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Crop wild relatives (CWR) provide a valuable resource for improving crops. They possess desirable traits that confer resilience to various environmental stresses. To fully utilize crop wild relatives in breeding and conservation programs, it is important to understand the genetic basis of their adaptation. Landscape genomics associates environments with genomic variation and allows for examining the genetic basis of adaptation. Our study examined the differences in allele frequency of 15,416 single nucleotide polymorphisms (SNPs) generated through genotyping by sequencing approach among 153 accessions of 15 wild eggplant relatives and two cultivated species from Africa, the principal hotspot of these wild relatives. We also explored the correlation between these variations and the bioclimatic and soil conditions at their collection sites, providing a comprehensive understanding of the genetic signals of environmental adaptation in African wild eggplant. Redundancy analysis (RDA) results showed that the environmental variation explained 6% while the geographical distances among the collection sites explained 15% of the genomic variation in the eggplant wild relative populations when controlling for population structure. Our findings indicate that even though environmental factors are not the main driver of selection in eggplant wild relatives, it is influential in shaping the genomic variation over time. The selected environmental variables and candidate SNPs effectively revealed grouping patterns according to the environmental characteristics of sampling sites. Using four genotype-environment association methods, we detected 396 candidate SNPs (2.5% of the initial SNPs) associated with eight environmental factors. Some of these SNPs signal genes involved in pathways that help adapt to environmental stresses such as drought, heat, cold, salinity, pests, and diseases. These candidate SNPs will be useful for marker-assisted improvement and characterizing the germplasm of this crop for developing climate-resilient eggplant varieties. The study provides a model for applying landscape genomics to other crops' wild relatives.
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Soil microbiome science, rapidly evolving, predominantly focuses on field crop soils. However, understanding garden soil microbiomes is essential for enhancing food production sustainability in garden environments. This study aimed to unveil the bacteriome diversity and composition in rooftop garden soils (RGS) and surface garden soils (SGS) across urban (Dhaka North and Dhaka South City Corporations) and peri-urban (Gazipur City Corporation) areas of Dhaka Division, Bangladesh. We analyzed 11 samples, including six RGS and five SGS samples from 11 individual gardens using 16S rRNA (V3-V4 region) gene-based amplicon sequencing. A total of 977 operational taxonomic units (OTUs), including 270 and 707 in RGS and SGS samples, respectively, were identified. The observed OTUs were represented by 21 phyla, 45 classes, 84 orders, 173 families, and 293 genera of bacteria. Alpha diversity indices revealed significantly higher bacterial diversity in SGS samples (p = 0.01), while beta diversity analyses indicated distinct bacteriome compositions between RGS and SGS samples (p = 0.028, PERMANOVA). Despite substantial taxonomic variability between sample categories, there was also a considerable presence of shared bacterial taxa. At the phylum level, Bacilliota (61.14%), Pseudomonadota (23.42%), Actinobacteria (6.33%), and Bacteroidota (3.32%) were the predominant bacterial phyla (comprising > 94.0% of the total abundances) in both types of garden soil samples. Of the identified genera, Bacillus (69.73%) and Brevibacillus (18.81%) in RGS and Bacillus (19.22%), Methylophaga (19.21%), Acinetobacter (6.27%), Corynebacterium (5.06%), Burkholderia (4.78%), Paracoccus (3.98%) and Lysobacter (2.07%) in SGS were the major bacterial genera. Importantly, we detected that 52.90% of genera were shared between RGS and SGS soil samples. Our data reveal unique and shared bacteriomes with probiotic potential in soil samples from both rooftop and surface gardens. Further studies should explore the functional roles of shared bacterial taxa in garden soils and how urban environmental factors affect microbiome composition to optimize soil health and sustainable food production.
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Bactérias , Jardins , Microbiota , RNA Ribossômico 16S , Microbiologia do Solo , Solo , Bangladesh , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , RNA Ribossômico 16S/genética , Solo/química , Monitoramento Ambiental , Biodiversidade , CidadesRESUMO
The introduction of plant pathogens can quickly reshape disease dynamics in island agro-ecologies, representing a continuous challenge for local crop management strategies. Xanthomonas pathogens causing tomato bacterial spot were probably introduced in Taiwan several decades ago, creating a unique opportunity to study the genetic makeup and adaptive response of this alien population. We examined the phenotypic and genotypic identity of 669 pathogen entries collected across different regions of Taiwan in the last three decades. The analysis detected a major population shift, where X. euvesicatoria and X. vesicatoria races T1 and T2 were replaced by new races of X. perforans. After its introduction, race T4 quickly became dominant in all tomato-growing areas of the island. The genomic analysis of 317 global genomes indicates that the Xanthomonas population in Taiwan has a narrow genetic background, most likely resulting from a small number of colonization events. However, despite the apparent genetic uniformity, X. perforans race T4 shows multiple phenotypic responses in tomato lines. Additionally, an in-depth analysis of effector composition suggests diversification in response to local adaptation. These include unique mutations on avrXv3 which might allow the pathogen to overcome Xv3/Rx4 resistance gene. The findings underscore the dynamic evolution of a pathogen when introduced in a semi-isolated environment and provide insights into the potential management strategies for this important disease of tomato.
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We announce the sequence of the Escherichia coli MTR_GS_S1457 strain isolated from a soil sample of a vegetable gardening system for the first time in Bangladesh. With a length of 4,918,647 bp, this strain contained one plasmid, two CRISPR arrays, 54 predicted antibiotic resistance genes, and 81 predicted virulence factor genes.
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Crop production often faces challenges from plant diseases, and biological control emerges as an effective, environmentally friendly, cost-effective, and sustainable alternative to chemical control. Wheat blast disease caused by fungal pathogen Magnaporthe oryzae Triticum (MoT), is a potential catastrophic threat to global food security. This study aimed to identify potential bacterial isolates from rice and wheat seeds with inhibitory effects against MoT. In dual culture and seedling assays, three bacterial isolates (BTS-3, BTS-4, and BTLK6A) demonstrated effective suppression of MoT growth and reduced wheat blast severity when artificially inoculated at the seedling stage. Genome phylogeny identified these isolates as Bacillus subtilis (BTS-3) and B. velezensis (BTS-4 and BTLK6A). Whole-genome analysis revealed the presence of genes responsible for controlling MoT through antimicrobial defense, antioxidant defense, cell wall degradation, and induced systemic resistance (ISR). Taken together, our results suggest that the suppression of wheat blast disease by seed endophytic B. subtilis (BTS-3) and B. velezensis (BTS-4 and BTLK6A) is liked with antibiosis and induced systemic resistance to wheat plants. A further field validation is needed before recommending these endophytic bacteria for biological control of wheat blast.
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This study announces the genome sequence of the Shigella flexneri MTR_GR_V146 strain isolated from a tomato (Solanum lycopersicum) sample in Bangladesh. This strain has a 4,624,521 bp genome length (coverage: 73.07×), 2 CRISPR arrays, 1 plasmid, 52 predicted antibiotic resistance genes, and 53 virulence factor genes.
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We announce a genome sequence of Citrobacter freundii MTR_GS_V1777 strain isolated from a vegetable sample in Bangladesh. This strain had a genome size of 4,997,753 bp (58.7× genome coverage) and contained two plasmids, typed as sequence type ST124, 38 predicted antibiotic resistance genes, and 77 predicted virulence factor genes.
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Reports indicate that vegetables are becoming a source of multidrug-resistant (MDR) bacteria, including Escherichia coli. Here, we present genome sequences of five MDR E. coli strains to assist future genomic analysis of this bacterium. These E. coli strains were isolated from vegetable samples of different gardening systems in Dhaka, Bangladesh.
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BACKGROUND: Neurogenesis is stimulated in the subventricular zone (SVZ) of mice with cortical brain injuries. In most of these injuries, newly generated neuroblasts attempt to migrate toward the injury, accumulating within the corpus callosum not reaching the perilesional area. METHODS: We use a murine model of mechanical cortical brain injury, in which we perform unilateral cortical injuries in the primary motor cortex of adult male mice. We study neurogenesis in the SVZ and perilesional area at 7 and 14 dpi as well as the expression and concentration of the signaling molecule transforming growth factor alpha (TGF-α) and its receptor the epidermal growth factor (EGFR). We use the EGFR inhibitor Afatinib to promote neurogenesis in brain injuries. RESULTS: We show that microglial cells that emerge within the injured area and the SVZ in response to the injury express high levels of TGF-α leading to elevated concentrations of TGF-α in the cerebrospinal fluid. Thus, the number of neuroblasts in the SVZ increases in response to the injury, a large number of these neuroblasts remain immature and proliferate expressing the epidermal growth factor receptor (EGFR) and the proliferation marker Ki67. Restraining TGF-α release with a classical protein kinase C inhibitor reduces the number of these proliferative EGFR+ immature neuroblasts in the SVZ. In accordance, the inhibition of the TGF-α receptor, EGFR promotes migration of neuroblasts toward the injury leading to an elevated number of neuroblasts within the perilesional area. CONCLUSIONS: Our results indicate that in response to an injury, microglial cells activated within the injury and the SVZ release TGF-α, activating the EGFR present in the neuroblasts membrane inducing their proliferation, delaying maturation and negatively regulating migration. The inactivation of this signaling pathway stimulates neuroblast migration toward the injury and enhances the quantity of neuroblasts within the injured area. These results suggest that these proteins may be used as target molecules to regenerate brain injuries.
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Lesões Encefálicas , Células-Tronco Neurais , Animais , Masculino , Camundongos , Lesões Encefálicas/metabolismo , Movimento Celular , Receptores ErbB/metabolismo , Células-Tronco Neurais/metabolismo , Neurogênese/fisiologia , Fator de Crescimento Transformador alfaRESUMO
Bacterial blight disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious constraints in rice production. The most sustainable strategy to combat the disease is the deployment of host plant resistance. Earlier, we identified an introgression line, IR 75084-15-3-B-B, derived from Oryza officinalis possessing broad-spectrum resistance against Xoo. In order to understand the inheritance of resistance in the O. officinalis accession and identify genomic region(s) associated with resistance, a recombinant inbred line (RIL) mapping population was developed from the cross Samba Mahsuri (susceptible to bacterial blight) × IR 75084-15-3-B-B (resistant to bacterial blight). The F2 population derived from the cross segregated in a phenotypic ratio of 3: 1 (resistant susceptible) implying that resistance in IR 75084-15-3-B-B is controlled by a single dominant gene/quantitative trait locus (QTL). In the F7 generation, a set of 47 homozygous resistant lines and 47 homozygous susceptible lines was used to study the association between phenotypic data obtained through screening with Xoo and genotypic data obtained through analysis of 7K rice single-nucleotide polymorphism (SNP) chip. Through composite interval mapping, a major locus was detected in the midst of two flanking SNP markers, viz., Chr11.27817978 and Chr11.27994133, on chromosome 11L with a logarithm of the odds (LOD) score of 10.21 and 35.93% of phenotypic variation, and the locus has been named Xa48t. In silico search in the genomic region between the two markers flanking Xa48t identified 10 putatively expressed genes located in the region of interest. The quantitative expression and DNA sequence analysis of these genes from contrasting parents identified the Os11g0687900 encoding an NB-ARC domain-containing protein as the most promising gene associated with resistance. Interestingly, a 16-bp insertion was noticed in the untranslated region (UTR) of the gene in the resistant parent, IR 75084-15-3-B-B, which was absent in Samba Mahsuri. The association of Os11g0687900 with resistance phenotype was further established by sequence-based DNA marker analysis in the RIL population. A co-segregating PCR-based INDEL marker, Marker_Xa48, has been developed for use in the marker-assisted breeding of Xa48t.
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Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), threatens global food security and the livelihood of small-scale rice producers. Analyses of Xoo collections from Asia, Africa and the Americas demonstrated complete continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemic African Xoo, carry Asian-type TAL effectors targeting the sucrose transporter SWEET11a and iTALes suppressing Xa1. Phylogenomics clustered these strains with Xoo from Southern-China. African rice varieties do not carry effective resistance. To protect African rice production against this emerging threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit all known TALe-binding elements in three SWEET promoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains of Xoo, including strains recently discovered in Tanzania. The strategy could help to protect global rice crops from BB pandemics.
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Oryza , Xanthomonas , Edição de Genes , Oryza/genética , Efetores Semelhantes a Ativadores de Transcrição , Xanthomonas/genética , Tanzânia , Doenças das Plantas/microbiologia , Resistência à Doença/genéticaRESUMO
Neuropathological aging is associated with memory impairment and cognitive decline, affecting several brain areas including the neurogenic niche of the dentate gyrus of the hippocampus (DG). In the healthy brain, homeostatic mechanisms regulate neurogenesis within the DG to facilitate the continuous generation of neurons from neural stem cells (NSC). Nevertheless, aging reduces the number of activated neural stem cells and diminishes the number of newly generated neurons. Strategies that promote neurogenesis in the DG may improve cognitive performance in the elderly resulting in the development of treatments to prevent the progression of neurological disorders in the aged population. Our work is aimed at discovering targeting molecules to be used in the design of pharmacological agents that prevent the neurological effects of brain aging. We study the effect of age on hippocampal neurogenesis using the SAMP8 mouse as a model of neuropathological aging. We show that in 6-month-old SAMP8 mice, episodic and spatial memory are impaired; concomitantly, the generation of neuroblasts and neurons is reduced and the generation of astrocytes is increased in this model. The novelty of our work resides in the fact that treatment of SAMP8 mice with a transforming growth factor-alpha (TGFα) targeting molecule prevents the observed defects, positively regulating neurogenesis and improving cognitive performance. This compound facilitates the release of TGFα in vitro and in vivo and activates signaling pathways initiated by this growth factor. We conclude that compounds of this kind that stimulate neurogenesis may be useful to counteract the neurological effects of pathological aging.
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Disfunção Cognitiva , Células-Tronco Neurais , Camundongos , Animais , Fator de Crescimento Transformador alfa/metabolismo , Fator de Crescimento Transformador alfa/farmacologia , Neurogênese , Células-Tronco Neurais/metabolismo , Neurônios/metabolismo , Hipocampo/metabolismo , Disfunção Cognitiva/metabolismo , Giro Denteado , Envelhecimento/metabolismoRESUMO
Harmonic mechanisms orchestrate neurogenesis in the healthy brain within specific neurogenic niches, which generate neurons from neural stem cells as a homeostatic mechanism. These newly generated neurons integrate into existing neuronal circuits to participate in different brain tasks. Despite the mechanisms that protect the mammalian brain, this organ is susceptible to many different types of damage that result in the loss of neuronal tissue and therefore in alterations in the functionality of the affected regions. Nevertheless, the mammalian brain has developed mechanisms to respond to these injuries, potentiating its capacity to generate new neurons from neural stem cells and altering the homeostatic processes that occur in neurogenic niches. These alterations may lead to the generation of new neurons within the damaged brain regions. Notwithstanding, the activation of these repair mechanisms, regeneration of neuronal tissue within brain injuries does not naturally occur. In this review, we discuss how the different neurogenic niches respond to different types of brain injuries, focusing on the capacity of the progenitors generated in these niches to migrate to the injured regions and activate repair mechanisms. We conclude that the search for pharmacological drugs that stimulate the migration of newly generated neurons to brain injuries may result in the development of therapies to repair the damaged brain tissue.
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Lesões Encefálicas , Células-Tronco Neurais , Animais , Neurogênese/fisiologia , Neurônios , Encéfalo/fisiologia , MamíferosRESUMO
Grafted tomato (Solanum lycopersicum L.) is widely used to manage soil-borne diseases (Lee et.al 2010). In Taiwan, grafting on eggplant (S. melongena L.) rootstock have been extensively used to reduce bacterial wilt in tomato production. In July 2019, wilting plants were found at a cherry tomato farm (~ 0.5 ha) located at Miaoli County. About 10% tomatoes of cv. 'Mint Shine' grafted onto the eggplant rootstock displayed wilt symptoms. Numerous leaflets with chlorosis, inter-vein yellowing, V-shaped necrotic lesions and withered leaves were observed on the affected plants. Some plants eventually wilted and died. A cut at the grafting site revealed the vascular discolorations on both scion (tomato) and rootstock (eggplant). A fungus with a compact whitish colony was consistently isolated from the symptomatic vascular tissue by using acidified potato dextrose agar (PDA) plates. Two isolates, Ve2 from eggplant and Ve4 from tomato, grown on PDA plates were characterized. Both Ve2 and Ve4 grow slowly (ca. 2.6 mm/day at 28 oC) and shared almost identical cultural and morphological characteristics. They first showed whitish mycelium and cream color in reverse within 1 week. Later, numerous microsclerotia developed evenly over the colony and the reverse color turned dark black. Microscopic observations revealed hyaline hyphae with black, elongated, irregularly spherical microsclerotia measuring 31.3 to 71.5 × 16.8 to 49.0 µm (average 50.4 × 28.5 µm) on a 3-week-old PDA culture. Abundant hyaline, single-celled, ellipsoida conidia measuring 2.7 to 4.7 × 0.9 to 3.2 µm (average 3.7 × 1.9 µm) and verticillate conidiophores were observed. The fungus was identified as Verticilium dahliae based on the consistent morphological characteristics (Hawksworth et. al 1970). To confirm the identity, the internal transcribed spacer regions of ribosomal DNA, amplified by PCR with universal primers ITS4/ITS5 (White et.al 1990), were sequenced. Both strains shared the same sequences (GenBank MZ734460; MZ736637), and BLASTn searching was 100% identical to many records of V. dahliae including an ex-epitype CBS130341. Pathogenicity was tested on 3-week-old seedlings of tomato cv. 'Bonny best' and eggplant cv. 'Longship' by a root dip method (Bhat & Subbarao 2007). Eighteen plants arranged into three replications were inoculated for each host-isolate combination, and incubated in the greenhouse at 25±3â. The pathogenicity test was repeated two times, with the result that both isolates were pathogenic to tomato and eggplant. Both isolates induced wilt symptoms in all inoculated plants within 14 days post-inoculation (DPI). Severe leaf drop, wilting and vascular discoloration in all inoculated eggplant whereas slight yellowing and mildly stunt growth in tomato were observed at 21 DPI. Koch's postulates were fulfilled by re-isolating the same fungus from both infected tomato and eggplant. All uninoculated plants remained health and no V. dahliae was isolated from them. To our knowledge, this is the first report of V. dahliae and Verticilium wilt of grafted tomato caused by this pathogen in Taiwan. This pathogen affects over 400 plant species and has resulted in significant economic losses in many regions of world (Subbarao 2020). It is important to investigate the distribution and extent of damage caused by this emerging pathogen on Solanaceous or other crops.
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Biofilms in milking equipment on dairy farms have been associated with failures in cleaning and sanitizing protocols. These biofilms on milking equipment can be a source of contamination for bulk tank milk and a concern for animal and public health, as biofilms can become on-farm reservoirs for pathogenic bacteria that cause disease in cows and humans. This report describes a cross-sectional study on 3 dairy farms, where hoses used to divert waste milk, transition milk, and colostrum were analyzed by culture methods and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to assess the presence of pathogenic bacteria such as Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella spp. In addition, the presence of biofilms was analyzed using scanning electron microscopy and confocal spectral microscopy. Biofilms composed of multispecies microbial communities were observed on the surfaces of all milk hoses. In two dairy farms, S. aureus, P. aeruginosa, Klebsiella pneumoniae, and Klebsiella oxytoca were isolated from the milk hose samples collected. Cleaning and sanitation protocols of all surfaces in contact with milk or colostrum are crucial. Hoses used to collect waste milk, colostrum, and transition milk can be a source of biofilms and hence pathogenic bacteria. Waste milk used to feed calves can constitute a biosecurity issue and a source of pathogens, therefore an increased exposure and threat for the whole herd health and, potentially, for human health.
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Achieving the distinctive complex behaviors of adult mammals requires the development of a great variety of specialized neural circuits. Although the development of these circuits begins during the embryonic stage, they remain immature at birth, requiring a postnatal maturation process to achieve these complex tasks. Understanding how the neuronal membrane properties and circuits change during development is the first step to understand their transition into efficient ones. Thus, using whole cell patch clamp recordings, we have studied the changes in the electrophysiological properties of layer V pyramidal neurons of the rat primary motor cortex during postnatal development. Among all the parameters studied, only the voltage threshold was established at birth and, although some of the changes occurred mainly during the second postnatal week, other properties such as membrane potential, capacitance, duration of the post-hyperpolarization phase or the maximum firing rate were not defined until the beginning of adulthood. Those modifications lead to a decrease in neuronal excitability and to an increase in the working range in young adult neurons, allowing more sensitive and accurate responses. This maturation process, that involves an increase in neuronal size and changes in ionic conductances, seems to be influenced by the neuronal type and by the task that neurons perform as inferred from the comparison with other pyramidal and motor neuron populations.
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A small library of phorbol 12,13-diesters bearing low lipophilicity ester chains was prepared as potential neurogenic agents in the adult brain. They were also used in a targeted UHPLC-HRMS screening of the latex of Euphorbia resinifera. Two new 12-deoxy-16-hydroxyphorbol 13,16-diesters were isolated, and their structures were deduced using two-dimensional NMR spectroscopy and NOE experiments. The ability of natural and synthetic compounds to stimulate transforming growth factor alpha (TFGα) release, to increase neural progenitor cell proliferation, and to stimulate neurogenesis was evaluated. All compounds that facilitated TGFα release promoted neural progenitor cell proliferation. The presence of two acyloxy moieties on the tigliane skeleton led to higher levels of activity, which decreased when a free hydroxyl group was at C-12. Remarkably, the compound bearing isobutyryloxy groups was the most potent on the TGFα assay and at inducing neural progenitor cell proliferation in vitro, also leading to enhanced neurogenesis in vivo when administered intranasally to mice.