Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeny and Biogeography of Erythronium (Liliaceae) Inferred from Chloroplast matK and Nuclear rDNA ITS Sequences

Abstract We investigated phylogenetic relationships within Erythronium using DNA sequences from the chloroplast gene matK and the internal transcribed spacer (ITS) of nuclear ribosomal DNA. Erythronium, Amana, and Tulipa form a strongly supported clade that appears to be of Asian origin. Erythronium is widely distributed in the Northern Hemisphere, and consists of three well supported and geographically distinct clades occurring in western North America, eastern North America, and Eurasia. ITS analyses suggest that the Eurasian and eastern North American clades form a monophyletic group that separated into two lineages following divergence from the western North American clade. Although the three clades are each characterized by distinct morphological features, convergence both among and within geographic areas is seen in several characters. The western North American clade exhibits greater morphological and molecular diversity than either of the other two clades, and many of its species hybridize, suggesting both recent and ongoing speciation. The geographic distribution of Erythronium suggests initial diversification in Tertiary mixed mesophytic forest, followed by fragmentation of the range during the late Tertiary or early Pleistocene and subsequent radiation in western North America.
A test of the vicariance hypothesis of western North American freshwater biogeography

Aim The biogeography of western North American freshwater molluscs has traditionally been attributed to vicariance associated with late Tertiary rearrangement of landscape based on distributional evidence and the putatively limited dispersal ability of these organisms. We examined the phylogeography of a widely ranging western springsnail (Pyrgulopsis wongi Hershler, 1989) to test this hypothesis and evaluate the relative importance of vicariance and dispersal in structuring the distribution of this species.
Immune modulation by antibodies and antibody receptors

Mucosal immunoregulation involves the unique cross-talk between epithelial cells and various immune system components. Mucosal secretions contain significant quantities of immunoglobulin (Ig) G. The neonatal Fc receptor for IgG (FcRn) is important in regulating host IgG levels and in transporting IgG and its associated antigens across polarized epithelial barriers. Through its ability to secrete and absorb IgG, FcRn integrates its encounters with luminal antigens with the systemic immune compartments. The FcRn thereby provides essential host defense and immunoregulatory functions at mucosal surfaces. In this review, we examine recent data on the use of FcRn and anti-CD3 for immune modulation. Recent preclinical studies have revealed the significant efficacy of using FcRn or orally administered antibodies as a means of immune modulation. For example, the oral administration of anti-CD3 was recently shown to be effective in the prevention and treatment of several animal models of immune-mediated disorders. In addition, the use of FcRn or orally administered antibodies were recently described in two patents as potential methods for inducing systemic tolerance and for treating immune-mediated disorders. The FcRn patent generally discussed the methods and products for initiating an immune response against an antigen. In particular, this patent described the trans-epithelial delivery of antigens to provoke tolerance and immunity. The anti-CD3 patent emphasized the advantages of an oral route of administration compared to a parenteral one. These advantages included easier chronic use and a reduction in the side effects that are associated with the parenteral use of anti-CD3.
A review of genetic approaches to the management of blister rust in white pines

Summary Since introduced a century ago, Cronartium ribicola has devastated many populations of North American white pines. However, significant genetic resistance to white pine blister rust occurs naturally and can be exploited. In this review, we discuss the progress and different approaches to breeding for resistance in North American white pines. Three broad categories of resistance are: (1) ontogenetic resistance, (2) R-gene resistance and (3) partial resistance. Ontogenetic resistance is associated with increased host age and indicated by higher susceptibility to infection in primary needles and young seedlings then in grafts and older trees. R-gene resistance (major gene resistance) is an example of the classic gene-for-gene system common in many rust diseases. R-gene resistance provides immunity but may not be durable. Host resistance and the corresponding rust virulence which defeats it are well described for sugar pine and western white pine. Host plants with partial resistance are able to retard or tolerate disease development without eliminating the pathogen. Partial resistance is also called slow-rusting resistance or low-level resistance and is revealed in seedlings by several responses, including slow-canker-growth, difficult-to-infect, needle-shed and bark-reaction. Most of these seedling responses are presumed to be multigenic; but needle-shed may be controlled by recessive genes. Long-term, field trials for verification of screening and selection results are sparse. Although 100% higher survival of selected material over unselected occurs in some trials, mortality is high under conditions of high hazard and heavy inoculum load. In several, long-term trials, some full-sib crosses expressed a strong phenotypic resistance that indicates specific combining ability between complimentary parents. These and other observations suggest that we might yet find strong and durable resistance. Study of Eurasian white pines infected by blister rust fungi could help us better understand endemic pathosystems. Different strategies are identified for deploying material selected for either R-gene or partial resistance. Current research suggests that resistance is more complex than previously modelled, but new molecular techniques offer useful methods for investigating the white pine blister rust pathosystem.
Hereditary Blindness in a Captive Wolf (Canis lupus) Population: Frequency Reduction of a Deleterious Allele in Relation to Gene Conservation

Numerous cases of hereditary diseases and disorders have been reported in wild animals bred in captivity, but little attention has been paid to the particular genetic management problems that arise when such defects occur. These problems include the obstacle of eliminating the deleterious allele(s) without contemporary loss of genetic variability. In this paper we use the statistical methods of pedigree analysis to address questions regarding a previously presumed hereditary form of blindness observed in a captive wolf population bred for conservation purposes in Scandinavian zoos. The most likely mode of inheritance coincides with an autosomal recessive allele with either a full penetrance or a reduced penetrance of 0.6 (depending on the reliability of studbook records). Using these two models of inheritance, we calculate the probability of carrying the blindness allele for each living animal. Analysis of the effect of removing high-probability carriers on founder allele survival and level of inbreeding demonstrates that the frequency of the deleterious allele can be significantly reduced without seriously affecting founder allele survival or current degree of inbreeding in the wolf population. Numerosos casos de enfermedades y desordenes hereditarios han sido reportados en animales salvajes criados en cautiverio, sin embargo, poca atencion se ha prestado a los particulares problemas de manejo genetico que se presentan cuando tales defectos ocurren. Estos problemas incluyen el obstaculo que se presenta para eliminar lo(s) alelo(s) deletereos sin la perdida simultanea de variabilidad genetica. En este trabajo nosotros utilizamos los metodos estadisticos de analisis de pedigre para considerar preguntas concernientes a una forma de ceguera, previamente considerada como hereditaria, que se observo en una poblacion cautiva de lobos criada con fines concervacionistas en zoologicos Escandinavos. El modo de transmision hereditaria coincide con un alelo recesivo autosomico con penetrancia total o con una penetrancia reducida de 0.6 (dependiendo de la confiabilidad de los registros cria). Usando estos dos modelos de transmision hereditaria calculamos la probabilidad de portar el alelo de ceguera para cada animal. El analisis del efecto de remover los individuos con alto riesgo de ser portadores sobre la supervivencia del alelo fundador y el nivel de endocria demuestra que la frecuencia de los alelos deletereos puede ser significativamente reducida sin afectar seriamente la supervivencia del alelo fundador o el nivel actual de endocria de la poblacion de lobos.
Localization of feeding of Anomalococcus indicus (Hemiptera: Lecanodiaspididae) and supplementary biological notes: towards the biological management of the invasive tree Vachellia nilotica indica (Fabales: Mimosoideae) in North-Eastern Australia

Summary. Management of the invasive Vachellia nilotica indica infesting tropical grasslands of Northern Australia has remained unsuccessful to date. Presently Anomalococcus indicus is considered a potential agent in the biological management of V. n. indica. Whereas generic biological details of A. indicus have been known, their feeding activity and details of their mouthparts and the sensory structures that are associated with their feeding action are not known. This paper provides details of those gaps. Nymphal instars I and II feed on cortical-parenchyma cells of young stems of V. n. indica, whereas nymphal instars III and adult females feed on phloem elements of older shoots. Nymphal instars and adults (females) trigger stress symptoms in the feeding tissue with cells bearing enlarged and disfigured nuclei, cytoplasmic shrinkage, cytoplasmic trabeculae, abnormal protuberances and uneven cell wall thickening, unusual cell membrane proliferation, and exhausted and necrosed cells. Continuous nutrient extraction by A. indicus can cause stem death. We provide evidence that A. indicus, by virtue of its continuous feeding activity and intense population build up, can be an effective biological-management agent to regulate populations of V. n. indica in infested areas.
Prokaryotic activities and abundance in pelagic areas of the Ionian Sea

The Ionian Sea represents a suitable basin for studying the biogeochemical processes mediated by microbial activities. Because of its characteristics as a crossing region between the western and eastern Mediterranean Sea, it is one of the sites most affected by changes in water mass composition and dynamics, caused by the Eastern Mediterranean Transient (EMT). To date, relatively few data exist on microbial activities in pelagic areas of the Ionian Sea. From 1998 to 2004, during different research cruises, prokaryotic parameters (abundance, extracellular enzyme activities leucine aminopeptidase, β-glucosidase, alkaline phosphatase, bacterial production and respiration) were measured together with culturable bacteria and the main physical, chemical and trophic parameters (temperature, salinity, nutrients, particulated organic matter). The aim of the study was to describe the spatial and temporal variability in microbial activities involved in the carbon and phosphorus cycles, in different layers. Results showed that organic matter transformation mediated by the microbial community displayed a significant increase in autumn, highlighting the occurrence of significant changes at meso- and bathypelagic depths. Unlike the dark ocean, bacterial growth efficiency in the Ionian Sea, which increased with depth, seemed to vary from being a source of carbon in the epipelagic layer to a sink in the meso- and bathypelagic layers. The mechanism of phosphatase regulation showed a weak inverse correlation between specific phosphatase and inorganic P in all seasons except autumn. It is worth mentioning that the reported results constitute, to the best of our knowledge, one of the available datasets giving information about microbial activities in the Ionian Sea.
The role of multidrug efflux pumps in biofilm formation of Salmonella enterica serovar Typhimurium

Multidrug resistance (MDR) efflux pumps and biofilm formation are two mechanisms by which bacteria can evade the action of many antimicrobials. MDR efflux pumps confer low level multidrug resistance and are over-expressed in MDR clinical isolates. Biofilms are three dimensional, complex communities of bacteria encased in a self produced extra cellular matrix. Biofilms protect the bacteria within them both physically by acting as a barrier to any external threats, and metabolically by containing high proportions of persister cells. This thesis explores the link between MDR efflux and biofilm formation in S. Typhimurium and shows that genetic inactivation of any one of the nine MDR efflux systems results in a biofilm defect. We found that the transcriptional repression of curli, an essential component of the Salmonella matrix, is the reason for the efflux mutants' inability to form a biofilm. The biofilm defect in a tolC mutant was rescued by inactivation of a gene encoding an osmolarity sensor, envZ, suggesting that membrane stress response is a possible link between efflux and biofilm formation. Chemical efflux inhibitors (EIs) were found to impart curli repression and cause subsequent biofilm defect. This finding is clinically important as biofilms are a major cause of infection EIs could be a potential novel anti-biofilm therapy.
Contribution Of Sigma B To Stress Response And Virulence In Listeria Monocytogenes Lineages I, Ii, Iiia, And Iiib

The widespread presence of Listeria monocytogenes in various diverse environments, including those that are natural (i.e., non-agricultural), agricultural, and food-associated, suggests that these environments may serve as sources or reservoirs of L. monocytogenes that can be transmitted to various hosts, including humans. As the vast majority of human listeriosis infections are recognized to occur through consumption of contaminated foods, and as animal listeriosis infections also appear to be predominantly feedborne, development of effective intervention strategies for reducing the incidence of listeriosis among susceptible human and animal populations will require elucidation of specific routes of L. monocytogenes transmission among different ecosystems and compartments within food and feed production systems. Current knowledge of L. monocytogenes ecology is presented to provide insight into the primary sources that appear to contribute to its introduction into human foodassociated environments and foods as well as its transmission among various compartments in food and agricultural production systems.
A revision of the American spiders of the genus Drassyllus (Araneae, Gnaphosidae). Bulletin of the AMNH ; v. 173, article 1

3 Introduction . 3 Collections Examined. 7 Drassyllus Chamberlin . 7 The fallens Group. 8 The lamprus Group. 18 The notonus Group. 29 The niger Group . 36 The novus Group. 42 The frigidus Group . 51 The mumai Group. 70 The insularis Group . 73 Literature Cited. 94 Index of Specific Names . 97
Increased nitrate availability in the soil of a mixed mature temperate forest subjected to elevated CO2 concentration (canopy FACE)

In a mature temperate forest in Hofstetten, Switzerland, deciduous tree canopies were subjected to a free‐air CO2 enrichment (FACE) for a period of 8 years. The effect of this treatment on the availability of nitrogen (N) in the soil was assessed along three transects across the experimental area, one under Fagus sylvatica, one under Quercus robur and Q. petraea and one under Carpinus betulus. Nitrate, ammonium and dissolved organic N (DON) were analysed in soil solution obtained with suction cups. Nitrate and ammonium were also captured in buried ion‐exchange resin bags. These parameters were related to the local intensity of the FACE treatment as measured from the 13C depletion of dissolved inorganic carbon in the soil solution. Over the 8 years of experiment, the CO2 enrichment reduced DON concentrations, did not affect ammonium, but induced higher nitrate concentrations, both in soil solution and resin bags. In the nitrate captured in the resin bags, the natural abundance of the isotope 15N increased strongly. This indicates that the CO2 enrichment accelerated net nitrification, probably as an effect of the higher soil moisture resulting from the reduced transpiration of the CO2‐enriched trees. It is also possible that N mineralization was enhanced by root exudates (priming effect) or that the uptake of inorganic N by these trees decreased slightly as the result of a reduced N demand for fine‐root growth. In this mature deciduous forest, we did not observe any progressive N limitation due to elevated atmospheric CO2 concentrations; on the contrary, we observed an enhanced N availability over the 8 years of our measurements. This may, together with the global warming projected, exacerbate problems related to N saturation and nitrate leaching, although it is uncertain how long the observed trends will last in the future.
MOLECULAR ANALYSIS OF THE CAMP- RESPONSE ELEMENT [CRE] ELEMENTS IN THE PROMOTER REGION AND EXON 1 OF THE SURVIVAL OF MOTOR NEURON 2 [SMN2] GENE IN MALAYSIAN SPINAL MUSCULAR ATROPHY PATIENTS; TO ELUCIDATE THEIR ROLE IN CIRCUMSCRIBING THE CLINICAL SEVERITY

Objective: In the Spinal muscular atrophy [SMA] genes [ SMN 1 and SMN 2 genes]; the CRE-II elements at -400 bp in the promoter region of the SMN genes and CRE-I element at +108 bp in the exon 1 of the SMN genes, are reported to have a role in c-AMP induce expression of the SMN genes through its binding affinity to CREB-1. This study was designed to determine the role of CRE sites in the circumscribing the clinical severity of SMA. Methods: Direct sequencing was performed for the PCR products of the promoter regions of the SMA patients with homozygous deletion of SMN 1, different copy number of SMN 2 and NAIP non deletion. Results: No variation among the CRE-I and CRE-II sites was found in all the clinical types as compare to normal healthy control showing no role of CRE sites in circumscribing the clinical severity of SMA. Conclusion: There was no sequence variation found in the CRE binding sites in the three different clinical types of SMA reflecting no role of CRE binding sites in circumscribing the clinical severity of SMA.
Isolation and characterisation of Gaeumannomyces graminis var. graminis melanin mutants

Gaeumannomyces graminis var. graminis produces 1,8-dihydroxynaphthalene (DHN) melanin in its hyphal and hyphopodial cell walls. We isolated G. graminis mutants that were affected in their melanin biosynthesis. One was unable to synthesize DHN-melanin and, because it accumulated 2-hydroxyjuglone, a DHN melanin pathway shunt product, it is most likely to be defective in the reductase that catalyzes the conversion of 1,3,8-trihydroxynaphthalene to vermelone, the penultimate reaction in DHN synthesis. Genetic crosses with our wild-type strain indicated that this trihydroxynaphthalene reductase deficiency was the result of a single mutation. Another mutant constitutively synthesized DHN melanin and genetic crosses with our wild-type strain suggested that this heavily melanized mutant had a single mutation responsible for its phenotype. This mutant produced more melanin than the wild-type strain as measured by Azure A binding to melanin. The wild type and constitutively melanized mutant hyphae were more hydrophobic and more resistant to lytic enzymes, benomyl, restrictive temperature, and uv light than the non-melanized mutant, which also autolysed more readily. The non-melanized mutant was not more sensitive to heavy metal than the melanized strains. In addition, the non-melanized mutant was unaltered in pathogenicity to rice, whereas the constitutively melanized mutant was less pathogenic. The constitutively melanized mutant produced less extracellular lytic enzymes than the wild-type and the non-melanized mutant, which may explain its reduced virulence.
Chorus size and call intensity : female choice in the painted reed frog, Hyperolius marmoratus

1. In two-choice phonotaxis experiments female painted reed frogs (Hyperolius marmoratus) preferentially chose the stimulus with the greater sound pressure level (SPL) at source when all other call parameters were identical. 2. However, this preference was not apparent when we increased the distance of the louder stimulus from the female such that the SPL of the two stimuli at the release point was equivalent. This suggests that females simply move up sound gradients ('passive attraction'). 3. Female choice of the loudest stimulus was also affected by the number of speakers. 4. There were significantly fewer responses to the loudest speaker in some four-choice compared to matched two-choice phonotaxis experiments. 5. Together these experimental results may partially account for the absence of a large male mating advantage in the field.
Avaliação do comportamento ingestivo de vacas leiteiras em pastejo de Brachiaria brizantha recebendo diferentes teores de concentrado na dieta

Objetivou-se avaliar o comportamento ingestivo de vacas leiteiras em pastagem de Brachiaria brizantha submetidas a diferentes niveis de suplementacao concentrada na dieta. Utilizaram-se 16 vacas lactantes ½ Holandes × ½ Zebu, com media de 80 ± 10,14 dias de lactacao e peso corporal de 454,7 ± 54,51 kg. Os animais foram distribuidos em quatro tratamentos, utilizando-se um quadrado latino 4 × 4. O comportamento foi avaliado a cada dez minutos, durante 24 horas no 16o dia de cada periodo. Utilizou-se a analise de variância e regressao a 0,05 de probabilidade. Os tempos despendidos em pastejo, ruminacao e outras atividades; os numeros de pastejo, ruminacao, de bocados por dia e de mastigacoes mericicas por bolo; os tempos de pastejo, alimentacao total e mastigacao total; a taxa de bocado; o tempo de degluticao; o tempo por bolo ruminado; a velocidade de mastigacao e a eficiencia de alimentacao para FDN nao sofreram alteracoes com o aumento nos teores de concentrado na dieta. O tempo de cocho, o periodo de cocho, o tamanho de bocado, o tempo por mastigacao de bolo, a eficiencia de alimentacao para MS, CNF, NDT e a eficiencia de ruminacao cresceram linearmente. O periodo de ruminacao, o numero de bocados por degluticao, o numero de bolos ruminados por dia e o numero de mastigacoes mericicas por dia decresceram linearmente com o aumento dos teores de concentrado na dieta. Houve efeito quadratico do teor de concentrado sobre o numero de periodos em outras atividades e sobre o tempo em outras atividades. A suplementacao com ate 33,8% de concentrado na dieta de vacas em pastejo nao promovem alteracoes nas atividades de pastejo e ruminacao nem o tempo gasto em outras atividades, porem aumenta o tempo que os animais permanecem no cocho. O aumento no teor de concentrado da dieta melhora as eficiencias de alimentacao e ruminacao.
Performance of Chip Processing Potato Varieties in Northeastern Florida

tubers. This resulted in overall better chip ratings for the numbered entries com- pared to ‘Atlantic’ tubers. A potential ﬁ t for B0564-8 and B0766-3 in northeastern Florida production may be as a late season chip variety when the potential for the development of internal heat necrosis increases.