bluuebunny/crossref_metadata_2025 huggingface dataset:
Performance Evaluation of the Scent Transfer Unit™ (STU‐100) for Organic Compound Collection and Release
Authors: Eckenrode Brian A. , Ramsey Scott A. , Stockham Rex A. , Van Berkel Gary J. , Asano Keiji G. , Wolf Dennis A.
Published: July 2006

ABSTRACT: The Scent Transfer Unit™ (STU‐100) is a portable vacuum that uses airflow through a sterile gauze pad to capture a volatiles profile over evidentiary items for subsequent canine presentation to assist law enforcement personnel. This device was evaluated to determine its ability to trap and release organic compounds at ambient temperature under controlled laboratory conditions. Gas chromatography‐mass spectrometry (GC‐MS) analyses using a five‐component volatiles mixture in methanol injected directly into a capture pad indicated that compound release could be detected initially and 3 days after the time of collection. Additionally, 15 compounds of a 39‐component toxic organic gaseous mixture (10–1000 parts per billion by volume [p.p.b.v]) were trapped, released, and detected in the headspace of a volatiles capture pad after being exposed to this mixture using the STU‐100 with analysis via GC‐MS. Component release efficiencies at ambient temperature varied with the analyte; however, typical values of c. 10% were obtained. Desorption at elevated temperatures of reported human odor/scent chemicals and colognes trapped by the STU‐100 pads was measured and indicated that the STU‐100 has a significant trapping efficiency at ambient temperature. Multivariate statistical analysis of subsequent mass spectral patterns was also performed.
Suicide With Associated Acts of Arson: Two Cases from Colorado
Authors: Adair Thomas W. , Fisher Angela
Published: July 2006

ABSTRACT: We report on two cases of suicide in which the victims started fires before their deaths. In one case the victim died of a single self‐inflicted gunshot wound to the head after setting several fires in his residence. In the second case the victim hung himself after setting several fires in his residence and an adjoining building. In both cases, the victim's position was not near the origin of the fires suggesting that the arson was not a failsafe device to the primary mechanism of suicide. Neither victim showed a significant percentage of carboxyhemoglobin, or thermal damage from the fires. Both cases are remarkable in that, had the fire caused more damage to the remains and dwellings, a finding of suicide may not have been reached. We discuss similar aspects between the two reported cases and discuss differences observed with similar events such as complex suicide, suicide by self‐immolation, and concealed homicide by burning. Similar cases should be reported to broaden our understanding of these complex events.
Evaluation of Real‐Time PCR Amplification Efficiencies to Detect PCR Inhibitors
Authors: Kontanis Elias J. , Reed Floyd A.
Published: July 2006

ABSTRACT: Real‐time PCR analysis is a sensitive template DNA quantitation strategy that has recently gained considerable attention in the forensic community. However, the utility of real‐time PCR methods extends beyond quantitation and allows for simultaneous evaluation of template DNA extraction quality. This study presents a computational method that allows analysts to identify problematic samples with statistical reliability by comparing the amplification efficiencies of unknown template DNA samples with clean standards. In this study, assays with varying concentrations of tannic acid are used to evaluate and adjust sample‐specific amplification efficiency calculation methods in order to optimize their inhibitor detection capabilities. Kinetic outlier detection and prediction boundaries are calculated to identify amplification efficiency outliers. Sample‐specific amplification efficiencies calculated over a four‐cycle interval starting at the threshold cycle can be used to detect reliably the presence of 0.4 ng of tannic acid in a 25 μL PCR reaction. This approach provides analysts with a precise measure of inhibition severity when template samples are compromised. Early detection of problematic samples allows analysts the opportunity to consider inhibitor mitigation strategies prior to genotype or DNA sequence analysis, thereby facilitating sample processing in high‐throughput forensic operations.
Allele Frequencies for Three STR Loci in Chinese Han Populations
Authors: Liu Zhiyong , Zhang Baohua , Chen Guodi , Yu Lin , Liao Miao , Wang Jing , Long Bing , Zhang Lin
Published: July 2006

POPULATION: Chinese.
Mycobacterial spindle cell pseudotumor of the skin
Authors: Shiomi Tatsushi , Yamamoto Tetsurou , Manabe Toshiaki
Published: July 2006

Background:  Mycobacterial spindle cell pseudotumor is a rare tumor‐like lesion characterized by the proliferation of spindle cells engorged with mycobacterial microorganisms. To our knowledge, only a few cases of cutaneous lesions have been described in the literature.

Case report:  A 58‐year‐old Japanese woman presented with a nodule in her left forearm. She had systemic lupus erythematosus and interstitial pneumonia for 17 years, treated with prednisolone and azathioprine. She was also receiving insulin treatment for diabetes mellitus.

Results:  Histologically, the lesion was located in the deep dermis with extension into the subcutaneous fat tissue and was composed mainly of spindle cells focally showing a vaguely storiform pattern. In limited focal areas, foam cells, epithelioid histiocytes, and multinucleated giant cells were seen sparsely. Ziehl–Neelsen staining showed numerous acid‐fast bacilli within the spindle cells and epithelioid histiocytes. The acid‐fast bacilli were determined by culture and polymerase chain reaction to be Mycobacterium intracellulare.

Conclusions:  We emphasize that mycobacterial spindle cell pseudotumor should be included in the differential diagnoses of a spindle cell lesion in the skin, especially in immunosuppressed patients.
Melanoma associated with a dermatofibroma
Authors: Kovach Bradley T. , Boyd Alan S.
Published: July 2006

Background:  Dermatofibromas are common benign cutaneous fibrohistiocytic neoplasms, whereas melanomas are potentially aggressive malignancies. Differentiating these two entities can occasionally be difficult.

Methods:  We report the case of a 56‐year‐old female presenting with a firm pink papule on the left thigh.

Results:  Histopathology revealed atypical melanocytes in the epidermis and papillary dermis with numerous mitotic figures and intraepidermal pagetoid spread. Within the dermis was a poorly demarcated collection of epithelioid and spindled cells with intermixed keloidal collagen. The atypical melanocytes stained for MART‐1 and S‐100, whereas the underlying fibrohistiocytic tumor took up factor XIIIa immunostain, confirming the diagnosis of invasive malignant melanoma occurring in association with a dermatofibroma.

Conclusions:  This case emphasizes the role of immunohistochemical stains in correctly diagnosing melanocytic and histiocytic neoplasms.
Cutaneous oncocytoma – a report of three cases and review of the literature
Authors: Coburn Victoria , Radfar Arash , Snook David , Mahalingam Meera
Published: July 2006

Abstract:  The oncocyte is a cell characterized by capacious, eosinophilic, finely granular cytoplasm, and lesions composed primarily of oncocytes are termed oncocytomas. Whereas oncocytic metaplasia has been reported in various cutaneous neoplasms, oncocytomas typically occur in the kidneys, thyroid and salivary glands and are uncommon in the dermatopathology literature. We present three cases of cutaneous oncocytoma so that dermatopathologists are cognizant of this uncommon entity. Although some believe that oncocytomas are locally aggressive lesions, our cases indicate that their clinical course is perhaps as banal as their histology.
Simian immunodeficiency viruses replication dynamics in African non‐human primate hosts: common patterns and species‐specific differences
Authors: Pandrea Ivona , Silvestri Guido , Onanga Richard , Veazey Ronald S. , Marx Preston A. , Hirsch Vanessa , Apetrei Cristian
Published: July 2006

Methods  To define potential common features of simian immunodeficiency virus (SIV) infections in different naturally infected host species, we compared the dynamics of viral replication in 31 African green monkeys (10 sabeus, 15 vervets and seven Caribbean AGMs), 14 mandrills and three sooty mangabeys (SMs) that were experimentally infected with their species‐specific viruses.

Results  After infection, these SIVs replicated rapidly reaching viral loads (VLs) of 105–109 copies/ml of plasma between days 9–14 post‐infection (p.i). Set point viremia was established between days 42 and 60 p.i., with levels of approximately 105–106 copies/ml in SM and mandrills, and lower levels (103–105 copies/ml) in AGMs. VL during the chronic phase did not correlate with viral genome structure: SIVmnd‐2 (a vpx‐containing virus) and SIVmnd‐1 (which does not contain vpu or vpx) replicated to similar levels in mandrills. VL was dependent on virus strain: vervets infected with three different viral strains showed different patterns of viral replication. The pattern of viral replication of SIVagm.sab, which uses both CCR5 and CXCR4 co‐receptors was similar to those of the other viruses.

Conclusions  Our results show a common pattern of SIV replication in naturally and experimentally infected hosts. This is similar overall to that observed in pathogenic SIV infection of macaques. This result indicates that differences in clinical outcome between pathogenic and non‐pathogenic infections rely on host responses rather than the characteristics of the virus itself.
Repetitive exposures with simian/human immunodeficiency viruses: strategy to study HIV pre‐clinical interventions in non‐human primates
Authors: Kim Caryn N. , Adams Debra R. , Bashirian Sheila , Butera Sal , Folks Thomas M. , Otten Ron A.
Published: July 2006

Background  Non‐human primate models for human immunodeficiency virus (HIV) infection represent a valuable pre‐clinical tool to evaluate interventions (e.g., topical microbicides, vaccines, and chemoprophylaxis) designed to prevent transmission or slow disease progression after infection. Standard transmission models use a single‐dose exposure with high, non‐physiologic levels of virus to approach 100% infection rates of control animals. These single‐exposure models do not represent the circumstances of mucosal HIV transmission in humans and may result in misleading data with regard to intervention efficacy. Therefore, we have developed a repetitive mucosal exposure model using doses of virus that better reflects human exposures.

Methods  The virus used for these evaluations was simian‐human immunodeficiency virus [SHIVSF162P3 (R5‐using, subtype B HIV‐1 envelope)] and the virus dose used (approximately 105–106 viral particle equivalents or approximately 10 tissue culture infectious doses per exposure) approximates viral loads observed in the semen during acute HIV‐1 infection. Using the repeated mucosal exposure approach, we have evaluated a candidate vaginal microbicide (cellulose acetate phthalate, CAP) given 15 minutes prior to each weekly virus exposure. Pig‐tailed macaques were exposed weekly by vaginal inoculations with and without microbicide until systemic viral RNA was detected.

Results  Groups of naïve control monkeys were infected after an average of three to four exposures for the vaginal route of inoculation. Data from the first application of this monkey model to evaluate the topical microbicide CAP suggested that protection from SHIV infection was possible with three of four CAP‐treated monkeys remaining uninfected after 12 exposures (P = 0.015). CAP efficacy was markedly improved from 66% in a previous single‐dose virus exposure study to 92% in this repeated exposure system.

Conclusion  Our experience with using repetitive virus exposures to study topical microbicides and the findings to date from this study provides a basis to refine monkey models to more closely resemble human exposure during HIV transmission. This model may be highly relevant to pre‐clinical evaluation for a variety of therapeutic interventions which is discussed here.
Foamy virus infection in primates
Authors: Murray S.M. , Linial M.L.
Published: July 2006

Foamy viruses (FV), the oldest known genus of Retroviridae, are unique among the retroviruses in having no disease association. It is not known why FV are non‐pathogenic while infection by their closest relatives can be deadly. This may be related to the estimated 60 million years of coevolution of FV and their primate hosts. We review the current state of knowledge of FV infection, including information about the sites of viral replication and host immune responses, and discuss the role these may play in establishing persistent yet non‐pathogenic infections. Whether FV has pathologic consequences in immunosuppressed hosts has not been thoroughly investigated. As most primates in HIV/SIV research are coinfected with FV, investigation into possible interactions between these viruses is of interest. The use of FV as a vector for gene therapy is also discussed.
Dynamic evolution of antibody populations in a rhesus macaque infected with attenuated simian immunodeficiency virus identified by surface plasmon resonance
Authors: Steckbeck J.D. , Grieser H.J. , Sturgeon T. , Taber R. , Chow A. , Bruno J. , Murphy‐Corb M. , Montelaro R.C. , Cole K.S.
Published: July 2006

Background  Increasing evidence suggests that an effective AIDS vaccine will need to elicit broadly neutralizing antibody responses. However, the mechanisms of antibody‐mediated neutralization have not been defined. Previous studies from our lab have identified significant differences in the rates of antibody binding to trimeric SIV envelope proteins that correlate with neutralization sensitivity. Importantly, these results demonstrate differences in monoclonal antibody (MAb) binding to neutralization‐sensitive and neutralization‐resistant envelope proteins, suggesting that one mechanism for virus neutralization may be related to the stability of antibody binding. To date, little has been done to evaluate the binding properties of polyclonal serum antibodies elicited by SIV infection or vaccination.

Methods  In the current study, we translate these findings with MAbs to study antibody binding properties of polyclonal serum antibody responses generated in rhesus macaques infected with attenuated SIV. Quantitative and qualitative binding properties of well‐characterized longitudinal serum samples to trimeric, recombinant SIV gp140 envelope proteins were analyzed using surface plasmon resonance (SPR) technology (Biacore).

Results  Results from these studies identified two antibody populations in most of the samples analyzed; one antibody population exhibited fast association/dissociation rates (unstable) while the other population demonstrated slower association/dissociation rates (stable). Over time, the percentage of the total binding response of each antibody population evolved, demonstrating a dynamic evolution of the antibody response that was consistent with the maturation of antibody responses defined using our standard panel of serological assays. However, the current studies provided a higher resolution analysis of polyclonal antibody binding properties, particularly with respect to the early time‐points post‐infection (PI), that is not possible with standard serological assays. More importantly, the increased stability of the antibody population with time PI corresponded with potent neutralization of homologous SIV in vitro.

Conclusions  These results suggest that the stability of the antibody–envelope interaction may be an important mechanism of serum antibody virus neutralization. In addition, measurements of the ‘apparent’ rates of association and dissociation may offer unique numerical descriptors to characterize the level of antibody maturation achieved by candidate vaccine strategies capable of eliciting broadly neutralizing antibody responses.
Optimization of in vitro expansion of macaque CD4+ T cells using anti‐CD3 and co‐stimulation for autotransfusion therapy
Authors: Onlamoon Nattawat , Hudson Krystal , Bryan Patsy , Mayne Ann E. , Bonyhadi Mark , Berenson Ron , Sundstrom Bruce J. , Bostik Pavel , Ansari Aftab A. , Villinger François
Published: July 2006

Background  Our laboratory has previously shown that adoptive transfer of in vitro‐expanded autologous purified polyclonal CD4+ T cells using anti‐CD3/CD28‐coated beads induced antiviral responses capable of controlling SIV replication in vivo.

Methods  As CD4+ T cells comprise several phenotypic and functional lineages, studies were carried out to optimize the in vitro culture conditions for maximal CD4+ T‐cell expansion, survival and delineate the phenotype of these expanded CD4+ T cells to be linked to maximal clinical benefit.

Results and Conclusions  The results showed that whereas anti‐monkey CD3γ/ɛ was able to induce T‐cell proliferation and expansion in combination with antibodies against multiple co‐stimulatory molecules, monkey CD3ɛ cross reacting antibodies failed to induce proliferation of macaque CD4+ T cells. Among co‐stimulatory signals, anti‐CD28 stimulation was consistently superior to anti‐4‐1BB, CD27 or ICOS while the use of anti‐CD154 failed to deliver a detectable proliferation signal. Increasing the relative anti‐CD28 co‐stimulatory signal relative to anti‐CD3 provided a modest enhancement of expansion. Additional strategies for optimization included attempts to neutralize free radicals, enhancement of glucose uptake by T cells or addition of T‐cell stimulatory cytokines. However, none of these strategies provided any detectable proliferative advantage. Addition of 10 autologous irradiated feeder cells/expanding T cell provided some enhancement of expansion; however, given the high numbers of T cell needed, this approach was deemed impractical and costly, and lower ratios of feeder to expanding T cells failed to provide such benefit. The most critical parameter for efficient expansion of purified CD4+ T cells from multiple monkeys was the optimization of space and culture conditions at culture inception. Finally, anti‐CD3/28‐expanded CD4+ T cells uniformly exhibited a central memory phenotype, absence of CCR5 expression, marked CXCR4 expression in vitro, low levels of caspase 3 but also of Bcl‐2 expression.
Induction of the myofibroblastic phenotype in human gingival fibroblasts by transforming growth factor‐β1: role of RhoA‐ROCK and c‐Jun N‐terminal kinase signaling pathways
Authors: Smith Patricio C. , Cáceres Mónica , Martinez Jorge
Published: July 2006

Background and Objectives:  Myofibroblastic differentiation is an important event in gingival wound healing and chronic inflammation. Transforming frowth factor‐β 1 (TGF‐β1) is a potent growth factor that has been implicated in this process. Gingival myofibroblasts have an increased ability to remodel the extracellular matrix and this feature has been associated with changes in the distribution of F‐actin and the expression of the myofibroblast marker α‐smooth muscle actin. In the present study we have analyzed the role of TGF‐β1 and the signaling routes activated by this factor in the cytoskeletal changes that characterize the myofibroblastic differentiation process in human gingival fibroblasts.

Materials and methods:  The signalling pathways involved in myofibroblastic differentiation were studied in primary cultures of human gingival fibroblasts using several signal transduction inhibitors. RhoA activation was analyzed through a pull‐down assay. Distribution of focal adhesions and actin cytoskeleton was assessed by means of immunofluorescence and western blot. A cell adhesion assay was performed in TGF‐β1‐stimulated cells. Smooth muscle actin expression was studied through western blot and imunofluorescence. c‐Jun N‐terminal kinase phosphorylation was assessed through western blot.

Results:  Our observations show that TGF‐β1 activated the GTPase RhoA, a key regulator of the actin cytoskeleton. As a consequence of this event, this growth factor stimulated the generation of actin stress fibers and the reinforcement of vinculin‐enriched focal adhesions. These responses were blocked after inhibiting ROCK, the main target of RhoA activation. TGF‐β1 also stimulated the adhesion of fibroblasts over fibronectin, an extracellular matrix molecule involved in myofibroblastic differentiation. Finally, induction of the myofibroblast marker α‐smooth muscle actin by TGF‐β1 was abolished by the c‐Jun N‐terminal protein kinase inhibitor SP600125, suggesting a role for this signaling pathway during the induction of this phenotype.

Conclusions:  We propose that TGF‐β1 may promote the differentiation of myofibroblasts through the stimulation of cell spreading and adhesion, the reinforcement of focal adhesions, the maturation of the actin cytoskeleton, and the induction of α‐smooth muscle actin. Activity of RhoA‐ROCK and c‐Jun N‐terminal protein kinase signaling pathways are probably involved in these cellular events.
Litter Characteristics of Gilts Artificially Inseminated with Transforming Growth Factor‐β
Authors: Rhodes Michelle , Brendemuhl Joel H. , Hansen Peter J.
Published: July 2006

Problem  Semen is a rich source of transforming growth factor‐β (TGF‐β) and it has been proposed that this molecule promotes embryonic survival by modifying immune responses to promote tolerance toward paternal antigens and by inducing release of cytokines that promote embryonic development. The role of TGF‐β was tested using pigs by evaluating whether its addition to washed sperm improves conceptus survival and fetal growth.

Methods of study  At estrus, gilts were artificially inseminated twice at 12‐hr intervals with 100 mL of either washed semen resuspended in a commercial semen extender supplemented with 2 mg/mL of gelatin or washed semen in the same extender containing 65 ng/mL of TGF‐β1. Three boars were used as semen donors. At day 80 (±4 days) of gestation, gilts were sacrificed and reproductive tracts harvested.

Results  Treatment had no effect (P > 0.10) on total or live fetuses per litter, implantation rate, fetal survival or percentage of corpora lutea resulting in live fetuses at day 80. Insemination with TGF‐β1 also did not affect total or average fetal weight or total placental weight. There was a tendency (P = 0.09) for average placental weight of live fetuses to be lower for pregnancies established in gilts treated with TGF‐β1. Also, placental efficiency (mass of fetus/mass of placenta) was greater (P < 0.05) for pregnancies established in gilts treated with TGF‐β1. The high fertility in control gilts (80% implantation rate and 11.5 live fetuses per litter) is indicative that soluble seminal factors are not necessary for the establishment of pregnancy.

Conclusions  Within the ranges tested, concentration of TGF‐β in the fluid phase of the inseminate is not an important determinant of conceptus survival or fetal and placental growth to day 80 of gestation in the pig.
Yeh1 Constitutes the Major Steryl Ester Hydrolase under Heme-Deficient Conditions in
Saccharomyces cerevisiae
Authors: Köffel René , Schneiter Roger
Published: July 2006

Steryl esters are stored in intracellular lipid droplets from which they are mobilized upon demand and hydrolyzed to yield free sterols and fatty acids. The mechanisms that control steryl ester mobilization are not well understood. We have previously identified a family of three lipases of
Saccharomyces cerevisiae
that are required for efficient steryl ester hydrolysis, Yeh1, Yeh2, and Tgl1 (R. Köffel, R. Tiwari, L. Falquet, and R. Schneiter, Mol. Cell. Biol. 25:1655-1668, 2005). Both Yeh1 and Tgl1 localize to lipid droplets, whereas Yeh2 is localized to the plasma membrane. To characterize the precise function of these three partially redundant lipases, we examined steryl ester mobilization under heme-deficient conditions.
S. cerevisiae
is a facultative anaerobic organism that becomes auxotrophic for sterols and unsaturated fatty acids in the absence of molecular oxygen. Anaerobic conditions can be mimicked in cells that are deficient for heme synthesis. We here report that Yeh1 is the sole active steryl ester hydrolase under such heme-deficient conditions, indicating that Yeh1 is activated whereas Yeh2 and Tgl1 are inactivated by the lack of heme. The heme-dependent activation of Yeh1 is mediated at least in part by an increase in steady-state levels of Yeh1 at the expense of Yeh2 and Tgl1 in exponentially growing cells. This increase in steady-state levels of Yeh1 requires Rox3, a component of the mediator complex that regulates transcription by RNA polymerase II. These data thus provide the first link between fat degradation and the transcriptional control of lipase activity in yeast.
Transcription Factor STE12α Has Distinct Roles in Morphogenesis, Virulence, and Ecological Fitness of the Primary Pathogenic YeastCryptococcus gattii
Authors: Ren Ping , Springer Deborah J. , Behr Melissa J. , Samsonoff William A. , Chaturvedi Sudha , Chaturvedi Vishnu
Published: July 2006

Cryptococcus gattiiis a primary pathogenic yeast, increasingly important in public health, but factors responsible for its host predilection and geographical distribution remain largely unknown. We have characterizedC. gattii STE12α to probe its role in biology and pathogenesis because this transcription factor has been linked to virulence in many human and plant pathogenic fungi. A full-lengthSTE12α gene was cloned by colony hybridization and sequenced using primer walk and 3′ rapid amplification of cDNA ends strategies, and aste12αΔ gene knockout mutant was created byURA5insertion at the homologous site. A semiquantitative analysis revealed delayed and poor mating inste12αΔ mutant; this defect was not reversed by exogenous cyclic AMP.C. gattiiparent and mutant strains showed robust haploid fruiting. Among putative virulence factors tested, the laccase transcript and enzymatic activity were down regulated in theste12αΔ mutant, with diminished production of melanin. However, capsule, superoxide dismutase, phospholipase, and urease were unaffected. Similarly, Ste12 deficiency did not cause any auxotrophy, assimilation defects, or sensitivity to a large panel of chemicals and antifungals. Theste12αΔ mutant was markedly attenuated in virulence in both BALB/c and A/Jcr mice models of meningoencephalitis, and it also exhibited significant in vivo growth reduction and was highly susceptible to in vitro killing by human neutrophils (polymorphonuclear leukocytes). In tests designed to simulate theC. gattiinatural habitat, theste12αΔ mutant was poorly pigmented on wood agar prepared from two tree species and showed poor survival and multiplication in wood blocks. Thus,STE12α plays distinct roles inC. gattiimorphogenesis, virulence, and ecological fitness.
FsFKS1, the 1,3-β-Glucan Synthase from the Caspofungin-Resistant FungusFusarium solani
Authors: Ha Young-sil , Covert Sarah F. , Momany Michelle
Published: July 2006

The cell wall, a mesh of carbohydrates and proteins, shapes and protects the fungal cell. The enzyme responsible for the synthesis of one of the main components of the fungal wall, 1,3-β-glucan synthase, is targeted by the antifungal caspofungin acetate (CFA). Clinical isolates ofCandida albicansandAspergillus fumigatusare much more sensitive to CFA than clinical isolates ofFusariumspecies. To better understand CFA resistance inFusariumspecies, we cloned and sequenced FsFKS1, which encodes theFusarium solanif. sp.pisiβ(1,3)-d-glucan synthase, used RNA interference to reduce its expression and complemented deletion of the essentialfksgene of the CFA-sensitive fungusA. fumigatuswith FsFKS1. Reduction of the FsFKS1message inF. solanif. sp.pisireduced spore viability and caused lysis of spores and hyphae, consistent with cell wall defects. Compensating for the loss ofA. fumigatus fks1with FsFKS1caused only a modest increase in the tolerance ofA. fumigatusfor CFA. Our results suggest that FsFKS1 is required for the proper construction ofF. solanicell walls and that the resistance ofF. solanito CFA is at best only partially due to resistance of the FsFKS1 enzyme to this antifungal agent.
Plasmodium falciparum
AMA1 Binds a Rhoptry Neck Protein Homologous to TgRON4, a Component of the Moving Junction in
Toxoplasma gondii
Authors: Alexander David L. , Arastu-Kapur Shirin , Dubremetz Jean-Francois , Boothroyd John C.
Published: July 2006

Plasmodium falciparum
apical membrane antigen 1 (PfAMA1) coimmunoprecipitates with the
Plasmodium
homologue of TgRON4, a secreted rhoptry neck protein of
Toxoplasma gondii
that migrates at the moving junction in association with TgAMA1 during invasion. PfRON4 also originates in the rhoptry necks, suggesting that this unusual collaboration of micronemes and rhoptries is a conserved feature of
Apicomplexa
.
Gene Expression Induced by Copper Stress in the DiatomThalassiosira pseudonana
Authors: Davis Aubrey K. , Hildebrand Mark , Palenik Brian
Published: July 2006

Utilizing a PCR-based subtractive cDNA approach, we demonstrated that the marine diatomThalassiosira pseudonanaexhibits a rapid response at the gene level to elevated concentrations of copper and that this response attenuates over 24 h of continuous exposure. A total of 16 copper-induced genes were identified, 11 of which were completely novel; however, many of the predicted amino acid sequences had characteristics suggestive of roles in ameliorating copper toxicity. Most of the novel genes were not equivalently induced by H2O2- or Cd-induced stress, indicating specificity in response. Two genes that could be assigned functions based on homology were also induced under conditions of general cellular stress. Half of the identified genes were located within two inverted repeats in the genome, and novel genes in one inverted repeat had mRNA levels induced by ∼500- to 2,000-fold by exposure to copper for 1 h. Additionally, some of the inverted repeat genes demonstrated a dose-dependent response to Cu, but not Cd, and appear to belong to a multigene family. This multigene family may be the diatom functional homolog of metallothioneins.
cis
-Acting Site Controlling Bidirectional Transcription at the Growth-Differentiation Transition in
Dictyostelium discoideum
Authors: Hirose Shigenori , Payne Samuel H. , Loomis William F.
Published: July 2006

A pair of adjacent genes,
impA
and
dia1
, are divergently transcribed but expressed at different stages in the life cycle of
Dictyostelium discoideum
. The intervening 654-bp region carries
cis
-acting regions that are essential for transcription in both directions as well as repression of
dia1
in growing cells. We have focused on a 112-bp region proximal to
dia1
that is essential for bidirectional transcription. Analyses of a set of internal deletions showed that the sequence between positions 80 and 97 (TTTGAATTTTTTGAATTT) is critical and that bases outside this region are dispensable. Site-directed mutations within this critical region confirmed the importance of this sequence for transcription both to the right and to the left. However, insertions of either 6 or 24 Ts into the run of 6 Ts separating the repeated GAA sequence had little effect on the functioning of the site in either direction, suggesting that factors recognize the half-sites TTGAATT separately. Inversion of the bases between positions 80 and 97 greatly reduced expression in both directions, indicating that orientation is critical for expression of both the nearby
impA
gene and the distal
dia1
gene, which is more than 500 bp away. Comparison of 38 mutant constructs with multiple random variations in the region indicated that transcription factors may bind to a range of related sequences and still retain function. All functional constructs directed transcription both leftward and rightward, while all nonfunctional constructs were impaired for transcription in both directions. It appears that the same transcription complex controls transcription of both
impA
and
dia1
.
A MADS Box Protein Interacts with a Mating-Type Protein and Is Required for Fruiting Body Development in the Homothallic Ascomycete
Sordaria macrospora
Authors: Nolting Nicole , Pöggeler Stefanie
Published: July 2006

MADS box transcription factors control diverse developmental processes in plants, metazoans, and fungi. To analyze the involvement of MADS box proteins in fruiting body development of filamentous ascomycetes, we isolated the
mcm1
gene from the homothallic ascomycete
Sordaria macrospora
, which encodes a putative homologue of the
Saccharomyces cerevisiae
MADS box protein Mcm1p. Deletion of the
S. macrospora mcm1
gene resulted in reduced biomass, increased hyphal branching, and reduced hyphal compartment length during vegetative growth. Furthermore, the
S. macrospora Δmcm1
strain was unable to produce fruiting bodies or ascospores during sexual development. A yeast two-hybrid analysis in conjugation with in vitro analyses demonstrated that the
S. macrospora
MCM1 protein can interact with the putative transcription factor SMTA-1, encoded by the
S. macrospora
mating-type locus. These results suggest that the
S. macrospora
MCM1 protein is involved in the transcriptional regulation of mating-type-specific genes as well as in fruiting body development.
A Mitogen-Activated Protein Kinase Controls Differentiation of Bloodstream Forms of
Trypanosoma brucei
Authors: Domenicali Pfister Debora , Burkard Gabriela , Morand Sabine , Renggli Christina Kunz , Roditi Isabel , Vassella Erik
Published: July 2006

African
trypanosomes undergo differentiation in order to adapt to the mammalian
host and the tsetse fly vector. To characterize the role of a
mitogen-activated protein (MAP) kinase homologue, TbMAPK5, in the
differentiation of
Trypanosoma brucei
, we constructed
a knockout in procyclic (insect) forms from a differentiation-competent
(pleomorphic) stock. Two independent knockout clones proliferated
normally in culture and were not essential for other life cycle stages
in the fly. They were also able to infect immunosuppressed mice, but
the peak parasitemia was 16-fold lower than that of the wild type.
Differentiation of the proliferating long slender to the
nonproliferating short stumpy bloodstream form is triggered by an
autocrine factor, stumpy induction factor (SIF). The knockout
differentiated prematurely in mice and in culture, suggestive of
increased sensitivity to SIF. In contrast, a null mutant of a cell line
refractory to SIF was able to proliferate normally. The differentiation
phenotype was partially rescued by complementation with wild-type
TbMAPK5 but exacerbated by introduction of a nonactivatable mutant
form. Our results indicate a regulatory function for TbMAPK5 in the
differentiation of bloodstream forms of
T. brucei
that might be exploitable as a target for chemotherapy against human
sleeping
sickness.
Changing Roles of Aurora-B Kinase in Two Life Cycle Stages of
Trypanosoma brucei
Authors: Li Ziyin , Wang C. C.
Published: July 2006

Aurora-B kinase is a chromosomal passenger protein essential for chromosome segregation and cytokinesis. In the procyclic form of
Trypanosoma brucei
, depletion of an aurora-B kinase homologue TbAUK1 inhibited spindle formation, mitosis, cytokinesis, and organelle replication without altering cell morphology. In the present study, an RNA interference knockdown of TbAUK1 or overexpression of inactive mutant TbAUK1-K58R in the bloodstream form also resulted in defects in spindle formation, chromosome segregation, and cytokinesis but allowed multiple rounds of nuclear DNA synthesis, nucleolus multiplication, and continuous replication of kinetoplast, basal body, and flagellum. The typical trypanosome morphology was lost to an enlarged round shape filled with microtubules. It is thus apparent that there are distinctive mechanisms of action of TbAUK1 in regulating cell division between the two developmental stages of trypanosome. While it exerts a tight control on mitosis, organelle replication, and cytokinesis in the procyclic form, it regulates cytokinesis without rigid control over either nuclear DNA synthesis or organelle replication in the bloodstream form. The molecular basis underlining these discrepancies remains to be explored.
CHAOTIFYING THE CONTROLLABLE LINEAR SYSTEM VIA SINGLE INPUT STATE FEEDBACK
Authors: WU ZHENG MAO , LU JUN GUO , XIE JIAN YING , LI JIE
Published: July 2006

An approach for chaotifying a stable controllable linear system via single input state-feedback is presented. The feedback controller designed is a sawtooth function of the system states, which can make the fixed point of the closed-loop system to be a snap-back repeller, thereby yielding chaotic dynamics. Based on the Marotto theorem, it is proven theoretically that the closed-loop system is chaotic in the sense of Li and Yorke. Finally, the simulation results are used to illustrate the effectiveness of the proposed theory.
HYDROGEN BONDING IN DIAMOND: A COMPUTATIONAL STUDY
Authors: OFER O. , ADLER JOAN , HOFFMAN A.
Published: July 2006

We present tight binding molecular dynamics simulations of the diffusion and bonding of hydrogen in bulk diamond. The motion of hydrogen atoms and the resultant structural and electronic energy level changes are investigated. The hydrogen atoms were found to have a tendency to migrate to the surface layer of diamond, resulting in a local deformation of the lattice, creating new energy states above and below the Fermi energy in the bandgap of the diamond density of states. In the diamond bulk, at high hydrogen concentrations, vacancies created by a hydrogen atom are quickly filled with other hydrogen atoms causing a deformation of the diamond lattice, inducing H 2 formation. This creates new energy states above the Fermi energy and reduces the secondary bandgap of the diamond density of states.
ON SPIRAL GLIDER-GUNS IN HEXAGONAL CELLULAR AUTOMATA: ACTIVATOR-INHIBITOR PARADIGM
Authors: WUENSCHE ANDREW , ADAMATZKY ANDREW
Published: July 2006

We present a cellular-automaton model of a reaction-diffusion excitable system with concentration dependent inhibition of the activator, and study the dynamics of mobile localizations (gliders) and their generators. We analyze a three-state totalistic cellular automaton on a two-dimensional lattice with hexagonal tiling, where each cell connects with 6 others. We show that a set of specific rules support spiral glider-guns (rotating activator-inhibitor spirals emitting mobile localizations) and stationary localizations which destroy or modify gliders, along with a rich diversity of emergent structures with computational properties. We describe how structures are created and annihilated by glider collisions, and begin to explore the necessary processes that generate this kind of complex dynamics.
A NOVEL SCHEME FOR FORCE TERM IN THE LATTICE BGK MODEL
Authors: DU RUI , SHI BAOCHANG
Published: July 2006

In this paper a novel scheme of the lattice BGK (LBGK) model with a force term has been proposed. Unlike the existing models, an appropriate term was added in the evolutionary equation. Through the Chapman–Enskog (C–E) procedure the Navier–Stokes (N–S) equations with a force term can be recovered with the kinetic viscosity. Three discrete methods of the added term have been discussed in detail. It can be proved that some existing models are the special cases of the model in this paper. We have taken the numerical simulation of the generalized Poiseuille flow driven by a constant force in a channel filled with a porous medium of porosity flow in 2D with different values of the parameters and compared the three models of different discrete schemes in the aspect of the numerical accuracy and stability.
UNIVERSAL CONSTRUCTION AND SELF-REPRODUCTION ON SELF-TIMED CELLULAR AUTOMATA
Authors: TAKADA YOUSUKE , ISOKAWA TEIJIRO , PEPER FERDINAND , MATSUI NOBUYUKI
Published: July 2006

This paper proposes a universal constructor implemented on a self-timed cellular automaton, which is a particular type of asynchronous cellular automaton. Our construction utilizes the asynchronous nature of the underlying cellular automaton in a direct way, as a result of which it is simpler than the conventional construction based on the simulation of a synchronous cellular automaton by an asynchronous cellular automaton. Our model employs 39 rotation-invariant rules and the state of each cell is encoded by 8 bits.
THE PENNA MODEL WITH EXTRAGENETIC DISEASE
Authors: PAN QIUHUI , LI MENGPING , HE MINGFENG
Published: July 2006

In Penna model, the genetic disease which influences the existence of individual has been described by bit-string. In fact, the individual will get extragenetic disease and die of that. In this paper we consider the extragenetic disease and discuss the influence of disease-resistant capability and cure on the existence of species.
SIMULATION OF LAMINAR CONFINED IMPINGING STREAMS USING LATTICE BOLTZMANN METHOD
Authors: LIU HONG JUAN , ZOU CHUN , TIAN ZHI WEI , ZHENG CHU GUANG
Published: July 2006

Numerical simulations are performed to study the flow characteristic of laminar confined impinging streams using the lattice Boltzmann method (LBM). The velocity distributions for different flow conditions and geometric configurations are presented. By examination of the contours for the velocity magnitude, the size of the impingement zone is measured out for the first time. It is found that both the inlet jet Reynolds number and the geometry of the system have effects on the size of the impingement zone. Simulation results demonstrated that LBM is a potentially reliable computational tool for simulations of impinging streams.
Maximal lengthening contractions increase p70 S6 kinase phosphorylation in human skeletal muscle in the absence of nutritional supply
Authors: Eliasson Jörgen , Elfegoun Thibault , Nilsson Johnny , Köhnke Rickard , Ekblom Björn , Blomstrand Eva
Published: July 2006

The aim of this study was to compare the training stimuli of eccentric (lengthening) and concentric (shortening) contractions regarding the effect on signaling enzymes involved in protein synthesis. Ten male subjects performed 4 × 6 maximal eccentric contractions on one leg followed by 4 × 6 maximal concentric contractions on the other. Six additional subjects performed the same protocol, but with maximal concentric and submaximal eccentric exercise of equal force to that of the maximal concentric contractions. Muscle biopsy samples were taken from the vastus lateralis before, immediately after, and 1 and 2 h after exercise in both legs. The average peak force produced during the maximal eccentric exercise was 31% higher than during the maximal concentric exercise, 2,490 (±100) vs. 1,894 (±108) N ( P < 0.05). The maximal eccentric contractions led to two- to eightfold increases in the phosphorylation of p70 S6 kinase (p70S6k) and the ribosomal protein S6 that persisted for 2 h into recovery but no significant changes in phosphorylation of Akt or mammalian target of rapamycin (mTOR). Maximal concentric and submaximal eccentric contractions did not induce any significant changes in Akt, mTOR, p70S6k, or S6 phosphorylation up to 2 h after the exercise. The results indicate that one session of maximal eccentric contractions activates p70S6k in human muscle via an Akt-independent pathway and suggest that maximal eccentric contractions are more effective than maximal concentric contractions in stimulating protein synthesis in the absence of a nutritional intake, an effect that may be mediated through a combination of greater tension and stretching of the muscle.
Regulation of contraction-induced FA uptake and oxidation by AMPK and ERK1/2 is intensity dependent in rodent muscle
Authors: Raney Marcella A. , Turcotte Lorraine P.
Published: July 2006

Muscle contraction activates AMP-activated protein kinase (AMPK) and extracellular signal-regulated kinase (ERK1/2), two signaling molecules involved in the regulation of muscle metabolism. The purpose of this study was to determine whether activation of AMPK and/or ERK1/2 contributes to the regulation of muscle fatty acid (FA) uptake and oxidation in contracting muscle. Rat hindquarters were perfused during rest (R) or electrical stimulation (E) of increasing intensity by manipulating train duration (E1 = 25 ms, E2 = 50 ms, E3 = 100 ms, E4 = 200 ms). For matched FA delivery, FA uptake was significantly greater than R during E1, E2, and E3 (7.8 ± 0.7 vs. 14.4 ± 0.3, 16.9 ± 0.8, 15.2 ± 0.5 nmol·min−1·g−1, respectively, P < 0.05), but not during E4 (8.3 ± 0.3 nmol·min−1·g−1, P > 0.05). FA oxidation was significantly greater than R during E1 and E2 (1.5 ± 0.1 vs. 2.3 ± 0.2, 2.5 ± 0.2 nmol·min−1·g−1, P < 0.05) before returning to resting levels for E3 and E4 (1.8 ± 0.1 and 1.5 ± 0.2 nmol·min−1·g−1, P > 0.05). A positive correlation was found between FA uptake and ERK1/2 phosphorylation from R to E3 ( R2 = 0.55, P < 0.05) and between FA oxidation and ERK1/2 phosphorylation from R to E2 ( R2 = 0.76, P < 0.05), correlations that were not maintained when the data for E4 and E3 and E4, respectively, were included in the analysis ( R2 = 0.04 and R2 = 0.03, P > 0.05). A positive correlation was also found between FA uptake and FA oxidation and AMPK activity for all exercise intensities ( R2 = 0.57, R2 = 0.65 respectively, P < 0.05). These results, in combination with previous data from our laboratory, suggest that ERK1/2 and AMPK are the predominant signaling molecules regulating FA uptake and oxidation during low- to moderate-intensity muscle contraction and during moderate- to high-intensity muscle contraction, respectively.
The PPARγ agonist pioglitazone modifies the vascular sodium-angiotensin II relationship in insulin-resistant rats
Authors: Zanchi Anne , Perregaux Christine , Maillard Marc , Cefai Daniel , Nussberger Juerg , Burnier Michel
Published: July 2006

Glitazones are efficient insulin sensitizers that blunt the effects of angiotensin II (ANG II) in the rat. Sodium chloride is another important modulator of the systemic and renal effects of ANG II. Whether glitazones interfere with the interaction between sodium and the response to ANG II is not known. Therefore, we investigated the effects of pioglitazone on the relationship between sodium and the systemic and renal effects of ANG II in rats. Pioglitazone, or vehicle, was administered for 4 wk to 8-wk-old obese Zucker rats. Animals were fed a normal-sodium (NS) or a high-sodium (HS) diet. Intravenous glucose tolerance tests, systemic and renal hemodynamic responses to ANG II, and the renal ANG II binding and expression of ANG II type 1 (AT1) receptors were measured. The results of our study were that food intake and body weight increased, whereas blood pressure, heart rate, filtration fraction, and insulin levels decreased significantly with pioglitazone in obese rats on both diets. Pioglitazone blunted the systemic response to ANG II and abolished the increased responsiveness to ANG II induced by a HS diet. Pioglitazone modified the renal hemodynamic response to changes in salt intake while maintaining a lower filtration fraction with ANG II perfusion. These effects were associated with a decrease in the number and expression of the AT1 receptor in the kidney. In conclusion, these data demonstrate that the peroxisome proliferator-activated receptor-γ agonist pioglitazone modifies the physiological relationship between sodium chloride and the response to ANG II in insulin-resistant rats.