Data Management Plans in the genomics research revolution of Africa: Challenges and Recommendations

Drafting and writing a data management plan (DMP) is increasingly seen as a key part of the academic research process. A DMP is a document that describes how a researcher will collect, document, describe, share, and preserve the data that will be generated as part of a research project. The DMP illustrates the importance of utilizing best practices through all stages of working with data while ensuring accessibility, quality, and longevity of the data. The benefits of writing a DMP include compliance with funder and institutional mandates; making research more transparent (for reproduction and validation purposes); and FAIR (findable, accessible, interoperable, reusable); protecting data subjects and compliance with the General Data Protection Regulation (GDPR) and/or local data protection policies. In this review, we highlight the importance of a DMP in modern biomedical research, explaining both the rationale and current best practices associated with DMPs. In addition, we outline various funders’ requirements concerning DMPs and discuss open-source tools that facilitate the development and implementation of a DMP. Finally, we discuss DMPs in the context of African research, and the considerations that need to be made in this regard

Development of a LAMP assay for detection of Leishmania infantum infection in dogs using conjunctival swab samples

Background: Leishmania infantum infections in dogs play a crucial role in the transmission of pathogens causing visceral leishmaniasis to humans in the Gansu province, northwest China. To be able to control zoonotic transmission of the parasite to humans, a non-invasive loop-mediated isothermal amplification (LAMP) assay to specifically detect L. infantum infections in dogs was developed. Methods: The primers used in the LAMP assay were designed to target kinetoplast DNA minicircle sequences of the L. infantum isolate MCAN/CN/90/SC and tested using DNA isolated from promastigotes of different Leishmania species. The LAMP assay was evaluated with conjunctional swab samples obtained from 111 and 33 dogs living in an endemic and a non-endemic region of zoonotic visceral leishmaniasis in the Gansu province, respectively. The LAMP assay was also compared with conventional PCR, ELISA and microscopy using conjunctional swab, serum and bone marrow samples from the dogs, respectively. Results: The LAMP assay detected 1 fg of L. infantum DNA purified from cultured promastigotes which was 10-fold more sensitive than a conventional PCR test using Leishmania genus-specific primers. No cross reaction was observed with DNA isolated from promastigotes of L. donovani, L. major, L. tropica, and L. braziliensis, and the L. infantum reference strain MHOM/TN/80/IPT1. The L. infantum-positive rates obtained for field-collected samples were 61.3%, 58.6%, 40.5% and 10.8% by LAMP, PCR, ELISA and microscopy, respectively. As only one out of the 33 samples from control dogs from the non-endemic region of zoonotic visceral leishmaniasis was positive by the LAMP assay and the PCR test, the observed true negative rate (specificity) was 97% for both methods. Conclusion: This study has shown that the non-invasive, conjunctional swab-based LAMP assay developed was more sensitive in the detection of leishmaniasis in dogs than PCR, ELISA and microscopy. The findings indicate that the LAMP assay is a sensitive and specific method for the field surveillance of domestic dogs, particularly of asymptomatic canines, in ZVL-endemic areas in western China

Mutations in the Mitochondrial Citrate Carrier SLC25A1 are Associated with Impaired Neuromuscular Transmission.

BACKGROUND AND OBJECTIVE: Congenital myasthenic syndromes are rare inherited disorders characterized by fatigable weakness caused by malfunction of the neuromuscular junction. We performed whole exome sequencing to unravel the genetic aetiology in an English sib pair with clinical features suggestive of congenital myasthenia. METHODS: We used homozygosity mapping and whole exome sequencing to identify the candidate gene variants. Mutant protein expression and function were assessed in vitro and a knockdown zebrafish model was generated to assess neuromuscular junction development. RESULTS: We identified a novel homozygous missense mutation in the SLC25A1 gene, encoding the mitochondrial citrate carrier. Mutant SLC25A1 showed abnormal carrier function. SLC25A1 has recently been linked to a severe, often lethal clinical phenotype. Our patients had a milder phenotype presenting primarily as a neuromuscular (NMJ) junction defect. Of note, a previously reported patient with different compound heterozygous missense mutations of SLC25A1 has since been shown to suffer from a neuromuscular transmission defect. Using knockdown of SLC25A1 expression in zebrafish, we were able to mirror the human disease in terms of variable brain, eye and cardiac involvement. Importantly, we show clear abnormalities in the neuromuscular junction, regardless of the severity of the phenotype. CONCLUSIONS: Based on the axonal outgrowth defects seen in SLC25A1 knockdown zebrafish, we hypothesize that the neuromuscular junction impairment may be related to pre-synaptic nerve terminal abnormalities. Our findings highlight the complex machinery required to ensure efficient neuromuscular function, beyond the proteomes exclusive to the neuromuscular synapse

Clinical trials in amyotrophic lateral sclerosis:a systematic review and perspective

Amyotrophic lateral sclerosis is a progressive and devastating neurodegenerative disease. Despite decades of clinical trials, effective disease modifying drugs remain scarce. To understand the challenges of trial design and delivery, we performed a systematic review of phase II, phase II/III and phase III amyotrophic lateral sclerosis clinical drug trials on trial registries and PubMed between 2008 and 2019. We identified 125 trials, investigating 76 drugs and recruiting more than 15000 people with amyotrophic lateral sclerosis. 90% of trials used traditional fixed designs. The limitations in understanding of disease biology, outcome measures, resources and barriers to trial participation in a rapidly progressive, disabling and heterogenous disease hindered timely and definitive evaluation of drugs in two-arm trials. Innovative trial designs, especially adaptive platform trials may offer significant efficiency gains to this end. We propose a flexible and scalable multi-arm, multi-stage trial platform where opportunities to participate in a clinical trial can become the default for people with amyotrophic lateral sclerosis

Morphological and Molecular Evolution Are Not Linked in Lamellodiscus (Plathyhelminthes, Monogenea)

Lamellodiscus Johnston & Tiegs 1922 (Monogenea, Diplectanidae) is a genus of common parasites on the gills of sparid fishes. Here we show that this genus is probably undergoing a fast molecular diversification, as reflected by the important genetic variability observed within three molecular markers (partial nuclear 18S rDNA, Internal Transcribed Spacer 1, and mitonchondrial Cytochrome Oxidase I). Using an updated phylogeny of this genus, we show that molecular and morphological evolution are weakly correlated, and that most of the morphologically defined taxonomical units are not consistent with the molecular data. We suggest that Lamellodiscus morphology is probably constrained by strong environmental (host-induced) pressure, and discuss why this result can apply to other taxa. Genetic variability within nuclear 18S and mitochondrial COI genes are compared for several monogenean genera, as this measure may reflect the level of diversification within a genus. Overall our results suggest that cryptic speciation events may occur within Lamellodiscus, and discuss the links between morphological and molecular evolution

The use of citrus pulp silage in Diplodus puntazzo nutrition

[EN] Purpose Studying the efect of citrus pulp silage in the growth performance, amino acid retention of sharpsnout sea bream juveniles. Methods Citrus pulp is an energy and protein source that has been used to replace wheat meal in Diplodus puntazzo fngerlings; 96 fsh of 21.5±0.67 g were nourished with two experimental diets for 105 days. The control diet (CON) contained 421.6 g/kg of protein and 22.6 MJ/kg of energy. The citrus pulp diet (CPD) included 442.7 g/kg of protein and 22.02 MJ/ kg of energy. Results At the end of this trial, the CPD did not afect the growth parameters, but the feed efciency values exhibited statistically signifcant diferences, with those fsh fed the CPD having higher values, possibly due to the presence of limonene in the diet. The CPD also resulted in a reduction in amino acid (AA) content due to the protein being bound to fbre; this consequence did not afect the fnal fsh AA profle. For AA retention, only arginine displayed signifcant diferences, although the rest of the AAs also showed efects of AA reduction from the CPD. Conclusion Citrus pulp silage can be used in D. puntazzo feeding, without adverse in the growth performance and the amino acid profle, although it did cause a reduction in feed efciencyNogales Mérida, S.; Tomas-Vidal, A.; Jover Cerda, M.; Sánchez Lozano, NB.; Velazco Vargas, JL.; Martínez-Llorens, S. (2018). The use of citrus pulp silage in Diplodus puntazzo nutrition. International Journal Of Recycling of Organic Waste in Agriculture (Online). 2018:1-8. https://doi.org/10.1007/s40093-018-0235-5S182018Alnaimy A, Gad AE, Mustafa MM, Atta MAA, Basuony HAM (2017) Using of citrus by-products in farm animals feeding. J Sci 1(3):58–67. https://doi.org/10.15406/oajs.2017.01.00014Amorim AB, Thomaz MC, Ruiz US, Pascoal LAF, Watanabe PH, Martinez JF, Daniel E, Martins MIEG, Masson GCIH (2011) Economic evaluation of the use of different levels of citrus pulp with or without the addition of enzyme complex in the diets of pigs. Arq Bras Med Vet Zootec 63(5):1181–1190. https://doi.org/10.1590/S0102-09352011000500020Amorim AB, Thomaz MC, Ruiz U, Dott S, Martinez JF, Pascoal LAF, Daniel E, Watanabe PH, Rosalen DL (2014) Citrus pulp and enzyme complex for growing and finishing pigs. Rev Bras Saúde Prod Anim Salv 15(2):369–380. https://doi.org/10.1590/S1519-99402014000200009AOAC (Association of official Analytical Chemists) (1990) Official methods of analysis, 15th edn. Association of Official Analytical Chemists, ArlingtonBasir R, Toghyani M (2017) Effect of dietary graded levels of dried lemon (Citrus aurantifulia) pulp on performance, intestinal morphology and humoral immunity in broiler chickens. Int J Recycl Org Waste Agric 6:125–132. https://doi.org/10.1007/s40093-017-0159-5Bosch L, Alegria A, Farré R (2006) Application of the 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC), reagent to the RP-HPLC determination of amino acids in infant foods. J Chromatogr B 831:176–183. https://doi.org/10.1016/j.jchromb.2005.12.002Chaouch H, Hamida OBA-BH, Ghorbel M, Jarboui O (2013) Diet composition and food habits of Diplodus puntazzo (Sparidae) from the Gulf of Gabès (Central Mediterranean). J Mar Biol Assoc UK 93(8):2257–2264. https://doi.org/10.1016/j.jchromb.2005.12.002Crosswhite JD, Myers NB, Adesogan AT, Brendemuhi JH, Johnson DD, Carr CC (2013) The effect of dietary citrus pulp on the growth, feed efficiency, carcass merit, and lean quality of finishing pigs. Prof Animal Sci 29:345–358Food and Agriculture Organization (FAO) (2017) Citrus fruit, fresh and processed. Statistical bulletin 2016. Trade and Markets Division, RomeFrancis G, Makker HPS, Becker K (2001) Antinutritional factors present in plant-derived alternate fish ingredients and their effects in fish. Aquaculture 199:197–227. https://doi.org/10.1016/S0044-8486(01)00526-9Fukada H, Furutani T, Shimizu R, Masumoto T (2014) Effects of yuzu (Citrus junos) peel from waste as an aquaculture feed supplement on growth, environmental load, and dark muscle discoloration in yellowtail Seriola quinqueradiata. J Aquat Food Prod T 23:511–521. https://doi.org/10.1080/10498850.2012.732201Hernández MD, Egea MA, Rueda FM, Aguado F, Martínez FJ, García B (2001) Effects of commercial diets with a different P/E ratio on sharpsnout sea bream (Diplodus puntazzo) growth and nutrient utilization. Aquaculture 195:321–329. https://doi.org/10.1016/S0044-8486(00)00564-0Krogdahl Å, Hemre G-I, Mommsen TP (2005) Carbohydrates in fish nutrition: digestion and absorption in postlarval stages. Aquacult Nutr 11(2):103–122. https://doi.org/10.1111/j.1365-2095.2004.00327.xLashkari S, Taghizadeh A (2012) Nutrient digestibility and evaluation of protein and carbohydrate fractionation of citrus by-products. J Anim Physiol Anim Nutr 97:701–709. https://doi.org/10.1111/j.1439-0396.2012.01312.xMarín FR, Soler-Rivas C, Benavente-García O, Castillo J, Pérez-Alvarez JA (2007) By-products from different citrus processes as a source of customized functional fibres. Food Chem 100:736–741. https://doi.org/10.1016/j.foodchem.2005.04.040Moreno Alvarez MJ, Hernández JG, Rovero R, Tablante A, Rangel L (2000) Alimentación de tilapias con raciones parciales de cáscaras de naranja. Cienc Technol Aliment 3(1):29–33. http://www.redalyc.org/articulo.oa?ld=72430204Mourão JL, Pinheiro VM, Pratesm JAM, Bessa RJB, Ferreira LMA, Fontes CMGA, Ponte PIP (2008) Effect of dietary dehydrated pasture and citrus pulp on the performance and meat quality of broiler chickens. Poult Sci 87:733–743. https://doi.org/10.3382/ps.2007-00411Nogales-Mérida S, Tomás-Vidal A, Martínez-Llorens S, Jover Cerdá M (2010) Sunflower meal as a partial substitute in juvenile sharpsnout sea bream (Diplodus puntazzo) diets: amino acid retention, gut and liver histology. Aquaculture 298:275–281. https://doi.org/10.1016/j.aquaculture.2009.10.025Oluremi OIA, Okafor FN, Adenkola AY, Orayaga KT (2010) Effect of fermentation of sweet orange (Citrus sinensis) fruit peel on its phytonutrients and the performance of broiler starter. Int J Poult Sci 9(6):546–549Piquer Querol O (2006) Whole citrus fruits in sheep nutrition. Dissertation, Universitat Politècnica de ValènciaPiquer O, Ródenas L, Casado C, Blas E, Pascual JJ (2009) Whole citrus fruits as an alternative to wheat grain or citrus pulp in sheep diet: effect on the evolution of ruminal parameters. Small Rumin Res 83:14–21. https://doi.org/10.1016/j.smallrumres.2008.11.009Rodriguez APO, Gominho-Rosa MDC, Cargnin-Ferreira E, De Francisco A, Fracalossi DM (2012) Different utilization of plant sources by the omnivores jundiá catfish (Rhamdia quelen) and Nile tilapia (Oreochromis niloticus). Aquacult Nutr 18:65–72. https://doi.org/10.1111/j.1365-2095.2011.00877.xSaleh HM, El-Mor M (2015) Feeding habits of the sharp snout sea bream, Diplodus puntazzo (Cetti, 1777) (Teleostei: Sparidae) from Benghazi Coast, Eastern Libya. Int J Bioassays 4:3860–3865Shan Y (2017) Comprehensive utilization of citrus by-products. Academic Press, AmsterdamShimada T, Shindu M, Miyazawa M (2002) Species differences in the metabolism of (+)− and (−)− Limonenes and their metabolites, carveols and carvones, by cytochrome P450 enzymes in liver microsomes of mice, rats, guinea pigs, rabbits, dogs monkeys, and humans. Drug Metab Pharmacokin 17(6):507–515Silva VK, Souza Morita V, Boleli IC (2013) Effect of pectin extracted from citrus pulp on digesta characteristics and nutrient digestibility in broilers chickens. R Bras Zootec 42(8):575–583. https://doi.org/10.1590/S1516-35982013000800007Spreen TH (2001) Projections of world production and consumption of citrus to 2010. In: China/FAO citrus symposium, Beijing, Popular Republic of China, 14–17 May 2001Wadhwa M, Bakshi MPS (2013) Fruit wastes as livestock feed. In: Makkar HPS(ed) Utilization of fruit and vegetable wastes as livestock feed and as substrates for generation of other value-added products. In: RAP publication 2013/04 FAO, APHCA, pp 11-14Wang C, Gao GL, Huang JX, Zhang KS, Zhong H, Wang HW, Su J, Xie M, Wang QG (2017) Nutritive value of dry citrus pulp and its effect on performance in geese from 35 to 70 days of age. J Appl Poult Res 26:253–259. https://doi.org/10.3382/japr/pfw069Watanabe PH, Thomaz MC, Martins MIEG, Ruiz US, Fraga AL, Santos VM, Pascoal LAF, Silva SZ (2009) Gross and partial net incomes and feeding cost of diets containing citrus pulp for pigs slaughtered with 130 kg of weight. Arq Bras Med Vet Zootec 61(1):203–210. https://doi.org/10.1590/S0102-09352009000100029Watanabe PH, Thomas MC, Ruiz US, Santos VM, Masson GCI, Fraga AL, Pascoal LAF, Robes-Huaynate RA, Silva SZ (2010) Carcass characteristics and meat quality of heavy swine fed different citrus pulp levels. Arq Bras Med Vet Zootec 62(4):921–929. https://doi.org/10.1590/S0102-09352010000400023Zang L, Shimada Y, Kawajiri J, Tanaka T, Nishimura N (2014) Effect of yuzu (Citrus junos Siebold ex Tanaka) peel on the diet-induced obesity in a zebrafish model. J Funct Foods 10:499–510. https://doi.org/10.1016/j.jff.2014.08.00