Analysis of AFLP Markers for Screening Resistance to Common Bean Roots Rot (Pythium spp.)

Aims: To investigate AFLPs for suitability as potential markers for identification of sources of Pythium resistance in bean genotypes preferred by poor small holder farmers. Place and Duration of Study: Department of biological sciences Masinde Muliro University of Science and Technology, Kenya and Bangor University, North Wales, United Kingdom, between September 2010 and December 2012. Methodology: 45 common bean accessions comprising 35 seed samples collected from farmers, market centers, as well as seed stockists and ten common bean lines generated from a conventional breeding program with differential resistance to the pathogen Pythium were subjected to AFLP analysis. Genetic characterization using cluster and principal component analysis were conducted to determine segregating patterns of bean accessions in relation to tolerant and Original Research Article Maryrose et al.; AJEA, 5(4): 374-391, 2015; Article no.AJEA.2015.039 375 susceptible bean lines. Average genetic distances were calculated and similarity coefficients subjected to unweighted pair group method of arithmetic averages to generate dendograms. Results: Two informative AFLP primer combinations yielded 194 polymorphic loci. Genetic distance of bean samples from KARI Kakamega had 56 to 414 base pairs with a variability index of 0.63 to 0.90. Combined analysis of bean accessions from KARI breeding program and market class common bean samples revealed a variability index range of 0.62 to 0.90 with 56 to 420 base pairs. PCA contributed about 51.58% on the genetic variation. Cluster analysis of the 10 KARI-Kakamega bean lines revealed that resistant bean varieties were genetically different from the susceptible bean varieties. The dendogram generated revealed four sub-groups and with the exception of Alulu, a mildly resistant cultivar, that segregated alongside resistant cultivars, resistant varieties clustered differently from susceptible cultivars. However, screening with farmers’ germplasm produced a dendogram that revealed a mixture of distinct and relatively non-distinct categorization with regard to resistance. Only resistant cultivars AN1062, R2075, R719 and R1946 and susceptible cultivars GLP2 and GLP585 clustered together as expected. The others segregated randomly alongside the farmers’ germplasm. Resistant varieties AND1062, R2075, R719, R1946 and SCAM80 were more genetically related to marketable class of beans. R1946 R719, R2075 and AND1062 are closely related genetically compared to Mw001, KK15, Alulu and GLP2. Conclusion: AFLP is a relatively informative technique that has a great potential of delineating susceptible and resistant Pythium root rot dry bean varieties, and can be used as a preliminary guide to carry out further analysis. It is notable that the AFLP markers used were not able to clearly distinguish all the cultivars comprehensively and should not be used alone in determining resistance levels. The information generated in this study will contribute to the propagation of acceptable market class bean lines with resistance to Pythium root rot for improved livelihood and increased food securit

Genetic Diversity of Dry Bean (Phaseolus vulgaris L.) Accessions of Kenya Using SSR Markers

Aims: To determine the genetic diversity existing within the Kenyan dry bean using SSR markers. Place and Duration of Study: This study was conducted in Western Kenya and Bangor University, North Wales, between September 2010 and December 2012.Methodology: Thirty five (35) marketable dry bean samples collected from farmers, market centers as well as seed stockists were subjected to SSR analysis. Data generated was subjected to analysis with the GenAlEx 6.4 software assuming Hardy-Weinberg equilibrium to determine gene diversity index, number of polymorphic loci and alleles, genetic distances, analysis of molecular Original Research Article Maryrose et al.; AJEA, 5(4): 306-319, 2015; Article no.AJEA.2015.030 307 variance (AMOVA) and principal components analysis (PCA). NYTS-pc 2.1 software was used to construct an unweighted pair group method arithmetic averages (UPGMA) dendogram using the generated similarity coefficients. Results: Of the 7 SSR primers tested, 5 SSR primers were found to be polymorphic and used to screen the bean samples. The 5 primer combinations generated 49 polymorphic bands in 35 samples. Analysis of molecular variance accredited 8% of the disparity to diversity among the populations while the majority of the diversity (92%), resided within populations. The gene diversity index ranged from 0.1267 in the market population to 0.2377 in the Western province population. The highlands of Eastern province had a gene diversity index of 0.1475 while the dry lands had 0.1991. Cluster analysis segregated the bean samples into 9 clusters. Conclusion: There exists considerable variation in the dry bean of Kenya that is narrowing. There is need to intensify efforts to broaden the bean variation for sustainability. The population genetics of dry beans of Kenya are a possible guide to future bean breeding and germplasm management in Kenya. Keywords: SSRs; Phaseolus vulgaris; dry bean; germplasm characterization; and genetic variatio

Motor modules during adaptation to walking in a powered ankle exoskeleton

Abstract Background Modules of muscle recruitment can be extracted from electromyography (EMG) during motions, such as walking, running, and swimming, to identify key features of muscle coordination. These features may provide insight into gait adaptation as a result of powered assistance. The aim of this study was to investigate the changes (module size, module timing and weighting patterns) of surface EMG data during assisted and unassisted walking in an powered, myoelectric, ankle-foot orthosis (ankle exoskeleton). Methods Eight healthy subjects wore bilateral ankle exoskeletons and walked at 1.2 m/s on a treadmill. In three training sessions, subjects walked for 40 min in two conditions: unpowered (10 min) and powered (30 min). During each session, we extracted modules of muscle recruitment via nonnegative matrix factorization (NNMF) from the surface EMG signals of ten muscles in the lower limb. We evaluated reconstruction quality for each muscle individually using R2 and normalized root mean squared error (NRMSE). We hypothesized that the number of modules needed to reconstruct muscle data would be the same between conditions and that there would be greater similarity in module timings than weightings. Results Across subjects, we found that six modules were sufficient to reconstruct the muscle data for both conditions, suggesting that the number of modules was preserved. The similarity of module timings and weightings between conditions was greater then random chance, indicating that muscle coordination was also preserved. Motor adaptation during walking in the exoskeleton was dominated by changes in the module timings rather than module weightings. The segment number and the session number were significant fixed effects in a linear mixed-effect model for the increase in R2 with time. Conclusions Our results show that subjects walking in a exoskeleton preserved the number of modules and the coordination of muscles within the modules across conditions. Training (motor adaptation within the session and motor skill consolidation across sessions) led to improved consistency of the muscle patterns. Subjects adapted primarily by changing the timing of their muscle patterns rather than the weightings of muscles in the modules. The results of this study give new insight into strategies for muscle recruitment during adaptation to a powered ankle exoskeleton.https://deepblue.lib.umich.edu/bitstream/2027.42/140718/1/12984_2017_Article_343.pd

Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments

Microbes have obligate requirements for trace metals in metalloenzymes that catalyse important biogeochemical reactions. In anoxic methane- and sulphide-rich environments, microbes may have unique adaptations for metal acquisition and utilization because of decreased bioavailability as a result of metal sulphide precipitation. However, micronutrient cycling is largely unexplored in cold (≤ 10°C) and sulphidic (> 1 mM ΣH_(2)S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5–270 nM), cobalt (0.5–6 nM), molybdenum (10–5600 nM) and tungsten (0.3–8 nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalysing anaerobic oxidation of methane (AOM) utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B_(12) biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulphate-reducing bacteria. Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrophilic microorganisms. Overall, our data suggest that AOM consortia use specialized biochemical strategies to overcome the challenges of metal availability in sulphidic environments

Radiative Corrections to the Inflaton Potential as an Explanation of Suppressed Large Scale Power in Density Perturbations and the Cosmic Microwave Background

The Wilkinson Microwave Anisotropy Probe microwave background data suggest that the primordial spectrum of scalar curvature fluctuations is suppressed at small wavenumbers. We propose a UV/IR mixing effect in small-field inflationary models that can explain the observable deviation in WMAP data from the concordance model. Specifically, in inflationary models where the inflaton couples to an asymptotically free gauge theory, the radiative corrections to the effective inflaton potential can be anomalously large. This occurs for small values of the inflaton field which are of the order of the gauge theory strong coupling scale. Radiative corrections cause the inflaton potential to blow up at small values of the inflaton field. As a result, these corrections can violate the slow-roll condition at the initial stage of the inflation and suppress the production of scalar density perturbations.Comment: 20 pages, 2 figures, v2: refs added, v3: JCAP versio

Prevalent Multimorbidity Combinations Among Middle-Aged and Older Adults Seen in Community Health Centers

BACKGROUND: Multimorbidity (≥ 2 chronic diseases) is associated with greater disability and higher treatment burden, as well as difficulty coordinating self-management tasks for adults with complex multimorbidity patterns. Comparatively little work has focused on assessing multimorbidity patterns among patients seeking care in community health centers (CHCs). OBJECTIVE: To identify and characterize prevalent multimorbidity patterns in a multi-state network of CHCs over a 5-year period. DESIGN: A cohort study of the 2014-2019 ADVANCE multi-state CHC clinical data network. We identified the most prevalent multimorbidity combination patterns and assessed the frequency of patterns throughout a 5-year period as well as the demographic characteristics of patient panels by prevalent patterns. PARTICIPANTS: The study included data from 838,642 patients aged ≥ 45 years who were seen in 337 CHCs across 22 states between 2014 and 2019. MAIN MEASURES: Prevalent multimorbidity patterns of somatic, mental health, and mental-somatic combinations of 22 chronic diseases based on the U.S. Department of Health and Human Services Multiple Chronic Conditions framework: anxiety, arthritis, asthma, autism, cancer, cardiac arrhythmia, chronic kidney disease (CKD), chronic obstructive pulmonary disease (COPD), congestive heart failure, coronary artery disease, dementia, depression, diabetes, hepatitis, human immunodeficiency virus (HIV), hyperlipidemia, hypertension, osteoporosis, post-traumatic stress disorder (PTSD), schizophrenia, substance use disorder, and stroke. KEY RESULTS: Multimorbidity is common among middle-aged and older patients seen in CHCs: 40% have somatic, 6% have mental health, and 24% have mental-somatic multimorbidity patterns. The most frequently occurring pattern across all years is hyperlipidemia-hypertension. The three most frequent patterns are various iterations of hyperlipidemia, hypertension, and diabetes and are consistent in rank of occurrence across all years. CKD-hyperlipidemia-hypertension and anxiety-depression are both more frequent in later study years. CONCLUSIONS: CHCs are increasingly seeing more complex multimorbidity patterns over time; these most often involve mental health morbidity and advanced cardiometabolic-renal morbidity

The impact of induction and/or concurrent chemoradiotherapy on acute and late patient-reported symptoms in oropharyngeal cancer:Application of a mixed-model analysis of a prospective observational cohort registry

BACKGROUND The goal of this study was to comprehensively investigate the association of chemotherapy with trajectories of acute symptom development and late symptom recovery in patients with oropharyngeal cancer (OPC) by comparing symptom burden between induction chemotherapy followed by concurrent chemoradiotherapy (ICRT), concurrent chemo-radiotherapy (CRT), or radiotherapy (RT) alone.METHODS Among a registry of 717 patients with OPC, the 28-item patient-reported MD Anderson Symptom Inventory-Head and Neck Module (MDASI-HN) symptoms were collected prospectively at baseline, weekly during RT, and 1.5, 3 to 6, 12, and 18 to 24 months after RT. The effect of the treatment regimen (ICRT, CRT, and RT alone) was examined with mixed-model analyses for the acute and late period. In the CRT cohort, the chemotherapy agent relationship with symptoms was investigated.RESULTS Chemoradiation (ICRT/CRT) compared with RT alone resulted in significantly higher acute symptom scores in the majority of MDASI-HN symptoms (ie, 21 out of 28). No late symptom differences between treatment with or without chemotherapy were observed that were not attributable to ICRT. Nausea was lower for CRT with carboplatin than for CRT with cisplatin; cetuximab was associated with particularly higher scores for acute and late skin, mucositis, and 6 other symptoms. The addition of ICRT compared with CRT or RT alone was associated with a significant increase in numbness and shortness of breath.CONCLUSION The addition of chemotherapy to definitive RT for OPC patients was associated with significantly worse acute symptom outcomes compared with RT alone, which seems to attenuate in the late posttreatment period. Moreover, induction chemotherapy was specifically associated with worse numbness and shortness of breath during and after treatment.LAY SUMMARYChemotherapy is frequently used in addition to radiotherapy cancer treatment, yet the (added) effect on treatment-induced over time is not comprehensively investigatedThis study shows that chemotherapy adds to the symptom severity reported by patients, especially during treatment</p