Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactions of temperate bacteriophages of Streptococcus salivarius subsp. thermophilus with lysogenic indicators affect phage DNA restriction patterns and host ranges

Summary After treatment with mitomycin C, 12 of the 120 strains of the French Collection of Lactic Acid Bacteria (CNRZ) belonging to the species Streptococcus salivarius subsp. thermophilus were found to be inducible and lysogenic. The corresponding temperate phages were multiplied on indicator strains and further characterized. It is noteworthy that some of the indicators were themselves lysogenic. The temperate phages belonged to Bradley's group B, or to the Siphoviridae family of the International Committee on Taxonomy of Viruses. Seven of them were shared among the two protein profiles previously established for virulent phages of Str. salivarius subsp. thermophilus. Seven different DNA restriction profiles were found for ten native temperate phages examined just after mitomycin C induction. Genome sizes varied from 40 to 45 kb and were classified into four related homology groups by DNA cross-hybridization, but there was no clear-cut relationship with the protein clusters previously shown. DNA homology with representatives of virulent phages was also found. The DNA restriction profiles of seven native temperate phages, examined just after mitomycin C induction of the lysogenic hosts, were noticeably different from those of the corresponding phages once they had been propagated on lysogenic indicators. Moreover, the host range of the latter phages was extended to a greater number of sensitive strains. The possible role of lysogenic strains of Str. salivarius subsp. thermophilus in the occurrence of phage outbreaks affecting this dairy streptococcal species is discussed.
A Synthetic Diet for the Spruce Budworm, Choristoneura fumiferana (Clem.) (Lepidoptera: Tortricidae)

Abstract The spruce budworm, Choristoneura fumiferana (Clemens), was reared on a synthetic diet. Comparison of two successive laboratory generations reared on synthetic diet and on frozen balsam fir buds showed that diet-fed insects had a higher survival, developed faster, were heavier, mated more successfully, and were more fecund.
Quantification of genetic diversity at allozyme loci

L'electrophorese sur gel d'amidon constitue une methode puissante et economiquement abordable pour estimer la variabilite genetique des especes vegetales et de leurs populations. Les loci d'alloenzymes representent des caracteres typiquement monogeniques, qui se recombinent de facon independante et affichent des alleles co-dominants. Des tailles d'echantillon variant de 30-50 individus analyses pour 10-20 loci polymorphes s'averent suffisantes pour caracteriser de facon adequate la diversite genetique d'une population et evaluer comment la diversite genetique se repartit parmi les populations. Les parametres qui devraient etre utilises sont le pourcentage de loci polymorphes (P), le nombre moyen d'alleles par locus polymorphe (AP), l'heterozygotie theorique (diversite genetique, H c ), la valeur G ST de Nei, l'identite genetique (I) et la distance genetique (D). Les auteurs presentent des exemples, en plus de faire un sommaire des tests qui permettent d'evaluer la confiance statistique des estimations de parametres.
Microsatellites indicate minimal barriers to mule deer Odocoileus hemionus dispersal across Montana, USA

To better understand the future spread of chronic wasting disease, we conducted a genetic assessment of mule deer Odocoileus hemionus population structure across the state of Montana, USA. Individual based analyses were used to test for population structure in the absence of a priori designations of population membership across the sampling area. Samples from the states of Wyoming, Colorado and Utah were also included in the analysis to provide a geographic context to the levels of population structure observed within Montana. Results showed that mule deer across our entire study region were characterized by weak isolation by distance and a lack of spatial autocorrelation at distances > 10 km. We found evidence for contemporary male bias in dispersal, with female mule deer exhibiting higher mean individual pairwise genetic distance than males. We tested for potential homogenizing effects of past translocations within Montana, but were unable to detect a genetic signature of these events. Our results indicate high levels of connectivity among mule deer populations in Montana and suggest few, if any, detectable barriers to mule deer gene flow or chronic wasting disease transmission.
AVALIAÇÃO BIOECONÔMICA DO USO DA TORTA DE DENDÊ NA ALIMENTAÇÃO DE VACAS LEITEIRAS

This work was carried out with the purpose of evaluating the bioeconomic effect of the inclusion of palm kernel cake (PKC) to the diet of dairy cows (0.0, 11.34, 22.78 and 34.17%). We evaluated the milk production expressed in kg/day (MP) and in percentage of body weight (MP%BW), feed efficiency (FE), the contents of protein, fat, fat:protein ratio, lactose, total solids (TS ), defatted dry extract (DDE) and milk urea nitrogen (MUN). A linear decreasing effect was observed on the MP and MP%BW with the inclusion of PKC. The FE increased linearly (0.008 points) with the inclusion of palm kernel cake. There was a linear reduction in protein and DDE contents. As for fat, lactose and TS contents, fat: protein ratio and MP corrected for 4% of fat expressed in % of BW there was no effect of the inclusion of PKC. There was a linear increasing effect of the inclusion of PKC to the diets on the levels of MUN. The inclusion of PKC to the diet of dairy cows implies in reduction of milk production, although it does not compromise its composition. The use of PKC should be made with reservation because it compromises milk production and body condition of the animal. KEYWORDS: biofuel; by-products; performance; ruminant.
Molecular cloning and expression analysis of hypoxia inducible factor 1α in tongue sole, Cynoglossus semilaevis (Actinopterygii: Pleuronectiformes: Cynoglossidae), subjected to acute hypoxia

Hypoxia-inducible factor-1 (HIF-1) is the master regulator of oxygen homeostasis by regulating more than 100 genes expression (Manolescu et al. 2009). HIF-1 is a heterodimer which is composed of two subunits, HIF-1α and HIF-1β. The two subunits belong to the helix-loop-helix (Bhlh)-Per-Arnt-Sim (PAS) family, which contain conserved structural domains, such as a bHLH domain and two PAS domains (Kewley et al. 2004). The HIF-1β subunit, also known as hydrocarbon nuclear translocator (ARNT), is constitutively expressed, and is not affected by oxygen tension (Wang et al. 1995). HIF-1α is constitutively transcribed under normoxic conditions, but it is rapidly degraded via an ubiquitin-dependent pathway. However, during hypoxia this pathway is inhibited and HIF-1α is translocated to the nucleus and dimerizes with HIF-1β, causing HIF-1 to bind with hypoxia response elements (HREs) of target genes to activate their transcription (Maynard and Ohh 2004). Currently, HIF-1 has been cloned and characterized in mammals (Gassmann et al. 2002), birds, amphibians, and some fish species (Cao et al. 2008, Kodama et al. 2012). ACTA ICHTHYOLOGICA ET PISCATORIA (2013) 43 (3): 201–209 DOI: 10.3750/AIP2013.43. 3.04
Phylogenetic relationships in the grass family (Poaceae) based on the nuclear single copy locus topoisomerase 6 compared with chloroplast DNA

Phylogenetic relationships within the grass family were studied using a newly obtained locus of the nuclear single copy gene topoisomerase 6 (Topo6) spanning the four exons 8–11 and the chloroplast matK gene. Data were evaluated using maximum parsimony, maximum likelihood and Bayesian methods. All analyses showed genera Streptochaeta and Anomochloa as early diverging, followed by Pharus as sister to the rest of the Poaceae, and monophyly of the subfamily Anomochlooideae was supported by the nuclear dataset. The remaining grasses formed a strongly supported and monophyletic group, which split into the major clades BEP and PACMAD in the Topo6 analyses. Monophyly of the BEP clade was strongly supported by the Topo6 data. The results showed clearly incongruity between the two sets of data, such as the different subfamilial relationships of Bambusoideae, Ehrhartoideae and Pooideae. Most of the analysed species are representatives of subfamily Pooideae, which was analysed in more detail by PCR fragment length differences of another Topo6 region spanning the exons 17–19. Monophyly of Pooideae was strongly supported by the matK data, whereas the nuclear data placed Brachyelytrum outside of the remaining Pooideae. Relationships within the early evolutionary lineages remained largely unresolved in the phylogenetic trees, but the ‘core’ Pooideae (Aveneae/Poeae tribe complex and Hordeeae) were highly supported in all analyses. The differences in amplification lengths illustrate the tribe and subtribe classification of Pooideae. The comparatively conserved structure of the newly studied Topo6 region makes it a promising marker from the nuclear genome that could be successfully PCR-amplified to study higher-level phylogenetic relationships within grasses and perhaps between families within the order Poales.
Pedossistemas da Mata Atlântica: considerações pertinentes sobre a sustentabilidade

A pedological analysis was carried out on the ecologically important Atlantic Forest system, as a contribution to the study of its biodiversity. Focus is placed on some factors that can influence local diversity, such as soil depth, that varies within short distances. The reasons for prohibiting the cultivation of hilly soils by small farmers is also questioned. It is suggested that radiation, water and nutrient resources, should be emphasized, since they are essential to ecosystem functioning, instead of indirect variables. Based on pedological information, ten great environments in the Atlantic Forest were identified. Comments related to water and nutrients, and observations related to use, fragility and ecological importance are made about each stratified ecosystem. Two great ecosystems are indicated as potentially very important to diversity: shallow soil areas and rock outcrops and humic soil areas (a very important carbon sink), in the higher portions of the landscape.
The role of setts in badger ( Meles meles ) group size, breeding success and status of TB ( Mycobacterium bovis )

This paper examines the relationship between the number of occupied setts in a badger social group territory and badger group size, breeding success, and status of infection with Mycobacterium bovis (TB). The data used were from a long-term epidemiological and ecological study of a high-density population of badgers Meles meles in south-west England. The number of occupied setts in a social group was significantly and positively related to the number of badgers caught in the social group, so that as a social group increases in size, badgers occupy more of the available setts. This relationship remained significant when numbers of adults, adult males and adult females were examined. The number of breeding females, number of cubs and sex ratio was not related to the number of occupied setts in a social group. It is possible that the advantages to breeding females of a larger number of setts available to breed in might be outweighed by the increased aggression found in larger groups. The TB score for prevalence and for incidence of social groups was significantly and positively related to the number of occupied setts in a social group, such that the more occupied setts there were in a territory, the higher the TB index of the group. Possibly the setts themselves contribute to the persistence of TB within social groups, or badgers infected with TB might show a difference in behaviour from uninfected badgers resulting in their increased use of outlying setts.
Molecular phylogeny and systematics of Neotropical toucanets in the genus Aulacorhynchus (Aves, Ramphastidae)

Bonaccorso, E. , Guayasamin, J. M. , Peterson, A. T. & Navarro‐Sigüenza, A. G. (2011). Molecular phylogeny and systematics of Neotropical toucanets in the genus Aulacorhynchus (Aves, Ramphastidae). —Zoologica Scripta, 40, 336–349.
Performance of community-based natural resource governance for the Kafue Flats (Zambia)

SUMMARY The performance obstacles surrounding community-based natural resource management (CBNRM) in southern Africa have much to do with understanding of environmental governance systems and how these are devolved. CBNRM appears to be failing because of flawed environmental governance systems compounded by their ineffective devolution. A case study in Zambia is used to illustrate why and how one CBNRM scheme for the most part faltered. It draws on practical experiences involving the devolution of decision-making and benefit-distribution processes on a floodplain wetland known as the Kafue Flats. While this CBNRM scheme was designed to facilitate the devolution of key components of an environmental governance system, the resultant efforts were largely unsuccessful because of the poor social relationships between government actors and local rural communities. It is argued that in Zambia, at least from an environmental governance system perspective, CBNRM has mostly failed. While generally bringing some marginal improvements to local communities, the construction and execution of an effective environmental governance system have been largely flawed.
Anaerobic metabolism of aromatic compounds via the benzoyl‐CoA pathway

Aromatic compounds are important growth substrates for microorganisms. They form a large group of diverse compounds including lignin monomers, amino acids, quinones, and flavonoids. Aerobic aromatic metabolism is characterized by the extensive use of molecular oxygen which is essential for the hydroxylation and cleavage of aromatic ring structures. The anaerobic metabolism of low molecular mass soluble aromatic compounds requires, of necessity, a quite different strategy. In most known cases, aromaticity is broken by reduction and the ring is subsequently opened hydrolytically. A small number of different central aromatic intermediates can be reduced, the most common of which is benzoyl-CoA, a compound that is formed as a central intermediate in the degradation of a large number of aromatic growth substrates. This review concentrates on the anaerobic aromatic metabolism via the benzoyl-CoA pathway. The peripheral pathways that transform growth substrates to benzoyl-CoA include various types of novel reactions, for example carboxylation of phenolic compounds, reductive elimination of ring substituents like hydroxyl or amino groups, oxidation of methyl substituents, O-demethylation reactions and shortening of aliphatic side chains. The central benzoyl-CoA pathway differs in several aspects in the denitrifying, phototrophic and fermenting bacteria studied. In denitrifying and phototrophic bacteria it starts with the two-electron reduction of benzoyl-CoA to a cyclic dienoyl-CoA driven by the hydrolysis of two molecules of ATP to ADP+Pi. This ring reduction is catalyzed by benzoyl-CoA reductase and requires a low-potential ferredoxin as an electron donor. In Rhodopseudomonas palustris the cyclic diene is further reduced to cyclohex-1-ene-1-carboxyl-CoA. In the denitrifying species Thauera aromatica, the cyclic diene is hydrated to give 6-hydroxycyclohex-1-ene-1-carboxyl-CoA. Subsequent β-oxidation results in the formation of a cyclic β-oxo compound, followed by hydrolytic carbon ring opening yielding 3-hydroxypimelyl-CoA in the case of T. aromatica and pimelyl-CoA in the case of R. palustris. These intermediates are further β-oxidized via glutaryl-CoA; final products are 3 acetyl-CoA and 1 CO2. In fermenting bacteria benzoyl-CoA may possibly be reduced to the level of cyclohex-1-ene-1-carboxyl-CoA in an ATP-independent reaction. The genes coding for the enzymes of the central benzoyl-CoA pathway have been cloned and sequenced from R. palustris, T. aromatica, and Azoarcus evansii. Sequence analyses of the genes support the concept that phototrophic and denitrifying bacteria use two slightly different pathways to metabolize benzoyl-CoA. The gene sequences have in some cases been very helpful for the identification of possible catalytic mechanisms that were not obvious from initial characterizations of purified enzymes.
Centric diatoms (Coscinodiscophyceae) of fresh and brackish water bodies of the southern part of the Russian Far East

Abstract Anotated list of centric diatoms (Coscinodiscophyceae) of fresh and brackish water bodies of the southern Russian Far East, based on the authors' data, supplemented by the published literature, is given. It includes 143 algae species (including varieties and forms - 159 taxa) representing 38 genera, 22 families and 14 orders.
Characterization of an EST Database for the Perennial Weed Leafy Spurge: An Important Resource for Weed Biology Research

Abstract Genomics programs in the weed science community have not developed as rapidly as that of other crop, horticultural, forestry, and model plant systems. Development of genomic resources for selected model weeds are expected to enhance our understanding of weed biology, just as they have in other plant systems. In this report, we describe the development, characteristics, and information gained from an expressed sequence tag (EST) database for the perennial weed leafy spurge. ESTs were obtained using a normalized cDNA library prepared from a comprehensive collection of tissues. During the EST characterization process, redundancy was minimized by periodic subtractions of the normalized cDNA library. A sequencing success rate of 88% yielded 45,314 ESTs with an average read length of 671 nucleotides. Using bioinformatic analysis, the leafy spurge EST database was assembled into 23,472 unique sequences representing 19,015 unigenes (10,293 clusters and 8,722 singletons). Blast similarity searches to the GenBank nonredundant protein database identified 18,186 total matches, of which 14,205 were nonredundant. These data indicate that 77.4% of the 23,472 unique sequences and 74.7% of the 19,015 unigenes are similar to other known proteins. Further bioinformatics analysis indicated that 2,950, or 15.5%, of the unigenes have previously not been identified suggesting that some may be novel to leafy spurge. Functional classifications assigned to leafy spurge unique sequences using Munich Information Center for Protein or Gene Ontology were proportional to functional classifications for genes of arabidopsis, with the exception of unclassified or unknowns and transposable elements which were significantly reduced in leafy spurge. Although these EST resources have been developed for the purpose of constructing high-density leafy spurge microarrays, they are already providing valuable information related to sugar metabolism, cell cycle regulation, dormancy, terpenoid secondary metabolism, and flowering. Nomenclature: Leafy spurge, Euphorbia esula L. EPHES, arabidopsis, Arabidopsis thaliana (L.) Heynh
Identification of Volatile Compounds Released by Leaves of the Invasive Plant Croftonweed (Ageratina adenophora, Compositae), and their Inhibition of Rice Seedling Growth

Abstract Several volatile allelochemicals were identified and characterized from fresh leaf tissues of the invasive croftonweed. A simple bioassay was used to demonstrate the release of volatile allelochemicals from leaf tissues. The bioassays revealed that foliar volatile components of croftonweed exhibited significant effects on the seedling growth of upland rice. Peroxidase (POD) activity, superoxide dismutase (SOD) activity, and root oxidizability rose as the concentration of volatiles increased. Activity for both POD and SOD significantly increased with exposure to 15 g and 20 g of croftonweed leaf tissue for 5 d. Root activity was significant at 10 g compared to the control. The volatile components also stimulated the development of the aerenchyma tissue and inhibited lateral root formation. Leaf volatiles of croftonweed were identified by gas chromatography coupled with mass spectrometry (GC–MS). Some of the compounds identified included &agr;-phellandrene, camphene, &rgr;-cymene, 2-carene, &agr;-pinene, limonene, and (z)-3-hexen-1-ol. Bioassays showed that four of these compounds could account for the observed phytotoxicity imparted by total leaf volatiles. Limonene, 2-carene, &agr;-pinene and camphene had no phytotoxic effect on shoot elongation. Phellandrene did cause inhibition in shoot growth at all concentrations. Both (z)-3-hexene-1-ol and &rgr;-cymene inhibited both shoot elongation and root elongation, but the effects of the two compounds on root length were more significant than on the shoot length. Nomenclature: Croftonweed, Ageratina adenophora (Spreng.) King and H. E. Robins; upland rice, Oryza sativa L.
Studies on the antibiotic sensitivity pattern of isolates of P. multocida from buffaloes.

Antibiotic susceptibility p attern of Pasteurella multocida causing hemorrhagic septicemia in buffaloes was determined. The Pasteurella multocida (n=11) were isolated from healthy (04) and diseased buffaloes (07) of four districts of Sargodha division. Isolates were identified by cul tural, biochemical and serological characteristics, and confirmed by specie specific polymerase chain reaction. All isolates were subjected to antibiotic susceptibility testing against gentamicin, erythromycin, amoxicillin, ampicillin, chloramphenicol, cip rofloxacin, norfloxacin, enrofloxacin, sulfadiazine and amikacin by disc diffusion method. Results revealed that P. multocida were highly sensitive to enrofloxacin (90.91 %) followed by gentamicin, chloramphenicol, ciprofloxacin and norfloxacin (72.73%). Susceptibility of P. multocida isolates was low against ampicillin and amoxicillin (45.45%), amikacin (36.36%), sulfadiazine (18.18%) and erythromycin (18.18%). It was concluded that quinolones (enrofloxacin, ciprofloxacin and norfloxacin) are better choice for the treatment of hemorrhagic septicemia as the level of resistance in P. multocida against the macrolides, sulfa drugs and beta lactams has increased enormously.
Supplementation with highly purified docosahexaenoic acid ethyl ester was associated with enhancement of hepatic fatty acid oxidation and greater apparent absorption of docosahexaenoic acid in rats.

Fish oil-derived fatty acid ethyl ester (EE) has been widely utilized as a supplement in Europe and United States. However, few studies have assessed the apparent absorption of docosahexaenoic acid (DHA) between non-purified DHA-EE (L-DHAEE) and highly purified DHA-EE (H-DHAEE). This study evaluated the effects of L-DHAEE and H-DHAEE on lipid metabolism and apparent absorption of DHA in rats. Groups of male Wistar rats were fed AIN93G diet containing 2.8% L-DHAEE or 1.0% H-DHAEE for 4 or 8 weeks. As parameters of lipid metabolism and apparent absorption of DHA-EE, serum and liver lipid contents, fecal EE excretion, lipid-metabolizing enzyme activities, and organ fatty acid composition were measured. The L-DHAEE diet increased fecal DHA-EE and total EE excretion compared with the H-DHAEE diet. In rats fed DHA-EE for 4 weeks, H-DHAEE was more efficacious than L-DHAEE at increasing liver DHA content, partly owing to the enhancement of apparent absorption. In addition, rats fed the H-DHAEE diet had higher fatty acid ? -oxidation activity in peroxisomes than rats fed the L-DHAEE diet for 8 weeks. These results suggest that H-DHAEE supplementation may have beneficial functions in the prevention of lifestyle-related diseases as compared with L-DHAEE supplementation.