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PubMed1995

Neutron diffraction analysis of the solvent accessible volume in cubic insulin crystals.

The average contact distance between protein and solvent surface atoms in cubic insulin crystals has been determined from two sets of 15 A resolution neutron diffraction data. A contact distance between the water hydrogen sites and the protein surface that is significantly shorter than the average protein-water oxygen contact distance implies that many water molecules are oriented with hydrogen atoms pointed towards the protein surface. The shape of the protein/solvent interface is consistent with the protein envelope obtained from atomic co-ordinates.

Animals↗
PubMed2000

A robust test for assortative mating.

Testing for random mating in human populations is difficult due to confounding factors such as ethnic preference and population stratification. With HLA, the high level of polymorphism is an additional problem since it is rare for couples to share the same haplotype. Focus on an ethnically homogeneous population, where levels of polymorphism at HLA loci are more limited, may provide the best situation in which to detect non-random mating. However, such populations are often genetic isolates where there may be inbreeding to an extent that is difficult to quantify and account for. We have developed a test for random mating at a multiallelic locus that is robust to stratification and inbreeding. This test relies on the availability of genotypic information from the parents of both spouses. The focus of the test is on families where there is allele sharing between the parents of both spouses, so that potential spouses could share an allele. Denoting the shared allele at the locus of interest by A, then under the assumption of random mating, heterozygous parents AX should transmit allele A equally as frequently as allele X to their offspring. When there is positive (negative) assortative mating, A will be transmitted more (less) often than X. The power of the test has been computed in a number of situations. Data on high resolution HLA haplotypes from the Hutterite population were reinvestigated by the proposed test. The test detects significant negative assortative mating when the parental origin of the shared haplotype is taken into account.

Alleles↗
PubMed1997

Molecular detection of minimal residual disease in adult and childhood acute lymphoblastic leukaemia reveals differences in treatment response.

Immunoglobulin heavy chain gene (IgH gene) rearrangements are found in the majority of patients with B lineage acute lymphoblastic leukaemia (ALL). Two hundred and three bone marrow samples from 54 patients (33 adults and 21 children) were analysed by PCR within specific time-points after diagnosis (ie 1, 2-3, 4-6 and 7-12 months) using FR1 and JH primers (fingerprinting with a sensitivity > or =1:5 x 10[3]). CDR3-derived allele specific oligoprimers (ASO to achieve a sensitivity between 1:10[4] and 1:10[5]) were applied to 12 children and 18 adults, while size of CDR3 region, oligoclonality and background problems prevented their application to the remaining patients. All patients were followed clinically for > or =24 months. Thirty adults and 16 children presented as newly diagnosed ALL, while the remaining eight patients were analysed in first or subsequent relapse. Patients destined to relapse showed a higher proportion of positive tests (> or =50%), particularly after 1 month, than in the remission group, irrespective of age. Among patients staying in remission, a decrease in MRD-positive tests occurred during the first 12 months in both age groups. However, the proportion of positive tests dropped below 15% at a later stage in adults (4-6 months) than in children (2-3 months). Among children, only patients destined to relapse were MRD positive beyond 1 month, with the exception of only one patient, still positive at 2-3 months in the remission group. The difference in MRD positivity between relapse and remission patients was statistically significant in children (P < 0.03) at any time of testing, but only at 4-6 months in adults (P < 0.01). These data suggest that resolution of MRD in ALL occurs more rapidly in children compared to adults, particularly within the first 6 months. Children and adults, studied in first or subsequent relapse, showed a higher proportion of positive tests during reinduction compared to newly diagnosed patients.

Adolescent↗
PubMed2003

Time-resolved and static-ensemble structural chemistry of hydroxymethylbilane synthase.

The enzyme hydroxymethylbilane synthase (HMBS, EC 4.3.1.8), 313 amino acid residues and MW 34 kDa, also known as porphobilinogen deaminase (PBGD), catalyses the stepwise polymerization of four molecules of porphobilinogen (PBG) to the linear tetrapyrrole 1-hydroxymethylbilane. Several crystallographic structures of HMBS have been previously determined, most recently including by time-resolved Laue protein crystallography of the Lys59Gln mutant form with reaction initiation undertaken by use of a flow cell carrying the substrate PBG. In this paper we review these structures and add new molecular graphics representations and analyses. Moreover we present a new structure refined at 1.66 A resolution using diffraction data recorded at cryo-temperature (100 K) in an attempt at trapping the polypeptide loop (residues 47 to 58) in the vicinity of the enzyme active site, missing in all previous structure determinations. This loop still has not appeared in the electron density maps, in spite of the advantage of cryo-temperature, but nevertheless the 1.66 A cryo-structure extends the ensemble of known HMBS structures. The cryomodel of protein, cofactor and 320 bound water molecules has been refined to a final R-factor and R-free of 0.198 and 0.247 respectively; the PDB deposition codes, coordinates and structure factors are 1GTK and R1GTKSF respectively. Finally a protein comparison study is presented of the Mycobacterium tuberculosis (MTb) HMBS, with the E. coli HMBS. This has been done as preparation for future structural studies on the MTb HMBS from this important disease bearing organism. The overall amino acid sequence identity is 41%. Most interestingly there is a two-residue reduction in length of the loop referred to above (Asp 50 and Gly 58 being missing in the MTb form). This gives the hope that this loop will be less flexible and thus might become visible to crystallographic analysis.

Crystallography, X-Ray↗
PubMed2004

An ordered array of cadmium clusters assembled in zeolite A.

We report the assembly of a cubic array of cationic cadmium clusters encapsulated in zeolite A, and its characterization through Rietveld analysis of powder synchrotron X-ray diffraction data and high resolution transmission electron microscopy.

Journal Article↗
PubMed2002

Subcellular localization of phosphatidylinositol 4,5-bisphosphate using the pleckstrin homology domain of phospholipase C delta1.

Ptd(4,5)P(2) is thought to promote and organize a wide range of cellular functions, including vesicular membrane traffic and cytoskeletal dynamics, by recruiting functional protein complexes to restricted locations in cellular membranes. However, little is known about the distribution of PtdIns(4,5)P(2) in the cell at high resolution. We have used the pleckstrin homology (PH) domain of phospholipase delta(1) (PLCdelta(1)), narrowly specific for PtdIns(4,5)P(2), to map the distribution of the lipid in astrocytoma and A431 cells. We applied the glutathione S-transferase-tagged PLCdelta(1) PH domain (PLCdelta(1)PH-GST) in an on-section labelling approach which avoids transfection procedures. Here we demonstrate PtdIns(4,5)P(2) labelling in the plasma membrane, and also in intracellular membranes, including Golgi (mainly stack), endosomes and endoplasmic reticulum, as well as in electron-dense structures within the nucleus. At the plasma membrane, labelling was more concentrated over lamellipodia, but not in caveolae, which contained less than 10% of the total cell-surface labelling. A dramatic decrease in signal over labelled compartments was observed on preincubation with the cognate headgroup [Ins(1,4,5)P(3)], and plasma-membrane labelling was substantially decreased after stimulation with thrombin-receptor-activating peptide (SFLLRN in the one-letter amino acid code), a treatment which markedly diminishes PtdIns(4,5)P(2) levels. Thus we have developed a highly selective method for mapping the PtdIns(4,5)P(2) distribution within cells at high resolution, and our data provide direct evidence for this lipid at key functional locations.

Blood Proteins↗
PubMed2003

Hepatitis C virus-polymerase chain reaction minipool testing: 3 years in the largest Swiss blood transfusion service.

BACKGROUND AND OBJECTIVES: Hepatitis C virus-polymerase chain reaction (HCV-PCR) minipool testing can improve the safety of labile blood products owing to a reduction in the diagnostic preseroconversion window period. In Switzerland, HCV-PCR minipool testing for the release of labile blood components became mandatory in September 1999. In the largest Swiss blood transfusion centre, HCV-PCR minipool testing began in January 1999. This report analyses the performance of the test during a 3-year period: 1 January 1999 to 31 December 2001. MATERIALS AND METHODS: EDTA-blood was collected in either standard tubes or plasma preparation (PPT) tubes from 10 blood transfusion services in Switzerland and then sent to the Blood Transfusion Service SRC Berne. Up to 48 donor samples were pooled overnight using Tecan Genesis RSP 200/8 pipettors. Viral RNA was extracted by using the Qiagen QIAamp 96 viral RNA BioRobot kit on a BioRobot 9604. For PCR amplification and detection of HCV or internal control (IC) sequences, the Roche Cobas Amplicor v2.0 test kit was used. Data management, pool resolution and identification of positive samples were performed using the PMS Software from Tecan. RESULTS: In the 3-year period from 1 January 1999 to 31 December 2001, 839056 blood donor samples were tested in minipools of up to 48 samples. Thirty-five HCV-PCR-positive donations were identified. Thirty-four samples had antibodies against HCV and were therefore also detected by screening for antibody to HCV (anti-HCV). In October 2001, one seronegative (but PCR-positive) donor was detected. CONCLUSIONS: HCV-PCR minipool testing was successfully introduced in the largest Swiss blood transfusion service. It was shown that the release of HCV-PCR minipool results can be accomplished concurrently with the results of serological analysis. The challenge with a seronegative, but PCR-positive, donor demonstrates that the minipool testing strategy adds additional safety to blood products.

Blood Preservation↗
PubMed2003

Systematic quantification of complex metabolic flux networks using stable isotopes and mass spectrometry.

Metabolic fluxes provide a detailed metric of the cellular metabolic phenotype. Fluxes are estimated indirectly from available measurements and various methods have been developed for this purpose. Of particular interest are methods making use of stable isotopic tracers as they enable the estimation of fluxes at a high resolution. In this paper, we present data validating the use of mass spectrometry (MS) for the quantification of complex metabolic flux networks. In the context of the lysine biosynthesis flux network of Corynebacterium glutamicum (ATCC 21799) under glucose limitation in continuous culture, operating at 0.1 x h(-1) after the introduction of 50% [1-13C]glucose, we deploy a bioreaction network analysis methodology for flux determination from mass isotopomer measurements of biomass hydrolysates, while thoroughly addressing the issues of measurement accuracy, flux observability and data reconciliation. The analysis enabled the resolution of the involved anaplerotic activity of the microorganism using only one labeled substrate, the determination of the range of most of the exchange fluxes and the validation of the flux estimates through satisfaction of redundancies. Specifically, we determined that phosphoenolpyruvate carboxykinase and synthase do not carry flux at these experimental conditions and identified a high futile cycle between oxaloacetate and pyruvate, indicating a highly active in vivo oxaloacetate decarboxylase. Both results validated previous in vitro activity measurements. The flux estimates obtained passed the chi2 statistical test. This is a very important result considering that prior flux analyses of extensive metabolic networks from isotopic measurements have failed criteria of statistical consistency.

Amino Acids↗
PubMed2000

Migraine attacks and sleep in children.

Falling asleep as a means of ending migraine attack was studied in 133 4-16-year-old children in out-patient settings. Children registered 999 migraine attacks in headache diaries using a visual analogue scale (VAS) in 409 attacks and a five-face scale in 590 attacks. The distribution of maximal pain intensity was similar on both scales; on VAS 88% assigned grades between 63 and 100, and on the face scale 93% assigned grades of 4 or 5. Children fell asleep during 33% of the attacks (n = 329), in 64% of these within the first hour (n = 209). Of the children, 68% (n = 91) had fallen asleep at least once during an attack. Falling asleep was more common in children under 8 years of age than in older children. In those under 8 years, 62% (95% confidence interval (CI) 49-75%) of attacks were resolved by sleep, in those aged 8-12 years 34% (26-41%), and in children >12 years 24% (15-33%) (ANOVA, P<0.0001). Pain was relieved without sleep in 43% (n = 431) of attacks, in 38% of these (n = 383) within the first 4 h. The data on migraine resolution were missing for 24% (n = 239) of the attacks, most often because the attack exceeded the 5-h observation period. This study confirms that migraine attacks in children are extremely painful and often resolve during an interval of sleep in children under 8 years of age.

Adolescent↗
PubMed2004

Potential energy curves of diatomic molecular ions from high-resolution photoelectron spectroscopy. I. The first six electronic states of Ar2+.

High-resolution photoelectron spectroscopic data have been used to determine the potential energy curves of the first six electronic states of Ar2+. The potential energy functions properly include the effects of the long-range interactions and of the spin-orbit interaction and are of spectroscopic accuracy (1-2 cm(-1)) over a wide range of internuclear distances. The total number of adjustable parameters could be reduced to only 12 by truncating the long-range interaction series after the R(-6) term and assuming an R-independent spin-orbit coupling constant. This assumption was verified to be valid to an accuracy of +/-2 cm(-1) over the range of internuclear distances between 3.0 and 4.6 A. The interaction potential proposed by Siska [P. E. Siska, J. Chem. Phys. 85, 7497 (1986)] was generalized to a form that is expected to be sufficiently flexible to describe chemical bonding in other diatomic molecular ions. The potential energy curves are more accurate than the best available ab initio curves by two orders of magnitude and provide quantitative information on dissociation energies and equilibrium internuclear distances. The local maximum between the two potential wells of the I(1/2g) state was determined to lie 62 cm(-1) below the Ar(1S0)+Ar(+)(2P(3/2)) dissociation limit, and the II(1/2g) state is found to be significantly more bound (De=177 cm(-1)) than previously assumed.

Argon↗
PubMed2001

Nondestructive, in situ, cellular-scale mapping of elemental abundances including organic carbon in permineralized fossils.

The electron microprobe allows elemental abundances to be mapped at the microm scale, but until now high resolution mapping of light elements has been challenging. Modifications of electron microprobe procedure permit fine-scale mapping of carbon. When applied to permineralized fossils, this technique allows simultaneous mapping of organic material, major matrix-forming elements, and trace elements with microm-scale resolution. The resulting data make it possible to test taphonomic hypotheses for the formation of anatomically preserved silicified fossils, including the role of trace elements in the initiation of silica precipitation and in the prevention of organic degradation. The technique allows one to understand the localization of preserved organic matter before undertaking destructive chemical analyses and, because it is nondestructive, offers a potentially important tool for astrobiological investigations of samples returned from Mars or other solar system bodies.

Carbon↗
PubMed2003

Pseudo-cryptic speciation in coccolithophores.

Coccolithophores are a group of calcifying unicellular algae that constitute a major fraction of oceanic primary productivity, play an important role in the global carbon cycle, and are key biostratigraphic marker fossils. Their taxonomy is primarily based on the morphology of the minute calcite plates, or coccoliths, covering the cell. These are diverse and include widespread fine scale variation, of which the biological/taxonomic significance is unknown. Do they represent phenotypic plasticity, genetic polymorphisms, or species-specific characters? Our research on five commonly occurring coccolithophores supports the hypothesis that such variation represents pseudocryptic speciation events, occurring between 0.3 and 12.9 million years ago from a molecular clock estimation. This finding suggests strong stabilizing selection acting on coccolithophorid phenotypes. Our results also provide strong support for the use of fine scale morphological characters of coccoliths in the fossil record to improve biostratigraphic resolution and paleoceanographic data retrieval.

Animals↗
PubMed2002

Carbon emissions from tropical deforestation and regrowth based on satellite observations for the 1980s and 1990s.

Carbon fluxes from tropical deforestation and regrowth are highly uncertain components of the contemporary carbon budget, due in part to the lack of spatially explicit and consistent information on changes in forest area. We estimate fluxes for the 1980s and 1990s using subpixel estimates of percent tree cover derived from coarse (National Oceanic and Atmospheric Administration's Advanced Very High Resolution Radiometer) satellite data in combination with a terrestrial carbon model. The satellite-derived estimates of change in forest area are lower than national reports and remote-sensing surveys from the United Nations Food and Agriculture Organization Forest Resource Assessment (FRA) in all tropical regions, especially for the 1980s. However, our results indicate that the net rate of tropical forest clearing increased approximately 10% from the 1980s to 1990s, most notably in southeast Asia, in contrast to an 11% reduction reported by the FRA. We estimate net mean annual carbon fluxes from tropical deforestation and regrowth to average 0.6 (0.3-0.8) and 0.9 (0.5-1.4) petagrams (Pg).yr(-1) for the 1980s and 1990s, respectively. Compared with previous estimates of 1.9 (0.6-2.5) Pg.yr(-1) based on FRA national statistics of changes in forest area, this alternative estimate suggests less "missing" carbon from the global carbon budget but increasing emissions from tropical land-use change.

Africa↗
PubMed1972

Structure of the radical form of clostridial flavodoxin: a new molecular model.

Interpretation of a new electron-density map at 3.25-A resolution has led to a somewhat revised model for the free radical (semiquinone) structure of flavodoxin from Clostridium MP. Although the general conformation of the molecule is very similar to that of oxidized Desulfovibrio vulgaris flavodoxin, flavin mononucleotide-protein interactions are not identical in the two flavodoxins. In the Cl. MP semiquinone molecule, the isoalloxazine ring appears to retain the essentially planar conformation characteristic of oxidized flavins; within the limits imposed by the resolution of the data, the map shows no evidence for bending of the isoalloxazine ring about N5-N10.

Clostridium↗
PubMed1973

A crystalline fragment of the double helix: the structure of the dinucleoside phosphate guanylyl-3',5'-cytidine.

The sodium salt of guanylyl-3',5'-cytidine crystallizes in a monoclinic unit cell with one molecule in the asymmetric unit. Each molecule is related to another molecule by a 2-fold rotation axis which results in the formation of an antiparallel, right-handed double helix with complementary hydrogen bonding between the guanine and cytosine residues. The crystal is heavily hydrated with 36 water molecules in the unit cell. The geometry of this crystalline double helix is very similar to those which have been derived from studies of fiber x-ray diffraction patterns of double-stranded RNA, even though the latter do not yield data at atomic resolution.

Cytosine Nucleotides↗
PubMed1981

Pyochelin: novel structure of an iron-chelating growth promoter for Pseudomonas aeruginosa.

Pyochelin, an endogenous growth promoter that solubilizes ferric iron, has been isolated from Pseudomonas aeruginosa, including clinical strains. The structure of pyochelin has been assigned as 2-(2-o-hydroxyphenyl-2-thiazolin-4-yl)-3-methylthiazolidine-4-carboxylic acid and is of a different type from those previously assigned to siderophores (siderochromes) from bacteria. The assignment rests on 1H and 13C NMR data, high-resolution (including field desorption) mass spectrometry, and spectroscopic properties of synthetic model compounds. Pyochelin is presumed to be biosynthesized from salicylic acid and two moles of cysteine.

Growth Substances↗
PubMed1985

The 2-A resolution structure of a thermostable ribonuclease A chemically cross-linked between lysine residues 7 and 41.

The crystal structure of Lys-7-(dinitrophenylene)-Lys-41-cross-linked ribonuclease A has been determined by molecular replacement and refined by restrained least-squares methods to an R factor of 0.18 at 2.0-A resolution. Diffraction intensity data were collected by using a conventional diffractometer and an x-ray area detector. Comparison of the thermostable cross-linked protein and the native enzyme shows them to be structurally similar, with a rms difference in backbone and side-chain atoms of 0.52 and 1.34 A, respectively. Native and modified proteins additionally show 35 common bound solvent sites and similar overall temperature factor behavior, despite localized differences resulting from cross-link introduction, altered crystal pH, or lattice interactions with neighboring molecules. These results are discussed in the context of proposals on the origins of thermostability in the cross-linked enzyme.

Amino Acid Sequence↗
PubMed1986

Molecular structure of the G.A base pair in DNA and its implications for the mechanism of transversion mutations.

The synthetic deoxydodecamer d(C-G-C-G-A-A-T-T-A-G-C-G) was analyzed by x-ray diffraction methods, and the structure was refined to a residual error of R = 0.17 at 2.5-A resolution (2 sigma data) with 83 water molecules located. The sequence crystallizes as a full turn of a B-DNA helix and contains 2 purine X purine (G.A) base pairs and 10 Watson-Crick base pairs. The analysis shows conclusively that adenine is in the syn orientation with respect to the sugar moiety whereas guanine adopts the usual trans orientation. Nitrogen atoms of both bases are involved in hydrogen bonding with the N-1 of guanine 2.84 A from the N-7 of adenine and the N-6 of adenine within 2.74 A of the O-6 of guanine. The C-1'...C-1' separation is 10.7 A close to that for standard Watson-Crick base pairs. The incorporation of the purine.purine base pairs at two steps in the dodecamer causes little perturbation of either the local or the global conformation of the double helix. Comparison of the structural features with those of the G.T wobble pair and the standard G.C pair suggests a rationale for the differential enzymatic repair of the two types of base-pair mismatches.

Chemical Phenomena↗