The SdiA-Regulated Gene srgE Encodes a Type III Secreted Effector

Salmonella enterica serovar Typhimurium is a food-borne pathogen that causes severe gastroenteritis. The ability of Salmonella to cause disease depends on two type III secretion systems (T3SSs) encoded in two distinct Salmonella pathogenicity islands, 1 and 2 (SPI1 and SPI2, respectively). S. Typhimurium encodes a solo LuxR homolog, SdiA, which can detect the acyl-homoserine lactones (AHLs) produced by other bacteria and upregulate the rck operon and the srgE gene. SrgE is predicted to encode a protein of 488 residues with a coiled-coil domain between residues 345 and 382. In silico studies have provided conflicting predictions as to whether SrgE is a T3SS substrate. Therefore, in this work, we tested the hypothesis that SrgE is a T3SS effector by two methods, a β-lactamase activity assay and a split green fluorescent protein (GFP) complementation assay. SrgE with β-lactamase fused to residue 40, 100, 150, or 300 was indeed expressed and translocated into host cells, but SrgE with β-lactamase fused to residue 400 or 488 was not expressed, suggesting interference by the coiled-coil domain. Similarly, SrgE with GFP S11 fused to residue 300, but not to residue 488, was expressed and translocated into host cells. With both systems, translocation into host cells was dependent upon SPI2. A phylogenetic analysis indicated that srgE is found only within Salmonella enterica subspecies. It is found sporadically within both typhoidal and nontyphoidal serovars, although the SrgE protein sequences found within typhoidal serovars tend to cluster separately from those found in nontyphoidal serovars, suggesting functional diversification.     

Genetic dissection of days to flowering via genome-wide association studies in Turkish common bean germplasm

Common bean is a nutrient‐dense legume crop serving as a source of food for millions of people. Characterization of unexplored common bean germplasm to unlock the phenotypic and genetic variations is still needed to explore the breeding potential of this crop. The current study aimed to dissect the genetic basis having association for days to flowering (DF). A total of 188 common bean accessions collected from 19 provinces of Turkey were used as plant material under five environments and two locations. Analysis of variance (ANOVA) revealed that genotypes and genotype by environment interaction have significant effects on DF. A total of 10 most stable accessions were evaluated from stability analysis. Overall maximum (75) and minimum (54) DF were observed for Hakkari-51 and Mus-46 accessions, respectively. The implemented constellation plot divided studied germplasm according to their DF and growth habit. A total of 7900 DArTseq markers were used for association analysis. Mixed linear model using the Q + K Model resulted a total of 18 DArTseq markers from five environments. DArT-8668385 marker identified in Bolu during 2016 was also associated with DF in Sivas during 2017. Combined data of five years resulted a total of four markers (DArT-22346534, DArT-3369768, DArT-3374613, and DArT-3370801) having significant association ( p  <  0.01 ) for DF. DArT-22346534 present on Pv 08 accounted a maximum of 9.89% variation to the studied trait. A total of four putative candidate genes were predicted from sequences reflecting homology to identified four DArTseq markers. We envisage that exploitation of identified DArTseq markers will hopefully beneficial for the development of new common bean varieties having better adaptation ability to changing climatic conditions.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-01029-8.     

Macrophage sub-populations and the lipoxin A4 receptor implicate active inflammation during equine tendon repair

Macrophages (Mφ) orchestrate inflammatory and reparatory processes in injured connective tissues but their role during different phases of tendon healing is not known. We investigated the contribution of different Mφ subsets in an equine model of naturally occurring tendon injury. Post mortem tissues were harvested from normal (uninjured), sub-acute (3-6 weeks post injury) and chronically injured (>3 months post injury) superficial digital flexor tendons. To determine if inflammation was present in injured tendons, Mφ sub-populations were quantified based on surface antigen expression of CD172a (pan Mφ), CD14(high)CD206(low) (pro-inflammatory M1Mφ), and CD206(high) (anti-inflammatory M2Mφ) to assess potential polarised phenotypes. In addition, the Lipoxin A(4) receptor (FPR2/ALX) was used as marker for resolving inflammation. Normal tendons were negative for both Mφ and FPR2/ALX. In contrast, M1Mφ predominated in sub-acute injury, whereas a potential phenotype-switch to M2Mφ polarity was seen in chronic injury. Furthermore, FPR2/ALX expression by tenocytes was significantly upregulated in sub-acute but not chronic injury. Expression of the FPR2/ALX ligand Annexin A1 was also significantly increased in sub-acute and chronic injuries in contrast to low level expression in normal tendons. The combination of reduced FPR2/ALX expression and persistence of the M2Mφ phenotype in chronic injury suggests a potential mechanism for incomplete resolution of inflammation after tendon injury. To investigate the effect of pro-inflammatory mediators on lipoxin A(4) (LXA(4)) production and FPR2/ALX expression in vitro, normal tendon explants were stimulated with interleukin-1 beta and prostaglandin E(2). Stimulation with either mediator induced LXA(4) release and maximal upregulation of FPR2/ALX expression after 72 hours. Taken together, our data suggests that although tenocytes are capable of mounting a protective mechanism to counteract inflammatory stimuli, this appears to be of insufficient duration and magnitude in natural tendon injury, which may potentiate chronic inflammation and fibrotic repair, as indicated by the presence of M2Mφ.     

Impacts of harvesting intensity on tree taxonomic diversity,structural diversity,population structure,and stability in a West African mangrove forest

Wetlands Ecology and Management - Understanding the impacts of wood harvesting intensity on the diversity and structure of ecosystems such as mangroves is essential for defining actions for their...     

Plants in traditional home gardens: richness,composition, conservation and implications for native biodiversity in Benin

Home gardens have received increasing attention and have been insistently presented as hotspots for agro-biodiversity over the last decades. However, apart from their exceptional high plant species diversity, there is little quantitative evidence of the effectiveness of plant species conservation in home gardens. This study examined this issue by assessing (i) the size and membership of garden flora and the contribution to the maintenance of the national flora, (ii) how home garden flora connects to the larger ecosystem it belongs to and (iii) the conservation status of plant species at the home garden level. 360 home gardens distributed in three agro-ecological zones and nine phyto-geographical districts in Benin were visited and inventoried. Diversity parameters at different taxonomic levels were calculated. Species accumulation and spatial occupancy, multivariate methods and rarity index were also used for data analysis. Findings showed that the 360 studied home gardens hosted up to 14.21% of plant species and 44.32% of plant families of the national flora. Home garden flora was constantly dominated by exotic plant species but strongly connected to their surrounding ecosystems, being composed of at least 60% of plant species from their phyto-geographical districts. Finally, home garden plant species were mostly rare and threatened at the home garden level. In this study, we acknowledge the contribution of home gardens to the maintenance of plant species diversity at regional and global levels than local level. Based on the observed prevalence of exotic species, HG effectiveness in sustainably conserving native plant species biodiversity remains questionable.     

Molecular Mimicry by an F-Box Effector of Legionella pneumophila Hijacks a Conserved Polyubiquitination Machinery within Macrophages and Protozoa

The ability of Legionella pneumophila to proliferate within various protozoa in the aquatic environment and in macrophages indicates a remarkable evolution and microbial exploitation of evolutionarily conserved eukaryotic processes. Ankyrin B (AnkB) of L. pneumophila is a non-canonical F-box-containing protein, and is the only known Dot/Icm-translocated effector of L. pneumophila essential for intra-vacuolar proliferation within both macrophages and protozoan hosts. We show that the F-box domain of AnkB and the ⁹L¹⁰P conserved residues are essential for intracellular bacterial proliferation and for rapid acquisition of polyubiquitinated proteins by the Legionella-containing vacuole (LCV) within macrophages, Dictyostelium discoideum, and Acanthamoeba. Interestingly, translocation of AnkB and recruitment of polyubiquitinated proteins in macrophages and Acanthamoeba is rapidly triggered by extracellular bacteria within 5 min of bacterial attachment. Ectopically expressed AnkB within mammalian cells is localized to the periphery of the cell where it co-localizes with host SKP1 and recruits polyubiquitinated proteins, which results in restoration of intracellular growth to the ankB mutant similar to the parental strain. While an ectopically expressed AnkB-⁹L¹⁰P/AA variant is localized to the cell periphery, it does not recruit polyubiquitinated proteins and fails to trans-rescue the ankB mutant intracellular growth defect. Direct in vivo interaction of AnkB but not the AnkB-⁹L¹⁰P/AA variant with the host SKP1 is demonstrated. Importantly, RNAi-mediated silencing of expression of SKP1 renders the cells non-permissive for intracellular proliferation of L. pneumophila. The role of AnkB in exploitation of the polyubiquitination machinery is essential for intrapulmonary bacterial proliferation in the mouse model of Legionnaires'' disease. Therefore, AnkB exhibits a novel molecular and functional mimicry of eukaryotic F-box proteins that exploits conserved polyubiquitination machinery for intracellular proliferation within evolutionarily distant hosts.     

Assessment and Clinical Utility of a Non-Next-Generation Sequencing-Based Non-Invasive Prenatal Testing Technology

Background: Rolling-circle replication (RCR) is a novel technology that has not been applied to cell-free DNA (cfDNA) testing until recently. Given the cost and simplicity advantages of this technology compared to other platforms currently used in cfDNA analysis, an assessment of RCR in clinical laboratories was performed. Here, we present the first validation study from clinical laboratories utilizing RCR technology. Methods: 831 samples from spontaneously pregnant women carrying a singleton fetus, and 25 synthetic samples, were analyzed for the fetal risk of trisomy 21 (T21), trisomy 18 (T18) and trisomy 13 (T13), by three laboratories on three continents. All the screen-positive pregnancies were provided post-test genetic counseling and confirmatory diagnostic invasive testing (e.g., amniocentesis). The screen-negative pregnancies were routinely evaluated at birth for fetal aneuploidies, using newborn examinations, and any suspected aneuploidies would have been offered diagnostic testing or confirmed with karyotyping. Results: The study found rolling-circle replication to be a highly viable technology for the clinical assessment of fetal aneuploidies, with 100% sensitivity for T21 (95% CI: 82.35–100.00%); 100.00% sensitivity for T18 (71.51–100.00%); and 100.00% sensitivity for T13 analyses (66.37–100.00%). The specificities were >99% for each trisomy (99.7% (99.01–99.97%) for T21; 99.5% (98.62–99.85%) for T18; 99.7% (99.03–99.97%) for T13), along with a first-pass no-call rate of 0.93%. Conclusions: The study showed that using a rolling-circle replication-based cfDNA system for the evaluation of the common aneuploidies would provide greater accuracy and clinical utility compared to conventional biochemical screening, and it would provide comparable results to other reported cfDNA methodologies.     

Species richness,cultural importance,and prioritization of wild spices for conservation in the Sudano-Guinean zone of Benin (West Africa)

Background

Spices have always been used for their flavor-enhancement characteristics and for their medicinal properties. In Benin, scientific research on spices is scarce, despite their importance in the local population’s daily needs. This study investigated the diversity of wild spices and documented the associated traditional knowledge that can be used for their valuation, domestication, and sustainable management in the Sudano-Guinean Zone of Benin.

Methods

Data were collected during field expeditions using semi-structured interviews in ten localities across the three phytodistricts of the zone. Species richness and Shannon’s diversity index were estimated using species accumulation curves. Use report (UR), cultural importance, use value (UV) index, and informant consensus factor (F_ic) were used to assess traditional knowledge on wild species, their local importance, and informants’ agreement among sociolinguistic groups. Priority wild spices were finally identified using an approach combining eight criteria (native status, economic value, ethnobotanical value, global distribution, national distribution, in-situ and ex-situ conservation status, legislation, and threats assessment) in four prioritization methods (point scoring procedure, point scoring procedure with weighting, compound ranking system, and binomial ranking system).

Results

A total of 14 species, belonging to 12 genera and 9 families, were inventoried. The most prominent families were Zingiberaceae (21.43%), Annonaceae (21.43%), and Rutaceae (14.29%). More than 200 specific uses were reported, with the Tchabè people holding the greatest level of knowledge (70 uses; UR?=?5.70?±?0.33). The culturally most important spices differed among sociolinguistic groups. Most of the informants agree on the use of the species among (F_ic = 0.72–0.98) and across the considered use categories (F_ic = 0.88–0.99). The highest UV were registered for Aframomum alboviolaceum (UV?=?0.93), Lippia multiflora (UV?=?0.76), and Aframomum angustifolium (UV?=?0.18). Overall, people perceived wild spices as declining due to agriculture, grazing, and drought. Five species, A. alboviolaceum, L. multiflora, Monodora tenuifolia, Xylopia aethiopica, and Z. zanthoxyloides, were the most prioritized for conservation.

Conclusions

This study provides information relevant for the implementation of conservation and domestication actions of wild spices in Benin. Priority species could be integrated into traditional agroforestry systems (e.g., home gardens). However, for this to be effective, further research should be undertaken on morphological and genetic diversity and propagation methods of priority wild spices.

     

Women’s Traditional Knowledge,Use Value,and the Contribution of Tamarind (<Emphasis Type="Italic">Tamarindus indica</Emphasis> L.) to Rural Households’ Cash Income in Benin

Women’s Traditional Knowledge, Use Value, and the Contribution of Tamarind ( Tamarindus indica L.) to Rural Households’ Cash Income in Benin. This study examined differences in knowledge, use values, and contribution of tamarind (Tamarindus indica) to women’s cash income during the dry season, focusing on seven tribal groups in Benin. Data were gathered using semistructured individual interviews and monitoring, and were analyzed using quantitative ethnobotanical methods. Principal component analysis was applied to describe the use value and use forms of tamarind according to different tribes. Tamarind was found to play an important role in local communities’ livelihoods. Overall, 26 different uses were mentioned for tamarind products. Most commonly, the fruit (pulp) was used to make beverages, as a laxative and purgative, and it seems to be the only plant part sold commercially. Bark was frequently used as a medicine to treat wounds, and leaves were used to make porridge and as an antibiotic. Medicinal, cultural, and material use categories were correlated best with the Fulani, whereas commerce was most correlated with Gourma tribes (PCA analysis). There were significant differences for tamarind utilization among the tribal groups, with overall ethnobotanical use values (EUV_T) ranging from 10 to 14, and contribution to cash income ranging from 8.8% to 56.4%. In view of its domestication potential, it is crucial that traditional tribal knowledge of tamarind be preserved and integrated into management policies. Further development and research needs for utilization and conservation are improvement of commercialization, organization of market channels, and extent of genetic diversity within and among populations.     

Xanthones inhibitors of α-glucosidase and glycation from Garcinia nobilis

One new xanthone, caroxanthone (1) together with six known xanthones, 4-prenyl-2-(3,7-dimethyl-2,6-octadienyl)-1,3,5,8-tetrahydroxyxanthone (2), smeathxanthone A (3), gartanin (4), euxanthone (5), 8-hydroxycudraxanthone G (6) and morusignin I (7) were isolated from the stem bark of Garcinia nobilis. The structures were determined by 1D- and 2D-NMR techniques. All these compounds were tested for anti-glycation, α-glucosidase and α-chymotrypsin activities. Some of them exhibited strong to moderate α-glucosidase activities, while none of them inhibited α-chymotrypsin. Compounds 6 and 7 were found to be modest α-glucosidase inhibitors with IC₅₀ values of 76 μM and 84 μM, respectively.