Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Water Extract from Enzymic-Treated Hamcho (Salicornia herbacea) on Lipid Metabolism in Rats Fed High Cholesterol Diet

This study was conducted to investigate the effects of water extract from enzymic-treated Salicornia herbacea (Hamcho) on lipid metabolism in rats fed high cholesterol diet. Experimental rats were divided into six groups which were composed of normal diet group, normal and Hamcho extract diet group, high cholesterol diet group, high cholesterol and Hamcho extracts diet groups. Body weight gain and food efficiency ratio (FER) of the high cholesterol diet group were significantly increased compared to the normal diet group, while those of the high cholesterol and Hamcho extracts diet groups were decreased compared to the high cholesterol diet group. Food intake was not significantly different among all experimental groups, The serum TG content of the high cholesterol diet group was significantly increased compared to the normal diet group, but that of the high cholesterol and extracts diet group was significantly decreased in dose-dependent concentration. The liver TG, total lipid and total cholesterol contents of the high cholesterol diet group were significantly increased compared to the normal diet group, while those of the high cholesterol and Hamcho extracts diet groups were significantly decreased compared to the high cholesterol diet group. The serum total cholesterol and LDL-cholesterol contents, and AI of the high cholesterol diet group were significantly increased compared to the normal diet group, while those of the high cholesterol and Hamcho extracts diet groups were decreased, and especially the high cholesterol and Hamcho extract diet group was significantly decreased compared to the high cholesterol diet group. Serum HDL-cholesterol contents of the high cholesterol diet group were significantly increased compared to the normal diet group. These results suggest that supplementation of water extract from enzymic-treated Salicornia herbacea may have a pronounced impact on lipid metabolism of serum and liver in the rats fed high cholesterol diet.
Genetic diversity and structure of domesticated strains of red sea bream, Pagrus major, inferred from microsatellite DNA markers

The genetic diversity and structure of nine domesticated strains of red sea bream used in a private hatchery were studied and compared to a wild population. A total of 313 individuals were genotyped at eight microsatellite loci. Average number of alleles per locus ranged from 5.5 to 9.4 in domesticated strains, but that of the wild population was 28.4. Heterozygosity of domesticated strains (ranged 0.697–0.804) was also lower compared to the wild population (0.952). Estimated Ne also decreased in all domesticated strains (ranged 10.3–126.0) compared to the wild population (1422.5). The UPGMA tree and 3-D FCA showed that there were two main clusters containing domesticated strains, and the wild population was at the middle of both of the domesticated clusters. The STRUCTURE analysis also supported the phylogenetic analysis, and revealed three sub-clusters in the domesticated strains. Pairwise FST revealed that all domesticated strains were statistically different from the wild population, and also the differentiation between domesticated strains was all statistically significant. Information on genetic diversity and structure of domesticated strains of red sea bream obtained in this study will be useful for future broodstock management and selective breeding programmes.
Mitochondrial DNA Variation in Chinook (Oncorhynchus tshawytscha) and Chum Salmon (O. keta) Detected by Restriction Enzyme Analysis of Polymerase Chain Reaction (PCR) Products

We analyzed intraspecific mitochondrial DNA variation in chinook salmon (Oncorhynchus tshawytscha) from drainages in the Yukon River (Alaska and Yukon Territory), the Kenai River (Alaska), and Oregon and California rivers; and chum salmon (O. keta) from the Yukon River and Vancouver Island, and Washington rivers. For each species, three different portions of the mtDNA molecule were amplified separately using the polymerase chain reaction and then digested with at least 19 restriction enzymes. Intraspecific sequence divergences between haplotypes were less than 0.01 base substitution per nucleotide. Nine chum salmon haplotypes were identified. Yukon River chum salmon stocks displayed more haplotypes (eight) than the stocks of Vancouver Island and Washington (two). The most common chum salmon haplotype occurred in all areas. Seven chinook salmon haplotypes were identified. Four haplotypes occurred in the Yukon and Kenai rivers and four occurred in Oregon/California, with only one haplotype shared between th.
ISOLATION AND CHARACTERIZATION OF PYOCINS FROM SEVERAL STRAINS OF PSEUDOMONAS AERUGINOSA

Two types of pyocins were found in Pseudomonas aeruginosa and named pyocin type S and type R. Production of both types of pyocin was inducible by ultraviolet ray or by mitomycin. An S-type pyocin was prepared from strain P28 and its nature was investigated. The pyocin activity was labile to heat or proteinase treatment. Its molecular weight was estimated to be around 1×105. The same type of pyocin was found in M11, a fertile strain originally isolated by Holloway.Pyocin type R, which has a structure very similar to some phage tails, was found among three strains of Japanese and Australian origin and named pyocin R2, R3, and R4. These pyocins distinguished by the difference in their action spectrum but were otherwise indiscernible. They behaved in the same manner during the purification process including DEAE-cellulose chromatography. Moreover an immunological cross reaction was observed among these R-type pyocins. Anti-pyocin R or R2 serum also neutralized other R-type pyocins. Electron microscopy revealed a similar dimension for each pyocin particle; 15A×1, 300A.
Lipid and hydrophobic modification of cationic carriers on route to superior gene vectors

Gene therapy has been pursued in the past two decades for treatment of diseases associated with defective gene expression. The insertion of a therapeutic gene into cells, followed by its expression, and consequently the inhibition or activation of target proteins constitute the general steps for a beneficial outcome in such an approach. However, the future of this approach will rely upon safe and effective gene carriers. Cationic polymers represent a class of non-viral carriers that can be optimally engineered to facilitate gene delivery to target cells and amphiphilic polymers have been particularly appealing due to delicate balance of physical properties that might optimize their functional performance. This review was complied with a focus on recent progress on lipid and hydrophobically modified polymers, and aims to provide new insights into development of this type of gene carriers. In particular, we will focus on the insertion of lipid or hydrophobic moieties into cationic carriers and its influence on the gene delivery performance. Critical parameters influencing the condensation of nucleic acids, surface properties and aggregation behavior of polyplexes, and the ability of the carrier-cargo complexes to dissociate will be described, all in the context of in vitro and in vivo performance of the carriers.
Growth, condition, and environmental relationships in Atlantic cod (Gadus morhua) in the northern Gulf of St. Lawrence and implications for management strategies in the Northwest Atlantic

Northern Gulf of St. Lawrence Atlantic cod (Gadus morhua) is one of several stocks that collapsed in eastern Canada following a long period of intensive exploitation. Surplus and net production per capita became nil or negative in the mid-1980s so that any level of exploitation would have caused a decline of the stock. This was partly explained by a marked decline in growth production and is consistent with smaller sizes-at-age but also lower condition factor values during the same period. Correlations between size-at-age and temperature were not significant when corrected for autocorrelation, but slopes were always positive, suggesting higher growth rates at higher temperatures. Smaller sizes-at-age in the 1980s were not associated with changes in the fishery or increased fishing mortality, nor were they consistent with the density-dependence hypothesis. Lengths at age 8 decreased by more than 10 cm as the stock decreased 10-fold in abundance. While size-at-age and temperature covary in cod when all stoc.
Environmentally Sound Harvesting Technologies in Commercial Forests in the Area of Northern Velebit – Functional Terrain Classification

Background and Purpose: The role of environmental effects in timber harvesting has great importance in decision making and planning logging operations. Consequently, more emphasis should be put on a planning system so that environmentally sensitive sites for a certain harvesting system can be recognized and the most suitablemachinery selected for given terrain conditions. Material and Methods: Four main data sources have been used for the model of ecoefficient harvesting system prediction: 1) a digital elevation model (DEM), 2) a digital network of forest roads, 3) forest inventory data and 4) ecoefficient limitations for harvesting systems. Software ArcGIS 9 was used for GIS processing and data analysis. Results: Amodel for selecting an ecoefficient harvesting system for commercial forests of Northern Velebit is based on three influencing factors: terrain slope, extraction distance and breast height diameter of trees. Based on the model, a harvesting system is determined for each forest subcompartment. The results show that breast height tree diameter restricts mechanized felling and processing. Fully mechanized harvesting systems could be used only over 7.27% of the researched area. Ground based extraction represents the main technology. Conclusions: In order to establish functional terrain classification, a model for determining an ecoefficient harvesting system should comprise a geographic information system, and terrain and forest stand data. Specific terrain (limestone combined with relief characteristics) and forest stand conditions (mixed selective forests with natural regeneration) limit the application of some harvesting systems which would otherwise be environmentally acceptable in many other cases.
Conservation and ecological implications of the use of space by chilla foxes and free-ranging dogs in a human-dominated landscape in southern Chile

We investigated whether domestic dogs (Canis lupus familiaris) influenced the use of space by chilla foxes (Lycalopex griseus) in southern Chile and tested the hypothesis that dogs interfere with chillas. We used scent stations and occurrence of scats within systematically placed plots to assess habitat use by both species and to test whether dogs were associated to the use of space by chillas. Activity data were obtained from captures for both species, and telemetry for foxes. Diet of both species was analysed in order to tease out the potential existence of exploitation competition.We found that, when active, chillas used prairies more and native forest less than expected according to availability, whereas inactive chillas (during the day) preferred native forest, the only habitat type that dogs did not use. The odds of dog occurrence increased at shorter distance to human houses, whereas the inverse pattern was observed for chillas. Poisson models showed that the number of chilla visits to scent stations was negatively correlated with the number of dog visits. We observed dogs persecuting and/or killing chillas which was also corroborated by local people that used dogs to prevent chilla-related poultry losses, supporting the idea that dogs harass foxes actively.The analysis of scats showed that dogs fed mainly on house food and domestic ruminant carcasses whereas foxes fed on hare, hens, mice and wild birds, thus suggesting that exploitation competition is not a strong alternative hypothesis as a proximate cause for the patterns observed. We conclude that dogs seem to constrain the use of space by wild carnivores via interference.
Molecular directionality of β-chitin biosynthesis

Abstract The molecular packing in β-chitin unit cells was experimentally determined by a combination of unidirectional degradation by Bacillus circulans chitinase A1 and microdiffraction electron crystallography using highly crystalline β-chitin microfibrils from the protective tubes secreted by Lamellibrachia satsuma . The mode of chain packing was found to be identical with that of the previously published crystal model for β-chitin, despite a controversial definition of the unit cell parameters. Here, a “parallel-down” packing was determined, where the reducing ends of chains point in an opposite direction to the crystallographic c -axis. Microdiffraction analyses of nascent β-chitin microfibrils generated from diatom Thalassiosira sp. showed that the c -axis of the crystal was directed toward the diatoms, and therefore the reducing end of a growing chain pointed away from the locus of biosynthesis. This mechanism agreed well with what we found recently in the cellulose biosynthesis system, and provides strong evidence that the polymerization by the processive glycosyl transferase takes place at the non-reducing end of the growing polysaccharide chains.
Evolution of the Genes Encoding Starch Synthase in Sorghum and Common Wheat

Starch synthases (SSs) play important roles in plant starch synthesis. Five enzymetic isoforms of starch synthases have been found in plant, some of isoforms have further diverged possibly via whole genome duplication events, which might result in two or three subclasses of the sequences in rice and maize. In this study, we found the retention of GBSS, SSII, and SSIII duplicators except for the SSIV duplicator in genomes of sorghum and wheat. The SSIV gene might have been lost in maize and sorghum genomes based on the synteny relationship among rice maize and sorghum. Expression analyses indicated that the SS duplicators were also diverged from the duplicators of SbGBSSI, SbSSIIIa in expression pattern, and SbSSIIa were expressed mainly in endosperm in sorghum, whereas SbGBSSII, SbSSIIb, and SbSSIIIb of sorghum, TaSSIIb and TaSSIIIb of common wheat, were expressed mainly in leaves. Our findings, in combination with previous studies, indicate that the SSIV duplicator should be not remained in all Gramineae species, while the expression of duplicated SS genes diverged similarly in the studied species.
Evaluation of a growth model of preruminant calves and modifications to simulate short-term responses to changes in protein intake

Recently, a mechanistic simulation model was developed which integrates protein and energy metabolism of preruminant calves of 80 to 240 kg live-weight (LW). The model can be used to predict the rate of gain of weight, protein and fat from nutrient input. A serial slaughter experiment was conducted to obtain an independent data set for model evaluation purposes. The objective of the model evaluation exercise was to evaluate model predictions to different protein intakes in three LW ranges: 80–120 kg (three levels of protein intake), 120–160 kg (three levels of protein intake) and 160–240 kg LW (two levels of protein intake). In this experiment, 64 calves were used, of which 36 were slaughtered to determine chemical body composition. Four calves were slaughtered as a reference group at 80 kg LW and subsequently four per protein intake level at each of the pre-determined target weights. Model predictions were found satisfactory for live-weight gain and protein deposition, with root mean-square prediction errors (RMSPE) expressed as a percentage of the observed mean of below 7%. For fat deposition, the RMSPE was 18% (on average 26 g day 1), of which 58% was due to a consistent underestimation. Closer examination of the experimental results from 80–120 kg LW revealed an adaptation of the calves to the sudden change in diets after the start of the experiment, still present at 120 kg LW and not predicted by the model. Modifications were made to the model, based on the hypotheses that (i) calves adapt their visceral protein mass quickly to a 13 Mod Nutrient ch12 30/8/00 4:06 pm Page 163
Song diversification and complexity in canaries and seedeaters (Serinus spp.)

Bird song is a composite trait that shows great variation in syntax and phonology between taxa, which hampers the precise quantification of complexity. This should be more feasible for closely-related species that share aspects of song organization. We conducted a comparative study of song and syllable characteristics in the largest fringillid genus, Serinus (canaries and seedeaters), with two objectives: (1) to describe and quantify song complexity in the genus and (2) to assess evolutionary dynamics of song, in particular whether interspecific song diversification evolved along intraspecific lines of covariation between syllable characteristics. We document a pattern of intense, very labile evolution of song in the genus. Well-known vocal constraints such as the relationship between frequency and body size did not appear to limit this evolution, and intraspecific trade-offs between different aspects of syllable complexity did not constrain interspecific diversification. Factor analysis returned an axis of variation that comprehensively expresses song complexity in the genus, and is defined by song speed, repertoire size, and also various aspects of syllable phonology. The species body size is not related to this axis of complexity, but to a minor axis that may indicate better respiratory capacity of larger birds. We discuss the pattern of song evolution in Serinus spp. in the context of the evolutionary dynamics of sexually selected traits. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92, 183–194.
Extra-pair fertilization and effective population size in the song sparrow Melospiza melodia

The concept of effective population size (N-e) is used widely by conservation and evolutionary biologists as an indicator of the genetic state of populations, but its precision and relation to the census population size is often uncertain. Extra-pair fertilizations have the potential to bias estimates of N-e when they affect the number of breeders or their estimated reproductive success tallied from social pedigrees. We tested if the occurrence of extra-pair fertilizations influenced estimates of N-e in a resident population of song sparrows Melospiza melodia using four years of detailed behavioural and genetic data. Estimates of N-e based on social and genetic data were nearly identical and averaged c. 65% of the census population size over four years, despite that 28% of 471 independent young were sired outside of social pairs. Variance in male reproductive success also did not differ between estimates based on social and genetic data, indicating that extra-pair mating had little effect on the distribution of reproductive success in our study population. Our results show that the genetic assignment will not always be necessary to estimate N-e precisely.
Modulation of lineage-specific cell differentiation by long non-coding RNAs

Mammalian genomes comprise thousands of non-protein-coding genes. These can produce small non-coding RNAs (such as rRNAs and tRNAs), as well as long non-coding RNAs (lncRNAs), which are >200nt and resemble mRNAs in their biogenesis. Although the functions of the vast majority of lncRNAs remain unknown, many are tissueand developmental stage-specific, suggesting roles in lineage-specific development. We generated deep transcriptome surveys from differentiating mouse red blood cells, and implemented a computational strategy for de novo lncRNA discovery to comprehensively catalog erythroid-expressed lncRNAs. We found >100 previously unannotated loci, many of which are erythroid-specific and are induced by key erythroid transcription factors during differentiation. We exploited these features to select 12 candidates for loss-of-function studies, and found that depleting 10 out of 12 impaired red cell maturation, inhibiting cell size reduction and subsequent enucleation. To study how lncRNAs regulate erythropoiesis, we focused on EC6, an unpolyadenylated lncRNA needed for silencing neighboring loci encoding NF-kB activators. De-repression of these genes upon EC6 knockdown leads to activation of NF-kB and other immune pathways that antagonize erythropoiesis, resulting in impaired proliferation and elevated apoptosis during differentiation. We showed that EC6 is retained in chromatin and binds the nuclear matrix factor hnRNP U, which may enable co-localization with its targets to mediate their repression. Extending our work to a different lineage, we reconstructed transcriptomes from distinct mouse adipose tissues and identified ~1500 lncRNAs. These included many brown fat-specific loci induced during differentiation which are targets of key adipogenic factors. Inhibiting one of them, lnc-BATE1, compomised brown adipocyte development, impairing activation of brown fat genes, mitochondrial biogenesis, and thermogenic function. We showed that lnc-BATE1 acts in trans and binds hnRNP U, which is also required for proper brown adipocyte maturation. This work demonstrates that lncRNAs modulate lineage-specific cell differentiation by promoting or suppressing competing gene expression programs controlling cell fate. Thesis Supervisors: Harvey F. Lodish, Alexander van Oudenaarden Titles: Professors of Biology
Does Competition Drive Dispersal

What distances would animals be expected to disperse if the only cost to staying on the natal site resulted from competition for resources limiting to reproduction? In such a situation the "best" dispersal distance would be zero, but the constraint of competition would prevent many individuals from achieving this ideal; the actual dispersal distances would be shaped by population demography. The models I describe predict the distribution of dispersal distances as a function of home range turnover probability for animals that move to the first uncontested home range they encounter and no farther. The models provide a good match to data for some, but not all, avian and mammalian data sets, suggesting (1) that competiton for resources limiting to reproduction may be the primary factor driving dispersal, and (2) that the action of inbreeding avoidance, habitat selection, and other processes suggested to influence dispersal distances can be detected as deviations from these model predictions.
Marbled lungfish growth rates in Lake Baringo, Kenya, estimated by mark-recapture

Mark-recapture was used to quantify the relationship between body mass (M T ) and individual growth rates of sub-adult marbled lungfish Protopterus aethiopicus in Lake Baringo, Kenya. Specific growth rate (in mass) was found to be a well defined and decreasing function of M T over the size range of recaptured fish. Growth trajectories based on this function indicated that Lake Baringo African lungfish reached maturity at an age of c. 3 years and had a low reproductive effort.