Miracle-dz/UniFAR-FTUs huggingface dataset:
Why Proteins Evolve at Different Rates: The Determinants of Proteins’Rates of Evolution

Proteins undergo changes in their amino acid sequences over evolutionary time, as a result of the accumulation of nonsynonymous mutations in their encoding genes. Genes and proteins act as “molecular clocks”, accumulating changes at a relatively constant rate, as mutations occur with a certain probability each time a nucleotide is replicated. From the very beginning of molecular evolution studies, it became apparent that different proteins evolve at very different rates, each evolving according to its own “molecular clock”. For instance, in their early studies Zuckerkandl and Pauling (1965) already noted that the high rate of evolution of hemoglobin was “spectacularly
Risk assessment of workers exposed to crystalline silica aerosols

ABSTRACT This study was conducted to determine the concentration of airborne respirable crystalline silica (ARCS) particles and to evaluate its risk level among workers employed in eight different workplaces in Iran. They included sandblasting operations, ceramic production, sand and gravel work, brick production, asphalt manufacturing, foundry operation, glass making, and stone cutting. Personal exposure to ARCS was measured in randomly selected samples from each workplace. The maximum and minimum average of ARCS concentration in the eight workplaces were observed in foundry operation (0.338 ± 0.110 mg/m3) and glass manufacturing (0.125 ± 0.093 mg/m3), respectively. The average concentration of ARCS in all assessed working conditions were higher than the permitted limit of occupational contact recommended by Technical Committee of the Iranian Ministry of Health, treatment and medical education (0.025 mg/m3). Overall, the results showed a serious lack of control in Iranian industries with respect to workers' exposures to ARCS.
Quality and Antioxidant Activity of Yogurt Supplemented with Roselle during Cold Storage

The purpose of this study was to determine the quality (physical, chemical, microbiological characteristics), total phenolic content, and antioxidant activity using 1,1-diphenyl-2-picrylhydrazyl radical (DPPH) inhibition assay of probiotic yogurt supplemented with roselle flower extract (Hibiscus sabdariffa L) during cold storage. The experiment used treatment for types of yogurt as follows: cow’s milk probiotic yogurt + roselle, goat’s milk probiotic yogurt + roselle, cow’s milk yogurt, and goat’s milk yogurt. The yogurt was stored in cold storage and evaluated the quality and antioxidant activity variables on days 0, 3, 6, 9, 12, and 15th. The results showed that there were interaction (P<0.05) between types of yogurt and storage time on pH value and total lactic acid bacteria (LAB), but no interaction effect on viscosity. The types of yogurt significantly affected (P<0.05) aw, total titrable acid (TTA), total phenolic content, and antioxidant activity. Cow’s milk probiotic yogurt + roselle and goat’s milk probiotic yogurt + roselle were the best yogurt that contributed to a good quality and high antioxidant activity up to 15 d at cold storage.
CARACTÉRISATION DES MUTATIONS DU VIRUS HERPÈS SIMPLEX IMPLIQUÉES DANS LA RÉSISTANCE AUX ANTIVIRAUX

Drug resistant HSV isolates are responsible form substantial morbidity among immunocompromised subjects. The genetic basis for resistance to nucleoside analogs such as acyclovir (ACV) have been mapped to point mutations in the viral thymidine kinase (TK) gene while mutations within the viral DNA pol gene, the main target for all antiherpetic drug actually available, could lead to a multidrug resistance phenotype. However, the distinction between viral mutations (TK and DNA pol) involved in antiviral resistance or part of viral polymorphism can be difficult to evaluate with current methodologies. OBJECTIVE: The aim of this research project is thus to evaluate the role of particular mutations within the HSV TK and DNA pol gene with regard to drug-resistance patterns and viral fitness, by designing new gene expression systems. METHODS: The protozoan parasite Leishmania stably transfected with a TK expression vector (pSP72αNEOα) was used as an heterologous system to evaluate the role of several different point mutations within the coding region of the TK gene in conferring resistance to nucleoside analogs. Susceptibility of TK-expressing parasites to nucleoside analogs can thus be tested very easily by a simple measurement of the optic density of cultures grown in the presence or in the absence of the drug. Finally, a set of overlapping viral cosmids and plasmids for the rapid generation of recombinant HSV-1 DNA pol mutants have been developed. RESULTS: Expression of the TK gene from ACV-susceptible clinical isolates resulted in Leishmania susceptibility to the antiviral, whereas expression of a TK gene with frameshift mutations or nucleotide substitutions from ACV-resistant isolates gave rise to parasites with high levels of antiviral resistance. Twenty HSV-1 recombinants with single or dual mutations within the DNA pol gene were successfully generated with the cosmid/plasmid based approach. Mutations within the central part of the enzyme’s catalytic domain (regions II and VI) were associated with resistance to ACV, FOS, and ADV, whereas mutations inserted within extremities (δ-region C, I, V, and VII) were mostly related to the replicative activity of the enzyme. CONCLUSION: Such new strategies provide an easy, reliable, and sensitive means of evaluating the functional role of viral mutations which should translate in improved management of drug-resistant HSV infections.
Proximate chemical composition and content of biologically active components in leaves of two quinoa cultivars (Salcedo and Altiplano) produced in Peru

Objective: The purpose of the presented study was to describe the proximate chemical composition and content of biologically active components in leaves of two quinoa cultivars (Salcedo and Altiplano) produced in Peru. Methodology: This study conducted by means of different analytical methods. It is describe changes of different phenological stages in relation to nutritional composition, pigment contents, polyphenols, flavonoids and antioxidant activity of plant extract evaluated by standard methods of DPPH (2,2-diphenyl-1-picrylhydrazyl) and ABTS (2,2 -azino-bis-3-ethylbenzthiazoline-6-sulphonic acid) assay and the correlation between mean antioxidant index scores were also analyzed. Results: The results presented no considerable variations. However, the ash content for Altiplano and Salcedo leaves was 2.8 and 3.6%, respectively. The total pigment content is much higher in the Salcedo leaves (4816.77 μg gG1 dry weight) when compared with Altiplano leaves (2662.92 μg gG1 dry weight). The total polyphenol and total flavonoid contents is similar in both samples for Salcedo (10.55 mg GAE gG1 and 8.69 mg rutin gG1) and Altiplano (10.72 mg GAE gG1 and 9.14 mg rutin gG1), respectively. The antioxidant activity as measured by DPPH and ABTS, expressed as Trolox Equivalent Antioxidant Capacity (TEAC), evaluated in Altiplano was higher than that found in Salcedo. The antioxidant potency composite index was 16.32 and 11.95, respectively. The antioxidant potency showed the positive correlation coefficients with phenolics (r2 = 0.6575), flavonoids (r2 = 0.3896) and the correlation between phenolics and flavonoids (r2 = 0.6744). Conclusion: These results indicated promising perspectives for the leaves of two quinoa cultivars (Salcedo and Altiplano) that are excellent resources of bioactive components and can be used in the food industry as infusions.
Differential expression and regulation of PDLIM4 in prostate cancer cells

Objective To analyze the differential expression of tumor suppressor PDLIM4 gene in nonneoplastic RWPE1 cells and prostate cancer(PC) cell lines and different drug-resistant cell lines.Methods Different cell lines including RWPE1,carcinoma cell lines(PC-3,DU145,and LNCaP),multidrug-resistant cells(PC-3/Doc,K562/A02,H460/Doc) were used to identify PDLIM4 expression by quantitative PCR(qPCR),Western blotting,and immunofluorescence(IF) assays.The expressions and activities of DNA methyltransferases(DNMTs) were also tested in PC-3 and PC-3/Doc cells by Western blotting and enzyme activity assays.Results PDLIM4 was overexpressed in RWPE1 cells,not expressed in DU145 or LNCaP cells,slightly detected in PC-3 cells but predominantly evidenced in its multidrug resistant PC-3/Doc cells,and this kind of high expression of PDLIM4 in drug-resistant cell lines is tissue-specific.Enzyme activity assays demonstrated that the activity of DNMTs were significantly reduced in PC-3/Doc compared to PC-3 cells,even though the expression levels of DNMTs were similar in both cell lines.Conclusion The expressions of PDLIM4 were dramatically reduced in PC cell lines,while this tissue-specific up-regulation of PDLIM4 in PC-3/Doc might result from the decreased enzyme activity of DNMTs when compared to PC-3 cells.
Geographic patterns of biodiversity in European coastal marine benthos

Within the COST action EMBOS (European Marine Biodiversity Observatory System) the degree and variation of the diversity and densities of soft-bottom communities from the lower intertidal or the shallow subtidal was measured at 28 marine sites along the European coastline (Baltic, Atlantic, Mediterranean) using jointly agreed and harmonized protocols, tools and indicators. The hypothesis tested was that the diversity for all taxonomic groups would decrease with increasing latitude. The EMBOS system delivered accurate and comparable data on the diversity and densities of the soft sediment macrozoobenthic community over a large-scale gradient along the European coastline. In contrast to general biogeographic theory, species diversity showed no linear relationship with latitude, yet a bell-shaped relation was found. The diversity and densities of benthos were mostly positively correlated with environmental factors such as temperature, salinity, mud and organic matter content in sediment, or wave height, and related with location characteristics such as system type (lagoons, estuaries, open coast) or stratum (intertidal, subtidal). For some relationships, a maximum (e.g. temperature from 15–20°C; mud content of sediment around 40%) or bimodal curve (e.g. salinity) was found. In lagoons the densities were twice higher than in other locations, and at open coasts the diversity was much lower than in other locations. We conclude that latitudinal trends and regional differences in diversity and densities are strongly influenced by, i.e. merely the result of, particular sets and ranges of environmental factors and location characteristics specific to certain areas, such as the Baltic, with typical salinity clines (favouring insects) and the Mediterranean, with higher temperatures (favouring crustaceans). Therefore, eventual trends with latitude are primarily indirect and so can be overcome by local variation of environmental factors.
El rol de los genes LSM en la regulación de los ritmos circadianos

Los relojes circadianos son mecanismos auto-regulatorios endogenos que controlan la periodicidad de multiples procesos biologicos. Estos proporcionan a los organismos una ventaja adaptativa que permite sincronizar distintos eventos fisiologicos y del desarrollo al momento mas adecuado del dia. La regulacion del reloj circadiano ocurre principalmente mediante circuitos de retroalimentacion transcripcional. Sin embargo, estudios recientes muestran que se requiere de mecanismos post-transcripcionales para el correcto funcionamiento del reloj. Uno de estos mecanismos es el splicing alternativo, mediante el cual se producen multiples variantes de ARNm a partir de un unico gen. En esta tesis se caracterizo el comportamiento circadiano de mutantes de factores de splicing cuyos transcriptos estan regulados por el reloj. Se encontro que mutaciones en los genes LSM5 y LSM4, que codifican para componentes del complejo spliceosomal U6 snRNP, alteran el periodo circadiano. Un analisis global del transcriptoma de ambas mutantes revelo enriquecimiento en genes implicados en la regulacion de la transcripcion y respuestas de estres, asi como alteraciones en el splicing alternativo de un subconjunto de genes, incluyendo genes centrales y de vias de salida del reloj. Los genes LSM tambien forman parte de otro complejo involucrado en el decaimiento del ARNm. Dado que LSM4 y LSM5 son parte de los dos complejos nos preguntamos si parte del efecto circadiano observado era debido a su rol sobre el decaimiento de ARNm. Se encontro que mutaciones en varios genes involucrados en decaimiento de ARNm tambien generan alteraciones en los ritmos circadianos. Estos resultados apoyan la idea de que ciertos genes LSM desempenan un rol en los ritmos circadianos, mediante la regulacion del splicing alternativo y del decaimiento de ARNm, lo cual contribuye a la sincronizacion de los ritmos biologicos con cambios ambientales.
Evaluation of Antioxidant Potential of Clarias Batrachus Oil in Alloxan Induced Diabetic Mice (Mus Musculus)

Introduction: Diabetes mellitus is a chronic disorder in human and responsible for different complications and also causes mortality and morbidity. Long chain fatty acids influence inflammation through a variety of mechanisms; many of these are mediated by, or at least associated with, changes in fatty acid composition of cell membranes. Hence the present study was performed to investigate the effect of fish oil extracted from Clarias batrachus which is a good source of PUFA n-3 among freshwater species on alloxan-induced diabetic mice. Material and method: Alloxan was administered at repetitive doses (100 mg/kg b.wt after every 5th day for a period of one month to induce diabetes in mice. Along with alloxan injection, 10% Clarias fish oil was supplemented to diabetic mice for a period of one month. Analysis of basic antioxidant and lipid peroxidation parameters in serum, liver, kidney, heart and pancreatic tissues was carried out. Result: The levels of antioxidant and lipid peroxidation markers were significantly (P<0.05) altered in all the tissues of alloxan-induced diabetic mice. The supplementation of fish oil to diabetic mice showed significant recovery in activity of enzymes SOD, Catalase and in concentration of Vitamin C which is decreased in diabetic control mice. Conclusion: The result of this study indicated fish oil supplementation in diabetic mice helped to reduce the elevated glucose and glycosylated haemoglobin level along with an increase in insulin concentration and helped to recover the altered antioxidant and enzyme activity, which specifies that long term treatment of diabetes with fish oil may help to reduce the diabetes induced tissue damages.
Impact of allosucking on growth of farmed red deer calves (Cervus elaphus)

It is generally presumed that allosucking brings benefits to the allosucking infants. Nevertheless, the data supporting such a presumption are rare. The aim of the study was to determine whether allosucking has any impact on growth rates of the allosucking calves. Fifty pregnant hinds were observed between 28 May (1st day of calving) and 2 September (abrupt weaning of all calves) on a red deer farm at Vimperk, South Bohemia, the Czech Republic. Of the 50 calves born the growth curve was calculated for 39 calves. During their 1st month of life these calves were observed in 1015 sucking bouts. In 690 cases the calves sucked from maternal hinds and in 325 cases non-maternal hinds. Only 25·64% of calves sucked exclusively from maternal hinds. The prevailing type of sucking behaviour was a combination of sucking from maternal hinds and allosucking (74·36%). Calves sucking from maternal and non-maternal hinds showed 1·6-fold higher sucking frequency than did calves feeding from maternal hinds only. Our results indicate that to some extend allonursing behaviour of the hind may affect their calves’ feeding behaviour. The more non-filial calves the maternal hind nursed, the higher frequency of the sucking by their calves occurred. The groups of calves did not differ in birth weight. With increasing age, the relative body weight increased faster in calves sucking maternal hinds only than in calves sucking maternal and non-maternal hinds. This gain in body weight was not essentially influenced by the fact whether or not the calf’s maternal hind nursed non-filial or exclusively filial calves. However, at weaning (99 days), the lowest body weight occurred in allosucking calves whose maternal hinds were allonursing. The results suggest that allosucking does not mean an extra profit to the allosucker. Instead, in our subjects, allosucking was rather attributed to compensation of nutritional requirements based on a combination of various factors, such as discrete differences in body weight at birth and also later and allonursing of the maternal hind.
Exogenous administration of dehydroepiendrosterone attenuates loss of superoxide dismuatse activity in the brain of old rats

The influence of exogenously administered dehyrocpiendrosterone (DHEA) on the activity of superoxide dismulase (SOD) was investigated in the mitochondrial and cylosolic fractions from cerebral cortex, cerebellum, hippocampus and medulla regions of the brains of 12- and 22-months old rats. DHEA was administered daily at the dose of 30 mg/kg/body wt, intrapcritonially (i.p) in both age groups of rats for 1 month. Results showed that SOD activity was significantly higher in the mitochondrial fraction than in the cytosolic fraction, in DHEA-treated animals in both age groups. This indicated that exogenous DHEA affected mitochondrial SOD more than the cytosolic SOD. In terms of percent increase, 22 months-old animals showed significant increase in the SOD activity in both the fractions of all the four brain regions than in the 12 months old DHEA-treated animals. This showed that exogenous DHEA provided more protection to the SOD in ageing brain of older rats (22 months) than the younger (12 month) ones. The study suggests that exogenous DHEA is more beneficial at old age in terms of neuroproteclion against oxidative stress-mediated brain dysfunctions and may protect age-related alterations in cognitive functions like learning and memory.
Comparison of Leaf Traits (SLA And LMA) on Different Populations of Alcea apterocarpa

Bu çalışmada, farklı lokalitelerdeki Alcea apterocarpa (Fenzl) Boiss popülasyonlarının yaprak alanı ve spesifik yaprak ağırlığı değerlerini karşılaştırdık. SLA ve LMA önemli yaprak karakterleridir. Çünkü SLA ve LMA yaprak besinleri, yaprak ekonomisi ve atmosferle gaz alışverişlerinde ilişkilidir. Bu nedenle bir çok tür yaprak karakterlerini çevresel gradientlere karşı uyarlamaktadır. A. apterocarpa ruderal bir türdür ve geniş yayılış alanlarına sahiptir. Ayrıca etnobotanik özelliğe sahip olan örnek tedavi edici bitki özelliğine sahiptir. Çalışma için üç farklı lokalitede 6 birey seçtik. Her bir lokalite farklı nüfus yoğunluğuna sahip bölgelerden seçilmiştir. Lokalitelerden olgun ve senesens yapraklar toplanmış ve yaprakların SLA ve LMA değerleri hesaplanmıştır. Sonuçlar, senesens ile olgun yapraklar ve lokaliteler arasında önemli farklılıkların olduğunu göstermiştir. Özellikle, şehir merkezindeki A. apterocarpa populasyonunda SLA değeri diğer lokalitelere göre en yüksek iken, LMA değeri en düşük bulunmuştur.
Assessment of promoter trap as a tool to study zygotic embryogenesis in Arabidopsis thaliana

L'utilisation de la methode de piege a promoteur dans l'etude de l'embryogenese zygotique a ete evaluee chez Arabidopsis thaliana. Les plantes ont ete transformees par une construction d'ADN-T comportant le gene rapporteur uidA (GUS) depourvu de promoteur. Le but de cette etude etait de rechercher des fusions transcriptionnelles fonctionnelles entre le gene rapporteur et des promoteurs de plante. Chez 100 plantes transformees, l'activite GUS a ete mesuree par fluorometrie dans differents organes. Dans 62% des plantes transgeniques, le gene GUS est exprime dans un organe au moins. Vingt-six plantes expriment GUS dans les jeunes siliques dont 2 de maniere specifique. Le profil d'expression GUS dans ces 26 lignees a ete visualise par histochimie. Six de ces lignees ont montre une expression dans l'embryon: 3 ont une expression constitutive, 1 presente une expression preferentielle dans les graines seches, 1 autre a une expression specifique de la graine et 1 seule plante a montre une expression specifique de l'embryon. Cependant, aucune de ces lignees n'a montre une expression specifique d'un stade de developpement de l'embryon. Dans un second lot de 186 transformants, nous avons isole une lignee a expression GUS specifique de la pointe de la racine et une autre presentant une expression specifique des cellules du suspenseur. L'interet de l'utilisation de la technique de piege a promoteur pour caracteriser des genes specifiques de cellules et tissus de l'embryon des plantes a fleurs est discute en fonction des strategies similaires employees chez la Drosophile
Quenching Measurements using Understanding the Light-Dark Kinetic Trace-2014 Chlorophyll Fluorescence

These measurements are usually determined after overnight dark adaptation and the after illumination a specific light level until steady state photosynthesis has been reached. However, Klughammer (2008) states that Y(NO) is not limited to steady state measurement if his simplified equations are used. Without a good understanding of the mechanisms that affect the light trace, machine artifacts and user errors can be included in measurements. Quenching relaxation for the lake and puddle model Kramer 2004 lake model parameters Quenching Measurements using Understanding the Light Dark Kinetic Trace 2014 Chlorophyll Fluorescence,
Climatic conditions driving a part of changes in the biochemical composition in land snails: Insights from the endangered Codringtonia(Gastropoda: Pulmonata)

Abstract Most land snails in order to ensure their survival under adverse environmental conditions interrupt their activity entering a state of dormancy. The transition from activity to dormancy is accompanied by several changes in the animals’ physiology. To identify these changes we examined the seasonal patterns in the biochemical composition and the LDH activity of three different tissues in four endangered land snail species. Additionally, within a phylogenetic framework we investigated the correlation of the measured parameters with the spatial and climatic variables of the sampling sites. Our results indicate that there are both differences and similarities in the pattern exhibited by the four species, depending on the physiological parameter investigated and the climatic conditions of the sampling sites, which sometimes have a significant effect on the seasonal pattern exhibited. Snails can successfully deal with the winter dormancy by maintaining high metabolite concentrations and stable water content whereas there is no indication of anaerobic pathways’ activation. At the same time, they deal successfully with the low humidity and high temperatures during the summer, but they are forced to maintain low metabolite concentrations and seem to activate anaerobic pathways to meet their energy demands. Therefore, from a biochemical perspective, it seems that winter is a less stressful period for snails compared to summer. According to the prevailing climate change scenarios, the Mediterranean region is going to exhibit a sudden transition towards a dryer and longer summer. This transition will exert a very high adaptation pressure on the already vulnerable Codringtonia species. Thus, it could be that this endemic Greek genus is truly on the verge of extinction.