Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional characterisation of the yeast tumour suppressor homologue Sro7p

Correct targeting of newly synthesized proteins to appropriate domains of the cell membrane is crucial to cellular architecture, polarity and function, making it no surprise that many proteins of the secretory machinery are conserved throughout evolution. This work presents a functional characterisation of the Saccharomyces cerevisiae cell polarity protein and tumour suppressor homologue, Sro7p. This protein, and its paralogue Sro77p, belong to the Lgl-family of WD-40 repeat proteins that are conserved from yeast to human. Deletion of Lgl genes produces different phenotypes that all seem to share the common denominator of defective targeting of critical cell surface proteins. Yeast cells lacking SRO7 become sensitive to NaCl and we here show that this defect is due to mis-targeting of the sodium transporter Ena1p. In sro7 mutants Ena1p becomes routed to the vacuole for degradation via the multi-vesicular body (MVB) pathway, instead of being properly expressed at the cell surface. Isolation and analysis of post-Golgi secretory vesicles showed a defective sorting of Ena1p into these vesicles from sro7 mutants, implying mis-sorting in late Golgi or early endosomes. The diversion of Ena1p into the MVB pathway further required ubiquitylation by the ubiquitin ligase Rsp5p. Isolation of suppressors of the sro7 salt sensitivity identified two genes of unknown function, RSN1 encoding a trans-membrane protein, and ART5 (RSN2), encoding an arrestin-like protein. Deletion of either gene in sro7 mutants re-establishes salt tolerance and retargets Ena1p to the cell surface. Previous proteomic studies have shown that Art5p interacts with Rsp5p and we showed that deletion of ART5 in sro7 mutants inhibits ubiquitylation of Ena1p. Our data are consistent with Art5p being a selective adaptor protein that helps Rsp5p recruiting Ena1p for ubiquitylation. To identify further candidate proteins for mis-sorting in salt stressed sro7 mutants we performed the first proteomic analysis of purified yeast post-Golgi vesicles (PGVs), using quantitative proteomics techniques. By this analysis we could identify 107 genuine vesicle residents in control yeast cells, including a number of cargo proteins not previously identified in PGVs. Vesicles derived from sro7 mutants contained essentially the same list of proteins but were depleted of a subset of proteins, thus being candidates for mis-routing. The present study finally analysed possible Lgl conservation in plants by characterising two Arabidopsis thaliana Lgl homologues. Sequence based modelling showed that both proteins can fold into the twin β-propellers shown by the published Sro7p crystal structure. However, only one of the proteins, AtLGL1, could partially substitute for the yeast Sro7/77 proteins. The other, AtLGL2 showed structural similarities with tomosyn that is known to regulate vesicle fusion in mammals. Homozygous T-DNA insertion mutants in A. thaliana exhibited defects in lateral root formation, a phenotype associated with changed celland tissue polarity. ISBN 978-91-628-7887-0
Prevalence of Multiple Drug Resistance among Avian Pathogenic E. coli Isolates from Commercial Poultry

Infections associated with Avian Pathogenic E. coli are responsible for huge economic losses for poultry industry worldwide. Particularly, its association with colibacillosis, a complex syndrome which is characterized by lesions of multiple organs i.e. peritonitis, pericarditis, air Sacculitis, osteomyelitis, salpingitis and yolk sac infections is responsible for high mortality and morbidity. Moreover, it causes respiratory tract infections among poultry birds, followed by septicaemia. Liver samples were collected from commercial poultry birds from the various retail shops located in Peshawar City. Bacteria were identified by biochemical and molecular methods. Out of all the tested isolates n=85, 98% were identified as Avian Pathogenic E. coli (APEC). Identified APEC samples were further tested against 23 different antibiotics including amoxicillin (89.40%), levofloxacin (62.40%), ciprofloxacin (71.80%), tobramycin (14.10%), gentamycin (34.10%),neomycin (53.00%), streptomycin (81.00%), tigecyclines (0.00%), oxytetracyclines (96.50%), doxycycline (61.20%), nitrofurantoin (1.00%), chloramphenicol (63.50%), cefixime (7%), cefepime (4.70%), ceftazidime (8.30%), cefotaxime (8.00%), cephalothin (43.50%), trimethoprim, sulfamethoxazole (77.60%), lincomycin (100%), augmentin (4.70%), carbapenem (4%) and polymyxin B (15%). Out of all n=85 isolates 99.9% were multi-drug resistant. Furthermore, ESBL encoding TEM, OXA, SHV were detected in following percentages 53.60%, 19.50%, 9.70% respectively genes.
β-amyrin synthase : investigating the structure and function of an oxidosqualene cyclase involved in disease resistance in oats

1 Chapter 1 Introduction . 2 1.1 Cereals and disease resistance . 2 1.1.1 The Gramineae: a family of the plant kingdom . 2 1.1.2 Susceptibility of cereals to pathogenic fungi . 2 1.1.3 Resistance mechanisms in plants . 3 1.2 Secondary metabolites . 5 1.2. 1 Secondary metabolites in plants . 5 1.2. 2 Saponins and disease resistance . 6 1.2. 3 Avenacins: Structure and function . 8 1.3 Pathway to avenacin production . 9 1.3. 1 Primary and secondary metabolism in plants . 9 1.3. 2 Sterol and triterpene synthesis: a branchpoint between primary and secondary metabolism . 9 1.3. 3 Applications of characterising secondary metabolic pathways . 13 1.3. 4 Elucidating biosynthetic pathways in plants . 14 1.3. 5 Identification of genes involved in avenacin biosynthesis in oats . 15 1.4 Oxidosqualene cyclases in plants, animals and fungi . 26 1.4. 1 Cloning of oxidosqualene cyclases involved in sterol production . 26 1.4. 2 Cloning of oxidosqualene cyclases involved in triterpene production . 27 1.4. 3 Alternative strategies for cloning plant oxidosqualene cyclase genes . 29 1.5 Structure-function relationships in plant OSCs . 30 1.5. 1 Conserved features: vast product differences . 30 1.5. 2 Solving the structures of triterpenoid cyclases . 31 1.5. 3 Insights into enzyme mechanism . 33 Chapter 2 Homology modelling of AsbAS1 . 37 2.
Cutting Edge: The Neurotoxic Prion Peptide Fragment PrP106–126 Is a Chemotactic Agonist for the G Protein-Coupled Receptor Formyl Peptide Receptor-Like 11 2

Prion diseases are transmissible and fatal neurodegenerative disorders which involve infiltration and activation of mononuclear phagocytes at the brain lesions. A 20-aa acid fragment of the human cellular prion protein, PrP106–126, was reported to mimic the biological activity of the pathologic isoform of prion and activates mononuclear phagocytes. The cell surface receptor(s) mediating the activity of PrP106–126 is unknown. In this study, we show that PrP106–126 is chemotactic for human monocytes through the use of a G protein-coupled receptor formyl peptide receptor-like 1 (FPRL1), which has been reported to interact with a diverse array of exogenous or endogenous ligands. Upon stimulation by PrP106–126, FPRL1 underwent a rapid internalization and, furthermore, PrP106–126 enhanced monocyte production of proinflammatory cytokines, which was inhibited by pertussis toxin. Thus, FPRL1 may act as a “pattern recognition” receptor that interacts with multiple pathologic agents and may be involved in the proinflammatory process of prion diseases.
Characterising the binding interactions and thermodynamics of odour binding protein 3

Odour Binding Proteins (OBPs) are found in the olfactory system of a range of species. Whilst invertebrate OBP function is well understood, the exact function of these proteins in the vertebrate nasal mucus is not fully understood. Multiple subtypes of rat OBPs have been identified and found to share less than 30% sequence identity. Studies have suggested each rat OBP binds to particular sets of odours, which may afford them a particularly important role within the olfactory system, pre-sorting odours. This study focuses on OBP3, closely examining the binding interaction of this protein with a range of odours. This has been done using Isothermal Titration Calorimetry which revealed that the binding of the highest affinity ligands, the heterocyclic compounds, is enthalpically driven. A defined odour series, the gamma-lactones showed that despite increasing ligand size and hydrophobicity, the free energy of binding of these ligands is maintained. Interactions with both 2-isobutylthiazole and the gamma-lactones were examinedusing NMR spectroscopy, which required the NMR assignment of OBP3 to be determined. In addition a homology model of OBP3 was created in order to structurally map the per-residue changes of OBP3 upon binding. It has been found that OBP3 is able to subtly adjust in order to accommodate each of these ligands. Protein engineering of the OBP3 binding pocket has been used to highlight the importance of its size and hydrophobicity. The importance of a tyrosine residue that appears to cover the opening to the binding pocket and is conserved across both the aBPs and the lipocalins family they are part of, has been demonstrated. Mutagenesis has also revealed the importance of a number of key residues for the binding of 2-isobutylthiazole. The ability to rationally improve the affinity of OBP3 for a particular odour has also been demonstrated.
Écologie de la reproduction de l'huître Crassostrea gigas en lagune méditerranéenne

Les lagunes mediterraneennes hebergent de nombreux usages anthropiques dont la conchyliculture depuis le debut du 20eme siecle. Importee en 1970, l'huitre creuse, Crassostrea gigas, s'y est adaptee parfaitement et a permis un developpement ostreicole important jusqu'en 2008, annee d'apparition des surmortalites de naissain liees a l'emergence d'un variant du virus OsHv1. La rarefaction du naissain et la speculation sur ce produit ont modifie regionalement les pratiques culturales et les modes d'approvisionnement en juveniles, avec notamment la volonte de developper une activite locale de captage. Mais le cycle de reproduction de l'espece et le recrutement de juveniles etaient mal connus en milieu lagunaire. Dans ce contexte, l'objectif de cette these est de caracteriser la variabilite de la reproduction et du recrutement de l'huitre creuse en lagune mediterraneenne. La configuration lagunaire offre des atouts de productivite pour le cheptel de geniteurs et de connectivite hydrodynamique pour les larves. Cependant, il apparait que le fonctionnement ecologique du systeme a la base de la production primaire joue un role essentiel sur les apports trophiques pour le succes de la reproduction des huitres. Ce travail s'inscrit, en outre, dans le contexte d'un ecosysteme en voie de restauration ecologique entamant un processus d'oligotrophisation dont nous decrivons les premiers effets sur le cycle de reproduction de l'huitre.
Modulation of neural plasticity by the ADAMTSs (a disintegrin and metalloproteinase with thrombospondin motifs)

Brevican, a proteoglycan of the lectican family, inhibits neurite outgrowth and may also stabilize synapses. Little is known about its expression or function in vitro. This study seeks to determine whether a brevican-containing matrix is present in neural cultures, and if so, how the production of brevican may be modulated. To accomplish this, the content of brevican and its proteolytic fragments were measured in primary cultures of neurons, astrocytes and microglia after treatment with cytokines. These experiments revealed that astrocytes and neurons express several isoforms of brevican, whereas microglia do not produce this proteoglycan. Cleavage fragments of brevican were found primarily in neuronal and astrocyte culture medium. ADAMTS4 (a disintegrin and metalloproteinase with thrombospondin motifs), a protease that selectively cleaves lecticans, was detected in cultures of neurons, astrocytes and microglia. When astrocytes were challenged with various cytokines, it was found that treatment with transforming growth factor β (TGFβ) resulted in a marked increase in intact brevican in the culture medium that was accompanied by a trend for a decrease in ADAMTS-generated fragments of brevican and apparent ADAMTS
Effect of heat treatment using palm oil on properties and durability of Semantan bamboo

This paper investigates the effect of heat treatment on Semantan bamboo (Gigantochloa scortechinii) with emphasis given to their properties and durability. Matured four-year-old bamboo culms were harvested and subjected to high temperature condition using palm oil as a heating media. Two groups of samples, green and air-dried, were used. The temperatures applied were 140Â°C, 180Â°C and 220Â°C, with exposure duration of 30, 60 and 90 min, respectively. The results of the investigations show that the heat-treated bamboos retained most of their original physical and strength properties after undergoing the heat treatment. Green or air-dried bamboo culms can be dried to an MC of 6-7% within 2-3 h of treatment. The basic densities of bamboo were found to improve slightly by the heat application. The overall strengths properties of the heat-treated bamboo were found to decrease. The modulus of elasticity in the bending strengths was reduced between 2 and 33% in the green- and 6-9% in the air-dried conditions. For the modulus of rupture in the bending strengths, the value was reduced between 1 and 23% in green- and 4-16% in air-dried conditions. The compression strengths were reduced in the range between 2 and 3% in green- and 2-35% in air-dried conditions. The shear strengths were reduced in the range between 16 and 24% and 12-24% in in green- and air-dried conditions, respectively.
Primary moult in non-breeding second-calendar-year Swifts Apus apus during summer in Europe

Little is known about the extent of primary moult in non-breeding second-calendar-year Swifts during summer in Europe. A sample of 352 Swifts of this age group was captured during May–July in a village in the Netherlands. Primary moult was almost completely restricted to July. During the first and second halves of July, respectively, 20% and 60% of the second-calendar-year Swifts were moulting. Moult was restricted to the first four inner primaries, but 62% of individuals moulted the innermost primary only. Surprisingly, in 63% of moulting birds, primary moult was asymmetric.
Actinomyces and Related Genera

1 Definition 2 Introduction and Historical Perspective 3 Habitat 4 Morphology 5 Cultural Characteristics 6 Metabolism 7 Cell Wall Composition; Antigenic Structure 8 Susceptibility to Antimicrobial Agents 9 Classification 10 Laboratory Isolation and Identification 11 Typing Methods 12 Role in the Normal Flora of Humans 13 Pathogenicity and Virulence 14 Acknowledgments Keywords: actinomyces and related genera; Actinomyces spp. -gram-positive rods; colonial morphology and appearance in broth; Actinomyces cellular and colonial morphology; Actinomyces spp. -cell walls typical of gram-positive bacteria; Actinomyces spp. and susceptibility to antimicrobial agents; Actinomyces spp. -mouths of humans and animals; actinomycotic infections in humans-involving A. israelii and A. gerencseriae with A. naeslundii
Effects of a compensatory dry-land training program on shoulder posture and scapular position of competitive female swimmers

Background: Competitive swimmers place a significant demand on the shoulder adductors and internal rotator muscles due to the repetitive nature of swimming movements.Objectives: To evaluate the effect of a compensatory dry-land training program on the shoulder posture and scapular position of competitive female swimmersMethod: 25 National Level female competitive swimmers received an 8-week intervention program focused on strengthening of posterior shoulder girdle muscles and stretching of anterior shoulder muscles. The study sample was exposed to a control period of 2 weeks and an intervention period of 8 weeks.Results: Significant differences were found after the intervention period, on both dominant and non-dominant sides, with respect to shoulder protraction (distance between the anterior aspect of the acromion to the wall – p < .05) and scapular abduction (distance between a medial line marked over the thoracic spinal process and the medial border of spina scapulae – p < .05; and distance between a medial line marked over the thoracic spinal process and the medial border of the spina scapulae – p < .05). Conclusions: The results revealed that the incorporation of a compensatory dry-land training program alongside a normal in-water training significantly reduced the distance of shoulder posture in protraction and scapular position in abduction.Key words: shoulder protraction, scapular abduction, dry-land training, swimming, female.
Rooting for Rewilding: Quantifying Wild Boar's Sus scrofa Rooting Rate in the Scottish Highlands

Rewilding is emerging as a promising framework within restoration ecology to help restore ecosystem function through species reintroduction. To manage effectively such projects it is necessary to predict and quantify the interactions between the reintroduced species and their environment. To date, this has not been a priority in restoration ecology. Here, we quantify wild boar's rooting rate at a range of stocking densities to explore their potential to aid the restoration of the Caledonian pine forest in the Scottish Highlands by reinvigorating the disturbance regime. Eleven enclosures of c. 0.5 ha within heather moorland, dominated by Caluna vulgaris, were used, situated on the Alladale Wilderness Reserve, 50 km north‐west of Inverness. Stocking densities varied between 4 and 15 boar/ha. The accumulation of rooted area was recorded weekly over a 13‐week period. A cost analysis was performed to compare the use of wild boar with other ground preparation techniques. The median per capita rooting rate was 42.4 m2/week (interquartile range [IQR] 45.5), but rooting rate varied temporally. Median rooting rates varied between 21.6 and 75.3 m2/week (IQR 5.6) in periods that varied in suitability for rooting. Rooting rates were consistent across stocking densities. The cost of using wild boar as a ground preparation tool ranged between £184 and £1,961 per hectare depending on stocking density and rate of rooting. This experiment has direct application for managing the impact of wild boar within free range farming conditions, managed woodland regeneration schemes, rewilding projects, and in the wild.
Antimicrobial Use and Multidrug-Resistant Salmonella spp., Escherichia coli, and Enterococcus faecalis in Swine from Northern Thailand

The aim of this study was to isolate antimicrobial-resistant bacteria from intensive commercial and backyard swine operations (farms) in Northern Thailand and to characterize antimicrobial usage among swine farmers. A total of 51 swine farms in Chiang Mai, Lampoon, and Nan provinces were visited from February to October 2011 to collect swine fecal samples for bacterial isolation ( Salmonella spp., Escherichia coli, Enterococcus faecalis ) and antimicrobial resistance testing. A survey about production intensity, management practices, animal health, and antimicrobial usage was conducted with a sub-set of farms (n = 20) located in Nan province. The farm-level prevalence of drug-resistant E. coli, E. faecalis, and Salmonella spp. was 96, 35, and 18%, respectively. Of the four surveyed commercial operations (median = 58 pigs/farm), 75% routinely administered antimicrobials to pigs (> 50% of animal life). In the 16 backyard farms surveyed (median = 6 pigs/farm), 89% used antimicrobials intermittently (10-50% of animal life) or episodically (< 10% of animal life) and one farm routinely administered antimicrobials to pigs. Herd size was moderately positively correlated (R 2 = 0.44) to the number of resistance traits identified on a farm. These data indicate that reservoirs of multidrug resistance are widely present in swine farms of all sizes in Northern Thailand and may be affected by farm size and antimicrobial usage practices on the farm.
Yetişkinlerde Geleneksel/Tamamlayıcı Tıp Tutumu ile Sağlık Okuryazarlığı ve Sağlık Algısı Arasındaki İlişk

Amac: Bu arastirma yetiskinlerde geleneksel/tamamlayici tip uygulamalari ile saglik okuryazarligi ve saglik algisi arasindaki iliskinin incelenmesi amaciyla yapilmistir. Gerec ve Yontem: Arastirma Kasim-Aralik 2017 tarihleri arasinda Istanbul’da 4 aile sagligi merkezine basvuran 18-65 yas arasi bireylerle tanimlayici olarak yurutuldu n=214 . Katilimda “gonulluluk” esas alinmistir. Arastirma verilerinin toplanmasinda katilimcilarin sosyo-demografik ozelliklerini belirleyen anket formu, Geleneksel Tamamlayici Tip Tutum Olcegi, Yetiskin Saglik Okuryazarligi Olcegi ve Saglik Algisi Olcegi kullanilmistir. Veri analizleri SPSS 23.0 istatistik programinda aritmetik ortalama, Mann Whitney U, Korelasyon Analizi ve One Sample-KS testleri kullanilarak yapildi. Bulgular: Arastirmaya katilanlarin yas ortalamasi 32.9±11.7 olup %71.7’i kadindir. Katilimcilarin %55.6’si universitesi mezunu, %81.8’i orta gelir grubundadir. %79.9’unun kronik bir hastaligi yoktur. Katilimcilarin %39.3’u geleneksel/tamamlayici tip yontemi kullanmaktadir. Kullanicilarin %34.6 ile en cok kullandiklari yontem bitkisel yontemler olup bunu %17.8 ile masaj ve %8.9 ile hacamat takip etmektedir. En az kullanilan yontemler %1.4 ile hipnoz yontemi olup bunu %0.9 ile larva uygulamalari ve %0.5 ile refleksoloji yontemi takip etmektedir. Katilimcilar Geleneksel Tamamlayici Tip Tutum Olceginden 189 puan uzerinden ortalama 103.99±22.03 puan almislardir. Yetiskin Saglik Okuryazarligi Olcegi puani ve Geleneksel Tamamlayici Tip Tutum Olcegi puani arasinda negatif yonlu zayif bir iliski bulunmustur r = -19; p . 05 . Geleneksel Tamamlayici Tip Tutum Olcegi puani ve Saglik Algisi Olcegi puani arasinda ise anlamli bir iliski bulunmamistir p> . 05 . Sonuc: Arastirma bulgularina gore yetiskin bireylerin saglik okuryazarlik duzeyleri arttikca geleneksel ve tamamlayici tipa karsi tutumlarinda azalma gorulmustur. Bu sonuc dogrultusunda etkinligi kanitlanmamis geleneksel/tamamlayici tip yontemlerinin kullaniminin engellenmesinde, saglik okuryazarligi seviyesinin yukseltilmesi koruyucu bir onlem olabilir.
Application of Gamma Irradiation for the Reduction of Residual Nitrite and Nitrosamine in Meat Products

Nitrite, a curing agent of meat products, is precursors of carcinogenic N-nitrosamines during processing of meat products or under human stomach conditions as well as having its own toxicity. Some researches have been conducted to evaluate the effects of ionizing radiation on the reduction of residual nitrite and N-nitrosamines in an aqueous model system and cured meat products with different packaging methods during storage. These results showed that the gamma irradiation was effective in reducing the residual nitrite and N-nitrosamines in an aqueous model system as well as meat products. Especially, irradiation combined with vacuum or modified atmosphere packaging was more effective in nitrite and N-nitrosamines reduction than aerobic packaging during storage. The objective of this review is to introduce the irradiation technology for the application of reducing the residual nitrite and N-nitrosamine contents in meat products.