Spontaneous Embedding of DNA Mismatches Within the RNA:DNA Hybrid of CRISPR-Cas9.

CRISPR-Cas9 is the forefront technology for editing the genome. In this system, the Cas9 protein is programmed with guide RNAs to process DNA sequences that match the guide RNA forming an RNA:DNA hybrid structure. However, the binding of DNA sequences that do not fully match the guide RNA can limit the applicability of CRISPR-Cas9 for genome editing, resulting in the so-called off-target effects. Here, molecular dynamics is used to probe the effect of DNA base pair mismatches within the RNA:DNA hybrid in CRISPR-Cas9. Molecular simulations revealed that the presence of mismatched pairs in the DNA at distal sites with respect to the Protospacer Adjacent Motif (PAM) recognition sequence induces an extended opening of the RNA:DNA hybrid, leading to novel interactions established by the unwound nucleic acids and the protein counterpart. On the contrary, mismatched pairs upstream of the RNA:DNA hybrid are rapidly incorporated within the heteroduplex, with minor effect on the protein-nucleic acid interactions. As a result, mismatched pairs at PAM distal ends interfere with the activation of the catalytic HNH domain, while mismatches fully embedded in the RNA:DNA do not affect the HNH dynamics and enable its activation to cleave the DNA. These findings provide a mechanistic understanding to the intriguing experimental evidence that PAM distal mismatches hamper a proper function of HNH, explaining also why mismatches within the heteroduplex are much more tolerated. This constitutes a step forward in understanding off-target effects in CRISPR-Cas9, which encourages novel structure-based engineering efforts aimed at preventing the onset of off-target effects

The Economics of Targeting and Sustaining a Niche Market: A Case Study of Green Pod Chickpea Marketing in Ethiopia

Ethiopia is a leading producer of chickpea in Sub-Saharan Africa and the crop plays substantial role in household food and nutrition security, soil fertility restoration and national export earnings. Recent market studies show that farmers often sell chickpea in grain form and it reaches the final consumer through complex and long supply channels involving various market actors. However, Green Pod Chickpea (GPCP) marketing is a recently evolving phenomenon as a niche market, and there has been a considerable boost in its supply over the past five years. The objective of this paper is to critically examine the main driving forces behind GPCP marketing and assess whether it is a viable and sustainable option for smallholder farmers. Despite the relevance of multilayer evidences, the research and development efforts to understand, evaluate and support GPCP marketing scheme are very much limited—the issue has not received the attention it deserves. Farmers are still relying on old varieties with very minimal extension support and the degree to which the niche market would be able to absorb the growing number of aspiring GPCP market participants is still unclear. In nutshell, there is limited information and knowledge about the size and characteristics of GPCP market. To the best of our understanding, this study is the first of its kind to critically examine the viability of GPCP marketing scheme, and we hope that the findings could help bridge the knowledge gap, provide policy inputs and serve as reference for further studies in the area. To answer the research questions, we have collected data from chickpea producers, extension workers and market actors, and the data has been analyzed using descriptive and econometric methods. The findings clearly show that GPCP marketing is variety-specific: the market strongly favors the localized black and improved Marye varieties mainly due to their taste. To make GPCP buying decision, market actors such as consumer and vendors consider certain crop parameters and attributes including, pod color, pod size, freshness, neatness, pods per plant, variety (Desi or Kabuli) etc. As the multiple regression results show, proximity to market, gender, livelihood status, family size, harvesting and post-harvesting costs, grain and GPCP price gap, and access to finance are the main factors affecting the amount of GPCP traded. Some farmers sell GPCP out of necessity motivated by cash deficit, whereas others are highly market-oriented and put effort to exploit the niche market led by profit maximization. The structure and functioning of GPCP market is quite different from that of grain market: it is less complex and involves few intermediaries with short supply chain. To widen market base, availing more GPCP products options and value addition efforts (cleaning, peeling, cooking, roasting, packaging, and labeling) could be crucial entry points. Besides, the research and extension system should address the concerns of GPCP producers and engage them during variety release, training provision and capacity building sessions. To shade more light on the scalability and future prospect of such marketing scheme, further studies pertinent to its structure and functioning are vital. At policy level, mainstreaming it into the food and nutrition product stream could have paramount importance

Non-Motor Symptoms and Associated Factors in Parkinson’s Disease Patients in Addis Ababa, Ethiopia: A Multicenter Cross-Sectional Study

BACKGROUND: Non-motor symptoms (NMSs) of Parkinson’s disease (PD) were often overlooked and less studied. Little is known about NMSs in Ethiopia. The aim of the study was to determine the prevalence of NMSs and associated factors.METHODS: A multi-center cross-sectional observational study was conducted. NMS questionnaire was used to screen for the NMSs. Both descriptive and analytical statistics were used to analyze the data.RESULTS: Total of 123 PD patients with median of 4 years were investigated. The mean age of PD patients was 62.9 years. The mean age of PD onset was 58.3 years. In 23.6% the age of onset was below age 50. Males accounted 72.4%. Majority of the patients were on Levodopa alone and 31.7% were on levodopa plus trihexyphenidyl. Longer duration of illness was associated with frequent occurrence of NMSs. Constipation was the commonest NMS (78%), followed by urinary urgency (67.5%) and nocturia (63.4%). An unexplained pain was reported by 45.5%, cognitive impairment (45.5%), and sleep disturbance was reported by 45.5% of the study participants. Neurophysciatric symptoms were reported by small proportion of the patients. Lower monthly earning was associated with swallowing problem, unexplained weight change, and lighheadness.CONCLUSION: The prevalence of NMS was high among PD patients in Ethiopia. Constipation was the commonest NMS. Longer duration of illness was associated with frequent occurrence of NMSs. Lower monthly earning was associated with swallowing problem, unexplained weight change, and lighheadness

Phenotypic heterogeneity of Campylobacter coli isolated from conventional and antimicrobial free swine at farm and slaughter

The aim of this study was to determine the phenotypic and genotypic diversity of multiple Campylobacter coli isolates (n = 3) present in the same pig fecal and carcass samples at fann and slaughter, respectively. We isolated 1459 C. coli (1110 on farm and 349 from slaughter) from 908 pigs and 757 carcasses and characterized them for their antimicrobial susceptibility profile to a panel of six antimicrobials using the agar dilution method. A subset of 40 isolates representing 10 pigs and eight carcass samples were further genotyped by multi-locus sequence typing (MLST). Phenotypic diversity of C. coli isolates at the four fold minimum inhibitory concentration (MIC) levels within the same sample was detected in 39% (n = 192) pigs and 40.2% (n = 58) carcass swabs with no significant difference between the two sources (P = 0.721). Phenotypic heterogeneity based on the resistance patterns was observed in 32.5% (n = 162) of the farm samples and in 30.5% (n = 44) carcass swabs at slaughter (P = 0.64). Genotypic diversity based on MLST was detected in the 40 isolates which were represented by 22 sequence types (ST). In conclusion, we detected multiple C. coli subtypes from individual pig or carcass samples. Our study clearly signifies the importance of testing multiple colonies to make appropriate and valid conclusions in epidemiological based studies

Evaluation of Two Estrus Synchronization Protocols in Dairy Cattle at North Shoa Zone Ethiopia

This study was initiated to change the hesitation of the farmer on the effectiveness of estrus synchronization under their (Ethiopian small holder) livestock management system using two synchronization protocols. Non-pregnant animals with normal reproductive tract and that fulfilled the preconditions for estrus synchronization were considered for treatment & assigned into two synchronization protocols (single PGF2α injection; and double PGF2α injection). Among 94 (27 heifer and 67 cows) synchronized cows using one and two injections of PGF2α protocols 26 heifers and 63 cows (89/94.7%) were exhibited estrus by visual observation and rectal palpation the remaining 5 (5.3%) did not illustrate heat. The overall pregnancy was 59.6 % with overall birth 94.3 %. High pregnancy was obtained in the double injection of PGF2α treatment group (63.1 %) than animals treated with one shot protocol 55.8 % there were statistically significant difference between treatments (p<0.05). Higher pregnancy was obtained from cross breed animals than local breeds. More over most of the animals come to estrus greater than 96 hrs. There was also significant difference between technicians on detecting the CL and conception. The estrus response, conception rate, pregnancy rate and calving rate was higher in both protocols so producers or farmers can use either the two protocols to achieve remarkable result but tight follow-ups and more resources are need to be exploited at farmer level

Prevalence of methicillin-resistant staphylococci (MRS+) in pigs and farm workers

This study aims to dctcnnine the prevalence of MRSA and other methicillin resistant staphylococci in swine and swine fann workers. We collected swab and fecal samples from 96 pigs of 6-9 weeks of age from four fam1s in Ohio. Swab samples were collected from both anterior nares and fecal samples directly from the rectum of corresponding pigs. Nasal and oropharyngeal samples were collected from consenting farm workers. Samples were processed following conventional cultural methods and we used methicillin resistant Staphylococcus aureus selective agar (MRSA Chromagar®)

Knowledge and perception towards net care and repair practice in Ethiopia.

BACKGROUND: Long-lasting insecticidal nets (LLINs) are a key malaria control intervention. Although LLINs are presumed to be effective for 3 years under field or programmatic conditions, net care and repair approaches by users influence the physical and chemical durability. Understanding how knowledge, perception and practices influence net care and repair practices could guide the development of targeted behavioural change communication interventions related to net care and repair in Ethiopia and elsewhere. METHODS: This population-based, household survey was conducted in four regions of Ethiopia [Amhara, Oromia, Tigray, Southern Nations Nationalities Peoples Region (SNNPR)] in June 2015. A total of 1839 households were selected using multi-stage sampling procedures. The household respondents were the heads of households. A questionnaire was administered and the data were captured electronically. STATA software version 12 was used to analyse the data. Survey commands were used to account for the multi-stage sampling approach. Household descriptive statistics related to characteristics and levels of knowledge and perception on net care and repair are presented. Ordinal logistic regression was used to identify factors associated with net care and repair perceptions. RESULTS: Less than a quarter of the respondents (22.3%: 95% CI 20.4-24.3%) reported adequate knowledge of net care and repair; 24.6% (95% CI 22.7-26.5%) of the respondents reported receiving information on net care and repair in the previous 6 months. Thirty-five per cent of the respondents (35.1%: 95% CI 32.9-37.4%) reported positive perceptions towards net care and repair. Respondents with adequate knowledge on net care and repair (AOR 1.58: 95% CI 1.2-2.02), and those who discussed net care and repair with their family (AOR 1.47: 95% CI 1.14-1.89) had higher odds of having positive perceptions towards net care and repair. CONCLUSIONS: The low level of reported knowledge on net care and repair, as well as the low level of reported positive perception towards net repair need to be addressed. Targeted behavioural change communication campaigns could be used to target specific groups; increased net care and repair would lead to longer lasting nets