bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryptococcus neoformans
Virulence Gene Discovery through Insertional Mutagenesis
Authors: Idnurm Alexander , Reedy Jennifer L. , Nussbaum Jesse C. , Heitman Joseph 
Published: April 2004

ABSTRACT

Insertional mutagenesis was applied to
Cryptococcus neoformans
to identify genes associated with virulence attributes. Using biolistic transformation, we generated 4,300 nourseothricin (
NAT
)-resistant strains, of which 590 exhibited stable resistance. We focused on mutants with defects in established virulence factors and identified two with reduced growth at 37°C, four with reduced production of the antioxidant pigment melanin, and two with an increased sensitivity to nitric oxide (NO). The
NAT
insertion and mutant phenotypes were genetically linked in five of eight mutants, and the DNA flanking the insertions was characterized. For the strains with altered growth at 37°C and altered melanin production, mutations were in previously uncharacterized genes, while the two NO-sensitive strains bore insertions in the flavohemoglobin gene
FHB1
, whose product counters NO stress. Because of the frequent instability of nourseothricin resistance associated with biolistic transformation,
Agrobacterium
-mediated transformation was tested. This transkingdom DNA delivery approach produced 100% stable nourseothricin-resistant transformants, and three melanin-defective strains were identified from 576 transformants, of which 2 were linked to
NAT
in segregation analysis. One of these mutants contained a T-DNA insertion in the promoter of the
LAC1
(laccase) gene, which encodes a key enzyme required for melanin production, while the second contained an insertion in the promoter of the
CLC1
gene, encoding a voltage-gated chloride channel. Clc1 and its homologs are required for ion homeostasis, and in their absence Cu
+
transport into the secretory pathway is compromised, depriving laccase and other Cu
+
-dependent proteins of their essential cofactor. The
NAT
resistance cassette was optimized for cryptococcal codon usage and GC content and was then used to disrupt a mitogen-activated protein kinase gene, a predicted gene, and two putative chloride channel genes to analyze their contributions to fungal physiology. Our findings demonstrate that both insertional mutagenesis methods can be applied to gene identification, but
Agrobacterium
-mediated transformation is more efficient and generates exclusively stable insertion mutations.
Cell Cycle Progression in G
1
and S Phases Is
CCR4
Dependent following Ionizing Radiation or Replication Stress in
Saccharomyces cerevisiae
Authors: Westmoreland Tammy J. , Marks Jeffrey R. , Olson John A. , Thompson Eric M. , Resnick Michael A. , Bennett Craig B. 
Published: April 2004

ABSTRACT

To identify new nonessential genes that affect genome integrity, we completed a screening for diploid mutant
Saccharomyces cerevisiae
strains that are sensitive to ionizing radiation (IR) and found 62 new genes that confer resistance. Along with those previously reported (Bennett et al., Nat. Genet. 29:426-434, 2001), these genes bring to 169 the total number of new IR resistance genes identified. Through the use of existing genetic and proteomic databases, many of these genes were found to interact in a damage response network with the transcription factor Ccr4, a core component of the CCR4-NOT and RNA polymerase-associated factor 1 (PAF1)-CDC73 transcription complexes. Deletions of individual members of these two complexes render cells sensitive to the lethal effects of IR as diploids, but not as haploids, indicating that the diploid G
1
cell population is radiosensitive. Consistent with a role in G
1
, diploid
ccr4
Δ cells irradiated in G
1
show enhanced lethality compared to cells exposed as a synchronous G
2
population. In addition, a prolonged
RAD9
-dependent G
1
arrest occurred following IR of
ccr4
Δ cells and
CCR4
is a member of the
RAD9
epistasis group, thus confirming a role for
CCR4
in checkpoint control. Moreover,
ccr4
Δ cells that transit S phase in the presence of the replication inhibitor hydroxyurea (HU) undergo prolonged cell cycle arrest at G
2
followed by cellular lysis. This S-phase replication defect is separate from that seen for
rad52
mutants, since
rad52
Δ
ccr4
Δ cells show increased sensitivity to HU compared to
rad52
Δ or
ccr4
Δ mutants alone. These results indicate that cell cycle transition through G
1
and S phases is
CCR4
dependent following radiation or replication stress.
A Novel Allele of
Saccharomyces cerevisiae NDC1
Reveals a Potential Role for the Spindle Pole Body Component Ndc1p in Nuclear Pore Assembly
Authors: Lau Corine K. , Giddings Thomas H. , Winey Mark 
Published: April 2004

ABSTRACT

Both the spindle pole body (SPB) and the nuclear pore complex (NPC) are essential organelles embedded in the nuclear envelope throughout the life cycle of the budding yeast
Saccharomyces cerevisiae
. However, the mechanism by which these two multisubunit structures are inserted into the nuclear envelope during their biogenesis is not well understood. We have previously shown that Ndc1p is the only known integral membrane protein that localizes to both the SPBs and the NPCs and is required for SPB duplication. For this study, we generated a novel temperature-sensitive (
ts
) allele of
NDC1
to investigate the role of Ndc1p at the NPCs. Yeast cells carrying this allele (
ndc1
-
39
) failed to insert the SPB into the nuclear envelope at the restrictive temperature. Importantly, the double mutation of
ndc1
-
39
and NPC assembly mutant
nic96
-
1
resulted in cells with enhanced growth defects. While nuclear protein import and NPC distribution in the nuclear envelope were unaffected,
ndc1
-
39
mutants failed to properly incorporate the nucleoporin Nup49p into NPCs. These results provide evidence that Ndc1p is required for NPC assembly in addition to its role in SPB duplication. We postulate that Ndc1p is crucial for the biogenesis of both the SPBs and the NPCs at the step of insertion into the nuclear envelope.
Tfs1p, a Member of the PEBP Family, Inhibits the Ira2p but Not the Ira1p Ras GTPase-Activating Protein in
Saccharomyces cerevisiae
Authors: Chautard Hélène , Jacquet Michel , Schoentgen Françoise , Bureaud Nicole , Bénédetti Hélène 
Published: April 2004

ABSTRACT

Ras proteins are guanine nucleotide-binding proteins that are highly conserved among eukaryotes. They are involved in signal transduction pathways and are tightly regulated by two sets of antagonistic proteins: GTPase-activating proteins (GAPs) inhibit Ras proteins, whereas guanine exchange factors activate them. In this work, we describe Tfs1p, the first physiological inhibitor of a Ras GAP, Ira2p, in
Saccharomyces cerevisiae. TFS1
is a multicopy suppressor of the
cdc25-1
mutation in yeast and corresponds to the so-called Ic CPY cytoplasmic inhibitor. Moreover, Tfs1p belongs to the phosphatidylethanolamine-binding protein (PEBP) family, one member of which is RKIP, a kinase and serine protease inhibitor and a metastasis inhibitor in prostate cancer. In this work, the results of (i) a two-hybrid screen of a yeast genomic library, (ii) glutathione
S
-transferase pulldown experiments, (iii) multicopy suppressor tests of
cdc25-1
mutants, and (iv) stress resistance tests to evaluate the activation level of Ras demonstrate that Tfs1p interacts with and inhibits Ira2p. We further show that the conserved ligand-binding pocket of Tfs1—the hallmark of the PEBP family—is important for its inhibitory activity.
Transcription Initiation and Termination on
Leishmania major
Chromosome 3
Authors: Martínez-Calvillo Santiago , Nguyen Dan , Stuart Kenneth , Myler Peter J. 
Published: April 2004

ABSTRACT

Genome projects involving
Leishmania
and other trypanosomatids have revealed that most genes in these organisms are organized into large clusters of genes on the same DNA strand. We have previously shown that transcription of the entire
Leishmania major
Friedlin (LmjF) chromosome 1 (chr1) initiates bidirectionally between two divergent gene clusters. Here, we analyze transcription of LmjF chr3, which contains two convergent clusters of 67 and 30 genes, separated by a tRNA gene, with a single divergent protein-coding gene located close to the “left” telomere. Nuclear run-on analyses indicate that specific transcription of chr3 initiates bidirectionally between the single subtelomeric gene and the adjacent 67-gene cluster, close to the “right” telomere upstream of the 30-gene cluster, and upstream of the tRNA gene. Transcription on both strands terminates within the tRNA-gene region. Transient-transfection studies support the role of the tRNA-gene region as a transcription terminator for RNA polymerase II (Pol II) and Pol III, and also for Pol I.
Mitochondrial Histone-Like DNA-Binding Proteins Are Essential for Normal Cell Growth and Mitochondrial Function in
Crithidia fasciculata
Authors: Avliyakulov Nuraly K. , Lukeš Julius , Ray Dan S. 
Published: April 2004

ABSTRACT

The
Crithidia fasciculata
KAP2 and KAP3 proteins are closely related kinetoplast-specific histone-like DNA-binding proteins. The
KAP2
and
KAP3
genes are 46% identical and are arranged in tandem on the chromosomal DNA. Disruption of both alleles of either gene alone shows no detectable phenotype. However, replacement of both copies of the sequence encoding the entire
KAP2
and
KAP3
locus increases maxicircle mRNA levels two- to fourfold. These double-knockout cells are viable but grow extremely slowly, have reduced respiration and very abnormal cell morphologies, and accumulate numerous large vacuoles. The extreme phenotype of these mutant cells suggests an important role for the KAP2 and KAP3 proteins in mitochondrial metabolism and cell growth.
Candida albicans
Biofilms: a Developmental State Associated With Specific and Stable Gene Expression Patterns
Authors: García-Sánchez Susana , Aubert Sylvie , Iraqui Ismaïl , Janbon Guilhem , Ghigo Jean-Marc , d'Enfert Christophe 
Published: April 2004

ABSTRACT

Like many bacteria, yeast species can form biofilms on several surfaces.
Candida albicans
colonizes the surfaces of catheters, prostheses, and epithelia, forming biofilms that are extremely resistant to antifungal drugs. We have used transcript profiling to investigate the specific properties of
C. albicans
biofilms. Biofilm and planktonic cultures produced under different conditions of nutrient flow, aerobiosis, or glucose concentration were compared by overall gene expression correlation. Correlation was much higher between biofilms than planktonic populations irrespective of the growth conditions, indicating that biofilm populations formed in different environments display very similar and specific transcript profiles. A first cluster of 325 differentially expressed genes was identified. In agreement with the overrepresentation of amino acid biosynthesis genes in this cluster, Gcn4p, a regulator of amino acid metabolism, was shown to be required for normal biofilm growth. To identify biofilm-related genes that are independent of mycelial development, we studied the transcriptome of biofilms produced by a wild-type, hypha-producing strain and a
cph1
/
cph1 efg1
/
efg1
strain defective for hypha production. This analysis identified a cluster of 317 genes expressed independently of hypha formation, whereas 86 genes were dependent on mycelial development. Both sets revealed the activation of the sulfur-amino acid biosynthesis pathway as a feature of
C. albicans
biofilms.
Dual-Color Imaging of Nuclear Division and Mitotic Spindle Elongation in Live Cells of
Aspergillus nidulans
Authors: Su Wenqi , Li Shihe , Oakley Berl R. , Xiang Xin 
Published: April 2004

ABSTRACT

We have developed a dual-color imaging system based on cyan fluorescent protein-labeled histone H2A and green fluorescent protein-labeled alpha tubulin to visualize DNA and spindles simultaneously in the same living cell of
Aspergillus nidulans
. This system allows new details of mitosis and nuclear movement to be revealed.
A Mitogen-Activated Protein Kinase That Senses Nitrogen Regulates Conidial Germination and Growth in
Aspergillus fumigatus
Authors: Xue Tao , Nguyen C. Kim , Romans Angela , May Gregory S. 
Published: April 2004

ABSTRACT

We show that the mitogen-activated protein (MAP) kinase pathway that responds to osmotic stress in
Aspergillus fumigatus
is also involved in nutritional sensing. This MAP kinase regulates conidial germination in response to the nitrogen source and is activated upon starvation for either carbon or nitrogen during vegetative growth.
Biosynthesis and Uptake of Siderophores Is Controlled by the PacC-Mediated Ambient-pH Regulatory System in
Aspergillus nidulans
Authors: Eisendle Martin , Oberegger Harald , Buttinger Rudolf , Illmer Paul , Haas Hubertus 
Published: April 2004

ABSTRACT

Biosynthesis and uptake of siderophores in
Aspergillus nidulans
are regulated not only by iron availability but also by ambient pH: expression of this high-affinity iron uptake system is elevated by an increase in the ambient pH. Mediation of this regulation by the transcriptional regulator PacC has been confirmed via acidity- and alkalinity-mimicking mutants.
Identification of Genes Dependent on the MADS Box Transcription Factor SrfA in
Dictyostelium discoideum
Development
Authors: Escalante Ricardo , Iranfar Negin , Sastre Leandro , Loomis William F. 
Published: April 2004

ABSTRACT

Analysis of microarrays containing 6,345
Dictyostelium discoideum
genes has identified 21 whose expression is dependent on the MADS box transcription factor SrfA. In wild-type cells, all of these genes are induced late in development. At least four of them are necessary for proper spore differentiation, stability, and/or germination.
Scurvy in the British Mercantile Marine in the 19th century, and the contribution of the Seamen’s Hospital Society
Authors: Cook G C 
Published: April 2004

Abstract
When long voyages in sailing vessels were commonplace, scurvy was a major health hazard in mariners of all nations. The observations of James Lind (1716–94) and others indicated that citrus fruits had both a preventive and curative role in this disease. In the light of this work, by 1800 the disease had been virtually eliminated from Britain’s Royal Navy. However, it continued in the merchant navies of all nations until the latter half of the 19th century. In 1867, the Merchant Shipping Amendment Act was passed by the British Parliament largely as a result of a concerted effort by the Seamen’s Hospital Society (SHS), one of whose physicians, Harry Leach (1836–79) was the major proselytiser for improved conditions in the merchant service. Examination of the SHS records before and after this event demonstrate a marked reduction in the prevalence of scurvy in the Port of London. Although other factors—such as the introduction of steam ships, which resulted in faster voyages—were clearly important, the compulsory administration of genuine lime juice under supervision in the merchant service seems to have exerted a significant effect.
Pneumocystis carinii pneumonia in chronic lymphocytic leukaemia
Authors: Vavricka S R , Halter J , Hechelhammer L , Himmelmann A 
Published: April 2004

Abstract
Pneumocystis carinii pneumonia in patients with chronic lymphocytic leukaemia (CLL) who have not been treated with fludarabin are rare, although clinically relevant CD4 T-cell depletion can occur in longstanding CLL without prior treatment with purine analogues. A 52 year old woman is reported who was on long term treatment with chlorambucil and taking a short course of prednisone for familial CLL before she developped progressive dyspnoea, and P carinii pneumonia was diagnosed in bronchoalveolar lavage fluid. Despite treatment with high dose co-trimoxazole the patient died.
Echocardiographic abnormalities in primary antibody deficiency
Authors: Johnston S L , Hill S J , Lock R J , Dwight J F , Unsworth D J , Gompels M M 
Published: April 2004

Abstract

Objective
To document cardiac abnormalities secondary to pulmonary disease in primary antibody deficiency.

Patients and methods
A cross sectional audit study of patients from a regional immunology centre. Subjects undergoing two dimensional and Doppler transthoracic echocardiography were reviewed. Ventricular dimensions and function, valvular competence, and estimated pulmonary artery pressure were recorded. Data were compared with clinical variables, pulmonary function tests, and thoracic computed tomography data.

Results
Nineteen patients with common variable immunodeficiency and one with IgG2 subclass deficiency were included, mean age at diagnosis 37.5 years, mean estimated diagnostic delay 10.94 years. Left ventricular impairment was found in 15% and right heart dilatation in 20%. Pulmonary hypertension (mean pulmonary artery pressure &gt;25 mm Hg) was found in 45% (9/20), graded as moderate (40–60 mm Hg) in 44% of cases. Pulmonary function was obstructive in 47% (9/19). Fifty five percent of the patients with computed tomography data within the last five years (10/18) had confirmed bronchiectasis. Patients with right heart dilatation and/or moderate pulmonary hypertension (n = 6) had a more prolonged diagnostic delay (p = 0.04) and more severe lung disease.

Conclusion
Echocardiographic abnormalities are common in primary antibody deficiency, associated with diagnostic delay and pulmonary complications. Pulmonary hypertension should be considered in those with severe lung disease and can be confirmed by echocardiography.
Establishing the Diploma in Tropical Medicine and Hygiene (DTM&H) course in the Sultanate of Oman
Authors: Scrimgeour E M 
Published: April 2004

Abstract
Until 1997, there was no formal teaching in tropical medicine in Arabian Peninsular countries, although many tropical diseases (for example, malaria, schistosomiasis, leishmaniasis, filariasis), are endemic in the region. A six month, part time Diploma in Tropical Medicine and Hygiene (DTM&H) course was established in the Sultan Qaboos University, Muscat, Sultanate of Oman, in 1997, for small groups of Omani doctors wishing to sit the annual DTM&H examination in London. To date, 21 doctors have been successful, and the Royal College of Physicians of London has accredited the Tropical Medicine School in Oman as an appropriate training centre for the examination. Since over 20 doctors apply each year for the six available places in the course, a full time DTM&H course for larger groups of doctors, from Oman and regional countries, is under consideration.
Modulation of Delayed-Type Hypersensitivity Responses in Hairless Guinea Pigs by Peptides Derived from Enkephalin
Authors: Sizemore Robert C. , Piva Marta , Moore LeeTerry , Gordonov Natalia , Heilman Edward , Godfrey Henry P. 
Published: April 2004

Although opioid peptides such as methionine (met)-enkephalin have been previously shown to enhance or suppress immune responses, few studies in animal models have addressed the immunomodulatory activity of their metabolic derivatives. Hairless (IAF/HA-HO) guinea pigs immunized with Freund’s complete adjuvant containing <i>Mycobacterium tuberculosis </i>and repeatedly skin tested with purified protein derivative of tuberculin (PPD) display high levels of stable delayed-type hypersensitivity (DTH) to PPD. Met-enkephalin (YGGFM) and two of its metabolites (YGG, YG) enhanced and accelerated PPD-elicited DTH inflammatory reactions when injected together with elicitor in these animals. At 24 h, 5 × 10<sup>–3</sup> pmol met-enkephalin significantly enhanced DTH responses by 30% over PPD alone, while 5 × 10<sup>–5</sup> pmol of YGG and 5 × 10<sup>–9</sup> pmol of YG significantly enhanced these responses by 62 and 32%, respectively. At much higher doses (5 × 10<sup>3</sup> pmol), met-enkephalin and its metabolites significantly suppressed DTH reactions by 25–32%. Tyrosine and glycine had no effect on PPD-elicited DTH. All DTH reactions (control, enhanced, suppressed) displayed typical perivascular mononuclear cell infiltrates. We conclude that the immunoactivity of met-enkephalin resides in its first two amino acids and suggest that cleavage of enkephalin molecules to YG occurs in serum and/or on the cell surface.
Rac2 is critical for neutrophil primary granule exocytosis
Authors: Abdel-Latif Dalia , Steward Melissa , Macdonald Dawn L. , Francis Gordon A. , Dinauer Mary C. , Lacy Paige 
Published: April 2004

AbstractNeutrophil degranulation is important in many inflammatory disorders, although the intracellular mechanisms underlying this process remain poorly understood. The Rho GTPase, Rac2, has been implicated in control of degranulation in earlier studies. We hypothesized that Rac2 selectively regulates neutrophil primary granule release. Using bone marrow and peritoneal exudate neutrophils from rac2-/- mice in comparison with similar cells from wild-type C57Bl/6 mice, we found that primary granule myeloperoxidase and elastase release was absent in Rac2-/- neutrophils in response to chemoattractant stimulation, cytochalasin B/f-Met-Leu-Phe (CB/fMLP), and CB/leukotriene B4. Rac2-/- neutrophils also failed to exhibit mobilization of the primary granule marker CD63+ during CB/fMLP stimulation as determined by confocal microscopy. Priming of Rac2-/- neutrophils with tumor necrosis factor (TNF) or by peritoneal elicitation did not rescue the defect in primary granule release. However, phosphorylation of p38 mitogen-activated protein (MAP) kinase in Rac2-/- neutrophils was evident in response to CB/fMLP and/or TNF. Primary granule density and morphology were normal in Rac2-/- neutrophils. Secondary specific and tertiary granule release, measured by lactoferrin immunoassay and zymography, was normal in response to CB/fMLP and adhesion to fibronectin. These findings suggest an obligatory role for Rac2 in regulation of primary granule release by neutrophils.
G-CSF receptor truncations found in SCN/AML relieve SOCS3-controlled inhibition of STAT5 but leave suppression of STAT3 intact
Authors: van de Geijn Gert-Jan M. , Gits Judith , Aarts Lambertus H. J. , Heijmans-Antonissen Claudia , Touw Ivo P. 
Published: April 2004

AbstractTruncated granulocyte colony-stimulating factor receptors (G-CSF-Rs) are implicated in severe congenital neutropenia (SCN) and the consecutive development of acute myeloid leukemia (AML). Mice expressing G-CSF-R truncation mutants (gcsfr-d715) show defective receptor internalization, an increased signal transducer and activator of transcription 5 (STAT5)/STAT3 activation ratio, and hyperproliferative responses to G-CSF treatment. We determined whether a lack of negative feedback by suppressor of cytokine signaling (SOCS) proteins contributes to the signaling abnormalities of G-CSF-R–d715. Expression of SOCS3 transcripts in bone marrow cells from G-CSF–treated gcsfr-d715 mice was approximately 60% lower than in wild-type (WT) littermates. SOCS3 efficiently suppressed STAT3 and STAT5 activation by WT G-CSF-R in luciferase reporter assays. In contrast, while SOCS3 still inhibited STAT3 activation by G-CSF-R–d715, STAT5 activation was no longer affected. This was due mainly to loss of the SOCS3 recruitment site Tyr729, with an additional contribution of the internalization defects of G-CSF-R–d715. Because Tyr729 is also a docking site for the Src homology 2–containing protein tyrosine phosphatase-2 (SHP-2), which binds to and inactivates STAT5, we suggest a model in which reduced SOCS3 expression, combined with the loss of recruitment of both SOCS3 and SHP-2 to the activated receptor complex, determine the increased STAT5/STAT3 activation ratio and the resulting signaling abnormalities projected by truncated G-CSF-R mutants.