Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting molecular markers of development and regeneration through integrative analysis of high-throughput genomics data

In biology and medicine, the expression of particular gene transcripts and proteins is often used to identify particular cell types, developmental states, or pathogenic states to which they are unique. In this context, such transcripts and proteins are termed molecular markers. Molecular markers are indispensable in many facets of scientific research and can ultimately be used to reveal the biology behind their functions as such. However, in many cases, knowledge of which markers are ideal for a given task is still an elusive goal. In particular, developmental and stem cell research strongly relies on both protein and nucleotide molecular markers for numerous aspects as cell state and identity is very important in these fields. To identify protein-coding transcripts which may indicate novel stem cell marker proteins, a database of heterogeneous murine stem cell microarray data was analyzed using a novel clustering method. Analysis of transcripts enriched in markers demarcating undifferentiated and differentiated cells revealed that aggregate functions could be defined for markers of differentiated cells, but not for those in undifferentiated cells. In addition, the results indicated that genes expressed in mammalian stem cells and their immediate derivatives have common ancestors in the sea urchin, suggesting that mechanisms governing mammalian stem cells were established very early in evolution. To identify novel non-coding RNA markers in a muscle system, a ncRNA prediction approach enabling the detection of longer ncRNAs was used to identify miRNA containing sites in the mouse genome. The use of EST data was determined to improve ncRNA prediction strategies during the development of this method by evaluating the performance of miRNA prediction by combining information regarding
SPM-1 in Europe -Lactamase β First Report of the Metallo-

El S al a bi, Allaa e d din, Tole m a n, M a rk Alexa n d e r Ho w a r d ORCID: h t t p s://o rcid.o rg/00 0 0-0 0 0 2-9 4 9 7-0 5 1 2, Weeks, Janis Lesley, Bru d e r er, T. , F r ei, R. a n d Walsh, Timot hy Ru tla n d ORCID: h t t p s://o rcid.o r g/00 0 0-0 0 0 3-4 3 1 5-4 0 9 6 2 0 0 9. Fi r s t r e po r t of t h e m e t allolac t a m a s e S P M-1 in E u ro p e. Antimic robial β Age n t s a n d Ch e mot h e r a py 5 4 (1) , p . 5 8 2. 1 0.11 2 8/AAC.007 1 9-0 9 file
Identification of Teas Cultivated in Eastern, Southeastern and Southern Asia Based on Nucleotide Sequence Comparison of Ribulose 1,5-bisphosphate Carboxylase Large-subunit of Chloroplast DNA and 18S Ribosomal RNA of Nuclear DNA

Nucleotide sequences of the ribulose 1,5-bisphosphate carboxylase large-subunit (rbcL) in chloroplast (cp) DNA and 18S ribosomal RNA encoded in nuclear DNA (nuclear-encoded 18S-rRNA) were determined to clarify genetic diversity among cultivated teas. The nucleotide sequence alignment of rbcL in cpDNA enabled the taxonomic distinction of the section Thea. On the basis of these data, the rbcL nucleotide sequences of 195 cultivated teas in the Asian region were classified. The cultivated teas are separated into five groups: CSs type (var. sinensis), CSa type (var. assamica), type CSaa (like var. assamica), CIt type of C. irrawadiensis, and CTa type of C. taliensis. All the cultivated teas from the East Asia (China, Korea, and Japan) region were of the CSs type, whereas the cultivated teas from Bangladesh, Laos, Sri Lanka and Thailand were CSa type. The cultivated teas from India were separated into CSs and CSa types. The rbcL nucleotide sequences of the teas currently cultivated in Yunnan, China were CSa and CIt types, and the teas of Vietnam were CSa, CSs and CIt types. On the other hand, the teas cultivated in Myanmar included all types of CSs, CSa, CSaa, CIt and CTa. In addition, differences in nucleotide sequences were observed at three positions in 870 nuclear-encoded 18S-rRNA nucleotide sequences. The different nucleotide sequences of nuclear-encoded 18S-rRNA distinguished C. sinensis (var. sinensis and var. assamica) from wild tea species. Similarly, almost all cultivars tested were divided into the Cs type of C. sinensis (var. sinensis and var. assamica) and Cw type of wild tea species by alignment of nuclear-encoded 18S-rRNA nucleotide sequences, with an interspecific hybrid between C. sinensis and C. taliensis identified in a region of Myanmar. Analysis of genetic relationships indicated that many teas cultivated in the Myanmar region differ from the tea groups of East and South Asia. Our data indicated that the endemically cultivated teas in parts of Myanmar are conservationally important as new sources of desirable teas for future breeding programs and improvement of tea products.
Isostrength Comparison of Large‐Strain (Fracture) Rheological Properties of Egg White and Whey Protein Gels

The effects of protein concentration and heating conditions on the physical properties of whey protein isolate (WPI) (in 50 mM NaCl, pH 7) and egg white (pH 9) gels were examined. Egg white and WPI gels had similar values for shear stress at fracture (i.e., isostrength), while trends for shear strain at fracture were protein-type specific. The rigidity ratio (R 0.3 ), ratio of the rigidity at fracture (G f ) to the rigidity at 30% of fracture strain, measured departure from the stress-strain relationship of an ideal Hookean solid. All gels fit master curves of G f vs R 0.3 , which were described by a power law model of R 0.3 =A(G f ) -0.19 , where A showed protein type-specific characteristics.
Polymorphism and association of microsatellite SJ01 with birth weight and early growth traits in pigs

Myostatin is a negative regulator of animal skeletal muscle development and SJ01 is a microsatellite locus flanking porcine myostatin gene. In the present study, the polymorphism of microsatellite SJ01 in three pig populations, that is, Duroc (n = 420), Yorkshire (n = 414) and Landrace (n = 119), were investigated, and its associations with birth weight and early growth traits were analyzed. The results indicated that genotype BB was predominant in Yorkshire pigs and allele B was predominant in both Yorkshire and Landrace pigs, whereas allele A was more prevalent in Duroc pigs. Among the three pig breeds, Duroc population had the highest heterozygosity and deviated from Hardy-Weinberg equilibrium (P < 0.05). The average daily gain from 28 d to 70 d in Yorkshire pigs and the body weight at 70 d in Landrace pigs were significantly different between SJ01 genotypes (P < 0.05). These results suggest that microsatellite SJ01 is a potential DNA marker for early growth trait selection in Yorkshire and Landrace pigs as well as for refining QTL for early growth traits on SSC15.
Effects of low concentrations of O3, leaf age and water stress on leaf diffusive conductance and water use efficiency in soybean

Peter B. Reich, Anna W. Schoettle and Robert G, AmundsonReich, P. B. , Schoettle, A. W. & Amundson, R. G. 1985. Effects of low con-centrations of O3, leaf age and water stress on leaf diffusive conductance and wateruse efficiency in soybean. - Physiol. Plant. 63: 5&-64.Ozone, leaf age and water stress each affected leaf conductance in soybean [Glycinemax (L.) Merr. Hodgson], but there were no mteractions among these factors. Expo-sure to increased concentrations of O, (0.01, 0.05, 0.09. aod 0.13 nl 1"') resulted inlinear declines in abaxial and adaxial conductances io leaves of all ages. There wereno differences in relative response to O3 between the two leaf surfaces. For well-wa-tered plants, water use efficiency also decreased with exposure to increased O, coo-ceotrations (water-stressed plants were not tested). Abaxial conductance increased asleaves aged from 4 to 10 days and then declioed with further aging. Adaxial con-ductance decreased with all increases in leaf age beyond 4 days, and the ratio ofabaxial/adaxial conductance increased continuously throughout the leaf lifespan.During water-stress cycles (water withheld for 2-3 days) leaves of water-stressedplants had tower conductances than those from well-watered plants, and there was nodifference in relative response between abaxial and adaxial stomata.Additional key words - Abaxial, adaxial, stomata.P. B. Reich (reprint requests), et al., Bovce Thompson Institute for Flam Research,Cornell Univ. Ithaca, NY 14S53 USA.Introduction
Gauging the impact of fishing mortality on non-target species

The most obvious effect of fishing on non-target species is direct mortality. To quantify this effect on the vulnerability of species requires measurement of the current fishing mortality rate and of the tolerance of the species to fishing mortality. These are difficult to estimate for the little-studied non-target species. We describe two potential methods for estimating current fishing mortality rate when data are limited. Their application is illustrated for dab (Limanda limanda) and grey gurnard (Eutrigula gurnardus), two common non-target species in the North Sea. We also develop approaches to define tolerance levels for fishing mortality for little-studied and rare species, based on the potential jeopardy level: the fishing mortality that causes a reduction in spawning stock biomass per recruit relative to the unexploited situation. We propose that for non-target species, models founded on basic knowledge of life history parameters, and on generally established relationships between these parameters, may offer the only practical approach.
Haemocytic Parasitosis in the farmed oyster Tiostrea chilensis

The present study was carried out in Chiloe island (Chile) in a period between late autumn and early summer in 1997. From a total of 167 specimens histologically analysed, there were two oysters with a haemocytic hyperplasic response in the mantle, gills and digestive gland. The parasited haemocytes contain in the citoplasm a variable number of spherically shapped parasites similar to the protozoan Bonamia. The genus Bonamia has been described in Tiostrea chilensis from aquaculture farms in New Zealand, which indicates the susceptibility of the Chilean oyster to this parasite. In the present study, an haemocytic parasitosis is histopathologically described from T. chilensis specimens cultivated in the area surrounding Chiloe, Chile.
Survival in the alpine landscape : genetic, demographic and reproductive strategies of the rare monocarpic perennial "Campanula thyrsoides" in the Swiss Alps

Campanula thyrsoides is one of the few monocarpic perennials in the Swiss Alps. Genetic connectivity among populations of this species is impeded due to the heterogeneity of the alpine environment and consequently, a significant pattern of decreasing population relatedness with increasing geographic distance can be found. The comparison with two other alpine species studied at the same spatial scale showed that the potential for long-distance seed dispersal does not necessarily translate into increased population similarity. The results further suggest that other life-history traits, especially the breeding system, may play an important role in genetic diversity partitioning. These findings corresponds well with the current knowledge about determinants of genetic diversity in plant populations. The molecular study also corroborates the theory on glacial refugia in the European Alps by delimiting two prominent areas of post-glacial plant migration. A very comforting result is the high amount of genetic diversity that can be found even in small populations such that the short-term adaptive potential of Campanula thyrsoides is assured. Demographic analysis of two populations revealed that survival and growth are the most important determinants of population persistence. C. thyrsoides seems to follow an evolutionary stable flowering strategy which is characterized by an optimal size-dependent flowering threshold. Age at reproduction varied largely in this species and such a pronounced generation overlap efficiently buffers environmental variability. Simulation approaches further showed that C. thyrsoides is most likely micrositelimited and consequently has a large potential for population growth. In general, this study confirms the findings of similar investigations and the novel combination of methods applied have proven powerful to study in depth the important demographic parameters of a long-lived alpine plant, potentially facilitating future research. The pollination experiment established firm proof for an obligatory outcrossing breeding system in C. thyrsoides which does not break down as flowers age. The study also demonstrated the minimal risk of population decline as a result of inbreeding depression. From the three studies summarized above and the information accumulated in the general life-history analysis I conclude that C. thyrsoides is well adapted to the variability of the alpine environment, that the genetic and demographic requirements for short-term adaptive capacity and long-term evolutionary potential of this species is assured and that no specific conservation measures have to be taken for this naturally rare species.
Diversity and Abundance of Plants with Flowers and Fruits from October 2001 to September 2002 in Paucarillo Reserve, Northeastern Amazon, Peru

En el presente trabajo damos a conocer la diversidad de fl oracion y fructifi cacion observada du- rante un ano de estudio fenologico en la Reserva de Paucarillo (noroeste de la Amazonia Peruana 3°41’ S, 72°24’ W). Registramos un total de 270 especies en 59 familias, de las cuales el 57% son representadas solamente por 1 individuo. Las Arecaceae y Rubiaceae fueron las familias dominantes en este sitio.
A SYSTEM ESTABLISHING COMPATIBILITY PROFILES FOR ARTIFICIAL OXYGEN CARRIERS AND OTHER SUBSTANCES

Worldwide, great efforts are being made to develop a clinically useful artificial oxygen carrier. Toxicological and immunological compatibility is generally tested using animal experiments but inflammatory parameters in particular show large species-specific differences. Therefore, we developed an in vitro system using human components to establish a compatibility profile of unknown compounds. The test system comprises induction of hemolysis, activation of complement (C3a), induction/suppression of cytokine production, influence on cell proliferation, direct toxicity on peripheral leukocytes, and phagocytosis of the material under test and of microbes. The test system will be described, along with results of various perfluorocarbon emulsions. When testing lecithin-based perfluorodecalin (PFD) emulsions, and comparing them to Pluronic-based PFD emulsions, we could show that Pluronic-based emulsions were virtually untoxic to peripheral human leukocytes. They neither inhibited cell proliferation nor caused any hemolysis, but caused mild to moderate inhibition of endotoxin-induced cytokine production. At the same time, lecithin-based PFD emulsion caused substantial cytotoxicity in phagocytic cells like monocytes (60–100% after 24 h incubation) and granulocytes (10–20% after 24 h incubation). They also suppressed endotoxin-induced cytokine production in monocytes to more than 98% and inhibited cell proliferation of an endothelial (ECV 304) and a monocytic cell line (MonoMac6) to more than 95%.
Use of Biotechnology to Improve the Tolerance in Rice (Oryza sativa) to Drought Stress

Abiotic stress factors are the main limitations to plant growth and yield inagriculture. Among them, drought stress, which is caused by water deficit, is probablythe most impacting adverse condition and the most widely encounter Rice (Oryza SativaL.) is one of the most important cereal crops that provides a staple diet for almost half ofthe world’s population. However, rice yield and quality are affected by environmentalstress. Drought is one of the most common environmental stresses affecting rice growthand productivity. There’s the possible development of biotechnological tools to addressthe critical problems of crop improvement for a sustainable agriculture. Among theavailable biotechnological tools, the in-vitro culture alone or combined with mutagenesis,which are induced with physicochemical or biological agents by using (PEG) can beexploited to increase genetic variability and mutants, as a potential source of newcommercial cultivars, in-vitro culture environments . Following this, it is preferred thatthere are more studies on finding the varieties of rice tolerant to drought stress by usingbiotechnological in order to reduce the risk of abiotic stress, which is the most importantstresses of drought on agriculture and rice production.
RANDOM DENDROGRAMS AND NULL HYPOTHESES IN CLADISTIC BIOGEOGRAPHY

Simberloff et al. (1981, pages 40-63 in Vicariance biogeography: A critique (G. Nelson and D. E. Rosen, eds.), Columbia Univ. Press, New York) proposed three different sampling distributions of trees for testing cladistic biogeographic hypotheses. Two of these distributions involved sampling from a uniform distribution of cladograms (either labeled or unlabeled), whereas the third distribution was calculated by a simple Markovian model. This paper presents a proof that the third distribution of cladograms is identical to the uniform distribution of dendrograms (rooted trees with internal nodes ranked). Hence, all three sampling distributions are uniform distributions that differ solely in the kind of tree being sampled. The paper concludes by suggesting ways of constructing nonuniform tree distributions. (Biogeography; cladistics; dendrograms; null hypotheses; random trees.)
A cohesion/tension model for the gating of aquaporins allows estimation of water channel pore volumes in Chara

The water permeability (hydraulic conductivity; Lp) of turgid, intact internodes of Chara corallina decreased exponentially as the concentration of osmolytes applied in the medium increased. Membranes were permeable to osmolytes and therefore they could be applied on both sides of the plasma membrane at concentrations of up to 2.0 m (5.0 MPa of osmotic pressure). Organic solutes of different molecular size (molecular weight, MW) and reflection coefficients (σs) were used [heavy water HDO, MW: 19, σs: 0.004; acetone, MW: 58, σs: 0.15; dimethyl formamide (DMF), MW: 73, σs: 0.76; ethylene glycol monomethyl ether (EGMME), MW: 76, σs: 0.59; diethylene glycol monomethyl ether (DEGMME), MW: 120, σs: 0.78 and triethylene glycol monoethyl ether (TEGMEE), MW: 178, σs: 0.80]. The larger the molecular size of the osmolyte, the more efficient it was in reducing cell Lp at a given concentration. The residual cell Lp decreased with increasing size of osmolytes. The findings are in agreement with a cohesion/tension model of the osmotic dehydration of water channels (aquaporins; AQPs), which predicts both reversible exponential dehydration curves and the dependence on the size of osmolytes which are more or less excluded from AQPs (Ye, Wiera & Steudle, Journal of Experimental Botany 55, 449–461, 2004). In the presence of big osmolytes, dehydration curves were best described by the sum of two exponentials (as predicted from the theory in the presence of two different types of AQPs with differing pore diameters and volumes). AQPs with big diameters could not be closed in the presence of osmolytes of small molecular size, even at very high concentrations. The cohesion/tension theory allowed pore volumes of AQPs to be evaluated, which was 2.3 ± 0.2 nm3 for the narrow pore and between 5.5 ± 0.8 and 6.1 ± 0.8 nm3 for the wider pores. The existence of different types of pores was also evident from differences in the residual Lp. Alternatively, pore volumes were estimated from ratios between osmotic (Pf) and diffusional (Pd) water flow, yielding the number of water molecules (N) in the pores. N-values ranged between 35 and 60, which referred to volumes of 0.51 and 0.88 nm3/pore. Values of pore volumes obtained by either method were bigger than those reported in the literature for other AQPs. Absolute values of pore volumes and differences obtained by the two methods are discussed in terms of an inclusion of mouth parts of AQPs during osmotic dehydration. It is concluded that the mouth part contributed to the absolute values of pore volumes depending on the size of osmolytes. However, this can not explain the finding of the existence of two different types or groups of AQPs in the plasma membrane of Chara.
Snail species identification by RFLP-PCR and designing of species-specific oligonucleotide primers

To enforce labeling regulations in the authentication of snail species it might be of importance to use nonmorphological methods. Snail meat of 2 species was analyzed by restriction fragment length polymorphism (RFLP) of the genes encoding mitochondrial 12S rRNA and 16S rRNA. Digestion of the polymerase chain reaction (PCR) products of 12S rRNA with the endonucleases Afi III, Dra I and Sty I, and the 16S rRNA PCR product with the endonucleases Nsp I, Sfu I and Taq I, yielded specific banding patterns characteristic for Helix pomatia and Helix lucorum. The meat of both species could additionally be differentiated with species-specific oligonucleotide primers based on 16S rRNA gene sequences characteristic for both species. Pour renforcer les normes d'etiquettage dans l'authentification des especes d'escargots, des methodes non morphologiques peuvent etre utiles. Cette etude evalue des methodes RFLP-PCR (polymorphisme de longueur de fragment de restriction - reaction en chaine par polymerase) pour l'identification et la differenciation de Helix pomatia et H. lucorum. L'analyse est basee sur 3 regions d'ADN mitochondrial dans le gene rRNA 12S, rRNA 16S et le cytochrome b. Les amorces specifiques a l'espece dans le gene rRNA 16S sont determinees et evaluees.
Collaboration among countries in marine conservation can achieve substantial efficiencies

Multinational collaboration is important for successfully protecting marine environments. However, few studies have assessed the costs and benefits incurred by taking collaborative action. One of the most complex marine regions in the world is the Mediterranean Sea biodiversity hotspot. The sea is shared by over 20 countries across three continents with a vast array of socio‐economic and political backgrounds. We aimed to examine how collaboration between countries of the Mediterranean Sea affects conservation plans when costs and threats are considered.
Determinants of Yield Gap in Small-scale Apple Farms in Balochistan, Pakistan

Amid declining yield of apple (Malus domestica) in Balochistan, this study analyzed yield gaps of commonly grown varieties ‘Katja’ (Malus domestica ’Katy’) and Red Delicious (Malus domestica ‘Borkh’) grown at experimental station and in farmers’ fields using data collected through a survey of 181 officially designated small farmers in Mastung district in Balochistan, Pakistan. The average actual yields of commonly grown Katja and Red Delicious apple in farmers’ fields were below one-third of the experimental station yields, leading to an average experimental-station based yield gap (YGE) of about 14,593 and 15,942 kg hectare−1, respectively. A significant variation in the yields of both varieties was also found within farmers’ fields. The average yield gaps between the model-farmer (farmer with highest yield) and common farmer yields (YGM) were 4960 and 7288 kg hectare−1 for Katja and Red Delicious, respectively. Yield gap indexes (YGI) were also developed to calculate yield variability between experimental station and current farmers’ yield (YGIE), and also within farmers’ yield variability (YGIM). The mean YGIE was 69.3%, whereas the mean YGIM was 46.5%, indicating the possibility of increasing yield by 53.5%. Farmer’s experience in apple farming, household labor force size, tree density, soil suitability, weed management, access to credit and extension services, and attendance of training on apple farming had significantly influenced apple yield gap. Landholding size and contract apple marketing system were other factors significantly expanding the yield gap. Addressing constraints to farmers’ access to yield-improving resources and farm management would be a vital step towards significant productivity improvements in apple farming.