Controlling Candida: immune regulation of commensal fungi in the gut

The intestinal microbiome harbors fungi that pose a significant risk to human health as opportunistic pathogens and drivers of inflammation. Inflammatory and autoimmune diseases are associated with dysbiotic fungal communities and the expansion of potentially pathogenic fungi. The gut is also the main reservoir for disseminated fungal infections. Immune interactions are critical for preventing commensal fungi from becoming pathogenic. Significant strides have been made in defining innate and adaptive immune pathways that regulate intestinal fungi, and these discoveries have coincided with advancements in our understanding of the fungal molecular pathways and effectors involved in both commensal colonization and pathogenesis within the gut. In this review, we will discuss immune interactions important for regulating commensal fungi, with a focus on how specific cell types and effectors interact with fungi to limit their colonization or pathogenic potential. This will include how innate and adaptive immune pathways target fungi and orchestrate antifungal immune responses, in addition to how secreted immune effectors, such as mucus and antimicrobial peptides, regulate fungal colonization and inhibit pathogenic potential. These immune interactions will be framed around our current understanding of the fungal effectors and pathways regulating colonization and pathogenesis within this niche. Finally, we highlight important unexplored mechanisms by which the immune system regulates commensal fungi in the gut.

Effects of empagliflozin on progression of chronic kidney disease: a prespecified secondary analysis from the empa-kidney trial

BACKGROUND

Sodium-glucose co-transporter-2 (SGLT2) inhibitors reduce progression of chronic kidney disease and the risk of cardiovascular morbidity and mortality in a wide range of patients. However, their effects on kidney disease progression in some patients with chronic kidney disease are unclear because few clinical kidney outcomes occurred among such patients in the completed trials. In particular, some guidelines stratify their level of recommendation about who should be treated with SGLT2 inhibitors based on diabetes status and albuminuria. We aimed to assess the effects of empagliflozin on progression of chronic kidney disease both overall and among specific types of participants in the EMPA-KIDNEY trial.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA), and included individuals aged 18 years or older with an estimated glomerular filtration rate (eGFR) of 20 to less than 45 mL/min per 1·73 m2, or with an eGFR of 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher. We explored the effects of 10 mg oral empagliflozin once daily versus placebo on the annualised rate of change in estimated glomerular filtration rate (eGFR slope), a tertiary outcome. We studied the acute slope (from randomisation to 2 months) and chronic slope (from 2 months onwards) separately, using shared parameter models to estimate the latter. Analyses were done in all randomly assigned participants by intention to treat. EMPA-KIDNEY is registered at ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and then followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroups of eGFR included 2282 (34·5%) participants with an eGFR of less than 30 mL/min per 1·73 m2, 2928 (44·3%) with an eGFR of 30 to less than 45 mL/min per 1·73 m2, and 1399 (21·2%) with an eGFR 45 mL/min per 1·73 m2 or higher. Prespecified subgroups of uACR included 1328 (20·1%) with a uACR of less than 30 mg/g, 1864 (28·2%) with a uACR of 30 to 300 mg/g, and 3417 (51·7%) with a uACR of more than 300 mg/g. Overall, allocation to empagliflozin caused an acute 2·12 mL/min per 1·73 m2 (95% CI 1·83-2·41) reduction in eGFR, equivalent to a 6% (5-6) dip in the first 2 months. After this, it halved the chronic slope from -2·75 to -1·37 mL/min per 1·73 m2 per year (relative difference 50%, 95% CI 42-58). The absolute and relative benefits of empagliflozin on the magnitude of the chronic slope varied significantly depending on diabetes status and baseline levels of eGFR and uACR. In particular, the absolute difference in chronic slopes was lower in patients with lower baseline uACR, but because this group progressed more slowly than those with higher uACR, this translated to a larger relative difference in chronic slopes in this group (86% [36-136] reduction in the chronic slope among those with baseline uACR <30 mg/g compared with a 29% [19-38] reduction for those with baseline uACR ≥2000 mg/g; ptrend<0·0001).

INTERPRETATION

Empagliflozin slowed the rate of progression of chronic kidney disease among all types of participant in the EMPA-KIDNEY trial, including those with little albuminuria. Albuminuria alone should not be used to determine whether to treat with an SGLT2 inhibitor.

FUNDING

Boehringer Ingelheim and Eli Lilly.

Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial

BACKGROUND

The EMPA-KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62-0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16-1·59), representing a 50% (42-58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1).

INTERPRETATION

In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease.

FUNDING

Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council.

The impact of CFTR modulator triple therapy on type 2 inflammatory response in patients with cystic fibrosis

BACKGROUND

Treatment of cystic fibrosis (CF) has been revolutionized by the use of cystic fibrosis transmembrane conductance regulator (CFTR) protein modulators such as elexacaftor/tezacaftor/ivacaftor (ETI) triple therapy. Prior studies support a role for type 2 (T2) inflammation in many people with CF (PwCF) and CF-asthma overlap syndrome (CFAOS) is considered a separate clinical entity. It is unknown whether initiation of ETI therapy impacts T2 inflammation in PwCF. We hypothesized that ETI initiation decreases T2 inflammation in PwCF.

METHODS

A single center retrospective chart review was conducted for adult PwCF. As markers of T2 inflammation, absolute eosinophil count (AEC) and total immunoglobulin E (IgE) data were collected longitudinally 12 months prior to ETI therapy initiation and 12 months following therapy initiation. Multivariable analyses adjusted for the age, gender, CFTR mutation, disease severity, inhaled steroid use, and microbiological colonization.

RESULTS

There was a statistically significant reduction (20.10%, p < 0.001) in 12-month mean total IgE following ETI initiation; this change remained statistically significant in the multivariate model. The longitudinal analysis demonstrated no change in AEC following therapy initiation.

CONCLUSION

This study demonstrates that there is a statistically significant percent reduction in mean total IgE but no change in AEC following ETI initiation. ETI may lead to decreased antigen and superantigen load in the airway as a result of improved mucociliary clearance and these changes may drive the decline in total IgE, without influencing the epigenetic drivers of eosinophilic inflammation. Further studies are warranted to determine the underlying mechanism of ETI impact on T2 inflammation and possible role for asthma immunomodulator therapy post ETI initiation in CFAOS.

SAT0409 BIOLOGIC TREATMENT IN PSORIATIC ARTHRITIS AND AXIAL SPONDYLOPATHY REDUCES SICKNOTES ISSUED BY GPS, DESPITE DELAYS IN DIAGNOSIS: A REAL-LIFE STUDY IN WALES

Background:

Seronegative inflammatory arthritis including psoriatic arthritis (PsA) and axial spondyloarthropathies (AxS) are chronic inflammatory diseases associated with significant morbidities. The National Institute of Health and Clinical Excellence (NICE) has produced several pieces of guidance on disease management including the use of biologic therapies which have been shown to improve patient outcomes and quality of life. However, there are limited real-life data on patient journey from symptom onset to diagnosis and treatment including with biologics in the UK.

Objectives:

The purpose of this study is to examine the real-life patient journey from symptom onset to diagnosis and treatment.

Methods:

Data from the Secure Anonymised Information Linkage (SAIL) databank in Wales, which holds over a billion anonymised records, were used to assess the treatment of patients with PsA or AxS, aged 18 years or over with at least one READ code present for PsA or AxS in their primary care records. We examined the drug use of patients across primary, secondary care and specialist rheumatology clinics to explore the use of NSAIDs, DMARDs and biologics in the real-life setting while exploring demographics, comorbidities and surgical procedures of 1829 PsA and 908 AxS patients.

Results:

The AxS patients were significantly younger at diagnosis and were predominantly male. Typical delays in diagnosis of 8-9 years from symptom onset were observed. The rate of stopping or switching a biologic medication was similar for AxS and PsA patients (Table 1). There was a significant reduction in sicknotes issued following biologic initiation for PsA (Difference: 14.6%, 95% CI: 8.7% to 20.4%) and AxS (Difference 16.9%, 95% CI: 10.5% to 23.3%)

Table 1.

Characteristics of treatment of PsA and AxS patients

PsA (n=1829)AxS (n=908)Difference (95% CI)Female (%, n)55.1% (1007)29.1% (264)26 (22.2 to 29.6)*Mean age at diagnosis (years, SD)46.9 (14)43.5 (14.4)3.4 (2.3 to 4.5)*BMI (Index, SD)30.3 (6.3)28 (5.8)2.3 (1.8 to 2.8)*Time from symptom to diagnosis (years, SD)8.9 (5.5)8.0 (5.6)0.9 (0.5 to 1.3)Hypertension at diagnosis (%, n)24.2% (442/1829)19.4% (176/908)4.8 (1.5 to 8.0)*Time from diagnosis to biologic (years, SD)6.3 (4.7)6.1 (5.0)0.2 (-0.9 to 0.5)Used a Biologic (%, n)23% (420/1829)36.8% (334/908)13.8 (10.2 to 17.5)*NSAIDs used pre-biologic (SD)11.3 (3.2)11.6 (3.2)0.3 (-0.2 to 0.8)Number of DMARDs used pre-biologic (SD)3.1 (1.5)2.5 (1.7)0.6 (0.4 to 0.8)*Biologic treatment change/failure (%, n)21.6% (92/425)22% (74/336)0.4 (-6.4 to 5.5)Sicknotes issued by GPᵻpre-biologic (SD)33.9% (144/425)33.6% (113/336)0.3 (-6.5 to 7.0)Sicknotes issued by GPᵻpost-biologic (SD)(%, n)19.3% (82/425)16.7% (56/336)2.6 (-2.9 to 8.0)Hospitalised for serious infection pre- diagnosis (%, n)7.2% (131/1829)6.3% (57/908)0.9 (-1.2 to 2.8)Hospitalised for serious infection post- diagnosis (%, n)10.4% (190/1829)11.6% (105/908)1.2 (-1.3 to 3.8)Hospitalised for serious infection post- biologic (%, n)5.6% (24/425)6.3% (21/336)0.7 (-2.8 to 4.2)

* Significant at p<0.05

ᵻ General practioner/Primary care physician

Conclusion:

Patients with PsA and AxS were treated with NSAIDs and DMARDs prior to receiving biologic medication in accordance with NICE guidelines. However, there was a long delay from symptom onset to diagnosis. Biologic treatment reduced sicknotes issued by GPs confirming the benefit of biologic treatment on work productivity observed in clinical trials.

Acknowledgments:

The work is funded by a Investigator-led grant from Novartis Pharmaceuticals UK Limited

Disclosure of Interests:

Ernest Choy Grant/research support from: Amgen, Bio-Cancer, Chugai Pharma, Ferring Pharmaceuticals, Novimmune, Pfizer, Roche, UCB, Consultant of: AbbVie, Amgen, AstraZeneca, Biogen, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Chelsea Therapeutics, Chugai Pharma, Daiichi Sankyo, Eli Lilly, Ferring Pharmaceuticals, GlaxoSmithKline, Hospita, Ionis, Janssen, Jazz Pharmaceuticals, MedImmune, Merck Sharp & Dohme, Merrimack Pharmaceutical, Napp, Novartis, Novimmune, ObsEva, Pfizer, R-Pharm, Regeneron Pharmaceuticals, Inc., Roche, SynAct Pharma, Sanofi Genzyme, Tonix, UCB, Speakers bureau: Amgen, Boehringer Ingelheim, Bristol-Myers Squibb, Chugai Pharma, Eli Lilly, Hospira, Merck Sharp & Dohme, Novartis, Pfizer, Regeneron Pharmaceuticals, Inc., Roche, Sanofi-Aventis, UCB, Sinead Brophy: None declared, Roxanne Cooksey: None declared, Lindsey Hanson Employee of: Lindsey Hanson is a permanent employee of Novartis Pharmaceuticals UK Limited, Anna Halliday Shareholder of: Anna Halliday owns Novartis share, Employee of: Anna Halliday is a permanent employee of Novartis Pharmaceuticals UK Ltd.

PSVI-3 Estimation of the optimal standardized ileal digestible valine to lysine ratio required for growing-finishing pigs in low crude protein diets

Aim was to determine standardized ileal digestible Val to Lys ratios for growing - finishing pigs fed low CP diets on performance, BUN and carcass characteristics. SID Val to Lys ratios for BW 42.5 to 70.3 kg, 70.3 to 98.1 kg and 98.1 to 128.7 kg pigs. Pigs (n = 400, 10 pens / treatment, 8 pigs / pen) blocked by BW and randomly assigned to 1 of 5 treatments. Diets were SID Val to Lys of 0.55, 0.60, 0.65, 0.70 and 0.75. Data analyzed as a RCBD with PROC MIXED procedure of SAS with pen (experimental unit), treatment (fixed effect), and BW block (random effect). In phase 1, linear and quadratic increase of ADG (Linear, P = 0.03; Quadratic, P = 0.04), BUN decreased (Linear, P = 0.01; Quadratic, P = 0.04). SID Val:Lys for ADG, linear broken-line and quadratic model were 0.64 and 0.66, respectively. BUN for SID Val:Lys were 0.63 (P = 0.01) and 0.70 (P = 0.04). In phase 2, ADG increased (Linear, P = 0.04; Quadratic, P = 0.01) and G:F increased (Linear, P = 0.02; Quadratic, P = 0.04). a linear (P = 0.04) and quadratic (P = 0.01) increase in ADG. SID Val:Lys ADG were 0.66 and 0.70. with the increase of SID Val:Lys ratios. SID Val:Lys for G:F were 0.70 and 0.75, respectively. In phase 3, the SID Val:Lys to maximize ADG were 0.67 (Linear, P = 0.04) and 0.72 (Quadratic, P < 0.01). as the SID Val:Lys increased. Supplementation of low CP diets with high levels of SID Val:Lys increase decreased (Linear, P = 0.02) fat depth, at 0.65. but no effect on other carcass characteristics. In conclusion, SID Val:Lys requirement for ADG in three phases were 0.64, 0.66, 0.67, and 0.66, 0.70, 0.72, using a linear broken-line and quadratic model respectively. BUN and fat thickness appears to be minimized at Val:Lys ratio of 0.65 and a potential to increase lean percentage.

PSV-24 Effects of non-animal protein in nursery diets on wean to finish pig performance and carcass characteristics

The aim of this study was to investigate the effects of a non-animal protein source in nursery diets on performance and carcass characteristics of wean to finish pigs. A total of 432 piglets with initial BW 6.31 ± 0.13 kg were blocked by BW and randomly assigned to 1 of 6 treatments. Treatments included PC1AP1: animal protein, nursery nutrient specifications without additives; PC2AP2: animal protein, growernutrientspecification without additives; NC1NP1: Non-animal protein, nursery specification without additives; NC2NP2: Non-animal protein, grower specification without additives; NC1 NP1 + FA[(Feed Additives)]: NC1 NP1 with additives; NC2 NP2 + FA: NC2 NP2 with additives. Feed Additives [Enzymes (Xylanase, β-Glucanase, Invertaseused), Oregano Essential Oil] were used in Treatments NP1 +FA and NP2 +FA. A linear model was used via the GLM procedure of SAS 9.4, with treatment as fixed effect and block as random effect. Pigs fed on the non-animal protein source and supplemented with feed additives had similar ADF, ADG, and G:F at finishing compared with treatment group on animal protein source (P > 0.05). No treatment differences (P > 0.05) for digesta, liver and serum based on a principal component AA analysis. (P>o.o5)[H2] No positive carry-over effects (P > 0.05) were found for performance except that pigs fed onthe animal protein source had greaterhad greater hot carcass weight (P < 0.05) than the non-animal protein group. In conclusion, wean pigs fed either animal or non-animal protein source at nursery had similar performance at finishing stage and similar carcass characteristics even though pigs on animal protein source had greater hot carcass weight relative to those on plant protein. [H1]Define FA [H2]Do not mention digesta, liver, or serum. Rather state the variables you analyzed in those samples.

A Type 1 Diabetes Genetic Risk Score Predicts Progression of Islet Autoimmunity and Development of Type 1 Diabetes in Individuals at Risk

OBJECTIVE

We tested the ability of a type 1 diabetes (T1D) genetic risk score (GRS) to predict progression of islet autoimmunity and T1D in at-risk individuals.

RESEARCH DESIGN AND METHODS

We studied the 1,244 TrialNet Pathway to Prevention study participants (T1D patients' relatives without diabetes and with one or more positive autoantibodies) who were genotyped with Illumina ImmunoChip (median [range] age at initial autoantibody determination 11.1 years [1.2-51.8], 48% male, 80.5% non-Hispanic white, median follow-up 5.4 years). Of 291 participants with a single positive autoantibody at screening, 157 converted to multiple autoantibody positivity and 55 developed diabetes. Of 953 participants with multiple positive autoantibodies at screening, 419 developed diabetes. We calculated the T1D GRS from 30 T1D-associated single nucleotide polymorphisms. We used multivariable Cox regression models, time-dependent receiver operating characteristic curves, and area under the curve (AUC) measures to evaluate prognostic utility of T1D GRS, age, sex, Diabetes Prevention Trial-Type 1 (DPT-1) Risk Score, positive autoantibody number or type, HLA DR3/DR4-DQ8 status, and race/ethnicity. We used recursive partitioning analyses to identify cut points in continuous variables.

RESULTS

Higher T1D GRS significantly increased the rate of progression to T1D adjusting for DPT-1 Risk Score, age, number of positive autoantibodies, sex, and ethnicity (hazard ratio [HR] 1.29 for a 0.05 increase, 95% CI 1.06-1.6; P = 0.011). Progression to T1D was best predicted by a combined model with GRS, number of positive autoantibodies, DPT-1 Risk Score, and age (7-year time-integrated AUC = 0.79, 5-year AUC = 0.73). Higher GRS was significantly associated with increased progression rate from single to multiple positive autoantibodies after adjusting for age, autoantibody type, ethnicity, and sex (HR 2.27 for GRS >0.295, 95% CI 1.47-3.51; P = 0.0002).

CONCLUSIONS

The T1D GRS independently predicts progression to T1D and improves prediction along T1D stages in autoantibody-positive relatives.

How do low back pain patients conceptualize their expectations regarding treatment? Content analysis of interviews

PURPOSE

The purpose of this study was to gain insight into how low back pain (LBP) patients conceptualize the construct of expectations regarding treatment.

METHODS

This study was nested within a mixed-method randomized clinical trial comparing three primary care interventions for LBP. A total of 77 participants with LBP lasting longer than 6 weeks were included; semi-structured interviews were conducted querying patients about their expectations for treatment. Also factors influencing their expectations were explored. Interviews were administered following enrollment into the study, but prior to study treatment. Two researchers independently conducted a content analysis using NVIVO 9 software.

RESULTS

LBP patients' expectations could be categorized in two main domains: outcome and process expectations, each with subdomains. Patients expressed expectations in all subdomains both as values (what they hoped) and probabilities (what they thought was likely). In multiple subdomains, there were differences in the nature (positive vs. negative) and frequency of value and probability expectations. Participants reported that multiple factors influenced their expectations of which past experience with treatment appeared to be of major influence on probability expectations.

CONCLUSION AND RECOMMENDATIONS

This study showed that LBP patients' expectations for treatment are multifaceted. Current measurement instruments do not cover all domains and subdomains of expectations. Therefore, we recommend the development of new or improved measures that make a distinction between value and probability expectations and assess process and/or outcome expectations covering multiple subdomains. Some of the influencing factors found in this study may be useful targets for altering patients' treatment expectations and improving health outcomes.

Advantage of rapamycin over mycophenolate mofetil when used with tacrolimus for simultaneous pancreas kidney transplants: randomized, single-center trial at 10 years

Simultaneous pancreas kidney transplantation (SPKT) is the treatment of choice for patients with type 1 diabetes and end-stage renal disease. Rapamycin and mycophenolate mofetil (MMF) have been used for maintenance immunosuppression with tacrolimus in SPKT; however, long-term outcomes are lacking. From September 2000 through December 2009, 170 SPKT recipients were enrolled in a randomized, prospective trial receiving Rapamycin (n = 84) or MMF (n = 86). All patients received dual induction therapy with thymoglobulin and daclizumab, and low-dose maintenance tacrolimus and corticosteroids. Compared to MMF, rates of freedom from first biopsy-proven acute kidney or pancreas rejection were superior for Rapamycin at year 1 (kidney: 100% vs. 88%; P = 0.001; pancreas: 99% vs. 92%; P = 0.04) and at year 10 (kidney: 88% vs. 71%, P = 0.01; pancreas: 99% vs. 89%, P = 0.01). The higher rates of rejection were associated with withholding MMF (vs. Rapamycin, p = 0.009), generally for gastrointestinal or bone marrow toxicity. There was no significant difference in creatinine, proteinuria, c-peptide, viral infections, lymphoproliferative disorders or posttransplant diabetes. HbA1C and lipid levels were normal in both groups, although higher in the Rapamycin arm. There were no significant differences in patient or allograft survival. In this 10-year SPKT study, Rapamycin in combination with tacrolimus was better tolerated and more effective than MMF. Overall, the patient and allograft survival were equivalent.

First Report of Fusarium torulosum Causing Dry Rot of Seed Potato Tubers in the United States

Fusarium dry rot of potato (Solanum tuberosum L.) is a postharvest disease caused by several Fusarium species and is of worldwide importance. Thirteen species of Fusarium have been implicated in fungal dry rots of potatoes worldwide. Among them, eight species have been reported in the northern United States (2). In Michigan potato production, F. sambucinum was the predominant species reported to be affecting seed potato in storage and causing seed piece decay after planting (3). Some previous identifications of F. sambucinum as dry rot may have been F. torulosum since F. torulosum was previously classified within F. sambucinum (4). To further investigate this, dry rot symptomatic tubers were collected from Michigan seed lots in the summers of 2009 and 2010. Small sections from the margins of necrotic regions were cut with a scalpel, surface sterilized in 0.5% sodium hypochlorite for 10 s, rinsed twice in sterile distilled water, and blotted with sterile filter paper. The tissue pieces were plated on half-strength potato dextrose agar (PDA) amended with 0.5 g/liter of streptomycin sulfate and incubated at 23°C for 5 to 7 days. Cultures resembling Fusarium species were transferred onto water agar, and single hyphal tips from actively growing isolates were removed and plated either on carnation leaf agar (CLA) or on half-strength PDA to generate pure cultures. Among the Fusarium isolates obtained, five isolates were identified as F. torulosum (GenBank Accessions Nos. JF803658-JF803660). Identification was based on colony and conidial morphology on PDA and CLA, respectively. These features included slow growth (2.8 ± 0.2 cm in 5 days), white mycelium that became pigmented with age, narrow concentric rings, red or white pigmentation on agar, macroconidia (32.4 ± 0.4 μm average length) with five septa, a pointed apical cell, and a foot-shaped basal cell (4). The identity was confirmed through DNA extraction followed by amplification and sequencing of the translation elongation factor (EF-1α) gene region (1). The Fusarium-ID.v (1) and the NCBI database were used to obtain the closest match (99%) to previously sequenced materials (GenBank Accession No. AJ543611). Pathogenicity testing was done on disease-free potato tubers cv. Red Norland. Tubers were surface sterilized for 10 min in 0.5% sodium hypochlorite and rinsed twice in distilled water. Three tubers per isolate were injected with 20 μl of a conidial suspension (10⁶ conidia/ml) made from F. torulosum cultures grown on PDA for 7 to 10 days. Control tubers were injected with 20 μl of sterile distilled water. All tubers inoculated with F. torulosum developed typical potato dry rot symptoms consisting of a brown and dry decay. There was no disease incidence on the control tubers. F. torulosum was reisolated from the symptomatic tubers. To our knowledge, this is the first report of F. torulosum causing potato dry rot in the United States. References: (1) D. Geiser et al. Eur. J. Plant Pathol. 110:473, 2004. (2) L. E. Hanson et al. Phytopathology 86:378, 1996. (3) M. L. Lacy and R. Hammerschmidt. Fusarium dry rot. Extension Bulletin. Retrieved from http://web1.msue.msu.edu/msue/iac/onlinepubs/pubs/E/E2448POT , 23 May 2010. (4) J. F. Leslie and B. A. Summerell. The Fusarium Laboratory Manual. Wiley-Blackwell, Hoboken, NJ, 2006.

First Report of in vitro Fludioxonil-Resistant Isolates of Fusarium spp. Causing Potato Dry Rot in Michigan

Fusarium dry rot of potato (Solanum tuberosum) is a postharvest disease caused by several Fusarium spp. Dry rot is managed primarily by reducing tuber bruising and promoting rapid wound healing. Dry rot symptomatic tubers were collected from Michigan seed lots in 2009 and 2010. The isolates may not have been exposed to fludioxonil because currently applications are restricted to seed not intended for seed production (3). Small sections were cut from the margins of necrotic regions with a scalpel, surface sterile in 10% sodium hypochlorite for 10 s, rinsed twice in sterile distilled water, and blotted with sterile filter paper. The tissue pieces were plated on half-strength potato dextrose agar (PDA) amended with 0.5 g/liter of streptomycin sulfate. The dishes were incubated at 23°C for 5 to 7 days. Cultures resembling Fusarium spp. were transferred onto water agar and hyphal tips from the margin of actively growing isolates were removed with a sterile probe and plated either on carnation leaf agar (CLA) or on half-strength PDA to generate pure cultures. Fusarium isolates were obtained and used for further studies. Among them, 54 were identified as Fusarium oxysporum and 23 as F. sambucinum. Identification was based on colony and conidial morphology on PDA and CLA, respectively. The identity was confirmed through DNA extraction followed by amplification and sequencing of the translation elongation factor (EF-1α) gene region. The Fusarium-ID v. (2) and the NCBI database were used to obtain the closest match to previously sequenced materials. Pathogenicity testing was done on disease-free potato tubers, cv. FL 1879. Tubers were surface sterilized for 10 min in 10% sodium hypochlorite and rinsed twice in distilled water. Three tubers per isolate were injected with 20 μl of a conidial suspension (10⁶ conidia/ml) made from cultures grown on PDA for 7 days. Control tubers were injected with 20 μl of sterile distilled water. All tubers inoculated with F. sambucinum and F. oxysporum developed typical potato dry rot symptoms consisting of dry brown decay lesions. F. sambucinum and F. oxysporum were reisolated from all symptomatic tubers. An effective concentration for 50% reduction in growth (EC₅₀) was determined for each F. sambucinum and F. oxysporum isolate for thiabendazole (TBZ), fludioxonil, and difenoconazole using the spiral gradient endpoint method (1). Sensitive and resistant F. sambucinum and F. oxysporum isolates were reported. Fifteen isolates of F. sambucinum and thirty-four of F. oxysporum were resistant to fludioxonil with EC₅₀ greater than 130 mg/liter. The remainder was sensitive to fludioxonil with EC₅₀ ranging from 0.8 to 4.9 mg/liter. To our knowledge, this is the first report of resistance to fludioxonil in isolates of F. sambucinum and F. oxysporum in Michigan. Fusarium insensitivity in laboratory studies may not translate directly to commercial production. This disparity may result from interactions not experienced in mixed populations or within a living host. There has been no compelling evidence to suggest that fludioxonil has failed to perform because of insensitivity to Fusarium. The occurrence of such isolated strains necessitates the development and registration of partner chemistries that can preempt any future concerns on lack of performance of products in use. References: (1) H. Förster et al. Phytopathology 94:163, 2004. (2) D. Geiser et al. Eur. J. Plant Pathol. 110:473, 2004. (3) R. D. Peters et al. Plant Dis. 92:172, 2008.

Genome size diversity in orchids: consequences and evolution

BACKGROUND

The amount of DNA comprising the genome of an organism (its genome size) varies a remarkable 40 000-fold across eukaryotes, yet most groups are characterized by much narrower ranges (e.g. 14-fold in gymnosperms, 3- to 4-fold in mammals). Angiosperms stand out as one of the most variable groups with genome sizes varying nearly 2000-fold. Nevertheless within angiosperms the majority of families are characterized by genomes which are small and vary little. Species with large genomes are mostly restricted to a few monocots families including Orchidaceae.

SCOPE

A survey of the literature revealed that genome size data for Orchidaceae are comparatively rare representing just 327 species. Nevertheless they reveal that Orchidaceae are currently the most variable angiosperm family with genome sizes ranging 168-fold (1C = 0.33-55.4 pg). Analysing the data provided insights into the distribution, evolution and possible consequences to the plant of this genome size diversity.

CONCLUSIONS

Superimposing the data onto the increasingly robust phylogenetic tree of Orchidaceae revealed how different subfamilies were characterized by distinct genome size profiles. Epidendroideae possessed the greatest range of genome sizes, although the majority of species had small genomes. In contrast, the largest genomes were found in subfamilies Cypripedioideae and Vanilloideae. Genome size evolution within this subfamily was analysed as this is the only one with reasonable representation of data. This approach highlighted striking differences in genome size and karyotype evolution between the closely related Cypripedium, Paphiopedilum and Phragmipedium. As to the consequences of genome size diversity, various studies revealed that this has both practical (e.g. application of genetic fingerprinting techniques) and biological consequences (e.g. affecting where and when an orchid may grow) and emphasizes the importance of obtaining further genome size data given the considerable phylogenetic gaps which have been highlighted by the current study.

Expression profiles of cloned channel catfish (Ictalurus punctatus) lymphoid cell lines and mixed lymphocyte cultures

Clonal channel catfish lymphoid cell lines and mixed lymphocyte cultures (MLCs) have proven extremely useful in examining immune responses at the cellular and molecular levels. To date clonal catfish cell lines and MLCs have been biologically and phenotypically characterized using a variety of techniques including reverse transcription polymerase chain reaction (RT-PCR), as well as Northern and Southern blotting. To expand the molecular characterization of these cultures, microarray analysis was employed. Clonal B (3B11), macrophage (42TA), and cytotoxic T cell (TS32.15 and TS32.17) lines and MLCs were examined using a cDNA array containing approximately 2500 probes derived from EST libraries prepared from the 42TA macrophage cell line, a MLC, and 5-14-day-old catfish fry. Analysis showed that each cell line displayed a unique RNA expression profile that included a variety of immune-related genes. Pearson correlation analysis indicated that one cytotoxic T cell line (TS32.15) clustered with the MLC, whereas a second cytotoxic T cell line (TS32.17) was more closely associated with a second cluster containing B cells and macrophages. This study illustrates the utility of microarray analyses in profiling RNA expression patterns in catfish lymphoid cell lines and will serve as a platform for examining catfish immune responses following virus infection or poly [I:C] treatment.

The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae)

BACKGROUND

In studies looking at individual polyploid species, the most common patterns of genomic change are that either genome size in the polyploid is additive (i.e. the sum of parental genome donors) or there is evidence of genome downsizing. Reports showing an increase in genome size are rare. In a large-scale analysis of 3008 species, genome downsizing was shown to be a widespread biological response to polyploidy. Polyploidy in the genus Nicotiana (Solanaceae) is common with approx. 40 % of the approx. 75 species being allotetraploid. Recent advances in understanding phylogenetic relationships of Nicotiana species and dating polyploid formation enable a temporal dimension to be added to the analysis of genome size evolution in these polyploids.

METHODS

Genome sizes were measured in 18 species of Nicotiana (nine diploids and nine polyploids) ranging in age from <200,000 years to approx. 4.5 Myr old, to determine the direction and extent of genome size change following polyploidy. These data were combined with data from genomic in situ hybridization and increasing amounts of information on sequence composition in Nicotiana to provide insights into the molecular basis of genome size changes.

KEY RESULTS AND CONCLUSIONS

By comparing the expected genome size of the polyploid (based on summing the genome size of species identified as either a parent or most closely related to the diploid progenitors) with the observed genome size, four polyploids showed genome downsizing and five showed increases. There was no discernable pattern in the direction of genome size change with age of polyploids, although with increasing age the amount of genome size change increased. In older polyploids (approx. 4.5 million years old) the increase in genome size was associated with loss of detectable genomic in situ hybridization signal, whereas some hybridization signal was still detected in species exhibiting genome downsizing. The possible significance of these results is discussed.

Punctuated genome size evolution in Liliaceae

Most angiosperms possess small genomes (mode 1C = 0.6 pg, median 1C = 2.9 pg). Those with truly enormous genomes (i.e. > or = 35 pg) are phylogenetically restricted to a few families and include Liliaceae - with species possessing some of the largest genomes so far reported for any plant as well as including species with much smaller genomes. To gain insights into when and where genome size expansion took place during the evolution of Liliaceae and the mode and tempo of this change, data for 78 species were superimposed onto a phylogenetic tree and analysed. Results suggest that genome size in Liliaceae followed a punctuated rather than gradual mode of evolution and that most of the diversification evolved recently rather than early in the evolution of the family. We consider that the large genome sizes of Liliaceae may have emerged passively rather than being driven primarily by selection.

Waves in interplanetary shocks: a wind/WAVES study

We describe results from the first statistical study of waveform capture data during 67 interplanetary (IP) shocks with Mach numbers ranging from approximately 1-6. Most of the waveform captures and nearly 100% of the large amplitude waves were in the ramp region. Although solitary waves, Langmuir waves, and ion acoustic waves (IAWs) are all observed in the ramp region of the IP shocks, large amplitude IAWs dominate. The wave amplitude is correlated with the fast mode Mach number and with the shock strength. The observed waves produced anomalous resistivities from approximately 1-856 Omega.m (approximately 10(7) times greater than classical estimates.) The results are consistent with theory suggesting IAWs provide the primary dissipation for low Mach number shocks.

Effect of drivers' age and push button locations on visual time off road, steering wheel deviation and safety perception

The study examined the effects of manual control locations on two groups of randomly selected young and old drivers in relation to visual time off road, steering wheel deviation and safety perception. Measures of visual time off road, steering wheel deviations and safety perception were performed with young and old drivers during real traffic. The results showed an effect of both driver's age and button location on the dependent variables. Older drivers spent longer visual time off road when pushing the buttons and had larger steering wheel deviations. Moreover, the greater the eccentricity between the normal line of sight and the button locations, the longer the visual time off road and the larger the steering wheel deviations. No interaction effect between button location and age was found with regard to visual time off road. Button location had an effect on perceived safety: the further away from the normal line of sight the lower the rating.

Epithelial cells as phagocytes: apoptotic epithelial cells are engulfed by mammary alveolar epithelial cells and repress inflammatory mediator release

Clearance of apoptotic cells is critical to tissue homeostasis and resolution of inflammatory lesions. Macrophages are known to remove dying cells and release anti-inflammatory mediators in response; however, many cells traditionally thought of as poor phagocytes can mediate this function as well. In the lactating mammary gland following weaning, alveolar epithelial cell death is massive, yet the gland involutes rapidly, attaining its prepregnancy state in a matter of days. We found histologic evidence of apoptotic cell phagocytosis by viable mammary epithelial cells (MEC) in the involuting mouse mammary gland. Cultured MEC were able to engulf apoptotic cells in vitro, utilizing many of the same receptors used by macrophages, including the phosphatidylserine receptor (PSR), CD36, the vitronectin receptor alpha(v)beta3, and CD91. In addition, MEC, like macrophages, produced TGFbeta in response to stimulation of the PSR by apoptotic cells or the anti-PSR ab 217G8E9, and downregulated endotoxin-stimulated proinflammatory cytokine production. These data support the hypothesis that amateur phagocytes play a significant role in apoptotic cell clearance and its regulation of inflammation.

Genomic relationships among diploid and hexaploid species of Andropogon (Poaceae)

Andropogon is a pantropical grass genus comprising 100-120 species and found mainly in the grasslands of Africa and the Americas. While the genomic relationships between many Andropogon species have been resolved by studying chromosome behavior in interspecific hybrids, relationships between the North and South American diploids have remained elusive. Further, the genome composition of two hexaploid species (including the important forage grass Andropogon lateralis Nees) has been unclear because of the strong hybridization barriers that exist between species. Consequently, genomic in situ hybridization was applied to shed light on these issues. The results confirmed that (i) both the South American (Andropogon selloanus (Hack.) Hack., Andropogon macrothrix Trin.) and North American (Andropogon gyrans Michx.) diploid species shared a common S genome and (ii) the S genome comprises just one of the three genomes in the hexaploids A. lateralis Nees and Andropogon bicornis L. The evolutionary and taxonomic implications of these findings are discussed.

Effect of button location on driver's visual behaviour and safety perception

Although buttons are a frequently used type of control in car interiors, little research has been undertaken on how the usage of buttons affects the visual behaviour of the driver. In this study, the aim was to analyse the effect of push button location and auditory feedback on drivers' visual time off road and safety perception when driving in a real traffic situation. The effect of six button locations (five on the centre stack, one near the gear stick) was tested. Drivers' visual behaviour was studied in real traffic on a motorway. An eye tracking system recorded the visual behaviour of eight drivers who, in 96 repeated trials each, were instructed to press a specific button. Data analysis focused on the drivers' visual time off road and safety perception in relation to the location of the button to be pressed. Auditory feedback did not show a significant effect on visual time off road. The time off road increased significantly as the angle increased between the normal line of sight and button location for the five buttons placed on the centre stack. Results for the button located close to the gear stick, with the highest eccentricity, produced a short time off road. This unexpected finding is discussed in terms of three potential explanations: 1) the role of perceptual discrimination; 2) risk perception; and 3) motor control.

Dogmas and controversies in the handling of nitrogenous wastes: ammonia tolerance in the oriental weatherloach Misgurnus anguillicaudatus

The oriental weatherloach Misgurnus anguillicaudatus is an extremely ammonia-tolerant fish. Many ammonia-protection mechanisms have been reported in this fish. Six strategies used by this fish to deal with the problem of excess ammonia are described. The fish can (1) reduce ammonia production through reduction in protein and/or amino acid catabolism; (2) reduce ammonia production and obtain energy through partial amino acid catabolism leading to alanine formation; (3) detoxify ammonia to glutamine; (4) tolerate very high ammonia levels in its tissues; (5) get rid of ammonia as NH(3) gas and, probably, (6) possesses background K(+) channels that are impermeable to NH(4)(+). The effects of extracellular ammonia on the contraction performance of the heart from this fish were found to be the same as in rainbow trout, an ammonia-sensitive fish. It suggests that the hearts of most, if not all, fish species are protected against ammonia. MK-801, an NMDA receptor blocker, was found to have a protective effect against ammonia intoxication in the oriental weatherloach, which suggests that the NMDA receptor, as in mammals, is involved in ammonia toxicity.