bluuebunny/crossref_metadata_2025_split huggingface dataset:
Florigen (II): It is a Mobile Protein
Authors: Yang Yuejun , Klejnot John , Yu Xuhong , Liu Xuanming , Lin Chentao 
Published: November 2007

Abstract The true identity of florigen – the molecule(s) that migrates from leaves to apical meristem to initiate flowering – was notoriously elusive, having made it almost the “Bigfoot” of plant biology. There was never a lack of drama in the field of florigen study, and florigen researchers have once again experienced such a swing in the last two years. We wrote a minireview last year in this journal (Yu et al. 2006) to excitedly salute, among other discoveries, the notion that the flowering locus T (FT) mRNA might be the molecular form of a florigen. However, this hypothesis was challenged in a little less than two years after its initial proposition, and the original paper proposed that the FT mRNA hypothesis was retracted (Huang et al. 2005; Bohlenius et al. 2007). Interestingly enough, the FT gene previously proposed to encode a florigen was never challenged. Rather, the FT protein, instead of the FT mRNA, is now believed to migrate from leaves to the apical meristem to promote floral initiation. In this update, we will share with our readers some entertaining stories concerning the recent studies of florigen in five different plant species. In addition to the published reports referenced in this update, readers may also refer to our previous minireview and references therein for additional background information (Yu et al. 2006).
Constraints on Anaerobic Respiration in the Hyperthermophilic Archaea
Pyrobaculum islandicum
and
Pyrobaculum aerophilum
Authors: Feinberg Lawrence F. , Srikanth R. , Vachet Richard W. , Holden James F. 
Published: November 2007

ABSTRACT

Pyrobaculum islandicum
uses iron, thiosulfate, and elemental sulfur for anaerobic respiration, while
Pyrobaculum aerophilum
uses iron and nitrate; however, the constraints on these processes and their physiological mechanisms for iron and sulfur reduction are not well understood. Growth rates on sulfur compounds are highest at pH 5 to 6 and highly reduced (<−420-mV) conditions, while growth rates on nitrate and iron are highest at pH 7 to 9 and more-oxidized (>−210-mV) conditions. Growth on iron expands the known pH range of growth for both organisms.
P. islandicum
differs from
P. aerophilum
in that it requires direct contact with insoluble iron oxide for growth, it did not produce any extracellular compounds when grown on insoluble iron, and it lacked 2,6-anthrahydroquinone disulfonate oxidase activity. Furthermore, iron reduction in
P. islandicum
appears to be completely independent of
c
-type cytochromes. Like that in
P. aerophilum
, NADH-dependent ferric reductase activity in
P. islandicum
increased significantly in iron-grown cultures relative to that in non-iron-grown cultures. Proteomic analyses showed that there were significant increases in the amounts of a putative membrane-bound thiosulfate reductase in
P. islandicum
cultures grown on thiosulfate relative to those in cultures grown on iron and elemental sulfur. This is the first evidence of this enzyme being used in either a hyperthermophile or an archaeon.
Pyrobaculum arsenaticum
and
Pyrobaculum calidifontis
also grew on Fe(III) citrate and insoluble iron oxide, but only
P. arsenaticum
could grow on insoluble iron without direct contact.
Kelch Repeat Protein Clakel2p and Calcium Signaling Control Appressorium Development inColletotrichum lagenarium
Authors: Sakaguchi Ayumu , Miyaji Toshihiko , Tsuji Gento , Kubo Yasuyuki 
Published: November 2007

ABSTRACTKelch repeat proteins are important mediators of fundamental cellular functions and are found in diverse organisms. However, the roles of these proteins in filamentous fungi have not been characterized. We isolated a kelch repeat-encoding gene ofColletotrichum lagenarium ClaKEL2, aSchizosaccharomyces pombe tea1homologue. Analysis of theclakel2mutant indicated thatClaKEL2was required for the establishment of cellular polarity essential for proper morphogenesis of appressoria and that there is a plant signal-specific bypass pathway for appressorium development which circumventsClaKEL2function. Clakel2p was localized in the polarized region of growing hyphae and germ tubes, and the localization was disturbed by a microtubule assembly blocker. Theclakel2mutants formed abnormal appressoria, and those appressoria were defective in penetration hypha development into cellulose membranes, an artificial model substrate for fungal infection. Surprisingly, theclakel2mutants formed normal appressoria on the host plant and retained penetration ability. Normal appressorium formation on the artificial substrate by theclakel2mutants was restored when cells were incubated in the presence of CaCl2or exudates from cucumber cotyledon. Furthermore, calcium channel modulators inhibited restoration of normal appressorium formation. These results suggest that there could be a bypass pathway that transduces a plant-derived signal for appressorium development independent ofClaKEL2and that a calcium signal is involved in this transduction pathway.
Binding of the Wheat Germ Lectin to
Cryptococcus neoformans
Suggests an Association of Chitinlike Structures with Yeast Budding and Capsular Glucuronoxylomannan
Authors: Rodrigues Marcio L. , Alvarez Mauricio , Fonseca Fernanda L. , Casadevall Arturo 
Published: November 2007

ABSTRACT

The capsule of
Cryptococcus neoformans
is a complex structure whose assembly requires intermolecular interactions to connect its components into an organized structure. In this study, we demonstrated that the wheat germ agglutinin (WGA), which binds to sialic acids and β-1,4-
N
-acetylglucosamine (GlcNAc) oligomers, can also bind to cryptococcal capsular structures. Confocal microscopy demonstrated that these structures form round or hooklike projections linking the capsule to the cell wall, as well as capsule-associated structures during yeast budding. Chemical analysis of capsular extracts by gas chromatography coupled to mass spectrometry and high-pH anion-exchange chromatography suggested that the molecules recognized by WGA were firmly associated with the cell wall. Enzymatic treatment, competition assays, and staining with chemically modified WGA revealed that GlcNAc oligomers, but not sialic acids, were the molecules recognized by the lectin. Accordingly, treatment of
C. neoformans
cells with chitinase released glucuronoxylomannan (GXM) from the cell surface and reduced the capsule size. Chitinase-treated acapsular cells bound soluble GXM in a modified pattern. These results indicate an association of chitin-derived structures with GXM and budding in
C. neoformans
, which may represent a new mechanism by which the capsular polysaccharide interacts with the cell wall and is rearranged during replication.
Pneumococcal Virulence Gene Expression and Host Cytokine Profiles during Pathogenesis of Invasive Disease
Authors: Mahdi Layla K. , Ogunniyi Abiodun D. , LeMessurier Kim S. , Paton James C. 
Published: November 2007

ABSTRACTPneumococcal disease continues to account for significant morbidity and mortality worldwide. For the development of novel prophylactic and therapeutic strategies against the disease spectrum, a complete understanding of pneumococcal behavior in vivo is necessary. We evaluated the expression patterns of the proven and putative virulence factor genesadcR,cbpA,cbpD,cbpG,cpsA,nanA,pcpA,piaA,ply,psaA,pspA, andspxBafter intranasal infection of CD1 mice with serotype 2, 4, and 6A pneumococci by real-time reverse transcription-PCR. Simultaneous gene expression patterns of selected host immunomodulatory molecules, CCL2, CCL5, CD54, CXCL2, interleukin-6, and tomor necrosis factor alpha, were also investigated. We show that pneumococcal virulence genes are differentially expressed in vivo, with some genes demonstrating niche- and serotype-specific differential expression. The in vivo expression patterns could not be attributed to in vitro differences in expression of the genes in transparent and opaque variants of the three strains. The host molecules were significantly upregulated, especially in the lungs, blood, and brains of mice. The pneumococcal-gene expression patterns support their ascribed roles in pathogenesis, providing insight into which protein combinations might be more appropriate as vaccine antigens against invasive disease. This is the first simultaneous comparison of bacterial- and host gene expression in the same animal during pathogenesis. The strategy provides a platform for prospective evaluation of interaction kinetics between invading pneumococci and human patients in culture-positive cases and should be feasible in other infection models.
Regulation of
l
-Lactate Utilization by the FadR-Type Regulator LldR of
Corynebacterium glutamicum
Authors: Georgi Tobias , Engels Verena , Wendisch Volker F. 
Published: November 2007

ABSTRACT

Corynebacterium glutamicum
can grow on
l
-lactate as a sole carbon and energy source. The NCgl2816-
lldD
operon encoding a putative transporter (NCgl2816) and a quinone-dependent
l
-lactate dehydrogenase (LldD) is required for
l
-lactate utilization. DNA affinity chromatography revealed that the FadR-type regulator LldR (encoded by NCgl2814) binds to the upstream region of NCgl2816-
lldD
. Overexpression of
lldR
resulted in strongly reduced NCgl2816-
lldD
mRNA levels and strongly reduced LldD activity, and as a consequence, a severe growth defect was observed in cells grown on
l
-lactate as the sole carbon and energy source, but not in cells grown on glucose, ribose, or acetate. Deletion of
lldR
had no effect on growth on these carbon sources but resulted in high NCgl2816-
lldD
mRNA levels and high LldD activity in the presence and absence of
l
-lactate. Purified His-tagged LldR bound to a 54-bp fragment of the NCgl2816-
lldD
promoter, which overlaps with the transcriptional start site determined by random amplification of cDNA ends-PCR and contains a putative operator motif typical of FadR-type regulators, which is
−1
TNGTNNNACNA
10
. Mutational analysis revealed that this motif with hyphenated dyad symmetry is essential for binding of LldD to the NCgl2816-
lldD
promoter.
l
-Lactate, but not
d
-lactate, interfered with binding of LldR
His
to the NCgl2816-
lldD
promoter. Thus, during growth on media lacking
l
-lactate, LldR represses expression of NCgl2816-
lldD
. In the presence of
l
-lactate in the growth medium or under conditions leading to intracellular
l
-lactate accumulation, the
l
-lactate utilization operon is induced.
Study of Anoxic and Oxic Cholesterol Metabolism by
Sterolibacterium denitrificans
Authors: Chiang Yin-Ru , Ismail Wael , Heintz Dimitri , Schaeffer Christine , Van Dorsselaer Alain , Fuchs Georg 
Published: November 2007

ABSTRACT

The initial enzymes and genes involved in the anoxic metabolism of cholesterol were studied in the denitrifying bacterium
Sterolibacterium denitrificans
Chol-1S
T
. The second enzyme of the proposed pathway, cholest-4-en-3-one-Δ
1
-dehydrogenase (AcmB), was partially purified. Based on amino acid sequence analysis, a gene probe was derived to screen a cosmid library of chromosomal DNA for the
acmB
gene. A positive clone comprising a 43-kbp DNA insert was sequenced. In addition to the
acmB
gene, the DNA fragment harbored the
acmA
gene, which encodes the first enzyme of the pathway, cholesterol dehydrogenase/isomerase. The
acmA
gene was overexpressed, and the recombinant dehydrogenase/isomerase was purified. This enzyme catalyzes the predicted transformation of cholesterol to cholest-4-en-3-one.
S. denitrificans
cells grown aerobically with cholesterol exhibited the same pattern of soluble proteins and cell extracts formed the same
14
C-labeled products from [
14
C]cholesterol as cells that were grown under anoxic, denitrifying conditions. This is especially remarkable for the late products that are formed by anaerobic hydroxylation of the cholesterol side chain with water as the oxygen donor. Hence, this facultative anaerobic bacterium may use the anoxic pathway lacking any oxygenase-dependent reaction also under oxic conditions. This confers metabolic flexibility to such facultative anaerobic bacteria.
ExoS Controls the Cell Contact-Mediated Switch to Effector Secretion in
Pseudomonas aeruginosa
Authors: Cisz Michelle , Lee Pei-Chung , Rietsch Arne 
Published: November 2007

ABSTRACT

Type III secretion is used by many gram-negative bacterial pathogens to directly deliver protein toxins (effectors) into targeted host cells. In all cases, secretion of effectors is triggered by host cell contact, although the mechanism is unclear. In
Pseudomonas aeruginosa
, expression of all type III secretion-related genes is up-regulated when secretion is triggered. We were able to visualize this process using a green fluorescent protein reporter system and to use it to monitor the ability of bacteria to trigger effector secretion on cell contact. Surprisingly, the action of one of the major type III secreted effectors, ExoS, prevented triggering of type III secretion by bacteria that subsequently attached to cells, suggesting that triggering of secretion is feedback regulated. Evidence is presented that translocation (secretion of effectors across the host cell plasma membrane) of ExoS is indeed self-regulated and that this inhibition of translocation can be achieved by either of its two enzymatic activities. The translocator proteins PopB, PopD, and PcrV are secreted via the type III secretion system and are required for pore formation and translocation of effectors across the host cell plasma membrane. Here we present data that secretion of translocators is in fact not controlled by calcium, implying that triggering of effector secretion on cell contact represents a switch in secretion specificity, rather than a triggering of secretion per se. The requirement for a host cell cofactor to control effector secretion may help explain the recently observed phenomenon of target cell specificity in both the
Yersinia
and
P. aeruginosa
type III secretion systems.
Methicillin-Resistant
Staphylococcus aureus
Nasal Carriage among Injection Drug Users: Six Years Later
Authors: Al-Rawahi G. N. , Schreader A. G. , Porter S. D. , Roscoe D. L. , Gustafson R. , Bryce E. A. 
Published: November 2007

ABSTRACT

A survey in 2000 to detect methicillin-resistant
Staphylococcus aureus
(MRSA) colonization in Vancouver downtown east side injection drug users (IDUs) revealed an MRSA nasal colonization incidence of 7.4%. This is a follow-up study to determine the current prevalence of MRSA colonization and to further characterize the isolates and risk factors for colonization. In this point prevalence study of MRSA nasal carriage among IDUs, nasal swabs were cultured to detect
S. aureus
. Isolates were studied for their antimicrobial susceptibility patterns and the presence of
mecA
and Panton-Valentine leukocidin (PVL) genes and by pulsed-field gel electrophoresis (PFGE).
S. aureus
was isolated from 119 of 301 (39.5%) samples; three (2.5%) participants had both methicillin-sensitive
S. aureus
(MSSA) and MRSA, resulting in 122 isolates. Of these, 54.1% were MSSA and 45.9% were MRSA, with an overall MRSA rate of 18.6%. USA-300 (CMRSA-10) accounted for 75% of all MRSA isolates; 25% were USA-500 (CMRSA-5). None of the USA-500 isolates were positive for PVL; 41 (97.6%) USA-300 isolates contained PVL. One MSSA isolate, from an individual also carrying USA-300, was positive for PVL. The PFGE pattern of this MSSA isolate was related to that of the MRSA strain. The antibiograms of USA-300 compared to USA-500 isolates showed 100% versus 7.1% susceptibility to trimethoprim-sulfamethoxazole (TMP-SMX) and 54.8% versus 7.1% susceptibility to clindamycin. MRSA nasal colonization in this population has increased significantly within the last 6 years, with USA-300 replacing the previous strain. Most of these strains are PVL positive, and all are susceptible to TMP-SMX.
Loop-Mediated Isothermal Amplification Method Targeting the TTS1 Gene Cluster for Detection of
Burkholderia pseudomallei
and Diagnosis of Melioidosis
Authors: Chantratita Narisara , Meumann Ella , Thanwisai Aunchalee , Limmathurotsakul Direk , Wuthiekanun Vanaporn , Wannapasni Saran , Tumapa Sarinna , Day Nicholas P. J. , Peacock Sharon J. 
Published: November 2007

ABSTRACT

Melioidosis is a severe infection caused by
Burkholderia pseudomallei
. The timely implementation of effective antimicrobial treatment requires rapid diagnosis. Loop-mediated isothermal amplification (LAMP) targeting the TTS1 gene cluster was developed for the detection of
B. pseudomallei
. LAMP was sensitive and specific for the laboratory detection of this organism. The lower limit of detection was 38 genomic copies per reaction, and LAMP was positive for 10 clinical
B. pseudomallei
isolates but negative for 5
B. thailandensis
and 5
B. mallei
isolates. A clinical evaluation was conducted in northeast Thailand to compare LAMP to an established real-time PCR assay targeting the same TTS1 gene cluster. A total of 846 samples were obtained from 383 patients with suspected melioidosis, 77 of whom were subsequently diagnosed with culture-confirmed melioidosis. Of these 77 patients, a positive result was obtained from one or more specimens by PCR in 26 cases (sensitivity, 34%; 95% confidence interval [CI], 23.4 to 45.4%) and by LAMP in 34 cases (sensitivity, 44%; 95% CI, 32.8 to 55.9%) (
P
= 0.02). All samples from 306 patients that were culture negative for
B. pseudomallei
were negative by PCR (specificity, 100%; 95% CI, 98.8 to 100%), but 5 of 306 patients (1.6%) were positive by LAMP (specificity, 98.4%; 95% CI, 96.2 to 99.5%) (
P
= 0.03). The diagnostic accuracies of PCR and LAMP were 86.7% (95% CI, 82.9 to 89.9%) and 87.5% (95% CI, 83.7 to 90.6%), respectively (
P
= 0.47). Both assays were very insensitive when applied to blood samples; PCR and LAMP were positive for 0 and 1 of 44 positive blood cultures, respectively. The PCR and LAMP assays evaluated here are not sufficiently sensitive to replace culture in our clinical setting.
Relationships of Nontypeable
Haemophilus influenzae
Strains to Hemolytic and Nonhemolytic
Haemophilus haemolyticus
Strains
Authors: McCrea Kirk W. , Xie Jingping , LaCross Nathan , Patel Mayurika , Mukundan Deepa , Murphy Timothy F. , Marrs Carl F. , Gilsdorf Janet R. 
Published: November 2007

ABSTRACT

Haemophilus influenzae
is both a human respiratory pathogen and pharyngeal commensal, while
H. haemolyticus
, the closest phylogenetic relative of
H. influenzae
, is arguably a strict pharyngeal commensal. A hemolytic phenotype has historically differentiated
H. haemolyticus
from
H. influenzae
, but the recent recognition of significant nonhemolytic
H. haemolyticus
colonization has decreased this trait's resolvability. Given this and the potential of recombination between the species, we examined the distribution of microbiologic and molecular traits between collections of
H. influenzae
and
H. haemolyticus
strains separated within a dendrogram obtained by multilocus sequence analysis (MLSA). All strains hybridizing with a probe to
iga
, a gene encoding an immunoglobulin A protease of
H. influenzae
, clustered apart from strains that did not hybridize with the probe. Other traits also segregated significantly along this division, suggesting a separation of the species. Of note, the LOS genes
licA
,
lic2A
, and
lgtC
of
H. influenzae
were approximately 2, 6, and 54 times, respectively, more prevalent in
H. influenzae
than in
H. haemolyticus
. In contrast to species separation, interspecies recombination was evidenced by the inability of single gene sequences to phylogenetically separate the species and by the “fuzzy” distribution of some species-specific traits across the species dividing line. Together, these data support the historically accurate and pragmatic division of these species while recognizing their potential for recombination. Future comparative genomic studies identifying common and distinctive genes could be useful in evaluating their role in the commensal or virulent growth, respectively, of
H. influenzae
.
The Logic of Being: Eriugena's Dialectical Ontology
Authors: Erismann Christophe 
Published: November 2007

AbstractIn his major work, the Periphyseon, the ninth century Latin philosopher John Scottus Eriugena gives, with the help of what he calls "dialectic", a rational analysis of reality. According to him, dialectic is a science which pertains both to language and reality. Eriugena grounds this position in a realist ontological exegesis of the Aristotelian categories, which are conceived as categories of being. His interpretation tends to transform logical patterns, such as Porphyry's Tree or the doctrine of the categories, into a structure which is both ontological and logical, and to use them as tools for the analysis of the sensible world. The combination of dialectic interpreted as a science of being, capable of expressing truths about the sensible world as well as about discourse, with an ontological interpretation of logical concepts allows Eriugena to develop his metaphysical theory, a strong realism. Eriugena not only supports a theological realism (of divine ideas), but also, and principally, an ontological realism, the assertion of the immanent existence of forms. Eriugena claims that genera and species really subsist in the individuals: they are completely and simultaneously present in each of the entities which belong to them.
The Turn of the Century North American Drought: Global Context, Dynamics, and Past Analogs*
Authors: Seager Richard 
Published: November 2007

Abstract
The causes and global context of the North American drought between 1998 and 2004 are examined using atmospheric reanalyses and ensembles of atmosphere model simulations variously forced by global SSTs or tropical Pacific SSTs alone. The drought divides into two distinct time intervals. Between 1998 and 2002 it coincided with a persistent La Niña–like state in the tropical Pacific, a cool tropical troposphere, poleward-shifted jet streams, and, in the zonal mean, eddy-driven descent in midlatitudes. During the winters reduced precipitation over North America in the climate models was sustained by anomalous subsidence and reductions of moisture convergence by the stationary flow and transient eddies. During the summers reductions of evaporation and mean flow moisture convergence drove the precipitation reduction, while transient eddies acted diffusively to oppose this. During these years the North American drought fitted into a global pattern of circulation and hydroclimate anomalies with noticeable zonal and hemispheric symmetry.
During the later period of the drought, from 2002 to 2004, weak El Niño conditions prevailed and, while the global climate adjusted accordingly, western North America remained, uniquely among midlatitude regions, in drought. The ensemble mean of the climate model simulations did not simulate the continuation of the drought in these years, suggesting that the termination of the drought was largely unpredictable in terms of global ocean conditions.
The global context of the most recent, turn of the century, drought is compared to the five prior persistent North American droughts in the instrumental record from the mid-nineteenth century on. A classic La Niña pattern of ocean temperature in the Pacific is common to all. A cold Indian Ocean, also typical of La Niña, is common to all five prior droughts, but not the most recent one. Except in southern South America the global pattern of precipitation anomalies of the turn of the century drought is similar to that during the five prior droughts. These comparisons suggest that the earlier period of this most recent drought is the latest in a series of multiyear droughts forced by persistent changes in tropical Pacific Ocean temperatures. Warm tropical North Atlantic Ocean temperatures may play a secondary role.