed region of a second GLP. CONCLUSION: Physical mapping and sequence comparison showed major haplotype divergence at the Sr2 locus between Hope and Chinese Spring. Candidate genes within the Sr2 region of Hope are being evaluated for the ability to confer stem rust resistance. Based on the detailed mapping and sequencing of the locus, we predict that Sr2 does not belong to the NB-LRR gene family and is not related to previously cloned, race non-specific rust resistance genes Lr34 and Yr36.

Intramolecular interaction influences binding of the Flax L5 and L6 resistance proteins to their AvrL567 ligands.

L locus resistance (R) proteins are nucleotide binding (NB-ARC) leucine-rich repeat (LRR) proteins from flax (Linum usitatissimum) that provide race-specific resistance to the causal agent of flax rust disease, Melampsora lini. L5 and L6 are two alleles of the L locus that directly recognize variants of the fungal effector AvrL567. In this study, we have investigated the molecular details of this recognition by site-directed mutagenesis of AvrL567 and construction of chimeric L proteins. Single, double and triple mutations of polymorphic residues in a variety of AvrL567 variants showed additive effects on recognition strength, suggesting that multiple contact points are involved in recognition. Domain-swap experiments between L5 and L6 show that specificity differences are determined by their corresponding LRR regions. Most positively selected amino acid sites occur in the N- and C-terminal LRR units, and polymorphisms in the first seven and last four LRR units contribute to recognition specificity of L5 and L6 respectively. This further confirms that multiple, additive contact points occur between AvrL567 variants and either L5 or L6. However, we also observed that recognition of AvrL567 is affected by co-operative polymorphisms between both adjacent and distant domains of the R protein, including the TIR, ARC and LRR domains, implying that these residues are involved in intramolecular interactions to optimize detection of the pathogen and defense signal activation. We suggest a model where Avr ligand interaction directly competes with intramolecular interactions to cause activation of the R protein.