Mitochondrial genome SNPs analysis of eight barley genotypes displaying hot spot regions,phylogenetic relationships and heteroplasmy

Abstract

Organellar genomes are small, circular entities that provide unique advantages as compared to the nuclear genome. The present study was aimed at evaluating the efficiency of utilizing mitochondrial single nucleotide polymorphisms (SNPs) approach in separating barley cultivars. Sequences generated via next-generation sequencing were further utilized to confirm the incidence of heteroplasmy in barley mitochondrial genome. The analysis involved seven cultivated barley (Hordeum vulgare subsp. vulgare) (VG) and one wild (H. vulgare subsp. spontaneum) (SP) genotypes. A total of 73 million paired-end reads per mitochondrial genomes across the eight barley genotypes were generated using Illumina HiSeq 2000 platform. Sequences of each genotype were separately aligned to the published barley mitochondrial reference genome, thus SNPs were detected. The overall results indicated the efficiency of using mitochondrial SNPs as a molecular marker in distinguishing among barley genotypes. Unique SNPs were determined in six out of the eight genotypes, where Giza131 and Giza129 had no specific mitochondrial SNPs, while Giza130 showed the largest number of unique mitochondrial SNPs. The phylogenetic tree indicated the close relationship between Giza129 and Giza130. Interestingly, SP was not clearly discriminated among genotypes.     

Monitoring Microbial Numbers in Food by Density Centrifugation

Some foods contain low numbers of microbes that may be difficult to enumerate by the plate count method due to small food particles that interfere with the counting of colonies. Ludox colloidal silicon was coated with reducing agents to produce a nontoxic density material. Food homogenates were applied to a layered 10 and 80% mixture of modified Ludox and centrifuged at low speed. The top and bottom of the tube contained the food material, and the Ludox-containing portion was evaluated by conventional pour plate techniques. Plate counts of the Ludox mixture agreed with plate counts of the food homogenate alone. The absence of small food particles from pour plates resulted in a plate that was more easily read than pour plates of the homogenate alone. Modified Ludox was evaluated for its effect on bacteria at 4°C during a 24-h incubation period. No inhibition was observed. This method is applicable to food products, such as doughnuts, spices, tomato products, and meat, in which small food particles often interfere with routine plate counts or low dilution may inhibit colony formation. Inhibitory substances can be removed from spices, resulting in higher counts. Ludox is more economical than similar products, such as Percoll. Modified Ludox is easily rendered nontoxic by the addition of common laboratory reagents. In addition, the mixture is compatible with microbiological media.     

Mechanisms of BCG action

Summary Donor mice were treated IV with BCG and after various time intervals the spleens from these animals were injected into syngeneic recipients which were simultaneously challenged with an allogeneic tumour. The spleen cells from the BCG-treated donors, but not untreated donors, conferred on the recipients an ability to induce a potentiated CMC reaction against the tumour. The transference of BCG-induced potentiating activity could not be explained by the transference of viable BCG organisms, but was mediated by a cell that was anti-Thy.1-sensitive, silica-resistant, plastic-nonadherent, and nylon wool-adherent, and was sensitive in vivo to anti-thymocyte serum but resistant to hydrocortisone. By the use of congenic strains of mice that differed at the Thy.1 allele, it was shown that the cells responsible were not precursors of the cytotoxic lymphocytes but were cells that produced an amplification of the response of the recipient host's precursor cytotoxic T cells.     

Epidemiological,clinical, and public health response characteristics of a large outbreak of diphtheria among the Rohingya population in Cox’s Bazar,Bangladesh, 2017 to 2019: A retrospective study

BackgroundUnrest in Myanmar in August 2017 resulted in the movement of over 700,000 Rohingya refugees to overcrowded camps in Cox’s Bazar, Bangladesh. A large outbreak of diphtheria subsequently began in this population.Methods and findingsData were collected during mass vaccination campaigns (MVCs), contact tracing activities, and from 9 Diphtheria Treatment Centers (DTCs) operated by national and international organizations. These data were used to describe the epidemiological and clinical features and the control measures to prevent transmission, during the first 2 years of the outbreak. Between November 10, 2017 and November 9, 2019, 7,064 cases were reported: 285 (4.0%) laboratory-confirmed, 3,610 (51.1%) probable, and 3,169 (44.9%) suspected cases. The crude attack rate was 51.5 cases per 10,000 person-years, and epidemic doubling time was 4.4 days (95% confidence interval [CI] 4.2–4.7) during the exponential growth phase. The median age was 10 years (range 0–85), and 3,126 (44.3%) were male. The typical symptoms were sore throat (93.5%), fever (86.0%), pseudomembrane (34.7%), and gross cervical lymphadenopathy (GCL; 30.6%). Diphtheria antitoxin (DAT) was administered to 1,062 (89.0%) out of 1,193 eligible patients, with adverse reactions following among 229 (21.6%). There were 45 deaths (case fatality ratio [CFR] 0.6%). Household contacts for 5,702 (80.7%) of 7,064 cases were successfully traced. A total of 41,452 contacts were identified, of whom 40,364 (97.4%) consented to begin chemoprophylaxis; adherence was 55.0% (N = 22,218) at 3-day follow-up. Unvaccinated household contacts were vaccinated with 3 doses (with 4-week interval), while a booster dose was administered if the primary vaccination schedule had been completed. The proportion of contacts vaccinated was 64.7% overall. Three MVC rounds were conducted, with administrative coverage varying between 88.5% and 110.4%. Pentavalent vaccine was administered to those aged 6 weeks to 6 years, while tetanus and diphtheria (Td) vaccine was administered to those aged 7 years and older. Lack of adequate diagnostic capacity to confirm cases was the main limitation, with a majority of cases unconfirmed and the proportion of true diphtheria cases unknown.ConclusionsTo our knowledge, this is the largest reported diphtheria outbreak in refugee settings. We observed that high population density, poor living conditions, and fast growth rate were associated with explosive expansion of the outbreak during the initial exponential growth phase. Three rounds of mass vaccinations targeting those aged 6 weeks to 14 years were associated with only modestly reduced transmission, and additional public health measures were necessary to end the outbreak. This outbreak has a long-lasting tail, with Rt oscillating at around 1 for an extended period. An adequate global DAT stockpile needs to be maintained. All populations must have access to health services and routine vaccination, and this access must be maintained during humanitarian crises.

Jonathan Polonsky and colleagues report on a diphtheria outbreak among Rohingya people in Cox’s Bazar, Bangladesh during 2017-19.     

Performance evaluation of broadcast and global combine operations in all-port wormhole-routed OTIS-Mesh interconnection networks

OTIS (Optical Transpose Interconnection System) optoelectronic architecture is an attractive high-speed interconnection network. As a continuation for the research work performed on OTIS, this paper investigates broadcast and global combine communication operations on the promising all-port wormhole-routed OTIS-Mesh using the Extended Dominating Node (EDN) approach, referred to as EDN-OTIS-Mesh. The performance of broadcast and global combine operations is evaluated, both analytically and by simulation, in terms of the number of communication steps, latency, and latency improvement. A comparative study is conducted among three interconnection networks’ architectures: the single-port wormhole-routed OTIS-Mesh, all-port wormhole-routed OTIS-Mesh, and all-port wormhole-routed EDN-OTIS-Mesh. The obtained analytical and simulation results show that the broadcast and global combine operations on all-port EDN-OTIS-Mesh significantly outperform the single-port and all-port OTIS-Mesh.     

Clinical Trial of a Combination of Lynestrenol and Mestranol (Lyndiol) as an Oral Contraceptive Agent

Contraception with lynestrenol-mestranol (Lyndiol) was studied in 332 Mexican women during a period of two and one-half years. Side effects were minimal or transient. No pregnancies occurred in those who took the medication according to instructions. The women were followed with yearly pelvic examinations and Papanicolaou smears, serial endometrial biopsies and extensive studies of blood, liver and glandular function. Complete ophthalmological studies were done on 30 patients. No clinical or laboratory evidence of harmful effects could be demonstrated. Return to ovulation (using pregnanediol excretion and endometrial biopsies as parameters) occurred in all of 22 women studied in the first three post-treatment cycles. Eight posttreatment pregnancies and the resulting offspring were normal. The first post-treatment cycle, as with other oral contraceptives, was unpredictable and tended to be prolonged. It varied in length from 22 to 60 days.     

Farnesyl pyrophosphate is a new danger signal inducing acute cell death

Cell death is a vital event in life. Infections and injuries cause lytic cell death, which gives rise to danger signals that can further induce cell death, inflammation, and tissue damage. The mevalonate (MVA) pathway is an essential, highly conserved and dynamic metabolic pathway. Here, we discover that farnesyl pyrophosphate (FPP), a metabolic intermediate of the MVA pathway, functions as a newly identified danger signal to trigger acute cell death leading to neuron loss in stroke. Harboring both a hydrophobic 15-carbon isoprenyl chain and a heavily charged pyrophosphate head, FPP leads to acute cell death independent of its downstream metabolic pathways. Mechanistically, extracellular calcium influx and the cation channel transient receptor potential melastatin 2 (TRPM2) exhibit essential roles in FPP-induced cell death. FPP activates TRPM2 opening for ion influx. Furthermore, in terms of a mouse model constructing by middle cerebral artery occlusion (MCAO), FPP accumulates in the brain, which indicates the function of the FPP and TRPM2 danger signal axis in ischemic injury. Overall, our data have revealed a novel function of the MVA pathway intermediate metabolite FPP as a danger signal via transient receptor potential cation channels.

Farnesyl pyrophosphate, a metabolic intermediate of the cholesterol synthesis pathway, functions as a novel danger signal to trigger acute cell necrosis, and collaborates with activation of the cation channel TRPM2 to play an important role in brain ischemic injury.     

Modeling the vestibular evoked myogenic potential

Measuring the vestibular evoked myogenic potential (VEMP) promises to become a routine method for assessing vestibular function, although the technique is not yet standardized. To overcome the problem that the VEMP amplitude depends not only on the inhibition triggered by the acoustic stimulation of the vestibular end organs in the inner ear, but also on the tone of the muscle from which the potential is recorded, the VEMP is often normalized by dividing through a measure of the electromyogram (EMG) activity. The underlying idea is that VEMP amplitude and EMG activity are proportional. But this would imply that the muscle tone is irrelevant for a successful VEMP recording, contradicting experimental evidence. Here, an analytical model is presented that allows to resolve the contradiction. The EMG is modeled as the sum of motor unit action potentials (MUAPs). A brief inhibition can be characterized by its equivalent rectangular duration (ERD), irrespective of the actual time course of the inhibition. The VEMP resembles a polarity-inverted MUAP under such circumstances. Its amplitude is proportional to both the ERD and the MUAP rate. The EMG activity, by contrast, is proportional to the square root of the MUAP rate. Thus, the normalized VEMP still depends on the muscle tone. To avoid confounding effects of the muscle tone, the standard deviation of the EMG could be considered. But the inhibition effect on the standard deviation is small so that the measuring time would have to be much longer than usual today.     

Utility of nuclear stress imaging for detecting coronary artery bypass graft disease

ABSTRACT: BACKGROUND: The value of Single Photon Emission Computed Tomography stress myocardial perfusion imaging (SPECT-MPI) for detecting graft disease after coronary artery bypass surgery (CABG) has not been studied prospectively in an unselected cohort. METHODS: Radial Artery Versus Saphenous Vein Graft Study is a Veterans Affairs Cooperative Study to determine graft patency rates after CABG surgery. Seventy-nine participants agreed to SPECT-MPI within 24 hours of their coronary angiogram, one-year after CABG. The choice of the stress protocol was made at the discretion of the nuclear radiologist and was either a symptom-limited exercise test (n=68) or an adenosine infusion (n=11). The SPECT-MPI results were interpreted independent of the angiographic results and estimates of sensitivity, specificity and accuracy were based on the prediction of a graft stenosis of [greater than or equal to]70% on coronary angiogram. RESULTS: A significant stenosis was present in 38 (48%) of 79 patients and 56 (22%) of 251 grafts. In those stress tests with an optimal exercise heart rate response (>80% maximum predicted heart rate) (n=26) sensitivity, specificity and accuracy of SPECT-MPI for predicting the graft stenosis was 77%, 69% and 73% respectively. With adenosine (n=11) it was 75%, 57% and 64%, respectively. Among participants with a suboptimal exercise heart rate response, the sensitivity of SPECT-MPI for predicting a graft stenosis was <50%. The accuracy of SPECTMPI for detecting graft disease did not vary significantly with ischemic territory. CONCLUSIONS: Under optimal stress conditions, SPECT-MPI has a good sensitivity and accuracy for detecting graft disease in an unselected patient population 1 year post-CABG.