Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Cloning, Characterization, and Expression of the M Antigen of Histoplasma capsulatum

ABSTRACT The major diagnostic antigens of Histoplasma capsulatumare the H and M antigens, pluripotent glycoproteins that elicit both humoral and T-cell-mediated immune responses. These antigens may play a role in the pathogenesis of histoplasmosis. M antigen is considered immunodominant because antibodies against it are the first precipitins to arise in acute histoplasmosis and are commonly present during all phases of infection. The biological activity of monomolecular M antigen and its ability to elicit a protective immune response to H. capsulatum are largely unknown. A molecular approach was used to identify the biological nature of M antigen, including its purification from histoplasmin, partial digestion with proteinases, and reverse-phase high-performance liquid chromatography to separate the released peptides. The amino acid sequences of the purified peptides were obtained by Edman degradation, and using degenerate oligonucleotide primers for PCR, a 321-bp fragment of the gene encoding the M antigen was amplified from genomic H. capsulatum DNA. This fragment was used to screen an H. capsulatum genomic DNA library, leading to the isolation, cloning, and sequencing of the full-length gene. The M gene consists of 2,187-bp DNA encoding a protein of 80,719 Da, which has significant homology to catalases from Aspergillus fumigatus, Aspergillus niger, and Eimericella nidulans. A cDNA was generated by reverse transcription-PCR and cloned into the expression vector pQE40. The identity of the cloned, expressed protein was confirmed by Western blotting. The recombinant fusion protein was immunoreactive with monoclonal antibodies raised against M antigen, with polyclonal mouse anti-M antiserum, and with a serum sample from a patient with histoplasmosis. The gene encoding the major immunodominant M antigen of H. capsulatum is a presumptive catalase, and the recombinant protein retains serodiagnostic activity.
Enhanced Factor H Binding to Sialylated Gonococci Is Restricted to the Sialylated Lacto-N-Neotetraose Lipooligosaccharide Species: Implications for Serum Resistance and Evidence for a Bifunctional Lipooligosaccharide Sialyltransferase in Gonococci

We isolated serologically identical (by serovar determination and porin variable region [VR] typing) strains of Neisseria gonorrhoeae from an infected male and two of his monogamous female sex partners. One strain (termed 398078) expressed the L1 (Gal (cid:1) 1 3 3Gal (cid:2) 1 3 4Glc (cid:2) 1 3 4HepI) lipooligosaccharide (LOS) structure exclusively; the other (termed 398079) expressed the lacto-N -neotetraose (LNT; Gal (cid:2) 1 3 4GlcNAc (cid:2) 1 3 3Gal (cid:2) 1 3 4Glc (cid:2) 1 3 4HepI) LOS structure. The strain from the male index case expressed both glycoforms and exhibited both immunotypes. Nuclear magnetic resonance analysis revealed that sialic acid linked to the terminal Gal of L1 LOS via an (cid:1)
Distinctive Epstein-Barr Virus Variants Associated with Benign and Malignant Pediatric Pathologies: LMP1 Sequence Characterization and Linkage with Other Viral Gene Polymorphisms

27 The ubiquitous Epstein-Barr virus (EBV) is related to the development of lymphomas and is also the 28 etiological agent for infectious mononucleosis (IM). Sequence variations in the LMP1 encoding gene 29 have been deeply studied in different pathologies and geographic regions. Controversial results 30 propose the existence of tumor-related variants while others argued in favor of a geographical 31 distribution of these variants. However, current reports assessing EBV variants in IM were performed 32 in adult patients who display multiple variant infections. In the present study, LMP1 variants in 15 33 pediatric patients with IM and 20 pediatric EBV-associated lymphomas from Argentina were 34 compared as representatives of benign and malignant infection in children, respectively. A three 35 months follow-up study of LMP1 variants in peripheral blood cells and in oral secretions of patients 36 with IM was performed. Moreover, an integrated linkage analysis was performed with variants of 37 EBNA1 and the promoter region of BZLF1. Similar sequence polymorphisms were detected in both 38 pathological conditions, IM and lymphoma, but these differ from those previously described in healthy 39 donors from Argentina and Brazil. The results suggest that certain LMP1 polymorphisms, namely the 40 30bp deletion and high copy number of the 33bp repeats, could be associated to EBV-related 41 pathologies, either benign or malignant instead of just tumor related. Additionally, this is the first 42 study to describe the Alaskan variant in EBV-related lymphomas previously restricted to 43 nasopharyngeal carcinomas from North America.
Annotated Checklist of Deep-sea Fishes of the Sea of Japan

A list of deep-sea fishes from the Sea of Japan is presented on the basis of a literature survey and specimens mainly collected in the years 2009-2013. A total of 363 species belonging to 104 families of 29 orders of deep-sea fishes is listed with remarks on the literature surveys and/or specimens.
Parrot Evolution and Paleogeographical Events: Mitochondrial DNA Evidence

*Departamento de Biologia, Instituto de Biocieˆncias–Universidade de Sa˜o Paulo, Sa˜o Paulo, Brazil; and †Department ofZoology, University of Leicester, Leicester, EnglandWe sequenced 1,771 bp of three mitochondrial genes (12S rDNA, 16S rDNA, and cytochrome b) of nine NewWorld parrot genera (Amazona aestiva, Anodorhynchus hyacinthinus, Ara ararauna, Aratinga aurea, Cyanopsittaspixii, Deroptyus accipitrinus, Guaruba guarouba, Pionus menstruus, and Pyrrhura picta) and compared them withthe corresponding sequence of Australian parakeet (Melopsittacus undulatus). Phylogenetic analyses (maximumparsimony and maximum likelihood) showed that the Neotropical species we studied constitute two monophyleticgroups: the long-tailed and the short-tailed species. The separation within the long-tailed species could be assignedto the late Oligocene–early Miocene, when paleoenvironmental changes might have inﬂuenced this radiation. Thelong-tailed Neotropical and Australasian species diverged during the Cretaceous–Tertiary boundary, when SouthAmerica and Australia were moving away from Antarctica (Gondwanaland ﬁssion). We also compared our datawith the cytochrome b sequences of seven different genera of Australasian parrots obtained by other investigators,and these comparisons also support the independent evolution of the Neotropical and Australasian species. Analysesperformed with 567 bp of partial sequences of 12S rDNA and cytochrome b did not support or refute the hypothesisof monophyly of the Neotropical parrots with respect to an African species whose sequences were available.However, this analysis supported the view that the divergence between Neotropical short- and long-tailed taxa wasolder than the Oligocene–Miocene divergence among the long-tailed genera.
Dissemination of Virulence Factors and Antimicrobial Resistance in Faecal Enterococci from Poultry

Epidemiological studies have emphasized the importance of Enterococcus spp. in regard to positive and negative role of these bacteria. Presented work investigated a relationship among some factors (cytolysin, gelatinase, esp and biofilm formation) on phenotypic and genotypic level in relation to antibiotic resistance (gentamicin -GEN, streptomycin- STR, and vancomycin-VAN) in 82 enterococcal isolates (18 isolates of Enteroccus faecium, 26 of E. faecalis, 35 of E. casseliflavus and 3 of E. gallinarum) taken from cloacal swabs of poultry and from the water intended for livestock breeding. For phenotypic determination, commercial cultivation methods were used. Genes for appropriate factors were detected by polymerase chain reaction. Among tested isolates, 53 (65%) carried gelE gene and consequently 43 (52%) isolates produced gelatinase. The presence of cyl operon was detected in 53 (65%) and production of haemolysin on horse blood agar was determined in 37 (45%). In 14 (17%) isolates, esp gene was detected, but 28 (34%) isolates including those without esp gene detection were considered as strong biofilm producers. In 11 isolates (13%), all three genes (esp/gelE/cylA) were present contrary to 18 (22%) strains with negative PCR reaction. Resistance to GEN and STR was detected in 1 and 3 isolates respectively. All enterococci tested were susceptible to VAN. No relationship between virulence factors and resistance to antimicrobials was found. The data of this study proved relatively wide distribution of virulence factors among enterococci of animal and environmental origin and suggested that such isolates can be a reservoir of virulence trait.
Evaluation of immunomodulatory and microbicidal potential of Thuja occidentalis

The present paper deals with the investigation for in vitro antimicrobial properties and immunomodulatory potential of Thuja occidentalis. Its various solvent extracts showed high potency of antimicrobial activities against bacterial pathogens. The growth of the bacteria Escherichia coli was found to be inhibited by all plant extracts. Staphylococcus aureus was found to be resistant to Hexane extract. While Ethanol extract inhibited the growth of Staphylococcus aureus. Salmonella typhimuruim cultures were inhibited by all extract. Water extracts were more effective against microbial cultures at high concentrations. Rapid rise in total WBC counts in treated organisms proved the plant to have high immunomodulatory property. Plant methanolic extract treated animals showed increased life span than untreated controls. ANOVA analysis of the results showed that the results were significant and reproducible.
Mercury resistance in aromatic compound degrading Pseudomonas strains

Six of ten Pseudomonas strains selected from environmental samples for their ability to degrade aromatic compounds were found to be mercury resistant. Mercury detoxification proceeded through Hg2+ volatilization and the genes involved were chromosomally located. All the mercury resistant strains proved able to degrade aromatic compounds in the presence of Hg2+.
Parental Behavior Controls Incubation Period and Asynchrony of Hatching in Magellanic Penguins

Abstract. In many species of birds, periods of incubation of eggs within a clutch depend on the order in which the eggs were laid and determine whether the eggs hatch asynchronously or on the same day. Magellanic Penguins (Spheniscus magellanicus) lay two eggs 4 days apart that hatch 2 days apart; first eggs take 41 days to hatch, and second eggs take 39 days. We tested whether temperatures of the two eggs differ and whether delayed onset of incubation caused this pattern. First eggs were cooler than second eggs during their first few days (P < 0.001). First eggs averaged 23.4 ± 0.3 °C in the first 24–48 hours after they were laid. Second eggs averaged 27.9 ± 0.3 °C, warm enough for development. Egg temperature did not stabilize (33.9 °C) until eggs were about 18 days old. We swapped first and second eggs of different nests to determine if parental behavior caused the differences in temperatures and incubation periods. First eggs treated as second eggs developed as fast as control second eggs, and second eggs treated as first eggs developed nearly as slowly (40 days) as control first eggs. First eggs that were stored in a cooler until second eggs were laid took 2 days longer to hatch than control first eggs. Parental incubation behavior explained why the incubation period of second eggs was shorter than that of first eggs and controlled asynchrony of hatching, which affects chick growth and survival.
Modelling the effects of management on population dynamics: some lessons from annual weeds.

Summary 1. Agricultural and invasive weeds are major threats to managed and natural ecosystems, costing billions of dollars annually. Models for arable and invasive weed population dynamics can contribute to the management of problem species through generating predictions of population densities, and how those are likely to respond to changing management. Frequently, however, little attention is paid to quantifying the errors in estimates of model parameters and how these may affect the robustness of model predictions. 2. Most weed models are parameterized using a combination of field-estimated and literature derived parameters. Only rarely are estimates of error available for all parameters, despite the fact that most parameters will be subject to considerable error. 3. Close to extinction boundaries, predictions of population densities may be highly sensitive to small errors in model parameters. However, because of their generally high reproductive capacities, many weeds may occur at high and economically significant densities while close to extinction. Consequently, models may be numerically unstable at ecologically realistic densities. 4. We review methods of dealing with parameter uncertainty in weed modelling. We stress that it is important to recognize that many models may be structurally incorrect and all stabilizing mechanisms may not have been identified. Also, alternative model forms have seldom been explored, although a variety of alternatives to conventional difference equations exist. 5. Synthesis and applications. Only when different management interventions have greatly contrasting effects on population sizes are most models of weed populations likely to provide qualitatively correct predictions of their effects. Quantitative predictions from demographic models will usually be subject to large errors. Modelling methods that account for spatial heterogeneity and other stabilizing effects may yield more accurate predictions; however, their parameterization will often require approaches for data collection very different from those currently used.
A Model Using Phenotypic Characteristics to Detect Introgressive Hybridization in Wild Westslope Cutthroat Trout and Rainbow Trout

Abstract Introgressive hybridization is a substantial threat to native populations of cutthroat trout Oncorhynchus clarki ssp. To assess the status of native cutthroat trout and protect existing pure (nonhybridized) populations, fisheries managers need to identify introgressive hybridization in wild populations. Genetic techniques are the most reliable methods for detecting introgression but are typically expensive and time-consuming. Phenotypic characteristics are generally easy to measure in the field and have been investigated for their value in identifying hybrids in several genera of fish. We developed a practical quantitative tool for detecting introgressive hybridization in westslope cutthroat trout O. c. lewisi by fitting a classification tree model to the phenotypic characteristics of known pure and hybrid individuals. We then tested it as a means of making site-level assessments of the level of introgression. The genotypes of individuals were determined using noncoding sequences of nuclear DNA.
Contracaecum sp (ANISAKIDAE) EN EL PEZ Hoplias malabaricus, CAPTURADO EN LA CIÉNAGA GRANDE DE LORICA, CÓRDOBA

Objetivo. Determinar la presencia de Contracaecum en el pez moncholo (Hoplias malabaricus). Materiales y metodos. Se utilizaron 45 peces recolectados en la cienaga grande de Lorica entre julio de 2006 y mayo de 2007. Una vez en el laboratorio fueron analizados biometricamente, posteriormente fueron eviscerados y analizados en busqueda de nematodos. Se les extrajo la musculatura esqueletica la cual fue disecada en laminas delgadas y observadas con luz ultravioleta para evidenciar la presencia de nematodos. Los nematodos encontrados fueron contabilizados, aislados y fijados en formol al 4% con glicerina al 5%. Para la identificacion de los nematodos se utilizaron claves morfometricas. Resultados. Los nematodos fueron encontrados solamente en visceras e identificados como Contracaecum sp en estado larval III. La prevalencia fue de 100% con tasas de infestacion leve (88.9%) y moderada (11.1%). El valor del factor de condicion fue de 0.036±0.04, los indices hepatosomatico, branquiosomaticos y bazosomatico de 1.65±0.37, 3.40±0.43, 0.09±0.04 respectivamente y sin relacion entre estos y el indice parasitario en moncholo (r 0.05). Conclusiones. Contracaecum sp parasita las visceras de moncholo de la Cienaga Grande de Lorica. El FC y los indices organosomaticos no sirven como predictores de esta situacion.
Budding of PPxY-Containing Rhabdoviruses Is Not Dependent on Host Proteins TSG101 and VPS4A

Budding of PPxY-Containing Rhabdoviruses Is Not Dependent on Host Proteins TSG101 and VPS4A Takashi Irie, Jillian M. Licata, James P. McGettigan, Matthias J. Schnell, and Ronald N. Harty Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Biochemistry and Molecular Pharmacology, Jefferson Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
Detection of Schistosoma mansoni DNA in Human Blood as a Diagnostic Method for Schistosomiasis

Material and Methods : The individuals under study were categorized into four groups. Group I included 36 patients with active intestinal schistosomiasis. Group II included 20 patients with past history of intestinal schistosomiasis. Group III included 20 patients with Schistosoma haematobium and other parasitic infections, and finally group IV which included 15 individuals serving as negative controls. For all groups under study stool and urine were examined for parasitic ova; serum was examined for S. mansoni circulating DNA by PCR and for the detection of bilharzial antibody by IHAT. Results: PCR proved highly significant in diagnosis of active intestinal schistosomiasis with a sensitivity of 97.2%, specificity of 100%, predictive value of positive (PVP) of 100%, predictive value of negative (PVN) of 98.2% and a diagnostic accuracy of 98.9%. All cases in group II, III, and IV were negative. IHAT results showed a sensitivity of 77.8% in group I, 90.0 % in group II, 25% in group III and in group IV all cases were negative. The specificity of IHAT in the diagnosis of active intestinal schistosomiasis was 85.7%, with PVP 84.8% and PVN 78.9%; the diagnostic accuracy was 81.6%. Conclusion : S. mansoni DNA detection may be used as a valuable and species specific test for diagnosis of early infection or in situations of low worm burden in which other diagnostic methods show low sensitivity and specificity. Early treatment of such cases avoids the occurrence of irreversible pathological damage by the deposited eggs.
Assessment of Genetic Diversity in Peruvian Amaranth (Amaranthus caudatus and A. hybridus) Germplasm using Single Nucleotide Polymorphism Markers

Repository Citation Jimenez, Felix; Maughan, Peter J.; Alvarez, Aquilino; Kielinski, Kiel D. ; Smith, Scott M. ; Pratt, Donald B. ; Elzinga, David B. ; and Jellen, Eric N. , "Assessment of Genetic Diversity in Peruvian Amaranth (Amaranthus caudatus and A. hybridus) Germplasm Using Single Nucleotide Polymorphism Markers [Abstract]" (2013). Faculty Publications. 57. https://scholarworks.sfasu. edu/biology/57
Initial density affects biomass–density and allometric relationships in self‐thinning populations of Fagopyrum esculentum

The form and generality of the biomass–density relationship, especially during self‐thinning of crowded stands, have been intensively debated in recent years. All models of self‐thinning assume that the trajectory is independent of the initial pre‐thinning density, so populations differing in initial density can be analysed together. As plant allometry is a determinant of the self‐thinning trajectory, and competition alters plants' allometric growth, initial density may have consequences for the self‐thinning trajectory. To ask whether initial density can influence allometric relationships and the biomass–density trajectory, we grew Fagopyrum esculentum populations at three high densities and measured shoot biomass, density and the height and diameter of individual plants at six harvests. Initial density did not affect the slope of the log biomass–log density relationship, but there was a clear and significant effect on the intercept. Populations sown at higher densities had significantly more biomass at a given density of survivors. If the data for all densities and harvests are analysed together, the log biomass–log density relationship is linear with a slope of −0.377, which is consistent with the predictions of Metabolic Scaling Theory. If the independent variable initial density is included as a factor, the estimated slope of the log B–log N relationship is much steeper and consistent with the classical ‘Self‐thinning Rule’. The position of the self‐thinning trajectory is determined in part by the biomass density: the relationship between mass and volume. Initial density could affect this by altering allometric growth in a way that influences architectural compactness. An alternative hypothesis is that competition at higher initial density is more size symmetric, which has been shown to reduce growth and mortality. Synthesis. The self‐thinning trajectory is not always independent of initial population density. Interpopulation scaling patterns, even within one species, do not reflect processes within populations, and this conflation lies behind much of the current debate about size–density relationships in plant populations and communities. Interactions among plants and allometry are more important than internal physiological scaling mechanisms in determining the self‐thinning trajectory of crowded stands.