APSIM-based modeling approach to understand sorghum production environments in Mali

Sorghum production system in the semi-arid region of Africa is characterized by low yields which are generally attributed to high rainfall variability, poor soil fertility, and biotic factors. Production constraints must be well understood and quantified to design effective sorghum-system improvements. This study uses the state-of-the-art in silico methods and focuses on characterizing the sorghum production regions in Mali for drought occurrence and its effects on sorghum productivity. For this purpose, we adapted the APSIM-sorghum module to reproduce two cultivated photoperiod-sensitive sorghum types across a latitude of major sorghum production regions in Western Africa. We used the simulation outputs to characterize drought stress scenarios. We identified three main drought scenarios: (i) no-stress; (ii) early pre-flowering drought stress; and (iii) drought stress onset around flowering. The frequency of drought stress scenarios experienced by the two sorghum types across rainfall zones and soil types differed. As expected, the early pre-flowering and flowering drought stress occurred more frequently in isohyets < 600 mm, for the photoperiod-sensitive, late-flowering sorghum type. In isohyets above 600 mm, the frequency of drought stress was very low for both cultivars. We quantified the consequences of these drought scenarios on grain and biomass productivity. The yields of the highly-photoperiod-sensitive sorghum type were quite stable across the higher rainfall zones > 600 mm, but was affected by the drought stress in the lower rainfall zones < 600 mm. Comparatively, the less photoperiod-sensitive cultivar had notable yield gain in the driest regions < 600 mm. The results suggest that, at least for the tested crop types, drought stress might not be the major constraint to sorghum production in isohyets > 600 mm. The findings from this study provide the entry point for further quantitative testing of the Genotype × Environment × Management options required to optimize sorghum production in Mali.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13593-023-00909-5.

Characterization of adaptation mechanisms in sorghum using a multireference back-cross nested association mapping design and envirotyping

Identifying the genetic factors impacting the adaptation of crops to environmental conditions is of key interest for conservation and selection purposes. It can be achieved using population genomics, and evolutionary or quantitative genetics. Here we present a sorghum multireference back-cross nested association mapping population composed of 3,901 lines produced by crossing 24 diverse parents to 3 elite parents from West and Central Africa-back-cross nested association mapping. The population was phenotyped in environments characterized by differences in photoperiod, rainfall pattern, temperature levels, and soil fertility. To integrate the multiparental and multi-environmental dimension of our data we proposed a new approach for quantitative trait loci (QTL) detection and parental effect estimation. We extended our model to estimate QTL effect sensitivity to environmental covariates, which facilitated the integration of envirotyping data. Our models allowed spatial projections of the QTL effects in agro-ecologies of interest. We utilized this strategy to analyze the genetic architecture of flowering time and plant height, which represents key adaptation mechanisms in environments like West Africa. Our results allowed a better characterization of well-known genomic regions influencing flowering time concerning their response to photoperiod with Ma6 and Ma1 being photoperiod-sensitive and the region of possible candidate gene Elf3 being photoperiod-insensitive. We also accessed a better understanding of plant height genetic determinism with the combined effects of phenology-dependent (Ma6) and independent (qHT7.1 and Dw3) genomic regions. Therefore, we argue that the West and Central Africa-back-cross nested association mapping and the presented analytical approach constitute unique resources to better understand adaptation in sorghum with direct application to develop climate-smart varieties.

Evaluation of the Impact of Population Management on the Genetic Parameters of Selected Spiral-Horned Antelopes

The rapid loss of biodiversity and the associated reduction and fragmentation of habitats means that ex situ populations have become an important part of species conservation. These populations, which are often established from a small number of founders, require careful management to avoid the negative effects of genetic drift and inbreeding. Although the inclusion of molecular data is recommended, their availability for captive breeding management remains limited. The aim of this study was to evaluate the relationship between the levels of genetic diversity in six spiral-horned antelope taxa bred under human care and their respective management strategies, conservation status, demography, and geographic origin, using 10 nuclear DNA microsatellite loci and mitochondrial control region DNA sequences. Our findings include associations between genetic diversity and management intensity but also with the diversity and contribution of wild populations to captive founders, with some populations apparently composed of animals from divergent wild lineages elevating captive genetic diversity. When population sizes are large, the potential advantages of maximizing genetic diversity in widely outcrossed populations may need careful consideration with respect to the potential disruption of adaptive diversity. Genetic data serve as a robust tool for managing captive populations, yet their interpretation necessitates a comprehensive understanding of species biology and history.

An Optimized and Cost-Effective RNA Extraction Method for Secondary Metabolite-Enriched Tissues of Norway Spruce (Picea abies)

Since the development of next-generation sequencing techniques and with the growing interest in transcriptomic studies, there is a demand for high-throughput RNA extraction techniques. General RNA extraction protocols are unreliable when it comes to the quality and quantity of isolated RNA obtained from different tissue types of different plant species. Despite Norway spruce (Picea abies) being one of the most significant and commercially valuable tree species in European forests, only limited genetic research is available. In this study, we developed a cetyltrimethylammonium bromide (CTAB) protocol by modifying the original method. We compared this CTAB protocol with other widely used methods for extracting RNA from different tissues (needle, phloem, and root) of Norway spruce, known for its richness in polyphenols, polysaccharides, and secondary metabolites. The modified CTAB method proves to be superior to the kit-based and TRIzol-based methods for extracting RNA from the metabolite-rich tissues of Norway spruce, resulting in high RNA quality and integrity values (RIN~7-9). The modified CTAB RNA extraction method is rapid, cost-effective, and relatively simple in yielding the desired RNA quality from Norway spruce tissues. It is optimal for RNA sequencing and other downstream molecular applications.

Substituting Solid Fossil Fuels with Torrefied Timber Products

As a push towards alternative and renewable resources for heat and power generation, biomass and thermally treated fuels from biomass may be viable options in the upcoming economic reality. This study the verified mass and energy balance of spruce woody biomass after low temperature pyrolysis between 250 and 550 °C. The results showed that low-temperature pyrolysis can yield high-grade biochar suitable for substitution of fossil fuels. Crucially, the net calorific value of biochar processed at 350 °C substantially exceeded that of brown coal. An economic analysis was carried out on the assumption of the current economic reality in the Czech Republic. It was shown that even if the price of the biochar slightly increased, it would still be beneficial to invest in torrefaction technology over paying carbon credits.

Same place, different time, head up: Multiple antipredator responses to a recolonizing apex predator

Prey adjust their antipredator behavioral tactics to minimize the risk of an encounter with predators. Spatiotemporal responses of prey to predators have been reported, but the nature of antipredator response is not ubiquitous and it is the object of increasing interest, especially considering the recent recovery of large carnivores in Europe, and the potential for behavioral antipredator responses to elicit consequences at the ecosystem level. We have tested multiple antipredator responses by fallow deer Dama dama to wolf Canis lupus in a Mediterranean protected area recently recolonized by this apex predator. Through intensive camera trapping, we tested for temporal and spatial association between predator and prey, and we have also studied deer vigilance in forest habitats where focal observations are usually impossible. Wolf detection rates were spatially associated with those of fallow deer. Accordingly, no evidence was found for fallow deer avoiding sites with higher predator detection rates. Temporal activity patterns were significantly different between the 2 species, with the wolf being mainly nocturnal whereas fallow deer was active especially during daylight. A comparison with a preliminary study strongly suggests an increase in the diurnal activity of fallow deer along with the stabilization of wolf presence in the area. Both the rate and the duration of vigilance of female fallow deer increased with the local frequency of wolf activity. We suggest an antipredator response based on temporal-rather than spatial-avoidance, as well as increased vigilance.

Chemical Composition of Essential Oils and Supercritical Carbon Dioxide Extracts from Amomum kravanh, Citrus hystrix and Piper nigrum 'Kampot'

The fruits of Amomum kravanh, Citrus hystrix and Piper nigrum 'Kampot' are traditionally used as spices in Cambodian cuisine. In this study, the chemical composition of essential oils (EOs) and supercritical CO2 extracts from all three species was determined using GC-MS, with two columns of different polarity (HP-5/DB-HeavyWAX). Differences between the chemical profile of the EOs and CO2 extracts were observed for all species. The greatest difference was detected in A. kravanh EO containing mainly eucalyptol (78.8/72.6%), while the CO2 extract was rich in fatty acids (13/55.92%) and long-chain alkanes (25.55/9.54%). Furthermore, the results for the CO2 extract of this species differed, where tricosane (14.74%) and oleic acid (29.26%) were the main compounds identified when utilizing the HP-5 or DB-HeavyWAX columns, respectively. Moreover, the EO and CO2 extract from P. nigrum 'Kampot' fruits and the CO2 extract from C. hystrix fruit peel, containing respective amounts 34.84/39.55% (for EO) and 54.21/55.86% (for CO2 extract) of β-caryophyllene and 30.2/28.9% of β-pinene, were isolated and analyzed for the first time. Generally, these findings suggest that supercritical CO2 could potentially be used for the extraction of all three spices. Nevertheless, further research determining the most efficient extraction parameters is required before its commercial application.

First Detection of SARS-CoV-2 in White Rhinoceros during a Small-Scale Coronavirus Surveillance in the Bandia Reserve, Senegal

The SARS-CoV-2 pandemic has heightened interest in the monitoring and surveillance of coronaviruses in wildlife. Testing for the virus in animals can provide valuable insights into viral reservoirs, transmission, and pathogenesis. In this study, we present the results of the molecular surveillance project focused on coronaviruses in Senegalese wildlife. During the project, we screened fecal samples of the wild animals living in the Bandia Reserve (ten non-human primates, one giraffe, and two white rhinoceros) and the free-living urban population of African four-toed hedgehogs in Ngaparou. The results showed the absence of coronaviruses in hedgehogs, non-human primates, and a giraffe. A single positive sample was obtained from a white rhinoceros. The sequencing results of amplified RdRp gene confirmed that the detected virus was SARS-CoV-2. This study represents the first documented instance of molecular detection of SARS-CoV-2 in white rhinoceros and, therefore, extends our knowledge of possible SARS-CoV-2 hosts.

Validation of Broth Macrodilution Volatilization Method for Testing of Essential Oils in Liquid and Vapor Phase: Chemical Composition, Cytotoxicity, and Antibacterial Effect of Indian Medicinal Plants against Pneumonia-Causing Pathogens

Essential oils (EOs) have great potential in inhalation therapy for the treatment of respiratory infections. However, innovative methods for evaluation of antimicrobial activity of their vapors are still needed. The current study reports validation of the broth macrodilution volatilization method for assessment of the antibacterial properties of EOs and shows the growth-inhibitory effect of Indian medicinal plants against pneumonia-causing bacteria in liquid and vapor phase. Among all samples tested, Trachyspermum ammi EO exhibits the strongest antibacterial effect against Haemophilus influenzae, with minimum inhibitory concentrations of 128 and 256 µg/mL in the liquid and vapor phases, respectively. Furthermore, Cyperus scariosus EO is found to be nontoxic to normal lung fibroblasts assessed by modified thiazolyl blue tetrazolium bromide assay. Chemical analysis performed using gas chromatography-mass spectrometry identified α-citral, cyperotundone, and thymol as the main constituents of Cymbopogon citratus, C. scariosus, and T. ammi EOs, respectively. In addition, β-cymene is identified as the major compound of T. ammi EO vapors when analyzed using solid-phase microextraction and gas-tight syringe sampling techniques. This study demonstrates the validity of the broth macrodilution volatilization method for antimicrobial screening of volatile compounds in the vapor phase and suggests the therapeutic potential of Indian medicinal plants in inhalation therapy.

Garcinia kola: a critical review on chemistry and pharmacology of an important West African medicinal plant

Garcinia kola Heckel (Clusiaceae) is a tree indigenous to West and Central Africa. All plant parts, but especially the seeds, are of value in local folklore medicine. Garcinia kola is used in treatment of numerous diseases, including gastric disorders, bronchial diseases, fever, malaria and is used to induce a stimulating and aphrodisiac effect. The plant is now attracting considerable interest as a possible source of pharmaceutically important drugs. Several different classes of compounds such as biflavonoids, benzophenones, benzofurans, benzopyran, vitamin E derivatives, xanthones, and phytosterols, have been isolated from G. kola, of which many appears to be found only in this species, such as garcinianin (found in seeds and roots), kolanone (fruit pulp, seeds, roots), gakolanone (stem bark), garcinoic acid, garcinal (both in seeds), garcifuran A and B, and garcipyran (all in roots). They showed a wide range of pharmacological activities (e.g. analgesic, anticancer, antidiabetic, anti-inflammatory, antimalarial, antimicrobial, hepatoprotective and neuroprotective effects), though this has only been confirmed in animal models. Kolaviron is the most studied compound and is perceived by many studies as the active principle of G. kola. However, its research is associated with significant flaws (e.g. too high doses tested, inappropriate positive control). Garcinol has been tested under better conditions and is perhaps showing more promising results and should attract deeper research interest (especially in the area of anticancer, antimicrobial, and neuroprotective activity). Human clinical trials and mechanism-of-action studies must be carried out to verify whether any of the compounds present in G. kola may be used as a lead in the drug development.

Ethnobotanical inventory of medicinal plants used by Cashinahua (Huni Kuin) herbalists in Purus Province, Peruvian Amazon

This study aims to document the diversity of medicinal plants used by the Cashinahua people (also known as Huni Kuin) of the Curanja River, as well as describe and compare their uses with pharmacological and phytochemical records from previously published studies. The ethnic has been studied to a limited extent from an ethnobotanical perspective. The study area is located in the Ucayali region, eastern Central Amazon, where ancestral knowledge is preserved due to the limited accessibility of the region. Between November 2010 and June 2015, a total of 11 months were spent on the survey, which included a short-term visit to complete voucher specimen collection and taxonomic identification. We conducted semi-structured interviews with 10 Cashinahua traditional healers and 10 midwives. Vernacular names, ethnomedicinal uses, plant parts used and forms of preparation and administration were recorded. Ethnopharmacological, pharmacological and phytochemical uses were checked through survey of the previously published papers indexed on Web of Science databases between 2018 and 2022. We obtained data on 467 plant taxa, among which we highlighted 79 species unreported or rarely cited for medicinal use or phytochemical analysis. These species were spread over 60 genera and 42 botanical families, with Acanthaceae being the most represented. Leaves were used the most frequently (93.56%). Among the 79 species, the most reported therapeutic activities involved pregnancy and birth disorders (13.84%), followed by poisonings, infections and infestations. The predominant application form was external (87%). Our study indicates that there are locally valuable species that have not yet been studied for their medical potential.

Postindustrial Landscapes Are Neglected Localities That May Play an Important Role in the Urban Ecology of Ticks and Tick-Borne Diseases-A Pilot Study

BACKGROUND

Numerous recent studies have shown that ticks and tick-borne pathogens pose a considerable threat in urban areas, such as parks, playgrounds, zoos, cemeteries, etc. Abandoned postindustrial localities, and other types of vague terrain, are other examples of urban wilderness areas that have been absolutely neglected in respect to ticks and tick-borne pathogens thus far, even though they provide ideal biotopes for ticks.

METHODS

The abundance of ticks and prevalence of Borrelia burgdorferi sensu lato spirochetes were compared between a city park and an adjacent abandoned construction waste disposal site in Prague, Czechia from June to October 2021.

RESULTS

The results showed that ticks and borrelia spirochetes are present at the city park as well as at the abandoned construction waste disposal site, although in lower numbers.

DISCUSSION

According to the best of our knowledge, this is the first report describing the presence of ticks and tick-borne pathogens in an urban postindustrial landscape. More detailed studies are needed to uncover the role of these localities in the ecology of ticks and ecoepidemiology of tick-borne diseases in urban areas.

Selective accumulation of pharmaceutical residues from 6 different soils by plants: a comparative study on onion, radish, and spinach

The accumulation of six pharmaceuticals of different therapeutic uses has been thoroughly investigated and compared between onion, spinach, and radish plants grown in six soil types. While neutral molecules (e.g., carbamazepine (CAR) and some of its metabolites) were efficiently accumulated and easily translocated to the plant leaves (onion > radish > spinach), the same for ionic (both anionic and cationic) molecules seems to be minor to moderate. The maximum accumulation of CAR crosses 38,000 (onion), 42,000 (radish), and 7000 (spinach) ng g-1 (dry weight) respectively, in which the most majority of them happened within the plant leaves. Among the metabolites, the accumulation of carbamazepine 10,11-epoxide (EPC - a primary CAR metabolite) was approximately 19,000 (onion), 7000 (radish), and 6000 (spinach) ng g-1 (dry weight) respectively. This trend was considerably similar even when all these pharmaceuticals applied together. The accumulation of most other molecules (e.g., citalopram, clindamycin, clindamycin sulfoxide, fexofenadine, irbesartan, and sulfamethoxazole) was restricted to plant roots, except for certain cases (e.g., clindamycin and clindamycin sulfoxide in onion leaves). Our results clearly demonstrated the potential role of this accumulation process on the entrance of pharmaceuticals/metabolites into the food chain, which eventually becomes a threat to associated living biota.

Assessment of the incubating environment for investment in biogas technology in Syria by using AHP and SWOT

In light of the massive energy supply shortage due to the Syrian war since 2011, renewable energy adoption has a high potential to cover the actual energy demand. Hence, this study aims to shed light on the factors that affect investment in biogas technology. With the scarcity of research on alternative energies in Syria, this paper focused on the characteristics of the Syrian environment toward biogas technology adoption. The results show that Syrian society accepts and desires to adopt new technologies, representing an optimal strategy to stimulate biogas technology use and the need to spread awareness about its benefits. The SWOT model was applied to identify strengths, weaknesses, opportunities, and threats facing biogas technology adoption. The analytical hierarchy process model was applied to set priorities and make better decisions related to the knowledge of biogas, acceptance of biogas technology, desire for and common approach for its use, the resulting organic fertilizer, and administrative and financial aspects. The work concludes that the southern region was at the forefront in the areas studied in terms of weights of biogas technology investment criteria, subsequently, the central and later the coastal regions. By presenting a systematic and comprehensive approach, this study represents a roadmap to assist decision-makers in inking decisions related to adopting and deploying biogas technology on a larger scale and contributes to developing a criterion for selecting biogas sites in Syria.

Machine Learning-Based Plant Detection Algorithms to Automate Counting Tasks Using 3D Canopy Scans

This study tested whether machine learning (ML) methods can effectively separate individual plants from complex 3D canopy laser scans as a prerequisite to analyzing particular plant features. For this, we scanned mung bean and chickpea crops with PlantEye (R) laser scanners. Firstly, we segmented the crop canopies from the background in 3D space using the Region Growing Segmentation algorithm. Then, Convolutional Neural Network (CNN) based ML algorithms were fine-tuned for plant counting. Application of the CNN-based (Convolutional Neural Network) processing architecture was possible only after we reduced the dimensionality of the data to 2D. This allowed for the identification of individual plants and their counting with an accuracy of 93.18% and 92.87% for mung bean and chickpea plants, respectively. These steps were connected to the phenotyping pipeline, which can now replace manual counting operations that are inefficient, costly, and error-prone. The use of CNN in this study was innovatively solved with dimensionality reduction, addition of height information as color, and consequent application of a 2D CNN-based approach. We found there to be a wide gap in the use of ML on 3D information. This gap will have to be addressed, especially for more complex plant feature extractions, which we intend to implement through further research.