Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of Molecular Tools for the Identification of Complex Bacterial Flora - Application to the Study of Galliform Gut Flora

This last decade knew a strong passion for the complex microfloras particularly for the floras associated symbiotically with their host like the digestive tract flora. The digestive floras indeed open many opportunities as well on the medical level as on the industrial and the biotechnological levels. In this manuscript, various works on the digestive flora of Galliforms are presented: study of the antibiotic action mode as growth promoter in chicken, search for substitutes to antibiotics in chicken and search of a putative pathogen of non specific enteritis in turkey. New tools useful for the bacterial identification were also developed in this writing. A new technique of clone screening, named CSbyDG, based on a discrimination of tri-band DGGE profiles, proved its effectiveness to screen clone libraries of 16S rDNA. To allow the regrouping of profile obtained in CSbyDG, a data-processing program coded in Visual Basic Application for Excel was developed. This program, named ProReg XL Tool, is able to regroup identical electrophoretic profiles. Its applicability is thus much broader than the only regrouping of profile of CSbyDG. In the long term, CSbyDG should allow, by various bearings, to identify a bacterium in a few hours.
Predicting protein efficiency ratio by the chemical determination of connective tissue content in meat.

The influence of connective tissue content on amino acid composition and rat PER was studied in an attempt to develop a regression equation for predicting PERs of meat from the simple chemical analysis of collagen. Collagen content was highly correlated to essential amino acid content and rat PER with correlation coefficients of -0.99 and -0.98, respectively. The developed regression equation, PER = -0.02290 (collagen content) + 3.1528, effectively predicted rat PER within ± 0.2 units when tested on various meat ingredients. These results indicated that the chemical determination of collagen content can be employed to provide a rapid, inexpensive and easily adaptable assay for the estimation of protein quality of meat. Mechanically deboned red meat had a reasonably good PER (2.65) and only a moderate level of collagen (19%); whereas, partially defatted chopped beef showed wide variation in PER as well as in collagen content with different processors. Both raw and cooked mechanically deboned chicken also showed good PERs, 3.0 and 2.6, respectively.
A proposal for an improved version of EigenAnt algorithm with performance evaluation on combinatorial optimization problems

O algoritmo denominado EigenAnt foi introduzido recentemente para a resolucao do problema de encontrar o menor caminho entre dois nos de um grafo, utilizando uma dinâmica com evaporacao local de feromonio. O referido algoritmo possui uma prova matematica de convergencia ao menor caminho. Nesta tese, realiza-se a analise de estabilidade e sensibilidade parametrica do algoritmo EigenAnt aplicado a problemas de caminhos minimos em cadeias binarias entre N nos. Motivado por esta analise, propoe-se uma extensao do algoritmo EigenAnt (denotado Improved EigenAnt), no qual a exploracao de distintos equilibrios estaveis e a velocidade de convergencia a estes podem ser ajustada independentemente. Realiza-se tambem uma analise comparativa entre os algoritmos EigenAnt, Improved EigenAnt e outros algoritmos existentes do tipo Colonia de Formigas, no contexto de problemas de caminho minimo em redes de roteamento. Adicionalmente, aplica-se o algoritmo novo proposto a problemas multidimensionais de mochileiro, por meio da modelagem destes como problemas de caminhos minimos em cadeias binarias entre N nos, com restricoes. Evaporacao local de feromonio e convergencia rapida sao propriedades de algoritmos da classe EigenAnt que tornam esta classe vantajosa para rastreamento de solucoes otimas de problemas de otimizacao dinâmica, nos quais as instâncias do problema, a funcao objetivo e os parâmetros das restricoes podem mudar ao longo do tempo. Uma investigacao experimental da aplicacao do algoritmo proposto (Improved EigenAnt) para rastrear a solucao otima em redes dinâmicas de roteamento e em problemas dinâmicos do mochileiro constituem uma outra contribuicao desta tese.
Role of nitric acid or H 2 O 2 in antioxidant defense system of Pisum sativum L. under drought stress

st century. Drought is an important environmental constraint limiting the productivity of many crops worldwide. Experiments were conducted to investigate the effects of seed pretreatment by hydrogen peroxide at 70 mM or sodium nitroprusside (SNP; nitric oxide donor) at 10 µM on drought tolerance in pea seedlings. Osmotic stress was provoked by addition polyethylene glycol to the nutrient solution at the flowering stage. H 2 O 2 or SNP are active molecules involved in mediation of various biotic and abiotic stress induced physiological responses in plants. H 2 O 2 or SNP pretreatment alleviate oxidative damage, accelerate proline accumulation and enhance total chlorophyll, carotenoid, photosynthetic activity ( 14 CO 2 -assimilation), and total yield/plant in leaves of pea seedlings subjected to osmotic stress. The results showed that osmotic stress induced decrease in the enzyme activities of ascorbate peroxidase, glutathione peroxidase, catalase and overproduction of O 2 y� in pea leaves, which in turn caused exacerbation of lipid peroxidation and depression of photosynthesis. Application of H 2 O 2 or SNP significantly increased the enzyme activities and decrease O 2 y� production and hence inhibited lipid peroxidation. Level of H 2 O 2 , proline and Evan blue uptake in seedlings pretreated with H 2 O 2 or SNP were markedly lower than under drought stress, indicating the operation of antioxidant system in them. Moreover, seedlings arising from H 2 O 2 or SNP pretreatment enhanced the membrane stability, as revealed from greatly reduced malondialdehyde content. The present data suggest that seed pretreatment in pea with H 2 O 2 or SNP, a stress signal, could trigger the activation of antioxidants in seeds, which persists in the seedlings to alleviate the oxidative damage, leading to improvements in physiological attributes for the seedling growth under drought. (Helal Ragab Moussa and Mohamed Abd El-Fattah Hassan Mohamed. Role of nitric acid or H 2 O 2 in antioxidant defense system of Pisum sativum L. under drought stress. World Rural Observations 2011;3(2):76-81); ISSN: 1944-6543 (Print); ISSN: 1944-6551 (Online). http://www.sciencepub. net/rural.
Proteolytic processing of the L-type Ca 2+ channel alpha 11.2 subunit in neurons

Background: The L-type Ca2+ channel Cav1.2 is a prominent regulator of neuronal excitability, synaptic plasticity, and gene expression. The central element of Cav1.2 is the pore-forming α 11.2 subunit. It exists in two major size forms, whose molecular masses have proven difficult to precisely determine. Recent work suggests that α 11.2 is proteolytically cleaved between the second and third of its four pore-forming domains (Michailidis et al,. 2014). Methods: To better determine the apparent molecular masses (M R)of the α 11.2 size forms, extensive systematic immunoblotting of brain tissue as well as full length and C-terminally truncated α 11.2 expressed in HEK293 cells was conducted using six different region–specific antibodies against α 11.2. Results: The full length form of α 11.2 migrated, as expected, with an apparent M R of ~250 kDa. A shorter form of comparable prevalence with an apparent M R of ~210 kDa could only be detected in immunoblots probed with antibodies recognizing α 11.2 at an epitope 400 or more residues upstream of the C-terminus. Conclusions: The main two size forms of α 11.2 are the full length form and a shorter form, which lacks ~350 distal C-terminal residues. Midchannel cleavage as suggested by Michailidis et al. (2014) is at best minimal in brain tissue.
Pharmacokinetic changes of halofantrine in experimentally-induced diabetes mellitus following oral drug administration

It was hypothesized in this study that alterations in plasma lipoprotein profile and disturbed gastrointestinal motility as observed in diabetes mellitus may influence the disposition of halofantrine (HF), a highly lipophilic antimalarial drug. Therefore, using a rat model of diabetes mellitus induced by administration of alloxan monohydrate, the effects of the disease on the pharmacokinetics of HF was investigated. Also, the drug binding to normal and diabetic plasma components was determined. Results showed that the mean Cmax values of HF and its major metabolite, desbutylhalofantrine (DHF), were markedly higher (up to 2.5 times) in the control than in diabetic rats (p 0.05). The binding of HF and DHF in diabetic plasma was significantly higher when compared to control (p pharmacokinetic-modulating processes induced by the disease. It is suggested that the significantly reduced Cmax of the drug and its metabolite in diabetes may have clinical implications since the clinical efficacy of HF is influenced by its peak plasma concentrations.
Methods of Event History Analysis in the Assessment of Crisis Impact on Sectors Related with the Real Estate Market in Poland

The subject of the article is the use of methods of event history analysis to assess the fall of prices and the subsequent increase of share prices of companies operating in the construction industry, developers (real estate) and building materials industry compared to other industries. The 328 examined companies were listed on the continuous market and the parallel market on the Stock Exchange in Warsaw. Share prices were observed in the period from 1 January 2008 to 31 December 2009 which was based on the earlier observations of stock quotes and the WIG index, the latter reaching its minimum in February 2009. The closing price of a share was taken into account. The 60% decrease and 80% growth in shares prices in particular sectors were analysed. What was assessed was the risk of fall in share prices and their chance for recovery. Additionally, the intensity of the increase of share prices and the probability of failure to reach the limit were examined.
Capture and Brief Invasive Procedures Using Electronarcosis Does Not Appear to Affect Postrelease Habits in Male Atlantic Sturgeon During the Spawning Season

AbstractWith advances in technology and demand for life history information, researchers are increasingly conducting invasive procedures on fish that require an anesthetic. This study examined the effectiveness of electronarcosis as a field anesthetic on Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus during the spawning season in the James River, Virginia. Concerns about sampling Atlantic Sturgeon during spawning runs prompted our examining whether movements after capture, narcosis, and tagging were noticeably modified. An electronarcosis system, which consisted of a power supply, fiberglass tank, and hardware cloth, were set up both on land and on a sampling boat. During the spawning season Atlantic Sturgeon were caught and implanted with Vemco V16 telemetry tags using electronarcosis as an anesthetic. Anesthesia induction, surgery, and recovery averaged 5 min. Telemetry data from the tagging year was compared with returning fish tagged in previous years. This showed movements during the spawning seas.
GENECFE-ANFIS: A NEURO-FUZZY INFERENCE SYSTEM TO INFER GENE-GENE INTERACTIONS BASED ON RECOGNITION OF MICROARRAY GENE EXPRESSION PATTERNS

A neuro-fuzzy inference system that recognizes the expression patterns of genes in microarray gene expression (MGE) data, called GeneCFE-ANFIS, is proposed to infer gene interactions. In this study, three primary features are utilized to extract genes' expression patterns and used as inputs to the neuro-fuzzy inference system. The proposed algorithm learns expression patterns from the known genetic interactions, such as the interactions confirmed by qRT-PCR experiments or collected through text-mining technique by surveying previously published literatures, and then predicts other gene interactions according to the learned patterns. The proposed neuro-fuzzy inference system was applied to a public yeast MGE dataset. Two simulations were conducted and checked against 112 pairs of qRT-PCR confirmed gene interactions and 77 TFs (Transcriptional Factors) pairs collected from literature respectively to evaluate the performance of the proposed algorithm.
Orchidaceae, Uttarakhand, Western Himalaya, India

A checklist of 237 species of orchids recorded from the state of Uttarakhand, India, is provided. Of these 127 are terrestrial, 99 epiphytic and 11 saprophytic. The present study shows that Poneorchis nana (King & Pantl.) Soo is a new record for Uttarakhand. Bulbophyllum secundum Hook. and Eulophia hormusjii Duthie that have earlier been merged into other species, during the present study after detailed scrutiny, have been treated as separate species. Androcorys pugioniformis (Lindl. ex Hook. f.) K.Y. Lang. has been rediscovered after a century gap. Nomenclature has been updated as far as possible with the help of available recent taxonomic literature.
Src promotes PKCδ degradation

Platelet-derived growth factor BB (PDGF) stimulates DNA synthesis through a mechanism that is at least partially dependent upon Src family tyrosine kinases, although the signal transduction pathway downstream of Src is poorly understood. We have studied the signaling between Src and different protein kinase C (PKC) isoforms and its possible role in the regulation of PDGF-stimulated DNA synthesis. We found that Src promoted the tyrosine phosphorylation of PKCd, and its subsequent degradation. Enforced expression of PKCd inhibited PDGF-stimulated DNA synthesis, whereas expression of PKCa and PKC« did not, a finding consistent with a model in which PKCd negatively regulates G1-to-S-phase progression. We used mutagenesis to map a critical Src phosphorylation site on PKCd to tyrosine 311. A mutant form of PKCd in which tyrosine 311 was replaced with phenylalanine (Y311F) was more stable in the presence of Src, suggesting that Src-induced degradation was a direct result of PKCd tyrosine phosphorylation. We conclude that PKCd is downstream of Src but is unlikely to play a positive role in the signaling pathway by which Src promotes DNA synthesis.
Scanning electron microscopy of six selected mealybug (Hemiptera: Pseudococcidae) species of Sri Lanka.

The Scanning Electron Microscope (SEM) is extremely useful for studying the detailed morphology of very small structures on insect cuticle, enabling quick and accurate representation. Scanning electron microscopy of mealy bugs (Hemiptera: Pseudococcidae) is challenging, due to the thinness and flexibility of the cuticle. The three- dimensional structure of the wax-producing pores of mealy bugs is complicated and can be best elucidated using the SEM. Only a few studies have reported on ultra structure and wax- secretion processes in the Pseudococcidae. The aim of this study was to enrich the understanding of the external morphology and wax-secreting pores of mealy bugs, using scanning electron microscopy. Six economically important pest mealy bug species in Sri Lanka were studied under the SEM namely, Coccidohystrix insolita (Green), Dysmicoccus brevipes (Cockerell), D. neobrevipes Beardsley, Maconellicoccus hirsutus (Green), Phenacoccus solenopsis Tinsley and Planococcus lilacinus (Cockerell). The specimens were subjected to dehydration, critical point drying and sputter coating, before being scanned using the SEM. The ultra structure of the antenna, ostiole, vulva, claw digitules, cerarius, circulus and wax-secreting pores were examined. Wax-secreting pores of different species showed remarkable structural variation. Minute characters of taxonomic importance that can only be seen under the SEM are discussed. Although the preparation of specimens for viewing under the SEM is time-consuming and expensive, the effort is worthwhile because the detailed information obtained may solve some difficult aspects of mealy bug taxonomy, and help to improve the understanding of the role of wax secretions in mealy bug biology.
Functional analysis of CDKF;1: a plant specificCAK-activating kinase

Cyclin-dependent protein kinases (CDKs) control checkpoint transitions of the cell cycle. Activation of CDKs requires phosphorylation of a conserved threonine residue in their T-loops by CDKactivating kinases (CAKs) that are analogously activated by CAK-activating kinases (CAKAKs). CDKF;1, a plant specific CAKAK, is reported to phosphorylate two of three known Arabidopsis CAKs (CDKD;2 and CDKD;3). Here we show that CDKF;1 and CDKDs purified from E. coli are auto-activated without cyclin binding and that CDKF;1 phosphorylates all three Arabidopsis CDKDs (CDKD;1, CDKD;2, and CDKD;3). We found that CDKF;1 and CDKD;2 are required for phosphorylation of the CTD domain of Arabidopsis RNA POLYMERASE II (RNAPII) largest subunit, which comprises of 15 consensus and 26 variant YSPTSPS tandem heptad repeats. CDKD;2 mediates Serine-5 phosphorylation of the CTD, suggesting its possible role in the control of transcription initiation and 5’ capping of nascent RNAs. CDKF;1 phosphorylates the Serine-7 residue of CTD heptapeptide repeats. Reduction of CTD-phosphorylation on Serine-7 in the cdkf;1 mutant causes overall defects in transcription and development, as well as in the production of small RNAs, including miR156, miR165, miR172, ta-siRNA1 (TAS1), and COPIA. CDKF;1 can also phosphorylate in vitro the VirD2 protein, which is covalently bound to the 5’-end of single-stranded intermediate of Agrobacterium transferred DNA (T-DNA/T-strand) and mediates its integration into the nuclear genomes of plant host cells. Previous data indicate that VirD2 interacts with the TATA-box-binding subunit of RNAPII and is phosphorylated in vivo by a CTD-associated CAK-like protein kinase. Studies of Arabidopsis CAKs show that CDKD;2 is found in association with cyclin H and CDKF;1 as part of the TFIIH complex, which is implicated in global genome and transcription-coupled repair. Our data demonstrate that mutations inactivating either CDKF;1 or its CAK substrate CDKD;2 result in dramatic reduction of tumour formation mediated by Agrobacterium tumefaciens C58. This suggests that CDKD;2 is an important mediator of VirD2 phosphorylation by CDKF;1, which is likely required for VirD2 recruitment to the TFIIH complex implicated in repair-recombination between the 5’-end of the T-strand and target sequences in the host chromosomes.
Coffee senna (Cassia occidentalis) germination and emergence is affected by environmental factors and seeding depth

Abstract Laboratory and greenhouse experiments were conducted to determine the effect of light, temperature, moisture stress, solution pH, and burial depth on coffee senna germination and emergence. Seeds germinated equally with or without light, and pretreatment with red or far-red light did not affect germination. Optimum temperature for germination was 25 C, and a high germination percentage (> 70%) occurred from 12.5 to 30 C. The low temperature threshold for germination was between 10 and 12.5 C, whereas the upper threshold was near 45 C. Coffee senna germination in response to moisture stress and solution pH differed at 15 and 30 C. At −0.4 MPa, no germination occurred at 15 C, whereas 15% germination occurred at 30 C. Optimum germination was at pH 6, but further increases in pH had a more negative effect on germination at 15 C than at 30 C. Coffee senna germination ranged from 9 to 12% at pH 3, but was 0% at pH 10, which indicates that coffee senna germination was more tolerant of acidic than basic solutions. Depth-mediated emergence inhibition was sigmoidal, with greatest emergence on the soil surface. Emergence from 2- to 10-cm depths reached 95% of the total emergence 1 to 3 d earlier in a sandy loam than in a sand soil. Mean emergence depth was 1.7 cm in the sand and 2.4 cm in the sandy loam soil. Knowledge gained from this research will be instrumental in developing a better understanding of the requirements for coffee senna germination and emergence, allowing further development and improvement of integrated weed management strategies specific to this troublesome weed. Nomenclature: Coffee senna, Cassia occidentalis L. CASOC.
Fire-induced colonization of a Flooding Pampa grassland by thistles: Remnant litter and interference effects

Abstract Winter and spring burnings constitute a traditional management practice of the Flooding Pampa grasslands which are dominated by the tussock grass Paspalum quadrifarium. In addition to increasing the primary productivity and the nutrient quality of the regrowth, this burning favours the establishment of opportunistic species, especially the legume Lotus glaber and the thistles Cirsium vulgare and Carduus acanthoides. The aims of the present study were to assess the effects of burning and those of the remnant litter on L. glaber and thistle recruitment, as well as the effects of L. glaber density on the emergence, survival and flowering of thistles. Two field experiments were carried out: 1. A completely randomized factorial design with occurrence of L. glaber and fire was applied in a mature Paspalum stand; 2. A completely randomized design with four L. glaber seed densities oversown on a burned Paspalum stand, as the treatments. Thistle and L. glaber recruitment within the Paspalum stand was dependent on fire, but their emergence in burnt plots was reduced by the presence of remnant litter. Remnant litter and interference from L. glaber provide complementary mechanisms to reduce fire-cued colonization by thistles. While seedling emergence of thistles was mostly affected by the presence of remnant litter, seedling survival depended on local density of L. glaber. By the end of the first post-fire growing season, the survivorship of established thistles was linearly reduced with increasing sowing density and above-ground biomass of L. glaber. The maintenance of a significant litter coverage and a high density of L. glaber in the pre-fire seed bank, as well as the oversowing of L. glaber after fire, may be useful tools in fire management of Paspalum stands aimed to improve their forage value with reduced dependence on chemical control of weeds. Nomenclature: Cabrera (1953).
Bioactivity of leaves of Macaranga species in tropical peat swamp and non-peat swamp environments.

Very few studies have been reported on the chemical properties of peat swamp plants compared with their non-peat swamp counterparts. In this study, the total phenolic content, antioxidant activity and antibacterial activity of fresh Macaranga gigantea, M. hosei, M. hypoleuca, M. kingii, M. pruinosa and M. triloba leaf extracts from four tropical peat swamp forests and three non-peat swamp forests were measured and compared. Total phenolic content was measured by the Folin-Ciocalteu assay. Antioxidant activity was determined using the 1,1-diphenyl-2-picrylhydrazyl free radical scavenging and ferric reducing power assays, while disc-diffusion technique was used to determine the antibacterial properties. Reversed-phase-high-performance liquid chromatography methods were used to identify and quantify the concentrations of phenolics. Antioxidant properties of leaf extracts from peat swamp forest species were 42 to 60% higher than those of the same plant species from non-peat swamp forest. However, no significant differences were observed for samples collected from within the same environmental conditions. No significant differences were found in antibacterial activities between peat swamp and non-peat swamp samples. The results suggest that trees in peat swamp forests are producing higher levels of phenolic compounds in response to extreme conditions. © 2014 Forest Research Institute Malaysia.