Miracle-dz/UniFAR-FTUs huggingface dataset:
Energy metabolism in halophilic and alkalophilic bacteria

This review summarizes the recent data on the energy metabolism of acetogenic bacteria isolated from saline and soda lakes. It provides a general description of saline and soda lakes as microbial habitats, performs a comparative analysis of the energy metabolism of neutrophilic acetogens, considers the adaptation strategies of halophilic and alkalophilic acetogens to high salinity and high pH values, while also discussing the mechanisms of energy accumulation under auto- and organotrophic conditions.
Physical quality of an Oxisol under no-tillage subjected to different cropping systems

The objective of this work was to evaluate the physical quality of an Oxisol under no-tillage subjected to different crop rotations and crop sequences. The experiment was carried out in a clayey Oxisol, during six years, in a randomized complete block design, with strip plots and three replicates. The following physical indicators of soil quality were evaluated: soil density and carbon content, as well as mean weight diameter and tensile strength of aggregates. Treatments consisted of three summer crop rotations – corn/corn (Zea mays), soybean/soybean (Glycine max), and soybean/corn – and of seven second crops (crop sequences) – corn, sunflower (Helianthus annuus), oilseed radish (Raphanus sativus), pearl millet (Pennisetum americanum), pigeon pea (Cajanus cajan), grain sorghum (Sorghum bicolor), and sun hemp (Crotalaria juncea). Crop rotations and sequences did not affect soil carbon contents. Corn, as a summer crop, increased the tensile strength and mean weight diameter of aggregates, similarly to pearl millet and sorghum as second crops. Soybean/corn rotation with sun hemp as a second crop increases soil physical quality, promoting higher tensile strengths and lower soil densities.
EFEITO DE Bacillus thuringiensis E Trichoderma sp. NO CRESCIMENTO DE FUNGOS FITOPATOGÊNICOS EFFECT OF Bacillus thuringiensis AND Trichoderma sp. ON THE GROWTH PATHOGENIC FUNGI

Biological control of plant disease does not only refer to the interaction between pathogen and host, but also to the result of this interaction and to the countless non-pathogens that rest on the infection site. The mechanisms of the antagonistic interaction can be: antibiosis, competition, parasitism, predation and defense induction of the host. This work aimed to evaluate the effects of some antagonistic agents on the mycelial growth of pathogenic fungi. The experiment was carried out in a completly randomized design with six repetitions, and the treatments were arranged in a factorial scheme 2 x 8 (antagonists: Trichoderma sp. and Bacillus thuringiensis and pathogens: Sclerotium rolfsii, Diaporthe phaseolorum, Pythium aphanidermatum, Monilinia fructicola, Sclerotinia sclerotiorum, Rhizoctonia solani, Fusarium solani and Bipolaris sorokiniana). In order to evaluate the antagonism, the pairing culture on petri dishes with the BDA medium was used, and a disk of mycelia pathogen was transferred to 1,5 cm of the border of the disk, and at the other end, a disk of the Trichoderma sp. antagonist mycelial or three furrows of B. thuringiensis were transferred. The dishes were incubated in a controlled environment. The diameter of the colonies was measured after 48 hours. On the control dishes, only the pathogen was tranferred. Again, the diameter of the colonies was evaluated after 48 hours. The bacterium B. thuringiensis was effective as an antagonist, controlling the majority of the pathogens. The percentage of growth inhibition varied from 39,41% to 7,99%, for S.rolfsii and B. sorokiniana, respectively. Trichoderma sp presented significant control only on S.rolfsii, but it did not prevent the development of sclerotia.
The determination of behavioural plasticity in yellow perch, Perca flavescens

iv ACKNOWLEDGEMENTS . v LIST OF FIGURES . ix LIST OF TABLES . xi LIST OF APPENDICES . xiii Chapter 1: General Introduction . 1 Knowledge Gaps in Behavioural Ecology . 5 References . 12 Chapter 2: Interaction of early rearing experience, genetic divergence, and ontogeny on the behavioural repertoire of yellow perch, Perca flavescens . 17 Introduction . 17 Methods . 23 Study Species . 23 Sampling . 24 Fish Husbandry . 26 Behavioural Experimental Design . 27 Statistical Analysis . 30 Results . 34 Survivorship across Trials . 34 Open Field Test PCA . 34 Novel Object Test PCA . 35 Stimulus Response Test . 35 Behavioural Correlations within Trials . 35 Linear Mixed Effects Modelling . 36 Discussion . 37 References . 45
Estimating in situ isotopic turnover in Rainbow Trout (Oncorhynchus mykiss) muscle and liver tissue

ABSTRACT Stable isotope analysis (SIA) is a powerful tool for assessing food webs and diet. However, the underlying assumptions that stable isotope ratios in an organism's tissues reflect that of its present diet may be complicated by isotopic turnover and retention time. Quantification of in situ isotopic turnover of study organisms and different tissues via field studies is essential to inform scientifically sound food web and diet studies utilizing SIA. Rainbow Trout white muscle and liver tissue were collected monthly from North Twin Lake, Washington during the 2013 growing season. Using ANCOVAs, we estimated stable carbon retention time of 154 (95% CI: 106–224) and 292 (95% CI: 257–763) days for Rainbow Trout liver and white muscle, respectively. For nitrogen, we estimated a retention time of 186 (95% CI: 114–329) days for both white muscle and liver. Our analyses suggest longer isotopic retention times (and therefore slower isotope turnover rates) for adult fish in a natural system relative to those commonly reported in the literature. These findings can improve interpretation of SIA in future aquatic food web and diet studies involving adult coldwater fish in freshwater systems.
DEVELOPMENT OF A SANDWICH-TYPE DNA ARRAY PLATFORM FOR THE DETECTION OF LABEL-FREE OLIGONUCLEOTIDE TARGETS

iv ÖZ. vi ACKNOWLEDGMENTS.ix TABLE OF CONTENTS.xi LIST OF TABLES.xiv LIST OF FIGURES.xv LIST OF ABBREVIATIONS . xviii CHAPTER 1 1.INTRODUCTION . 1 1.1 Biosensors . 1 1.2 DNA Biosensors . 2 1.3 Microarray Technology . 4 1.3.1 Protein Microarrays . 5 1.3.2 DNA Arrays . 7 1.3.2.1 Immobilization of DNA on Glass Surface . 7 1.3.2.2 DNA Surface Hybridization . 9 1.4 Sandwich Hybridization . 11 1.5 Sandwich Type DNA Arrays . 14 1.6 Aim of the Study . 16 2.MATERIALS AND METHODS . 17 xii 2.1 Materials . 17 2.1.1 Chemicals . 17 2.1.2 Support Materials . 17 2.1.3 Heterobifunctional Cross-linkers and Oligonucleotides . 17 2.2 Methods . 18 2.2.1 Construction of Array Platform . 18 2.2.1.1 Cleaning the Glass Slides . 18 2.2.1.2 Aminosilane Coating of the Slides . 19 2.2.1.3 Labeling Slides . 19 2.2.1.3.1 Type 1 Labeling Design . 19 2.2.1.3.2 Type 2 Labeling Design . 20 2.2.1.4 Surface Activation . 20 2.2.1.5 Capture Probe Immobilization . 21 2.2.1.6 Surface Blocking . 22 2.2.1.7 Hybridization. 22 2.2.2 Determination of Surface Coating Agent . 22 2.2. 3 Determination of Capture Probe Immobilization Technique . 23 2.2. 4 Capture Probe Optimization . 23 2.2. 5 Signal Probe Optimization . 23 2.2. 6 Optimization of Hybridization Conditions. 24 2.2. 7 Determination of Sensitivity . 24 2.2. 8 Multiplex Assay . 25 2.2. 9 Slide Scanning and Image Analysis . 27 2.2.10 Statistical Analysis . 27 xiii 3.RESULTS AND DISCUSSION . 29 3.1 Determination of Solid Support . 30 3.2 Surface coating agent choice . 30 3.3 Determination of Capture Probe Immobilization . 37 3.4 Capture Probe (P1) concentration optimization. 42 3.5 Signal Probe (P2) Concentration Optimization . 45 3.6 Optimization of Hybridization Conditions . 47 3.6. 1 Optimization of Hybridization Duration . 48 3.6. 2 Optimization of Hybridization Temperature . 50 3.6. 3 Optimization of Hybridization Sequence of the Probes . 53 3.7 Sensitivity of the Array Platform . 55 3.8. Selectivity of the Array Platform . 58 4.CONCLUSION . 64 REFERENCES.66 APPENDICES 76 A.PREPARATION OF SOLUTIONS AND BUFFERS.76 B.TABULATED VALUES OF NET FLUORESCENCE INTENSITIES . 78
Biofilm formation in Bacillus cereus group bacteri : screening of strains and initial molecular studies

In this study we have established a method for screening a collection of strains, from the Bacillus cereus group of bacteria, for biofilm formation, including soil isolates, strains from culture collections, reference strains, dairy isolates, and clinical strains from different types of human infections. Certain strains from the B. cereus group, which includes the opportunistic human pathogen B. cereus, insecticidal B. thuringiensis, and the obligate human and animal pathogen B. anthracis, are known to have the ability to form biofilm, an attached state in which cells are closely packed and firmly attached to each other and usually a solid surface. In biofilm, microorganisms aggregate and excrete a protective and adhesive matrix of a polymeric, usually carbohydrate-containing, substance. The matrix may provide beneficial functions, such as protection from antibiotics and the immune system during infection and giving bacterial cells the ability to communicate during growth. Biofilm formation is known, at least for certain bacterial pathogens, to contribute to the aetiology of human disease, exemplified by Pseudomonas aeruginosa infections in cystic fibrosis patients. In this study 81 strains have been screened for biofilm formation, resulting in the confirmation of 7 strains, which form biofilm. The ability to form biofilm has not been observed to specifically correlate with strain origin; however strains isolated outside their natural environment (soil and insect intestine) have shown a higher propensity to form biofilm. We have also initiated gene disruption studies in a candidate regulatory gene, the pleiotropic transcriptional regulator plcR, to reveal its possible involvement in biofilm formation in Bacillus cereus ATCC 10987, a strain closely related to B. anthracis, isolated from spoiled cheese in the 1930s.
Phylogeny and circumscription of the genus Orinus (Poaceae: Eragrostideae): evidence from NRDNA its sequences = Filogenia ITS e a circunscrição do gênero Orinus (Poaceae: Eragrostideae): evidência das sequências its do NRDNA

In this study, ITS sequences of the nuclear ribosomal DNA were conducted for six putative species of Orinus ( O . alticulmus , O . anomala , O . kokonorica , O . longiglumis , O . thoroldii and O . tibeticus ) with 572 individuals from 73 populations. The results found that the six species formed two monophyletic groups: the one ( O . anomala Keng ex Keng f. and L. Liou) with O . alticulmus , O . anomala and O . kokonorica , and another ( O . thoroldii (Stapfex Hemsl.) Bor) with O . longiglumis , O . thoroldii and O . tibeticus . The taxonomic data from ITS sequences were not congruent with those from morphological characteristics, likely resulting from rapid speciation trigged by the uplifts of the Qinghai-Tibetan Plateau and its adjacent regions and the extensive selection pressure under the alpine environments. The ITS data suggest that the classification of the six species within the genus Orinus should be reduced to two species. We include a complete taxonomic revision of the genus and a key to distinguish the two species. Therefore, it is very necessary to make the comprehensive revision and arrangement of these taxa, strictly regulate the taxa confusion of genus and species order, and do new reports on belonging to the genus taxa.
The integrated function of cardiac, skeletal, and vascular smooth muscle: limitations to oxygen transport and utilization in healthy aging and disease

The purpose of this dissertation was to investigate the integration of cardiac, skeletal, and vascular smooth muscle in the process of oxygen (O2) transport and utilization. The goal of the first study was to examine the vasomotor function of human skeletal muscle feed arteries (SMFAs), utilizing pressure myography, with a focus on the impact of age. In this study, we demonstrated that in response to an increased shear stress, the SMFAs likely contribute to the regulation of vascular resistance/conductance in vivo. Furthermore, aging likely blunts the capacity to delivery O2 due to reduced endothelial function in these SMFAs identified by attenuated kinetics of vasodilation and maximum vasodilatory capacity. Additionally, this attenuated vascular function was associated with a reduction in the shear-induced activation of eNOS, and elevated free radical production in SMFAs with age. The second study using normal healthy donor hearts (HdH) as a reference, sought to examine the impact of heart failure (HF) etiology on mitochondrial function in the pathology. Specifically, this study examined cardiac muscle mitochondrial function and free radical production in patients with ischemic HF (iHF) in comparison to that of patients with non-ischemic HF (niHF). Both mitochondrial quality and quantity were compromised in HF compared to HdH. Interestingly, a lower tissue mass specific oxidative phosphorylation (OXPHOS) capacity was documented in iHF compared to niHF, which was predominantly due to reduced mitochondrial content. However, increased non-phosphorylating respiration, and elevated mitochondrial derived free
Insulin-Stimulated Protein Kinase C λ/ζ Activity Is Reduced in Skeletal Muscle of Humans With Obesity and Type 2 Diabetes: Reversal With Weight Reduction

In humans with obesity or type 2 diabetes, insulin target tissues are resistant to many actions of insulin. The atypical protein kinase C (PKC) isoforms λ and ζ are downstream of phosphatidylinositol-3 kinase (PI3K) and are required for maximal insulin stimulation of glucose uptake. Phosphoinositide-dependent protein kinase-1 (PDK-1), also downstream of PI3K, mediates activation of atypical PKC isoforms and Akt. To determine whether impaired PKCλ/ζ or PDK-1 activation plays a role in the pathogenesis of insulin resistance, we measured the activities of PKCλ/ζ and PDK-1 in vastus lateralis muscle of lean, obese, and obese/type 2 diabetic humans. Biopsies were taken after an overnight fast and after a 3-h hyperinsulinemic-euglycemic clamp. Obese subjects were also studied after weight loss on a very-low-calorie diet. Insulin-stimulated glucose disposal rate is reduced 26% in obese subjects and 62% in diabetic subjects (both comparisons P
Nucleotide sequences of a part of Barley yellow dwarf virus-PAV and Cereal yellow dwarf virus-RPV genome from Iran

Barley yellow dwarf disease is one of the most important and destructive diseases in cereals in Iran. Two isolates of each predominant virus including Barley yellow dwarf virus-PAV (BYDV-PAV) and Cereal yellow dwarf virus-RPV (CYDV-RPV) were selected for sequence characterizations. The segment of PAV-IR genome (1264 nt) comprising a partial genes for coat protein (CP), read through protein (RTP) and movement protein (MP) showed a high sequence identity to PAV isolates from USA, France and Japan (96-97%). In a phylogenetic analysis it was placed into PAV group I together with PAV isolates of barley and oats. The fragment of RPV-IR (719 nt) contained partial genes for CP, RTP and MP was putatively identified as belonging to CYDV-RPV. However, RPV-IR showed a similar sequence identity with both RPV and Cereal dwarf virus-RPS (CYDV-RPS) at 90-91%, and the phylogenetic analyses suggested that it might be more closely related to RPS. These sequences are the first ones of BYD-causing viruses from Iran and Southwest Asia.
What is the real Hormotila? (Chlorophyceae)

It is shown by the heterogenous nature of Borzi’s description and illustrations that Hormotila mucigena Borzi, the generitype of Hormotila, should be redefined. Borzi’s original description and accompanying illustrations of Hormotila (constituting the protologue) correspond to a minimum of five distinct genera of green algae. Two distinct concepts of the genus have persisted over the years. The genus has become based on a combination of palmelloid and physiologically stressed forms of two of the component algae. Our understanding of the genus is further confused by the incorporation of unrelated unicellular and colonial coccoid forms. There are only one or two distinctive attributes that would allow the selection of any one of the five forms as representing the genus and species. One of Borzi’s original figures is proposed to redefine the original species of the genus, Hormotila mucigena.
Molecular diversity and phylogeny of Triticum-Aegilops species possessing D genome revealed by SSR and ISSR markers

Abstract The aim of this study is investigation the applicability of SSR and ISSR markers in evaluating the genetic relationships in twenty accessions of Aegilops and Triticum species with D genome in different ploidy levels. Totally, 119 bands and 46 alleles were detected using ten primers for ISSR and SSR markers, respectively. Polymorphism Information Content values for all primers ranged from 0.345 to 0.375 with an average of 0.367 for SSR, and varied from 0.29 to 0.44 with the average 0.37 for ISSR marker. Analysis of molecular variance (AMOVA) revealed that 81% (ISSR) and 84% (SSR) of variability was partitioned among individuals within populations. Comparing the genetic diversity of Aegilops and Triticum accessions, based on genetic parameters, shows that genetic variation of Ae. crassa and Ae. tauschii species are higher than other species, especially in terms of Nei’s gene diversity. Cluster analysis, based on both markers, separated total accessions in three groups. However, classification based on SSR marker data was not conformed to classification according to ISSR marker data. Principal co-ordinate analysis (PCoA) for SSR and ISSR data showed that, the first two components clarified 53.48% and 49.91% of the total variation, respectively. This analysis (PCoA), also, indicated consistent patterns of genetic relationships for ISSR data sets, however, the grouping of accessions was not completely accorded to their own geographical origins. Consequently, a high level of genetic diversity was revealed from the accessions sampled from different eco-geographical regions of Iran.
Note on the Thermal Conductivity of Beeswax

SummaryThe thermal conductivities of two types of beeswax were determined using a line heat-source technique. Values for both crude rendered wax and foundation wax were influenced by temperature, the conductivity being higher at the two extremes of −15° and +40°C used, and relatively constant between 0 and 25°. Conductivity of the crude rendered wax was consistently higher than that of the foundation material.
Prediction of three-dimensional structure of Chlamydia trachomatis heat shock protein 60: An immunodominant antigen.

Chlamydia trachomatis infections are the most prevalent sexually transmitted infection in the world and are often associated with various fertility disorders. C. trachomatis heat shock protein 60 (cHSP60) or GroEL has been identified as an immunodominant antigen, being strong target of both humoral and cell mediated immune responses. A homology modeling was used for the prediction of three-dimensional (3-D) structure of cHSP60 by using the comparative modeling module of MODELLER. Since the MODELLER-aligned alignments led to asymmetric matching, the necessary sequence alignments were done using ClustalW and mGenTHREADER. The template used was the file with code 1kp8 from the Protein Data Bank (PDB), which gives the crystal structure of GroEL of Escherichia coli. The structure was energy minimized by MODELLER’s inherent minimization module. From the Ramachandran plot analysis, it was found that 91.8% of residues falls in the most favoured region. Further, this study could shed light on characterizing cHSP60 in wet laboratory.
Identification of bacteria from the rhizosphere of Jatropha curcas with characteristics of biotechnological interest.

In the present study Pseudomonas sp. S18 (PMa-76), Pseudomonas aeruginosa N7B1 (PMa-83), Pseudomonas sp. (PMa-88), Pseudomonas nitroreducens TX1 (PMa-89), Pseudomonas strains sp. bf1 (PHx -97), Pseudomonas aeruginosa F23 (PHx -98), Pseudomonas aeruginosa F23 (PHx -101) strains were isolated from the rhizosphere of physic nut. The PMa-83 PMa-88 PMa-89, PHx -97, PHx -98, PHx -101 strains grew up in the presence of phenol 0.05% and benzene 1.0%, as a sole carbon source, as well as in the presence of zinc, copper and cobalt in concentrations of 0.1 and 5 mg/ml. The Pseudomonas sp. S18 (PMa-76) strain was the one that had the highest capacity to solubilize phosphate (9.6 mm). Moreover indole production in 6 strains were detected and while biosurfactants production was detected in 5 strains. Furthermore, the presence of nifH genes in PMa-83, PHx -97, PHx-98 and PHx P-101 strains were also detected, indicating the ability to fix nitrogen. PMa 83 is the strain in which the growth in phenol, benzene and metals were detected, thus indole production, the presence of biosurfactants and nif H genes which are characteristics of biotechnological interest.
Hydrolysis of agricultural residues and kraft pulps by xylanolytic enzymes from alkaliphilic Bacillus sp. strain BK

An alkaliphilic bacterium, Bacillus sp. strain BK, was found to produce extracellular cellulase-free xylanolytic enzymes with xylan-binding activity. Since the pellet-bound xylanase is eluted with 2% TEA from the pellet of the culture, they contain a xylan-binding region that is stronger than the xylan-binding xylanase of the extracellular enzyme. The xylanases had a different molecular weight and xylan-binding ability. The enzyme activity of xylanase in the extracellular fraction was 6 times higher than in the pellet-bound enzyme. Among the enzymes, xylanase had the highest enzyme activity. When Bacillus sp. strain BK was grown in pH 10.5 alkaline medium containing xylan as the sole carbon source, the bacterium produced xylanase, arabinofuranosidase, acetyl esterase, and β-xylosidase with specific activities of 1.23, 0.11, 0.06, and 0.04 unit per mg of protein, respectively. However, there was no cellulase activity detected in the crude enzyme preparation. The hydrolysis of agricultural residues and kraft pulps by the xylanolytic enzymes was examined at 50°C and pH 7.0. The rate of xylan hydrolysis in corn hull was higher than those of sugarcane bagasse, rice straw, corn cop, rice husk, and rice bran. In contrast, the rate of xylan hydrolysis in sugarcane pulp was 2.01 and 3.52 times higher than those of eucalyptus and pine pulp, respectively. In conclusion, this enzyme can be used to hydrolyze xylan in agricultural residues and kraft pulps to breach and regenerate paper from recycled environmental resources.