bluuebunny/crossref_metadata_2025 huggingface dataset:
Erdheim‐Chester Disease With Cutaneous Features in an Indian Patient
Authors: Garg Taru , Chander Ram , Gupta Tanvi , Mendiratta Vibhu , Jain Manjula
Published: May 2008

A 60‐year‐old Indian woman presented with multiple asymptomatic, firm swellings over the face that had been progressively increasing for the past 3.5 years. She complained of dry cough and dyspnea of 2 years' duration, which was diagnosed as interstitial lung disease (ILD) based on chest radiography and high‐resolution computed tomography. Apart from occasional backaches, the patient had no other systemic complaints. The results of the general physical examination was normal, with no lymphadenopathy. Cutaneous examination revealed multiple (5) firm, yellowish to skin‐colored well‐defined nodules with irregular margins ranging in size from 1× 1 cm to 4×8 cm present over the left periorbital region and right jawline, with overlying telangiectasias on the skin (Figure 1). On examination of the chest, she had generalized rhonchi and crepts; the remainder of the systemic examination results were normal. Fine needle aspiration cytology from the nodule in the periorbital area revealed a dispersed population of spindle cells, numerous foam cells, and giant cells suggestive of xanthogranuloma. Histopathology from the nodule on the jawline showed abundant foamy histiocytes in the dermis with few multinucleated giant cells and lymphocytes (Figure 2). The foamy histiocytes were periodic acid‐Schiff‐positive. On immunohistochemistry, histiocytes were CD68‐positive. Findings of routine investigations including hemogram, peripheral blood smear, and blood chemistry were normal. Radiography of the lumbosacral spine showed mixed osteolytic and osteosclerotic lesions involving L5‐S1, the left sacroiliac joint, and the left iliac blade. Findings from radiography of the long bones and skull were normal. Contrast‐enhanced computed tomographic scan of the abdomen and pelvis showed areas of osteolysis, with marginal sclerosis present bilaterally that involved the iliac blades and the right half of the sacrum. A methylene diphosphate bone scan revealed increased tracer uptake seen at the fifth lumbar vertebrae, bilateral sacroiliac bone, and left iliac bone and areas of photopenia in sacrum. Bone marrow aspiration from the sternum showed normal cells with a normal erythroid‐to‐myeloid ratio. Ultrasonographic B scanning of the eyes showed no retro‐orbital involvement. Erdheim‐Chester disease was diagnosed in this patient on the basis of diagnostic histopathology, radiologic features involving bones, and ILD and treatment with 40 mg oral prednisolone daily was started. Surgical debulking of her skin lesions was planned, but the patient refused due to her worsening ILD.

Photograph showing xanthomatous coalescing nodules with overlying telangiectasias and crusted fine needle aspiration cytology site.

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Photomicrograph showing foamy histiocytes, giant cells, and lymphocytes (hematoxylin and eosin stain, original magnification ×40).

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Tacrolimus‐Induced Hyperpigmentation in a Patch of Vitiligo
Authors: De Dipankar , Kanwar Amrinder Jit
Published: May 2008

A 10‐year‐old boy had vitiligo vulgaris involving limited areas and was prescribed topical tacrolimus ointment (0.03%), as the lesions were present in the infraorbital area in addition to other areas including the arms, thighs, and around the knees and ankles. Within 2 months of starting treatment, he had evidence of diffuse repigmentation of all the patches of vitiligo. Two months later, all the lesions repigmented completely with excellent color matching except those in the infraorbital area. The parents were anxious due to brownish hyperpigmentation in the previous patch of vitiligo in infraorbital area (Figure). He had no irritation or burning sensation in the areas of application. There was no history of photosensitivity. The patient was applying tacrolimus once at night, and no photoprotection was advised. Due to location of the lesion in the infraorbital area, a cosmetically important site, the parents did not consent for punch biopsy. The hyperpigmentation was temporary, with reappearance of depigmentation within 1 month of discontinuing topical tacrolimus application.

Brownish hyperpigmentation in the site of previous vitiligo patch.

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Arterial Stiffness and Vascular Load in Heart Failure
Authors: Ooi Henry , Chung William , Biolo Andreia
Published: May 2008

“Men are born soft and supple; dead, they are stiff and hard. Plants are born tender and pliant; dead, they are brittle and dry. Thus whoever is stiff and inflexible is a disciple of death. Whoever is soft and yielding is a disciple of life. The hard and stiff will be broken. The soft and supple will prevail.”—Lao Tzu, 6th century BC

Vascular load is an important determinant of ventricular function. This is particularly true of the failing heart, which is exquisitely load‐sensitive. Vascular load comprises 2 major components: resistive load, which arises primarily at the arteriolar resistance vessels, and pulsatile load, which is primarily determined by aortic stiffness and early return of reflected waves from the periphery to the heart. Assessment of pulsatile load is gaining increasing prominence as evidence grows of a significant pathophysiologic role for arterial stiffness in cardiovascular disease, including heart failure. Assessment of arterial stiffness and vascular load is reviewed here. The importance of optimal ventricular‐vascular coupling to maximize the efficiency of cardiac ejection is discussed. Current knowledge of arterial stiffness, vascular load, and ventricular‐vascular coupling in systolic heart failure and in heart failure with a normal ejection fraction (“diastolic failure”) is described. Reducing aortic stiffness may form an important future therapeutic target in patients with heart failure.
Etiology and Management of Anemia in Patients With Heart Failure: How Much Iron Is Missing?
Authors: Silva Luis Beck da , Rohde Luis E. , Clausell Nadine
Published: May 2008

Anemia is common among patients with heart failure (HF) and has been associated with worse prognosis. To date, it is not well known whether correction of anemia in these patients can improve outcome. Proposed modalities for correction of anemia have been either administration of erythropoiesis‐stimulating proteins, which appears plausible in patients with concomitant renal failure (so‐called cardiorenal syndrome), or iron supplementation, which is particularly attractive in patients with no overt renal failure and chronic disease anemia with some degree of iron deficiency. This article reviews the rationale for anemia correction and the latest randomized clinical trial assessing clinical utility of erythropoiesis‐stimulating proteins and/or iron supplementation through oral or intravenous administration in anemic HF patients.
Reliability-Based Optimization With Discrete and Continuous Decision and Random Variables
Authors: McDonald Mark , Mahadevan Sankaran
Published: May 2008

Engineering design problems frequently involve both discrete and continuous random and design variables, and system reliability may depend on the union or intersection of multiple limit states. Solving reliability-based design optimization (RBDO) problems, where some or all of the decision variables must be integer valued, can be expensive since the computational effort increases exponentially with the number of discrete variables in discrete optimization problems, and the presence of both system and component level reliability makes RBDO more expensive. The presence of discrete random variables in a RBDO problem has usually necessitated the use of Monte Carlo simulation or some other type of enumeration procedure, both of which are computationally expensive. In this paper, the theorem of total probability is used to allow for the use of the first-order reliability method in solving mixed-integer RBDO problems. Single-loop RBDO formulations are developed for three classes of mixed-integer RBDO with both discrete and continuous random variables and component and system-level reliability constraints. These problem formulations can be solved with any appropriate discrete optimization technique. This paper develops, for each of the three problem classes, greedy algorithms to find an approximate solution to the mixed-integer RBDO problem with both component and system reliability constraints and/or objectives. These greedy algorithms are based on the solution of a relaxed formulation and require hardly additional computational expense than that required for the solution of the continuous RBDO problem. The greedy algorithms are verified by branch and bound and genetic algorithms. Also, this paper develops three algorithms, which can allow for calibration of reliability estimation with a more accurate reliability analysis technique. These algorithms are illustrated in the context of a truss optimization problem.
Engineering Product Design Optimization for Retail Channel Acceptance
Authors: Williams N. , Azarm S. , Kannan P. K.
Published: May 2008

Significant recent research has focused on the marriage of consumer preferences and engineering design in order to improve profitability. The extant literature has neglected the effects of marketing channels, which are becoming increasingly important. At the crux of the issue is the fact that channel dominating retailers, like Wal-Mart, have the ability to unilaterally control manufacturer’s design decisions as gatekeepers to the consumers or market. In this paper, we propose a new methodology that accounts for this power asymmetry. A chance constrained optimization framework is used to model retailer acceptance of possible engineering designs and accounts for the important effect on the profitability of the retailer’s assortment through a latent class estimation of demand from conjoint surveys. Our approach allows the manufacturer to optimize a product design for its own profitability while reliably ensuring that the product will make it to market by making the retailer more profitable with the addition of the new product to the assortment. As a demonstrative example, we apply the proposed approach for product design selection in the case of an angle grinder. For this example, we analyze the market and are able to improve expected manufacturer profitability while simultaneously presenting the designer with trade-offs between slotting allowances, market share, and risk of retailer acceptance.
Housing Influence on Churning Losses in Geared Transmissions
Authors: Changenet C. , Velex P.
Published: May 2008

In a previous paper (Changenet, and Velex, 2007, “A Model for the Prediction of Churning Losses in Geared Transmissions—Preliminary Results,” ASME J. Mech. Des., 129(1), pp. 128–133), a series of empirical formulas were presented enabling accurate predictions of churning losses for one gear, which is typical of automotive transmission geometry. However, this formulation does not take into account the influence of flanges and deflectors. In order to extend the proposed methodology, a test rig has been set up in which several movable walls can be inserted, thus making it possible to modify the radial and axial clearances, i.e., the distances between the tested gear and the walls. Based on a qualitative evaluation of the various fluid flow regimes possible in gearboxes, the influence of the global volume of the oil sump on churning losses is analyzed. By considering a number of flange and deflector arrangements, the following conclusions are drawn: (a) Radial clearances have a weaker influence than axial clearances and (b) power losses can be minimized by properly chosen axial clearances.
Closed-Loop Analysis in Semantic Tolerance Modeling
Authors: Wang Yan
Published: May 2008

A semantic tolerance modeling scheme based on generalized intervals was recently proposed to allow for embedding more tolerancing intents in specifications with a combination of numerical intervals and logical quantifiers. By differentiating a priori and a posteriori tolerances, the logic relationships among variables can be interpreted, which is useful to verify completeness and soundness of numerical estimations in tolerance analysis. In this paper, we present a semantic tolerance analysis approach to estimate size and geometric tolerance stackups based on closed loops of interval vectors. An interpretable linear system solver is constructed to ensure interpretability of numerical results. A direct linearization method for nonlinear systems is also developed. This new approach enhances traditional numerical analysis methods by preserving logical information during computation such that more semantics can be derived from variation estimations.
Type Synthesis of Six-DOF Wrist-Partitioned Parallel Manipulators
Authors: Kong Xianwen , Gosselin Clément M.
Published: May 2008

A six-DOF wrist-partitioned parallel manipulator is a parallel manipulator in which three of the six actuated joints are used to control the position of a point on the moving platform while the other three are further used to control the orientation of the moving platform. Such parallel manipulators are, in fact, the parallel counterparts of the wrist-partitioned serial manipulators, which are widely used in industry. Unlike parallel manipulators of a general structure, a six-DOF wrist-partitioned parallel manipulator usually has simple kinematic characteristics such as its forward displacement analysis and singularity analysis are easy to solve. This paper deals with the type synthesis of six-DOF wrist-partitioned parallel manipulators. An approach is first proposed for the type synthesis of this class of parallel manipulators. Using the proposed approach, six-DOF wrist-partitioned parallel manipulators can be constructed from the types of three-DOF nonoverconstrained spherical parallel manipulators. A large number of six-DOF wrist-partitioned parallel manipulators are then obtained, and several types of practical relevance are also identified.
Static Equilibrium of Spatial Mechanisms With Cylindrical Joints
Authors: Fischer Ian S.
Published: May 2008

The components of force and torque acting on a joint of a link in static equilibrium are partitioned according to the type of joint so that the equations of static equilibrium can be set up automatically by computer where the type of each joint has been specified in the input data. Special attention is given to the cylindrical joint, and the implications of the geometry of an intermediate link with a cylindrical joint on both ends are examined. While the methodology is demonstrated for the RCCC mechanism, which features a revolute input joint and cylindrical intermediate and output joints, it is adaptable to closed-loop mechanisms of binary links with any kind of joint in any position.
Potent In Vitro Antifungal Activities of Naturally Occurring Acetylenic Acids
Authors: Li Xing-Cong , Jacob Melissa R. , Khan Shabana I. , Ashfaq M. Khalid , Babu K. Suresh , Agarwal Ameeta K. , ElSohly Hala N. , Manly Susan P. , Clark Alice M.
Published: May 2008

Our continuing effort in antifungal natural product discovery has led to the identification of five 6-acetylenic acids with chain lengths from C
16
to C
20
: 6-hexadecynoic acid (compound 1), 6-heptadecynoic acid (compound 2), 6-octadecynoic acid (compound 3), 6-nonadecynoic acid (compound 4), and 6-icosynoic acid (compound 5) from the plant
Sommera sabiceoides
. Compounds 2 and 5 represent newly isolated fatty acids. The five acetylenic acids were evaluated for their in vitro antifungal activities against
Candida albicans, Candida glabrata, Candida krusei, Candida tropicalis, Candida parapsilosis, Cryptococcus neoformans, Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Trichophyton mentagrophytes
, and
Trichophyton rubrum
by comparison with the positive control drugs amphotericin B, fluconazole, ketoconazole, caspofungin, terbinafine, and undecylenic acid. The compounds showed various degrees of antifungal activity against the 21 tested strains. Compound 4 was the most active, in particular against the dermatophytes
T. mentagrophytes
and
T. rubrum
and the opportunistic pathogens
C. albicans
and
A. fumigatus
, with MICs comparable to several control drugs. Inclusion of two commercially available acetylenic acids, 9-octadecynoic acid (compound 6) and 5,8,11,14-eicosatetraynoic acid (compound 7), in the in vitro antifungal testing further demonstrated that the antifungal activities of the acetylenic acids were associated with their chain lengths and positional triple bonds. In vitro toxicity testing against mammalian cell lines indicated that compounds 1 to 5 were not toxic at concentrations up to 32 μM. Furthermore, compounds 3 and 4 did not produce obvious toxic effects in mice at a dose of 34 μmol/kg of body weight when administered intraperitoneally. Taking into account the low in vitro and in vivo toxicities and significant antifungal potencies, these 6-acetylenic acids may be excellent leads for further preclinical studies.
Inactivation of the Type IV Secretion System Reduces the Th1 Polarization of the Immune Response toBrucella abortusInfection
Authors: Rolán Hortensia García , Tsolis Renée M.
Published: May 2008

TheBrucella abortustype IV secretion system (T4SS), encoded by thevirBoperon, is essential for establishing persistent infection in the murine reticuloendothelial system. To gain insight into the in vivo interactions mediated by the T4SS, we compared host responses elicited byB. abortuswith those of an isogenic mutant in thevirBoperon. Mice infected with theB. abortus virBmutant elicited smaller increases in serum levels of immunoglobulin G2a, gamma interferon (IFN-γ), and interleukin-12p40 than did mice infected with wild-typeB. abortus. Despite equal bacterial loads in the spleen, at 3 to 4 days postinfection, levels of IFN-γ were higher in mice infected with wild-typeB. abortusthan in mice infected with thevirBmutant, as shown by real-time PCR, intracellular cytokine staining, and cytokine levels. IFN-γ-producing CD4+T cells were more abundant in spleens of mice infected with wild-typeB. abortusthan invirBmutant-infected mice. Similar numbers of IFN-γ-secreting CD8+T cells were observed in the spleens of mice infected withB. abortus2308 or avirBmutant. These results suggest that early differences in cytokine responses contribute to a stronger Th1 polarization of the immune response in mice infected with wild-typeB. abortusthan in mice infected with thevirBmutant.
Francisella tularensis
subsp.
tularensis
Schu S4 Disulfide Bond Formation Protein B, but Not an RND-Type Efflux Pump, Is Required for Virulence
Authors: Qin Aiping , Scott David W. , Mann Barbara J.
Published: May 2008

Francisella tularensis
subsp.
tularensis
is a highly virulent bacterium that is a CDC select agent. Despite advancements in the understanding of its biology, details pertaining to virulence are poorly understood. In previous work, we identified a transposon insertion mutant in the FTT0107c locus that was defective in intracellular survival in HepG2 and J77A.1 cells. Here, we report that this mutant was also highly attenuated in vivo. The FTT0107c locus is predicted to encode an ortholog of the disulfide bond formation B protein (DsbB). This designation was confirmed by complementation of an
Escherichia coli dsbB
mutant. This
dsbB
mutant of Schu S4 was highly attenuated in mice, but unlike what has been reported for
Francisella novicida
, intranasal immunization with a sublethal dose did not induce protection against wild-type challenge.
dsbB
was found to be transcribed in an operon with
acrA
and
acrB
, which encode an RND-type efflux pump. However, this pump did not make a significant contribution to virulence because strains with nonpolar deletions in
acrA
and
acrB
behaved like wild-type strain Schu S4 with respect to intracellular growth and in vivo virulence. This result is in contrast to a report that an
acrB
mutant of a live vaccine strain of
F. tularensis
has decreased virulence in mice. Overall, these results demonstrate key differences between the virulence requirements of Schu S4 and less virulent subspecies of
Francisella
. We have shown that DsbB is a key participant in intracellular growth and virulence, and our results suggest that there are critical virulence factors that contain disulfide bonds.
Pure and applied mycology
Authors: Trinci A. P. J.
Published: May 2008

Pure research is defined as experimental or theoretical work undertaken primarily to acquire new knowledge without any particular application or use in view. By contrast, applied research, which, of course, is also undertaken to acquire new knowledge, is directed primarily towards practical aims or objectives. In recent years governments worldwide have used Technology Foresight Exercises, to enable them to direct basic research in universities towards areas of science with commercial potential. There is, of course, but a short step between this approach and the direct involvement of universities in applied research. Using examples from four areas of research in mycology, this article advocates the need to maintain a broad base of pure (curiosity-driven) research in universities and research institutes, as well as identifying a need for government to provide additional funding for areas of research perceived to be of national importance. Key words: fungal diversity, Fusarium graminearum, protein production, Quorn® mycoprotein, Schizosaccharomyces pombe, technology foresight.
Correlates of pathogen species richness in the grass family
Authors: Clay Keith
Published: May 2008

Factors contributing to the species richness of fungal pathogens infecting grasses were explored through statistical analyses of data derived from a computerized data base on fungi on plants in the United States and from grass floras. The total number of fungal species infecting each grass species, as well as numbers of smuts, rusts, and systemic clavicipitaceous fungi, were compiled. Host characteristics included grass subfamily, the number of species in the genus, geographic range, life history, and their status as native versus alien species, and crop versus noncrop species. Analyses indicated that the best predictor of pathogen species richness per host is host geographical range. Grass subfamily, life history, and status as crops or native species also were significantly correlated with pathogen load but explained less variation than host geographical range. Pathogen species richness per host showed a strong trend to increase with increasing latitude. Extensive sampling of fungal pathogens from selected grass species is needed to provide an independent measure of accuracy of the data base. Key words: biodiversity, fungi, grasses, pathogens, species richness.
Functional diversity in fungi
Authors: Miller Steven L.
Published: May 2008

Diversity has various meanings but generally they reflect the variation in species assemblages within a community. Species establish interpopulation relationships that lead to stable community structure, and stable and resilient communities by definition contain a certain level of diversity. Communities with too great or too little diversity predictably undergo rapid change. Studies of fungal diversity have been limited by taxonomic and logistical difficulties in collecting and defining fungal individuals and species. Succession of fungi on substrates, seasonal fluctuations, inconsistent isolation techniques, and other considerations have also led to problems in assessing fungal species diversity. Although the problem has now been identified it is not likely that significant additions to our taxonomic knowledge will soon be useful in saving rapidly disappearing ecosystems. However, calculations of fungal diversity are not limited to taxonomic information. Several approaches provide measurements of functional diversity in situations where taxonomic information is poorly defined. These include using binary biochemical and physiological descriptors to characterize isolates, evaluating enzymatic capabilities for utilizing particular substrates and extracting DNA or RNA from the soil or other substrate and probing for genes that code for functional enzymes. Such functional approaches can provide timely information on the contribution of fungi to community diversity and toward the establishment of predictors of community stability. This paper reviews the problems in assessing fungal diversity and evaluates potential techniques for determining fungal diversity from a functional perspective. Key words: fungal, microbial diversity, biodiversity, ecology.
Fungi as biocontrol agents of weeds: a tropical perspective
Authors: Evans Harry C.
Published: May 2008

The two approaches, classical and inundative, which can be used to exploit fungi for weed biocontrol, are described and discussed. It is concluded that classical biological control involving the release of coevolved natural enemies, typically highly specific biotrophs into an exotic ecosystem, is the most environmentally and economically acceptable long-term strategy for controlling alien weeds, particularly in conservation areas. Mycoherbicides, based mainly on endemic nectrotrophs, have still not realized their full potential, mainly owing to problems with formulation, application, and market size, but with improved technology these may play an increasingly significant role in agricultural ecosystems. Virulent pathogens with broad host ranges offer the most commercial potential, if these can be tailored to suit individual crop systems. The initial selection of suitable biocontrol agents, based on field, herbarium, and literature surveys is outlined, whilst the problems involved in making the final selection are analysed in detail, especially those relating to taxonomy, biology, and host specificity. Examples are given of fungal pathogens that are being or could be employed for control of some major tropical weed species. Key words: fungi, classical biocontrol, mycoherbicides, tropics, conservation.
Ecological succession and biological control in the phyllosphere
Authors: Marois J. J. , Coleman P. M.
Published: May 2008

Understanding biological control of plant diseases is dependent on an understanding of succession in microbial communities. The colonization of aboveground plant parts by saprophytic microbes is not well understood, but it appears to follow the same model as that in soil communities. When a nutrient source is added, such as plant debris, there is a succession of organisms organized along a spectrum of complexity of carbohydrate utilization. A similar phenomenon may occur during the colonization of plant parts newly exposed by natural development or by wounds, upon which many pathogens depend to serve as sites of infection. These nutrient utilization strategies have been interpreted as indicative of r (rapidly utilizing simple sugars) and K (slowly utilizing lignin) life strategies. If the concepts of r and K species are applicable to microbes, it could indicate what type of interaction would be most likely to be successful for biological control. For example, pathogens that are r species may be better controlled by competition, and K pathogenic species better controlled by parasitism. However, for any interaction to take place, the control agent's environmental requirements, both biotic and abiotic, must overlap with that of the pathogen. The concepts of ecological succession and r and K species, if appropriate for microorganisms, may prove very valuable when developing biological control strategies. Key words: antibioses, competition, island biogeography, parasitism.
Fungal biocontrol of root diseases: endomycorrhizal suppression of cylindrocarpon root rot
Authors: Traquair James A.
Published: May 2008

Many reviews in the past decade outline the need to understand the complex interactions between fungal pathogens of roots, mycorrhizal fungi, mycorrhizosphere associates, and various climatic and edaphic factors to develop stable mycorrhizal biocontrol strategies. Cylindrocarpon root rot caused by Cylindrocarpon destructans is a good example of a replant disorder that is amenable to this type of control in nurseries and new or renovated orchard sites. Cylindrocarpon root rot was reduced by endomycorrhizal colonization of potted peach rootstocks with Glomus aggregatum under controlled environment conditions using Turface or natural, untreated orchard soils. Several mechanisms of suppression are discussed including tolerance to the pathogen through increased host vigor and reduced exudation, competition for space and nutrients, and induced host resistance. Technical innovations and new concepts of fungal community ecology are improving the odds of developing effective biocontrols with mycorrhizae. Exploitation of natural and integrated disease management using multiple mechanisms of pathogen inhibition may offset the difficulties in inoculum preparation. Key words: Cylindrocarpon destructans, antagonism, competition, rhizosphere, mycorrhizosphere.
Turgor pressure and the mechanics of fungal penetration
Authors: Money Nicholas P.
Published: May 2008

This article explores the relationship between cellular turgor pressure and mechanisms used by fungi to invade solid substrates. In the oomycete Saprolegnia ferax, the rate of hyphal growth through solid medium decreases as turgor is reduced and the effect is most pronounced at high agar concentrations. This is the first clear evidence that turgor provides the force for invasive hyphal growth. Among pathogenic fungi, the role of turgor in plant infection has been established by experiments on the rice blast fungus Magnaporthe grisea, which can punch through the surface of rice leaves and a variety of synthetic membranes. In common with other walled organisms, fungal growth hinges on an interplay between turgor and the resistance offered by the wall; irrespective of turgor, no cellular expansion or substrate deformation can occur unless the wall yields. Turgor is the only logical source of the necessary force when fungi penetrate plastics, lift the lids of Petri dishes, or burst through asphalt paving. In other cases, fungi use exoenzymes to soften the substrate in advance of the invading cells. This process is particularly significant in plant infection, which involves a combination of physical force and the secretion of cuticle- and wall-degrading enzymes. Key words: hyphae, osmotic stress, Oomycetes, Magnaporthe, Saprolegnia, turgor pressure.
Independent nuclear motility and hyphal tip growth
Authors: Aist James R.
Published: May 2008

Independent nuclear motility is involved in many important aspects of fungal life cycles, including the following: nuclear division; population of hyphal tip cells, branches, and spores with nuclei; dikaryotization; and karyogamy. Spindle pole bodies are almost constantly in motion during all phases of the nuclear cycle, and they have been linked to most instances of independent nuclear motility. A role for microtubules in this process is now well established, and research is being focused on which set of them, astral or cytoplasmic, is utilized as well as on the microtubule-associated motor proteins that may generate the force. In some cases, F-actin may interact with the microtubules or even provide an alternative cytoskeleton supporting nuclear migration. Hyphal tip growth and independent nuclear motility are coordinated and interrelated processes, making the elucidation of the signals, processes, and structures involved an attractive area for further research. Key words: actin, microtubule, microtubule associated protein, microtubule organizing center, motility, nucleus.
Role of cytosolic pH in axis establishment and tip growth
Authors: Kropf Darryl L. , Gibbon Bryan C. , Money Nicholas P.
Published: May 2008

The role of cytosolic pH (pHc) in determining the growth site and in tip elongation has been investigated by measuring and manipulating pHc. pHcacidifies by 0.1–0.2 units as the growth axis is established. Concomitantly, cells accumulate KCl, which increases the cellular osmotic pressure, resulting in the generation of turgor pressure. The K+taken up is apparently compartmentalized as the free cytosolic K+activity remains constant. At present, the relation between pHc, K+, and turgor pressure is not well understood. A small but statistically significant cytosolic pH gradient, acid at the future growth site, is also detectable during axis establishment. As growth is initiated the intensity of the gradient increases to approximately 0.3 pH units. The magnitude of the pH gradient correlates with the rate of tip elongation. The gradient may regulate tip elongation in a number of ways, including local control of the assembly and stability of cytoskeletal elements. Key words: cytosolic pH gradients, tip growth, turgor pressure, weak acids and bases, SNARF 1, pH-sensitive microelectrodes.
Integration and regulation of hyphal tip growth
Authors: Heath I. Brent
Published: May 2008

Hyphal tip growth is an exquisitely controlled process that forms developmentally regulated, species-specific, even-diameter tubes at rates of up to about 50 μm/min. The traditional view is that this process results from the balance between the expansive force of turgor pressure and the controlled extensibility of the apical cell wall. While these elements are involved, the model places regulation into either the global domain (turgor pressure) or the extracellular environment (the cell wall), neither of which seem well suited to the level of control evinced. Recent evidence suggests that F-actin-rich elements of the cytoskeleton are important in tip morphogenesis. Our current models propose that tip expansion is regulated (restrained under normal turgor pressure and protruded under low turgor) by a peripheral network of F-actin that is attached to the plasmalemma and the cell wall by integrin-containing linkages, thus placing control in the cytoplasm where it is accessible to normal intracellular regulatory systems. The F-actin system also functions in cytoplasmic and organelle motility; control of plasmalemma-located, stretch-activated, Ca2+-transporting, ion channel distribution; vectoral vesicle transport; and exocytosis. Regulation of the system may involve Ca2+, the concentration of which is influenced by the tip-high gradient of the stretch-activated channels, thus suggesting a possible feedback regulation mechanism. Key words: tip growth, fungi, stretch-activated channels, F-actin, Ca2+, hyphae.
Nitrogen metabolite repression inAspergillus nidulans: an historical perspective
Authors: Arst Jr. Herbert N.
Published: May 2008

The paper of Arst and Cove (Mol. Gen. Genet. 126: 111 – 141, 1973) on "Nitrogen metabolite repression in Aspergillus nidulans" has influenced studies and perceptions of gene regulation in filamentous fungi during the past 21 years. Here I attempt to appraise the contributions of that paper and assess its role in further developments. Nitrogen metabolite repression, carbon catabolite repression, pathway-specific and integrated induction, as-acting regulatory mutations, a useful class of growth inhibitors, and a homologous Neurospora crassa gene are all discussed. Key words: Aspergillus nidulans, carbon catabolite repression, nitrogen metabolite repression.
The roles of PUT3, URE2, and GLN3 regulatory proteins in the proline utilization pathway ofSaccharomyces cerevisiae
Authors: Brandriss Marjorie C. , Falvey Darlene A. , des Etages Shelley Ann G. , Xu Shiwei
Published: May 2008

The yeast Saccharomyces cerevisiae can use alternative nitrogen sources such as allantoin, urea, γ-aminobutyrate, or proline when preferred nitrogen sources such as asparagine, glutamine, or ammonium ions are unavailable in the environment. To use proline as the sole nitrogen source, cells must activate the expression of the proline transporters and the genes that encode the catabolic enzymes proline oxidase (PUT1) and Δ1-pyrroline-5-carboxylate dehydrogenase (PUT2). Transcriptional activation of the PUT genes requires the PUT3 regulatory protein, proline, and relief from nitrogen repression. PUT3 is a 979 amino acid protein that binds a short DNA sequence in the promoters of PUT1 and PUT2, independent of the presence of proline. The functional domains of PUT3 have been studied by biochemical and molecular tests and analysis of activator-constitutive and activator-defective mutant proteins. Mutations in the URE2 gene relieve nitrogen repression, permitting inducer-independent transcription of the PUT genes in the presence of repressing nitrogen sources. The GLN3 protein that activates the expression of many genes in alternative nitrogen source pathways is not required for the expression of the PUT genes under inducing, derepressing conditions (proline) or noninducing, repressing conditions (ammonia). Although it has been speculated that the URE2 protein antagonizes the action of GLN3 in the regulation of many nitrogen assimilatory pathways, URE2 appears to act independently of GLN3 in the proline-utilization pathway. Key words: Saccharomyces cerevisiae, proline utilization, nitrogen repression.
The Mauriceville and Varkud plasmids: primitive retroelements found inNeurosporamitochondria
Authors: Lambowitz Alan M. , Chiang Chia-Chien
Published: May 2008

The Mauriceville and closely related Varkud plasmids are small circular DNAs (3.6 and 3.7 kb, respectively) found in the mitochondria of certain Neurospora spp. strains isolated from nature. The plasmids replicate via reverse transcription and appear to be primitive retroelements that may be related to the early ancestors of retroviruses. Recent studies have shown that the plasmid reverse transcriptase closely resembles certain viral RNA-dependent RNA polymerases in initiating (−) strand cDNA synthesis de novo (i.e., without a primer) at a tRNA-like structure at the 3′ end of the plasmid transcript. The plasmid reverse transcriptase can also use DNA or RNA primers and can carry out template-switching reactions that lead to the generation of suppressive mutant plasmids or the integration of the plasmids into mitochondrial DNA. The characteristics of the plasmids and their reverse transcription mechanism suggest an evolutionary connection between RNA and DNA replication and raise the possibility that the plasmids are related to the earliest DNA-based life forms that emerged at the time of transition from an RNA to a DNA world. Key words: DNA synthesis, evolution, retrovirus, reverse transcriptase, RNA virus.
A robust fungal phytogeny using the mitochondrially encoded NAD5 protein sequence
Authors: Paquin Bruno , Roewer Ingeborg , Wang Zhang , Lang B. Franz
Published: May 2008

We present a fungal phylogeny based on mitochondrial NAD5 (subunit of the NADH dehydrogenase) protein sequences. The tree topology is well supported by bootstrap analysis and mostly congruent with trees inferred from nuclear sequences, ultrastructural data, or mitochondrial COX1 and COX3 (subunits of the cytochrome oxidase) protein sequences. The NAD5 tree points to (i) an early divergence of the Chytridiomycetes, (ii) an appearance of Zygomycetes prior to the divergence of Ascomycetes and Basidiomycetes, and (iii) Oomycetes as clearly unrelated to fungi. In addition, this analysis predicts a common ancestor of fungi and animals, to the exclusion of green algae and plants. Our results reinforce the view that protein sequences are of high value in the reconstruction of the phylogenetic history of mitochondria. Key words: protein sequences, mitochondria, phylogeny, fungi, Oomycetes.
Retrograde regulation: a novel path of communication between mitochondria, the nucleus, and peroxisomes in yeast
Authors: Chelstowska Anna , Jia Yankai , Rothermel Beverly , Butow Ronald A.
Published: May 2008

Alterations in mitochondrial function result in changes in nuclear gene expression, a process we have called retrograde regulation. Here we summarize studies on the effects of the mitochondrial state on expression of the C1T2 gene, which encodes citrate synthase 2, an enzyme that functions in the glyoxylate cycle and is located in peroxisomes. Various defective mitochondria result in up to a 30-fold transcriptional activation of the gene, a process which could provide additional citrate to mitochondria when the TCA cycle is limiting. We have identified three new genes, RTG1, RTG2, and RTG3, that are required for C1T2 expression. RTG1 and RTG3 encode basic helix–loop–helix transcription factors that bind to the 5′ flanking region of C1T2. RTG2 is a protein of unknown function. Both RTG1 and RTG2 are also required for oleic acid induction of peroxisomes. These studies reveal a complex pattern of interorganelle communication among mitochondria, the nucleus and peroxisomes. Key words: yeast, mitochondria, peroxisomes, organelle communication.
The replication of yeast chromosomes: lessons fromSaccharomyces cerevisiaechromosome III
Authors: Newlon Carol S.
Published: May 2008

To understand how a eukaryotic chromosome is replicated, a systematic analysis of chromosome III of Saccharomyces cerevisiae has been undertaken. Replication origins are specified by autonomously replicating sequence (ARS) elements, whose sequences can be dissected using a simple plasmid assay. Only a subset of ARS elements are active as chromosomal replication origins. Replication origins are required for normal chromosome transmission, but they appear to be redundant; several origins can be deleted without affecting chromosome stability. Replication origin position has been conserved on chromosome III in diverged strains, suggesting that origin position is important for chromosome function. The inability of some ARS elements to function as chromosomal replication origins appears likely to result from chromosomal context or position effects. Replication termination occurs over broad regions between active replication origins. The position of termination can be altered by deleting origins, suggesting that no specific replication termination elements are required. Replication forks appear to move at a relatively constant rate through the chromosome. A replication pause site associated with the centromere results from the kinetochore protein complex that binds the centromere to mediate chromosome segregation. Key words: Saccharomyces cerevisiae, ARS elements, replication origins, replication termination, DNA replication intermediates.
Independent synaptic behavior of sister chromatids inCoprinus cinereus
Authors: Pukkila Patricia J. , Shannon Katie B. , Skrzynia Cécile
Published: May 2008

Sister and nonsister chromatids behave in distinct ways during meiosis. We have shown that homologous synapsis does not require the presence of sister chromatids. In mutants that fail to undergo premeiotic DNA replication, synaptonemal complex of normal appearance is observed in diploid nuclei, but not in triploid nuclei. Our results indicate that homologous alignment does not depend on DNA replication. In addition, the differences observed in diploid and triploid nuclei indicate that sister chromatids can exhibit independent synaptic behavior, although ordinarily, they are constrained to act as a single unit. Key words: Coprinus cinereus, meiosis, synaptonemal complex, meiotic mutants, DNA replication, triploid nuclei.
Methylation of repeated DNA sequences and genome stability inAscobolus immersus
Authors: Colot Vincent , Goyon Christophe , Faugeron Godeleine , Rossignol Jean-Luc
Published: May 2008

In the ascomycete Ascobolus immersus, artificially repeated DNA fragments are subject to a process of methylation induced premeiotically (MIP). Artificially repeated genes are inactivated as a consequence of this methylation. Once established, both methylation and inactivation are stably maintained (although they can be reversed) through vegetative as well as sexual reproduction, even after the different copies of the repeat have segregated from each other. Therefore, MIP constitutes a process of epimutation. The biological significance of MIP remains unknown. Two likely hypotheses, which are not mutually exclusive, are that MIP acts to limit the spread of transposable elements throughout the genome or that it acts to reduce ectopic recombination between dispersed sequences. In this second hypothesis, targets for MIP are also likely to be mainly transposable elements. For these reasons, we have recently started a search for such elements in Ascobolus. Results obtained so far indicate that several types of transposable elements or remnants of them are present in Ascobolus. Analysis of their methylation status suggests that they are indeed likely targets of MIP and in one case points to a possible strategy that transposons might use to escape MIP, simply by reducing their size. Key words: DNA repeats, methylation, genome stability, Ascobolus immersus.
The shape of things to come: morphogenesis in yeast and related patterns in other systems
Authors: Mischke Michelle D. , Chant John
Published: May 2008

The elaboration of cell form has fascinated biologists for generations. A vast body of literature details the life cycles, anatomy, and developmental programs of many species. The mechanisms responsible for the observed diversity of structure involve polarization, directed growth, and spatial memory. These issues of morphogenesis are currently under study in the budding yeast Saccharomyces cerevisiae and other fungi. In yeast, a number of genes are known that specifically affect either the orientation or the assembly of a polarity axis. These include the bud-site selection genes, BUD1–BUD5, as well as the polarity establishment genes, CDC24, CDC42, CDC43, and BEM1. Members of each of these classes encode elements in signal transduction type pathways. This review examines our present understanding of the molecular machinery responsible for orienting and assembling cell polarity as best understood in S. cerevisiae, and speculates about how similar machinery might function in other fungi. Key words: morphogenesis, polarity, yeast, Saccharomyces, development.
Relationships between sexual processes and parasitic interactions in the host–pathogen systemAbsidia glauca–Parasitella parasitica
Authors: Wöstemeyer J. , Wöstemeyer A. , Burmester A. , Czempinski K.
Published: May 2008

Parasitella parasitica is a facultative parasite of many Mucorales including Absidia glauca. The infection process includes the formation of a plasmatic continuum between host and parasite, which allows the invasion of the host by nuclei of the parasite. This process gives rise to interspecies recombinants. Auxotrophic A. glauca mutants are complemented by the transfer of genes from the parasite to the host. At the molecular level, we could show that plasmid-coded genes are also transferred. The successful formation of infection structures is mating-type dependent. Parasitella parasitica exclusively infects hosts belonging to the complementary mating type. The formation of infection structures is correlated with the ability to synthesise the sex pheromone trisporic acid, which is produced in mixed cultures by compatible combinations between host and parasite. Normally, trisporic acid is formed by a cooperative biosynthesis involving both mating types. Trisporic acid seems to be involved also in mediating the recognition between P. parasitica and A. glauca. To test the hypothesis of direct hormonal correlations between sex and parasitism, we have isolated one of the key enzymes for trisporic acid synthesis, dihydromethyltrisporic acid dehydrogenase, sequenced the N-termini of some proteolytic cleavage products, and have started to isolate the corresponding gene. Key words: mycoparasitism, zygomycetes, trisporic acid, Absidia glauca, Parasitella parasitica, Mucor.