Miracle-dz/UniFAR-FTUs huggingface dataset:
Elucidation of the primary structure of the lantibiotic epilancin K7 from Staphylococcus epidermidis K7. Cloning and characterisation of the epilancin-K7-encoding gene and NMR analysis of mature epilancin K7.

Lantibiotics are bacteriocins that contain unusual amino acids such as lanthionines and alpha, beta-didehydro residues generated by posttranslational modification of a ribosomally synthesized precursor protein. The structural gene encoding the novel lantibiotic epilancin K7 from Staphylococcus epidermidis K7 was cloned and its nucleotide sequence was determined. The gene, which was named elkA, codes for a 55-residue preprotein, consisting of an N-terminal 24-residue leader peptide, and a C-terminal 31-residue propeptide which is posttranslationally modified and processed to yield mature epilancin K7. In common with the type-A lantibiotics nisin A and nisin Z, subtilin, epidermin, gallidermin and Pep5, pre-epilancin K7 has a so-called class-Al leader peptide. Downstream and upstream of the elkA gene, the starts of two open-reading-frames, named elkP and elkT, were identified. The elkP and elkT genes presumably encode a leader peptidase and a translocator protein, respectively, which may be involved in the processing and export of epilancin K7. The amino acid sequence of the unmodified pro-epilancin K7, deduced from the elkA gene sequence, is in full agreement with the amino acid sequence of mature epilancin K7, determined previously by means of NMR spectroscopy [van de Kamp, M. , Horstink, L. M. , van den Hooven, M. W. , Konings, R. N. M. , Hilbers, C. W. , Sahl, H. -G. , Metzger, J. W. & van de Ven, F. J. M. (1995) Eur. J. Biochem. 227, 757-771]. The first residue of mature epilancin K7 appears to be modified in a way that has not been described for any other lantibiotic so far. NMR experiments show that the elkA-encoded serine residue at position +1 of pro-epilancin K7 is modified to a 2-hydroxypropionyl residue in the mature protein.
Configurations in Graphs of Large Minimum Degree, Connectivity, or Chromatic Number

Wagner [42] proved that a graph of large chromatic number contains a subgraph that can be contracted into a large complete graph. Modifying Wagner's proof, Dirac [lo] and Jung [17] proved that, for every natural number k there exists a natural number f , ( k ) such that every graph G of chromatic number at leastf,(k) contains a subdivision of the complete graph K, . These results have inspired several investigations on configurations, in particular, paths, cycles, and subdivision, in graphs or digraphs of large minimum degree, connectivity, or chromatic number. In the undirected case there is a richness of such results, while one very quickly encounters unsolved questions, counterexamples, and NP-complete problems in the directed case. Reference [39] gives a survey of these results and problems, and in the present paper we indicate more possible directions in this area. We also consider infinite graphs. In particular, we give a short proof of the recent result of Thomas [30] that the tree-width (to be defined later) of an infinite graph (of finite tree-width) is the maximum of the tree-widths of its finite subgraphs. Combined with results of Robertson and Seymour [ZS] this proves the conjecture of the author [38], as pointed out by Seese and Nesetril and Seymour (private communication) that every infinite graph of sufficiently large connectivity has a subgraph that is contractible to any prescribed finite planar graph.
Meat and carcass quality in two pig lines of different stress-susceptibility genotype and their crosses.

In order to investigate differences in carcass and meat quality between lines of different stress susceptibility, 150 pigs were slaughtered on 15 slaughter days, consisting of equal numbers of stress-susceptible (nn) pigs of a boar line, stress-resistant (NN) pigs of a sow line and stress-carrier (Nn) crosses of these two lines. Carcass quality was determined by a SKGII-device which combined four physical measurements into a carcass lean estimate and a conformation score, and meat quality traits were measured on the carcass and on a loin slice. Killing-out proportion was lower for the NN line compared with the Nn crosses and the nn line. Lean content increased and conformation score improved as the number of n alleles in the respective genotypes increased but the Nn genotype was closer to the nn genotype than to the NNgenotype. Similarly, a large difference in meat quality was found between the NN and the nn line, whereas the difference in meat quality between the Nn and the nn genotype was smaller than expected. This was probably due to the low-voltage stunning procedure. In addition, the method of transporting the pigs to the abattoir (by truck or by foot, for a distance 125 m) had a pronounced effect on meat quality in the loin.
Forecasting plant community impacts of climate variability and change: when do competitive interactions matter?

1. A change in a climate variable may alter a species’ abundance not only through a direct effect on that species’ vital rates, but also through ‘indirect’ effects mediated by species interactions. While recent work has highlighted cases in which indirect effects overwhelm the direct effects of climate, we lack robust generalizations to predict the strength of indirect effects.
Overexpression of Glucose-6-phosphate Dehydrogenase (G6PD) in NIH 3T3 Cells Enhances Cell Proliferation

Glucose-6-phosphate dehydrogenase (G6PD) functions to catalyze the first step in the pentose phosphate pathway. The major physiological function of G6PD is to provide NADPH, which is required for reductive biosynthesis and for detoxification of free radicals and peroxides in mature red blood cells. We previously showed that overexpression of human G6PD in NIH3T3 cells may alter the cellular redox status by enhancing intracellular NADPH and GSH levels (Kuo and Tang, 1998a). In this report, we provide evidence that an increase in G6PD activity is important for cell proliferation. To investigate the role of G6PD in cell growth, we stably transfected human G6PD cDNA into NIH 3T3 cells. Two G6PD-overexpressing clones which had a 6-fold (H6) and a 16-fold (H7) increase, respectively, in their intracellular G6PD activity were compared with control cells transfected with a vector alone. Overexpression of G6PD promoted cell growth at both low (0.5%) and high (10%) serum conditions. When treated with dihydroepiandrosterone (DHEA), a potent G6PD inhibitor, stimulated cell growth in G6PD-overexpressing cells was significantly suppressed. Furthermore, cells expressing high levels of human G6PD were able to grow to a higher cell density and proliferated in a low serum concentration, which are characteristicws of transformed phenotypes. These results show that G6PD activity is important not only in modulating intracellular redox status, but also in regulating cell proliferation.
Sucrose accumulation in sugarcane stalks does not limit photosynthesis and biomass production

Until now raw sugar has been the predominant commodity produced from sugarcane (Saccharum spp. hybrids) with the exception of Brazil where fermentable sugars are used to produce ethanol. Worldwide interest in renewable energy has focussed attention on total biomass production of ‘energy canes’ rather than sucrose yield alone. Clones selected for biomass tend to have high fibre contents derived from the wild type, S. spontaneum. It is possible that high fibre genotypes can produce higher biomass yields than high sucrose types due to feedback on photosynthesis either by sucrose or sucrose signalling compounds as proposed in several recent publications on feedback responses in sugarcane leaves. Up to 20 sugarcane clones with either high fibre or high sucrose content were grown in one field and three pot experiments to elucidate some of the processes from source to sink that could be responsible for high rates of biomass accumulation expected in high fibre clones. We were particularly interested in the possibility that clones with high sucrose content may have reduced photosynthesis as sucrose levels increased in upper internodes due to feedback mechanisms. Photosynthesis of whole plants and of single leaves decreased with crop development as much as 60% in some cases. Maintenance of photosynthesis was not associated with low content of sugars in leaves or in internodes. Sink strength for sucrose storage in the upper internodes was strong in both high fibre and high sucrose clones despite plants being grown for 12 months in conditions controlled to achieve high sucrose contents. Our data supported previous conclusions about localised feedback on photosynthesis by sugars accumulating in the leaf resulting in reduced photosynthesis of small segments of individual young leaves. However, whole-plant photosynthesis did not decline through the day indicating that older leaves may compensate for reduced photosynthesis in younger leaves in the afternoon. While photosynthesis declined with crop age and sucrose content increased we found no evidence to suggest that photosynthesis declined because sucrose content increased. An increase in biomass yield through breeding and selection may not necessarily result in reduced sucrose content and increased fibre content.
Use of Various Ratios of Extruded Fullfat Soybean Meal and Dehulled Solvent Extracted Soybean Meal in Broiler Diets

A study was conducted in which whole unextracted soybeans were processed by passing the beans through a roller mill and then extruding without steam. The processed beans were then included into nutritionally adequate broiler diets, replacing solvent extracted soybean meal in ratios of 0/100, 25/75, 50/50, and 0/100 % with dietary energy levels of 3200, 3300, and 3400 ME kcal/kg. This resulted in a 3 x 4 factorial arrangement of treatments. Each treatment was fed to six replicate pens of 60 male chicks of a commercial broiler strain from 1 to 42 days of age. The results of the study demonstrate that the inclusion of extruded fullfat soybean in a pelleted broiler diet supported chick performance equal or superior to that of dehulled solvent extracted soybean meal, and that extruded soybeans could partially or completely replace soybean meal without any adverse effects on body weight, feed conversion, mortality, dressing percentage, or abdominal fat content provided the diets are nutritionally balanced.
Phylogeny and classification of Eucalyptus subgenus Eudesmia (Myrtaceae) based on nuclear ribosomal DNA, chloroplast DNA and morphology

Phylogenetic analysis of Eucalyptus subgenus Eudesmia is presented on the basis of the following three datasets: sequences of the internal transcribed spacer (ITS) and the external transcribed spacer (ETS) regions from nuclear rDNA, sequences of the psbA–trnH intergenic spacer region from chloroplast DNA, and morphological characters, including stamen bundling, operculum development, seeds and trichomes. Studies of floral development were essential for understanding the morphology of mature flowers and interpretation of synapomorphy and homoplasy. A summary phylogeny was constructed from a maximum parsimony analysis of those nodes coded as characters that had support in the molecular trees together with morphological characters. A revised infra-subgeneric classification is presented on the basis of the summary phylogeny, and compared with classifications of Hill and Johnson (1998) and Brooker (2000). Differences relate to relationships between clades and taxonomic rank (sections, series and subseries) and valid names of Brooker (2000) are conserved where possible. One main clade of 14 species (section Limbatae), many of mallee growth form, was found in all analyses; this clade is distributed in the South-West of Western Australia and adjacent Interzone and desert areas. A second main clade (section Complanatae) occurs in the northern and eastern tropical and subtropical regions of Australia, including Kimberley, Arnhem, Queensland and New South Wales. This section includes E. tetrodonta, previously treated as an isolated taxon in a monotypic section; however, this species is related to E. baileyana, E. similis, E. lirata and series Miniatae. The hypothesised phylogeny provides a framework for further analyses of biogeography and ecology, including functional traits.
Increasing ocean temperature reduces the metabolic performance and swimming ability of coral reef damselfishes

Tropical coral reef teleosts are exclusively ectotherms and their capacity for physical and physiological performance is therefore directly influenced by ambient temperature. This study examined the effect of increased water temperature to 3 °C above ambient on the swimming and metabolic performance of 10 species of damselfishes (Pomacentridae) representing evolutionary lineages from two subfamilies and four genera. Five distinct performance measures were tested: (a) maximum swimming speed (Ucrit), (b) gait‐transition speed (the speed at which they change from strictly pectoral to pectoral‐and‐caudal swimming, Up−c), (c) maximum aerobic metabolic rate (MO2−MAX), (d) resting metabolic rate (MO2−REST), and (e) aerobic scope (ratio of MO2−MAX to MO2−REST, ASC). Relative to the control (29 °C), increased temperature (32 °C) had a significant negative effect across all performance measures examined, with the magnitude of the effect varying greatly among closely related species and genera. Specifically, five species spanning three genera (Dascyllus, Neopomacentrus and Pomacentrus) showed severe reductions in swimming performance with Ucrit reduced in these species by 21.3–27.9% and Up−c by 32.6–51.3%. Furthermore, five species spanning all four genera showed significant reductions in metabolic performance with aerobic scope reduced by 24.3–64.9%. Comparisons of remaining performance capacities with field conditions indicate that 32 °C water temperatures will leave multiple species with less swimming capacity than required to overcome the water flows commonly found in their respective coral reef habitats. Consequently, unless adaptation is possible, significant loss of species may occur if ocean warming of ≥3 °C arises.
Metabolism and resources of spherical colonies of Nostoc zetterstedtii

Constraints imposed by the spherical form and gelatinous matrix of centimeter‐thick colonies of the cyanobacterium Nostoc zetterstedtii on its functional properties were tested by examining the scaling of its composition, light absorption, photosynthesis, and respiration to individual size. In three summer experiments with colonies collected from the bottom of oligotrophic lakes of low inorganic carbon concentrations (dissolved inorganic C, DIC), metabolism and pigment density of colonies were scaled to their surface area as most algal filaments were confined to a 2‐mm‐thick outer shell. Nostoc absorbed 96% of incident light from the surface to the center because of high areal pigment density, but absorbed photons were used with low quantum efficiency (11–38 mmol O2 mol−1 photon) and photosynthesis was low relative to dark respiration (2.0–5.4). Therefore, N. zetterstedtii is threatened by reduced light availability and only extended to lake depths receiving about 12% of surface irradiance, whereas mosses, characeans, and angiosperms with thin photosynthetic tissues grew deeper (3.1–7.5% of surface irradiance). Nostoc ameliorated the restrictions of low lake DIC and long diffusion paths by active transport that could extract most external DIC, accumulate DIC in the colony 150–fold above external concentrations, and retain respiratory CO2. The energy cost of solute transport and gel formation in Nostoc colonies and extensive self shading restrict their potential growth, whereas colony formation should prevent grazing and increase longevity and nutrient recirculation. Nostoc zetterstedtii has become one of rarest freshwater macroalgae because of widespread lake eutrophication reducing water transparency and increasing competition from taller and faster‐growing stands of filamentous algae and higher plants.
Chemosensory signals in stream habitats: implications for ecological interactions

Abstract The combination of varying aquatic habitats and flow regimes creates a complex stimulus environment from which sensory information can be extracted. Previous studies with crayfish in artificial stream settings have shown that altering the temporal and spatial structure of an odor plume modifies orientation behavior. Exposure to more temporally complex odor signals enables crayfish to locate food more efficiently. To link these studies to a more natural setting, we examined how odor signals are dispersed in 3 physically different habitats within the Maple River in Pellston, Michigan, USA, by simultaneously measuring flow patterns and odor plume characteristics. These microhabitats consisted of sections of the stream with gravel, transition (gravel and sand), or sand substrate. Flow measurements were taken using an Acoustic Doppler Velocimeter while simultaneous in situ odor plume measurements were made with an Epsilon electrochemical system. Flow had more turbulent energy in gravel and transition habitats than in sand habitat. Mean velocity was significantly higher in gravel (67.8 ± 2.00 cm/s) than in transition (30.5 ± 0.46 cm/s) and sand (30.6 ± 0.27 cm/s) habitats. In addition, eddy diffusivity rates were higher in gravel (173.3 cm2/s3) than in sand (9.74 cm2/s3) and transition (129.7 cm2/s3) habitats. Differences in turbulent flow profoundly affected the fine-scale distribution of the chemical signal. The concentration of dopamine tracer in odor pulses was significantly lower in sand (range: 8.1–6.9 µmol/L) and transition (range: 26.2–8.9 µmol/L) habitats than in gravel (range: 46.5–5.39 µmol/L) habitat. Background (natural) concentrations of dopamine are undetectable with our current technology. Furthermore, spectral density of odor pulses showed larger fluctuations in chemical concentration at all frequencies (0.1–10 Hz) in gravel habitat than in sand or transition habitats. Our results illustrate the dynamic nature of turbulence structure within natural stream systems and its influence on the distribution of chemical odor signals. Our results provide evidence that natural stream settings influence both the distribution and concentration of chemical odors available for ecological and behavioral interactions. The combination of turbulence and odor plume variation creates habitat-specific information that influences orientation behavior of organisms within a river.
Monitoreo de la ictiofauna usando grupos taxonómicos superiores en el Parque Nacional Cabo Pulmo, México

The uses of biological indicators allow to save time, resources and staff efforts when monitoring programs are conducted. The reef fishes are among the species with biggest potential as indicators since they are conspicuous, easy to identify in the field and have ecological and economical importance. The objective of this study was to evaluate the usefulness of higher taxa to predict fish ecological indices in Cabo Pulmo reef. We generated multiple stepwise regression equations with species abundance data grouped at genera and family levels as factors, and using ecological indices (H', J', delta*) as dependent variables. To test the efficiency of the models, the expected indexes were compared with those observed in the field during independent test surveys. Results showed that all models were highly significant, and the best fit occurred at genus level to H', while those used for delta*, based on family data level, were less precise. The proportion of variables required to apply prediction models of any ecological index never exceeded 41% of the total taxa (genera or families). In conclusion, the use of regression methods to determine higher taxa indicators is adequate and represents a good potential to be used in monitoring programs. In addition, the use of genera and families as indicators provide logistic benefits as training for monitors is less intense and expensive. Finally, the use of expected-observed comparisons to measure the quality of the evaluations can be useful for managers in order to interpret and communicate results of the scientific endeavors to the society, so they in turn can participate and help to improve and facilitate long-term monitoring at Cabo Pulmo National Park.
Occurrence and Abundance of Epiphytic Cyanolichens in Protected Areas of Nova Scotia, Canada

Epiphytic cyanolichens occurrence and abundance was recorded in thirteen Wilderness Areas and one Nature Reserve in Nova Scotia, Canada. Twenty-one species were found. Very common species include those in the genus Lobaria, as well as Collema subflaccidum, Leptogium cyanescens and Parmeliella triptophylla. Uncommon species include Collema furfuraceum, Collema nigrescens, Nephroma bellum and Pseudocyphellaria crocata. Rare species are Coccocarpia palmicola, Degelia plumbea, Erioderma pedicellatum, Leptogium corticola, Leptogium laceroides, Leptogium saturninum, Nephroma laevigatum, Nephroma helveticum, Pannaria conoplea, Pseudocyphellaria perpetua and Sticta fuliginosa.
The nervous system of a pilidium larva: evidence from electron microscope reconstructions

The principal ultrastructural features of a pilidium larva from Friday Harbor (pilidium A, unidentified as to species) are summarized and, based on electron microscope reconstructions, the larval nervous system is described for the first time. Ciliary effectors in the larva include the marginal ciliary band, which is drawn out to form a small accessory ridge at each of the junctions between lobes, and a pair of suboral (buccal) ridges, one on either side of the stomodeum, that run between the mouth and marginal band. The nervous system consists of a small intratrochal nerve supplying the marginal band, an oral nerve that encircles the mouth at the junction of stomodeum and stomach, and a pair of nerves connecting these that run beneath the suboral ridges. The nerve fibres appear to arise from uniciliate cells in the marginal band and the suboral region. The organization, innervation, and behavior of pilidium A are discussed briefly with reference to Muller's larva, a related larva with a similar type of t.
A 420 Kb Deletion within the Minimum Critical Region of the 15q24 Microdeletion Syndrome in a Female Infant

Recurrent deletions of the chromosomal region 15q24 have recently been identified as the underlying cause of a novel microdeletion syndrome. A recent study comparing patients with 15q24 deletions of variable size defined a minimum critical deletion region of 1.7 Mb. The corresponding clinical phenotype includes intellectual disability, developmental delay, muscle hypotonia, dysmorphic facial features, skeletal anomalies, cardiac defects, and male genital anomalies. To date, 34 patients with a 15q24 deletion based on array CGH have been reported in the medical literature. Little is known about the genotype phenotype correlation for this genomic region. Case Report: We report a female newborn infant with a 420 Kb deletion within the reported 1.7 Mb critical region of the 15q24 deletion that was identified by array CGH. The infant had tetralogy of Fallot and dysmorphic facial features including a flat nasal bridge, hypertelorism, retro- and micrognathia. The 420 Kb deletion included 11 known genes: COMMD4, NEIL1, MIR631, MAN2C1, SIN3A, PTPN9, SNUPN, IMP3, SNX33, CSPG4, and ODF3L1. The 420 Kb deletion defines the minimum critical region of the 15q24 microdeletion syndrome. Conclusion: Thirty-one of 35 reported patients including the patient presented here, were classified phenotypically according to breakpoints and size. Haplo-insufficiency of the genes in the minimum region may contribute to the clinical phenotype observed in affected patients.