Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of protein oxidation in ageing & disease

Ageing is a natural phenomenon of the human lifecycle, yet it is still not understood what causes the deterioration of the human body near the end of the lifespan. One popular theory is the Free Radical Theory of Ageing, which proposes that oxidative damage to biomolecules causes ageing of tissues. The ageing population is affected by many chronic diseases. This study focused on sarcopenia (muscle loss in ageing) and obesity as two models for comparison of oxidative damage in muscle proteins in mice. The aim of the study was to develop advanced mass spectrometry methods to detect specific oxidative modifications to mouse muscle proteins, including oxidation, nitration, chlorination, and carbonyl group formation, but western blotting was also used to provide complementary information on the oxidative state of proteins from aged and obese muscle. Mass spectrometry proved to be a powerful tool, enabling identification of the types of modifications present, the sites at which they were present and percentage of the peptide populations that were modified. Targeted and semi-targeted mass spectrometry methods were optimised for the identification and quantitation of the oxidised residues in muscle proteins. The development of the quantitative methods enabled comparisons of mass spectrometry instruments. Both the Time of Flight and QTRAP systems showed advantages of using the different mass analysers to quantify oxidative modifications. Several oxidised residues were characterised and quantified in both the obese and sarcopenic models, and higher levels of oxidation were found compared to their control counterparts. Residues found to be oxidised were oxidation of proline, tyrosine and tryptophan, dioxidation of methionine, allysine and nitration of tyrosine. However quantification was performed on methionine dioxidation and cysteine trioxidation containing residues in SERCA. The combination of measuring residue susceptibility and functional studies could contribute to understanding the overall role of oxidation in ageing and obesity.
The Effect of Light Quality on Shoot Extension Growth in Three Species of Grasses

The effect of light quality on the extension growth of vegetative shoots and on the final size of their leaves was investigated in plants of Lolium multiflorum, Sporobolus indicus and Paspalum dilatatum. Three experimental approaches were used, (a) red or far-red end-of-day irradiations of sunlight-grown plants, (b) different red/far-red ratios of white light in a growth room and (c) sunlight enrichment with radiation of different red/far-red ratios or with different amounts of far-red light during the photoperiod. Plants treated with end-of-day far-red or low red/far-red ratios throughout the photoperiod developed longer leaves and, as a result, longer shoots. This effect was more marked in leaf sheaths than in blades. Tiller extension and leaf sheath length increased with the amount of far-red added to sunlight in a simple hyperbolic relationship. These results show that vegetative grass shoots respond to light quality in a way similar to internodes of dicotyledonous plants.
Interactions between helicase and primase are crucial for DNA replication in the enteropathogen Clostridium difficile

DNA replication is an essential and conserved process in all domains of life and may serve as a target for the development of new antimicrobials. However, such developments are hindered by a limited understanding of DNA replication in pathogenic micro-organisms. Clostridium difficile is the main cause of health-care associated diarrhea and its DNA replication machinery is virtually uncharacterized. We identified the replicative helicase (CD3657), the helicase loader ATPase (CD3654) and primase (CD1454) of C. difficile and reconstitute helicase and primase activity in vitro. We demonstrate a direct and ATP-dependent interaction between the helicase loader and the helicase. We find that helicase activity is dependent on the presence of primase in vitro. The trinucleotide specificity of primase, which we find to be determined by a single lysine residue, is similar to extreme thermophile Aquifex aeolicus but the presence of helicase allows more efficient de novo synthesis of RNA primers from non-preferred trinucleotides. Thus, helicase-primase interactions constitute a crucial aspect of DNA replication initiation in C. difficile and helicase loading and activation in this organism differs critically from that of the Gram-positive model organism Bacillus subtilis.
Mastitis: The diseases under aspects of milk quality and hygiene

(1) Les changements inflammatoires dans la glande mammaire influencent le processus de la synthese du lait d'un point de vue quantitatif et qualitatif. Les modifications dans les constituants du lait ont un effet sur les composants principaux (lactose, graisse, proteines), de meme que sur les acides gras, les fractions de proteine, les caseines, les seroproteines, les anions et cations, la conductivite, les enzymes etc. Avec le nombre croissant de cellules somatiques la croissance des levains dans le lait peut etre influencee de maniere opposee. Le temps de coagulation et la stabilite du lait a la chaleur peuvent etre deteriores. (2) La valeur hygienique du lait cru est determinee par les microorganismes pathogenes et saprophytes, des residus et les contaminants. En cas de mammite des microorganismes pathogenes peuvent apparaitre qui sont infectieux aussi pour l'homme (p.ex. streptocoques B, Escherichia coli) ou qui a certaines conditions forment des toxines (p.ex. Staphylococcus aureus, Escherichia coli). (3) Les residus resultant du traitement de la mammite comprennent surtout des antimicrobiens comme des antibiotiques et des sulfonamides. La presence des residus antibiotiques dans lait est dicutee sous deux aspects: - la valeur du lait basee sur la qualite technologique (,,inhibiteurs) et - la sante publique et le regime des lois alimentaires. (4) Concernant l'effet des residus antibiotiques sur la sante humaine un grand nombre d'aspects doit etre pris en consideration (effets toxicologiques, microbiologiques et immunopathologiques). Du point de vue technologique la sensibilite des levains thermophiles et mesophiles aux antibiotiques divers peut varier largement. L'etablissement des limites maximum de residus (MRLs) pour un nombre d'antimicrobiens a mene a la difficulte de que le resultat negatif d'un test inhibiteur n'indique pas necessairement des concentrations d'antimicrobiens au dessous les MRLs. Un nouveau systeme integre pour la determination d'antimicrobiens a ete developpe, qui tient compte des aspects technologiques et toxicologiques. (5) L'emploi des desinfectants pour le trempage du trayon avant et apres la traite doit etre evaluee critiquement. Il faut prende en consideration non seulement les ingredients actifs (iode, chlorhexidine, chlorure etc.) mais aussi d'autres composants (p.ex. des detergents, des additifs). (6) Le nombre de cellules somatiques dans le lait est un indicateur des caracteristiques qualitatives et hygieniques et refletent la situation actuelle de la mammite dans le troupeau. Les mesures de controle de la mammite doivent avoir pour objet primairement de fournir un lait avec une teneur reduite en cellules somatiques selon les attentes des producteurs et des consommateurs des points de vue qualitatif et hygienique.
New data on the spider genus Troglohyphantes (Araneae, Linyphiidae) in the Italian Alps, with the description of a new species and a new synonymy

In this paper we describe Troglohyphantes lanai n. sp. from Pennine Alps and the unknown female of T. bonzanoi, from Ligurian Alps. Based on the collection of new material and on the examination of the paratypes, T. delmastroi Pesarini, 2001 is proposed as junior synonym of T. iulianae Brignoli, 1971 (new synonymy). We also provide new faunistic and ecological data on the Italian species of Troglohyphantes, focusing mainly on Central Italian Alps. Phenetic species groups previously proposed in literature for the Italian species have been updated in view of recent literature and new findings. Pesarini’s complexes of species are used to map the species distribution in the Italian Alps.
Isolation of Proteins for Microsequence Analysis

The first basic protocol in this unit can be used to determine the amino‐terminal sequence of polypeptides or proteins. It is particularly appropriate for large fragments of insoluble or hydrophobic proteins or proteins that cannot be purified to >90% molar purity without electrophoresis. Although the efficacy of this technique varies with the protein, it is possible to obtain useful sequence information starting with less than 50 pmol of the protein of interest. If the protein is blocked at the amino terminus, chemical cleavage or partial enzymatic digestion must be performed prior to electrophoresis. Upon isolation, the internal amino acid sequence is analyzed as described in the second basic protocol. This method requires ˜200 pmol of protein for analysis.
The effects of crocin (active contstituent of saffron) treatment on brain antioxidant enzyme mRNA levels in diabetic rats / Diyabetik ratlarda safranın aktif içeriği olan krosin tedavisinin beyindeki antioksidan enzimlerin mRNA seviyeleri üzerine etkisi

Abstract Objective: The aim of the present study is to evaluate the effect of crocin on mRNA expression of antioxidant enzymes, SOD, CAT and GPX in the brain of the STZ induced diabetic rats. Methods: Thirty animals randomized in three groups containing ten animals in each group as follows; control (non-diabetic rats), DM (STZ-induced untreated diabetic rats), DM+crocin (STZ-induced diabetic rats treated with crocin,). Crocin was given at a dose of 20 mg/kg bw/day by gavage for 21 days. Results: STZ injection caused a significant increase in mRNA expression of antioxidant enzymes, SOD, CAT and GPX when compared to control group. Crocin given to diabetic rats significantly decreased mRNA expression of antioxidant enzymes, SOD, CAT and GPX when compared to DM group. Conclusion: The present study demonstrates that crocin can modulate mRNA expression of antioxidant enzymes, SOD, CAT and GPX and oxidative stress in the brain of the STZ induced diabetic rats.
Influence of thinning intensity and canopy type on Scots pine stand and growth dynamics in a mixed managed forest

Aim of the study : We analysed the effects of thinning intensity and canopy type on Scots pine growth and stand dynamics in a mixed Scots pine-beech forest. Area of the study : Western Pyrenees. Material and methods : Three thinning intensities were applied in 1999 (0, 20 and 30% basal area removed) and 2009 (0, 20 and 40%) on 9 plots. Within each plot, pure pine and mixed pine-beech patches are distinguished. All pine trees were inventoried in 1999, 2009 and 2014. The effects of treatments on the tree and stand structure variables (density, basal area, stand and tree volume), on the periodic annual increment in basal area and stand and tree volume, and on mortality rates, were analysed using linear mixed effects models. Main Results: The enhancement of tree growth was mainly noticeable after the second thinning. Growth rates following thinning were similar or higher in the moderate than in the severe thinning. Periodic stand volume annual increments were higher in the thinned than in the unthinned plots, but no differences were observed between the thinned treatments. We observed an increase in the differences of the Tree volume annual increment between canopy types (mixed < pure) over time in the unthinned plots, as beech crowns developed. Research highlights : Moderate thinning is suggested as an appropriate forest practice at early pine age in these mixed forests, since it produced higher tree growth rates than the severe thinning and it counteracted the negative effect of beech on pine growth observed in the unthinned plots. Keywords: competition; Fagus sylvatica L. ; Pinus sylvestris L. ; forest management; mortality; Mediterranean forest.
Synthesis and preliminary evaluation of novel alkyl diamine linked bivalent β-carbolines as angiogenesis inhibitors

A series of novel bivalent β-carbolines linked with an alkyl diamine spacer at the C-3 position were synthesized and evaluated as potent angiogenesis inhibitors. The results demonstrated that most bivalent β-carbolines displayed significant anti-proliferative effects against EA.HY926 human umbilical vein cell lines. Compound 8z was found to be the most potent anti-proliferative agent with an IC50 value of 1.10 μM against EA.HY926 cell lines. Preliminary investigations on the mechanisms of action revealed that compound 8z could dramatically inhibit EA.HY926 cell migration and tube formation in a dose-dependent manner. Moreover, compound 8z exhibited significant angiogenesis inhibitory effects in CAM assay, and the anti-angiogenic potency was comparable with that of the reference drug Endostar. These molecules might serve as candidates for further development into vascular-targeting antitumor drugs.
Effects of dietary vitamin B6 on the skeletal muscle protein metabolism of growing rabbits

This study aimed to evaluate the effects of dietary vitamin B6 on the skeletal muscle protein metabolism and expression of transcription and growth factor of growing rabbits. Two hundred, healthy, rabbits with similar bodyweights were randomly assigned to one of five dietary groups with 40 animals per group. The dietary groups consisted of the following different vitamin B6 supplementation levels: 0, 5, 10, 20 and 40 mg/kg. The feeding trial lasted 60 days. The results showed that dietary vitamin B6 elicited significant effects on the fore and hind leg muscle ratio (the fore and hind leg muscle weight/the liveweight; P < 0.05) and on serum total amino acids (T-AA), blood urea and insulin-like growth factor 1 (IGF1) content (P < 0.05). Additionally, expression of IGF1, myogenic determination factor (MYOD) and myogenin (MYOG), myocyte regulation factor 5 (MYF5), myostatin (MSTN) and WW domain-containing E3 proteasome ubiquitin ligase 1 (WWP1) mRNA in the loin (M. longissimus dorsi) were affected by vitamin B6 in diets (P < 0.05). The immunoblot analysis revealed that dietary vitamin B6 elicited significant effects on IGF1, MYOG and WWP1 expression in the loin (P < 0.05). Our results indicate that the addition of dietary vitamin B6 can significantly alter the protein metabolism of growing rabbits and that an appropriate vitamin B6 supplementation level is 20 mg/kg for 3–5-month-old growing rabbits (the basic diet vitamin B6 content was 4.51 mg/kg).
Leaf Disc Stress Tolerance Assay for Tobacco

[Abstract] Stress tolerance is a multigenic trait that depends on the coordinated action of several genes. Various physiological parameters, such as plant height and weight, total yield, chlorophyll content, photosynthesis rate, level of reactive oxygen species (ROS) and anti-oxidant activity could be correlated directly with the level of stress tolerance potential of any particular genotype. To evaluate the stress tolerance potential of a plant, leaf disc stress tolerance assay is a very rapid and widely acceptable experiment with minimum instrumentation facilities.
Natural zeolite (chabazite/phillipsite) dietary supplementation influences faecal microbiota and oxidant status of working dogs

Abstract We evaluated whether chabazite/phillipsite dietary supplementation might affect the faecal microbiota, oxidant and antioxidant status of working dogs at rest undergone to a trial test. Forty English Setter dogs were involved in two replicate trials. At each replicate, dogs were divided into two homogeneous groups (10 dogs/group). During a period of 28 days, diet was supplemented (Z group) or not supplemented (C group) with chabazite/phillipsite at the dose of 5 g/head/day. On day 29, dogs were subjected to a trial test. Faecal characteristics were assessed at 0 and 29 days (within two hours from the end of the trial test). Faecal consistency was not affected by dietary supplementation (p > .05). On day 29, Lactobacillus spp. and Enterococcus spp. counts were higher and Enterobacteriaceae were lower in Z than in C group (p < .05). At day 0 and at day 29, immediately before and within one hour from the end of the trial test, blood samples were recorded to evaluate the oxidant and antioxidant status. A reduction of 40% in thiobarbituric acid reactive substances (TBARS) levels was observed in Z compared to the C group (p < .05). Differences in nitric oxide and antioxidant enzymatic system levels were not significant (p > .05). Our results suggest that chabazite/phillipsite dietary supplementation, improves the intestinal microbiota ecosystem and may counteract the oxidative damage caused by physical stress in hunting dogs at the beginning of the working season.
A new species of Gomphrena (Amaranthaceae) from the Bonaparte Archipelago, Western Australia

Barrett, R.L. & Palmer, J. A new species of Gomphrena (Amaranthaceae) from the Bonaparte Archipelago, Western Australia. Nuytsia 26: 143–147 (2015). Gomphrena splendida R.L. Barrett & J.Palmer is described as a new species endemic to islands of the Bonaparte Archipelago in the northwest Kimberley region of Western Australia. This new species has a highly restricted distribution. It is unusual among the Australian species of Gomphrena L. in being a large, fleshy, perennial with very large flowers, giving this species significant horticultural potential in tropical areas. A modified key and images are presented.
Modulation of the GABAA receptor by CaMK-II dependent phosphorylation

Phosphorylation is an important mechanism for the modulation of ligand- gated ion channel function. CaMK-II dependent modulation of GABAa receptors was investigated through analysis of GABAA receptor mediated currents recorded by whole-cell patch clamp from non-neuronal and neuronal cell lines and from primary neurones in culture. Application of pre-activated a-CaMK-II had no effect on recombinant receptors expressed in HEK293 cells. Whole-cell currents recorded from cerebellar granule cells were significantly increased in peak amplitude on application of pre- activated a-CaMK-II. Analysis of spontaneous (s)IPSCs recorded from cerebellar granule cells in culture in the presence of pre-activated a-CaMK-II revealed an increase in sIPSC amplitude and decay time constants. Expression of recombinant GABAa receptors in the neuronal cell line NG108-15 allowed the functional effect of CaMK-II to be studied in a recombinant system. CaMK-II was able to up-regulate the function of cd/SlS and al/ftS GABAA receptors but not alfil'il receptors. This modification of function occurred through phosphorylation of Ser on the /33 subunit and through a downstream activation of a tyrosine kinase and subsequent phosphorylation of the 72S subunit at previously identified sites of tyrosine kinase phosphorylation, Tyr357 and Tyr359. Tyrosine kinase phosphorylation of 72S occurred when co-expressed with cd/31 or cd/33 but not with cd/2. Transfection of different GABAA receptor subunits into cerebellar granule cells was carried out to confirm the importance of these sites in a neuronal environment. Analysis of sIPSCs recorded from cerebellar granule cell cultures prepared from /52 subunit knockout mice revealed a-CaMK-II modification of /32 subunit-containing receptors at the synapse, resulting in an increase in sIPSC amplitude with no change in decay times. This was in contrast to the lack of any functional modulation of cd/52y2S receptors observed in NG108-15 cells. These findings are potentially important for understanding the mechanisms of CaMK-II dependent modulation of the GABAA receptor and may also have significant implications for the understanding of inhibitory synaptic plasticity.
Efficiency of threonine utilization in the growing pigs

ABSTRACT Objective. This study aimed to determine the marginal efficiency of threonine utilization in growing pigs by using the nitrogen balance technique. Materials and methods. Twelve castrated pigs with an average live weight of 72±2 kg were housed in metabolic cages maintained in a temperature controlled room of 22±3°C. The treatments consisted of four diets calculated to meet 30, 45, 60 and 70% of the nutritional requirements of standardized ileal digestible threonine. The amino acids others than threonine were maintained at least 15% above threonine requirements, expressed in terms of ideal levels. The amount of feed supplied was calculate to provide 2.6 times the metabolizable energy requirements for maintenance and adjusted daily according to an expected daily gain rate of 0.8 kg. Results. Pigs consumed 1.65 g kg-1 BW0.75 nitrogen daily, on average and 61% was retained and, as a result, 39% was excreted, being 31% through the feces and the remainder (69%) in the urine. The pigs showed a linear retention of threonine in response to the increase of standardized threonine intake. For each gram of standardized threonine intake 0.37 g were lost during the metabolism. Conclusions. It is concluded that for calculating nutritional requirements of standardized threonine of pigs by the factorial method, it is possible to use the utilization marginal efficiency of 0.63. RESUMEN Objetivo. El objetivo de este estudio fue determinar la eficiencia marginal del uso de treonina para cerdos en fase de crecimiento, por medio de la tecnica de balance de nitrogeno. Material y metodos. Fueron utilizados doce cerdos machos castrados con peso promedio de 72±2 kg alojados en jaulas metabolicas climatizadas a una temperatura ambiente de 22±3°C. Los tratamientos consistieron en cuatro dietas calculadas para 30, 45, 60 y 70% de las necesidades nutricionales de treonina digestible estandarizada. Los demas aminoacidos se anadieron a las dietas para lograr una proporcion de al menos 15% de sus necesidades expresadas con relacion a la treonina. La cantidad de alimento proporcionado se calculo para suministrar 2.6 veces la energia metabolizable y ajustada todos los dias, segun una tasa de ganancia media diaria de 0.8 kg. Resultados. Los cerdos consumieron 1.65 g kg-1 PV0.75 de nitrogeno por dia. En promedio 61% de nitrogeno ingerido se conservo y 39% fue excretado por el animal. El 31% se excreto en las heces y el resto (69%) en la orina. Los cerdos mostraron una retencion lineal de treonina, con relacion al aumento en la ingesta de treonina digestible estandarizada. Por cada gramo de treonina digestible estandarizada ingerido 0.37 g se perdieron durante el metabolismo. Conclusiones. Se concluye que, para el calculo de las necesidades nutricionales de treonina digestible estandarizada para cerdos por metodo factorial, es posible utilizar la eficiencia marginal del uso de treonina a 0.63.