Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein expression upon desiccation and imbibition of Magnolia ovata A. St.-Hil seeds

ABSTRACT The effect of seed drying and imbibition was studied by differential protein expression using two dimensional gel electrophoresis. After drying to a range of water contents, seeds were germinated to assess the viability. Seeds of Magnolia ovata did not withstand the desiccation down to 0.10 g H 2 O · g -1 dw. The critical water content below which the desiccation sensitivity became apparent was around 0.18 g H 2 O · g -1 dw (-26.5 MPa). Total protein was extracted and separated by 2D electrophoresis from fresh seeds (0.28 g H 2 O · g -1 dw), mild dried seeds (0.25 g H 2 O · g -1 dw) and seeds at low water content (0.10 g H 2 O · g -1 dw) before and after imbibition for 10 days. The proteome profile revealed the presence of 588 spots on each silver stained gel, from which 21 showed differential expression, correlated with desiccation and germination, by increased or decreased expression. After MS/MS sequencing, three protein spots produced spectra that matched to a Magnolia salicifolia legumin precursor. Results suggested an involvement of this protein in the events taking place during the drying and subsequent imbibitions of the dried seeds. Key words: desiccation tolerance, forest seed, legumin, proteomics
Isolation and identification of cultivable lactic acid bacteria in traditional fermented milk of Tibet in China

One hundred and seventy-one strains of lactic acid bacteria were isolated from 44 traditional fermented milk samples from different region of Tibet. Among these samples, the concentrations of lactic acid bacteria varied from 105to 109colony forming unit/mL. The ratio of rod bacteria (71.3%) was higher than that of cocci (28.7%), and was considered to be the major population. Lactobacillus fermentum (31%) and Lactobacillus casei (28%) were the most predominant species among all these isolates. This study systematically analysed the microbial composition of traditional fermented milk in China, which may become a valuable source for further starter selection.
Fork formation and other signs of osteophagia on a long bone swallowed by a red deer stag (Cervus elaphus)

A right anterior cannon bone (os metacarpale 3 + 4) of a red deer that was found in the reticulum of a 7-year-old red deer stag is described. The bone, which had accidentally been swallowed by the stag, showed clear signs of bone chewing (osteophagia), the most prominent being the formation of a fork at its distal end. Knowledge of the possible bone changes brought about by ruminant osteophagia may prevent the erroneous interpretation of skeletal remains as being worked by hominids.
Adult Cardiac Sca-1-positive Cells Differentiate into Beating Cardiomyocytes*

Although somatic stem cells have been reported to exist in various adult organs, there have been few reports concerning stem cells in the heart. We here demonstrate that Sca-1-positive (Sca-1+) cells in adult hearts have some of the features of stem cells. Sca-1+ cells were isolated from adult murine hearts by a magnetic cell sorting system and cultured on gelatin-coated dishes. A fraction of Sca-1+ cells stuck to the culture dish and proliferated slowly. When treated with oxytocin, Sca-1+ cells expressed genes of cardiac transcription factors and contractile proteins and showed sarcomeric structure and spontaneous beating. Isoproterenol treatment increased the beating rate, which was accompanied by the intracellular Ca2+ transients. The cardiac Sca-1+ cells expressed oxytocin receptor mRNA, and the expression was up-regulated after oxytocin treatment. Some of the Sca-1+ cells expressed alkaline phosphatase after osteogenic induction and were stained with Oil-Red O after adipogenic induction. These results suggest that Sca-1+ cells in the adult murine heart have potential as stem cells and may contribute to the regeneration of injured hearts.
Survival and Straying of Auke Creek, Alaska, Pink Salmon Marked with Coded Wire Tags and Thermally Induced Otolith Marks

Abstract Pink salmon Oncorhynchus gorbuscha fry from Auke Creek, Alaska, were marked with coded wire tags (CWTs) and, in some cases, thermally induced otolith marks, to investigate the effects of the CWT process on survival and straying. Pink salmon from Gastineau Hatchery that had been thermally marked provided a point of comparison. Marked fish were also used to estimate the natal composition of fish in nearby streams and at Auke Creek and Gastineau Hatchery. The survival of fish with both CWTs and thermal marks was significantly lower than that of fish with thermal marks alone but not significantly different from that of fish with CWTs alone. No effect of CWTs on straying was detected. The estimated straying rates were 4.4% and 6.7% for early-run and late-run Auke Creek fish, respectively, and 6.9% for Gastineau Hatchery fish. The observed straying and run composition estimates indicated a large-scale interchange of adult pink salmon among local streams, which may promote rapid colonization and recover.
Inhibition of Nitric-oxide Synthase-I (NOS-I)-dependent Nitric Oxide Production by Lipopolysaccharide plus Interferon-γ Is Mediated by Arachidonic Acid

Previous results have indicated that lipopolysaccharide (LPS) plus interferon-γ (IFNγ) inhibits nitric-oxide synthase (NOS)-I activity in glial cells. We report here that arachidonic acid (AA) plays a pivotal role in this response, which was consistently reproduced in different glial cell lines and in primary rat astrocytes. This notion was established using pharmacological inhibitors of phospholipase A2 (PLA2), cytosolic PLA2 (cPLA2) antisense oligonucleotides, and AA add-back experiments. This approach not only allowed the demonstration that AA promotes inhibition of NOS-I activity but also produced novel experimental evidence that LPS/IFNγ itself is a potential stimulus for NOS-I. Indeed, LPS/IFNγ fails to generate nitric oxide (NO) via NOS-I activation simply because it activates the AA-dependent signal that impedes NOS-I activity. Otherwise, LPS/IFNγ promotes NO formation, sensitive to exogenous AA, in cells in which cPLA2 is pharmacologically inhibited or genetically depleted. Because NO suppresses the NFκB-dependent NOS-II expression, inactivation of NOS-I by the LPS/IFNγ-induced AA pathway provides optimal conditions for NFκB activation and subsequent NOS-II expression. Inhibition of cPLA2 activity, while reducing the availability of AA, consistently inhibited NFκB activation and NOS-II mRNA induction and delayed NO formation. These responses were promptly reestablished by addition of exogenous AA. Finally, we have demonstrated that the LPS/IFNγ-dependent tyrosine phosphorylation of NOS-I and inhibition of its activity are mediated by endogenous AA.
Bioenergetics Model for Larval and Juvenile Walleyes: An in Situ Approach with Experimental Ponds

Abstract We used an in situ approach to redefine allometric parameters of consumption and metabolism in a percid bioenergetics model for young-of-year (age-0) walleyes Stizostedion vitreum (0.0021–0.8237 g wet weight; 8–49 mm total length) in ponds across a range of densities (10–50 fish·m–3). Of three methods used to estimate evacuation rates, only the one based on whole-gut fullness of larvae and stomach fullness of juveniles in food-free enclosures proved reliable, The intercepts for allometry of maximum consumption and resting metabolism for age-0 walleyes were higher than the intercepts for adults; however, slopes of age-0 and adult allometry were similar. Activity costs (ACT = ratio of active metabolism to resting metabolism) for age-0 walleyes varied across body weights and with fish density; patterns of activity costs at different fish densities reflected patterns of food availability. Activity and p-values (proportion of maximum consumption realized) were correlated with powers of zooplankton bio.
Bird and mammal conservation in Gaoligongshan Region and Jingdong County, Yunnan, China: patterns of species richness and nature reserves

Abstract Elevational and latitudinal patterns of species richness for birds and mammals were compared with human population density in relation to nature reserve designation in two areas of Yunnan Province, China. Results suggest that species richness is not the same for the two areas. In Gaoligongshan Region, species richness is inversely correlated with elevation and altitude, while reserve designation is positively correlated with elevation and latitude. In Jingdong County, reserve designations are positively correlated with elevation, but species richness shows no clear trends. In general, the present situation is strongly influenced by human activities. It appears that reserve designation is mismatched with species richness in Gaoligongshan Region, while there is a better fit between the two in Jingdong County. In both areas, however, it appeared that reserves were located primarily in order to reduce conflict with humans rather than to maximize conservation of biodiversity, probably because humans were responsible for forest—especially primary forest—destruction and degradation in the low-lying areas.
Temperature and salinity tolerance of juvenile Rhabdosargus holubi [Steindachner (Teleostei: Sparidae)]

Temperature and salinity tolerances of juvenile Rhabdosargus holubi (Steindachner) were determined experimentally. Results indicated that they are tolerant over a wide range of salinities (0.7–70‰) and temperatures (10–30°C) and that little interaction between temperature and salinity occurs. R. holubi is restricted to the warm temperate waters of southeastern Africa. It is absent from the subtropical Indian Ocean and from temperate Atlantic Ocean waters. The juveniles occur mainly in the inshore waters and estuaries. Evidence from tolerance experiments and salinity and temperature data from southern African estuaries suggested that the distribution of R. holubi is controlled by temperature.
PPARβ regulates vitamin A metabolism-related gene expression in hepatic stellate cells undergoing activation Published, JLR Papers in Press, November 16, 2002. DOI 10.1194/jlr.M200376-JLR200

Activation of cultured hepatic stellate cells correlated with an enhanced expression of proteins involved in uptake and storage of fatty acids (FA translocase CD36, Acyl-CoA synthetase 2) and retinol (cellular retinol binding protein type I, CRBP-I; lecithin:retinol acyltransferases, LRAT). The increased expression of CRBP-I and LRAT during hepatic stellate cells activation, both involved in retinol esterification, was in contrast with the simultaneous depletion of their typical lipid-vitamin A (vitA) reserves. Since hepatic stellate cells express high levels of peroxisome proliferator activated receptor β (PPARβ), which become further induced during transition into the activated phenotype, we investigated the potential role of PPARβ in the regulation of these changes. Administration of L165041, a PPARβ-specific agonist, further induced the expression of CD36, B-FABP, CRBP-I, and LRAT, whereas their expression was inhibited by antisense PPARβ mRNA. PPARβ-RXR dimers bound to CRBP-I promoter sequences. Our observations suggest that PPARβ regulates the expression of these genes, and thus could play an important role in vitA storage. In vivo, we observed a striking association between the enhanced expression of PPARβ and CRBP-I in activated myofibroblast-like hepatic stellate cells and the manifestation of vitA autofluorescent droplets in the fibrotic septa after injury with CCl4 or CCl4 in combination with retinol.
Human Cytosolic 3α-Hydroxysteroid Dehydrogenases of the Aldo-keto Reductase Superfamily Display Significant 3β-Hydroxysteroid Dehydrogenase Activity

The source of NADPH-dependent cytosolic 3β-hydroxysteroid dehydrogenase (3β-HSD) activity is unknown to date. This important reaction leads e.g. to the reduction of the potent androgen 5α-dihydrotestosterone (DHT) into inactive 3β-androstanediol (3β-Diol). Four human cytosolic aldo-keto reductases (AKR1C1–AKR1C4) are known to act as non-positional-specific 3α-/17β-/20α-HSDs. We now demonstrate that AKR1Cs catalyze the reduction of DHT into both 3α- and 3β-Diol (established by 1H NMR spectroscopy). The rates of 3α- versus 3β-Diol formation varied significantly among the isoforms, but with each enzyme both activities were equally inhibited by the nonsteroidal anti-inflammatory drug flufenamic acid. In vitro, AKR1Cs also expressed substantial 3α[17β]-hydroxysteroid oxidase activity with 3α-Diol as the substrate. However, in contrast to the 3-ketosteroid reductase activity of the enzymes, their hydroxysteroid oxidase activity was potently inhibited by low micromolar concentrations of the opposing cofactor (NADPH). This indicates that in vivo all AKR1Cs will preferentially work as reductases. Human hepatoma (HepG2) cells (which lack 3β-HSD/Δ5–4 ketosteroid isomerase mRNA expression, but express AKR1C1–AKR1C3) were able to convert DHT into 3α- and 3β-Diol. This conversion was inhibited by flufenamic acid establishing the in vivo significance of the 3α/3β-HSD activities of the AKR1C enzymes. Molecular docking simulations using available crystal structures of AKR1C1 and AKR1C2 demonstrated how 3α/3β-HSD activities are achieved. The observation that AKR1Cs are a source of 3β-tetrahydrosteroids is of physiological significance because: (i) the formation of 3β-Diol (in contrast to 3α-Diol) is virtually irreversible, (ii) 3β-Diol is a pro-apoptotic ligand for estrogen receptor β, and (iii) 3β-tetrahydrosteroids act as γ-aminobutyric acid type A receptor antagonists.
People, species richness and human population growth

Aim To investigate how the magnitude of conservation conflicts arising from positive relationships between human population size and species richness is altered during a period of marked human population growth (2% year − 1 ). Location South Africa. Methods Anuran and avian species richness were calculated from atlas distribution maps, and human population was measured in 1996 and 2001, all at a quarter-degree resolution. We investigated the relationships between human population size in, and its change during, these two periods and environmental energy availability. We then investigated the nature of relationships between species richness and human population size in both time periods, and its change during them; these analyses were conducted both with and without taking environmental energy availability into account. Finally, we investigated the nature of the relationships between human population size, and its change, and the proportion of protected land. Analyses were conducted both without and with taking spatial autocorrelation into account; the latter was achieved using mixed models that fitted a spatial covariance structure to the data. Results Change in human population size between 1996 and 2001 exhibited marked spatial variation, with both large increases and decreases, but was poorly correlated with environmental energy availability. The nature of the relationship between human population size and environmental energy availability did not, however, exhibit statistically significant differences regardless of whether the former was measured in 1996 or 2001. Similarly, relationships between species richness and human population size did not exhibit significant differences between the two periods. The strengths of the species‐ human relationships were markedly reduced when energy availability was taken into account. Change in human population size was poorly correlated with species richness. The proportion of protected land was negatively, albeit rather weakly, correlated with human population size in 1996 and 2001, and with its change between these two periods. Main conclusions Positive species‐human relationships arise largely, but not entirely, because both species richness and human population size exhibit similar responses to environmental energy availability. During a period of rapid human population growth, and marked changes in the spatial variation in human population size, positive correlations remained between human population size and both anuran and avian species richness. The slope of these correlations did not, however, alter, and the most species-rich areas are not those with the largest increases in human population. Despite marked population growth, the magnitude of conservation conflicts arising from positive species‐human relationships thus appears to have remained largely unchanged.
Transpiration Response of Maize Hybrids to Atmospheric Vapour Pressure Deficit

Maize (Zea mays L.) yield is often restricted by low soil water availability, particularly late in the growing season. To increase yields, genetic options for more effective use of available soil water are being explored. One option is to select genotypes that have restricted transpiration rate under high vapour pressure deficit (VPD) conditions so that soil water is conserved for use later in the growing season. While genetic variation for this trait has been identified within several crop species, such variation has never been explored in maize. The objective of this study was to examine transpiration rate of 35 single-cross hybrids to determine whether hybrids can be identified that express limited transpiration under high VPD. Two sets of experiments were undertaken in which plants were exposed to a range of VPD in chambers. A two-phase transpiration response was observed in 11 hybrids in which there was a threshold VPD above which transpiration rate was restricted. The VPD threshold varied from 1.7 to 2.5 kPa among these hybrids. Eight hybrids were included in both sets of experiments, and the same results were obtained in both experiments, indicating that expression of the trait was consistent.
Root growth and nitrogen uptake of carrot, early cabbage, onion and lettuce following a range of green manures

An experiment was performed to study the significance of rooting depth of four vegetable crops on their utilization of green manure nitrogen (N). Rates of rooting depth development were estimated as approximately 0.2, 0.7, 1.2 and 1.2 mm day °C−1 for onion, carrot, lettuce and cabbage, respectively. At harvest, onion and lettuce were found to be shallow‐rooted with final rooting depths of only 0.3 and 0.6 m, respectively, whereas carrot and cabbage reached rooting depths of at least 1.1 m. The two deep‐rooted vegetables increased their N uptake by 46, 24 and 7 kg N ha−1 when following winter‐hardy legumes, non‐hardy legumes and rye, respectively; the equivalent responses by the two shallow‐rooted crops were 23, 9 and 15 kg N ha−1, respectively. Thus the deep‐rooted crops used the legume N more efficiently but the shallow‐rooted crops made better use of N left by the non‐legume rye crop. These interactions between green manure type and vegetable crop N response are the result of the dual effects of the green manures: biological N fixation by the legumes, and the variable ability of the green manure crops to concentrate available N in the topsoil. Before shallow‐rooted crops, the ability of rye to concentrate N in the topsoil may be as important as the N fixing ability of legumes.
Establishing and managing switchgrass as an energy crop.

When it was first adopted as a crop, switchgrass was evaluated and improved for forage uses; but it has more recently been extensively studied as an energy crop, where its biomass might be used as feedstock for bioenergy. Of the two morphological forms or cytotypes of switchgrass, the lowland cultivars tend to produce more biomass; but upland cultivars are generally of more northern origin and more cold tolerant and therefore are usually preferred in the North. Attention to weed control, planting date, planting depth, and seed dormancy can greatly increase establishment success with this species. Stands of switchgrass should be harvested no more than twice per year, and one cutting often provides as much biomass as two. Harvesting after aboveground biomass has senesced can aid persistence, facilitate harvest operations, conserve N, and improve feedstock quality; but other harvest patterns may provide a better fit in some situations. If its biology is properly taken into consideration, switchgrass can offer great potential as an energy crop. Reference: Parrish, D. J., Fike, J. H. , Bransby, D. I. , and Samson, R. 2008. Establishing and managing switchgrass as an energy crop. Online. Forage and Grazinglands doi:10.1094/FG-20080220-01-RV.
Economic and social impacts of organic production systems

Given relatively low adoption levels to date, the potential benefits of organic farming systems are not yet very visible. However, there is growing evidence in the literature that adoption of such systems produces multiple environmental, social, and financial benefits that can solve pressing agricultural problems in Canada. Compared with their duration as conventional operations, most organic farms in North America perform better under organic management. This outcome is usually a product of lower input costs, more diversified production and marketing channels, resilience in the face of variable market conditions, higher premiums, and a better capacity to adapt to weather extremes. However, the performance of farming systems including some horticultural and animal production systems, for which our ecological understanding is limited, is still frequently inferior. The data on social impacts are less conclusive, but there is some evidence that when a community has many sustainable (including organic) produc.
Phylogenetic analysis and differentiation of Veronica subgenus Stenocarpon in the Balkan Peninsula

The Balkan Peninsula is considered the most important refugium for species during the Pleistocene glaciations and today harbours c. 2000 endemic species, but we know surprisingly little about the evolution of taxa in this region. Veronica saturejoides, V. thessalica and V. erinoides are a group of closely related alpine taxa endemic to the Balkan Peninsula. Here, we analyse four DNA regions [the nuclear chalcone synthase intron (CHSi) and ribosomal internal transcribed spacer (ITS) region and the plastid rpoB-trnC spacer and trnL-trnL-trnF region] and amplified fragment length polymorphism (AFLP) fingerprints to provide a phylogenetic hypothesis for the relationships among these taxa. Additionally, we analyse leaf morphological characters used to distinguish the three subspecies of V. saturejoides. The analyses support the distinction of the three subspecies based on previously intuitively suggested characters. Nuclear chalcone synthase intron data indicate that the southern taxa are genetically much more diverse than the more northern V. saturejoides subsp. saturejoides. Phylogenetic relationships inferred from this region and AFLP fingerprints support the monophyly of V. saturejoides. In contrast, plastid DNA regions suggest a closer relationship of V. saturejoides subsp. saturejoides to V. thessalica. The most likely scenario involves introgression into V. saturejoides subsp. saturejoides from V. thessalica. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159, 616‐636. ADDITIONAL KEYWORDS: amplified fragment length polymorphism (AFLP) ‐ chalcone synthase intron ‐ glacial refugia ‐ internal transcribed spacer (ITS) ‐ leaf morphology ‐ phylogeography ‐ rpoB-trnC spacer ‐ trnL-trnL-trnF-region.