Miracle-dz/UniFAR-FTUs huggingface dataset:
Resistance and resilience of ecosystem metabolism in a flood-prone river system

1. Gross primary production (GPP) and ecosystem respiration (ER) were analysed for 18 months in two reaches of the River Thur, a prealpine river in Switzerland. The upper reach at 655 m above sea level (a.s.l.) is bedrock constrained, has a high slope (0.60%) and a catchment area of 126 km 2 . The lower reach at 370 m a.s. l. has a more extensive hyporheic zone, a lower slope (0.17%) and a catchment of 1696 km 2 . 2. In both reaches, temporal patterns of stream metabolism reflected the occurrence of bed-moving spates. Average reductions of GPP and ER by spates were 53 and 24% in the upper reach, and 37 and 14% in the lower reach, respectively. The greater resistance of ER than GPP in both reaches shifted the ecosystem metabolism towards heterotrophy (decrease of the ratio of GPP to ER (P/R)) following spates. 3. Recovery of GPP was significantly faster in the lower reach and exhibited distinct seasonal variation (positive correlation with incident light). The differences in stability (both resistance and resilience) between reaches reflected differences in geomorphic settings and disturbance regime. 4. Stepwise regression analysis was used to explore the potential influence of season, disturbance and prevailing environmental conditions on stream metabolism in each reach. Time since spate plus temperature explained 73 and 86% of variation in ER and GPP, respectively, in the upper reach and 55% of variation in ER in the lower reach. Season plus prevailing environmental conditions explained 67% of variation in GPP in the lower reach. 5. To test how the perception of stability may change with increasing scale of observation, the disturbance regimes of 12 sites were compared with the disturbance regime of the entire Thur catchment. The analysis suggests that stream metabolism at the catchment scale is far more resistant to high flow events than at the reach scale.
Expression, characterization, and variation of the porcine calpain 7 gene

Abstract This study was designed to clone the porcine calpain 7 gene, CAPN7, to characterize its tissue expression, and to investigate its genetic variation. The cDNA sequence that contains a 2442 bp open reading frame encoding 813 amino acids was obtained by reverse transcription–polymerase chain reaction and rapid amplification of cDNA ends methods based on in slico cloning and homologous cloning, and five introns were identified. Quantitative real-time PCR showed that CAPN7 was ubiquitously expressed in all tissues examined, and the mRNA level in muscles was low at 1–7-days-old and high from 90 to 270-days-old. In addition, two single nucleotide polymorphisms in coding sequence were identified and the polymerase chain reaction–restriction fragment length polymorphism methods were established to detect the polymorphisms. At each site, the distribution of three genotypes is significantly different (P<0.01) in Yorkshire, Duroc, Wild boar, and Min pigs.
Chicken fatness: from QTL to candidate gene

Excessive fat is a well known problem in poultry. It depresses feed efficiency, has no commercial value, and is less appreciated by consumers. Therefore, considerable research effort has been applied around the world to study factors associated with fat deposition and methods of decreasing it.his dissertation concerns the identification of genes controlling fat deposition in broilers. The strategy used to identify these genes is the so-called positional candidate gene approach. This approach moves from mapping quantitative trait loci (QTL) towards the identification of candidate genes. A total genome scan of a large three generation broiler population has resulted in the localization of QTL for fat deposition. Several of these QTL are confirmed as well as new QTL are identified in an advanced intercross line produced from this broiler population. The construction of high resolution comparative maps has helped to identify potential candidate genes for fat deposition mapped in the QTL regions. These genes and the polymorphisms within these genes will be of interest for future research. Identified SNPs can be used to refine the map position of the QTL by analysing linkage and linkage disequilibrium.Finally, a causal link between the genetic trait and the candidate genes can be established from functional evidence.
Changes in rumen biohydrogenation intermediates and ciliate protozoa diversity after algae supplementation to dairy cattle

During an in vivo trial with four rumen-fistulated dairy cows, the effect of dietary supplementation of docosahexaenoic acid (DHA; 22:6 n-3)-enriched microalgae (Schizochytrium sp., 2% on feed intake) on the fatty acid metabolism and microbial community in the rumen was investigated. Algal supplementation resulted in lower concentrations of saturated fatty acids while the concentrations of monounsaturated and polyunsaturated fatty acids increased as compared to the control treatment. An incomplete biohydrogenation of linoleic (18:2 n-6) and linolenic (18:3 n-3) acid was observed, resulting in a strong accumulation of 18:1 t11, 18:1t10 and 18:2 t11c15. Denaturing gradient gel electrophoresis (DGGE) was performed to study the rumen bacterial and ciliate population. Algal supplementation provoked changes in both communities. Ciliate DGGE profiles suggested a decreased abundance of Isotricha prostoma and I. intestinalis and some species of Epidinium caudatum, Eudiplodinium maggii and Diplodinium dentaturn in the rumen of algae-fed cows. Moreover, quantitative PCR indicated that incomplete biohydrogenation through algal addition was associated with decreased ciliate numbers. The simultaneous accumulation of hydrogenation intermediates and the disappearance of ciliates suggest that ciliates and/or their associated bacteria could play a role in rumen biohydrogenation.
Mating strategy in Aleochara bilineata: sperm storage and allocation

Abstract By contrast to females that can maximize reproductive success with only one or a few copulations, males generally increase their fitness with frequency of mating. Sperm storage and allocation is therefore crucial for both male and female fitness. Sperm storage in Aleochara bilineata (Coleoptera; Staphylinidae) is investigated by measuring the number of spermatozoa stored in the female spermatheca after single, double or triple successive copulations with different males. The potential advantages of polyandry are studied in terms of the number of sperm stored by females mated twice with the same male (i.e. repeated copulation), compared with females mated twice with two different virgin males (i.e. polyandry). Level of polygyny is also estimated by measuring sperm allocation when ten successive mates are offered to a virgin male. Aleochara bilineata females store the sperm of the same or different males additively, suggesting no advantage for polyandry in terms of the number of sperm stored. A virgin male is able to inseminate ten different females but the number of sperm transferred decreases linearly. Finally, the latencies and durations of copulations are measured in all experiments to estimate changes according to the male or female status (i.e. virgin or mated). The latency before mating is higher when females are virgin than when females have already mated.
The trigeminal jaw adductors of primitive snakes and their homologies with the lacertilian jaw adductors

The trigeminal jaw adductor musculature of anilioid snakes is analysed. The group is characterised by primitive characters, viz. the presence of an extensive bodenaponeurosis and of a quadrate aponeurosis. A temporal tendon gives rise to superficial (lb) fibres which are not observed in other snakes: this may be a primitive or a derived feature. Jaw adductor muscles in snakes are usually subdivided following their relative position in an antero–posterior direction. Lacertilian jaw adductors are subdivided in a transverse plane. A detailed comparison of the anilioid and primitive lacertilian jaw adductors establishes correspondences (homologies) of parts in the transverse plane in both groups. These homologies are corroborated by innervational patterns. Platynotan lizards are widely accepted as potential snake ancestors. A comparison of homologue jaw adductors shows different evolutionary trends to characterise platynotan lizards and snakes. Theoretically, these findings do not rule out primitive platynotan lizards as snake ancestors. On the basis of the structure of jaw adductors, snakes are to be derived from a primitive lacertilian pattern, be it platynotan or not.
Loss of genetic variability in reintroduced roach (Rutilus rutilus) populations

Genetic variation at five microsatellite loci and in mtDNA was surveyed in reintroduced and ‘control’ populations of roach (Rutilus rutilus) in Sweden. Microsatellite allelic richness and allele size ranges were significantly reduced in reintroduced populations, and mtDNA diversity was nearly significantly reduced in reintroduced populations. These measures of genetic variability were strongly correlated with lake characteristics that influence population size and food availability.
Pathogenic and molecular variability in bean common mosaic virus infecting common bean in India

Pathogenic variability studies in bean common mosaic virus (BCMV) infecting common bean (Phaseolus vulgaris L.) revealed the existence of two pathogroups PG-I and PG-II and four strains (NL-1, NL-1n, NL-7 and NL-7n) in Himachal Pradesh, a North-Western Himalayan state of India. Two strains, NL-1 and NL-7 were identical to the previously described NL-1 and NL-7 strains from Europe and USA, whereas the other two designated as NL-1n and NL-7n differed from earlier identified strains with respect to their necrotic reaction on cultivar Jubila at high temperature (>30°C). Reverse phase HPLC peptide profiling of tryptic digests of coat protein of these strains further confirmed that NL-1, NL-1n, NL-7 and NL-7n are distinct from each other. This study constitutes the first record of pathogenic variability in BCMV infecting common bean in India.
Size spectra, body width and morphotypes of intertidal nematodes: an ecological interpretation

Nematode species from three intertidal assemblages (St Lawrence Estuary, Quebec, Canada) were studied in order to form an ecological interpretation of three allometric attributes: body width, size spectra, and morphotypes. The three assemblages were characterized by a very similar sediment grain median (Md) but different silt–clay proportions: A1 (upper-tidal level; Md=122 μm; silt=34.8%), A3 (mid-tidal level; Md=182 μm; silt=12.8%), and A5 (lower-tidal level; Md=122 μm; silt=6.8%). Silt–clay proportions were an influential factor in determining the mean nematode body width, used as a morphological discriminant between burrowing and interstitial organisms. A plot of the number of species vs the body width-classes showed two peaks: between 19.3 and 22.6 μm (interstitial), and between 32.0 and 45.5 μm (burrowers). As for the size spectra, in sandy sediments the mean nematode individual biomass was smaller than in muddy sediments. As a consequence, the estimated mean individual respiration rate was greater in muddy (A1=2.26 nl O2 h−1) than sandy sediments (A3=1.25 nl O2 h−1; A5=1.12 nl O2 h−1). In contrast, estimated metabolic ratios were lower in A1 (2.78 nl O2 h−1 μg−1 dry weight, DW) than in A3 (2.95 nl O2 h−1 μg−1 DW) and A5 (3.01 nl O2 h−1 μg−1 DW) suggesting different productivity and/or physiological adaptations to different lifestyles (burrowing vs interstitial) between species inhabiting muddy or sandy sediments. Morphotypes (body width/body length ratio=w/l ratio) were found to be associated with feeding groups. Small w/l ratios were typical of microvores, while greater ratios were typical of epigrowth feeders and predators. Ciliate-feeders, deposit-feeders and facultative predators had intermediate ratios. A morphotype food-related hypothesis is proposed: the species morphotype reflects the quality of exploited food; a small w/l ratio (i.e. long gut) would favour digestive efficiency and would be an adaptation to low quality food (microvores); inversely, a greater w/l ratio (i.e. short gut) would be an adaptation to high quality food (epigrowth-feeders and predators).
The effects of fasting and feeding on hepatic thyroxine 5′-monodeiodinase activity in the rainbow trout, Oncorhynchus mykiss

The effects of fasting and feeding on the activity and kinetics of the hepatic microsomal L-thyroxine (T4) 5′-monodeiodinase enzyme system (5′D) responsible for generating 3,5,3′-triiodo-L-thyronin.
Effectiveness of Transgenic Bt Cottons Against Noctuids in the Lower Rio Grande Valley of Texas

Abstract. The comparative efficacy of Bacillus thuringiensis (Berliner) Bollgard, Bollgard II, WideStrike, and non-Bt expressing cotton, Gossypium hirsutum L. , for control of the noctuid complex of bollworm, Helicoverpa zea (Boddie); fall armyworm, Spodoptera frugiperda (J. E. Smith); beet armyworm, Spodoptera exigua (Hübner); and cabbage looper, Trichoplusia ni (Hübner); was evaluated in the Lower Rio Grande Valley of Texas during 2004–2008. When noctuids were abundant, leaves or fruit were significantly less damaged and fewer live larvae were found on Bollgard II cotton compared with non-Bt cotton throughout the growing season. With few to moderate Lepidoptera, cotton with either of the two Bt traits had similar damage. One insecticide application to cotton with Bollgard, Bollgard II, WideStrike, or non-Bt traits resulted in significantly fewer bollworm and beet armyworm larvae and less damage on fruiting structures compared to nontreated cotton. Beet armyworm larval survival and damage to leaves on non-Bt cotton were 3.6-fold greater than on Bollgard II or WideStrike cotton and 1.5-fold greater than on cotton varieties with the Bollgard trait.
Precipitation of Plasma Lipoproteins by PEG-6000 and Its Evaluation with Electrophoresis and Ultracentrifugation

A neutral polymer precipitation procedure for fractionation of human plasma lipoproteins is described. The method was also tested preliminarily for fractionation of rat plasma lipoproteins. Polyethylene glycol-6000 (PEG-6000) at a concentration of about 12% and at pH 7.9 precipitated human plasma very low density (VLDL) and low-density (LDL) lipoproteins completely. Precipitation was independent of time and temperature. VLDL and LDL could not be precipitated separately. Polyethylene glycol-6000 precipitation can be used for rapid determination of high-density (HDL) lipids and of the ratio of HDL to LDL lipids.
Biogeography and Breeding System Evolution of the Woody Bencomia Alliance (Rosaceae) in Macaronesia Based on ITS Sequence Data

Abstract The origin of the flora of the Macaronesian archipelagos has been a subject of controversy for over a century with the traditional opinion asserting that it is a relictual fragment of a widespread Tertiary subtropical European flora. A phylogenetic investigation of the three Macaronesian genera of the Bencomia alliance (Bencomia, Dendriopoterium, and Marcetella) using sequence data from the nuclear rDNA Transcribed Spacer region (ITS) has provided evidence relevant to the origin of the Macaronesian flora and the evolution of morphological characters of interest to students of island biology. In the ITS phylogeny, the Bencomia alliance, Sarcopoterium, a monotypic genus of the eastern Mediterranean, and Sanguisorba ancistroides, also a Mediterranean species, form a clade that is sister to the Eurasian Sanguisorba minor. These relationships contradict the relictual hypotheses and show that the endemic Macaronesian Rosaceae are sister to Mediterranean Sanguisorbeae. The data also contradict a recent placement of Dendriopoterium and Marcetella together in a subgenus of Sanguisorba. The ITS tree demonstrates that dioecy evolved in the islands from a continental monoecious or gynomonecious ancestor and that there has been an increase in plant size and woodiness compared to continental relatives rather than the decrease suggested by previous workers. Communicating Editor: Matt Lavin
Low genetic diversity and allozymic evidence for autopolyploidy in the tetraploid Pyrenean endemic larkspur Delphinium montanum (Ranunculaceae)

Allozyme electrophoresis was conducted to survey the levels and distribution of genetic diversity in the tetraploid perennial larkspur Delphinium montanum (Ranunculaceae), which is endemic to the eastern Pyrenees of Spain and France and considered to be endangered. Seven populations were sampled, resolving 14 putative enzymatic loci belonging to eight enzymes. Banding patterns stained in gels revealed several enzymatic duplications attributable to autotetraploidy, such as the presence of both balanced and unbalanced heterozygotes and the lack of fixed heterozygosity. However, variability in D. montanum (P = 23.8%, A = 1.48, and He = 0.082) was lower than that expected for an autotetraploid species. This, in addition to the scarcity of loci showing three or four different alleles, could indicate that this species has suffered genetic erosion through population bottlenecks, or, alternatively, that it is undergoing diploidization. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 155, 211–222.
Apical Development and Growth of Barley under Different CO2 and Nitrogen Regimes

Increases in atmospheric carbon dioxide (CO2) concentration have stimulated interest in the response of agricultural crops to elevated levels of CO2. Several studies have addressed the response of C3 cereals to CO2, but the interactive effect of nutrient supply and CO2 on apical development and spikelet set and survival has not been investigated thoroughly. Hence, an experiment was conducted in the greenhouse to evaluate the effect of high (700 μmol CO2mol−1 air) and low (400 μmol mol−1) levels of atmospheric CO2 on apical development, spikelet set and abortion, and pre- and post-anthesis growth in spring barley (Hordeum vulgare L.) grown under high N (0.3 g N pot−1 before sowing −1–0.11 g N pot−1 week−1) and low N (0.3 g N pot−1) regimes. The plants were grown in 5 L pots. Development of spike was hastened due to CO2 enrichment, and the C+ plants pollinated few days earlier than the C— plants. Carbon dioxide enrichment had no effect on date of ripening. Development of spike slowed following application of extra N, and plants pollinated 10 days later and matured 2 weeks later when compared with plants under low N. Carbon dioxide enrichment did not affect the number of spikelets at anthesis. Excess N decreased spikelet abortion and the increased maximum number of spikelets under both [CO2]. Barley plants did not tiller when grown in low [CO2] and low N. Increased endogenous IAA concentration in those plants, recorded three days before tillers appeared in other treatments, may have contributed to this. Carbon dioxide enrichment increased the C concentration of plants, but decreased the N concentration under high N regime. Both the C and N concentration of plants were increased under high N regime. Carbon dioxide enrichment increased the total dry matter of mature plants by 9 % under high N regime and by 21 % under low N regime. Under high [CO2] increased kernel number on tiller spikes, and increased kernel weight both on main stem and on tiller spikes resulted in a 23 % increase in kernel yield under low N regime and 76 % increase in kernel yield under high N regime. The rate of N application influenced growth and yield components to a greater extent than CO2 enrichment. At maturity, plant dry matter, kernel weight, the number of kernels per spike, and the number of spikes per plant were higher under high N regime than under low N regime. Long days (16 h), low light intensity (280 μmol m−2s−1), and at constant temperature of 20 °C high [CO2] increased kernel weight and the number of kernels on tiller spikes under high and low N application rate, but did not increase the number of kernels on main stem spike, or the number of tillers or tiller spikes per plant.
Developmental expression of the αIELβ7 integrin on T cell receptor γδ and T cell receptor αβ T cells

A novel monoclonal antibody, 2E7, was shown by immunoprecipitation to be reactive with the αIELβ7 integrin and was employed to analyze the expression of this integrin in lymphocyte subsets and during T cell ontogeny. In adult lymph nodes, αIEL was expressed at low levels by 40–70% of CD8+ T cells and < 5% of CD4+ T cells. However, virtually all intestinal intraepithelial lymphocytes and ˜20% of lamina propria CD4+ T cells were 2E7+, indicating a preferential expression of this integrin on mucosal T cells. Examination of αIEL integrin expression during thymus ontogeny revealed that ˜3–5% of fetal or adult thymocytes were 2E7+. Interestingly, early in fetal thymus ontogeny, ˜40% of 2E7+ cells expressed T cell receptor (TcR)‐γδ and this subset persisted through birth. A developmental switch occurred such that 2E7+ TcR− CD4−8+ cells detected on fetal day 19 were followed by 2E7+ TcR‐αβ CD4−8+ cells in the neonatal thymus. The latter population persisted throughout thymus ontogeny into adulthood. Interestingly, a subset of TcR‐γδ Vγ3+ day 16 fetal thymocyte dendritic epidermal cell (DEC) precursors were 2E7+, but all mature DEC expressed high levels of αIEL integrin, suggesting that the αIEL integrin was acquired late in DEC maturation. This possibility was strenghthened by immunohistochemical localization of the majority of 2E7+ γδ and αβ T cells to the medullary regions of the thymus. Overall, the results demonstrate a developmentally ordered expression pattern of the αIELβ7 integrin that suggests a common function for this integrin during TcR‐γδ and ‐αβ CD4−8+ T cell thymocyte development or perhaps in effector functions for these subsets.
The purple saxifrage, Saxifraga oppositifolia, in Svalbard: two taxa or one?

Several studies have demonstrated high levels of genetic (DNA), ecophysiological, ecological, and morphological variation within the species purple saxifrage, Saxifraga oppositifolia, in Svalbard. It has recently been proposed that S. oppositifolia is represented by two conspicuously different subspecies in this archipelago: ssp. reptans, a late-flowering, prostrate ecotype of snow-protected, damp habitats, and ssp. pulvinata, an early-flowering, cushion-like ecotype of dry, wind-exposed heaths and ridges. It has also been suggested that the subspecies may be differentiated at the tetraploid and diploid levels, respectively, which would promote reproductive isolation. These hypotheses are tested by examining variation in morphology, ecology, and pollen size and stainability in 150 plants of S. oppositifolia growing in 50 vegetation samples at four sites in the Kongsfjorden area. Although analyses of the various data sets demonstrated the large variation within the species, the material could not be separated into distinct groups. The morphological variation was continuous along local ecological gradients. The pollen grains were fully stainable and the pollen diameter data showed a unimodal distribution, suggesting that the plants analysed represent only one ploidal level. These results reject a hypothesis that the morphologically intermediate plants are hybrids between two taxa at different ploidal levels. Thus, the conspicuous variation in S. oppositifolia in Svalbard probably results from local, in situ ecoclinal differentiation. Although this variation clearly is without taxonomic significance, it is important in the broader context of arctic conservation biology and the potential impact of global warming on arctic vegetation.