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Potentionmetric and spectroscopic (EPR, CD and absorption spectra) data have shown that a fragment of envelope proteins of the hepatitis B virus could be very specific bind molecules for Cu2+ ions using arginine lateral NH2 donor sites. The presence of Pro and Asp residues makes Arg binding not only very specific, but also very efficient.
1. A new population of neurons with transient expression of NPY immunoreactivity was described in the developing hamster paraventricular thalamic area. The present study was performed to discover whether this phenomenon is due to programmed cell death or apoptosis. 2. Toward this aim, immunocytochemical and electron microscopic examination of the paraventricular thalamic region, as well as DNA electrophoresis of tissue extracted from the described area, was performed on different stages of embryonic and postnatal development. 3. A sudden increase in neuropeptide Y immunoreactivity (NPY-IR) in the paraventricular thalamic area at embryonic day 14 (E14) was the first symptom of neuronal degeneration. 4. Electron microscopy revealed many neurons with large masses of condensed chromatin within nuclei and extracellular bodies. The affected cells had a convoluted shape and condensed cytoplasm. 5. DNA electrophoresis revealed a ladder of bands between 150 and 1000 bp that is specific for internucleosomal DNA fragmentation. 6. The data strongly suggest that developmental disappearance of NPY-IR neurons within the hamster dorsal thalamic area is due to apoptosis.
Modern research techniques have led to exponential growth in the volume and complexity of scientific data. Consequently, managing these volumes securely and efficiently has become a major challenge. While all research domains face these challenges, life science research is particularly affected because current approaches often rely on a large set of different file formats, with metadata stored in separated databases or spreadsheets. This leads to fragmented datasets, orphaned data, and compromised research reproducibility. Traditional solutions also force researchers to choose between security and accessibility, with encrypted files preventing selective access and indexed formats lacking adequate security for sensitive data. These limitations are particularly problematic in large-scale genomic studies where researchers must decompress multi-gigabyte files to access specific regions, creating computational bottlenecks and inefficient network usage when working with cloud-stored datasets. We introduce Pithos, a next-generation file format specifically designed for scientific data management in distributed cloud environments. The format uses content-defined chunking to enable efficient deduplication across distributed storage systems, thereby reducing storage costs and bandwidth requirements. The append-only structure ensures data immutability and allows for incremental updates without compromising content. Benchmark results show that Pithos outperforms existing solutions in read and write performance, with comparable or improved storage efficiency.
There is no knowledge of the transport mechanisms by which solutes cross the cat placenta or any other endotheliochorial placenta. Here, we investigated whether the amino acid transport systems beta and A are present in the cat placenta using a placental fragment uptake technique. Data were compared with studies in the human placenta, in which the presence of these two transport systems has been well established. A time course of [(3)H]taurine (substrate for system beta) and [(14)C]MeAIB (nonmetabolizable substrate for system A) uptake was determined in the term cat and human placental fragments in the presence and absence (choline substituted) of Na(+), and further studies were carried out over 15 min. Taurine uptake into both cat and human placenta fragments was found to be Na(+) and Cl(-) dependent, and Na(+)-dependent taurine uptake was blocked by excess beta-alanine. MeAIB uptake was found to be Na(+) dependent, and Na(+)-dependent MeAIB uptake was blocked by excess MeAIB or glycine. Western blotting and immunohistochemistry performed on cat and human placenta showed expression of TAUT and ATA2 (SNAT2), proteins associated with system beta and system A activity, respectively. This study therefore provides the first evidence of the presence of amino acid transport systems beta and A in the cat placenta.
BACKGROUND: Geographic patterns of suicide are associated with area levels of social fragmentation. It is unknown whether this reflects higher levels of severe mental illness in socially fragmented areas. METHOD: Data on psychiatric inpatient admissions and suicides amongst people aged 15-64 living in the City of Bristol [1991-1992] were postcode matched to the city's 34 electoral wards. Ecological associations of psychiatric admission (used as a 'proxy' measure of prevalence of severe mental illness) and suicide rates with levels of social fragmentation were investigated using negative binomial regression models. RESULTS: Psychiatric hospital admission rates were higher in areas with high levels of socioeconomic deprivation than in areas with high levels of social fragmentation. In contrast, associations with suicide were stronger in relation to social fragmentation than socioeconomic deprivation. Association of suicide with social fragmentation was only moderately attenuated in models controlling for psychiatric admission rate and socio-economic deprivation, RR 1.23 (95 % C. I. 1.09-1.38) per quartile increase in social fragmentation, compared to 1.29 (95% C. I. 1.16-1.44) before adjustment. CONCLUSION: The association between social fragmentation and suicide is not explained by socioeconomic deprivation or the prevalence of severe mental illness within socially fragmented areas as measured by psychiatric admission rate.
One of the core features of developmental stuttering is part-word repetition followed by fluent production (resolution) of the target word. The purpose of the study is to compare the spectro-temporal dimensions of fragments with the spectro-temporal dimensions of the resolution to define fragment types and develop articulatory interpretation of termination-restart cycles. From the acoustic recordings of six adult males who stutter, 142 stuttering events on words beginning with stops were isolated, excerpted, and digitized. The stuttering events occurred during either spontaneous speech or reading. The consecutive articulatory phases of fragments were classified and compared with the corresponding phases in resolutions. We found that (a) there are two basic types of fragments--those with vowels and those without, (b) the type of fragment produced is strongly influenced by the voicing status of the stop, (c) the fragments without vowels tend to have longer stop closure duration than the stops in the resolutions, (d) there are two subtypes in fragments with vowels--those with vowels shorter than and those with vowels longer than the vowels in the resolutions, (e) the shorter vowels differ spectro-temporally from the vowels in resolutions, and (f) the longer vowels differ temporally from the vowels in the resolutions. We discuss the articulatory implications of the acoustic data for each fragment type in the context of speech as an act designed to achieve contextually conditioned acoustic goals.
Southern blot analysis of genomic cattle DNA was carried out using murine cDNA probes representing the Tcp-1 gene of the t complex. Excellent cross-hybridization was obtained, and the probes apparently hybridized to at least two bovine TCP1 genes. Two independent restriction fragment length polymorphisms, each composed of two allelic variants, were detected; the inheritance of the restriction fragment length polymorphisms was confirmed by family data. One of the restriction fragment length polymorphisms, designated TCP1B, was evidently due to a gene duplication and was revealed with any restriction enzyme used. The duplication was found in three different cattle breeds investigated. Family segregation data indicated that TCP1B is linked to major histocompatibility complex genes. The result was consistent with close linkage to the major histocompatibility complex class II DO beta gene, whereas a fairly high recombination frequency was indicated between TCP1B/DO beta and other major histocompatibility complex genes. The result assigns TCP1B to a bovine linkage group previously comprising major histocompatibility complex class I and class II genes and blood group locus M. The similarity between this linkage group and parts of mouse chromosome 17 (t-H-2) and human chromosome 6 (TCP1-HLA) is discussed.
Previous work in our laboratory (Montague, J., Gaido, M., Frye, C., and Cidlowski, J. (1994) J. Biol. Chem. 269, 18877-18880) has shown that human recombinant cyclophilins A, B, and C have sequence homology with the apoptotic nuclease NUC18 and that denatured cyclophilins can degrade DNA. We have now evaluated the nucleolytic activity of recombinant cyclophilins under native conditions. We show that nuclease activity inherent to cyclophilins is distinct from cis-trans-peptidylprolyl isomerase activity and is similar to that described for apoptotic nucleases. Cyclophilin nucleolytic activity is stimulated by Ca2+ and/or Mg2+, with a combination of the two being optimal for cyclophilins A and B. Mg2+ alone is sufficient for cyclophilin C nuclease activity. pH optimums are in the range of pH 7.5-9.5. Cyclophilins can degrade both single-stranded and double-stranded DNA. Additionally, cyclophilins produce 3'-OH termini in linear double-stranded substrates, suggesting the cuts produced are similar to those of apoptotic cells. Cyclophilins also display endonucleolytic activity, demonstrated by their ability to degrade supercoiled DNA. In the absence of ions, cyclophilins bind linearized DNA. When added to nuclei from nonapoptotic cells, cyclophilin C induces 50-kilobase pair DNA fragmentation but not internucleosomal fragmentation. Together, these data suggest that cyclophilins are involved in degradation of the genome during apoptosis.
Mutations in presenilin (PS) 1 or PS2 genes account for the majority of early-onset familial Alzheimer's disease, and these mutations have been shown to increase production of species of amyloid beta peptide (Abeta) ending at residue 42, i.e. the most amyloidogenic form of Abeta. To gain insight into the molecular mechanisms whereby mutant PS induces overproduction of Abeta42, we constructed cDNAs encoding mutant and/or truncated forms of PS2 and examined the secretion of Abeta42 from COS or neuro2a cells transfected with these genes. Cells expressing full-length PS2 harboring both N141I and M239V mutations in the same polypeptide induced overproduction of Abeta42, although the levels of Abeta42 were comparable with those in cells engineered to express PS2 with one or the other of these PS2 mutations. In contrast, cells engineered to express partially truncated PS2 (eliminating the COOH-terminal third of PS2 while retaining the endoproteolytic NH2-terminal fragment) and harboring a N141I mutation, as well as cells expressing COOH-terminal fragments of PS2, did not overproduce Abeta42, and the levels of Abeta42 were comparable with those in cells that expressed full-length, wild-type PS2 or fragments thereof. These data indicate that: (i) the Abeta42-promoting effects of mutant PS2 proteins reach the maximum level with a given single amino acid substitution (i.e. N141I or M239V); and (ii) the expression of full-length mutant PS2 is required for the overproduction of Abeta42. Hence, cooperative interactions of NH2- and COOH-terminal fragments generated from full-length mutant PS2 may be important for the overproduction of Abeta42 that may underlie familial Alzheimer's disease.
Hirudin is an anticoagulant polypeptide isolated from a medicinal leech that inhibits thrombin with extraordinary potency (Kd = 0.2-1.0 pM) and selectivity. Hirudin is composed of a compact N-terminal region (residues 1-47, cross-linked by three disulfide bridges) that binds to the active site of thrombin, and a flexible C-terminal tail (residues 48-64) that interacts with the exosite I of the enzyme. To minimize the sequence of hirudin able to bind thrombin and also to improve its therapeutic profile, several N-terminal fragments have been prepared as potential anticoagulants. However, the practical use of these fragments has been impaired by their relatively poor affinity for the enzyme, as given by the increased value of the dissociation constant (Kd) of the corresponding thrombin complexes (Kd = 30-400 nM). The aim of the present study is to obtain a derivative of the N-terminal domain 1-47 of hirudin displaying enhanced inhibitory potency for thrombin compared to the natural product. In this view, we have synthesized an analogue of fragment 1-47 of hirudin HM2 in which Val1 has been replaced by tert-butylglycine, Ser2 by Arg, and Tyr3 by beta-naphthylalanine, to give the BugArgNal analogue. The results of chemical and conformational characterization indicate that the synthetic peptide is able to fold efficiently with the correct disulfide topology (Cys6-Cys14, Cys16-Cys28, Cys22-Cys37), while retaining the conformational properties of the natural fragment. Thrombin inhibition data indicate that the effects of amino acid replacements are perfectly additive if compared to the singly substituted analogues (De Filippis V, Quarzago D, Vindigni A, Di Cera E, Fontana A, 1998, Biochemistry 37:13507-13515), yielding a molecule that inhibits the fast or slow form of thrombin by 2,670- and 6,818-fold more effectively than the natural fragment, and that binds exclusively at the active site of the enzyme with an affinity (Kd,fast = 15.4 pM, Kd,slow = 220 pM) comparable to that of full-length hirudin (Kd,fast = 0.2 pM, Kd,slow = 5.5 pM). Moreover, BugArgNal displays absolute selectivity for thrombin over the other physiologically important serine proteases trypsin, plasmin, factor Xa, and tissue plasminogen activator, up to the highest concentration of inhibitor tested (10 microM).
The fragmentation pathways of protonated peptides are reviewed in the present paper paying special attention to classification of the known fragmentation channels into a simple hierarchy defined according to the chemistry involved. It is shown that the 'mobile proton' model of peptide fragmentation can be used to understand the MS/MS spectra of protonated peptides only in a qualitative manner rationalizing differences observed for low-energy collision induced dissociation of peptide ions having or lacking a mobile proton. To overcome this limitation, a deeper understanding of the dissociation chemistry of protonated peptides is needed. To this end use of the 'pathways in competition' (PIC) model that involves a detailed energetic and kinetic characterization of the major peptide fragmentation pathways (PFPs) is proposed. The known PFPs are described in detail including all the pre-dissociation, dissociation, and post-dissociation events. It is our hope that studies to further extend PIC will lead to semi-quantative understanding of the MS/MS spectra of protonated peptides which could be used to develop refined bioinformatics algorithms for MS/MS based proteomics. Experimental and computational data on the fragmentation of protonated peptides are reevaluated from the point of view of the PIC model considering the mechanism, energetics, and kinetics of the major PFPs. Evidence proving semi-quantitative predictability of some of the ion intensity relationships (IIRs) of the MS/MS spectra of protonated peptides is presented.
The analysis of data within multi-generational, genealogical, electrospray ionization/MS(n) fragmentation maps is discussed in reference to the structure elucidation of morphinans, an important class of pharmacological compounds. Various general approaches to separate and understand observed processes are discussed. These include: (1) Simple synthetic schemes incorporating deuterium and (13)C into morphinans to study later-generation, O-methyl group migration; (2) labeling to understand 'intense' signals for even-electron to odd-electron ion 'switching' events; (3) gas phase 'synthesis' of proposed MS(3) ions via an independent route, using chemical ionization (CI) MS/MS of naphthalenes and analysis via a bench-top El/Cl ion trap; (4) a useful synthetic paradigm for generating proposed carbonium ion structures at MS(4) via electrospray ionization (ESI) of easily synthesized amines; (5) the analysis of an oxidation product and correlation of MS(n) data of a switched, odd-electron species with electron ionization and low-pressure, low-energy charge exchange data; and (6) a new way of summarizing MS(n) data. Copyright -Copyright 2000 John Wiley & Sons, Ltd.
Loop-size chromatin fragmentation frequently observed upon apoptotic cell death is thought to be initiated by ss nicks. Here we show that the agarose-embedded, deproteinized chromatin of normal, non-apoptotic murine and human cells, as well as yeast protoplasts, falls apart to 50-300 kb ss fragments upon heat denaturation, as revealed by urea-TAE field-inversion agarose gel electrophoresis resolving ss and ds fragments alike. These data were in line with S1digestion experiments. The nicks (gaps) observed are best explained either by enzymatic cleavages occurring upon cell lysis instantaneously or by preexisting discontinuities becoming manifest upon heat denaturation. These discontinuities go unnoticed in the usual nondenaturaing circumstances but seem to be inevitably present in any DNA preparation. The loop-size ds DNA fragmentation in apoptosis may be based on these pre-existing or "ready-to-go" (upon cell lysis) ss discontinuities of the normal cellular chromatin.
The reproducibility of low-temperature anaerobic biological wastewater treatment trials was evaluated. Two identical anaerobic expanded granular sludge bed bioreactors were used to treat synthetic volatile fatty acid-based industrial wastewater under ambient conditions (18-20 degrees C) and to investigate the effect of various environmental perturbations on reactor performance and microbial community dynamics, which were assessed by chemical oxygen demand removal or effluent volatile fatty acid determination and terminal restriction fragment length polymorphism analysis, respectively. Methanogenic activity was monitored using specific methanogenic activity assays. Reactor performance and microbial community dynamics were each well replicated between Reactor 1 and Reactor 2. Archaeal dynamics, in particular, were associated with reactor operating parameters. Terminal restriction fragment length polymorphism data suggested dynamic acetoclastic and hydrogenophilic methanogenic populations and were in agreement with temporal specific methanogenic activity data. Putative psychrophilic populations were observed in anaerobic bioreactor sludge for the first time.
Fragment D (Mr 100 000) prepared from a terminal plasmin digest of fibrinogen was isolated and used to study its effect on fibrin formation. Increasing amounts of fragment D added to a solution of fibrinogen and thrombin decrease the rigidity of the resultant gel (10% of control at 2 mol of fragment D/mol of fibrinogen). Half-maximal inhibition is achieved at 1 mol of fragment D/mol of fibrinogen for non-cross-linked clots and at 1/2 mol of fragment D/mol of fibrinogen for cross-linked clots. "Clottability' decreases concomitantly with the rigidity. Only small amounts of fragment D (less than 10% for non-cross-linked gels) are incorporated into the gel. Light-scattering shows an increase in the final fibre thickness at fragment D concentrations up to 2 mol of fragment D/mol of fibrinogen, from 60 molecules/cross-section for the control to 120 molecules/cross-section. Higher fragment D concentrations lead to a decrease in the final fibre thickness. The limit fibre thickness is 8 nm, with a length of 80 nm, which is equivalent to a fibrin trimer. On the basis of results of synthetic-substrate and fibrinopeptide-release assays, it is clear that thrombin inactivation is not responsible for this effect. These data suggest that fragment D may inhibit fibrin formation by blocking the bimolecular polymerization of activated fibrin monomer molecules to form protofibrils, although additional effects on subsequent assembly steps may also be involved.
The atmospheric-pressure matrix-assisted laser desorption/ionisation quadrupole ion trap (AP-MALDI-QIT) analysis of tryptic peptides is reported following capillary liquid chromatographic (LC) separation and direct analysis of a protein digest. Peptide fragments were identified by peptide mass fingerprinting from mass spectrometric data and sequence analysis obtained by tandem mass spectrometry of the principal mass spectral peaks using a data-dependent scanning protocol. These data were compared with those from mass spectrometric analysis using capillary LC/MALDI-time-of-flight (TOF) and capillary LC/electrospray ionisation (ESI)-quadrupole TOF. For all three configurations the resulting data were searched against the MSDB database, using MASCOT and the sequence coverage compared for each technique. Complementary data were obtained using the three techniques.
Cholera toxin peptide 3 (CTP3) is a 15-residue peptide corresponding in sequence to an immunogenic loop on the surface of the B-subunits of both cholera toxin and the heat-labile toxin from Escherichia coli. TE33 is the Fab fragment of a monoclonal antibody elicited against CTP3. The crystal structure of the TE33-CTP3 complex at 2.3 A resolution reveals an antigen-binding pocket, 13 A deep and 13 A wide, which is lined with many aromatic residues. The N-terminal portion of the peptide antigen CTP3 forms a type II beta-turn that fits snugly into this pocket. At gln7 the peptide backbone of CTP3 forms a kink followed by an extended C-terminal chain that seals off the cleft and buries the beta-turn underneath it. All six complementarity-determining regions of TE33 contribute to the binding of CTP3. The antibody-peptide contacts include, in addition to van der Waals' interactions and hydrogen bonds, also one salt bridge and one water molecule, which mediates the interaction.
The three-dimensional structure of the complex of a second anti-peptide antibody (Fab 26/9) that recognizes the same six-residue epitope of an immunogenic peptide from influenza virus hemagglutinin (HA1; 75-110) as Fab 17/9 with the peptide has been determined at 2.8 A resolution. The amino acid sequence of the variable region of the 26/9 antibody differs in 24 positions from that of 17/9, the first antibody in this series for which several ligand-bound and free structures have been determined and refined. Comparison of the 26/9-peptide with the 17/9-peptide complex structures shows that the two Fabs are very similar (r.m.s.d. 0.5 to 0.8 A) and that the peptide antigen (101-107) has virtually the same conformation (r.m.s.d. 0.3 to 0.8 A) when bound to both antibodies. A sequence difference in the 26/9 binding pocket (L94; His in 26/9, Asn in 17/9) results in an interaction with a bound water molecule that is not seen in the 17/9 structures. Epitope mapping shows that the relative specificity of 26/9 and 17/9 antibodies for individual positions of the peptide antigen are slightly different. Amino acid substitutions in the peptide, particularly at position SerP107, are tolerated to different extents by 17/9 and 26/9. Structural and sequence analysis suggests that amino acid differences near the peptide-binding site are responsible for altering slightly the specificity of 26/9 for three peptide residues and illustrates how amino acid substitutions can modify antibody-antigen interactions and thereby modulate antibody specificity.