bluuebunny/crossref_metadata_2025_split huggingface dataset:
What functions do linker histones provide?
Authors: Harvey Anne C. , Downs Jessica A. 
Published: July 2004

SummaryLinker histones have long been known to facilitate chromatin condensation in vitro. For many years, this activity led to speculation that these proteins function as global repressors of transcription. However, work from numerous systems has demonstrated that this is not the case, and that linker histones appear to affect only the transcription of a small subset of genes, and, in fact, act to activate as well as repress transcription. Furthermore, there is evidence that suggests that linker histones are not required for mitotic condensation. In this review, we focus on studies of biological functions of linker histones primarily performed in unicellular eukaryotes. We highlight recent developments pointing towards linker histone involvement in DNA repair and ageing, which raise the possibility that the biological functions of linker histones are more varied than previously imagined.
Rafts and sphingolipid biosynthesis in the kinetoplastid parasitic protozoa
Authors: Denny Paul W. , Smith Deborah F. 
Published: July 2004

SummaryAlthough the concept of eukaryotic lipid rafts arouses controversy, recent biophysical studies strongly indicate that inducible, stable and relatively large rafts are a feature of activated mammalian cells. These studies allow us to consider the functional role of lipid rafts in kinetoplastid parasites, which are particularly rich in lipid‐anchored surface molecules. Morphological, biochemical and genetic studies indicate that lipid rafts (and sphingolipid biosythesis) are important in the differentiation of extracellular Leishmania to mammalian‐infective metacyclic promastigotes, perhaps orchestrating the clearly observable reorganization of the plasma membrane during this process that leads to an activated metacyclic primed for invasion. However, the first step in the sphingolipid biosynthetic pathway (mediated by serine palmitoyltransferase), and at least regulated, de novo sphingoid base and ceramide synthesis, are not essential for the pathogenesis of intramacrophage Leishmania amastigotes.
Endocytosis, membrane recycling and sorting of GPI‐anchored proteins: Trypanosoma brucei as a model system
Authors: Overath Peter , Engstler Markus 
Published: July 2004

SummaryIn the flagellated protozoon Trypanosoma brucei, endo‐ and exocytosis are restricted to a small area of the plasma membrane, the flagellar pocket. All endosomal compartments and the single Golgi complex are located within the posterior part of the cell between the flagellar pocket and the nucleus. The use of reverse genetic tools, including RNA interference, in combination with quantitative 3D‐fluorescence and electron microscopic techniques has provided an insight into endosomal membrane traffic, which occurs at a very high rate and appears to exhibit a lower level of complexity than in mammalian cells. The flagellate is an excellent model system for studies on endocytosis, sorting and recycling of glycosylphosphatidylinositol‐anchored glycoproteins, because 107 molecules of the variant surface glycoprotein form a dense coat at the cell's surface. Because the endocytic rate varies widely at different stages in the parasite's life cycle, trypanosomes may be used for investigating developmental aspects of their endocytic system.
A prospective association between cocoon use in infancy and childhood asthma
Authors: Trevillian L. F. , Ponsonby A. L. , Dwyer T. , Lim L. L. Y. , Kemp A. , Cochrane J. , Carmichael A. 
Published: July 2004

SummaryThere is increasing evidence for a role for bedding items in the development of asthma. The use of some forms of synthetic bedding, such as foam mattresses and pillows, is associated with a significantly increased risk of childhood wheeze. Our aim was to examine prospectively whether the use of synthetic cocoon/baby nests in infancy is associated with the subsequent development of wheeze in childhood. Data collected in 1988 as part of the Tasmanian Infant Health Survey were linked to the cross‐sectional Childhood Asthma Survey conducted in 1995 in Tasmania, Australia.We were able to match 863 records out of the 1111 in the 1988 survey. Information including parental, child‐care, and the infant's sleeping environment was collected at home interview in 1988 when the infant was 1 month of age. Data including sleep environment and asthma symptoms were available for each child at age 7 years. A generalised linear model was used to calculate the adjusted relative risk (RR) estimates for symptoms of wheeze and infant cocoon use. For children who were placed in a cocoon in infancy, there was an increased risk of recent wheeze (adjusted RR = 4.33 [95% CI 2.08, 9.02]) and night wheeze (adjusted RR = 3.35 [95% CI 1.52, 7.39]) at age 7 years.In view of the increasing prevalence of childhood asthma, the identification of potentially modifiable environmental factors which might operate in infancy is of importance. The present findings implicate infant bedding choice as a significant factor and further studies on the infant sleeping environment are indicated.
Transition from Birth to Ten to Birth to Twenty: the South African cohort reaches 13 years of age
Authors: Richter Linda M. , Norris Shane A. , De Wet Thea 
Published: July 2004

SummaryBirth to Ten now Birth to Twenty (BT20), is the largest and longest running longitudinal birth cohort study in Africa. In this paper, the methods, magnitude and significance of recruitment, follow‐up and attrition are described. Although more than 5000 births were notified in the area in the 7‐week enrolment period in early 1990, only 3275 children were established to have been born to women who were residents in the Greater Johannesburg Metropolitan area for at least the first 6 months of the child's life. Seventy per cent of these children and their families have been followed up for more than 12 years, indicating an average attrition rate of less than 3% per annum, with most attrition occurring in the first 2 years of the study. The most common reason for attrition was movement out of the study area, although detailed follow‐up, and the extent of contact re‐established at later points, indicate very high levels of circular migration among women and young children between urban and rural areas, as well as very high levels of residential mobility within urban areas. There has been no differential loss of vulnerable families and children. African women living in Soweto are the most consistent participants in the study. A bias, by population group membership and residential area, was introduced in the recruitment phases of the project by the difficulty of enrolling the small proportion of people in the metropolis, largely Whites, who used private delivery services in 1989–90.
The ACR4 receptor‐like kinase is required for surface formation of epidermis‐related tissues in Arabidopsis thaliana
Authors: Watanabe Masaru , Tanaka Hirokazu , Watanabe Daisuke , Machida Chiyoko , Machida Yasunori 
Published: July 2004

SummaryIn higher plants, an outer layer of meristematic cells, the protoderm, forms early in embryogenesis and this layer gives rise to the epidermis in differentiating tissues. We proposed previously that an Arabidopsis thaliana homolog of crinkly4 (ACR4), a gene for a receptor‐like protein kinase, would be involved in differentiation and/or maintenance of epidermis‐related tissues. In the present study, we isolated loss‐of‐function acr4 mutants by a reverse genetic approach. Our extensive analyses using the transmission electron microscopy and the toluidine blue test – a method that has recently been developed for the rapid visualization of defects in the leaf cuticle – showed that the acr4 mutations significantly affected the differentiation of leaf epidermal cells, suggesting similar roles for ACR4 and CR4 in the differentiation of leaf epidermis. Our acr4 mutants also had various abnormalities related to epidermal differentiation, which included disorganized cell layers in the integument and endothelium of ovules. In addition, the green fluorescent protein fused to ACR4 was localized preferentially on the lateral and basal plasma membranes in the epidermis of the leaf primordia, suggesting a role for ACR4 in epidermal differentiation at cell surfaces that make contact with adjacent cells. Furthermore, the loss‐of‐function mutations in the ACR4 and ABNORMAL LEAF SHAPE1 (ALE1) genes, which encode a putative subtilisin‐like serine protease, synergistically affected the function of the epidermis such that most leaves fused. Thus, ACR4 seems to play an essential role in the differentiation of proper epidermal cells in both vegetative and reproductive tissues.
Site‐directed mutagenesis and protein 3D‐homology modelling suggest a catalytic mechanism for UDP‐glucose‐dependent betanidin 5‐O‐glucosyltransferase from Dorotheanthus bellidiformis
Authors: Hans Judith , Brandt Wolfgang , Vogt Thomas 
Published: July 2004

SummaryIn livingstone daisy (Dorotheanthus bellidiformis), betanidin 5‐O‐glucosyltransferase (UGT73A5) is involved in the regiospecific glucosylation of betanidin and various flavonols. Based on sequence alignments several amino acid candidates which might be essential for catalysis were identified. The selected amino acids of the functionally expressed protein, suggested to be involved in substrate binding and turnover, were substituted via site‐directed mutagenesis. The substitution of two highly conserved amino acids, Glu378, located in the proposed UDP‐glucose binding site, and His22, located close to the N‐terminus, led to the complete loss of enzyme activity. A 3D model of this regiospecific betanidin and flavonoid glucosyltransferase was constructed and the active site modelled. This model was based on the crystallographic structure of a bacterial UDP‐glucose‐dependent glucosyltransferase from Amycolatopsis orientalis used as a template and the generated null mutations. To explain the observed inversion in the configuration of the bound sugar, semiempirical calculations favour an SN‐1 reaction, as one plausible alternative to the generally proposed SN‐2 mechanism discussed for plant natural product glucosyltransferases. The calculated structural data do not only explain the abstraction of a proton from the acceptor betanidin, but further imply that the reaction mechanism might also involve a catalytic triad, with similarities described for the serine protease family.
The fusarium wilt resistance locus Fom‐2 of melon contains a single resistance gene with complex features
Authors: Joobeur Tarek , King Joseph J. , Nolin Shelly J. , Thomas Claude E. , Dean Ralph A. 
Published: July 2004

SummaryThe soil‐borne fungus Fusarium oxysporum f.sp. melonis causes significant losses in the cultivated melon, a key member of the economically important family, the Cucurbitaceae. Here, we report the map‐based cloning and characterization of the resistance gene Fom‐2 that confers resistance to race 0 and 1 of this plant pathogen. Two recombination events, 75 kb apart, were found to bracket Fom‐2 after screening approximately 1324 gametes with PCR‐based markers. Sequence analysis of the Fom‐2 interval revealed the presence of two candidate genes. One candidate gene showed significant similarity to previously characterized resistance genes. Sequence analysis of this gene revealed clear polymorphisms between resistant and susceptible materials and was therefore designated as Fom‐2. Analysis of susceptible breeding lines (BL) presenting a haplotype very similar to the resistant cultivar MR‐1 indicated that a gene conversion had occurred in Fom‐2, resulting in a significant rearrangement of this gene. The second candidate gene which shared high similarity to an essential gene in Arabidopsis, presented an almost identical sequence in MR‐1 and BL, further supporting Fom‐2 identity. The gene conversion in Fom‐2 produced a truncated R gene, revealing new insights into R gene evolution. Fom‐2 was predicted to encode an NBS‐LRR type R protein of the non‐TIR subfamily. In contrast to most members of this class a coiled‐coil structure was predicted within the LRR region rather than in the N‐terminal. The Fom‐2 physical region contained retroelement‐like sequences and truncated genes, suggesting that this locus is complex.
LeSTIG1, an extracellular binding partner for the pollen receptor kinases LePRK1 and LePRK2, promotes pollen tube growth in vitro
Authors: Tang Weihua , Kelley Dior , Ezcurra Inés , Cotter Robyn , McCormick Sheila 
Published: July 2004

SummaryAs pollen tubes grow through the pistil they are thought to perceive and respond to diverse signals. The tomato pollen‐specific receptor kinases LePRK1 and LePRK2 might participate in signaling during pollen tube growth. We previously showed that the extracellular domain of LePRK2 interacts with a pollen protein, LAT52, before but not after pollen germination. To determine whether LePRK2 might have different binding partner(s) after pollen germination, we characterized two more proteins that, like LAT52, were identified in yeast two‐hybrid screens using the extracellular domains of LePRK1 and LePRK2 as baits. We show that LeSHY, a leucine‐rich repeat protein from pollen, and LeSTIG1, a small cysteine‐rich protein from pistil, can bind the extracellular domains of both LePRK1 and LePRK2 in vitro. In vitro binding assays with the extracellular domain of LePRK2 suggested that LeSTIG1 could displace binding of LAT52, consistent with the idea that LePRK1 and LePRK2 might interact with different ligands at different stages of pollen tube growth. Exogenous LeSTIG1 promotes pollen tube growth in vitro. The interaction of these pollen kinases with LeSTIG1 supports the notion that LePRK1 and LePRK2 are involved in mediating pollen–pistil interactions.
Endoplasmic reticulum‐resident proteins are constitutively transported to vacuoles for degradation
Authors: Tamura Kentaro , Yamada Kenji , Shimada Tomoo , Hara‐Nishimura Ikuko 
Published: July 2004

SummarySoluble endoplasmic reticulum (ER)‐resident proteins have very long lives because of their ER residency. This residency depends largely on ER‐retrieval signals at their C‐terminus. We examined the long‐term destiny of endogenous ER‐resident proteins, a lumenal binding protein (BiP) and a protein disulfide isomerase (PDI), with cultured cells of Arabidopsis. ER residents, in contrast to vacuolar proteinases, were considerably degraded in cells at the stationary phase. A subcellular fractionation analysis suggested that ER residents were transported into the vacuoles, which accumulated the residents lacking the ER‐retrieval signals. We showed that the PDI located in the vacuoles had high mannose glycans, but not complex glycans, which suggested that the ER resident was transported to the vacuoles independent of the medial/trans‐Golgi complex. To visualize the pathway of transport of ER‐resident proteins, tobacco BY‐2 cells were transformed with a chimeric gene encoding an ER‐targeted green fluorescent protein (30 kDa GFP‐HDEL). In the transformed cells at the stationary phase, GFP fluorescence was observed in the vacuoles. A subcellular fractionation revealed that a trimmed form of 27 kDa GFP was localized in the vacuoles. Treatment with E‐64d, an inhibitor of papain‐type cysteine proteinases that inhibits the degradation of GFP in the vacuoles, resulted in a stable accumulation of 27 kDa GFP in the vacuoles, even in the logarithmic phase. Our results suggest that endogenous ER residents are transported constitutively to the vacuoles by bypassing the Golgi complex and are then degraded.
Increased prevalence of latex‐sensitization among children with chronic renal failure
Authors: Dehlink E. , Prandstetter C. , Eiwegger T. , Putschögl B. , Urbanek R. , Szépfalusi Z. 
Published: July 2004

Background:  Type‐I‐allergy to natural rubber latex (NRL) has been shown to be more prevalent among certain groups of patients. Children suffering from chronic renal failure (CRF) could be a suspected risk group because of their intense exposure to latex through catheters, gloves and anesthetic equipment during frequent hospitalizations from early life on. We investigated the prevalence of latex‐sensitization among this group of patients and sought to identify risk factors.Methods:  Ninety‐three patients (mean age 10.5 years) suffering from CRF were assessed by questionnaire‐based history (details on renal disease, number and kind of surgical procedures, family and personal history of atopic diseases, allergic reactions to NRL, and the use of pacifiers) and by measurement of total and latex‐specific serum immunoglobulin (Ig)E.Results:  Ten of 93 (10.8%) patients showed elevated latex‐specific IgE‐levels. One of 10 patients reported clinical symptoms to latex‐allergen, but no allergic reactions to NRL during medical care were reported. Sensitized patients were significantly more likely to be atopic, reflected by a positive history of other allergies as well as elevated total serum IgE‐levels, and had a significantly higher number of urogenital surgeries (P = 0.02 in all cases, Fisher's exact and Wilcoxon test, respectively).Conclusion:  This study demonstrates that children with CRF are at increased risk of latex‐hypersensitivity. Significant associations with atopy and repeated surgeries were observed. Larger studies are required to elucidate whether these children are also at increased risk of anaphylaxis and therefore deserve preventive measures.
D‐2‐Hydroxy‐4‐Methylvalerate Dehydrogenase from Lactobacillus Delbrueckii Subsp. Bulgaricus— I. Kinetic Mechanism and pH Dependence of Kinetic Parameters, Coenzyme Binding and Substrate Inhibition
Authors: Alvarez Josep A. , Gelpí Josep Li. , Johnsen Keyji , Bernard Nathalie , Delcour Jean , Clarke Anthony R. , Holbrook J. John , Cortés Antonio 
Published: July 2004

The steady‐state kinetics of D‐2‐hydroxy‐4‐methylvalerate dehydrogenase have been studied at pH 8.0 by initial velocity, product inhibition, and dead‐end inhibition techniques. The mechanism is rapid‐equilibrium ordered in the NAD4+ plus D‐2‐hydroxy‐4‐methylvalerate direction, and steady‐state ordered in the other direction. In both cases coenzyme is the first substrate added and both the E‐NADH‐D‐2‐hydroxy‐4‐methylvalerate and E‐NAD+‐2‐oxo‐4‐methylvalerate give rise to abortive complexes which cause excess substrate inhibition. Steady‐state measurements show that the rate‐limiting step in both directions at pH 8.0 is between formation of the enzyme‐coenzyme‐substrate ternary complex and the release of the first product of the reaction. Transient kinetics combined with primary kinetic deuterium isotope effects show that in the NADH → NAD+ direction there is a slow, rate‐limiting rearrangement of the E‐NADH‐oxoacid complex while hydride transfer is very fast. The release of NAD+ at pH 8.0 is 200‐times faster than kcat, (NADH → NAD+) whereas the release of NADH is only 5‐times faster than kcat (NAD+→ NADH). The pH dependence of NADH binding depends upon the presence of two ionizable residues with a pKa of about 5.9. The pH dependence of kinetic parameters is explained by a third ionizable residue with pKa values 7.2 (in the E‐NADH complex) and 6.4 (in the E‐NAD+ complex) which may be the proton donor and acceptor for the chemical reaction.At pH 6.5 the mechanism changes in the NADH → NAD+ direction to be partly limited by the chemical step with a measured primary kinetic isotope effect of 5.7 and partly by an only slightly faster dissociation of NAD+. In addition the inhibition by excess oxo‐4‐methylvalerate is more pronounced. The mechanism implies that removing the positive charges created by the the two groups which control coenzyme affinity could both enhance the catalytic rate at pH 6.5 and diminish excess substrate inhibition to provide an enzyme better suited to the bulk synthesis of D‐2‐hydroxyacids.
A New Kinetic Model for the Mode of Action of Soluble and Membrane‐Immobilized Glutathione Peroxidase from Bovine Erythrocytes — Effects of Selenium
Authors: Carsol Marie Ange , Pouliquen‐Sonaglia Isabella , Lesgards Guy , Marchis‐Mouren Guy , Puigserver Antoine , Santimone Marius 
Published: July 2004

Kinetic studies on the oxidative reaction of glutathione by hydrogen peroxide were performed using soluble and membrane‐bound ox erythrocyte glutathione peroxidase of various types. The effects of organic and inorganic selenium on the glutathione peroxidase activity were also examined.The kinetic behaviour of the enzyme was investigated using a coupled reaction within a relatively large range of hydrogen peroxide and glutathione concentrations. Non‐parallel double‐reciprocal plots were obtained which suggested that a sequential ordered rather than a ping‐pong mechanism was involved. Similar results were obtained with soluble and membrane‐bound enzyme, whatever the type of crosslinking used.Crosslinking was performed on a nylon support using various alkylating agents and bifunctional molecules. With all three types of immobilized enzyme thus obtained, a slight but significant increase in the Km was observed.The effects of selenium were then studied. Using soluble enzyme, a slight increase in the activity was observed in the presence of inorganic selenium (sodium selenite) but not with organic selenium (seleno‐l‐methionine).Inorganic selenium alone was also found to have a slight effect on the membrane‐bound enzyme. An increase in the catalytic efficiency was observed when glutathione peroxidase was bound using lysine as the bifunctional agent and either glutaraldehyde or triethyloxonium tetrafluoroborate as the reticulation agent, after a three‐month period of incubation.
Conformation and Microenvironment of the Active Site of Xylose Reductase Inferred by Fluorescent Chemoaffinity Labeling
Authors: Rawat Urmila B. , Rao Mala B. 
Published: July 2004

Conformation and microenvironment at the active site of xylose reductase (XR) from Neurospora crassa was probed with fluorescent chemoaffinity labeling (FCAL) using o‐phthalaldehyde as a chemical initiator. Formation of a single isoindole derivative resulted in complete inactivation of the enzyme as judged by spectroscopic and fluorescence studies. Kinetic analysis of the 2,4,6‐trinitrobenzenesulfonic‐acid‐modified XR implicated the presence of an essential lysine residue at the active site of XR. Modification of lysine in XR abolished the ability of the enzyme to form isoindole derivative, indicating that the lysine residue involved in the reaction with 2,4,6‐trinitrobenzenesulfonic acid and o‐phthalaldehyde is the same and that the probe o‐phthalaldehyde is directed to the active site.Fluorescence studies revealed that inactivation of XR by Gdn/HCl precedes gross conformational change and the possibility of secondary‐conformational change was eliminated by acrylamide quenching studies. The enzyme inactivated by low concentrations of Gdn/HCl retained its ability to form the fluorescent XR‐isoindole derivative indicating that inactivation is not due to conformational changes at or near the active site of XR. Gdn/HCl also had no effect on the high‐affinity and low‐affinity NADPH‐binding sites of XR. Energy‐transfer experiments further revealed structural integrity at the active site of the Gdn/HCl‐inactivated XR. Changes in the fluorescence emission maximum of 1‐(β‐hydroxyethylthio)‐2‐β hydroxyethyl isoindole (EA adduct) in solvents of varying polarity was studied, the data obtained were utilized to interpret the fluorescence behaviour of XR‐isoindole derivative and assess the polarity at the active site. Experimental evidence presented here serves to suggest that the inactivation of XR by Gdn/HCl precedes conformational changes at the active site located in a microenvironment of low polarity.