Reporting Charcoal Rot in Chia and Developing a Susceptibility Assay

Chia (Salvia Hispanica) cross breeds were planted in the summer of 2018 with the intent of selective breeding for agricultural benefit. Preexisting pathogens in the soil caused 40-50% fatality of adult plants. This was surprising due to the precursory knowledge that chia has antibiotic and antifungal oils (Elshafie et. al. 2018); chia was only recently documented to be susceptible to Fusarium wilt (Fusarium oxysporum). The primary pathogen responsible was identified as Macrophomina phaseolina (aka charcoal rot); a widespread soilborne pathogen which has multiple commercial hosts (Su et. al. 2001). M. phaesolina on wheat seed vector where used as inoculums (Brandari 2017) for chia to evaluate disease progression and symptoms in chia. Samples of this trial produced M. phaseolina from diseased chia tissues confirming susceptibility to M. phaseolina; in addition carefully sampled root and stem fractions identified the pathology of fungus from root to stem. The two parental varieties of the cross, chia-Pinta and chia-Tropic continue to be compared for their disease resistance to M. phaseolina. Identifying disease resistant genes allows for breeding of resistant cultivars, improving the marketability of chia

Simultaneous aortic and renal artery reconstruction: Evolution of an eighteen-year experience

AbstractPurpose: We reviewed an 18-year experience with combined abdominal aortic and renal artery reconstruction (AOR) with a particular focus on patients' clinical risk profile and surgical results in contemporary practice as compared with earlier experience.Methods: One hundred seventy patients underwent AOR during the interval January 1, 1976 to June 30, 1994. To examine parameters representative of current practice, the cohort was divided into group I patients (n = 110) treated before 1990 and group II (n = 60) treated between 1990 and 1994. Median follow-up duration for the entire cohort was 8.4 ± 0.6 years. Renal artery reconstruction patency and patient survival rates were calculated by life-table methods. Logistic and Cox regression analysis were used to determine predictors of perioperative and long-term morbidity/mortality rates.Results: Although demographic features changed little over the review period, the detection (56% vs 73%, p = 0.03) and treatment with percutaneous transluminal coronary angioplasty/coronary artery bypass grafting (11% vs 40%, p = 0.0001) of associated coronary artery disease were more frequent in group II versus group I patients. Alternatively, renal insufficiency was more frequent in group I patients. The operative mortality rate for the entire cohort was 6.5% (group I = 9% vs group II = 2%, p = 0.06). Changing trends of surgical techniques over the review period included (group I vs II, respectively) increased use of bilateral simultaneous renal artery repair (12% vs 25%, p < 0.005) and transaortic endarterectomy as the renal artery reconstruction technique (3% vs 25%, p < 0.0001). Favorable response in blood pressure control was noted in 68% of group II patients. The cumulative 5-year survival rate for all patients was 75% with an initial serum creatinine of 2.0 mg/dl or greater being the only negative predictor of late survival after regression analysis.Conclusion: The current operative mortality rate for AOR is in the range anticipated for aortic surgery alone, and this appears to be related to improved detection and treatment of associated coronary artery disease and intervention before major deterioration in renal function. These findings coupled with currently available natural history data relative to renovascular disease justify an aggressive approach with AOR when significant renal artery stenosis is detected during evaluation of aortic disease. (J VASC SURG 1995;21:916-25.

Renal artery reconstruction for the preservation of renal function

AbstractPurpose: We reviewed a 13-year experience with an emphasis on long-term survival and renal function response when renal artery reconstruction (RAR) was performed primarily for the preservation or restoration of renal function in patients who had atherosclerotic renovascular disease.Methods: From January 1, 1980, to June 30, 1993, 139 patients underwent RAR for renal function salvage and were retrospectively reviewed. Inclusion criteria were either preoperative serum creatinine level >2.0 mg/dl (67% of patients) or RAR to the entire functioning renal mass irrespective of baseline renal function. Patient survival was calculated by life-table methods. Cox regression analysis was used to determine relative risk (RR) estimates for the late outcomes of continued deterioration of renal function and late survival after RAR. A logistic regression model was used to evaluate variables associated with perioperative complications.Results: Clinical characteristics of the cohort were notable for advanced cardiac (history of congestive heart failure, 27%; angina, 22%; previous myocardial infarction, 19%) and renal disease (serum creatinine level <2.0 mg/dl, 33%; 2.0 mg/dl to 3.0 mg/dl, 40%, >3.0 mg/dl, 27%). Cardiac disease was the principle cause of early (6 of 11 operative deaths) and late death. Operative management consisted of aortorenal bypass in 47%, extraanatomic bypass in 45%, and endarterectomy in 8%; 45% of patients required combined aortic and RAR. The operative mortality rate was 8%; significant perioperative renal dysfunction occurred in 10%. Major operative morbidity was associated with increasing azotemia (RR = 2.1; p = 0.001; 95% confidence interval [CI], 1.3 to 4.7 for each 1.0 mg/dl increase in baseline creatinine level). Of those patients who had a baseline creatinine level ≥2.0 mg/dl, 54% had ≥20% reduction in creatinine level after RAR. Late follow-up data were available for 87% of operative survivors at a mean duration of 4 years (range, 6 weeks to 12.6 years). Actuarial survival at 5 years was 52% ± 5%. Continued deterioration in renal function occurred in 24% of patients who survived operation, and eventual dialysis was required in 15%. Deterioration of renal function after RAR was associated with increasing levels of preoperative creatinine (RR = 1.6; 95% CI, 1.2 to 1.8; p = 0.001 for each 1.0 mg/dl increment in baseline creatinine level), and inversely related to early postoperative improvement in creatinine level (RR = 0.41; 95% CI, 0.2 to 0.9; p = 0.04).Conclusions: Intervention before major deterioration in renal function and an aggressive posture toward the frequently associated coronary artery disease are necessary to improve long-term results when RAR is performed for renal function salvage. (J Vasc Surg 1996;24:371-82.

Full characterization of vibrational coherence in a porphyrin chromophore by two-dimensional electronic spectroscopy

In this work we present experimental and calculated two-dimensional electronic spectra for a 5,15-bisalkynyl porphyrin chromophore. The lowest energy electronic Qy transition couples mainly to a single 380 cm–1 vibrational mode. The two-dimensional electronic spectra reveal diagonal and cross peaks which oscillate as a function of population time. We analyze both the amplitude and phase distribution of this main vibronic transition as a function of excitation and detection frequencies. Even though Feynman diagrams provide a good indication of where the amplitude of the oscillating components are located in the excitation-detection plane, other factors also affect this distribution. Specifically, the oscillation corresponding to each Feynman diagram is expected to have a phase that is a function of excitation and detection frequencies. Therefore, the overall phase of the experimentally observed oscillation will reflect this phase dependence. Another consequence is that the overall oscillation amplitude can show interference patterns resulting from overlapping contributions from neighboring Feynman diagrams. These observations are consistently reproduced through simulations based on third order perturbation theory coupled to a spectral density described by a Brownian oscillator model

Immunity and other defenses in pea aphids, Acyrthosiphon pisum

The genome of the pea aphid Acyrthosiphon pisum lacks genes thought to be crucial in other insects for recognition, signaling and killing of microbes

FRUITFULL controls SAUR10 expression and regulates Arabidopsis growth and architecture

[EN] MADS-domain transcription factors are well known for their roles in plant development and regulate sets of downstream genes that have been uncovered by high-throughput analyses. A considerable number of these targets are predicted to function in hormone responses or responses to environmental stimuli, suggesting that there is a close link between developmental and environmental regulators of plant growth and development. Here, we show that the Arabidopsis MADS-domain factor FRUITFULL (FUL) executes several functions in addition to its noted role in fruit development. Among the direct targets of FUL, we identified SMALL AUXIN UPREGULATED RNA 10 (SAUR10), a growth regulator that is highly induced by a combination of auxin and brassinosteroids and in response to reduced R:FR light. Interestingly, we discovered that SAUR10 is repressed by FUL in stems and inflorescence branches. SAUR10 is specifically expressed at the abaxial side of these branches and this localized activity is influenced by hormones, light conditions and by FUL, which has an effect on branch angle. Furthermore, we identified a number of other genes involved in hormone pathways and light signalling as direct targets of FUL in the stem, demonstrating a connection between developmentally and environmentally regulated growth programs.We thank Arjo Meijering for assistance with the light measurements, Niek Stortenbeker for contributions to the manuscript, and Ueli Grossniklaus (University of Zurich) for financial and technical support. MB was supported by the Dutch Organization for Scientific research (NWO) in the framework of the ERA-NET on Plant Genomics (ERA-PG) program project CISCODE and by an NWO Veni-grant. In part, this work was performed in Ueli Grossniklaus' laboratory at the University of Zurich with support through an EMBO LT Fellowship to MB and a grant from the Swiss National Science Foundation to Ueli Grossniklaus. HM was supported by an NWO Vidi-grant, granted to KK.Bemer, M.; Van Mourik, H.; Muiño, JM.; Ferrandiz Maestre, C.; Kaufmann, K.; Angenent, G. (2017). FRUITFULL controls SAUR10 expression and regulates Arabidopsis growth and architecture. Journal of Experimental Botany. 68(13):3391-3403. https://doi.org/10.1093/jxb/erx184S33913403681

The severity of pandemic H1N1 influenza in the United States, from April to July 2009: A Bayesian analysis

Background: Accurate measures of the severity of pandemic (H1N1) 2009 influenza (pH1N1) are needed to assess the likely impact of an anticipated resurgence in the autumn in the Northern Hemisphere. Severity has been difficult to measure because jurisdictions with large numbers of deaths and other severe outcomes have had too many cases to assess the total number with confidence. Also, detection of severe cases may be more likely, resulting in overestimation of the severity of an average case. We sought to estimate the probabilities that symptomatic infection would lead to hospitalization, ICU admission, and death by combining data from multiple sources. Methods and Findings: We used complementary data from two US cities: Milwaukee attempted to identify cases of medically attended infection whether or not they required hospitalization, while New York City focused on the identification of hospitalizations, intensive care admission or mechanical ventilation (hereafter, ICU), and deaths. New York data were used to estimate numerators for ICU and death, and two sources of data - medically attended cases in Milwaukee or self-reported influenza-like illness (ILI) in New York - were used to estimate ratios of symptomatic cases to hospitalizations. Combining these data with estimates of the fraction detected for each level of severity, we estimated the proportion of symptomatic patients who died (symptomatic case-fatality ratio, sCFR), required ICU (sCIR), and required hospitalization (sCHR), overall and by age category. Evidence, prior information, and associated uncertainty were analyzed in a Bayesian evidence synthesis framework. Using medically attended cases and estimates of the proportion of symptomatic cases medically attended, we estimated an sCFR of 0.048% (95% credible interval [CI] 0.026%-0.096%), sCIR of 0.239% (0.134%-0.458%), and sCHR of 1.44% (0.83%-2.64%). Using self-reported ILI, we obtained estimates approximately 7-96lower. sCFR and sCIR appear to be highest in persons aged 18 y and older, and lowest in children aged 5-17 y. sCHR appears to be lowest in persons aged 5-17; our data were too sparse to allow us to determine the group in which it was the highest. Conclusions: These estimates suggest that an autumn-winter pandemic wave of pH1N1 with comparable severity per case could lead to a number of deaths in the range from considerably below that associated with seasonal influenza to slightly higher, but with the greatest impact in children aged 0-4 and adults 18-64. These estimates of impact depend on assumptions about total incidence of infection and would be larger if incidence of symptomatic infection were higher or shifted toward adults, if viral virulence increased, or if suboptimal treatment resulted from stress on the health care system; numbers would decrease if the total proportion of the population symptomatically infected were lower than assumed.published_or_final_versio

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems

Circadian regulation of hormone signaling and plant physiology

The survival and reproduction of plants depend on their ability to cope with a wide range of daily and seasonal environmental fluctuations during their life cycle. Phytohormones are plant growth regulators that are involved in almost every aspect of growth and development as well as plant adaptation to myriad abiotic and biotic conditions. The circadian clock, an endogenous and cell-autonomous biological timekeeper that produces rhythmic outputs with close to 24-h rhythms, provides an adaptive advantage by synchronizing plant physiological and metabolic processes to the external environment. The circadian clock regulates phytohormone biosynthesis and signaling pathways to generate daily rhythms in hormone activity that fine-tune a range of plant processes, enhancing adaptation to local conditions. This review explores our current understanding of the interplay between the circadian clock and hormone signaling pathways