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At least 433 records · Page 24Linked to original sources
PubMed1996

Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database.

Numerous Escherichia coli proteins have already been characterized by two-dimensional gel electrophoresis (2-D PAGE), using carrier ampholytes in the first dimension (VanBogelen, R. A., Sankar, P., Clark, R. L., Bogan, J. A. and Neidhardt, F. C., Electrophoresis 1992, 13, 1014-1054). We present here a reference protein map of E. coli obtained with immobilized pH gradients (IPG) and available in a SWISS-2DPAGE format. Out of the protein spots identified in the E. coli gene protein database by Neidhardt's group, 153 have been identified in the E. coli gene protein database by Neihardt's group, 153 have been identified on the E. coli SWISS-2DPAGE database map by gel comparison and most of them were confirmed either by the analysis of amino acid composition (AAC) and/or N-terminal microsequencing. Additionally, five as yet unsequenced proteins were found. The E. coli SWISS-2DPAGE database is part of the ExPASy molecular biology server accessible through the Word Wide Web network.

Amino Acid Sequence↗
PubMed2004

Cell wall proteomics of the green alga Haematococcus pluvialis (Chlorophyceae).

The green microalga Haematococcus pluvialis can synthesize and accumulate large amounts of the ketocarotenoid astaxanthin, and undergo profound changes in cell wall composition and architecture during the cell cycle and in response to environmental stresses. In this study, cell wall proteins (CWPs) of H. pluvialis were systematically analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) coupled with peptide mass fingerprinting (PMF) and sequence-database analysis. In total, 163 protein bands were analyzed, which resulted in positive identification of 81 protein orthologues. The highly complex and dynamic composition of CWPs is manifested by the fact that the majority of identified CWPs are differentially expressed at specific stages of the cell cycle along with a number of common wall-associated 'housekeeping' proteins. The detection of cellulose synthase orthologue in the vegetative cells suggested that the biosynthesis of cellulose occurred during primary wall formation, in contrast to earlier observations that cellulose was exclusively present in the secondary wall of the organism. A transient accumulation of a putative cytokinin oxidase at the early stage of encystment pointed to a possible role in cytokinin degradation while facilitating secondary wall formation and/or assisting in cell expansion. This work represents the first attempt to use a proteomic approach to investigate CWPs of microalgae. The reference protein map constructed and the specific protein markers obtained from this study provide a framework for future characterization of the expression and physiological functions of the proteins involved in the biogenesis and modifications in the cell wall of Haematococcus and related organisms.

Cell Cycle↗
PubMed2005

Normalization of relative peptide ratios derived from in-gel digests: applications to protein variant analysis at the peptide level.

The ability to detect protein variants and post-translational modifications by mass spectrometry has become increasingly important. Unfortunately, the ability to detect variants in large intact proteins (>80,000 Da) is limited. Even in the analysis of smaller proteins, algorithms are required to determine the presence of a 2 Da mass shift in an intact 13 kDa protein because the isotopic distribution of the multiply charged ions of the variant overlaps the wild-type distribution. Fortunately, most modern instruments are capable of detecting variants in tryptic peptides derived from intact proteins. If a single common variant protein is known, the presence of a variant tryptic peptide can be easily demonstrated. A more difficult issue is the case where a multiplicity of peptides with multiple amino acid substitutions can be associated with pathology. In these cases a decrease in the relative amount of a variant peptide relative to other internal tryptic fragments would be diagnostic. However, the variability associated with the analysis of in-gel or solution digests of proteins, related to efficiencies in digestion, extraction and ionization, confounds variant analysis at the peptide level. A strategy was developed to normalize for this variability by utilizing multiple isotopically labeled internal standards for multiple peptides derived from the same protein. Erythrocyte spectrin from 36 normal and 25 abnormal osmotic fragility samples was analyzed as a test case. Three isotopically labeled target peptides comprising the alpha/beta-spectrin self-association sites were added to purified digested alpha-spectrin. The utilization of multiple internal standards demonstrates the capability to normalize for sample variability due to ionization efficiency, solvent effects, digestion and extraction efficiency.

Algorithms↗
PubMed1983

A neuroanatomical study on the organization of the central antennal pathways in insects. III. Neuroanatomical characterization of physiologically defined response types of deutocerebral neurons in Periplaneta americana.

1. Single unimodal (olfactory) or multimodal (olfactory and mechanosensory) neurons in the antennal lobe of the deutocerebrum of the American cockroach were characterized functionally by microelectrode recording, and their morphological types and positions in the brain were established by dye injection. Thus individual, physiologically identified neurons of known shape could be mapped in reference to the areas of soma groups, glomeruli, tracts and their projection regions in the brain. 2. All of these neurons send processes to deutocerebral glomeruli, i.e., the regions in which the axons of antennal sensory cells terminate. Output neurons have axons that leave the deutocerebrum whereas local interneurons are anaxonic. 3. An output neuron innervates only one glomerulus, sending its axon into the calyces of the corpora pedunculata (CP) in the protocerebrum, where by multiple branching they reach many CP neurons. The same axons send collaterals into the lateral lobe of the protocerebrum. Because of this arrangement, each deutocerebral glomerulus is represented individually and separately in the two projection regions. The fine structure of the endings of the deutocerebral axons in the protocerebrum is described. In the CP calyces they form microglomeruli with typical divergent connectivity. 4. A local interneuron innervates many glomeruli without sending processes to other parts of the brain. 5. Unimodal olfactory and multimodal neurons can be either output neurons or local interneurons; multimodal information is sent to the protocerebrum directly, in parallel with the unimodal information. 6. At least one glomerulus--the macroglomerulus of the male deutocerebrum--is specialized so as to provide an exclusive topographic representation of certain olfactory stimuli not represented elsewhere (female sexual pheromone).

Animals↗
PubMed1996

A prosody tutorial for investigators of auditory sentence processing.

In this tutorial we present evidence that, because syntax does not fully predict the way that spoken utterances are organized, prosody is a significant issue for studies of auditory sentence processing. We describe the basic elements and principles of current prosodic theory, review the psycholinguistic evidence that supports an active role for prosodic structure in sentence representation, and provide a road map of references that contain more complete arguments about prosodic structure and prominence. Because current theories do not predict the precise prosodic shape that a particular utterance will take, it is important to determine the prosodic choices that a speaker has made for utterances that are used in an auditory sentence processing study. To this end, we provide information about practical tools such as systems for signal display and prosodic transcription, and several caveats which we have found useful to keep in mind.

Algorithms↗
PubMed2003

Location of independent root-knot nematode resistance genes in plum and peach.

Prunus species express different ranges and levels of resistance to the root-knot nematodes (RKN) Meloidogyne spp. In Myrobalan plum ( Prunus cerasifera), the dominant Ma gene confers a high-level and wide-spectrum resistance to the predominant RKN, Meloidogyne arenaria, Meloidogyne incognita, Meloidogyne javanica and the isolate Meloidogyne sp. Florida which overcomes the resistance of the Amygdalus sources. In Japanese plum ( Prunus salicina), a similar wide-spectrum dominant resistance gene, termed R(jap), has been hypothesized from an intraspecific segregating cross. In peach, two crosses segregating for resistance to both M. incognita and M. arenaria were used to identify single genes that each control both RKN species in the Shalil ( R(Mia557)) and Nemared ( R(MiaNem)) sources. Localisation of these genes was made possible using the RFLP and SSR- saturated reference Prunus map TxE, combined with a BSA approach applied to some of the genes. The Ma1 allele carried by the Myrobalan plum accession P.2175 was localised on the linkage group 7 at an approximate distance of 2 cM from the SSR marker pchgms6. In the Japanese plum accession J.222, the gene R(jap) was mapped at the same position in co-segregation with the SSR markers pchgms6 and CPPCT022. The peach genes R(Mia557) and R(MiaNem), carried by two a priori unrelated resistance sources, were co-localized in a subtelomeric position on linkage group 2. This location was different from the more centromeric position previously proposed by Lu et al. (1999) for the resistance gene Mij to M. incognita and M. javanica in Nemared, near the SSR pchgms1 and the STS EAA/MCAT10. By contrast, R(Mia557) and R(MiaNem) were flanked by STS markers obtained by Yamamoto and Hayashi (2002) for the resistance gene Mia to M. incognita in the Japanese peach source Juseitou. Concordant results for the three independent sources, Shalil, Nemared and Juseitou, suggest that these peach RKN sources share at least one major gene resistance to M. incognita located in this subtelomeric position. We showed that plum and peach genes are independent and, thus, can be pyramided into interspecific hybrid rootstocks based on the plum and peach species.

Animals↗
PubMed2004

QTL analysis and comparative genomics of herbage quality traits in perennial ryegrass (Lolium perenne L.).

Genetic control of herbage quality variation was assessed through the use of the molecular marker-based reference genetic map of perennial ryegrass (Lolium perenne L.). The restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP) and genomic DNA-derived simple sequence repeat-based (SSR) framework marker set was enhanced, with RFLP loci corresponding to genes for key enzymes involved in lignin biosynthesis and fructan metabolism. Quality traits such as crude protein (CP) content, estimated in vivo dry matter digestibility (IVVDMD), neutral detergent fibre content (NDF), estimated metabolisable energy (EstME) and water soluble carbohydrate (WSC) content were measured by near infrared reflectance spectroscopy (NIRS) analysis of herbage harvests. Quantitative trait locus (QTL) analysis was performed using single-marker regression, simple interval mapping and composite interval mapping approaches, detecting a total of 42 QTLs from six different sampling experiments varying by developmental stage (anthesis or vegetative growth), location or year. Coincident QTLs were detected on linkage groups (LGs) 3, 5 and 7. The region on LG3 was associated with variation for all measured traits across various experimental datasets. The region on LG7 was associated with variation for all traits except CP, and is located in the vicinity of the lignin biosynthesis gene loci xlpomt1 (caffeic acid-O-methyltransferase), xlpccr1 (cinnamoyl CoA-reductase) and xlpssrcad 2.1 (cinnamyl alcohol dehydrogenase). Comparative genomics analysis of these gene classes with wheat (Triticum aestivum L.) provides evidence for conservation of gene order over evolutionary time and the basis for cross-specific genetic information transfer. The identification of co-location between QTLs and functionally associated genetic markers is critical for the implementation of marker-assisted selection programs and for linkage disequilibrium studies, which will enable future improvement strategies for perennial ryegrass.

Chromosome Mapping↗
PubMed1997

Genetical and physical assignments of equine microsatellites--first integration of anchored markers in horse genome mapping.

Twenty equine microsatellites were isolated from a genomic phage library, and their genetical and physical localization was sought by linkage mapping and fluorescent in situ hybridization (FISH). Nineteen of the markers were found to be polymorphic with, in most cases, heterozygosities exceeding 50%. The markers were mapped in a Swedish reference family for gene mapping, comprising eight half-sib families from Standardbred and Icelandic horse sires. Segregation was analyzed against a set of 35 other markers typed in the pedigree. Thirteen of the microsatellites showed linkage to at least one other marker, with a total of 21 markers being involved in these linkages. In parallel, 18 of the microsatellites could be assigned to their chromosomal region by FISH. These assignments involved eight equine autosomes: ECA1, 2, 4, 6, 9, 10, 15, and 16. The genetical and physical mappings revealed by this study represent a significant extension of the current knowledge of the equine genome map.

Alleles↗
PubMed2003

Genomic distribution and characterization of EST-derived resistance gene analogs (RGAs) in sugarcane.

A large sugarcane EST (expressed sequence tag) project recently gave us access to 261,609 EST sequences from sugarcane, assembled into 81,223 clusters. Among these, we identified 88 resistance gene analogs (RGAs) based on their homology to typical pathogen resistance genes, using a stringent BLAST search with a threshold e-value of e(-50). They included representatives of the three major groups of resistance genes with NBS/LRR, LRR or S/T KINASE domains. Fifty RGAs showed a total of 148 single-dose polymorphic RFLP markers, which could be located on the sugarcane reference genetic map (constructed in cultivar R570, 2n=approximately 115). Fifty-five SSR loci corresponding to 134 markers in R570 were also mapped to enable the classification of the various haplotypes into homology groups. Several RGA clusters were found. One cluster of two LRR-like loci mapped close to the only disease resistance gene known so far in sugarcane, which confers resistance to common rust. Detailed sequence comparison between two NBS/LRR RGA clusters in relation to their orthologs in rice and maize suggests their polyphyletic origins, and indicates that the degree of divergence between paralogous RGAs in sugarcane can be larger than that from an ortholog in a distant species.

Amino Acid Sequence↗
PubMed1988

Characterization of two antigens in parkinsonian Lewy bodies.

Two antigens, G7 and G9, which are labelled by monoclonal antibodies in Lewy bodies in brains from patients with Parkinson's disease, were characterized by two-dimensional electrophoresis, followed by electroblotting, in order to explore their possible relationship with neuronal degeneration in this disease. The G7 antigen was found in the substantia nigra of subjects with Parkinson's disease and progressive supranuclear palsy, as well as in normal subjects. It was also found in the dopaminergic nucleus paranigralis and the locus coeruleus. The G9 antigen was found in the substantia nigra and locus coeruleus, but also in the caudate nucleus, terminal region of the nigrostriatal dopaminergic neurons, and in the cortex and cerebellum, terminal regions of the noradrenergic neurons in the locus coeruleus. The identity of the antigens remains unknown. They do not correspond to tyrosine hydroxylase or neurofilaments previously detected in Lewy bodies, or to other cytoskeletal proteins. Nor are they related to the presence of neuromelanin in the cells that degenerate in Parkinson's disease. The proteins, or at least the epitopes labelled by the antibodies, are found in normal brain, suggesting that these proteins do not play a causal role in the formation of the Lewy bodies in degenerating neurons in Parkinson's disease. The G7 antigen is absent from the cholinergic substantia innominata, where Lewy bodies are also found, indicating that these antigens are not essential for the formation of the corpuscle.

Antigens↗
PubMed1988

Characterisation of a slow component of normal human serum albumin.

A minor component of albumin was isolated from normal human serum. It had reduced electrophoretic mobility, reacted normally with specific albumin antiserum and, in contrast to normal albumin, did not bind nickel. Sequence analysis showed that the minor band contained components with Ala-His-Lys- and His-Lys- N-terminal sequences, indicating removal of Asp and Asp-Ala respectively from the parent albumin which was found to have the expected N-terminal sequence of Asp-Ala-His-Lys. Both normal albumin and the minor component had an average of 0.32 residues of glucose bound as fructosamine.

Amino Acid Sequence↗
PubMed1987

Evidence for Renshaw cell-motoneuron decoupling during tonic vestibular stimulation in man.

The influence of static head-body tilts in the sagittal plane on the activity of Renshaw cells coupled to the soleus extensor alpha-motoneurons was studied in eight human subjects. Head-body rotation was carried out using a tilting seat and its effect was evaluated at 80 degrees (normal sitting position) and at 40 degrees of backward inclination (nose-up). Renshaw cell activity was assessed through a specially designed method of paired H-reflexes first described by Bussel and Pierrot-Deseilligny. alpha-Motoneuron excitability was also independently studied by mapping a reference H-reflex amplitude as a function of static head-body displacements. In almost all subjects Renshaw cell activity was increased at 40 degrees backward inclination with respect to control values at 80 degrees. These changes were attributed to the tonic labyrinthine reflexes capable of decoupling Renshaw cell activity from their motoneurons when the body was tilted backward from the upright position. We discuss the hypothetical functional modalities of the recurrent inhibitory circuit during postural adjustments elicited by labyrinthine input.

Electric Stimulation↗
PubMed2004

Comparative proteomic analysis of human whole saliva.

Human saliva performs a wide variety of biological functions that are critical for the maintenance of the oral health. Various functions include lubrication, buffering, antimicrobial protection, and the maintenance of mucosal integrity. In addition, whole saliva may be analysed for the diagnosis of human systemic diseases, since it can be readily collected and contains identifiable serum constituents. By using proteomic approach, we have established a reference proteome map of human whole saliva allowing for the resolution of greater than 200 protein spots in a single two-dimensional polyacrylamide gel. Fifty-four protein spots, comprised of 26 different proteins, were identifies using N-terminal sequencing, mass spectrometry, and/or computer matching with protein database. Ten proteins, whose levels were significantly different when bleeding had occurred in the oral cavity, were discussed in this study. These 10 proteins include alpha-1-antrypsin, apolipoprotein A-I, cystatin A, SA, SA-III, and SN, enolase I, hemoglobin beta-chain, thioredoxin peroxiredoxin B, as well as a prolactin-inducible protein. The proteomic approach identifies candidates from human whole saliva that may prove to be of diagnostic and therapeutic significance.

Adult↗
PubMed2005

Comparative proteomic analysis of mammalian animal tissues and body fluids: bovine proteome database.

Characterizing the complete proteome of multicellular organisms is a challenging task using the currently available technologies. With the increasing degree of genetic complexity, animals acquire a broader repertoire of options to meet environmental challenges. Mammalian cells from different tissues/body fluids express different thousands of proteins with a predicted dynamic range of up to five to six orders of magnitude, thus necessitating the whole arsenal of dedicated analytical strategies for a detailed proteome characterization. Nevertheless, 2D-E analysis of whole cellular lysates still remains the most used initial approach for the proteomic description of specialized cells. It enables to obtain an overview of the main soluble protein components of a specific tissue/body fluid, allowing comparison between different cellular types and molecular description of organ specialization. Massive proteomic investigations have been reported mainly in the case of human, mouse and rat, allowing comparative analysis. For this reason, a research project focused on the 2D-E characterization of tissues and biological fluids from other domestic mammals has been undertaken in our laboratory. A number of high-resolution reference electrophoretic maps have been established for liver, kidney, muscle, plasma and red blood cells samples from Holstein Friesian bovine female individuals. Among the 1863 distinct protein features detected, 534 species were identified and associated to 209 different genes by a combination of MALDI-TOF mass fingerprint, capillary LC-ESI-IT-MS-MS and image gel matching procedures. Identified polypeptide species and differences in expression profiles between various tissues/fluids clearly reflected organ biochemical specialization. This experimental output allowed establishing a 2D-E bovine database accessible at the URL address for image comparison.

Animals↗
PubMed2024

SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis.

Cell atlases serve as vital references for automating cell labeling in new samples, yet existing classification algorithms struggle with accuracy. Here we introduce SIMS (scalable, interpretable machine learning for single cell), a low-code data-efficient pipeline for single-cell RNA classification. We benchmark SIMS against datasets from different tissues and species. We demonstrate SIMS's efficacy in classifying cells in the brain, achieving high accuracy even with small training sets (<3,500 cells) and across different samples. SIMS accurately predicts neuronal subtypes in the developing brain, shedding light on genetic changes during neuronal differentiation and postmitotic fate refinement. Finally, we apply SIMS to single-cell RNA datasets of cortical organoids to predict cell identities and uncover genetic variations between cell lines. SIMS identifies cell-line differences and misannotated cell lineages in human cortical organoids derived from different pluripotent stem cell lines. Altogether, we show that SIMS is a versatile and robust tool for cell-type classification from single-cell datasets.

Single-Cell Analysis↗
PubMed2004

The evolutionary history of human chromosome 7.

We report on a comparative molecular cytogenetic and in silico study on evolutionary changes in human chromosome 7 homologs in all major primate lineages. The ancestral mammalian homologs comprise two chromosomes (7a and 7b/16p) and are conserved in carnivores. The subchromosomal organization of the ancestral primate segment 7a shared by a lemur and higher Old World monkeys is the result of a paracentric inversion. The ancestral higher primate chromosome form was then derived by a fission of 7b/16p, followed by a centric fusion of 7a/7b as observed in the orangutan. In hominoids two further inversions with four distinct breakpoints were described in detail: the pericentric inversion in the human/African ape ancestor and the paracentric inversion in the common ancestor of human and chimpanzee. FISH analysis employing BAC probes confined the 7p22.1 breakpoint of the pericentric inversion to 6.8 Mb on the human reference sequence map and the 7q22.1 breakpoint to 97.1 Mb. For the paracentric inversion the breakpoints were found in 7q11.23 between 76.1 and 76.3 Mb and in 7q22.1 at 101.9 Mb. All four breakpoints were flanked by large segmental duplications. Hybridization patterns of breakpoint-flanking BACs and the distribution of duplicons suggest their presence before the origin of both inversions. We propose a scenario by which segmental duplications may have been the cause rather than the result of these chromosome rearrangements.

Animals↗
PubMed1999

ELISA methods for the analysis of antibody responses induced in multiple sclerosis patients treated with recombinant interferon-beta.

Upon treatment with protein therapeutics, a subset of patients will typically develop antibodies against the drug. These anti-drug antibodies can be of concern because they have the potential to alter the drug's therapeutic activity. In the case of relapsing-remitting multiple sclerosis (RRMS) patients receiving recombinant interferon-beta (IFN-beta), those receiving BETASERON (IFN-beta-1b; E. coli expressed, non-glycosylated, des-Met-1, Cys17Ser recombinant IFN-beta) have a higher incidence of IFN-beta specific antibodies compared to those receiving AVONEX (IFN-beta-1a; mammalian cell-expressed, natural sequence, glycosylated recombinant IFN-beta). The current study reports the development and characterization of ELISAs that detect distinct components of the anti-IFN-beta response in patients' sera, and therefore can potentially be used to characterize the composition of the anti-IFN-beta antibody response. ELISAs were developed using a constant detecting reagent but a variety of IFN-beta-derived test antigens (e.g., native IFN-beta, biotinylated IFN-beta, IFN-beta peptides) and capture methods. Assays were characterized using serum samples from a small number of patients treated with recombinant IFN-beta (either BETASERON or AVONEX). Assays in which IFN-beta was captured via a specific mAb, or in which biotinylated IFN-beta was captured via streptavidin, detected serum antibodies that recognize IFN-beta in its native structural state. In contrast, assays in which IFN-beta was coated directly onto the assay plates detected antibodies that recognize forms of IFN-beta possessing a folded structure distinct from the native structure. Certain epitopes present on native IFN-beta were not represented in these assays in which the test antigen was directly coated on plastic. Antibodies specific for linear epitopes could be detected using linear peptides as test antigens; the locations of these epitopes were mapped by reference to the X-ray crystal structure of IFN-beta-1a. Together, these data show that the mode of antigen presentation employed in IFN-beta ELISAs determines which antibody specificities are detected, and can affect whether or not a given serum sample is identified as positive for anti-IFN-beta antibodies. As a consequence, screening samples in a single ELISA format presenting IFN-beta in a non-native form may lead to underestimation of the incidence of IFN-beta treated MS patients that have generated antibodies specific to the native, active form of the drug.

Antibodies↗