bluuebunny/crossref_metadata_2025 huggingface dataset:
Classification ofCryptosporidiumSpecies from Patients with Sporadic Cryptosporidiosis by Use of Sequence-Based Multilocus Analysis following Mutation Scanning
Authors: Jex Aaron R. , Pangasa Aradhana , Campbell Bronwyn E. , Whipp Margaret , Hogg Geoff , Sinclair Martha I. , Stevens Melita , Gasser Robin B.
Published: May 2008

In the present study, we analyzed genetic variation inCryptosporidiumspecies from humans (n= 62) with clinical cryptosporidiosis in South Australia. Sequence variation was assessed in regions within the small subunit of nuclear rRNA (p-SSU), the 70-kDa heat shock protein (p-hsp70), and the 60-kDa glycoprotein (p-gp60) genes by employing single-strand conformation polymorphism analysis and sequencing. Based on the analyses of p-SSU and p-hsp70,Cryptosporidium hominis(n= 38) andCryptosporidium parvum(n= 24) were identified. The analysis of p-gp60revealed eight distinct subgenotypes, classified asC. hominisIaA17R1 (n= 3), IbA9G3R2 (n= 14), IbA10G2R2 (n= 20), and IfA12G1R1 (n= 1), as well asC. parvumIIaA18G3R1 (n= 15), IIaA20G3R1 (n= 6), IIaA22G4R1 (n= 2), and IIcA5G3R2 (n= 1). Subgenotypes IaA17R1 and IIaA22G4R1 are new. Of the six other subgenotypes, IbA10G2R2, IIaA18G3R1, IIaA20G3R1, and IIcA5G3R2 were reported previously from the state of Victoria. This is the fourth record in Australia ofC. parvumsubgenotype IIaA18G3R1 from humans, which, to date, has been isolated only from cattle in other countries. This subgenotype might be a significant contributor to sporadic human cryptosporidiosis and may indicate a greater zoonotic contribution to the infection of humans in the area of study. Comparative analyses revealed, for the first time, the differences in the genetic makeup ofCryptosporidiumpopulations between two relatively close, major metropolitan cities.
Tuberculosis Diagnosis and Multidrug Resistance Testing by Direct Sputum Culture in Selective Broth without Decontamination or Centrifugation
Authors: Grandjean Louis , Martin Laura , Gilman Robert H. , Valencia Teresa , Herrera Beatriz , Quino Willi , Ramos Eric , Rivero Maribel , Montoya Rosario , Escombe A. Roderick , Coleman David , Mitchison Denis , Evans Carlton A.
Published: May 2008

Tuberculosis culture usually requires sputum decontamination and centrifugation to prevent cultures from being overgrown by contaminating bacteria and fungi. However, decontamination destroys many tuberculous bacilli, and centrifugation often is not possible in resource-poor settings. We therefore assessed the performance of
Mycobacterium tuberculosis
culture with unprocessed samples plated directly by using tuberculosis-selective media and compared this procedure to conventional culture using centrifuge decontamination. Quadruplicate aliquots of strain H37RV were cultured in 7H9 broth with and without selective antimicrobials and after centrifuge decontamination. The subsequent comparison was made with 715 sputum samples. Split paired sputum samples were cultured conventionally with centrifuge decontamination and by direct culture in tuberculosis-selective media containing antibiotics. Centrifuge decontamination reduced tuberculosis H37RV colonies by 78% (
P
< 0.001), whereas direct culture in tuberculosis-selective media had no inhibitory effect. Similarly, in sputum cultures that were not overgrown by contaminants, conventional culture yielded fewer tuberculosis colonies than direct culture (
P
< 0.001). However, the sensitivity of conventional culture was greater than that of direct culture, because samples were less affected by contamination. Thus, of the 340 sputum samples that were tuberculosis culture positive, conventional culture detected 97%, whereas direct culture detected 81% (
P
< 0.001). Conventional and direct cultures both took a median of 8.0 days to diagnose tuberculosis (
P
= 0.8). In those direct cultures that detected drug resistance or susceptibility, there was a 97% agreement with the results of conventional culture (Kappa agreement statistic, 0.84;
P
< 0.001). Direct culture is a simple, low-technology, and rapid technique for diagnosing tuberculosis and determining drug susceptibility. Compared to that of conventional culture, direct culture has reduced sensitivity because of bacterial overgrowth, but in basic laboratories this deficit may be outweighed by the ease of use.
Multifunctional T-Cell Characteristics Induced by a Polyvalent DNA Prime/Protein Boost Human Immunodeficiency Virus Type 1 Vaccine Regimen Given to Healthy Adults Are Dependent on the Route and Dose of Administration
Authors: Bansal Anju , Jackson Bethany , West Kim , Wang Shixia , Lu Shan , Kennedy Jeffrey S. , Goepfert Paul A.
Published: May 2008

A phase I clinical vaccine study of a human immunodeficiency virus type 1 (HIV-1) vaccine regimen comprising a DNA prime formulation (5-valent
env
and monovalent
gag
) followed by a 5-valent Env protein boost for seronegative adults was previously shown to induce HIV-1-specific T cells and anti-Env antibodies capable of neutralizing cross-clade viral isolates. In light of these initial findings, we sought to more fully characterize the HIV-1-specific T cells by using polychromatic flow cytometry. Three groups of participants were vaccinated three times with 1.2 mg of DNA administered intradermally (i.d.; group A), 1.2 mg of DNA administered intramuscularly (i.m.; group B), or 7.2 mg of DNA administered i.m. (high-dose group C) each time. Each group subsequently received one or two doses of 0.375 mg each of the gp120 protein boost vaccine (i.m.). Env-specific CD4 T-cell responses were seen in the majority of participants; however, the kinetics of responses differed depending on the route of DNA administration. The high i.m. dose induced the responses of the greatest magnitude after the DNA vaccinations, while the i.d. group exhibited the responses of the least magnitude. Nevertheless, after the second protein boost, the magnitude of CD4 T-cell responses in the i.d. group was indistinguishable from those in the other two groups. After the DNA vaccinations and the first protein boost, a greater number of polyfunctional Env-specific CD4 T cells (those with ≥2 functions) were seen in the high-dose group than in the other groups. Gag-specific CD4 T cells and Env-specific CD8 T cells were seen only in the high-dose group. These findings demonstrate that the route and dose of DNA vaccines significantly impact the quality of immune responses, yielding important information for future vaccine design.
The Hepatitis E Virus ORF3 Protein Modulates Epidermal Growth Factor Receptor Trafficking, STAT3 Translocation, and the Acute-Phase Response
Authors: Chandra Vivek , Kar-Roy Anindita , Kumari Sudha , Mayor Satyajit , Jameel Shahid
Published: May 2008

The hepatitis E virus (HEV) causes acute viral hepatitis, but its characterization is hampered by the lack of an efficient in vitro infection system that can be used to study the effects of HEV proteins on cellular processes. Previous studies suggest that the viral ORF3 protein (pORF3) is essential for infection in vivo and is likely to modulate the host response. Here, we report that pORF3 localizes to early and recycling endosomes and causes a delay in the postinternalization trafficking of epidermal growth factor receptor (EGFR) to late endosomes/lysosomes. The cytoplasmic phosphorylated signal transducer and activator of transcription 3 (pSTAT3) proteins require growth factor receptor endocytosis for their translocation from the cytoplasm to nucleus. Consequently, lower levels of pSTAT3 were found in the nuclei of ORF3-expressing Huh7 human hepatoma cells stimulated with EGF. This results in downregulation of the acute-phase response, a major determinant of inflammation in the host. We propose that through its effects on EGFR trafficking, pORF3 prolongs endomembrane growth factor signaling and promotes cell survival. The effects on STAT3 translocation would result in a reduced inflammatory response. Both of these events are likely to contribute positively to viral replication.
Cell Adhesion Promotes Ebola Virus Envelope Glycoprotein-Mediated Binding and Infection
Authors: Dube Derek , Schornberg Kathryn L. , Stantchev Tzanko S. , Bonaparte Matthew I. , Delos Sue E. , Bouton Amy H. , Broder Christopher C. , White Judith M.
Published: May 2008

Ebola virus infects a wide variety of adherent cell types, while nonadherent cells are found to be refractory. To explore this correlation, we compared the ability of pairs of related adherent and nonadherent cells to bind a recombinant Ebola virus receptor binding domain (EboV RBD) and to be infected with Ebola virus glycoprotein (GP)-pseudotyped particles. Both human 293F and THP-1 cells can be propagated as adherent or nonadherent cultures, and in both cases adherent cells were found to be significantly more susceptible to both EboV RBD binding and GP-pseudotyped virus infection than their nonadherent counterparts. Furthermore, with 293F cells the acquisition of EboV RBD binding paralleled cell spreading and did not require new mRNA or protein synthesis.
Human Cytomegalovirus Secretome Contains Factors That Induce Angiogenesis and Wound Healing
Authors: Dumortier Jerome , Streblow Daniel N. , Moses Ashlee V. , Jacobs Jon M. , Kreklywich Craig N. , Camp David , Smith Richard D. , Orloff Susan L. , Nelson Jay A.
Published: May 2008

Human cytomegalovirus (HCMV) is implicated in the acceleration of a number of vascular diseases including transplant vascular sclerosis (TVS), the lesion associated with chronic rejection (CR) of solid organ transplants. Although the virus persists in the allograft throughout the course of disease, few cells are directly infected by CMV. This observation is in contrast to the global effects that CMV has on the acceleration of TVS/CR, suggesting that CMV infection indirectly promotes the vascular disease process. Recent transcriptome analysis of CMV-infected heart allografts indicates that the virus induces cytokines and growth factors associated with angiogenesis (AG) and wound healing (WH), suggesting that CMV may accelerate TVS/CR through the induction and secretion of AG/WH factors from infected cells. We analyzed virus-free supernatants from HCMV-infected cells (HCMV secretomes) for growth factors, by mass spectrometry and immunoassays, and found that the HCMV secretome contains over 1,000 cellular proteins, many of which are involved in AG/WH. Importantly, functional assays demonstrated that CMV but not herpes simplex virus secretomes not only induce AG/WH but also promote neovessel stabilization and endothelial cell survival for 2 weeks. These findings suggest that CMV acceleration of TVS occurs through virus-induced growth factors and cytokines in the CMV secretome.
Neutralizing Antibody Blocks Adenovirus Infection by Arresting Microtubule-Dependent Cytoplasmic Transport
Authors: Smith Jason G. , Cassany Aurelia , Gerace Larry , Ralston Robert , Nemerow Glen R.
Published: May 2008

Neutralizing antibodies are commonly elicited by viral infection. Most antibodies that have been characterized block early stages of virus entry that occur before membrane penetration, whereas inhibition of late stages in entry that occurs after membrane penetration has been poorly characterized. Here we provide evidence that the neutralizing antihexon monoclonal antibody 9C12 inhibits adenovirus infection by blocking microtubule-dependent translocation of the virus to the microtubule-organizing center following endosome penetration. These studies identify a previously undescribed mechanism by which neutralizing antibodies block virus infection, a situation that may be relevant for other nonenveloped viruses that use microtubule-dependent transport during cell entry.
Severe Acute Respiratory Syndrome Coronavirus Protein 6 Accelerates Murine Hepatitis Virus Infections by More than One Mechanism
Authors: Hussain Snawar , Perlman Stanley , Gallagher Thomas M.
Published: May 2008

The severe acute respiratory syndrome coronavirus (SARS-CoV) encodes numerous accessory proteins whose importance in the natural infection process is currently unclear. One of these accessory proteins is set apart by its function in the context of a related murine hepatitis virus (MHV) infection. SARS-CoV protein 6 increases MHV neurovirulence and accelerates MHV infection kinetics in tissue culture. Protein 6 also blocks nuclear import of macromolecules from the cytoplasm, a process known to involve its C-terminal residues interacting with cellular importins. In this study, protein 6 was expressed from plasmid DNAs and accumulated in cells prior to infection by wild-type MHV. Output of MHV progeny was significantly increased by preexisting protein 6. Protein 6 with C-terminal deletion mutations no longer interfered with nuclear import processes but still retained much of the capacity to augment MHV infections. However, some virus growth-enhancing activity could be ascribed to the C-terminal end of protein 6. To determine whether this augmentation provided by the C terminus was derived from interference with nuclear import, we evaluated the virus-modulating effects of small interfering RNAs (siRNAs) directed against importin-β mRNAs, which down-regulated classical nuclear import pathways. The siRNAs did indeed prime cells for enhanced MHV infection. Our findings indicated that protein 6-mediated nuclear import blocks augmented MHV infections but is clearly not the only way that this accessory protein operates to create a milieu conducive to robust virus growth. Thus, the SARS-CoV protein 6 accelerates MHV infections by more than one mechanism.
Caractéristiques ultrastructurales de Ceratocystis ulmi en milieux naturel et artificiel
Authors: Chamberland Hélène , Ouellette G. B.
Published: May 2008

The ultrastructure of Ceratocystis ulmi (Buism.) C. Moreau was studied in both synthetic and natural media (infected tissues of elm). In fungal cells located at the cultures' margin and therefore considered young, a primitive ultrastructure with the following characteristics was observed. (1) The relatively voluminous nuclear area has irregular contours and appears to be devoid of an enclosing membrane; structures identified as developing mitochondria are contiguous to the nuclear area; endoplasmic reticulum is not evident. (2) As aging and septation of cells occur, the cytoplasm becomes less dense and organelles appear to be better delimited. Use of the goniometer has permitted the confirmation in many cases of the absence of membranes, and in others, their presence. Radioautographic studies of material labeled with [6-3H]thymidine showed that incorporation was greater in younger cells than older ones. Labeling in the latter occurred in association with fibrillar material within the nuclear areas, developing mitochondria, and other unidentified fibrillar masses. The importance of these observations is discussed. A mimeographed English version of results and discussion parts is available from the junior author.
Ypsilonia, Acanthotheciella, and Kazulia gen. nov.
Authors: Raj T. R. Nag
Published: May 2008

The pyrenomycete genus Acanthotheciella Höhn. is revised to include three species: A. harbata, A. mirabilis, and A. tropicalis sp. nov. The form genus Ypsilonia is accepted as its conidial state and is shown to belong in the Coelomycetes. Four species are shown to belong in Ypsilonia: the Ypsilonia state of A. barbota, Y. mirabilis, Y. tropicalis, and Y. cuspidata. Ypsilonia corticalis Wolf is considered as a nomen dubium, and Y. vagans Speg. isredisposed in a new genus of Hyphomycetes, Kazulia.
Effect of habitat and substrate quality on Douglas fir litter decomposition in western Oregon
Authors: Fogel Robert , Cromack Jr. Kermit
Published: May 2008

Linear regression models were developed for Douglas fir needle, female cone, branch, and bark decomposition in seven stands representing four mature vegetation types in western Oregon. Rate constants (k) for annual weight loss of needles ranged from 0.22 to 0.31 year−1, from 0.047 to 0.083 year−1 for cones, from 0.059 to 0.089 year−1 for branches, and from 0.005 to 0.040 year−1 for bark. The decomposition constant (k) of needles had a negative linear correlation (P < 0.01) with maximum plant moisture stress and temperature growth index of the seven stands. In comparing substrate quality of needle and woody litter components, k was more closely correlated with lignin content than with C:N ratio.
A new species of Moellerodiscus from India
Authors: Singh R. N. , Tewari V. P.
Published: May 2008

A new species of Moellerodiscus, M. dennisii, is described from India. This species, growing on rotting leaves of an unidentified angiospermic plant, has poorly developed stroma and biguttulate ascospores. The ectal excipulum is composed of flattened textura globulosa with large excipular hairs.
Cytological relationships between three diploid species of the fern genus Ceratopteris
Authors: Hickok Leslie G.
Published: May 2008

The cytological and reproductive characteristics of synthesized hybrids involving three diploid species of the homosporous fern genus Ceratopteris Brongn. have been examined. Cytological data indicate that the three species have major chromosomal homologies but differ with respect to a few structural rearrangements involving translocations and inversions. All of the hybrids were semi-sterile but F2 generations were obtained in which moderate to full fertility was evident. No relationship was evident between the degrees of morphological similarities between the species and the degrees of cytological and genetic differences expressed in the hybrids. These factors have confused species relationships among the diploid members of the genus. The behavior of the diploid hybrids is unique among the homosporous ferns in that cytological differences between the species involve individual chromosome differences rather than differences or similarities at the genomic level.
The role of fungi in the control of grasshoppers
Authors: Goettel Mark S. , Johnson Dan L. , Inglis G. Douglas
Published: May 2008

Fungi are among the most important microbial pathogens of grasshoppers with potential for development as biological control agents. Unlike most other insect pathogens that must be ingested to initiate disease, fungi generally invade insects via the external cuticle. The most common fungi that are pathogenic to grasshoppers are Beauveria bassiana, Metarhizium anisopliae, Metarhizium flavoviride, Sorosporella sp., and fungi in the Entomophaga grylli complex. A review of the latest information on the development of these fungi as microbial control agents of grasshoppers is presented. Species in the E. grylli complex are being used in classical biocontrol. This has resulted in controversy as there are indigenous nonpest grasshopper species that may be affected through introduction of the nonindigenous fungal strains. Beauveria bassiana and M. flavoviride are being developed for inundative control. These fungi can be mass produced and applied with equipment used for conventional pesticides. Conidia are applied either at ultralow volume in oil, as oil emulsions, or as bran-bait formulations. Field trials in Africa and North America have demonstrated significant grasshopper reductions. Improvements in formulation and inoculum targeting may further improve their efficacy. Key words: grasshoppers, locusts, microbial control, Beauveria bassiana, Entomophaga grylli, Metarhizium spp.
Sequences and proteins required for iron-regulated expression ofsid1ofUstilago maydis
Authors: Leong S. A. , An Z. , Mei B. , McEvoy J. , Zhao Q. , Markley J.
Published: May 2008

The molecular biology of the high affinity, siderophore-mediated iron uptake system of the basidiomycete fungus Ustilago maydis is under investigation. Ustilago maydis produces two cyclic peptide siderophores, ferrichrome and ferrichrome A. Biosynthesis of both siderophores is initiated by ornithine-N5-oxygenase, the product of sid1. sid1 mRNA accumulates only during growth under iron starvation conditions in wild-type cells or constitutively in urbs1 mutants, urbs1 encodes a 100-kDa protein with putative Zn finger domains that share sequence identity with those of the GATA family of transcription factors. The promoter region of sid1 was defined by deletion analysis of a 3.0-kb region 5′ to the translational start of sid1 using the Escherichia coli GUS gene as a reporter. Three regions were defined by this analysis to be critical to expression of sid1. These include (i) a 306-bp region containing two GATA sequences and mapping 2.4 kb from the start of translation; (ii) a 439-bp region immediately 5′ to the start of transcription; and (iii) a region encompassing the first intron of sid1. Deletion of the GATA sequences resulted in deregulated expression of sid1, while elimination of the latter two sequences ablated expression of the gene under all circumstances. Current efforts are focused on determining whether Urbsl interacts directly with the sid1 promoter via the GATA sequences and whether this interaction is dependent upon iron. Key words: GATA, transcription factor, siderophore, ferrichrome, iron, Urbs1.
The protein import apparatus of the mitochondrial outer membrane
Authors: Court Deborah A. , Lill Roland , Neupert Walter
Published: May 2008

The majority of proteins within mitochondria are synthesized on cytosolic ribosomes and imported into the organelles. Protein complexes in the mitochondrial outer membrane harbour both the receptors that recognize these preproteins, and a translocation pore. These "receptor complexes" are the entry points for most preproteins, which are subsequently targeted to their final submitochondrial locations. The outer membrane complexes cooperate with the import machinery of the inner membrane to target preproteins to the inner membrane itself, the matrix, or, in some cases, to the intermembrane space. In isolated outer membranes, these complexes are capable of accurately importing preproteins destined for the outer membrane. Our current understanding of the composition, function, and biogenesis of these outer membrane receptor complexes is the focus of this article. Key words: mitochondria, outer membrane, protein import, receptors.
Senescence is coupled to induction of an oxidative phosphorylation stress response by mitochondrial DNA mutations inNeurospora
Authors: Bertrand Helmut
Published: May 2008

In Neurospora and other genera of filamentous fungi, the occurrence of a mutation affecting one or several genes on the chromosome of a single mitochondrion can trigger the gradual displacement of wild-type mitochondrial DNA by mutant molecules in asexually propagated cultures. As this displacement progresses, the cultures senesce gradually and die if the mitochondrial mutation is lethal, or develop respiratory deficiencies if the mutation is nonlethal. Mitochondrial mutations that elicit the displacement of wild-type mitochondrial DNAs are said to be "suppressive." In the strictly aerobic fungi, suppressiveness appears to be associated exclusively with mutations that diminish cytochrome-mediated mitochondrial redox functions and, thus, curtail oxidative phosphorylation. In Neurospora, suppressiveness is connected to a regulatory system through which cells respond to chemical or genetic insults to the mitochondrial electron-transport system by increasing the number of mitochondria approximately threefold. Mutant alleles of two nuclear genes, osr-1 and osr-2, affect this stress response and abrogate the suppressiveness of mitochondrial mutations. Therefore, we propose that mitochondrial mutations are suppressive because their phenotypic effect is limited to the organelles within which the mutant DNA is located. Consequently, mitochondria that are "homozygous" for a mutant allele are functionally crippled and are induced to proliferate more rapidly than the normal mitochondria with which they coexist in a common protoplasm. While this model provides a plausible explanation for the suppressiveness of mitochondrial mutations in the strictly aerobic fungi, it may not account for the biased transmission of mutant mitochondrial DNAs in the facultatively anaerobic yeasts. Key words: mitochondria, mitochondrial DNA, mutations, suppressiveness, oxidative phosphorylation, stress response.
Determinants of fungal cell wall morphology: the vesicle supply center
Authors: Bartnicki-Garcia S. , Bartnicki D. D. , Gierz G.
Published: May 2008

Because fungal cell walls are shaped during construction, factors that regulate wall biogenesis must play a decisive role in morphogenesis. By delivering ingredients for wall formation in vesicles, fungi have a de facto mechanism to mold their own shape. The gradients in wall formation required for cell morphogenesis ensue from the pattern of vesicle discharge. A vesicle-based, mathematical model of fungal morphogenesis revealed that a relatively simple process could establish these gradients. The model and its underlying hyphoid equation assumes that wall-building vesicles emanate from a vesicle supply center (VSC). The VSC serves as an organizing center from which vesicles would move radially to the cell surface in all directions at random. VSC displacement is then an immediate cause of morphogenesis: a sustained linear displacement of the VSC would generate a polarized pattern of exocytosis required to make a hypha. The model predicts that the Spitzenkörper functions as a VSC. We have tested this prediction by analyzing instances where dislocations in Spitzenkörper position result in hyphal deformations. When the VSC was programmed to duplicate the movements of the Spitzenkörper before, during, and after a deformation, the resulting shapes mimicked closely the observed deformations. These correlations support the contention that the position and movement of the VSC determines the morphology of the fungal cell wall. The computer model has been refined to incorporate transverse random oscillations of the VSC to simulate more realistically the meandering shape of fungal hyphae. The model predicts that hyphal ring formation results from a sustained directional bias to the transverse oscillations of the Spitzenkörper. Key words: hyphal morphogenesis, Spitzenkörper, vesicle supply center, mathematical model, hyphoid equation, hyphal curvature.
Early interactions, adhesion, and establishment of the infection court byErysiphe graminis
Authors: Nicholson Ralph L. , Kunoh Hitoshi
Published: May 2008

The establishment of a fungal pathogen on the surface of its host is essential to the success of the infection process. For many fungi, establishment on the host is an active process that may depend on recognition of the host surface through chemical or topographic signals. Events that allow for establishment may be considered to represent the "preparation of the infection court" by the pathogen. This sometimes involves the adhesion of the pathogen to the host and possibly the alteration of the host's surface topography or chemistry. Adhesion is often presumed to be a single, chemically mediated event associated with germ tube or appressorium formation. However, adhesion of ungerminated propagules may also occur, and evidence suggests that it is mediated by the release of adhesive materials directly from the propagule upon contact with a suitable substratum. Fungi may require either a hydrophobic or a hydrophilic surface to initiate the infection process. The barley powdery mildew pathogen, Erysiphe graminis, requires a hydrophilic surface for appressorium formation, yet the barley leaf is extremely hydrophobic. The problem is resolved by the release of an exudate from conidia that makes the hydrophobic leaf surface hydrophilic. In contrast, Colletotrichum graminicola requires a hydrophobic surface for the initiation of its infection process. Ungerminated conidia of this fungus release materials that allow for the rapid adhesion of conidia, which ensures that germination and appressorium formation occur, initiating the infection process. For both fungi, these events happen well in advance of germination and establish the pathogen at the site of the infection court. Key words: adhesion, cuticle, cutinase, surface hydrophobicity, infection process.
A critique of DNA sequence analysis in the taxonomy of filamentous Ascomycetes and ascomycetous anamorphs
Authors: Seifert Keith A. , Wingfield Brenda D. , Wingfield Michael J.
Published: May 2008

The validity of reclassifying filamentous, ascomycetous anamorphs solely on the basis of ribosomal DNA sequences is examined. We suggest that emotional reactions to the debate are a consequence of often unacknowledged philosophical biases. From the perspective of the scientific method, neither morphological nor sequence-based taxonomic studies are inherently superior. A review of published information on the internal transcribed spacer of filamentous Ascomycetes and ascomycetous anamorphs demonstrates that uniform species concepts based on DNA sequences alone are presently infeasible. Because a phylogenetic scheme should classify species, the concept that fungi can be typified or classified solely by DNA sequences is challenged. Similarly, because no adequate nonmorphological species concept exists for anamorphic fungi that lack a sexual state, integration of the Deuteromycetes into the holomorphic classification on the basis of DNA sequences alone is also presently impractical. Key words: DNA sequencing, fungal taxonomy, internal transcribed spacer, species concepts.
Progress toward a phylogenetic classification of the Polyporaceae through parsimony analysis of mitochondrial ribosomal DNA sequences
Authors: Hibbett David S. , Donoghue Michael J.
Published: May 2008

We used sequence data from mitochondrial small-subunit ribosomal DNA to infer phylogenetic relationships of the Polyporaceae. We examined 62 species representing 14 families of Aphyllophorales and Agaricales. Parsimony analyses of these sequences suggest that the Polyporaceae are polyphyletic. Higher order relationships are poorly resolved, but seven groups of species are generally well supported (as measured by bootstrapping) or are congruent with previous taxonomic hypotheses. Group 1 includes Polyporus s.str., seven other genera of Polyporaceae, Lentinus, and Ganoderma. Because this clade contains the type species of Polyporus, it may serve as the core for a future recircumscription of the Polyporaceae. Group 2 is morphologically and ecologically diverse, but all members have amyloid, ornamented spores (with the possible exception of Heterobasidion). This group includes Bondarzewia, Heterobasidion, Hericium, Echinodontium, Lentinellus, Auriscalpium, and Russula. Group 3 includes five exemplars of the Hymenochaetaceae, as well as Oxyporus and Trichaptum. Trichaptum and members of the Hymenochaetaceae are unusual among the holobasidiomycetes in their possession of imperforate parenthosomes. Group 4 represents the Boletaceae and includes Boletus and Suillus. Group 5 includes Bjerkandera, which is a polypore, and Pulcherricium and Phanerochaete, which are corticioid. In Group 5 the corticioid habit may have been derived by reduction. Group 6 includes Fomitopsis, Piptoporus, and Daedalea, all of which are brown rot polypores with bipolar mating systems. Group 7 includes Laetiporus and Phaeolus. Laetiporus is classified in Polyporaceae, but Phaeolus has been placed in both the Polyporaceae and Hymenochaetaceae. In general, our results suggest that macromorphology is evolutionarily flexible, but that certain anatomical and physiological characters, while not free from homoplasy, contain clues to higher order relationships of polypores. Key words: Aphyllophorales, basidiomycetes, classification, phylogeny, Polyporaceae, ribosomal DNA.
Influence of habitat on the physiological and metabolic diversity of fungi
Authors: Wildman Howard G.
Published: May 2008

It is well known that there are variations in secondary metabolite production between different isolates of the same species of fungus in different habitats and geographic locations. What is less well known, however, is how much intrinsic variability in secondary metabolite production exists between different isolates of the same species within a particular habitat. The theory of adaptive polymorphism predicts that populations occupying wide ecological niches show greater variation than populations occupying narrow niches. As a test of this theory the influence of the habitat variability on the physiological and metabolic diversity of fungi occupying that habitat is reported using examples from the literature and from the author's own work with fungi colonizing wood in deserts of the southwest U.S.A. Key words: Fusarium spp., adaptive polymorphism, physiological diversity, metabolic diversity, secondary metabolites, habitat.
Bioconversion and biodegradation of aliphatic hydrocarbons
Authors: Lindley Nicholas D.
Published: May 2008

Aliphatic hydrocarbons represent a substantial energy reserve but also constitute a useful feedstock for the biotechnological production of various alkane-derived commodity chemicals. In addition, the biodegradation of aliphatic hydrocarbons continues to pose problems for fuel stocks with associated corrosion and eventual motor filter blocking. A relatively high number of yeasts and filamentous fungi have been described that degrade n-alkanes, but relatively few have received thorough investigation. Early work exploiting hydrocarbons as a potential substrate for unicellular protein production, though never commercially successful, enabled high-performance fermentation strategies to be developed that overcame many of the inherent problems caused by the use of high energy content insoluble liquid substrates. The biochemical pathways and physiological characteristics have been sufficiently established, as have the subcellular localization of the alkane-specific pathways, though many of the regulatory phenomena remain obscure. Currently, interest lies in the exploitation of such species, or their enzymes, in bioconversion processes and the unicellular yeasts, whose amenability to rational genetic engineering strategies exceeds that of filamentous species, are currently attracting renewed research interest. In view of this, the existing knowledge and potential for alkane-based biotechnology will be reviewed. Key words: alkane metabolism, bioconversion, biotechnology, aliphatic hydrocarbons, yeasts, filamentous fungi.
Application of baker's yeast in bioorganic synthesis
Authors: Ward O. P.
Published: May 2008

Baker's yeast has been widely used as a biocatalyst in organic synthesis, primarily because it is inexpensive and readily available. The majority of studies on the biotransformation capability of yeast deal with reductions of carbonyl groups and carbon–carbon double bonds. Reactions involving carbon–carbon bond formation are of great interest in chemical synthesis. Most of these biocatalytic reactions have been carried out in aqueous media. The conversion of benzaldehyde and pyruvate to L-phenylacetyl carbinol (a precursor of ephedrine) was one of the first commercial processes to utilize an enzyme biotransformation step. During this biotransformation, a proportion of the benzaldehyde is also reduced to benzyl alcohol. Detailed investigations have been carried out on factors affecting product formation by whole yeast cells, mainly in aqueous systems. The reaction mechanisms involved in pyruvate decarboxylase mediated formation of L-phenylacetyl carbinol have been reported. Recent studies on biocatalysis of benzaldehyde and substituted benzaldehyde to benzyl alcohol by whole cells of wild-type and mutant strains of baker's yeast in nonconventional media have established the effects of organic solvents and substrate hydrophobicity on reaction performance. The effect of solvent and substituted benzaldehyde substrate hydrophobicity on the kinetics of yeast alcohol dehydrogenase catalyzed reactions in nonconventional media will also be discussed. Key words: Saccharomyces, baker's yeast, biotransformations, organic synthesis.
Antibody immunity andCryptococcus neoformans
Authors: Casadevall Arturo
Published: May 2008

Recently there has been renewed interest in the potential of antibody immunity for the prevention and therapy of human Cryptococcus neoformans infections. Historically, the role of antibody immunity in protection against C. neoformans has been controversial. Experiments with polyclonal sera have produced evidence for and against the importance of antibody immunity in host defence. However, three groups have now shown that administration of monoclonal antibody (mAb) to the C. neoformans capsular polysaccharide (CPS) can modify the course of infection in mice. The quantity, isotype, and specificity of mAb appear to be important parameters of antibody efficacy against C. neoformans. Protective and nonprotective mAbs to CPS have been identified, suggesting a possible explanation for the divergent results obtained with polyclonal preparations, which presumably contain both types of antibodies. mAb administration has been shown to prolong survival, decrease organ fungal burden, and reduce serum polysaccharide antigen. The mechanism(s) by which mAb modify the course of infection is uncertain. In vitro experiments strongly suggest that antibodies mediate protection by enhancing effector cell function. The combination of antibody and amphotericin B is more effective than either agent alone for the treatment of murine cryptococcosis. Human–mouse chimeric antibodies with activity against C. neoformans have been constructed that may have advantages over mouse mAbs for therapy of human infections. A highly immunogenic capsular polysaccharide–protein vaccine has been made that can elicit protective antibodies in mice. Antibody immunity can modify the course of infection to the benefit of the host and may be useful in the prevention and treatment of human cryptococcosis. Key words: antibody, Cryptococcus neoformans, macrophage, vaccine, AIDS.
Effects of Environmental pH on the Hepatic Mixed Function Oxidases in Atlantic Salmon (Salmo salar)
Authors: Willis Douglas E. , Edwards Allison J. , Addison Richard F.
Published: May 2008

Atlantic salmon (Salmo salar) were held for some months in the Medway River, N.S., at pH 5.2–5.5 and in the Westfield River, N.S., in either untreated ("acidic") water at pH 4.7–5.2 or limed water at pH 51.–5.9 and were examined for effects on hepatic monooxygenases. Fish from the Westfield'acidic regime had lower body weights than those from the other two regimes, but similar liver weights. Females generally had higher hepatic microsomal protein contents than males, but this variable was not affected by environmental pH. Westfield acidic fish usually had higher benzo[a]pyrene hydroxylase and lower ethoxyresorufin O-deethylase activity than those from the other two regimes. Cytochromes P450 and b5 showed no clear difference between groups. Although the different pH environments affected reproductive success and steroid hormone metabolism, such changes were not reflected in these components of the hepatic monooxygenase system.
Effect of Temperature and Size on Development, Mortality, and Survival Rates of the Pelagic Early Life History Stages of Marine Fish
Authors: Pepin Pierre
Published: May 2008

This paper presents a comprehensive summary of development, mortality, and survival rates of fish eggs, yolk-sac larvae, and postlavae in relation to temperature and size. The general temperature- and, where applicable, size-dependent models explained 30–81% of the variance in vital rates. Daily development and mortality rates generally increased with increasing temperature. Temperature had an equal but opposite effect on stage-specific cumulative mortality rates of eggs and yolk-sac larvae. Stage-specific (length-dependent) cumulative mortality rates of postlarval fish were independent of temperature due to equal effects of temperature on daily growth and daily mortality rates. Size had no significant effect on daily or cumulative mortality rates of egg and yolk-sac stages. Daily mortality rates of postlarval fish were significantly influenced by mean size (i.e. length). The compensation of temperature effects between stages and/or vital rates may reduce the impact of environmental uncertainty on survival rates. It is suggested that the general temperature- and/or size-dependent relationships described in this study can serve as basic frameworks to assess whether there are significant effects resulting from species/stock-specific characteristics or environmental factors on the vital rates of the early life history stages of fish.
Acoustic Measures of the Abundance and Size of Pelagic Planktivores in Lake Michigan
Authors: Brandt Stephen B. , Mason Doran M. , Patrick E. Vincent , Argyle Ray L. , Wells L. , Unger Philip A. , Stewart Donald J.
Published: May 2008

Based on acoustic data taken at night and vertically stratified by bottom depth (3–110 m only), the total number (± 95% CI) of pelagic fishes in Lake Michigan was 43.4 ± 10.1 × 109 or 226.0 ± 55.2 kt in spring (mean density 0.7–3.8 fish∙m−2 or 1.6–12.8 g∙m−2) and 115.8 ± 18.3 × 109 or 313.2 ± 74.3 kt in late summer, 1987 (mean density 1.1–7.9 fish∙m−2 or 3.0–13.2 g∙m−2); approximately 30% of this increase in numbers (35% of biomass) occurred within Green Bay. Abundance estimates from horizontally stratified (by water column depth) data were within 9–11% of vertically stratified estimates during spring but over 20% higher during summer. By extrapolation to all water depths, we estimated total pelagic biomass as 274.6 kt for spring and 410.8 kt for summer. During both seasons, smaller fishes were nearer to the surface and nearer shore than larger individuals, and acoustic measures of size approximated the sizes of fishes caught in trawls. Bioenergetic model simulations suggest that 60% of the available production of alewife (Alosa pseudoharengus) was either consumed by stocked salmonines (52.9%) or commercially harvested (7.1%) in 1987. Underwater acoustics proved a valuable tool for lakewide assessments of fish abundances in the Great Lakes.
Responses of Diatom and Chrysophyte Assemblages in Lake 227 Sediments to Experimental Eutrophication
Authors: Zeeb Barbara A. , Christie Catherine E. , Smol John P. , Findlay David L. , Kling Hedy J. , Birks H. J. B.
Published: May 2008

We examined the diatom and chrysophyte assemblages preserved in Lake 227 sediments prior to, during, and following the annual additions of phosphorus (P) and nitrogen (N) (from 1969–1989). Premanipulation (1957–1968) diatom and chrysophyte assemblages were dominated by taxa characteristic of acidic, unproductive lake conditions. In 1969, the assemblages immediately shifted in response to increased nutrient availability and/or increased pH values in the epilimnion. Large increases in the relative abundance of Synedra PIRLA 2 and S. rumpens var. familiaris, Mallomonas crassisquama, M. doignonii var. tenuicostis, and cysts 1, 15, 29, 233, and 120 largely replaced the prefertilization assemblages. From 1970–1990, the diatom assemblage was dominated by alkaliphilic or pH-indifferent taxa. A second chrysophyte assemblage shift, which coincided with a lowering of the N:P addition ratio in 1975, was characterized by decreases in M. crassisquama and cysts 1, 15, 29, 233, and 120, and corresponding increases in Synura sphagnicola Korshikov scales and cysts 62 and 33. The stratigraphical analyses and numerical rate-of-change analyses clearly showed that diatom and chrysophyte species composition, particularly chrysophyte cysts, closely tracked short-term changes in lakewater chemistry. The amount of variance in the stratigraphic assemblages explained by lake-water chemical changes was high (68–90%), indicating the close algae–chemistry relationships in Lake 227 from 1969–1989.
Larval fish drift in the Valley River, Manitoba: influence of abiotic and biotic factors, and relationships with future year-class strengths
Authors: Johnston Thomas A. , Gaboury Marc N. , Janusz Richard A. , Janusz Laureen R.
Published: May 2008

We examined patterns in the spring drift of larval fishes in the Valley River, Manitoba. White sucker (Catostomus commersoni) and walleye (Stizostedion vitreum) were the most common species. The median date of larval drift for walleye was significantly earlier than for all other species. Capture rates of all species were significantly greater during the night than during the day. Larval abundance was positively related to river discharge in the 35 d preceding the median date of larval drift. Larval abundance was also positively related to mature female biomass in Dauphin Lake for walleye, but not for white sucker. Year-class strength of a cohort (catch per unit effort of 3- or 4-year-old fish) in Dauphin Lake was positively related to total larval drift of the same cohort (3 or 4 years earlier) in the Valley River for walleye, but not for white sucker. Our results suggest that the year-class strength of Dauphin Lake walleye is determined very early in the life history and that factors which enhance the natural production of walleye larvae will enhance walleye recruitment.
Modulation of ventilatory mechanics during exercise in ventilation-limited populations
Authors: Butcher Scott J.
Published: May 2008

The aim of this thesis was to examine the impact of modifications to ventilatory constraint in populations who have reductions in expiratory flow and ventilatory limitations during exercise. The first study examined the effect of the self-contained breathing apparatus (SCBA) regulator on work of breathing (WOB) and lung volume changes in healthy subjects. The second study further examined the effect of the SCBA on the above outcomes, as well as on pulmonary function and respiratory muscle fatigue during stair-stepping (in healthy subjects). In addition, the effect of breathing heliox on the aforementioned variables was studied. The third thesis study examined the effect of heliox on ventilatory constraint, exercise tolerance, and leg muscle fatigue in patients with chronic obstructive pulmonary disease (COPD). The main results of the first study were that, compared with a low-resistance breathing valve (RV), the SCBA regulator increased inspiratory elastic (32%), expiratory resistive (59%), and total WOB (13%), and increased end-expiratory lung volume creating a plateau in end-inspiratory lung volume at approximately 90% of vital capacity. When these variables were examined with the full SCBA and compared with the RV in the second study, similar results were found. In addition, resting pulmonary function was reduced with the SCBA. Exercise with the SCBA induced reductions in both inspiratory and expiratory maximal pressures indicating the presence of respiratory muscle fatigue. When compressed air was replaced with heliox in the SCBA, end-expiratory lung volume, total WOB, and respiratory muscle fatigue were reduced. These observations regarding the effect of heliox on ventilatory function led to the third study, which found that heliox increased exercise tolerance (53%) and leg muscle fatigue (15%) in patients with COPD, but only in those limited by ventilatory constraints and who did not have a significant level of leg fatigue while breathing room air. Those patients who did have leg fatigue on room air did not increase exercise tolerance despite reduced ventilatory constraint. Together, these findings indicate that reducing ventilatory constraint during exercise can have specific positive effects on exercise performance in populations who are ventilatory limited and have implications for occupational or rehabilitation exercise training.
Impact of DHEA(S) and cortisol on immune function in aging: a brief review
Authors: Buford Thomas W. , Willoughby Darryn S.
Published: May 2008

A decline in the human immune system that occurs with aging is known as immunosenescence. Several factors are involved in the process, including reduced neutrophil function and cytotoxic capacity of natural killer (NK) cells, thymus atrophy and reduced naïve T cell number, and lowered B cell antibody production in response to antigen. The endocrine system, specifically the hypothalamus–pituitary–adrenal axis, plays an important role in modulating immune function. With aging an imbalance occurs between two adrenal hormones, cortisol and DHEA, that have opposing actions on immune function. This brief review explores the interactions between cortisol and DHEA and their effects on immune function in aging, as well as potential methods to combat the endocrine-related contribution to immunosenescence, including DHEA supplementation and exercise.