-
Frontiers in Neuroscience 2015Basic and neutral neurohypophyseal (NH) nonapeptides have evolved from vasotocin (VT) by a gene duplication at the base of the gnathostome lineage. In teleosts, VT and...
Molecular cloning, sequencing and tissue expression of vasotocin and isotocin precursor genes from Ostariophysian catfishes: phylogeny and evolutionary considerations in teleosts.
Basic and neutral neurohypophyseal (NH) nonapeptides have evolved from vasotocin (VT) by a gene duplication at the base of the gnathostome lineage. In teleosts, VT and IT are the basic and neutral peptides, respectively. In the present study, VT and IT precursor genes of Heteropneustes fossilis and Clarias batrachus (Siluriformes, Ostariophysi) were cloned and sequenced. The channel catfish Icatalurus punctatus NH precursor sequences were obtained from EST database. The catfish NH sequences were used along with the available Acanthopterygii and other vertebrate NH precursor sequences to draw phylogenetic inference on the evolutionary history of the teleost NH peptides. Synteny analysis of the NH gene loci in various teleost species was done to complement the phylogenetic analysis. In H. fossilis, the NH transcripts were also sequenced from the ovary. The cloned genes and the deduced precursor proteins showed conserved characteristics of the NH nonapeptide precursors. The genes are expressed in brain and ovary (follicular envelope) of H. fossilis with higher transcript abundance in the brain. The addition of the catfish sequences in the phylogenetic analysis revealed that the VT and IT precursors of the species-rich superorders of teleosts have a distinct phylogenetic history with the Acanthopterygii VT and IT precursors sharing a less evolutionary distance and the Ostariophysi VT and IT having a greater evolutionary distance. The genomic location of VT and IT precursors, and synteny analysis of the NH loci lend support to the phylogenetic inference and suggest a footprint of fish- specific whole genome duplication (3R) and subsequent diploidization in the NH loci. The VT and IT precursor genes are most likely lineage-specific paralogs resulting from differential losses of the 3R NH paralogs in the two superorders. The independent yet consistent retention of VT and IT in the two superorders might be directed by a stringent ligand-receptor selectivity.
PubMed: 26029040
DOI: 10.3389/fnins.2015.00166 -
ACS Nano May 2024Electrospinning has been applied to produce ceramic fibers using sol gel-based spinning solutions consisting of ceramic precursors, a solvent, and a polymer to control...
Electrospinning has been applied to produce ceramic fibers using sol gel-based spinning solutions consisting of ceramic precursors, a solvent, and a polymer to control the viscosity of the solution. However, the addition of polymers to the spinning solution makes the process more complex, increases the processing time, and results in porous mechanically weak ceramic fibers. Herein, we develop a coelectrospinning technique, where a nonspinnable sol (<10 mPa s) consisting of only the ceramic precursor(s) and solvent(s) is encapsulated inside a polymeric shell, forming core-shell precursor fibers that are further calcined into ceramic fibers with reduced porosity, decreased surface defects, uniform crystal packing, and controlled diameters. We demonstrate the versatility of this method by applying it to a series of nonspinnable sols and creating high-quality ceramic fibers containing TiO, ZrO, SiO, and AlO. The polycrystalline TiO fibers possess excellent flexibility and a high Young's modulus reaching 54.3 MPa, solving the extreme brittleness problem of the previously reported TiO fibers. The single-component ZrO fibers exhibit a Young's modulus and toughness of 130.5 MPa and 11.9 KJ/m, respectively, significantly superior to the counterparts prepared by conventional sol-gel electrospinning. We also report the creation of ceramic fibers in micro- and nanospring morphologies and examine the formation mechanisms using thermomechanical simulations. The fiber assemblies constructed by the helical fibers exhibit a density-normalized toughness of 3.5-5 times that of the straight fibers due to improved fracture strain. This work expands the selection of the electrospinning solution and enables the development of ceramic fibers with more attractive properties.
PubMed: 38717374
DOI: 10.1021/acsnano.3c12659 -
Molecular and Cellular Biology Nov 1996The cytosolic heat shock cognate 70-kDa protein (hsc70) is required for efficient import of ornithine transcarbamylase precursor (pOTC) into rat liver mitochondria (K....
The cytosolic heat shock cognate 70-kDa protein (hsc70) is required for efficient import of ornithine transcarbamylase precursor (pOTC) into rat liver mitochondria (K. Terada, K. Ohtsuka, N. Imamoto, Y. Yoneda, and M. Mori, Mol. Cell. Biol. 15:3708-3713, 1995). The requirement of hsc70 for mitochondrial import of various precursor proteins and truncated pOTCs was studied by using an in vitro translation import system in which hsc70 was completely depleted. hsc70-dependent import of pOTC was about 60% of the total import, while import of the aspartate aminotransferase precursor, the serine:pyruvate aminotransferase precursor, and 3-oxoacyl coenzyme A thiolase was about 50, 30, and 0%, respectively. The subunit sizes of these four precursor proteins were 40 to 47 kDa. When pOTC was serially truncated from the COOH terminal, the hsc70 requirement decreased gradually and was not evident for the shortest truncated pOTCs of 90 and 72 residues. These truncated pOTCs were imported and proteolytically processed rapidly in 0.5 to 2 min at 25 degrees C, and the processed mature portions and the presequence portion were rapidly degraded. Sucrose gradient centrifugation analysis followed by import assay showed that pOTC synthesized in rabbit reticulocyte lysate forms an import-competent complex of about 11S in an hsc70-dependent manner. S values of import-competent forms of aspartate aminotransferase precursor, serine:pyruvate aminotransferase precursor, and 3-oxoacyl coenzyme A thiolase were 9S, 9S, and 4S, respectively. Thus, the S value decreased as the hsc70 dependency decreased. Precursor proteins were coimmunoprecipitated from the reticulocyte lysate containing the newly synthesized precursor proteins with an hsc70 antibody. The amount of coimmunoprecipitated proteins was much larger in the absence of ATP than in its presence. Among the four precursor proteins, the amount of coimmunoprecipitated protein decreased as the hsc70 dependency decreased.
Topics: Acetyl-CoA C-Acyltransferase; Alanine Transaminase; Animals; Aspartate Aminotransferases; Cattle; DNA-Directed RNA Polymerases; Enzyme Precursors; HSP70 Heat-Shock Proteins; Kinetics; Macromolecular Substances; Mitochondria, Liver; Ornithine Carbamoyltransferase; Protein Biosynthesis; Protein Processing, Post-Translational; Rabbits; Rats; Reticulocytes; Transcription, Genetic
PubMed: 8887640
DOI: 10.1128/MCB.16.11.6103 -
Foods (Basel, Switzerland) Mar 2023The metabolic modulation of major flavor precursors during coffee cherry ripening is critical for the characteristic coffee flavor formation. However, the formation...
The metabolic modulation of major flavor precursors during coffee cherry ripening is critical for the characteristic coffee flavor formation. However, the formation mechanism of flavor precursors during coffee cherry ripening remains unknown. In the present study, a colorimeter was employed to distinguish different maturity stages of coffee cherry based on the coffee cherry skin colors, and proteomics and metabolomics profiles were integrated to comprehensively investigate the flavor precursor dynamics involved in Arabica coffee cherry ripening. The data obtained in the present study provide an integral view of the critical pathways involved in flavor precursor changes during coffee cherry ripening. Moreover, the contributions of critical events in regulating the development of flavor precursors during the four ripening stages of coffee cherries, including the biosynthesis and metabolism pathways of organic acids, amino acids, flavonoids, and sugars, are discussed. Overall, a total of 456 difference express metabolites were selected, and they were identified as being concentrated in the four maturity stages of coffee cherries; furthermore, 76 crucial enzymes from the biosynthesis and metabolism of sugars, organic acids, amino acids, and flavonoids contributed to flavor precursor formation. Among these enzymes, 45 difference express proteins that could regulate 40 primary amino acids and organic acids flavor precursors were confirmed. This confirmation indicates that the metabolic pathways of amino acids and organic acids played a significant role in the flavor formation of Arabica coffee cherries during ripening. These results provide new insights into the protease modulation of flavor precursor changes in Arabica coffee cherry ripening.
PubMed: 37048253
DOI: 10.3390/foods12071432 -
Chemical Research in Toxicology Dec 2022Analytical methods and tools for the characterization of the human exposome by untargeted mass spectrometry approaches are advancing rapidly. Adductomics methods have...
Analytical methods and tools for the characterization of the human exposome by untargeted mass spectrometry approaches are advancing rapidly. Adductomics methods have been developed for untargeted screening of short-lived electrophiles, in the form of adducts to proteins or DNA, . The identification of an adduct and its precursor electrophile in the blood is more complex than that of stable chemicals. The present work aims to illustrate procedures for the identification of an adduct to N-terminal valine in hemoglobin detected with adductomics, and pathways for the tracing of its precursor and possible exposure sources. Identification of the adduct proceeded via preparation and characterization of standards of adduct analytes. Possible precursor(s) and exposure sources were investigated by measurements in blood of adduct formation by precursors and adduct levels . The adduct was identified as hydroxypropanoic acid valine (HPA-Val) by verification with a synthesized reference. The HPA-Val was measured together with other adducts (from acrylamide, glycidamide, glycidol, and acrylic acid) in human blood ( = 51, schoolchildren). The HPA-Val levels ranged between 6 and 76 pmol/g hemoglobin. The analysis of reference samples from humans and rodents showed that the HPA-Val adduct was observed in all studied samples. No correlation of the HPA-Val level with the other studied adducts was observed in humans, nor was an increase in tobacco smokers observed. A small increase was observed in rodents exposed to glycidol. The formation of the HPA-Val adduct upon incubation of blood with glycidic acid (an epoxide) was shown. The relatively high adduct levels observed in relation to the measured reactivity of the epoxide, and the fact that the epoxide is not described as naturally occurring, suggest that glycidic acid is not the only precursor of the HPA-Val adduct identified . Another endogenous electrophile is suspected to contribute to the HPA-Val adduct level.
Topics: Child; Humans; Epoxy Compounds; Hemoglobins; Valine; Lactic Acid; Animals; Rats
PubMed: 36395356
DOI: 10.1021/acs.chemrestox.2c00208 -
PloS One 2022Identification of peptides by analysis of data acquired by the two established methods for bottom-up proteomics, DDA and DIA, relies heavily on the fragment spectra. In...
Identification of peptides by analysis of data acquired by the two established methods for bottom-up proteomics, DDA and DIA, relies heavily on the fragment spectra. In DDA, peptide features detected in mass spectrometry data are identified by matching their fragment spectra with a peptide database. In DIA, a peptide's fragment spectra are targeted for extraction and matched with observed spectra. Although fragment ion matching is a central aspect in most peptide identification strategies, the precursor ion in the MS1 data reveals important characteristics as well, including charge state, intensity, monoisotopic m/z, and apex in retention time. Most importantly, the precursor's mass is essential in determining the potential chemical modification state of the underlying peptide sequence. In the timsTOF, with its additional dimension of collisional cross-section, the data representing the precursor ion also reveals the peptide's peak in ion mobility. However, the availability of tools to survey precursor ions with a wide range of abundance in timsTOF data across the full mass range is very limited. Here we present a de novo feature detector called three-dimensional intensity descent (3DID). 3DID can detect and extract peptide features down to a configurable intensity level, and finds many more features than several existing tools. 3DID is written in Python and is freely available with an open-source MIT license to facilitate experimentation and further improvement (DOI 10.5281/zenodo.6513126). The dataset used for validation of the algorithm is publicly available (ProteomeXchange identifier PXD030706).
Topics: Algorithms; Amino Acid Sequence; Databases, Factual
PubMed: 36449500
DOI: 10.1371/journal.pone.0277122 -
The Journal of Biological Chemistry Jul 1991Secretin is a 27-amino acid gastrointestinal hormone that stimulates the secretion of bicarbonate-rich pancreatic fluid. We isolated and analyzed the coding region of...
Secretin is a 27-amino acid gastrointestinal hormone that stimulates the secretion of bicarbonate-rich pancreatic fluid. We isolated and analyzed the coding region of the gene for the rat secretin precursor. The entire coding region spans 692 base pairs and is divided into four regions corresponding to the signal peptide and NH2-terminal peptide, the secretin peptide and processing signal sequences, a part of the COOH-terminal peptide, and the remainder of the COOH-terminal peptide, which are interrupted by three short introns (81, 105, and 104 base pairs). The organization is similar to those of the genes for other members of the secretin family, glucagon and VIP/PHI-27 precursors, supporting the assumption that the genes for the secretin family peptide precursors originated from a common ancestral gene. We also demonstrated that the secretin precursor gene is widely expressed in the brain and in the hypophysis. The regional expression pattern of the secretin precursor gene in the brain is quite different from those of the glucagon and VIP/PHI-27 precursor genes. The secretin precursor gene is highly expressed in the medulla oblongata and pons of the brain and the hypophysis, the expression levels of which are comparable to those in the duodenum. The secretin precursor mRNA in the brain and the hypophysis has the same coding sequence as that in the duodenum, indicating that secretin in the brain and the hypophysis is produced from the same secretin precursor protein as that in the duodenum. This is the first evidence to be reported that the secretin precursor gene is definitely expressed in the brain.
Topics: Amino Acid Sequence; Animals; Base Sequence; Brain Chemistry; Duodenum; Electrophoresis, Agar Gel; Molecular Sequence Data; Pituitary Gland, Anterior; Polymerase Chain Reaction; Protein Precursors; RNA, Messenger; Rats; Restriction Mapping; Secretin
PubMed: 2061329
DOI: No ID Found -
Trends in Hearing 2023The perceived azimuth of a target sound is determined by the interaural time difference and the interaural level difference (ILD) and is subject to contextual effects...
The perceived azimuth of a target sound is determined by the interaural time difference and the interaural level difference (ILD) and is subject to contextual effects from precursor sounds. This study characterized ILD-based precursor effects (PEs) for high-frequency stimuli in a total of seven normal-hearing listeners. In Experiment 1, precursor and target were band-pass-filtered noises approximately centered at 4 kHz (1.2- and 1-octave bandwidth, respectively) separated by a 10-ms gap. The effects of precursor location (ipsilateral, contralateral, and central) on the perceived target azimuth were measured using a head-pointing task. Relative to control trials without a precursor, ipsilateral precursors biased the perceived target azimuth toward midline (medial bias) and contralateral precursors biased it contralaterally (lateral bias). Central precursors caused a symmetric lateral bias. An auditory periphery model that determines the "internal" ILD at the auditory nerve level, including either realistic efferent compression control or auditory nerve adaptation, explained about 50% of the variance in the PEs. These within-trial PEs were accompanied by an across-trial PE, inducing medial bias. Experiment 2 studied the role of sequential segregation in the within-trial PE by introducing a pitch difference between precursor and target. Segregation conditions caused increased PE for ipsilateral, no effect for contralateral, and either no effect or reduced PE for central precursors. Overall, the ILD-based within-trial PE appears to be preshaped already in the auditory periphery and the mechanism underlying at least the ipsilateral PE appears to be immune against sequential segregation.
Topics: Humans; Cochlear Nerve; Sound; Auditory Perception
PubMed: 37161352
DOI: 10.1177/23312165231171988 -
Open Biology Apr 2015Neuropeptides are ancient regulators of physiology and behaviour, but reconstruction of neuropeptide evolution is often difficult owing to lack of sequence conservation....
Neuropeptides are ancient regulators of physiology and behaviour, but reconstruction of neuropeptide evolution is often difficult owing to lack of sequence conservation. Here, we report that the receptor for the neuropeptide NGFFFamide in the sea urchin Strongylocentrotus purpuratus (phylum Echinodermata) is an orthologue of vertebrate neuropeptide-S (NPS) receptors and crustacean cardioactive peptide (CCAP) receptors. Importantly, this has facilitated reconstruction of the evolution of two bilaterian neuropeptide signalling systems. Genes encoding the precursor of a vasopressin/oxytocin-type neuropeptide and its receptor duplicated in a common ancestor of the Bilateria. One copy of the precursor retained ancestral features, as seen in highly conserved vasopressin/oxytocin-neurophysin-type precursors. The other copy diverged, but this took different courses in protostomes and deuterostomes. In protostomes, the occurrence of a disulfide bridge in neuropeptide product(s) of the precursor was retained, as in CCAP, but with loss of the neurophysin domain. In deuterostomes, we see the opposite scenario-the neuropeptides lost the disulfide bridge, and neurophysin was retained (as in the NGFFFamide precursor) but was subsequently lost in vertebrate NPS precursors. Thus, the sea urchin NGFFFamide precursor and receptor are 'missing links' in the evolutionary history of neuropeptides that control ecdysis in arthropods (CCAP) and regulate anxiety in humans (NPS).
Topics: Amino Acid Sequence; Animals; Chromatography, High Pressure Liquid; Cloning, Molecular; Evolution, Molecular; Humans; Mass Spectrometry; Molecular Sequence Data; Neuropeptides; Phylogeny; Protein Precursors; Receptors, Neuropeptide; Strongylocentrotus purpuratus; Vertebrates
PubMed: 25904544
DOI: 10.1098/rsob.150030 -
Molecules and Cells Apr 2017MicroRNAs (miRNAs) are single-stranded, small RNAs (21-23 nucleotides) that function in gene silencing and translational inhibition via the RNA interference mechanism....
MicroRNAs (miRNAs) are single-stranded, small RNAs (21-23 nucleotides) that function in gene silencing and translational inhibition via the RNA interference mechanism. Most miRNAs originate from host genomic regions, such as intergenic regions, introns, exons, and transposable elements (TEs). Here, we focused on the palindromic structure of medium reiteration frequencies (MERs), which are similar to precursor miRNAs. Five MER consensus sequences (MER5A1, MER53, MER81, MER91C, and MER117) were matched with paralogous transcripts predicted to be precursor miRNAs in the horse genome (equCab2) and located in either intergenic regions or introns. The MER5A1, MER53, and MER91C sequences obtained from RepeatMasker were matched with the eca-miR-544b, eca-miR-1302, and eca-miR-652 precursor sequences derived from Ensembl transcript database, respectively. Each precursor form was anticipated to yield two mature forms, and we confirmed miRNA expression in six different tissues (cerebrum, cerebellum, lung, spleen, adrenal gland, and duodenum) of one thorough-bred horse. MER5A1-derived miRNAs generally showed significantly higher expression in the lung than in other tissues. MER91C-derived miRNA-5p also showed significantly higher expression in the duodenum than in other tissues (cerebellum, lung, spleen, and adrenal gland). The MER117-overlapped expressed sequence tag generated polycistronic miRNAs, which showed higher expression in the duodenum than other tissues. These data indicate that horse MER transposons encode miR-NAs that are expressed in several tissues and are thought to have biological functions.
Topics: Adrenal Glands; Animals; Cerebellum; DNA Transposable Elements; Duodenum; Gene Expression Regulation; Genome; Horses; Humans; Introns; Inverted Repeat Sequences; Lung; MicroRNAs; RNA Precursors; Spleen
PubMed: 28320202
DOI: 10.14348/molcells.2017.2295