Disentangling the role of soil in structuring tropical tree communities at Tarap Hill Reserve of Bangladesh

Tarap Hill Reserve, the largest upland reserve of Bangladesh, is situated along the Indo-Burma Biodiversity Hotspot. It encompasses the last remaining patches of natural vegetation in the Northeastern Tarap Mountain System and harbors 87 % of the nationally declared red-listed vascular plant species. Despite requiring high conservation priority, this is one of the least studied reserves in the tropics. In this study, we collected vegetation and soil (eight variables) data from 68 sample plots. We identified the tree communities by cluster analysis and verified them using the multi-response permutation procedure and detrended correspondence analysis. Species richness, diversity, and compositional similarity between the communities were also estimated. In total, 116 tree species representing 69 genera were recorded within the four identified tree community types. Finally, canonical correspondence analysis with associated Monte Carlo permutation tests (499 permutations) was performed to explore the patterns of variation in tree species distribution explained by the soil variables. Soil phosphorus, organic matter content, and pH were most closely correlated with tree compositional variation. Thus, conservation strategies that take into account variations in these influential soil factors may aid in the conservation of trees in the reserve.     

Inorganic Phosphate and Sodium Ions Are Cogerminants for Spores of Clostridium perfringens Type A Food Poisoning-Related Isolates

Clostridium perfringens type A isolates carrying a chromosomal copy of the enterotoxin (cpe) gene are involved in the majority of food poisoning (FP) outbreaks, while type A isolates carrying a plasmid-borne cpe gene are involved in C. perfringens-associated non-food-borne (NFB) gastrointestinal diseases. To cause diseases, C. perfringens spores must germinate and return to active growth. Previously, we showed that only spores of FP isolates were able to germinate with K⁺ ions. We now found that the spores of the majority of FP isolates, but none of the NFB isolates, germinated with the cogerminants Na⁺ and inorganic phosphate (NaP_i) at a pH of ∼6.0. Spores of gerKA-KC and gerAA mutants germinated to a lesser extent and released less dipicolinic acid (DPA) than did wild-type spores with NaP_i. Although gerKB spores germinated to a similar extent as wild-type spores with NaP_i, their rate of germination was lower. Similarly, gerO and gerO gerQ mutant spores germinated slower and released less DPA than did wild-type spores with NaP_i. In contrast, gerQ spores germinated to a slightly lesser extent than wild-type spores but released all of their DPA during NaP_i germination. In sum, this study identified NaP_i as a novel nutrient germinant for spores of most FP isolates and provided evidence that proteins encoded by the gerKA-KC operon, gerAA, and gerO are required for NaP_i-induced spore germination.Clostridium perfringens is a gram-positive, anaerobic, spore-forming, pathogenic bacterium that causes a wide array of gastrointestinal (GI) diseases in both animals and humans (14, 15). However, Clostridium perfringens type A food poisoning (FP) is the most common C. perfringens-associated illness among humans and is currently ranked as the third most commonly reported food-borne disease (14). Mostly type A isolates that produce the C. perfringens enterotoxin have been associated with C. perfringens-related GI illnesses (14). C. perfringens cpe-positive isolates can carry the cpe gene on either the chromosome or a plasmid (3, 4). Interestingly, the majority of C. perfringens type A FP isolates carry a chromosomal copy of the cpe gene, while all non-food-borne (NFB) GI disease isolates carry a plasmid copy of cpe (3, 4, 11, 29). The genetic differences involved in the pathogenesis differences between C. perfringens FP and NFB isolates seem to involve more factors than the simple location of the cpe gene. For example, spores of FP isolates are strikingly more resistant than spores of NFB isolates to heat (100°C) (27), cold (4°C), and freezing (−20°C) temperatures (12) and to chemicals used in food industry settings (13), making FP spores more suited for FP environments. Under favorable environmental conditions, these dormant spores germinate to return to active growth, proliferate to high numbers, and then produce toxins to cause disease (14).Bacterial spores germinate when they sense the presence of nutrients (termed germinants) in the environment through their cognate receptors located in the spore inner membrane (18). For C. perfringens, some nutrients that initiate germination include l-asparagine, KCl, a mixture of l-asparagine and KCl, and a 1:1 chelate of Ca²⁺ and dipicolinic acid (DPA) (Ca-DPA) (20). The main receptor(s) involved in sensing these compounds is the GerKA and/or GerKC receptor(s), which is required for l-asparagine and Ca-DPA and only partially required for KCl and an l-asparagine-KCl mixture (20, 21). Upon binding of the germinant to its cognate receptor, a variety of biophysical events take place, including the release of monovalent ions (i.e., Na⁺, K⁺, and Li⁺) followed by the release of the spore''s large depot of Ca-DPA (28). In Bacillus subtilis, release of Ca-DPA acts as a signal for activation of the cortex-lytic enzyme CwlJ (17). In contrast, Ca-DPA release from the spore core has no role in triggering cortex hydrolysis during C. perfringens spore germination (19, 22, 23); instead, Ca-DPA induces germination via the GerKA and/or GerKC receptor(s) (20, 21). Degradation of the cortex in both species leads to hydration of the spore core up to levels found in growing bacteria, allowing resumption of enzymatic activity and metabolism, and consequently outgrowth (22, 28).The ability of bacterial spores to sense different nutrients appears to be tightly regulated by their adaptation to different environmental niches. For example, spores of FP isolates, but not NFB isolates, are capable of germinating with KCl (20), an intrinsic mineral of meats that are most commonly associated with FP, suggesting an adaptation of FP isolates to FP environments. In addition, the level of inorganic phosphate (P_i) is also significant in meat products (42 to 60 mM) (USDA [http://fnic.nal.usda.gov/nal_display/index.php?info_center=4&tax_level=1&tax_subject=242]). Similarly, sodium ions are also present in meats (∼30 mM), especially in processed meat products (∼300 to 400 mM) (USDA). Consequently, in this study we found that Na⁺ and P_i at ∼100 mM and pH 6.0 are unique cogerminants for spores of C. perfringens type A FP isolates, act through the GerKA and/or GerKC and GerAA receptors, and also require the presence of the putative Na⁺/K⁺-H⁺ antiporter, GerO, for normal germination.     

Sources of Nitrogen in Combination with Systems of Irrigation Influence the Productivity of Modern Rice (<i>Oryza sativa</i> L.) Cultivars during Dry Season in Sub-Tropical Environment

In irrigated agricultural systems, nitrogen (N) and water are the vital resources for sustainability of the crop production in the modern era of climate change. The current study aimed to assess the impact of water and N management on the productivity of irrigated rice cultivars. In the context, a field observation was done at the research farm of Bangladesh Agricultural University, Mymensingh, during dry seasons in consecutive two years (2018–2019 and 2019–2020). The experiments were set up following split-plot design assigning water management in the main plots, nitrogen management in the sub-plots, and the cultivars were approved in the split-split plot with three replications. After two years observation, it was revealed that rice cultivar Binadhan-8 gave the maximum value of leaf area index, number effective tillers hill^-1 and grains panicle^-1 which lead to the higher grain yield (GY). Substantial relationships were observed among the concentration of N, growth, total dry matter (TDM) and N content, N uptake, N utilization effectiveness, and GY. However, with little exception, the Combined effect of water and N, cultivars and water management were varied significantly for all parameters. Finally, the results of the current study concluded that application of irrigation at 8 days after the disappearance of ponded water and source of 105 kg N ha^-1 from PU + Poultry manure are the best management approach for the excellent performance of rice cultivar Binadhan-8.     

High prevalence of sulfadoxine/pyrimethamine resistance alleles in Plasmodium falciparum parasites from Bangladesh

In Bangladesh, despite the official introduction of artemisinin combination therapy in 2004, chloroquine+sulfadoxine/pyrimethamine has been used for the treatment of uncomplicated malaria. To assess the distribution of pfcrt, pfmdr1, dhfr, and dhps genotypes in Plasmodium falciparum, we conducted hospital- and community-based surveys in Bandarban, Bangladesh (near the border with Myanmar) in 2007 and 2008. Using nested PCR followed by digestion, 139 P. falciparum isolates were genotyped. We found fixation of a mutation at position 76 in pfcrt and low prevalence of a mutation at position 86 in pfmdr1. In dhfr, the highest pyrimethamine resistant genotype quadruple mutant was found in 19% of isolates, which is significantly higher prevalence than reported in a previous study in Khagrachari (1%) in 2002. Microsatellite haplotypes flanking dhfr of the quadruple mutants in Bangladesh were identical or very similar to those found in Thailand and Cambodia, indicating a common origin for the mutant in these countries. These observations suggest that the higher prevalence of the dhfr quadruple mutant in Bandarban is because of parasite migration from Myanmar. However, continuous use of sulfadoxine/pyrimethamine would have also played a role through selection for the dhfr quadruple mutant. These results indicate an urgent need to collect molecular epidemiological information regarding dhfr and dhps genes, and a review of current sulfadoxine/pyrimethamine usage with the aim of avoiding the widespread distribution of high levels of resistant parasites in Bangladesh.     

Association of beta2 toxin production with Clostridium perfringens type A human gastrointestinal disease isolates carrying a plasmid enterotoxin gene

Clostridium perfringens type A isolates carrying an enterotoxin (cpe) gene are an important cause of human gastrointestinal diseases, including food poisoning, antibiotic-associated diarrhoea (AAD) and sporadic diarrhoea (SD). Using polymerase chain reaction (PCR), the current study determined that the cpb2 gene encoding the recently discovered beta2 toxin is present in <15% of food poisoning isolates, which typically carry a chromosomal cpe gene. However, >75% of AAD/SD isolates, which usually carry a plasmid cpe gene, tested cpb2(+) by PCR. Western blot analysis demonstrated that >97% of those cpb2(+)/cpe(+) AAD/SD isolates can produce CPB2. Additional PCR analyses, sequencing studies and pulsed field gel electrophoresis experiments determined that AAD/SD isolates carry cpb2 and cpe on the same plasmid when IS1151 sequences are present downstream of cpe, but cpb2 and cpe are located on different plasmids in AAD/SD isolates where IS1470-like sequences are present downstream of cpe. Those analyses also demonstrated that two different CPB2 variants (named CPB2h1 or CPB2h2) can be produced by AAD/SD isolates, dependent on whether IS1470-like or IS1151 sequences are present downstream of their cpe gene. CPB2h1 is approximately 10-fold more cytotoxic for CaCo-2 cells than is CPB2h2. Collectively, these results suggest that CPB2 could be an accessory toxin in C. perfringens enterotoxin (CPE)-associated AAD/SD.     

Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily

Flap endonuclease (FEN1), essential for DNA replication and repair, removes RNA and DNA 5' flaps. FEN1 5' nuclease superfamily members acting in nucleotide excision repair (XPG), mismatch repair (EXO1), and homologous recombination (GEN1) paradoxically incise structurally distinct bubbles, ends, or Holliday junctions, respectively. Here, structural and functional analyses of human FEN1:DNA complexes show structure-specific, sequence-independent recognition for nicked dsDNA bent 100° with unpaired 3' and 5' flaps. Above the active site, a helical cap over a gateway formed by two helices enforces ssDNA threading and specificity for free 5' ends. Crystallographic analyses of product and substrate complexes reveal that dsDNA binding and bending, the ssDNA gateway, and double-base unpairing flanking the scissile phosphate control precise flap incision by the two-metal-ion active site. Superfamily conserved motifs bind and open dsDNA; direct the target region into the helical gateway, permitting only nonbase-paired oligonucleotides active site access; and support a unified understanding of superfamily substrate specificity.     

Bioactivity of secoiridoid glycosides from Centaurium erythraea.

As part of our on-going search for bioactive compounds from Scottish plants, two secoiridoid glycosides, swertiamarin and sweroside, have been isolated from the aerial parts of Centaurium erythraea Rafn (Family: Gentianaceae) by reversed-phase preparative HPLC coupled with a photo-diode-array detector. The structures of these compounds were elucidated unambiguously by UV, FABMS and extensive 1D and 2D NMR spectroscopic analyses and also by comparing experimental data with literature data. Antibacterial, free radical scavenging activities and general toxicity of these glycosides have been assessed. Both compounds inhibited the growth of Bacillus cereus, Bacillus subtilis, Citrobacter freundii and Escherichia coli. While swertiamarin was also active against Proteus mirabilis and Serratia marcescens, sweroside inhibited the growth of Staphylococcus epidermidis. Swertiamarin and sweroside exhibited significant general toxicity in brine shrimp lethality bioassay and the LD50 values were 8.0 microg/ml and 34 microg/ml, respectively, whereas that of the positive control podophyllotoxin, a well known cytotoxic lignan, was 2.79 microg/ml. Chemotaxonomic implications of these compounds in the family Gentianaceae have also been discussed briefly.     

Comparison of the Levels of Heat Resistance of Wild-Type, cpe Knockout, and cpe Plasmid-Cured Clostridium perfringens Type A Strains

An enterotoxin (cpe) plasmid was cured from a Clostridium perfringens non-food-borne gastrointestinal disease (NFBGID) isolate, and the heat resistance levels of wild-type, cpe knockout, and cpe plasmid-cured strains were compared. Our results demonstrated that (i) wild-type cpe has no influence in mediating high-level heat resistance in C. perfringens and (ii) the cpe plasmid does not confer heat sensitivity on NFBGID isolates.     

Ebselen inhibits NO-induced apoptosis of differentiated PC12 cells via inhibition of ASK1-p38 MAPK-p53 and JNK signaling and activation of p44/42 MAPK and Bcl-2

Ebselen, a selenium-containing heterocyclic compound, prevents ischemia-induced cell death. However, the molecular mechanism through which ebselen exerts its cytoprotective effect remains to be elucidated. Using sodium nitroprusside (SNP) as a nitric oxide (NO) donor, we show here that ebselen potently inhibits NO-induced apoptosis of differentiated PC12 cells. This was associated with inhibition of NO-induced phosphatidyl Serine exposure, cytochrome c release, and caspase-3 activation by ebselen. Analysis of key apoptotic regulators during NO-induced apoptosis of differentiated PC12 cells showed that ebselen blocks the activation of the apoptosis signaling-regulating kinase 1 (ASK1), and inhibits phosphorylation of p38 mitogen-activated protein kinase (MAPK) and c-jun N-terminal protein kinase (JNK). Moreover, ebselen inhibits NO-induced p53 phosphorylation at Ser15 and c-Jun phosphorylation at Ser63 and Ser73. It appears that inhibition of p38 MAPK and p53 phosphorylation by ebselen occurs via a thiol-redox-dependent mechanism. Interestingly, ebselen also activates p44/42 MAPK, and inhibits the downregulation of the antiapoptotic protein Bcl-2 in SNP-treated PC12 cells. Together, these findings suggest that ebselen protects neuronal cells from NO cytotoxicity by reciprocally regulating the apoptotic and antiapoptotic signaling cascades.