Miracle-dz/UniFAR-FTUs huggingface dataset:
Local adaptation and effect of host genotype on the rate of pathogen evolution: an experimental test in a plant pathosystem

Abstract Virulence is thought to be a driving force in host–pathogen coevolution. Theoretical models suggest that virulence is an unavoidable consequence of pathogens evolving towards a high rate of intrahost reproduction. These models predict a positive correlation between the reproductive fitness of a pathogen and its level of virulence. Theoretical models also suggest that the demography and genetic structure of a host population can influence the evolution of virulence. If evolution occurs faster in pathogen populations than in host populations, the predicted result is local adaptation of the pathogen population. In our studies, we used a combination of molecular and physiological markers to test these hypotheses in an agricultural system. We isolated five strains of the fungal pathogen Mycosphaerella graminicola from each of two wheat cultivars that differed in their level of resistance to this pathogen. Each of the 10 fungal strains had distinct genotypes as indicated by different DNA fingerprints. These fungal strains were re‐inoculated onto the same two host cultivars in a field experiment and their genotype frequencies were monitored over several generations of asexual reproduction. We also measured the virulence of these 10 fungal strains and correlated it to the reproductive fitness of each fungal strain. We found that host genotypes had a strong impact on the dynamics of the pathogen populations. The pathogen population collected from the moderately resistant cultivar Madsen showed greater stability, higher genotype diversity, and smaller selection coefficients than the pathogen populations collected from the susceptible cultivar Stephens or a mixture of the two host cultivars. The pathogen collection from the mixed host population was midway between the two pure lines for most parameters measured. Our results also revealed that the measures of reproductive fitness and virulence of a pathogen strain were not always correlated. The pathogen strains varied in their patterns of local adaptation, ranging from locally adapted to locally maladapted.
Assessing the risk of invasive success in Pinus and Banksia in South African mountain fynbos

South African mountain fynbos has been severely invaded by trees and shrubs introduced from other mediterranean-climate regions. Management of these invasions should involve controlling current invaders and screening future introductions. Invasion windows are described and functional groups are defined for pines based on life history attributes important for invasion in the fire-prone mountain fynbos. The most successful invasive pines here (Pinus halepensis, P. pinaster and P. radiata) are fire-resilient and have small seeds, low seed-wing loadings, short juvenile periods, moderate to high degrees of serotiny and relatively poor fire-tolerance as adults. Other species with these attributes, especially from mediterranean-climate regions, wouldbe high-risk introductions. Taxa in other functional groups have not become major weeds even with widespread man-aided dissemination. Experience with pine invaders was used to define functional groups in western Australian Banksia species (Proteaceae), shrubs and trees which include taxa with similar attributes to fynbos invaders (e.g. Hakea and Pinus spp.). Banksias have only recently been introduced to the Cape, and are likely to be increasingly cultivated for the cut flower market. Tall serotinous shrubs with many small seeds per plant, short juvenile periods and low fire tolerance were identified as high risk introductions. This group includes thicket-forming species which maintain very large viable seed banks, e.g. Banksia burdettii, B. hookeriana and B. leptophylla. Low sprouting shrubs with few large seeds per plant and long juvenile periods are unlikely to become invasive in mountain fynbos. The approach of defining functional groups based on life history attributes and invasion windows is valuable for predicting the probability of invasive success. Chance interactions suchas an opportunistic dispersal mutualism between Pinus pinea and an introduced squirrel sometimes confound these predictions and underscore the idiosyncracies inherent in biological invasions.
Possibilities to improve the antioxidative capacity of beer by optimized hopping regimes

Different hopping regimes were evaluated to investigate the effect on the oxidative stability of wort and beer. Compared with a single hop dosage at the beginning of wort boil, it was possible to increase the concentration of α-acids in pitching wort and beer by applying incremental hop dosage, dry hopping or the use of a pre-isomerized hop product in combination with an α-acid extract, which concomitantly resulted in lower iron concentrations and an enhanced flavour stability as indicated by standard wort and beer analyses, atomic absorption spectroscopy, electron spin resonance spectroscopy and sensory analysis of fresh and force-aged beers. The functional principle of hop dosage variations is explained by saving of α-acids throughout the wort production process, which yields an increased formation and precipitation of pro-oxidative acting transition metal ions (e.g. Fe) in α-acid-complexes during the whirlpool rest and fermentation. Consequently, fewer reactive oxygen species are generated. Additional laboratory trials simulating wort cooling and beer storage in buffered model solutions proved that un-isomerized α-acids are strong iron chelators and confirmed the functional principle of the applied hopping regimes. Negative effects of higher α-acid contents on fermentation performance and depletion of the zinc concentration, which is an essential nutrient for yeast, could be excluded. Copyright © 2014 The Institute of Brewing & Distilling
Functional Proteomics in Silico : Putative Protein Interaction Analysis

During the past few years, protein interaction networks of some viral, prokaryotic and eukaryotic species have been established gradually. The proteome of those organisms were used as alignment templates to identify novel genes in different species. Many studies also support that the functional related proteins of different species were regulated in similar mechanism, suggested the evolutionarily conserved strategies among living organisms, including yeast, worm, fly and human. Accumulated sequences of genome projects lead us to extend our interests in uncovering genes in a comparative scope. We have developing sophisticated and integrated tools for constructing database of putative interlogs based on known protein interaction networks by comparative proteomic studies. Interlogs signify interacting proteins from one species whose homologous proteins from another species also interact. Through visualized presentation in web-based interface, it will be easy to realize the interactions of protein network. And following the web links, more details of interested proteins will be shown. This database can provide candidates for further high-throughput screening experiments and also can map regulatory and metabolic pathways for analysis of gene expression.
Disruption of Transforming Growth Factor-β Signaling in ELF β-Spectrin-Deficient Mice

Disruption of the adaptor protein ELF, a β-spectrin, leads to disruption of transforming growth factor–β (TGF-β) signaling by Smad proteins in mice. Elf −/− mice exhibit a phenotype similar tosmad2 +/−/smad3 +/−mutant mice of midgestational death due to gastrointestinal, liver, neural, and heart defects. We show that TGF-β triggers phosphorylation and association of ELF with Smad3 and Smad4, followed by nuclear translocation. ELF deficiency results in mislocalization of Smad3 and Smad4 and loss of the TGF-β–dependent transcriptional response, which could be rescued by overexpression of the COOH-terminal region of ELF. This study reveals an unexpected molecular link between a major dynamic scaffolding protein and a key signaling pathway.
Litter and soil arthropod colonization in reforested semi‐deciduous seasonal Atlantic forests

The recovery of soil ecological processes during the restoration of tropical forests is greatly influenced by arthropods that live in the litter and soil. However, these communities present complex dynamics, and their colonization patterns are not well understood. In this study, we examined the response patterns of litter and soil arthropods to the ecosystem regeneration process by assessing reforestation sites from two regions of São Paulo State, Brazil, and we compared the data obtained from these sites with data from mature forests. We assessed the arthropod communities using similarity indices and high‐level taxa abundance, with the level of forest succession and the locations of the restoration areas as factors. Forest succession correlated with the species composition as communities from the reforestation sites gradually became more similar to communities from the mature forests, while their quantitative patterns were minimally related. Forest maturation positively affected the richness of the litter community and the abundance of some minor groups, such as Protura, Diplura, and Symphyla. The region influenced the species composition but did not influence the manner in which the communities changed during the maturation process. We also found a convergent soil colonization pattern as arthropod communities from different sites became more similar during forest succession. This finding is consistent with both empirical data and theoretical predictions from the specialized literature, although the subject has been poorly explored until now. We conclude that reforestation allows the colonization of soil and litter fauna in a biased manner.
Plasmid Profiling of Japanese Flavobacterium psychrophilum Isolates

Abstract Flavobacterium psychrophilum is the causative agent of bacterial coldwater disease and rainbow trout fry syndrome in salmonids, cyprinids, and ayu Plecoglossus altivelis. To investigate genetic variability of this bacterium, plasmid profiling analysis was undertaken in 104 isolates of F. psychrophilum from Japan (n = 92), Europe (n = 9) and the USA (n = 3). Plasmids were isolated by a simple and inexpensive procedure using silica particles and then analyzed by agarose gel electrophoresis. Seventy-two of 104 isolates (69.2%) possessed plasmids, which were distributed at 2.8 kilobases (kb) (n = 33), 3.4 kb (n = 15), 4.1 kb (n = 23), and 5.2 kb (n = 1). The type strain of F. psychrophilum possessed a 2.8-kb plasmid, and a 3.4-kb plasmid was found mainly in isolates from rainbow trout O. mykiss. The 4.1-kb and 5.2-kb plasmids were found in Japanese isolates. Although the functions of these plasmids remain cryptic, no plasmids were associated with antibiotic resistance to ampicillin, sodium nifurstyre.
Funktionelle Analyse von komplexen Hepatitis-B-Virus-Varianten, assoziiert mit Leberzirrhose bei Immunsupprimierten

deutsch) Obwohl der Wildtyp des Hepatitis-B-Virus (HBV) nicht zytopathogen und die Pathogenese der Hepatitis B generell immunvermittelt ist, können in immunsupprimierten Nierentransplantatempfängern mit chronischer Hepatitis B schwere Leberschäden bis hin zu Leberzirrhose und Leberversagen entstehen. Die Entwicklung von Leberzirrhose in den Nierentransplantierten ist assoziiert mit der Akkumulation und Persistenz von komplexen HBV-Varianten mit Mutationen im Core-Promotor / X-Gen, Deletionen im Core (C)-Gen und teilweise zusätzlichen Deletionen im präS-Bereich. Dies lässt eine Rolle der Varianten in der speziellen Pathogenese bei Immunsupprimierten vermuten. In der vorliegenden Arbeit wurden funktionelle Analysen der komplexen Varianten im Vergleich zu ReferenzWildtypgenomen und Wildtyp-ähnlichen Genomen der Patienten aus der frühen Infektionsphase durchgeführt, um Hinweise auf den potentiellen Beitrag der Varianten zur Pathogenese zu erlangen. Die Analysen erfolgten durch transiente Transfektion der humanen Hepatomazelllinie HuH7 mit repräsentativen HBV-Gesamtgenomen, die aus 2 Patienten während des Krankheitsverlaufs von einer asymptomatischen Infektion hin zur Leberzirrhose isoliert und kloniert worden waren. Trotz einiger Unterschiede im Detail wiesen die komplexen Varianten einen gemeinsamen, drastisch vom Wildtyp abweichenden Phänotyp auf. Dieser war gekennzeichnet durch eine veränderte Transkription mit reduzierten präCund Oberflächen-mRNAs und verstärkter Expression der prägenomischen RNA, eine starke Reduktion des häufigsten Spleißprodukts der prägenomischen RNA, SP1, eine extrem reduzierte oder fehlende Expression und/oder Sekretion aller Oberflächenproteine und des HBeAg, ein verändertes intrazelluläres Verteilungsmuster des schwach exprimierten CoreProteins und teilweise der Oberflächenproteine sowie eine erhöhte Replikation und Anreicherung gegenüber Wildtyp-HBV aufgrund einer verstärkten reversen Transkription der prägenomischen RNA. Dieser Phänotyp basierte zum Teil auf den Mutationen in CorePromotor und C-Gen, wurde jedoch deutlich durch zusätzliche Mutationen in den übrigen Genomabschnitten beeinflusst. Die vielfältigen Veränderungen der Varianten unterstützen ihren vermuteten Beitrag zur Pathogenese.
Assignment1 of β-centractin (CTRN2) to human chromosome 2 bands q11.1→q11.2 with somatic cell hybrids and in situ hybridization

The centractins are a group of actin-related proteins that comprise the majority of the mass of the dynactin complex, a regulator of cytoplasmic dynein-mediated functions (Schroer, 1996). Centractins are F50% identical to actin at the amino acid level and 170% similar. Centractins are highly conserved molecules and multiple isoforms of centractin (Arp1) are known to exist, including ·, ß, and Á. The · and ß isoforms are expressed in a wide variety of similar tissues, but the ß-isoform is expressed at a much lower level than the ·-isoform (Clark et al., 1994). Arp1-Á appears to be more tissue-specific and restricted to the heart, lung, and skeletal muscle (Clark et al., 1994). Utilizing two separate methods, we report the chromosome location of ß-centractin, Arp1-ß (gene symbol CTRN2).
Ecological response surfaces for North American boreal tree species and their use in forest classification

Empirical ecological response surfaces were derived for eight dominant tree species in the boreal forest region of Canada. Stepwise logistic regression was used to model species dominance as a response to five climatic predictor variables. The predictor variables (annual snowfall, degree-days, absolute minimum temperature, annual soil moisture deficit, and actual evapotranspiration summed over the summer months) influence the response of plants more directly than the annual or monthly measures of temperature and precipitation commonly used in response surface modeling. The response surfaces provided estimates of the probability of species dominance across the spatial extent of North America with a high degree of success. Much of the variation in the probability of dominance is apparently related to the species' individualistic response to climatic constraints within different airmass regions. A forest type classification for the Canadian boreal forest region was derived by a cluster analysis based on the probability estimates. Five major forest types were distinguished by the application of a stopping rule. The predicted forest types showed a high degree of geographic correspondence with the distribution of forest types in the actual vegetation mosaic. The distribution of the predicted types also bears a direct relationship to seasonal airmass dynamics in the boreal forest region.
Molecular genetic analysis of abruptio placentae

Abruptio placentae is the premature separation of the normally implanted placenta from the uterine wall, resulting in haemorrhage before delivery of the fetus. This has serious maternal and neonatal implications, and is one of the leading causes of perinatal and maternal mortality and morbidity in South Africa. Placental vasculopathies, such as abruptio placentae, are believed to result from faults occurring in early placental development. Placental protein 13 (PP13) is a member of the pregnancy-related protein family, and is believed to function in a number of important physiological processes such as trophoblast invasion, placentation and implantation. The aim of this study was to investigate whether DNA sequence variants in the LGALS13 gene (encoding PP13), underlie and/or confer susceptibility to abruptio placentae. The gene was screened and genotyped in a cohort of patients whose pregnancies were complicated by abruptio placentae, as well as an ethnically matched control cohort. Statistical and in silico analyses were performed in order to identify potential susceptibility factors in this South African cohort and to predict whether the identified variants may impact on gene expression or the structure and function of PP13. In addition, the luciferase reporter gene assay was employed to investigate the functionality of the -98A/C variant identified in the 5’ untranslated region of the LGALS13 gene. Statistically significant differences were observed between patient and control groups at the following loci in the Coloured population: -98A/C, IVS2 -36G/A, IVS2 -22A/G and the hotspot variant in exon 3 (p<0.05). These variants could represent a susceptibility profile of this population or alternatively have implications in the pathogenesis of abruptio placentae. The deletion of a single thymine in exon 3 was shown to result in truncation of PP13 and subsequent disruption of a number of cysteine residues and putative phosphorylation sites, which could impact on dimerization and ultimately, the function of the protein. The reporter gene assay revealed a significant reduction (p=0.004) in luciferase activity by the -98 C allele.
Salinity-resistant plant growth promoting rhizobacteria ameliorates sodium chloride stress on tomato plants

Abstract Salinity is one of the major anthropogenic as well as environmental stresses that reduce plant growth. Results show that even after being adapted up to 6% sodium chloride (NaCl) concentration, all selected isolates were able to solubilize phosphate, and produce phytohormones, siderophores and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase enzyme. NT1 was found to exhibit the highest phosphate solubilization zones (25 mm), siderophore production (1000 µg ml−1) as well as ACC deaminase production (50 µMmg−1h−1) potential under laboratory conditions. On the other hand, pot studies conducted on tomato plants under 2% NaCl stress proved that C4 and T15 were the best growth promoters. C4 showed 50% enhancement in root and shoot length as compared to NaCl added untreated plants as well as in absence of NaCl. C4 also enhanced salinity tolerance in plants with the lowest uptake of NaCl thereby reducing the salt stress on plants. C5 enhanced biomass production in tomato plants with increased uptake of the salts by plants, thereby reducing the salt concentration in the soil. The study thus shows that the selected isolates can be used for the plant growth promotion of plants under salinity stress.
Targeted photosensitizer nanoconjugates based on human serum albumin selectively kill tumor cells upon photo-irradiation

A photosensitizer (Chlorin e6, Ce6) nanoconjugate based on human serum albumin (HSA) was designed and prepared for tumor cell targeted photodynamic therapy. The resulting nanoconjugates consisted of multiple cyclic Arg–Gly–Asp–D-Tyr–Cys peptides (cRGD) and about 5.4 Ce6 on each HSA molecule (RGD–HSA–Ce6). RGD–HSA–Ce6 exhibited small size with a mean diameter of 31.1 nm and negative charge with −15.9 mV. Due to the incorporation of targeting moiety, RGD–HSA–Ce6 could be specifically recognized by αvβ3 integrin overexpressed tumor cells, as well as internalized into late endosomes and lysosomes efficiently. In addition, RGD–HSA–Ce6 exhibited low dark toxicity in both tumor and normal cell lines. Upon photo-irradiation, RGD–HSA–Ce6 exhibited high phototoxicity against αvβ3 integrin overexpressed A375 melanoma cells, indicating the considerable potential for effective photodynamic therapy. Combined with the low phototoxicity to normal fibroblast 3T3 cells, RGD–HSA–Ce6 developed in this study may provide an effective tool for targeted photodynamic therapy to tumor cells.
A cold-inducible modifier QTL affecting fertility restoration of WA CMS in rice

populations of cross Neda-A X IR36, was studied in normal and cold conditions by means of QTL method. In cold condition the number of fertile plants was reduced in favor of sterility. The distributions of individuals in pollen fertility suggested that fertility restoration was mainly controlled by major genes. The population cultivated in normal conditions showed a 15 (F): 1(S) ratio; however, the one cultivated in cold condition deviated from 15 (F): 1(S) ratio, in which 2 QTLs were detected. The obtained results showed that one major QTL (qRf-1-1) localized on the short arm of 1st chromosome near RFLP marker RG140 and the other one (qRf-1-2) localized on the same chromosome between RM7180 and RM6100d. The detected QTLs explained 62 and 44% of the total variation of the trait, respectively. The minor QTL (qFer1-2) is expected to be a cold - inducible modifier QTL for fertility restoration. Key words:
A Twin-head “V” High-wire Greenhouse Cucumber Production System for Reducing Crop Start-up Costs

A high-wire system, in which the plant is trained into a single stem, is gaining popularity in year-round greenhouse cucumber (Cucumis sativus) production, especially with supplemental lighting, as it allows for uniform foliar and light distribution and higher yield and quality. However, this system requires much higher plant densities than the conventional umbrella system, resulting in increased crop start-up costs. A technique for raising twin-head transplants and a twin-head “V” high-wire cucumber system were developed to address this issue. The twin-head transplants were raised by topping the seedlings after the appearance of the fourth true leaf and then two strong lateral shoots were allowed to develop and be trained into a “V” system after planting. The twin-head system achieved similar plant growth and fruit yield as the conventional single-head system on two long English seedless cucumber cultivars (Bodega and Myrthos) and two breeding lines (2005A and 24–119) tested over 2 years. The twin-head system also improved the fruit grades in ‘Bodega’ by increasing the percentage of fruit in medium size while reducing the percentage of fruit in small size. Because the twin-head system achieved the same fruit yield as the conventional single-head system while using only half the number of transplants, we can conclude that the twin-head “V” high-wire system is a more cost-effective high-wire system for year-round greenhouse cucumber production.
Mobility of brown trout in south-central Wyoming streams

Stream-resident brown trout (Salmo trutta) have often been considered to have small home ranges. To test this hypothesis, positions of adult brown trout in two streams were monitored from mid-June to early December 1991 and from late September 1992 to early June 1993 by using radiotelemetry. Thirty-seven of the 54 brown trout that were relocated at least once had home ranges greater than 50 m, trout larger than 340 mm moved more than did smaller brown trout, and movement of all fish tended to be greater in autumn. Different movement patterns of large and small fish imply the existence of two life-history strategies.