bluuebunny/crossref_metadata_2025 huggingface dataset:
Bovine hemoglobin (glutamer‐250, Hemopure)‐specific immunoglobulin G antibody cross‐reacts with human hemoglobin but does not lyse red blood cells in vitro
Authors: Hamilton Robert G. , Kickler Thomas S.
Published: March 2007

BACKGROUND: Bovine hemoglobin (Hb)‐based oxygen carrier (HbOC‐201; Hb glutamer‐250, Hemopure, Biopure Corp.) is a blood replacement and augmentation drug that increases oxygen‐carrying capacity of circulating blood in patients with anemia and acute blood loss. The objective of this study was to assess the biologic significance (cross‐reactivity, hemolysis) of humoral immune responses in humans receiving repetitive HbOC‐201 administrations.

STUDY DESIGN AND METHODS: Serum samples containing immunoglobulin G (IgG) anti‐HbOC‐201 (n = 146) or no antibody (n = 16) were collected from subjects receiving HbOC‐201 in clinical studies. IgG anti‐HbOC‐201 levels were quantified and the extent of cross‐reactivity to human hemoglobin (HuHb) was assessed in direct‐binding and competitive‐inhibition immunoassays. Serum samples containing the highest levels of IgG anti‐HbOC‐201 were studied in a complement‐mediated hemolysis assay for their ability to lyse human red cells (RBCs).

RESULTS: The IgG anti‐HbOC‐201 levels in the antibody‐positive serum samples ranged from 0.7 to 86.8 μg per mL. Of the 146 IgG anti‐HbOC‐201–positive serum samples, 88.4 percent contained IgG antibodies whose binding to solid‐phase HbOC‐201 was competitively inhibited by incubation with soluble HuHb (11.6% [<20% inhibition]; 63% [20%‐80% inhibition]; and 25.4% [>81% inhibition]). Direct‐binding analysis to solid‐phase HuHb confirmed that 74 percent contained IgG antibodies reactive with HuHb. Dichotomous competitive inhibition and direct‐binding IgG anti‐HuHb data correlated significantly (r2 = 0.77, p < 0.001). Serum samples with the highest levels of IgG anti‐HuHb, as identified from clinical studies, did not lyse human RBCs in the presence of exogenous complement or induce the direct sensitization of RBCs with human IgG or complement.

CONCLUSION: These analyses indicate that HbOC‐201 administration elicits IgG antibodies in humans that react with bovine and HuHb, but do not cause hemolysis in vitro.
Synthesis, Physical, and Mechanical Properties of Bulk Zr3Al3C5Ceramic
Authors: He Lingfeng , Zhou Yanchun , Bao Yiwang , Lin Zhijun , Wang Jingyang
Published: March 2007

Anin situreactive hot‐pressing process using zirconium (zirconium hydride), aluminum, and graphite as staring materials and Si and Y2O3as additives was used to synthesize bulk Zr3Al3C5ceramics. This method demonstrates the advantages of easy synthesis, lower sintering temperature, high purity and density, and improved mechanical properties of synthesized Zr3Al3C5. Its electrical and thermal properties were measured. Compared with ZrC, Zr3Al3C5has a relatively low hardness (Vickers hardness of 12.5 GPa), comparable stiffness (Young's modulus of 374 GPa), but superior strength (flexural strength of 488 GPa) and toughness (fracture toughness of 4.68 MPa·m1/2). In addition, the stiffness decreases slowly with increasing temperature and at 1600°C remains 78% of that at ambient temperature, indicating that Zr3Al3C5is a potential high‐temperature structural ceramic.
CNTs/Ta3N5 Nanocomposite with Enhanced Photocatalytic Activity Under Visible Light Irradiation
Authors: Fu Bo , Gao Lian , Yang Songwang
Published: March 2007

Carbon nanotubes (CNTs)/Ta3N5 nanocomposite is presented as a novel photocatalyst working under visible light irradiation. The results of Fourier transform infrared analyses and transmission electron microscopy indicate that a good interfacial combination has formed between CNTs and Ta3N5 nanoparticles. The CNTs/Ta3N5 nanocomposite shows strong absorption in the visible light range compared with pure Ta3N5 and has a bandgap energy of 2.01 eV. The photocatalytic experiments show that the nanocomposite has a higher photocatalytic activity than Ta3N5 nanoparticles.
Time trends in Swedish patch test data from 1992 to 2000. A multi‐centre study based on age‐ and sex‐adjusted results of the Swedish standard series
Authors: Lindberg Magnus , Edman Björn , Fischer Torkel , Stenberg Berndt
Published: March 2007

Allergic contact dermatitis is recognized as a public health problem and some major allergens have been subject to intervention aiming at lowering skin exposure. There is an obvious interest in evaluating the effect of such interventions. Population studies are difficult to perform and epidemiological studies based on clinical data from testing patients with contact dermatitis are common surrogates. Our objective was to gather Swedish clinical standard series test data on two occasions in order to monitor trends in sensitization rates. Consecutive patch test results from the Swedish standard series were collected from 9 centres from 1991 to 1993 and from 1999 to 2001. In total, 3680 and 3790 patients, respectively, were included. Crude, age‐adjusted and age‐stratified prevalence are given separately for women and men. Our top 10 allergens are much in line with newly published European test data. Significant changes among those allergens are increasing sensitization rates for Myroxylon pereirae and decreasing rates for colophony, 5‐chloro‐2‐methyl‐4‐isothiazolin‐3‐one, Amerchol L 101 and thiuram mix. Nickel allergy is decreasing among young women. Among less common allergens, a noteworthy increase of sensitization to 4‐phenylendiamine is found. In conclusion, significant trends in sensitization rates of important allergen, reflecting changes in exposure, have been found.
Plasma concentration of selected neuropeptides in patients suffering from psoriasis
Authors: Reich Adam , Orda Alina , Wiśnicka Beata , Szepietowski Jacek C.
Published: March 2007

Abstract:  The aim of this study was to evaluate plasma levels of substance P (SP), calcitonin gene‐related peptide (CGRP), vasoactive intestinal peptide (VIP) and neuropeptide Y (NPY) during psoriasis course.

Methods:  Seventy‐three patients with psoriasis and 32 healthy volunteers were included. Detailed demographic and disease anamnesis was obtained from every patient. The disease severity was assessed using the Psoriasis Area and Severity Index score. Plasma levels of SP, CGRP, VIP and NPY were measured radioimmunologically.

Results:  Plasma levels of SP and NPY did not significantly differ between patients with psoriasis and controls (median SP: 52.8 and 57.9 pg/ml, respectively; P = 0.32; median NPY: 8.5 and 8.2 pg/ml, respectively; P = 0.67). CGRP plasma concentration was significantly elevated in psoriatic individuals both before (median 43.1 pg/ml) and after treatment (median 45.4 pg/ml), in comparison with healthy donors (median 13.5 pg/ml; P < 0.01 and P = 0.03, respectively). Treatment did not significantly influence plasma CGRP levels (P = 0.3). Median VIP plasma concentration in psoriatics before treatment was significantly higher compared with healthy controls (medians 66.9 and 60.1 pg/ml, respectively; P = 0.04), but the therapy resulted in significant decrease in VIP plasma level (median 19.0 pg/ml; P < 0.001). In psoriatic patients significant correlations were noted between NPY and VIP (R = 0.34; P < 0.01), and VIP and CGRP plasma levels, both before (R = 0.28; P = 0.03) and after the treatment (R = 0.44; P < 0.01).

Conclusions:  Based on our results and previous literature data it could be suggested that neuropeptides may be involved in the development of psoriatic lesions.
Regulation of Phagocytosis in Dictyostelium by the Inositol 5‐Phosphatase OCRL Homolog Dd5P4
Authors: Loovers Harriët M. , Kortholt Arjan , de Groote Hendrie , Whitty Leslie , Nussbaum Robert L. , van Haastert Peter J. M.
Published: March 2007

Phosphoinositides are involved in endocytosis in both mammalian cells and the amoeba Dictyostelium discoideum. Dd5P4 is the Dictyostelium homolog of human OCRL (oculocerebrorenal syndrome of Lowe); both have a RhoGAP domain and a 5‐phosphatase domain that acts on phosphatidylinositol 4,5‐bisphosphate/phosphatidylinositol 3,4,5‐trisphosphate (PI(3,4,5)P3). Inactivation of Dd5P4 inhibits growth on liquid medium and on bacteria. Dd5p4‐null cells are impaired in phagocytosis of yeast cells. In wild‐type cells, PI(3,4,5)P3 is formed and converted to PI(3,4)P2 just before closure of the phagocytic cup. In dd5p4‐null cells, a phagocytic cup is formed upon contact with the yeast cell, and PI(3,4,5)P3 is still produced, but the phagocytic cup does not close. We suggest that Dd5P4 regulates the conversion of PI(3,4,5)P3 to PI(3,4)P2 and that this conversion is essential for closure of the phagocytic cup. Phylogenetic analysis of OCRL‐like 5‐phosphatases with RhoGAP domains reveal that D. discoideum Dd5P4 is a surprisingly close homolog of human OCRL, the protein responsible for Lowe syndrome. We expressed human OCRL in dd5p4‐null cells. Growth on bacteria and axenic medium is largely restored, whereas the rate of phagocytosis of yeast cells is partly restored, indicating that human OCRL can functionally replace Dictyostelium Dd5P4.
The Best Interests Standard for Incompetent or Incapacitated Persons of All Ages
Authors: Kopelman Loretta M.
Published: March 2007

When making decisions for adults lacking decision-making capacity and having no discernable preferences, widespread support exists for using the Best Interests Standard. For example, the President's Council on Bioethics supports this view in its publication, Taking Care: Ethical Caregiving in Our Aging Society. The President's Council maintains that decision-makers should seek the best available care for incapacitated adults, yet clarifies the best care does not always extend biological life for the longest time and advocates careful attention to comfort care and pain control. Their recommendations for making medical decisions for incapacitated adults match guidelines by American Academy of Pediatrics (AAP) committees and by the U.K’.s Nuffield Council on Bioethics report for making medical decisions for children and infants.

For reasons of consistency, fairness, and compassion, this guidance should be applied to all people lacking decision-making capacity. Uniform guidelines, however, would be incompatible with a policy for infants based on the Child Abuse Prevention and Treatment Act (CAPTA) amendments, widely known as the “Baby Doe” Rules.
New insights concerning the role of carnitine in the regulation of fuel metabolism in skeletal muscle
Authors: Stephens Francis B. , Constantin‐Teodosiu Dumitru , Greenhaff Paul L.
Published: March 2007

In skeletal muscle, carnitine plays an essential role in the translocation of long‐chain fatty‐acids into the mitochondrial matrix for subsequent β‐oxidation, and in the regulation of the mitochondrial acetyl‐CoA/CoASH ratio. Interest in these vital metabolic roles of carnitine in skeletal muscle appears to have waned over the past 25 years. However, recent research has shed new light on the importance of carnitine as a regulator of muscle fuel selection. It has been established that muscle free carnitine availability may be limiting to fat oxidation during high intensity submaximal exercise. Furthermore, increasing muscle total carnitine content in resting healthy humans (via insulin‐mediated stimulation of muscle carnitine transport) reduces muscle glycolysis, increases glycogen storage and is accompanied by an apparent increase in fat oxidation. By increasing muscle pyruvate dehydrogenase complex (PDC) activity and acetylcarnitine content at rest, it has also been established that PDC flux and acetyl group availability limits aerobic ATP re‐synthesis at the onset of exercise (the acetyl group deficit). Thus, carnitine plays a vital role in the regulation of muscle fuel metabolism. The demonstration that its availability can be readily manipulated in humans, and impacts on physiological function, will result in renewed business and scientific interest in this compound.
Effect of Sedimentation on Ice-Sheet Grounding-Line Stability
Authors: Alley Richard B. , Anandakrishnan Sridhar , Dupont Todd K. , Parizek Byron R. , Pollard David
Published: March 2007

Sedimentation filling space beneath ice shelves helps to stabilize ice sheets against grounding-line retreat in response to a rise in relative sea level of at least several meters. Recent Antarctic changes thus cannot be attributed to sea-level rise, strengthening earlier interpretations that warming has driven ice-sheet mass loss. Large sea-level rise, such as the ≈100-meter rise at the end of the last ice age, may overwhelm the stabilizing feedback from sedimentation, but smaller sea-level changes are unlikely to have synchronized the behavior of ice sheets in the past.
Diversity of Lactic Acid Bacteria Associated with Fish and the Fish Farm Environment, Established by Amplified rRNA Gene Restriction Analysis
Authors: Michel Christian , Pelletier Claire , Boussaha Mekki , Douet Diane-Gaëlle , Lautraite Armand , Tailliez Patrick
Published: March 2007

Lactic acid bacteria have become a major source of concern for aquaculture in recent decades. In addition to true pathogenic species of worldwide significance, such as
Streptococcus iniae
and
Lactococcus garvieae
, several species have been reported to produce occasional fish mortalities in limited geographic areas, and many unidentifiable or ill-defined isolates are regularly isolated from fish or fish products. To clarify the nature and prevalence of different fish-associated bacteria belonging to the lactic acid bacterium group, a collection of 57 isolates of different origins was studied and compared with a set of 22 type strains, using amplified rRNA gene restriction analysis (ARDRA). Twelve distinct clusters were delineated on the basis of ARDRA profiles and were confirmed by sequencing of
sodA
and 16S rRNA genes. These clusters included the following:
Lactococcus raffinolactis
,
L. garvieae
,
Lactococcus l
.,
S. iniae
,
S. dysgalactiae
,
S. parauberis
,
S. agalactiae
,
Carnobacterium
spp., the
Enterococcus
“
faecium
” group, a heterogeneous
Enterococcus
-like cluster comprising indiscernible representatives of
Vagococcus fluvialis
or the recently recognized
V. carniphilus
,
V. salmoninarum
, and
Aerococcus
spp. Interestingly, the
L. lactis
and
L. raffinolactis
clusters appeared to include many commensals of fish, so opportunistic infections caused by these species cannot be disregarded. The significance for fish populations and fish food processing of three or four genetic clusters of uncertain or complex definition, namely,
Aerococcus
and
Enterococcus
clusters, should be established more accurately.
Characterization of Nontoxic and Toxin-Producing Strains ofAlexandrium minutum(Dinophyceae) in Irish Coastal Waters
Authors: Touzet Nicolas , Franco Jose M. , Raine Robin
Published: March 2007

A comparative analysis of the morphology, toxin composition, and ribosomal DNA (rDNA) sequences was performed on a suite of clonal cultures of the potentially toxic dinoflagellateAlexandrium minutumHalim. These were established from resting cysts or vegetative cells isolated from sediment and water samples taken from the south and west coasts of Ireland. Results revealed that strains were indistinguishable, both morphologically and through the sequencing of the D1-D2 domain of the large subunit and the ITS1-5.8S-ITS2 regions of the rDNA. High-performance liquid chromatography fluorescence detection analysis, however, showed that only strains derived from retentive inlets on the southern Irish coast synthesized paralytic shellfish poisoning (PSP) toxins (GTX2 and GTX3), whereas all strains ofA. minutumisolated from the west coast were nontoxic. Toxin analysis of net hauls, taken whenA. minutumvegetative cells were in the water column, revealed no PSP toxins in samples from Killary Harbor (western coast), whereas GTX2 and GTX3 were detected in samples from Cork Harbor (southern coast). These results confirm the identity ofA. minutumas the most probable causative organism for historical occurrences of contamination of shellfish with PSP toxins in Cork Harbor. Finally, random amplification of polymorphic DNA was carried out to determine the degree of polymorphism among strains. The analysis showed that all toxic strains from Cork Harbor clustered together and that a separate cluster grouped all nontoxic strains from the western coast.
Effect of Protein, Polysaccharide, and Oxygen Concentration Profiles on Biofilm Cohesiveness
Authors: Ahimou Francois , Semmens Michael J. , Haugstad Greg , Novak Paige J.
Published: March 2007

It is important to control biofilm cohesiveness to optimize process performance. In this study, a membrane-aerated biofilm reactor inoculated with activated sludge was used to grow mixed-culture biofilms of different ages and thicknesses. The cohesions, or cohesive energy levels per unit volume of biofilm, based on a reproducible method using atomic force microscopy (F. Ahimou, M. J. Semmens, P. J. Novak, and G. Haugstad, Appl. Environ. Microbiol. 73:2897-2904, 2007), were determined at different locations within the depths of the biofilms. In addition, the protein and polysaccharide concentrations within the biofilm depths, as well as the dissolved oxygen (DO) concentration profiles within the biofilms, were measured. It was found that biofilm cohesion increased with depth but not with age. Level of biofilm cohesive energy per unit volume was strongly correlated with biofilm polysaccharide concentration, which increased with depth in the membrane-aerated biofilm. In a 12-day-old biofilm, DO also increased with depth and may therefore be linked to polysaccharide production. In contrast, protein concentration was relatively constant within the biofilm and did not appear to influence cohesion.
Bacterial Degradation of
N,N
-Diethyl-
m
-Toluamide (DEET): Cloning and Heterologous Expression of DEET Hydrolase
Authors: Rivera-Cancel Giomar , Bocioaga Daniela , Hay Anthony G.
Published: March 2007

Pseudomonas putida
DTB grew aerobically with
N,N
-diethyl-
m
-toluamide (DEET) as a sole carbon source, initially breaking it down into 3-methylbenzoate and diethylamine. The former was further metabolized via 3-methylcatechol and
meta
ring cleavage. A gene from DTB,
dthA
, was heterologously expressed and shown to encode the ability to hydrolyze DEET into 3-methylbenzoate and diethylamine.
Competition for Light between Toxic and Nontoxic Strains of the Harmful Cyanobacterium
Microcystis
Authors: Kardinaal W. Edwin A. , Tonk Linda , Janse Ingmar , Hol Suzanne , Slot Pieter , Huisman Jef , Visser Petra M.
Published: March 2007

The cyanobacterium
Microcystis
can produce microcystins, a family of toxins that are of major concern in water management. In several lakes, the average microcystin content per cell gradually declines from high levels at the onset of
Microcystis
blooms to low levels at the height of the bloom. Such seasonal dynamics might result from a succession of toxic to nontoxic strains. To investigate this hypothesis, we ran competition experiments with two toxic and two nontoxic
Microcystis
strains using light-limited chemostats. The population dynamics of these closely related strains were monitored by means of characteristic changes in light absorbance spectra and by PCR amplification of the rRNA internal transcribed spacer region in combination with denaturing gradient gel electrophoresis, which allowed identification and semiquantification of the competing strains. In all experiments, the toxic strains lost competition for light from nontoxic strains. As a consequence, the total microcystin concentrations in the competition experiments gradually declined. We did not find evidence for allelopathic interactions, as nontoxic strains became dominant even when toxic strains were given a major initial advantage. These findings show that, in our experiments, nontoxic strains of
Microcystis
were better competitors for light than toxic strains. The generality of this finding deserves further investigation with other
Microcystis
strains. The competitive replacement of toxic by nontoxic strains offers a plausible explanation for the gradual decrease in average toxicity per cell during the development of dense
Microcystis
blooms.
Survival of
Mycobacterium avium
,
Legionella pneumophila
,
Escherichia coli
, and Caliciviruses in Drinking Water-Associated Biofilms Grown under High-Shear Turbulent Flow
Authors: Lehtola Markku J. , Torvinen Eila , Kusnetsov Jaana , Pitkänen Tarja , Maunula Leena , von Bonsdorff Carl-Henrik , Martikainen Pertti J. , Wilks Sandra A. , Keevil C. William , Miettinen Ilkka T.
Published: March 2007

Most of the bacteria in drinking water distribution systems are associated with biofilms. In biofilms, their nutrient supply is better than in water, and biofilms can provide shelter against disinfection. We used a Propella biofilm reactor for studying the survival of
Mycobacterium avium
,
Legionella pneumophila
,
Escherichia coli
, and canine calicivirus (CaCV) (as a surrogate for human norovirus) in drinking water biofilms grown under high-shear turbulent-flow conditions. The numbers of
M. avium
and
L. pneumophila
were analyzed with both culture methods and with peptide nucleic acid fluorescence in situ hybridization (FISH) methods. Even though the numbers of pathogens in biofilms decreased during the experiments,
M. avium
and
L. pneumophila
survived in biofilms for more than 2 to 4 weeks in culturable forms. CaCV was detectable with a reverse transcription-PCR method in biofilms for more than 3 weeks.
E. coli
was detectable by culture for only 4 days in biofilms and 8 days in water, suggesting that it is a poor indicator of the presence of certain waterborne pathogens. With
L. pneumophila
and
M. avium
, culture methods underestimated the numbers of bacteria present compared to the FISH results. This study clearly proved that pathogenic bacteria entering water distribution systems can survive in biofilms for at least several weeks, even under conditions of high-shear turbulent flow, and may be a risk to water consumers. Also, considering the low number of virus particles needed to result in an infection, their extended survival in biofilms must be taken into account as a risk for the consumer.
Temperature-Dependent Expression ofListeria monocytogenesInternalin and Internalin-Like Genes Suggests Functional Diversity of These Proteins among the Listeriae
Authors: McGann Patrick , Ivanek Renata , Wiedmann Martin , Boor Kathryn J.
Published: March 2007

TheListeria monocytogenesgenome contains genes encoding several internalins and internalin-like proteins. AsL. monocytogenesis present in many environments and can infect numerous, diverse host species, the environmental temperature was hypothesized to be a signal that might affect internalin gene transcription. A subgenomic microarray was used to investigate temperature-dependent transcription of 24 members of the internalin gene family inL. monocytogenes10403S. The levels of internalin gene transcripts for cells grown at 37°C were compared to the levels of transcripts for cells grown at 16, 30, and 42°C using competitive microarray hybridization, and the results were confirmed by performing quantitative reverse transcriptase PCR for 14 internalin genes. Based on these studies, the internalin genes can be grouped into the following five temperature-dependent categories: (i) four σB-dependent internalin genes (inlC2,inlD, lmo0331, and lmo0610) with the highest levels of transcripts at 16°C and generally the lowest levels of transcripts at 37°C; (ii) three partially PrfA-dependent internalin genes (inlA,inlB, andinlC) with the lowest levels of transcripts at 16°C and the highest levels of transcripts at 37 and 42°C; (iii) four genes (inlG,inlJ, lmo0514, and lmo1290) with the lowest levels of transcripts at 16°C and the highest levels of transcripts at 30 and/or 37°C; (iv) one gene (lmo0327) with the highest levels of transcripts at 16°C and low levels of transcripts at higher temperatures; and (v) 12 internalin genes with no differences in the levels of transcripts at the temperatures used in this study. The temperature-dependent transcription patterns suggest that the relative importance of different internalins varies by environment, which may provide insight into the specific functions of these proteins.
Development of a Genetic System for the Chemolithoautotrophic Bacterium
Thiobacillus denitrificans
Authors: Letain Tracy E. , Kane Staci R. , Legler Tina C. , Salazar Edmund P. , Agron Peter G. , Beller Harry R.
Published: March 2007

Thiobacillus denitrificans
is a widespread, chemolithoautotrophic bacterium with an unusual and environmentally relevant metabolic repertoire, which includes its ability to couple denitrification to sulfur compound oxidation; to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV); and to oxidize mineral electron donors. Recent analysis of its genome sequence also revealed the presence of genes encoding two [NiFe]hydrogenases, whose role in metabolism is unclear, as the sequenced strain does not appear to be able to grow on hydrogen as a sole electron donor under denitrifying conditions. In this study, we report the development of a genetic system for
T. denitrificans
, with which insertion mutations can be introduced by homologous recombination and complemented in
trans
. The antibiotic sensitivity of
T. denitrificans
was characterized, and a procedure for transformation with foreign DNA by electroporation was established. Insertion mutations were generated by in vitro transposition, the mutated genes were amplified by the PCR, and the amplicons were introduced into
T. denitrificans
by electroporation. The IncP plasmid pRR10 was found to be a useful vector for complementation. The effectiveness of the genetic system was demonstrated with the
hynL
gene, which encodes the large subunit of a [NiFe]hydrogenase. Interruption of
hynL
in a
hynL
::kan mutant resulted in a 75% decrease in specific hydrogenase activity relative to the wild type, whereas complementation of the
hynL
mutation resulted in activity that was 50% greater than that of the wild type. The availability of a genetic system in
T. denitrificans
will facilitate our understanding of the genetics and biochemistry underlying its unusual metabolism.
Expression and Interstrain Variability of the
YPS3
Gene of
Histoplasma capsulatum
Authors: Bohse Megan L. , Woods Jon P.
Published: March 2007

The
YPS3
locus of the dimorphic fungus
Histoplasma capsulatum
encodes a secreted and surface-localized protein specific to the pathogenic yeast phase. In this study we examined this locus in 32
H. capsulatum
strains and variants. Although protein production is limited to a select group of strains, the North American restriction fragment length polymorphism class 2/NAm 2 isolates, the locus was present in all the strains we examined. The
YPS3
gene is well conserved in its 5′ and 3′ regions but displays an intragenic hypervariable region of tandem repeats that fluctuates in size between strains. This feature is similar to that seen with genes encoding several cell surface proteins in other fungi.
Spatial Patterns of DNA Replication, Protein Synthesis, and Oxygen Concentration within Bacterial Biofilms Reveal Diverse Physiological States
Authors: Rani Suriani Abdul , Pitts Betsey , Beyenal Haluk , Veluchamy Raaja Angathevar , Lewandowski Zbigniew , Davison William M. , Buckingham-Meyer Kelli , Stewart Philip S.
Published: March 2007

It has long been suspected that microbial biofilms harbor cells in a variety of activity states, but there have been few direct experimental visualizations of this physiological heterogeneity. Spatial patterns of DNA replication and protein synthetic activity were imaged and quantified in staphylococcal biofilms using immunofluorescent detection of pulse-labeled DNA and also an inducible green fluorescent protein (GFP) construct. Stratified patterns of DNA synthetic and protein synthetic activity were observed in all three biofilm systems to which the techniques were applied. In a colony biofilm system, the dimensions of the zone of anabolism at the air interface ranged from 16 to 38 μm and corresponded with the depth of oxygen penetration measured with a microelectrode. A second zone of activity was observed along the nutrient interface of the biofilm. Much of the biofilm was anabolically inactive. Since dead cells constituted only 10% of the biofilm population, most of the inactive cells in the biofilm were still viable. Collectively, these results suggest that staphylococcal biofilms contain cells in at least four distinct states: growing aerobically, growing fermentatively, dead, and dormant. The variety of activity states represented in a biofilm may contribute to the special ecology and tolerance to antimicrobial agents of biofilms.
Genetic Analysis of
Helicobacter pylori
Strain Populations Colonizing the Stomach at Different Times Postinfection
Authors: Salama Nina R. , Gonzalez-Valencia Gerardo , Deatherage Brooke , Aviles-Jimenez Francisco , Atherton John C. , Graham David Y. , Torres Javier
Published: March 2007

Genetic diversity of the human gastric pathogen
Helicobacter pylori
in an individual host has been observed; whether this diversity represents diversification of a founding strain or a mixed infection with distinct strain populations is not clear. To examine this issue, we analyzed multiple single-colony isolates from two to four separate stomach biopsies of eight adult and four pediatric patients from a high-incidence Mexican population. Eleven of the 12 patients contained isolates with identical random amplified polymorphic DNA, amplified fragment length polymorphism, and
vacA
allele molecular footprints, whereas a single adult patient had two distinct profiles. Comparative genomic hybridization using whole-genome microarrays (array CGH) revealed variation in 24 to 67 genes in isolates from patients with similar molecular footprints. The one patient with distinct profiles contained two strain populations differing at 113 gene loci, including the
cag
pathogenicity island virulence genes. The two strain populations in this single host had different spatial distributions in the stomach and exhibited very limited genetic exchange. The total genetic divergence and pairwise genetic divergence between isolates from adults and isolates from children were not statistically different. We also analyzed isolates obtained 15 and 90 days after experimental infection of humans and found no evidence of genetic divergence, indicating that transmission to a new host does not induce rapid genetic changes in the bacterial population in the human stomach. Our data suggest that humans are infected with a population of closely related strains that vary at a small number of gene loci, that this population of strains may already be present when an infection is acquired, and that even during superinfection genetic exchange among distinct strains is rare.
Developmental contexts and sporting success: birth date and birthplace effects in national hockey league draftees 2000–2005
Authors: Baker Joseph , Logan A Jane
Published: March 2007

Objectives:To examine relative age and birth place effects in hockey players drafted to play in the National Hockey League (NHL) between 2000 and 2005 and determine whether these factors influenced when players were chosen in the draft.

Methods:1013 North American draftees were evaluated from the official NHL website, which provided birthplace, date of birth and selection order in the draft. Population size was collected from Canadian and American census information. Athletes were divided into four quartiles on the basis of selection date to define age cohorts in hockey. Data between the Canadian and American players were also compared to see if the optimal city sizes differed between the two nations.

Results:Relative age and birthplace effects were found, although the optimal city size found was dissimilar to that found in previous studies. Further, there were inconsistencies between the Canadian and American data.

Conclusion:Contextual factors such as relative age and size of birthplace have a significant effect on likelihood of being selected in the NHL draft.
Environmental risk factors for Parkinson’s disease and parkinsonism: the Geoparkinson study
Authors: Dick F D , De Palma G , Ahmadi A , Scott N W , Prescott G J , Bennett J , Semple S , Dick S , Counsell C , Mozzoni P , Haites N , Wettinger S Bezzina , Mutti A , Otelea M , Seaton A , Söderkvist P , Felice A
Published: March 2007

Objective:

To investigate the associations between Parkinson’s disease and other degenerative parkinsonian syndromes and environmental factors in five European countries.

Methods:

A case–control study of 959 prevalent cases of parkinsonism (767 with Parkinson’s disease) and 1989 controls in Scotland, Italy, Sweden, Romania and Malta was carried out. Cases were defined using the United Kingdom Parkinson’s Disease Society Brain Bank criteria, and those with drug-induced or vascular parkinsonism or dementia were excluded. Subjects completed an interviewer-administered questionnaire about lifetime occupational and hobby exposure to solvents, pesticides, iron, copper and manganese. Lifetime and average annual exposures were estimated blind to disease status using a job-exposure matrix modified by subjective exposure modelling. Results were analysed using multiple logistic regression, adjusting for age, sex, country, tobacco use, ever knocked unconscious and family history of Parkinson’s disease.

Results:

Adjusted logistic regression analyses showed significantly increased odds ratios for Parkinson’s disease/parkinsonism with an exposure–response relationship for pesticides (low vs no exposure, odds ratio (OR) = 1.13, 95% CI 0.82 to 1.57, high vs no exposure, OR = 1.41, 95% CI 1.06 to 1.88) and ever knocked unconscious (once vs never, OR = 1.35, 95% CI 1.09 to 1.68, more than once vs never, OR = 2.53, 95% CI 1.78 to 3.59). Hypnotic, anxiolytic or antidepressant drug use for more than 1 year and a family history of Parkinson’s disease showed significantly increased odds ratios. Tobacco use was protective (OR = 0.50, 95% CI 0.42 to 0.60). Analyses confined to subjects with Parkinson’s disease gave similar results.

Conclusions:

The association of pesticide exposure with Parkinson’s disease suggests a causative role. Repeated traumatic loss of consciousness is associated with increased risk.
Decline in lung function and mortality: implications for medical monitoring
Authors: Sircar Kanta , Hnizdo Eva , Petsonk Edward , Attfield Michael
Published: March 2007

Aim:To investigate the risk of death associated with selected cut-off points for rate of decline of forced expiratory volume in one second (FEV1).

Methods:Mortality rates of a cohort of 1730 coal miners who had performed two pulmonary function tests 12.8 years apart were followed up for an additional 12 years. Based on previous studies, cut-off points for FEV1rate of decline (ml/year) were selected as 30, 60 and 90 ml/year. Cox proportional hazard regression was used to estimate multivariate risk ratio of death in each category.

Results:The risk ratios (compared to “below 30 ml/year”) were 1.39 (95% CI 0.99 to 1.97) in the “60 to less than 90 ml/year” category and 1.90 (95% CI 1.32 to 2.76) in the “90 ml/year and above” category. Rates of decline above 90 ml/year were consistently related to excess mortality. In non-smokers and those with neither restrictive nor obstructive patterns at the first survey, rates of decline above 60 ml/year were significantly associated with increased mortality.

Conclusions:Risk of death increases in individuals with rates of decline above about 60 ml/year and is statistically significant with declines of 90 ml/year or more. These results should be useful to healthcare providers in assessing lung function declines observed in individuals.
Characteristics of metabolically obese normal-weight (MONW) subjects
Authors: Conus Florence , Rabasa-Lhoret Rémi , Péronnet François
Published: March 2007

The existence of a subgroup of normal-weight individuals displaying obesity-related phenotypic characteristics was first proposed in 1981. These individuals were identified as metabolically obese but normal weight (MONW). It was hypothesized that these individuals might be characterized by hyperinsulinemia and (or) insulin resistance, as well as by hypertriglyceridemia and high blood pressure despite having a body mass index (BMI) < 25 kg/m2. Such characteristics could confer upon MONW subjects a higher cardiovascular risk; however, scientific data on MONW subjects are scarce since only 9 publications are directly related to this topic. Despite differences in the criteria for identifying MONW subjects and the small number of subjects involved in most of these studies, their consistent results indicate that: (i) the prevalence of the MONW syndrome ranges between 5% and 45%, depending on the criteria used, age, BMI, and ethnicity; (ii) when compared with control subjects, MONW subjects display an altered insulin sensitivity, a higher abdominal and visceral adiposity, a more atherogenic lipid profile, a higher blood pressure, and a lower physical activity energy expenditure; and (iii) MONW subjects are at higher risks for type 2 diabetes and cardiovascular diseases.
Nutritional strategies in the prevention and treatment of metabolic syndrome
Authors: Feldeisen Sabrina E. , Tucker Katherine L.
Published: March 2007

The metabolic syndrome (MetS) is a clustering of metabolic abnormalities that increase the risk of developing atherosclerotic cardiovascular disease and type 2 diabetes. The exact etiology remains unclear, but it is known to be a complex interaction between genetic, metabolic, and environmental factors. Among environmental factors, dietary habits are of central importance in the prevention and treatment of this condition. However, there is currently no firm consensus on the most appropriate dietary recommendations. General recommendations include decreasing obesity, increasing physical activity, and consuming an anti-atherogenic diet, and have traditionally focused on low total fat intake. A major problem with the focus on low fat is that high-carbohydrate diets can contribute to increasing triglyceride and decreasing high-density lipoprotein (HDL) concentrations. Low-carbohydrate diets have been popular in recent years. However, such diets are typically higher in saturated fat and lower in fruits, vegetables, and whole grains than national dietary recommendations. More recently the quality of carbohydrate has been studied in relation to MetS, including a focus on dietary fiber and glycemic index. Similarly, there has been a move from limiting total fat to a focus on the quality of the fat, with evidence of beneficial effects of replacing some carbohydrate with monounsaturated fat. Other nutrients examined for possible importance include calcium, vitamin D, and magnesium. Together, the evidence suggests that the components of diet currently recommended as “healthy” are likely also protective against MetS, including low saturated and trans fat (rather than low total fat) and balanced carbohydrate intake rich in dietary fiber, as well as high fruit and vegetable intake (rather than low total carbohydrate); and the inclusion of low-fat dairy foods. Accelerating research on gene–diet interactions is likely to contribute interesting information that may lead to further individualized dietary guidance in the future.
Genetics of the metabolic syndrome
Authors: Terán-García Margarita , Bouchard Claude
Published: March 2007

The concept of a metabolic syndrome (MetS), a cluster of pre-clinical metabolic alterations commonly associated with obesity, is the object of much debate. Genetic studies have the potential to contribute to some of the key questions, including the true nature of the cluster of pre-clinical features and whether it is associated with human genetic variation. This review summarizes the evidence for the presence of familial aggregation for the individual components of MetS and their heritability levels. It also provides an overview of the studies that have dealt with candidate genes for MetS. Potential leads from genome-wide linkage scans are also discussed. The assumption is made that obesity, ectopic fat deposition and abnormal adipose tissue metabolism are responsible for alterations in lipid metabolism, which in turn generates the commonly observed pre-clinical shifts in glucose tolerance, lipids and lipoprotein profile, blood pressure, inflammatory markers, endothelial function, and a prothrombotic state. Progress in the understanding of the genetic basis of MetS should occur as soon as a consensus is reached on the true nature of MetS, its components and diagnostic criteria.
From “Simple” DNA-Protein Interactions to the Macromolecular Machines of Gene Expression
Authors: von Hippel Peter H.
Published: March 2007

The physicochemical concepts that underlie our present ideas on the structure and assembly of the “macromolecular machines of gene expression” are developed, starting with the structure and folding of the individual protein and DNA components, the thermodynamics and kinetics of their conformational rearrangements during complex assembly, and the molecular basis of the sequence specificity and recognition interactions of the final assemblies that include the DNA genome. The role of diffusion in reduced dimensions in the kinetics of the assembly of macromolecular machines from their components is also considered, and diffusion-driven reactions are compared with those fueled by ATP binding and hydrolysis, as well as by the specific covalent chemical modifications involved in rearranging chromatin and modifying signal transduction networks in higher organisms.
Gene Regulation: Gene Control Network in Development
Authors: de-Leon Smadar Ben-Tabou , Davidson Eric H.
Published: March 2007

Controlling the differential expression of many thousands of genes is the most fundamental task of a developing organism. It requires an enormous computational device that has the capacity to process in parallel a vast number of regulatory inputs in the various cells of the embryo and come out with regulatory outputs that are tissue specific. The regulatory genome constitutes this computational device, comprising many thousands of processing units in the form of cis-regulatory modules. The interconnected cis-regulatory modules that control regulatory gene expression create a network that is the underlying mechanism of specification. In this review we use the gene regulatory network that governs endomesoderm specification in the sea urchin embryo to demonstrate the salient features of developmental gene regulatory networks and illustrate the information processing that is done by the regulatory sequences.
Insights from Crystallographic Studies into the Structural and Pairing Properties of Nucleic Acid Analogs and Chemically Modified DNA and RNA Oligonucleotides
Authors: Egli Martin , Pallan Pradeep S.
Published: March 2007

Chemically modified nucleic acids function as model systems for native DNA and RNA; as chemical probes in diagnostics or the analysis of protein–nucleic acid interactions and in high-throughput genomics and drug target validation; as potential antigene-, antisense-, or RNAi-based drugs; and as tools for structure determination (i.e., crystallographic phasing), just to name a few. Biophysical and structural investigations of chemically modified DNAs and RNAs, particularly of nucleic acid analogs with more significant alterations to the well-known base-sugar-phosphate framework (i.e., peptide or hexopyranose nucleic acids), can also provide insights into the properties of the natural nucleic acids that are beyond the reach of studies focusing on DNA or RNA alone. In this review we summarize results from crystallographic analyses of chemically modified DNAs and RNAs that are primarily of interest in the context of the discovery and development of oligonucleotide-based therapeutics. In addition, we re-examine recent structural data on nucleic acid analogs that are investigated as part of a systematic effort to rationalize nature's choice of pentose in the genetic system.
Small-Angle X-Ray Scattering from RNA, Proteins, and Protein Complexes
Authors: Lipfert Jan , Doniach Sebastian
Published: March 2007

Small-angle X-ray scattering (SAXS) is increasingly used to characterize the structure and interactions of biological macromolecules and their complexes in solution. Although still a low-resolution technique, the advent of high-flux synchrotron sources and the development of algorithms for the reconstruction of 3-D electron density maps from 1-D scattering profiles have made possible the generation of useful low-resolution molecular models from SAXS data. Furthermore, SAXS is well suited for the study of unfolded or partially folded conformational ensembles as a function of time or solution conditions. Here, we review recently developed algorithms for 3-D structure modeling and applications to protein complexes. Furthermore, we discuss the emerging use of SAXS as a tool to study membrane protein-detergent complexes. SAXS is proving useful to study the folding of functional RNA molecules, and finally we discuss uses of SAXS to study ensembles of denatured proteins.
Visualizing Flexibility at Molecular Resolution: Analysis of Heterogeneity in Single-Particle Electron Microscopy Reconstructions
Authors: Leschziner Andres E. , Nogales Eva
Published: March 2007

It is becoming increasingly clear that many macromolecules are intrinsically flexible and exist in multiple conformations in solution. Single-particle reconstruction of vitrified samples (cryo-electron microscopy, or cryo-EM) is uniquely positioned to visualize this conformational flexibility in its native state. Although heterogeneity remains a significant challenge in cryo-EM single-particle analysis, recent efforts in the field point to a future where it will be possible to tap into this rich source of biological information on a routine basis. In this article, we review the basic principles behind a few relatively new and generally applicable methods that show particular promise as tools to analyze macromolecular flexibility. We also discuss some of their recent applications to problems of biological interest.
Cardiac-restricted angiotensin-converting enzyme overexpression causes conduction defects and connexin dysregulation
Authors: Kasi Vijaykumar S. , Xiao Hong D. , Shang Lijuan L. , Iravanian Shahriar , Langberg Jonathan , Witham Emily A. , Jiao Zhe , Gallego Carlos J. , Bernstein Kenneth E. , Dudley Samuel C.
Published: March 2007

Renin-angiotensin (RAS) system activation is associated with an increased risk of sudden death. Previously, we used cardiac-restricted angiotensin-converting enzyme (ACE) overexpression to construct a mouse model of RAS activation. These ACE 8/8 mice die prematurely and abruptly. Here, we have investigated cardiac electrophysiological abnormalities that may contribute to early mortality in this model. In ACE 8/8 mice, surface ECG voltages are reduced. Intracardiac electrograms showed atrial and ventricular potential amplitudes of 11% and 24% compared with matched wild-type (WT) controls. The atrioventricular (AV), atrio-Hisian (AH), and Hisian-ventricular (HV) intervals were prolonged 2.8-, 2.6-, and 3.9-fold, respectively, in ACE 8/8 vs. WT mice. Various degrees of AV nodal block were present only in ACE 8/8 mice. Intracardiac electrophysiology studies demonstrated that WT and heterozygote (HZ) mice were noninducible, whereas 83% of ACE 8/8 mice demonstrated ventricular tachycardia with burst pacing. Atrial connexin 40 (Cx40) and connexin 43 (Cx43) protein levels, ventricular Cx43 protein level, atrial and ventricular Cx40 mRNA abundances, ventricular Cx43 mRNA abundance, and atrial and ventricular cardiac Na+ channel (Scn5a) mRNA abundances were reduced in ACE 8/8 compared with WT mice. ACE 8/8 mice demonstrated ventricular Cx43 dephosphorylation. Atrial and ventricular L-type Ca2+ channel, Kv4.2 K+ channel α-subunit, and Cx45 mRNA abundances and the peak ventricular Na+ current did not differ between the groups. In isolated heart preparations, a connexin blocker, 1-heptanol (0.5 mM), produced an electrophysiological phenotype similar to that seen in ACE 8/8 mice. Therefore, cardiac-specific ACE overexpression resulted in changes in connexins consistent with the phenotype of low-voltage electrical activity, conduction defects, and induced ventricular arrhythmia. These results may help explain the increased risk of arrhythmia in states of RAS activation such as heart failure.