Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbe‐mediated control of Aspergillus flavus in stored rice grains with a focus on aflatoxin inhibition and biodegradation

Biological control of mycotoxigenic fungi using antagonistic microbes is a promising alternative to agricultural chemicals for postharvest storage. In this study, we evaluated rice-derived bacterial strains to identify biocontrol agents to inhibit Aspergillus flavus in stored rice grains. Consequently, we obtained three potential biocontrol strains (Microbacterium testaceum KU313, Bacillus megaterium KU143 and Pseudomonas protegens AS15) from 26 tested strains that were prescreened from the 460 strains isolated from rice grains. The three selected strains proved to be effective biocontrol agents showing antifungal activity against A. flavus and good colonisation ability on rice grains, along with inhibition of the fungal growth and aflatoxin production. In particular, P. protegens AS15 greatly inhibited the aflatoxins produced by A. flavus on rice grains to 8.68 (percent aflatoxin reduction relative to control = 82.9%) and 18.05 (68.3 %) ng g−1 dry weight of rice grains, compared with the 50.89 and 56.97 ng g−1 dry weight of rice grains of the MgSO4 control at 1 and 2 weeks after inoculation, respectively. In addition, strain AS15 had a significant ability to not only degrade aflatoxin B1 (the most harmful aflatoxin), but also utilise the toxin for bacterial growth in a nutrient-deficient medium. Therefore, the selected bacterial strains could be environmentally sound alternatives for the management of A. flavus and aflatoxin production by reducing the fungal damage to stored rice grains. This would also reduce the human and animal health hazards associated with the consumption of fungus-contaminated rice grains. To our knowledge, this is the first report of the potential of the bacterial species M. testaceum and P. protegens as biocontrol agents for controlling aflatoxigenic A. flavus on stored rice grains.
Protective effect of some chelating agents and antioxidants on the biohazards produced from water pollution by heavy metals in Wistar rats: biological, genetic and histopathological study

Background: Heavy metals that normally cause problems are mercury (HgCl2) and lead acetate (LA). Chelating and inhibitor agents are the target to treat and overcome metal toxicity. The current study has been carried out to evaluate the protective effects of N-acetyl cysteine (NAC) and meso 2,3 dimercaptosuccinic acid (DMSA) against HgCl2 and LA toxicity. Materials and Methods: Ninety male Wistar rats were divided into nine equal groups. The groups were administered NAC and/or DMSA in presence or absence of LA (LA; 0.2% in drinking water) or HgCl2 (2 mg/kg BW) for 2 consecutive months. Serum and organs were collected for biochemical, genetic and histopathological changes. Results: Biochemical results revealed that LA and HgCl2 significantly increased the levels of liver and kidney biomarkers. Administration of NAC and DMSA considerably improved these altered changes. LA and HgCl2 decreased serum levels of antioxidants and were ameliorated in NAC and DMSA administered rats. LA and HgCl2 administration upregulated expression of IL-1β and IL-8 that were normalized by NAC and DMSA. Kidneys of LA and HgCl2 groups showed intraluminal hyaline casts. Kidneys of DMSA-administrated rats showed mild hydropic degeneration of renal tubular epithelium in LA and HgCl2 groups. Kidneys of NAC administrated rats showed atrophy of capillary tufts. Kidneys of LA and HgCl2 administered rats which received DMSA and NAC showed normal glomerular structure. Liver histopathology showed sever changes that were ameliorated by NAC and DMSA. Conclusion: Taken together, usage of NAC and DMSA provide significant protection against LA and HgCl2-induced hepatotoxicity and nephrotoxicity in male Wistar rats.
An integrative taxonomic study of European Eupelmus (Macroneura) (Hymenoptera: Chalcidoidea: Eupelmidae), with a molecular and cytogenetic analysis of Eupelmus (Macroneura) vesicularis: several species hiding under one name for 240 years

Author’s visits to BMNH, HNHM, MNCN, and MNHN were supported by the SYNTHESYS Project (http://www.synthesys.info/), financed by European Community Research Infrastructure Action under the FP7 ‘Capacities’ Program (GB-TAF-490, HU-TAF-2949, ES-TAF-1816, and FR-TAF-1155), and his research is currently sustained by the internal grant GI-2015-02 awarded by the Al. I. Cuza University of Iasi.
Growth and reproduction of the chaetognaths Eukrohnia hamata and Parasagitta elegans in the Canadian Arctic Ocean: capital breeding versus income breeding

In Arctic seas, primary production and the availability of food for zooplankton are strongly pulsed over the short productive summer. We tested the hypothesis that Eukrohnia hamata and Parasagitta elegans, two similar and sympatric arctic chaetognaths, partition resources through different reproductive strategies. The two species had similar natural longevities of around 2 years. Eukrohnia hamata, which occurred at epiand meso-pelagic depths, spawned two distinct broods in autumn and spring. Offspring production coincided with drops in the frequency of E. hamata with visible lipid reserves, characteristic of capital breeders. Growth was positive from April to January and negative in February and March. Growth and maturation were similar for the two broods. Storage reserves contained in an oil vacuole may allow E. hamata to reproduce and grow outside the short production season. Parasagitta elegans produced one brood in summer–autumn during peak production in near-surface waters, characteristic of income breeders. In winter, P. elegans co-inhabited meso-pelagic waters with E. hamata, where it neither grew nor reproduced. As the Arctic warms, the development of an autumn phytoplankton bloom could favour the summer–autumn brood of P. elegans.
Antibacterial activity of essential oils extracted from medicinal plants against multi-drug resistant Staphylococcus aureus.

Multi-drug resistant Staphylococcus aureus has been a major contributor to treatment failure in the last decade in Pakistan and indigenous plants focused for screening of new therapeutic options. Antibacterial properties of indigenous medicinal plants essential oils were determined against MDR S. aureus isolates from patients, associated healthcare workers and healthy community. Antibacterial activity was determined by agar well diffusion assay. Minimum inhibitory concentrations (MIC) of essential oils exhibiting activity against selected MDR S. aureus were calculated using Micro broth dilution method. Five plants essential oils Carum copticum, Anethum sowa, Cuminum cyminum, Myristica fragrans and Zingiber officinale were tested for antibacterial activity against selected MDR S. aureus isolates from three sampling groups. Out of five essential oils, Carum copticum was found to be the most effective followed by Zingiber officinale and Cuminum cyminum. Upon qualitative analysis of five essential oils, Carum copticum, Cuminum cyminum and Zingiber officinale essential oils showed zones of inhibition greater than the standards Vancomycin and Linezolid. Anethum sowa and Myristica fragrans essential oils showed no activity against MDR S. aureus. The mean MIC values obtained for Carum copticum against selected MDR S. aureus isolates from patients, healthcare workers and community were 4. 2μl, 1.7 μl and 3.0 μl, respectively. Mean MIC value for Zingiber officinale were 10.8 μl, 3.5 μl and 6.8 μl and for Cuminum cyminum were 43.8 μl, 23.8 μl and 40 μl. The MIC value of Carum copticum essential oil was least against MDR S. aureus isolates and considered most effective plant oil.
Comparative Seed Germination in Species of Turbinicarpus: an Endangered Cacti Genus

All species of the genus Turbinicarpus are considered to be at risk and are thus included in CITES Appendix I. Ex situ plant reproduction has been suggested to reduce illegal extraction of these species. However, literature regarding seed germination of these species is scarce and often contradic- tory. Propagation requirements among 17 taxa (including 12 species, six subspecies, and one hybrid) were analyzed. We used fresh seeds for all taxa plus aged seeds for five species. The response vari- able measured was Germinative Value (GV), which measures germination quality resulting from three variables: germinability, germination speed, and germination uniformity. For fresh seeds, significant differences were found between taxa. Germination varied broadly across taxa from 8% to 97% and GV ranged from 0.848 to 20.112. The two taxa with lower GV, T. lophophoroides and T. pseudopectinatus, showed higher GV in old seeds than in fresh seeds, which indicates this species might form seed-banks in the soil. T. knuthianus did not show significant differences between fresh and old seeds, which can be interpreted as a strategy to produce both seeds for immediate propagation and seeds for securing the medium and long-term survival of the species. In contrast, T. swobodae and T. valdezianus showed higher GV in fresh seeds than in old seeds, which would appear to represent an adaptation to germinate as soon as rainfall occurs. Our results contribute to understanding germination biology of a threatened genus and the potential role of soil seed banks. In addition, results presented here could contribute to in situ conservation of Turbinicarpus spp. populations, through promoting natural regeneration, and ex situ conservation, by promoting large numbers of cultivated individuals outside their habitats.
STAPHYLOCOCCUS AUREUS FROM READY-TO-EAT FOOD AS A SOURCE OF MULTIPLE ANTIBIOTIC RESISTANCE GENES

The emergence of antibiotic-resistant strains of S. aureus such as methicillin-resistant S. aureus (MRSA) is a worldwide problem. Ready-to-eat (RTE) food which does not need thermal processing before consumption could be a vehicle for the spread of antibiotic-resistant microorganisms. The present study evaluated the molecular genetic characteristics (RAPD) and pheno- and genotypical antimicrobial resistance profile of S. aureus isolated from 75 RTE food samples (sushi, hamburgers, salads). All of the isolates (n=32) were resistant to at least one class of antibiotic tested of which 75% strains were classified as multidrug resistant. Most of the isolates were resistant to cefoxitin (87,5%) followed by clindamycin (78,1%), tigecycline and quinupristin/dalfopristin (53,1%). All methicillin resistant staphylococci harbored mec A gene. Among tetracycline resistance isolates all of them harbored at least one gene: tet (M), tet (L) and/or tet (K) and 78,9% of them were positive for the Tn 916 /Tn 1545 -like integrase family gene. Our results indicated that retail RTE food could be considered an important route for transmission of antibiotic resistant staphylococci harboring multiple antibiotic resistance genes.
Green Synthesis of Zinc Oxide Nanoparticles Using Parthenium hysterophorus Leaf Extract and Evaluation of their Antibacterial Properties

Parthenium hysterophorus an annual herbaceous weed, is known for its vigorous growth and as a causative agent for contact dermatitis, hay fever and diarrhea in humans and systemic toxicity in livestock. However, in spite of all the problems associated with this weed, it has been reported to have pharmacological activities. The objective of this study is to evaluate the potential of Parthenium hysterophorus leaf extracts for the synthesis of zinc oxide nanoparticles and their antimicrobial properties. Nanoparticles were extracted with the help of aqueous, methanolic and ethanolic solutions of P. hysterophorus leaves. Since a higher yield of nanoparticles was observed when synthesised using aqueous extract therefore these were used in further experiments. Synthesised nanoparticles were characterised using UV-Vis spectroscopy with maximum absorbance peak at 400 nm. SEM and TEM analysis revealed that the particles were spherical and cylindrical in shape with average particle size ranging from 16-45 nm. The chemical group association and elemental composition of nanoparticles was analysed using FTIR and SEM-EDX. Green synthesized zinc oxide nanoparticles were evaluated for antimicrobial activities against Gram positive and Gram negative bacteria. Zinc nanoparticles exhibited maximum zone of inhibition against Enterobacter aerogenes (36 mm) while least activity was seen against Staphylococcus aureus and Bacillus subtilis.
Expression pattern and ligand‐binding properties of odorant‐binding protein 13 from Monochamus alternatus hope

Odorant‐binding proteins (OBPs) are believed to play an important role in olfactory recognition. In this study, expression pattern and fluorescence binding characteristics of MaltOBP13 from the Japanese pine sawyer beetle, Monochamus alternatus Hope, were investigated via qPCR analysis of MaltOBP13 mRNA level and binding assay of MaltOBP13 and ligands. qPCR monitoring indicated MaltOBP13 mainly expressed in newly emerged males, particularly highly expressed in the last abdominal segment of males, and the expression level was significantly higher in 13‐day‐old mated adults than those of other stages. To further understand the function of the MaltOBP13 protein in odorant reception, the binding affinity of recombinant MaltOBP13 to ligands was tested by fluorescence binding assays with N‐phenyl‐1‐naphthylamine as a fluorescent probe. The results of this assay indicated that MaltOBP13 exhibited a high binding affinity for pine volatiles and binding capacity was higher in acidic conditions than in neutral environment, indicating a possible role in finding host plants.
Habitat complexity dampens selection on prey activity level

Editor: E. Hebets Abstract Conspecific prey individuals often exhibit persistent differences in behavior (i.e., animal personality) and consequently vary in their susceptibility to predation. How this form of selection varies across environmental contexts is essential to predicting ecological and evolutionary dynamics, yet remains currently unresolved. Here, we use three separate predator–prey systems (sea star–snail, wolf spider–cricket, and jumping spider–cricket) to independently examine how habitat structural complexity influences the selection that predators impose on prey behavioral types. Prior to conducting staged predator–prey interaction encounters, we ran prey individuals through multiple behavioral assays to determine their average activity level. We then allowed individual predators to interact with groups of prey in either open or structurally complex habitats and recorded the number and individual identity of prey that were eaten. Habitat complexity had no effect on overall predation rates in any of the three predator–prey systems. Despite this, we detected a pervasive interaction between habitat structure and individual prey activity level in determining individual prey survival. In open habitats, all predators imposed strong selection on prey behavioral types: sea stars preferentially consumed sedentary snails, while spiders preferentially consumed active crickets. Habitat complexity dampened selection within all three systems, equalizing the predation risk that active and sedentary prey faced. These findings suggest a general effect of habitat complexity that reduces the importance of prey activity level in determining individual predation risk. We reason this occurs because activity level (i.e., movement) is paramount in determining risk within open environments, whereas in complex habitats, other behavioral traits (e.g., escape ability to a refuge) may take precedence.
Myelin is remodeled cell-autonomously by oligodendroglial macroautophagy

Myelin is remodeled cell-autonomously by oligodendroglial macroautophagy Etan Aber Myelination of axons in the CNS by oligodendrocytes (OLs) is critical for the rapid and reliable conduction of action potentials down neuronal axons, as evidenced by the severe disabilities associated with myelin loss in multiple sclerosis and other diseases of myelin. The specification, differentiation, and maturation of OLs along with myelin formation by OLs have been thoroughly characterized. How myelin is turned over, however remains unclear. It is unsurprising that little is known about myelin turnover considering that for decades following their discovery, myelin and OLs were considered static elements in the adult nervous system. Recent evidence, however, shows that myelin in the CNS is actually plastic. Moreover, myelin remodeling in humans has been suggested to be mediated by mature OLs. As mature OLs have limited capacity to generate new myelin sheaths, we must ask whether mature OLs can remodel the myelin at preexisting myelin sheaths. One intriguing but unproven possibility is that myelin at individual internodes may be remodeled cell-autonomously by mature OLs to modulate neuronal circuit function. Macroautophagy (MA) is responsible for the lysosome-mediated elimination of cytosolic proteins, lipids, and organelles. MA achieves this by capturing cargo in bulk or selectively in a transient, multilamellar structure known as an autophagosome (AP). In this study, we used a combination of in vivo and cellular approaches to test the hypothesis that MA in OLs may be important for myelin remodeling in the adult CNS. We establish that myelin of individual internodes is remodeled, and does so through the coordinated efforts of endocytosis and MA. We found that autophagy protein Atg7 is essential for myelin remodeling in vivo: loss of Atg7 in OLs leads to an age-dependent increase of myelin at the internode and the formation of aberrant myelin structures, most notably myelin outfoldings. In addition, we find that MA has the potential to occur throughout the mature OL, and examination of OLs in culture suggests that formation of a mature AP structure, the amphisome, is required to facilitate the efficient degradation of myelin-containing endocytic structures. Together, we propose that myelin is a dynamic structure that is regularly remodeled through the cooperative efforts of MA and endocytosis. These findings raise the possibility that myelin remodeling is involved in neural plasticity and the tuning of neural circuits.
The First Occurrence of Cynognathus crateronotus (Cynodontia: Cynognathia) in Tanzania and Zambia, with Implications for the Age and Biostratigraphic Correlation of Triassic Strata in Southern Pangea

ABSTRACT Cynognathus crateronotus is a species of large carnivorous cynodont, first named and best known from the Triassic Burgersdorp Formation (Beaufort Group, Karoo Basin) of South Africa. Fossils of the genus have also been reported from the upper Fremouw Formation of Antarctica, the Upper Omingonde Formation of Namibia, and the Río Seco de la Quebrada Formation of Argentina. Without associated cranial material, however, distinguishing the postcrania of Cynognathus from that of the closely related cynognathian, Diademodon tetragonus, has proven difficult. Here we provide a more comprehensive diagnosis for Cynognathus crateronotus and describe two novel occurrences. First, parts of a medium-sized individual were recovered from a scrambled mass of dental and semiarticulated postcranial material from the lower Ntawere Formation of Zambia, a horizon that previously produced fossils of Diademodon and Kannemeyeria. Second, a large individual was collected from a recently discovered locality within the lower part of the Lifua Member of the Manda Beds of Tanzania. A large proportion of the postcranial skeleton, along with some craniodental remains, was found ex situ in a sandy streambed just downstream from a quarry that has produced the dicynodont Dolichuranus, an azendohsaurid archosauromorph, and the avemetatarsalian Teleocrater rhadinus. The widespread occurrence of Cynognathus across southern Pangea demonstrates its utility as a biostratigraphic marker, but recently published radiometric age estimates from Argentina suggest that either the genus persisted for over 10 million years or African strata traditionally interpreted as Middle Triassic are better understood as Late Triassic in age.
Molecular basic of chemosensory: Biofilm and cell-to-cell signaling in different species of pseudomonas

1 RESUMEN . 5 INTRODUCTION . 11 1. BACTERIAL SENSING . 13 1.1. One-component systems . 15 1.2. Two-component systems . 15 1.3. Chemosensory pathways . 16 1.3.1. The prototypal chemotaxis pathway (E. coli) . 18 1.3.2. More complex chemotaxis pathways: Pseudomonas . 19 1.3.3. Information available on Pseudomonas MCP . 22 2. BACTERIAL LIFESTYLE . 24 2.1. Biofilm in Pseudomonas . 27 2.2. Chemosensory signaling pathways control biofilm formation and colonization. 29 3. CELL TO CELL COMMUNICATION IN BACTERIA . 30 3.1. Quorum sensing . 30 3.1.1. QS in Pseudomonas aeruginosa . 32 3.2. LuxR-type proteins . 35 3.2.1. Classes of LuxR-type proteins . 37 3.2.2. LuxR-type proteins oligomeric state . 38 3.2. 3. General model for LuxR-type proteins . 39 3.3. Quorum quenching . 40 3.3.1. Degrading bacterial QSS . 41 3.3.2. Interference with QSS receptor . 42 3.4. Inter-kingdom signaling . 43 AIM OF THE THESIS AND SPECIFIC OBJECTIVES . 47 METHODOLOGY . 51 Experimental Procedures . 53 Microbiologic and molecular biology techniques . 53 Bioinformatics analysis. 55 Protein purification . 56 Biophysical analysis . 57 Genotypic studies . 60 Gene expression studies . 61 Phenotypic studies . 62 Plant studies . 65 RESULTS AND DISCUSSION . 67 CHAPTER 1 Assessment of the contribution of MCP-based signaling to biofilm formation . 71 Brief introduction . 71 Results . 74 Construction of bacterial MCP mutants and their analysis . 74 Identification of PP2249 as a chemotaxis receptor for Lamino acids . 79 Identification of PP1228 as a polyamine chemotaxis receptor . 81 Influence of MCP mutations on competitive plant root colonization . 85 Discussion . 86 Supplementary material . 90 CHAPTER 2 Purification of functional recombinant LasR and RhlR of Pseudomonas aeruginosa from Escherichia coli cultures. 105 Brief Introduction . 105 Results . 107 LasR and RhlR can be produced as recombinant proteins in E. coli in the absence of added AHL . 107 LasR and RhlR bind different acyl-homoserine lactones with similar affinity . 108 LasR and RhlR unfold at temperatures beyond 60 °C and AHL binding does not alter protein stability significantly . 110 AHL binding does not alter the oligomeric state of RhlR and LasR . 112 RhlR and LasR bind to promoter DNA . 114 RhlR stimulates transcription in vitro in a protein and AHL concentration dependent manner . 115 Differential impact of AHL ligands on the RhlR mediated upregulation of gene expression . 117 Discussion . 119 Supplementary material . 122 CHAPTER 3 Rosmarinic acid is a homoserine lactone mimic produced by plants that activates a bacterial quorum sensing regulator . 129 Brief introduction . 129 Results . 131 Rosmarinic binds to purified RhlR with high affinity . 131 Rosmarinic acid stimulates RhlR-mediated transcription . 133 Rosmarinic acid stimulates QS gene expression in vivo . 134 Rosmarinic acid increases biofilm formation, pyocyanin production, and elastase synthesis . 139 Discussion . 142 Supplementary material . 144 CONCLUSIONS . 147 CONCLUSIONES . 153 BIBLIOGRAPHY . 159 PUBLICATIONS . 187