A stable Escherichia coli-mycobacteria shuttle vector 'pSO246' in Mycobacterium bovis BCG

Abstract The most widely used plasmid vector system in mycobacteria is based on pAL5000 from Mycobacterium fortuitum . The derivatives of the pAL5000-based shuttle vectors between Escherichia coli and mycobacteria, which we have utilized to secrete recombinant antigens, were generated. The stability of the vectors was assessed in Mycobacterium bovis BCG (BCG). The plasmid vector pSO246 was stable in BCG for at least 50 generations.     

Genetic diversity of the Plasmodium falciparum GTP-cyclohydrolase 1, dihydrofolate reductase and dihydropteroate synthetase genes reveals new insights into sulfadoxine-pyrimethamine antimalarial drug resistance

Plasmodium falciparum parasites resistant to antimalarial treatments have hindered malaria disease control. Sulfadoxine-pyrimethamine (SP) was used globally as a first-line treatment for malaria after wide-spread resistance to chloroquine emerged and, although replaced by artemisinin combinations, is currently used as intermittent preventive treatment of malaria in pregnancy and in young children as part of seasonal malaria chemoprophylaxis in sub-Saharan Africa. The emergence of SP-resistant parasites has been predominantly driven by cumulative build-up of mutations in the dihydrofolate reductase (pfdhfr) and dihydropteroate synthetase (pfdhps) genes, but additional amplifications in the folate pathway rate-limiting pfgch1 gene and promoter, have recently been described. However, the genetic make-up and prevalence of those amplifications is not fully understood. We analyse the whole genome sequence data of 4,134 P. falciparum isolates across 29 malaria endemic countries, and reveal that the pfgch1 gene and promoter amplifications have at least ten different forms, occurring collectively in 23% and 34% in Southeast Asian and African isolates, respectively. Amplifications are more likely to be present in isolates with a greater accumulation of pfdhfr and pfdhps substitutions (median of 1 additional mutations; P<0.00001), and there was evidence that the frequency of pfgch1 variants may be increasing in some African populations, presumably under the pressure of SP for chemoprophylaxis and anti-folate containing antibiotics used for the treatment of bacterial infections. The selection of P. falciparum with pfgch1 amplifications may enhance the fitness of parasites with pfdhfr and pfdhps substitutions, potentially threatening the efficacy of this regimen for prevention of malaria in vulnerable groups. Our work describes new pfgch1 amplifications that can be used to inform the surveillance of SP drug resistance, its prophylactic use, and future experimental work to understand functional mechanisms.     

Proteomic analysis of necroptotic extracellular vesicles

Necroptosis is a regulated and inflammatory form of cell death. We, and others, have previously reported that necroptotic cells release extracellular vesicles (EVs). We have found that necroptotic EVs are loaded with proteins, including the phosphorylated form of the key necroptosis-executing factor, mixed lineage kinase domain-like kinase (MLKL). However, neither the exact protein composition, nor the impact, of necroptotic EVs have been delineated. To characterize their content, EVs from necroptotic and untreated U937 cells were isolated and analyzed by mass spectrometry-based proteomics. A total of 3337 proteins were identified, sharing a high degree of similarity with exosome proteome databases, and clearly distinguishing necroptotic and control EVs. A total of 352 proteins were significantly upregulated in the necroptotic EVs. Among these were MLKL and caspase-8, as validated by immunoblot. Components of the ESCRTIII machinery and inflammatory signaling were also upregulated in the necroptotic EVs, as well as currently unreported components of vesicle formation and transport, and necroptotic signaling pathways. Moreover, we found that necroptotic EVs can be phagocytosed by macrophages to modulate cytokine and chemokine secretion. Finally, we uncovered that necroptotic EVs contain tumor neoantigens, and are enriched with components of antigen processing and presentation. In summary, our study reveals a new layer of regulation during the early stage of necroptosis, mediated by the secretion of specific EVs that influences the microenvironment and may instigate innate and adaptive immune responses. This study sheds light on new potential players in necroptotic signaling and its related EVs, and uncovers the functional tasks accomplished by the cargo of these necroptotic EVs.Subject terms: Necroptosis, Cell death and immune response     

Prediction of the three-dimensional structure of aflatoxin of Aspergillus flavus by homology modelling

Aflatoxins are polyketide-derived secondary metabolites produced by Aspergillus spp. The toxic effects of aflatoxins have adverse consequences for human health and agricultural economics. The aflR gene, a regulatory gene for aflatoxin biosynthesis, encodes a protein containing a zinc-finger DNA-binding motif. AFLR-Protein three-dimensional model was generated using Robetta server. The modeled AFLR-Protein was further optimization and validation using Rampage. In the simulations, we monitored the backbone atoms and the C-α-helix of the modeled protein. The low RMSD and the simulation time indicate that, as expected, the 3D structural model of AFLR-protein represents a stable folding conformation. This study paves the way for generating computer molecular models for proteins whose crystal structures are not available and which would aid in detailed molecular mechanism of inhibition of aflatoxin.     

New records of endoparasitic helminths in alien invasive fishes from the Carpathian region

Six non-native invasive fish species from the Slovak part of the Tisa River basin, namely Carassius gibelio, Pseudorasbora parva, Ameiurus melas, A. nebulosus, Lepomis gibbosus, Perccottus glenii, and three gobiid species from the Danube River, namely Neogobius melanostomus, N. fluviatilis and N. kessleri, were investigated for endohelminth parasites. The expanding Asian cestode Nippotaenia mogurndae (syn. Amurotaenia perccotti) (Nippotaeniidea) has been introduced to Europe with its invasive host P. glenii. Pumpkinseed, Lepomis gibbosus, is a new definitive host of Proteocephalus percae and it is reported as the second intermediate host of the bothriocephalidean cestode Triaenophorus nodulosus in Slovakia.     

Differences in surface-dwelling beetles of grasslands invaded and non-invaded by goldenrods (Solidago canadensis,S. gigantea) with special reference to Carabidae

We evaluated surface-dwelling Coleoptera with special reference to ground beetles (Coleoptera: Carabidae) using pitfall traps across fourteen stands of grasslands invaded and non-invaded by invasive goldenrods (Solidago canadensis L. and S. gigantea Ait.) over a 3 year period. We analysed differences in assemblages of invaded and non-invaded grasslands and tested responses of surface-dwelling beetles and carabids to invasion of goldenrods. We identified 29 Coleoptera families and 91 Carabidae species. Solidago invaded grasslands showed significantly higher activity-abundance of rove and carrion beetles and supported greater diversity and significantly higher evenness of surface-dwelling Coleoptera and the number of sampled families and individuals was higher too. We found lower taxonomic richness and significantly lower activity-abundance of carabids across goldenrods stands. Several less common Carabidae species and significantly higher representation of stenotopic brachypterous habitat specialists were also observed within invaded stands. We confirmed that differences in plant cover connected with invasion of goldenrods, soil moisture and abandonment of invaded habitats are the driving mechanisms of changes in surface-dwelling Coleoptera and ground beetles assemblages composition across Solidago invaded grasslands. Overall, changes of grassland biotopes connected with invasion of goldenrods significantly alter Coleoptera families and Carabidae assemblages, but not necessarily reduce diversity.     

Mapping the amino acid properties of constituent nucleoporins onto the yeast nuclear pore complex

Visualization of molecular structures aids in the understanding of structural and functional roles of biological macromolecules. Macromolecular transport between the cell nucleus and cytoplasm is facilitated by the nuclear pore complex (NPC). The ring structure of the NPC is large and contains several distinct proteins (nucleoporins) which function as a selective gate for the passage of certain molecules into and out of the nucleus. In this note we demonstrate the utility of a python code that allows direct mapping of the physiochemical properties of the constituent nucleoporins on the scaffold of the yeast NPC׳s cytoplasmic view. We expect this tool to be useful for researchers to visualize the NPC based on their physiochemical properties and how it alters when specific mutations are introduced in one or more of the nucleoporins. The code developed using Python is available freely from the authors.     

The 4a/4a genotype of the VNTR polymorphism for endothelial nitric oxide synthase (eNOS) gene predicts risk for proliferative diabetic retinopathy in Slovenian patients (Caucasians) with type 2 diabetes mellitus

Thus far only a limited number of studies examined the association between endothelial nitric oxide synthase (eNOS) polymorphisms and proliferative diabetic retinopathy (PDR). In this report, two polymorphisms in the eNOS gene have been investigated, namely the 894G>T (Glu298Asp) and a 27 bp VNTR (4b/4a), to assess their possible relationships to PDR among Slovenian (Caucasians) type 2 diabetic patients. This cross-sectional case–control study enrolled 577 unrelated Slovenian subjects (Caucasians) with type 2 diabetes mellitus. The case group consisted of 172 patients with PDR and the control group had 405 patients who had no clinical signs of diabetic retinopathy (DR) but did have type 2 diabetes for more than 10 years’ duration. Genotyping of eNOS polymorphisms was carried out with conventional and real-time PCR assays. A significantly higher frequency of the eNOS minor “4a” allele was found in patients with PDR than in controls (23.6 versus 17.7%, p = 0.01). Moreover, the univariate analysis showed a significant association of the 27 bp VNTR 4a/4a genotype and PDR in the recessive model. The odds ratio (OR) of PDR for the 4a/4a genotype to 4b/4a plus 4b/4b was 2.9 (95% CI 1.3–6.2, p = 0.005). Further, the presence of 4a/a genotype was associated with a 3.4-fold (95% CI 1.4–8.6, p = 0.009) increased risk for PDR while adjusted for other risk factors. This is the first study to implicate eNOS 4a/4a homozygous deletion, and hence the “4a” allele, as the genetic risk factors for PDR in Caucasians.     

Respiration characteristics of mitochondria in parental and giant transformed cells of the murine Nemeth-Kellner lymphoma

Respiration characteristics of mitochondria of the parental and giant cells of murine NK/Ly (Nemeth-Kellner lymphoma) were studied. The giant cell-enriched ascites were obtained by serial intraperitoneal injections of vinblastine in tumour-bearing mice. Ascites containing >70% giant cells were used. Their diameter of was over 17 μm (~2800 μm(3)), while the diameter of the parental cells was 12.7 μm (1100 μm(3)). The respiration rate of mitochondria in situ was measured by oxygen consumption in intact and digitonin-permeabilized NK/Ly cells. Endogenous respiration of intact giant NK/Ly cells was three times higher compared to the parental ones, roughly in agreement with the volume change. The giant NK/Ly cells were far more resistant to permeabilization with digitonin than the parental cells, as shown by Trypan Blue and LDH (lactate dehydrogenase) release tests. After digitonin permeabilization, oxygen consumption was reduced to a minimal level (0.06 ng atom O/(s × 106 cells) in both types of cells. Addition of α-ketoglutarate or succinate to the incubation medium increased oxygen consumption in the parental cells by 46 and 164% respectively. In the giant NK/Ly cells, the corresponding increases were 164 and 276%. Addition of ADP to α-ketoglutarate- or succinate-supplemented medium further stimulated oxygen consumption of the permeabilized NK/Ly cells; however, the effect of ADP was more pronounced in the giant cells. In addition, indices of respiratory control were significantly higher in the giant cells. Oligomycin suppressed considerably the respiration of the intact giant cells but had a much weaker effect on parental cells. Thus, giant NK/Ly cells possess much higher respiration rates and show tighter coupling between the respiration and oxidative phosphorylation compared with parental cells.