Miracle-dz/UniFAR-FTUs huggingface dataset:
DOCKING OF CTX-M-9 GROUP OF ENZYMES WITH DRUGS AND INHIBITORS AND THEIR EVOLUTIONARY RELATIONSHIP

Background: Among the type of ESBLs, CTX-M-type ESBLs represent a new and rapidly growing family of molecular class-A ESBLs. The prevalence of CTX-M-type ESBLs poses a serious threat to the clinical use of third generation cephalosporins for the treatment of severe infections. Objective: The objectives of the present study are computational study of CTX-M-9, 14 and 27 of bla CTX-M sequences. Based on resistance to organisms, docking of drugs (cefotaxime, cefixime and cefepime) as well as inhibitors (clavulanate, sulbactam and tazobactam) with CTX-M-9, 14 and 27 for the identification of amino acid residues crucial to the enzyme-drug and enzyme-inhibitor interaction. Method: Bioactivity analysis was done using Pubchem, and docking of drugs and inhibitors with CTX-M-9 group of enzymes were done using Schrodinger to identify the amino acid residues that are crucial for interaction. Phylogenetic analysis was constructed by Neighbor-Joining method for calculating minimum distance and bootstrapping values was done for 1000 replicates to obtain >70percent recombination. Results: Schrodinger analysis revealed the amino acid residues that interacted with CTX-M-9, 14 and 27 and they were found to be ASP 101, ASN 136, LYS 137, ASP 101, GLU 166, SER 130, ASN 132, THR 235, SER 237, and ASP 240 respectively. Among the drugs, cefotaxime, cefixime and among inhibitors clavulanic acid and tazobactam were found to interact with CTX-M-9, 14 and 27. Minimum distance obtained from Neighbor-Joining analysis was 0.02 evolutionary rate of divergence, and only two nodes connecting (CTX-M-3, 55 and CTX-M-9, 16, 51) of bootstrapping values revealed 100 and 88percent respectively, whereas other CTX-M-9 group of enzymes showed less than 70percent recombination. Conclusion: The current study revealed the amino acid residues crucial to ‘CTX-M-drug’ and ’CTX-M-inhibitor’ interactions among CTX-M-9 group of enzymes using different bioinformatics tools which would be useful for the development of a versatile CTX-M-inhibitor. Key words : ESBL, blaCTX-M, Docking, Neighbor-Joining.
Effect of Root Temperature on the Concentration and Fatty Acid Composition of Phospholipids in Cucumber and Figleaf Gourd Roots

The effect of root temperature on phospholipid concentration and its fatty acid composition in the roots was studied with cucumber (Cucumis sativus L., cvs. Kurume-ochiai H and Suyo) and figleaf gourd (Cucurbita ficifolia Bouche) which have contrasting tolerance to low root temperature.Phospholipid concentration in roots increased at 14°C and more so at 12°C in figleaf gourd, which is highly tolerant of low root temperature compared to cucumber. In both cultivars of cucumber, however, the concentration increased only at 12°C. The increase in phospholipid concentration in figleaf gourd roots was assumed to be due to the net increase of phospholipid synthesis within roots, but that in cucumber roots seemed to be a result of root growth inhibition. Composition of phospholipids was relatively unaffected by root temperature in all crops; phosphatidylcholine (PC) and phosphatidylethanolamine (PE) were the main phospholipid species in the roots of all three crops.The degree of fatty acid unsaturation of total phospholipids increased steadily in figleaf gourd as the root temperature was lowered from 25 to 12°C. By contrast, in‘Suyo’, which is the most intolerant of low root temperature among the three crops used, degree of fatty acid unsaturation was highest at 17°C and tended to decrease toward the lowest root temperature. In‘Kurume-ochiai H’it was almost unaffected by root temperature. With reduction in root temperature, fatty acid unsaturation of PE increased with little changes in that of PC in figleaf gourd. Conversely, in both cultivars of cucumber fatty acid unsaturation of PE varied little, and instead, that of PC decreased at 12°C, more greatly in‘Suyo’. From these results it is suggested that the response of roots to low root temperature in phospholipid synthesis and its fatty acid unsaturation is related to different tolerance of these crops to low root temperature.
Genotypic Differences in Root Hair Deformation and Subsequent Nodulation for Red Clover under Different Additions of Starter N Fertilization

Red clover cultivars, including diploid and tetraploid, are commonly used in legume-based pasture mixtures. However, information on nodulation under different starter N regimens is limited. We hypothesized that there is genetic variability among different red clover cultivars for nodulation. A root hair deformation assay was conducted using three diploid (AC Christie, Tapani and CRS15) and three tetraploid (Tempus, CRS18 and CRS39) red clover cultivars by inoculating them with Rhizobium leguminosarum biovar trifolii. Nodulation and morphological characteristics of two selected red clover cultivars, AC Christie and Tempus, were determined under five starter N concentrations (0, 0.2, 0.4, 0.8 and 1.6 mg per plant). Inoculation with rhizobia increased root hair deformation with significant interaction across cultivars. Nodulation was delayed under high starter N concentrations, and genotypic differences were evident for days-to-nodule initiation. There was a positive quadratic response to starter N for AC Christie and a negative quadratic response for Tempus for nodulation. Tempus had more active nodules (92 %) than AC Christie (73 %). The genetic variability of red clover cultivars should be considered in N fixation studies and their response to availability of initial N.
Epithelial sensory structures of trochids

The ciliated epithelial sensory cells of the tentacle papillae and of the concave epipodial sense organ (e.s.o.) surface of the trochids Margaretes helicinus, Gibbula cineraria, G. umbilicalis, Monodonta lineata, Diloma nigerrima and D. zealandica are primary sensory cells with intra-epithelial nuclei. The 5–7 cells of a single papilla bear many cilia. Each e.s. o. cell has one cilium surrounded by 8–9 specialized microvilli. Both kinds of sensory cell show structural similarities with known mechanoreceptors.
Conservation genetics and ecology of the endangered Black Bog Ant, Formica picea

In this study I aimed to investigate the genetic and ecological factors that may Influence the distribution and conservation of the Black Bog Ant, Formica picea, within the UK, where it is classed as an endangered species. All main UK F. picea sites known at the start of this study (Cors Goch Llanllwch, Carmarthenshire Rhossili Down, West Glamorgan Hartland Moor, Dorset the New Forest, Hampshire) were investigated. The first study of its kind of a UK ant species, this investigation involved measuring micro-geographic ecological parameters and using both microsatellite and mitochondrial DNA markers for genetic analyses. High percentage cover of Bell Heather (Erica tetralix) and Deer Grass ( Trichophorum cespitosum) in the immediate vicinity of the nest and a low density of Heather (Calluna vulgaris) in the local area occupied by F. picea appear to contribute to favourable habitat. Water table level may be the most influential determinant of F. picea nest distribution, however, as an unoccupied area appearing favourable in terms of E. tetralix and T. cespitosum cover revealed significantly lower relative humidity and vegetation height in 2003. Colonies of all studied populations were highly polygynous, containing multiple reproducing queens per colony, and two populations revealed significant levels of inbreeding. Isolation by distance was detected in two populations, suggesting nest reproduction by budding and poor dispersal. All populations were genetically differentiated from one another, with the exception of the physically closest pair. Within Cors Goch Llanllwch a degree of social polymorphism was identified, with two sectors showing differing levels of polygyny and polydomy (multiple nests per colony). Aggression between non-nestmates was absent in this population, suggesting a largely unicolonial organisation. Despite relatively large population sizes conferred by polygyny, UK populations of F. picea are at risk due to ecological specificity, inbreeding and limited dispersal. Within this study I make suggestions for conservation management including detailed ecological analyses and colony relocation.
Targeting Tumors and the Kidney with siRNA Nanoparticles and Evaluation of Extracellular MicroRNA-based Methodologies to Track Their Activity

The goal of my thesis work is to discover new ways to enable the use of nanoparticle therapeutics to treat human disease. The work presented here touches on several areas in medicine and is united by a common theme: engineering ways to make, use, and evaluate therapeutics that maximize the benefit to the patient and minimize the harm. I have explored three interrelated strategies to achieve my objectives: (1) the use of targeted-nanoparticle-based therapeutics to deliver therapeutic entities to specific sites in the body, (2) the use of a highly specific type of therapeutic, siRNA, and (3) the evaluation of strategies for using extracellular microRNAs to non invasively monitor therapeutic activity and disease response to that activity. In Chapter 2, I present the first evidence of targeted-nanoparticle delivery of siRNA to solid tumors following systemic administration to patients. My coworkers and I demonstrate both dose-dependent accumulation of the siRNA nanoparticles and evidence of gene knockdown via the canonical RNAi mechanism. Chapters 3 – 5 describe the therapeutic potential of targeted nanoparticles (one version used in the clinic and described in Chapter 2) for: (i) targeting ribonucleotide reductase subunit M2 in human melanoma cell lines (Chapter 3), (ii) Herceptin-targeted nanoparticles containing siRNA against Her2 in Her2(+) breast cancer (Chapter 4), and (iii) siRNA targeting the “undruggable” protein N-Ras for N-Ras mutant melanomas (Chapter 5). Chapters 6 – 8 focus on the interaction of nanoparticles with the kidney. Chapter 6 explores a previously unknown phenomenon of size-dependent glomerular accumulation of nanoparticles. In Chapter 7, a new mechanism of clearance for polycation-polymer-based nucleic acid delivery systems is demonstrated, based on interactions between polymer components in the nanoparticle and the anionic surface of the renal filtration barrier, explaining the rapid clearance of these siRNA nanoparticle systems. Chapter 8 illustrates targeted-nanoparticle delivery of siRNA to the kidney. In Chapter 9, I test the hypothesis that analysis of tumor-secreted microRNAs within patient blood samples can be used as real-time markers of drug pharmacodynamics. Specifically, I focus on efforts to characterize microRNA expression patterns following pharmacologic inhibition of the oncogene BRAF in melanoma cells and their secreted exosomes.
Escarabeíneos (Coleoptera: Scarabaeidae: Scarabaeinae) de uma área de campo nativo no bioma Pampa, Rio Grande do Sul, Brasil

This work presents a survey of Scarabaeinae species from a natural grassland area in Bage, state of Rio Grande do Sul, Brazil. Samplings were carried out with flight intercept traps and pitfall traps baited with human feces, rotten banana and rotten meat, from December 2005 to November 2006. A total of 4,573 individuals, belonging to 14 genera and 30 species were collected. Onthophagus aff. hirculus Mannerheim, 1829, Canthon podagricus Harold, 1868, Ontherus sulcator (Fabricius, 1775) and Canthidium moestum Harold, 1867 were the most abundant species. Most of the captured assemblage is composed by species coprophagous and generalists preferably necrophagous. Few species were strictly necrophagous and none was classified as saprophagous. The rollers and tunnelers were represented by similar numbers of species.
Identification and characterization of genetic interactors of the Rho Guanine-nucleotide exchange factor Pebble in Drosophila

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Conservation Status of Freshwater Gastropods of Canada and the United States

ABSTRACT This is the first American Fisheries Society conservation assessment of freshwater gastropods (snails) from Canada and the United States by the Gastropod Subcommittee (Endangered Species Committee). This review covers 703 species representing 16 families and 93 genera, of which 67 species are considered extinct, or possibly extinct, 278 are endangered, 102 are threatened, 73 are vulnerable, 157 are currently stable, and 26 species have uncertain taxonomic status. Of the entire fauna, 74% of gastropods are imperiled (vulnerable, threatened, endangered) or extinct, which exceeds imperilment levels in fishes (39%) and crayfishes (48%) but is similar to that of mussels (72%). Comparison of modern to background extinction rates reveals that gastropods have the highest modern extinction rate yet observed, 9,539 times greater than background rates. Gastropods are highly susceptible to habitat loss and degradation, particularly narrow endemics restricted to a single spring or short stream reaches. Compil.
Age-Dependent Changes in Brain, CSF, and Plasma Amyloid β Protein in the Tg2576 Transgenic Mouse Model of Alzheimer's Disease

The accumulation of amyloid β protein (Aβ) in the Tg2576 mouse model of Alzheimer's disease (AD) was evaluated by ELISA, immunoblotting, and immunocytochemistry. Changes in Aβ begin at 6–7 months as SDS-insoluble forms of Aβ42 and Aβ40 that require formic acid for solubilization appear. From 6 to 10 months, these insoluble forms increase exponentially. As insoluble Aβ appears, SDS-soluble Aβ decreases slightly, suggesting that it may be converting to an insoluble form. Our data indicate that it is full-length unmodified Aβ that accumulates initially in Tg2576 brain. SDS-resistant Aβ oligomers and most Aβ species that are N-terminally truncated or modified develop only in older Tg2576 mice, in which they are present at levels far lower than in human AD brain. Between 6 and 10 months, when SDS-insoluble Aβ42 and Aβ40 are easily detected in every animal, histopathology is minimal because only isolated Aβ cores can be identified. By 12 months, diffuse plaques are evident. From 12 to 23 months, diffuse plaques, neuritic plaques with amyloid cores, and biochemically extracted Aβ42 and Aβ40 increase to levels like those observed in AD brains. Coincident with the marked deposition of Aβ in brain, there is a decrease in CSF Aβ and a substantial, highly significant decrease in plasma Aβ. If a similar decline occurs in human plasma, it is possible that measurement of plasma Aβ may be useful as a premorbid biomarker for AD.
Functional properties and amino acid content of a protein isolate from mung bean flour

Summary A protein isolate was prepared from mung bean flour by extraction with 0.001 NNaOH, precipitation at pH4.5, neutralization of the dispersed precipitate to pH6.8–7.0, and subsequent freeze drying. the isolate's amino acid composition was determined and found to be similar to that of mung bean flour except for cystine which was destroyed during isolate preparation. the following properties of the protein isolate were investigated: nitrogen solubility, buffer capacity, foamability, gelation. Except for buffer capacity, the isolate demonstrated good functional abilities in simple systems under laboratory conditions.
A review of Gammaridae (Crustacea: Amphipoda): the family extent, its evolutionary history, and taxonomic redefinition of genera

By molecular analysis of a high number of gammarids, including 29 out-group genera, we could assure the monophyly of Gammaridae. To avoid the paraphyly of the family, we propose the omission of Pontogammaridae, Typhlogammaridae, and all Baikalian families. Similarly, the genera Fontogammarus, Sinogammarus, Lagunogammarus, Pephredo, Neogammarus, and Laurogammarus may be cancelled. But, tens of Baikal genera, nested within Gammarus, are so diverse that they must be retained, although rendering Gammarus paraphyletic. Besides we propose the polyphyletic Echinogammarus–Chaetogammarus group to be divided into monophyletic genera Echinogammarus s. str. , Homoeogammarus, Parhomoeogammarus, Marinogammarus, Relictogammarus gen. nov., Chaetogammarus, and Trichogammarus gen. nov. These solutions made it possible to complete the first analysis of the family evolution in light of its phylogeny. Perimarine clades are mainly basally split clades, whereas in some ancient lakes extremely rich endemic faunas had developed polyphyletically. The troglobiotic Typhlogammarus group from Dinarides and Caucasus formed a monophylum, whereas the troglobiotic assemblage of Gammarus species is highly polyphyletic. Reduction of the uropod III endopodite, which classically distinguishes between the genera Gammarus and Echinogammarus, appeared to be highly polyphyletic. Protective dorsal pleonal projections occur scattered across the family and beyond, whereas lateral projections were limited to species of ancient lakes, so both structures were polyphyletic. The evolutionary history of Gammaridae was investigated with ten different calibration schemes, which produced incompatible results; however, the most probable scenario is a late rise of the family, which can only explain the absence of Gammaridae species around the Indo-Pacific. © 2015 The Linnean Society of London
A revision of Phlomoides sect. Thyrsiflorae (Lamiaceae)

The taxonomic status of Phlomoides sect. Thyrsiflorae in Flora Iranica is reviewed. A new species of this section is reported for the first time from the dry-stony zone in a mountainous region in Kerman Province of Iran, at an elevation of 2250 m, far disjunct (c.700 km) from the Phlomoides thyrsiflora in Afghanistan. This new species is described and illustrated as Phlomoides kermanica. On the basis of data on morphology, ecology and chorology, the new species is reported and its affinities and differences with regard to close species are discussed. Phlomoides sect. Thyrsiflorae is recorded for the first time from Iran. In addition, a key to all species of this section is presented.
The use of constant effort mist-netting to measure between-year changes in the abundance and productivity of common passerines

The Constant Effort Sites (CES) Ringing Scheme of the British Trust for Ornithology aims to provide annual measures of change in the abundance and productivity of common breeding passerines in scrub and wetland habitats in Britain and Ireland. Changes in the sizes of the annual catches, from a set of standard mist nets operated during 12 summer (May–August) visits, are combined across sites to produce estimates of the percentage change in adult and juvenile numbers. The proportion of juveniles in the catch is used as a relative measure of breeding productivity. Methods are presented for calculating standard errors of between-year changes in both adult and juvenile catches, and changes in the proportion of juveniles. Present levels of precision are summarized and predictions are made concerning likely improvements in precision from a larger CES Scheme. For most of the species considered there was little evidence that between-year changes in catches of adults at CE sites have differed between habitats, regi.
Long-term fertilizer experiments as a data base for calculating the carbon sink potential of arable soils

Long-term experiments in Müncheberg, Braunschweig and Livada were used to understand the complex issue of carbon sequestration in soil. The investigations were focused on: effects of land use changes on the fate of soil organic carbon; options of agronomic practices to maintain or to increase soil organic carbon; relationships between organic fertilization and changes in soil organic carbon. The long-term observations showed that the amount of soil organic matter is primarily a function of the prevailing land use. Clearly marked differences were observed between long-term arable farming with lower and short-term with higher soil organic carbon content. Agricultural practices lead to a decrease of soil organic carbon with the result that arable soils are rather sources of carbon than sinks. The carbon sequestration potential is caused by the agronomic management to different extents. The combination of organic and mineral fertilization increased the soil organic carbon content compared to exclusive mineral fertilization. Optimum values of organic fertilizer application for maintaining soil organic carbon were calculated. Liming reduced the soil carbon pool when applied in large amounts. Long-term fertilization experiments are a useful tool for calculating the carbon sink or source potential of arable soils.
Genetic variations of avian Pasteurella multocida as demonstrated by 16S-23S rRNA gene sequences comparison

Summary Pasteurella multocida is known as an important heterogenic bacterial agent causes some severe diseases such as fowl cholera in poultry and haemorrhagic septicaemia in cattle and buffalo. A polymerase chain reaction (PCR) assay was developed using primers derived from conserved part of 16S-23S rRNA gene. The PCR amplified a fragment size of 0.7 kb using DNA from nine avian P. multocida isolates. Sequence alignment of the 16S-23S rRNA genes (ITS) revealed a considerable heterogenicity among the isolates. The percentage of similarity varied from 83.3 to 100% among the isolates. An interesting finding from this study was the presence of an inserted sequence (seven nucleotides) in the 16S-23S rRNA region in 55% of the isolates. According to phylogenic analysis based on ITS sequence alignment, the P. multocida isolates classified into 2 distinct clusters. The virulence of isolates in cluster II were higher than those in cluster I. Ribotyping of P. multocida by using 16S-23S rRNA gene PCR sequencing could be used as a marker in epidemiologic studies.
An Immunocytochemical Technique Offering Increased Sensitivity and Lowered Cost with a Streptavidin-Horseradish Peroxidase Conjugate

AbstractImmunocytochemists seek methodologies that yield high sensitivity and excellent signal to noise ratios while remaining cost effective. We report on a three step labeled avidinbiotin (LAB) immunoperoxidase that has been used successfully in our laboratory for the past three years. The technique uses commercially available detection reagents that are purchased undiluted and used at high dilutions, resulting in a cost per slide of 3 – 5 cents. Excellent sensitivity has been achieved, which allows the dilution of primary antibody and detection system reagents (commercially available primary antibodies) to a range of 0.1–0.01 ug/ml, thereby saving on costly reagents. The method is easy to perform, accommodates busy technologists' schedules, and provides preparations with strong specific labeling and virtually no background interference. (The J Histotechnol 12:273, 1989)
N-Benzylideneaniline and N-Benzylaniline are Potent Inhibitors of Lignostilbene-α,β-dioxygenase, a Key Enzyme in Oxidative Cleavage of the Central Double Bond of Lignostilbene

Lignostilbene-α,β-dioxygenase (LSD, EC 1.13.11.43) is involved in oxidative cleavage of the central double bond of lignostilbene to form the corresponding aldehydes by a mechanism similar to those of 9-cis-epoxycarotenoid dioxygenase and β-carotene 15,15′-dioxygenase, key enzymes in abscisic acid biosynthesis and vitamin A biosynthesis, respectively. In this study, several N-benzylideneanilines and amine were synthesized and examined for their efficacy as inhibitors of LSD. N-(4-Hydroxybenzylidene)-3-methoxyaniline was found to be a potent inhibitor with IC50 = 0.3 µM and N-(4-hydroxybenzyl)-3-methoxyaniline was also active with IC50 = 10 µM. The information obtained from the structure-activity relationships study here can aid in discovering inhibitors of both abscisic acid and vitamin A biosynthesis.