Plant genomics in Africa: present and prospects

Plants are the world’s most consumed goods. They are of high economic value and bring many health benefits. In most countries in Africa, the supply and quality of food will rise to meet the growing population’s increasing demand. Genomics and other biotechnology tools offer the opportunity to improve subsistence crops and medicinal herbs in the continent. Significant advances have been made in plant genomics, which have enhanced our knowledge of the molecular processes underlying both plant quality and yield. The sequencing of complex genomes of African plant species, facilitated by the continuously evolving nextgeneration sequencing technologies and advanced bioinformatics approaches, has provided new opportunities for crop improvement. This review summarizes the achievements of genome sequencing projects of endemic African plants in the last two decades. We also present perspectives and challenges for future plant genomic studies that will accelerate important plant breeding programs for African communities. These challenges include a lack of basic facilities, a lack of sequencing and bioinformatics facilities, and a lack of skills to design genomics studies. However, it is imperative to state that African countries have become key players in the plant genome revolution and genome derived-biotechnology. Therefore, African governments should invest in public plant genomics research and applications, establish bioinformatics platforms and training programs, and stimulate university and industry partnerships to fully deploy plant genomics, particularly in the fields of agriculture and medicine

Seasonal variability of picophytoplankton under contrasting environments in northern Tunisian coasts, southwestern Mediterranean Sea

We investigated at the single cell level during 16 months (June 2012 to September 2013) the temporal distribution of picophytoplankton (picoeukaryotes, Synechococcus and Prochlorococcus) communities in two contrasted ecosystems: the Bay of Bizerte characterised by an oligotrophic regime typical of the Mediterranean Sea and the Bizerte Lagoon that exhibits a mesotrophic/eutrophic state. We aimed at depicting seasonal variations and quantifying the relationships between the environmental factors and the structure and abundance of picophytoplankton communities. Results showed that picophytoplankton groups were able to grow under a wide range of environmental conditions varying seasonally, although their abundances and contributions to the total chlorophyll biomass significantly varied and showed importance in the Bay of Bizerte. Synechococcus was the most abundant group reaching 225 * 10(3) cells.cm(-3) in the Bay and 278 * 10(3) cells.cm(-3) in the lagoon. This group was present all over the year in both ecosystems. Structural equation model results pointed out a different configuration regarding the picophytoplankton environmental drivers. The complexity of the configuration, i.e. number of significant links within the system, decreased under enhanced eutrophication conditions. The less exposure to anthropogenic stress, i.e. in the Bay of Bizerte, highlight a larger role of nutrient and hydrological conditions on the seasonal variations of picophytoplankton, whereas a negative effect of eutrophication on picophytoplankton communities was unveiled in the Bizerte Lagoon. We stress that such influence may be exacerbated under expected scenarios of Mediterranean warming conditions and nutrient release in coastal ecosystems

Seasonal variability of picophytoplankton under contrasting environments in northern Tunisian coasts, southwestern Mediterranean Sea

Highlights: • Picophytoplankton was able to grow under a wide range of environmental conditions varying seasonally. • Picophytoplankton variability was more marked in the bay than in the lagoon. • Picophytoplankton decreased in the lagoon under enhanced anthropogenic stress. • Synechococcus, the most abundant group of the community, was frequently present in both ecosystems during the monitoring. We investigated at the single cell level during 16months (June 2012 to September 2013) the temporal distribution of picophytoplankton (picoeukaryotes, Synechococcus and Prochlorococcus) communities in two contrasted ecosystems: the Bay of Bizerte characterised by an oligotrophic regime typical of the Mediterranean Sea and the Bizerte Lagoon that exhibits a mesotrophic/eutrophic state. We aimed at depicting seasonal variations and quantifying the relationships between the environmental factors and the structure and abundance of picophytoplankton communities. Results showed that picophytoplankton groups were able to grow under a wide range of environmental conditions varying seasonally, although their abundances and contributions to the total chlorophyll biomass significantly varied and showed importance in the Bay of Bizerte. Synechococcus was the most abundant group reaching 225*103 cells·cm-3 in the Bay and 278*103 cells·cm-3 in the lagoon. This group was present all over the year in both ecosystems. Structural equation model results pointed out a different configuration regarding the picophytoplankton environmental drivers. The complexity of the configuration, i.e. number of significant links within the system, decreased under enhanced eutrophication conditions. The less exposure to anthropogenic stress, i.e. in the Bay of Bizerte, highlight a larger role of nutrient and hydrological conditions on the seasonal variations of picophytoplankton, whereas a negative effect of eutrophication on picophytoplankton communities was unveiled in the Bizerte Lagoon. We stress that such influence may be exacerbated under expected scenarios of Mediterranean warming conditions and nutrient release in coastal ecosystems

Validation of the Collaborative Outcomes study on Health and Functioning during Infection Times (COH-FIT) questionnaire for adults

Background: The Collaborative Outcome study on Health and Functioning during Infection Times (COH-FIT; www.coh-fit.com) is an anonymous and global online survey measuring health and functioning during the COVID-19 pandemic. The aim of this study was to test concurrently the validity of COH-FIT items and the internal validity of the co-primary outcome, a composite psychopathology “P-score”. Methods: The COH-FIT survey has been translated into 30 languages (two blind forward-translations, consensus, one independent English back-translation, final harmonization). To measure mental health, 1–4 items (“COH-FIT items”) were extracted from validated questionnaires (e.g. Patient Health Questionnaire 9). COH-FIT items measured anxiety, depressive, post-traumatic, obsessive-compulsive, bipolar and psychotic symptoms, as well as stress, sleep and concentration. COH-FIT Items which correlated r ≥ 0.5 with validated companion questionnaires, were initially retained. A P-score factor structure was then identified from these items using exploratory factor analysis (EFA) and confirmatory factor analyses (CFA) on data split into training and validation sets. Consistency of results across languages, gender and age was assessed. Results: From >150,000 adult responses by May 6th, 2022, a subset of 22,456 completed both COH-FIT items and validated questionnaires. Concurrent validity was consistently demonstrated across different languages for COH-FIT items. CFA confirmed EFA results of five first-order factors (anxiety, depression, post-traumatic, psychotic, psychophysiologic symptoms) and revealed a single second-order factor P-score, with high internal reliability (ω = 0.95). Factor structure was consistent across age and sex. Conclusions: COH-FIT is a valid instrument to globally measure mental health during infection times. The P-score is a valid measure of multidimensional mental health

Physical and mental health impact of COVID-19 on children, adolescents, and their families: The Collaborative Outcomes study on Health and Functioning during Infection Times - Children and Adolescents (COH-FIT-C&A)

Background: The COVID-19 pandemic has altered daily routines and family functioning, led to closing schools, and dramatically limited social interactions worldwide. Measuring its impact on mental health of vulnerable children and adolescents is crucial. Methods: The Collaborative Outcomes study on Health and Functioning during Infection Times (COH-FIT – www.coh-fit.com) is an on-line anonymous survey, available in 30 languages, involving >230 investigators from 49 countries supported by national/international professional associations. COH-FIT has thee waves (until the pandemic is declared over by the WHO, and 6–18 months plus 24–36 months after its end). In addition to adults, COH-FIT also includes adolescents (age 14–17 years), and children (age 6–13 years), recruited via non-probability/snowball and representative sampling and assessed via self-rating and parental rating. Non-modifiable/modifiable risk factors/treatment targets to inform prevention/intervention programs to promote health and prevent mental and physical illness in children and adolescents will be generated by COH-FIT. Co-primary outcomes are changes in well-being (WHO-5) and a composite psychopathology P-Score. Multiple behavioral, family, coping strategy and service utilization factors are also assessed, including functioning and quality of life. Results: Up to June 2021, over 13,000 children and adolescents from 59 countries have participated in the COH-FIT project, with representative samples from eleven countries. Limitations: Cross-sectional and anonymous design. Conclusions: Evidence generated by COH-FIT will provide an international estimate of the COVID-19 effect on children's, adolescents’ and families’, mental and physical health, well-being, functioning and quality of life, informing the formulation of present and future evidence-based interventions and policies to minimize adverse effects of the present and future pandemics on youth

The collaborative outcomes study on health and functioning during infection times in adults (COH-FIT-Adults): Design and methods of an international online survey targeting physical and mental health effects of the COVID-19 pandemic

Background:. High-quality comprehensive data on short-/long-term physical/mental health effects of the COVID-19 pandemic are needed. Methods:. The Collaborative Outcomes study on Health and Functioning during Infection Times (COH-FIT) is an international, multi-language (n=30) project involving >230 investigators from 49 countries/territories/regions, endorsed by national/international professional associations. COH-FIT is a multi-wave, on-line anonymous, cross-sectional survey [wave 1: 04/2020 until the end of the pandemic, 12 months waves 2/3 starting 6/24 months threreafter] for adults, adolescents (14-17), and children (6-13), utilizing non-probability/snowball and representative sampling. COH-FIT aims to identify non-modifiable/modifiable risk factors/treatment targets to inform prevention/intervention programs to improve social/health outcomes in the general population/vulnerable subgrous during/after COVID-19. In adults, co-primary outcomes are change from pre-COVID-19 to intra-COVID-19 in well-being (WHO-5) and a composite psychopathology P-Score. Key secondary outcomes are a P-extended score, global mental and physical health. Secondary outcomes include health-service utilization/functioning, treatment adherence, functioning, symptoms/behaviors/emotions, substance use, violence, among others. Results:. Starting 04/26/2020, up to 14/07/2021 >151,000 people from 155 countries/territories/regions and six continents have participated. Representative samples of ≥1,000 adults have been collected in 15 countries. Overall, 43.0% had prior physical disorders, 16.3% had prior mental disorders, 26.5% were health care workers, 8.2% were aged ≥65 years, 19.3% were exposed to someone infected with COVID-19, 76.1% had been in quarantine, and 2.1% had been COVID 19-positive. Limitations:. Cross-sectional survey, preponderance of non-representative participants. Conclusions:. Results from COH-FIT will comprehensively quantify the impact of COVID-19, seeking to identify high-risk groups in need for acute and long-term intervention, and inform evidence-based health policies/strategies during this/future pandemics

Validation of the Collaborative Outcomes study on Health and Functioning during Infection Times (COH-FIT) questionnaire for adults

Background: The Collaborative Outcome study on Health and Functioning during Infection Times (COH-FIT; www.coh-fit.com) is an anonymous and global online survey measuring health and functioning during the COVID-19 pandemic. The aim of this study was to test concurrently the validity of COH-FIT items and the internal validity of the co-primary outcome, a composite psychopathology “P-score”. Methods: The COH-FIT survey has been translated into 30 languages (two blind forward-translations, consensus, one independent English back-translation, final harmonization). To measure mental health, 1–4 items (“COH-FIT items”) were extracted from validated questionnaires (e.g. Patient Health Questionnaire 9). COH-FIT items measured anxiety, depressive, post-traumatic, obsessive-compulsive, bipolar and psychotic symptoms, as well as stress, sleep and concentration. COH-FIT Items which correlated r ≥ 0.5 with validated companion questionnaires, were initially retained. A P-score factor structure was then identified from these items using exploratory factor analysis (EFA) and confirmatory factor analyses (CFA) on data split into training and validation sets. Consistency of results across languages, gender and age was assessed. Results: From >150,000 adult responses by May 6th, 2022, a subset of 22,456 completed both COH-FIT items and validated questionnaires. Concurrent validity was consistently demonstrated across different languages for COH-FIT items. CFA confirmed EFA results of five first-order factors (anxiety, depression, post-traumatic, psychotic, psychophysiologic symptoms) and revealed a single second-order factor P-score, with high internal reliability (ω = 0.95). Factor structure was consistent across age and sex. Conclusions: COH-FIT is a valid instrument to globally measure mental health during infection times. The P-score is a valid measure of multidimensional mental health