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PubMed1985

Putative repressor binding sites in the regions mediating transcriptional control of viral and cellular genes.

In this study, the sequences of several cellular genes (c-myc, c-fos, c-sis, c-mos, and the genes for urokinase, heat shock proteins, interleukin-2 and its receptor), thought to be controlled by negative regulatory factors, were examined. As a result of this comparison, multiple (and often clustered) copies of a 12 basepair (bp) element were identified in the flanking regions of these genes. Moreover, sequences with close homology to this 12 bp element were identified in specific control regions of some DNA and RNA tumor viruses. A consensus sequence (TTG nnn TTTTTT) was derived from an analysis of 111 of these elements. These sequence homologies have yielded a coherent first hypothesis, namely that this 12 bp element is the binding site of a transcriptional repressor protein.

Animals↗
PubMed1990

Genomic amplification in the cotyledon parenchyma of common bean.

The cotyledon parenchyma cells of common bean (Phaseolus vulgaris L.) produce large quantities of storage proteins during embryo maturation; throughout this period, these cells also accumulate nuclear DNA (nDNA). To investigate the basis of this nDNA accumulation, we have measured storage protein mRNA pools, nDNA mass, and gene copy number at specific stages of cotyledon development. RNA blotting and hybridization show that transcripts encoding the major embryo-specific storage proteins are present very early in cotyledon development, accumulate in coordinate fashion to peak during mid-maturation, and fall in abundance prior to the onset of dormancy. During this same period, nDNA mass per parenchyma cell nucleus, as measured by Feulgen microspectrophotometry, increases from 2C-4C to about 64C (C being the haploid germ cell genomic complement). The nDNA values do not cluster around integral multiples of the diploid 2C amount. DNA blotting and hybridization are used to evaluate the relative representations of different classes of the bean genome in DNA samples isolated from vegetative tissues, from cotyledons beginning to accumulate storage proteins, and from cotyledons of late maturation embryos entering dormancy. The results demonstrate that the observed DNA accumulation in the cotyledon parenchyma is due to overlapping rounds of replication of the complete genome and not to disproportionate amplification of specific sequences nor to random DNA synthesis.

Cell Nucleus↗
PubMed2003

Sequence variation and genomic organization of fatty acid desaturase-2 (fad2) and fatty acid desaturase-6 (fad6) cDNAs in maize.

Increased levels of oleic acid may enhance the nutritional and functional value of corn. Corn oil is primarily composed of palmitic, stearic, oleic, linoleic and linolenic fatty acids. Delta-12 desaturase in plants converts oleic acid (18:1) to linoleic acid (18:2) by inserting a double bond at the delta-12 position. Fatty acid desaturase-2 (fad2) encodes delta-12 desaturase that functions in the endoplasmic reticulum while fatty acid desaturase-6 (fad6) encodes delta-12 desaturase that functions in plastids. Complementary DNA (cDNA) clones from putative maize homologs for fad2 and fad6 were identified and the entire clones DNA sequenced. The maize fad2 cDNAs showed an amino-acid identity of 67-77% to fad2 of Glycine, Arabidopsis and Brassica species. Our cDNA sequence comparisons suggested that more than one fad2 gene is transcribed in maize embryos. Two different fad2 cDNAs from an embryo cDNA library map to separate chromosomal positions, providing evidence consistent with two different isoforms of fad2 expressed in the embryo. The fad2 cDNAs from multiple tissue sources clustered into three groups on a phenogram, and map to different positions on chromosomes 4, 5 and 10, which suggests at least three different isoforms of fad2 may be expressed in the maize plant. The two maize fad6 cDNAs share 81% amino-acid identity with the Arabidopsis fad6 and map to chromosome 1. Northern analysis revealed that fad2 is transcribed in embryos at 14, 21, 28 and 35 days after pollination, with the highest level observed at day 14. None of the fad2 or fad6 clones mapped to maize chromosome bins associated with QTLs for the ratio of oleic/linoleic acid, notably bin 6.04 which contains the linoleic1 locus and the largest reported QTL for the oleic/linoleic ratio. This suggests, but does not prove, that some of the QTLs for the oleic/linoleic acid ratio do not involve allelic variants of fad2 or fad6 but rather involve other genes that may influence flux through the enzymes encoded by fad2 or fad6.

DNA, Complementary↗
PubMed1999

Applications of amorphous track models in radiation biology.

The average or amorphous track model uses the response of a system to gamma-rays and the radial distribution of dose about an ion's path to describe survival and other cellular endpoints from proton, heavy ion, and neutron irradiation. This model has been used for over 30 years to successfully fit many radiobiology data sets. We review several extensions of this approach that address objections to the original model, and consider applications of interest in radiobiology and space radiation risk assessment. In the light of present views of important cellular targets, the role of target size as manifested through the relative contributions from ion-kill (intra-track) and gamma-kill (inter-track) remains a critical question in understanding the success of the amorphous track model. Several variations of the amorphous model are discussed, including ones that consider the radial distribution of event-sizes rather than average electron dose, damage clusters rather than multiple targets, and a role for repair or damage processing.

Animals↗
PubMed2026

A chromosome-scale genome of Capsicum pubescens provides insights into candidate terpene-associated gene clusters and pan variation of terpene synthases.

A chromosome-scale genome of Capsicum pubescens and comparative pan-TPS analysis support structural characterization and gene-level prioritization of a chromosome-9 terpene-associated candidate locus in this accession. Capsicum pubescens is one of the five domesticated Capsicum species, mainly cultivated in mid- to high-elevation regions of the Americas. Despite its distinctive morphology and fruit traits, genomic resources for C. pubescens remain less developed than those for the widely cultivated C. annuum. Here, we assembled a chromosome-scale reference genome for accession HNUCP0001, spanning 3.70 Gb with a scaffold N50 of 278.01 Mb. Comparative genomics revealed 679 significantly expanded gene families enriched in sesquiterpenoid and triterpenoid biosynthesis. Genome-wide biosynthetic gene-cluster mining identified multiple terpene-associated candidate loci, which were subsequently prioritized using genome-derived structural criteria and Capsicum pubescens-specific expression evidence. Subsequently, we curated the terpene synthase (TPS) repertoire and, across 16 Capsicum genomes, resolved 36 TPS orthogroups with pronounced presence/absence variation, highlighting dynamic lineage-specific diversification. Together, these analyses establish HNUCP0001 as an accession-specific genomic resource and provide a comparative framework for prioritizing terpene-associated TPS genes and candidate BGCs in Capsicum. These candidate loci, together with accession-level transcriptomic and metabolomic evidence, offer testable hypotheses for future functional studies of specialized terpenoid metabolism in C. pubescens.

Alkyl and Aryl Transferases↗
PubMed2026

NFS1 activates PI3K/AKT/mTOR signaling to upregulate GPX4 expression and enhance ferroptosis resistance in osteosarcoma.

Osteosarcoma continues to exhibit poor survival outcomes due to chemoresistance and metastasis, with metabolic reprogramming and ferroptosis resistance being key features of tumor heterogeneity, yet their upstream regulators remain poorly defined. NFS1, a cysteine desulfurase essential for iron-sulfur cluster biogenesis, protects multiple cancers from ferroptosis, but its role in osteosarcoma is unknown. In this study, we performed a transcriptomic meta-analysis and found that NFS1 expression was significantly upregulated in osteosarcoma tissues, with further elevation in metastatic lesions, and high NFS1 expression correlated with poor overall survival. Genome‑wide CRISPR screening data revealed a marked NFS1 dependency in osteosarcoma cell lines. Functionally, NFS1 promoted cell proliferation, migration, and invasion, whereas its knockdown suppressed these phenotypes. Using single‑cell RNA sequencing data from 27 osteosarcoma specimens, we applied a multi‑algorithm glycolytic scoring framework and observed NFS1 enrichment in highly glycolytic malignant cells, along with an association with PI3K/AKT/mTOR pathway activation. Mechanistically, NFS1 selectively enhanced PI3K, AKT, and mTOR phosphorylation without altering total protein levels, and upregulated GPX4, a central ferroptosis suppressor, leading to elevated ferroptosis resistance scores in NFS1‑high malignant cells. Collectively, these findings identify a previously unrecognized NFS1-PI3K/AKT/mTOR-GPX4 regulatory axis in osteosarcoma, linking metabolic reprogramming to ferroptosis resistance, and suggest that NFS1 functions as an oncogenic driver, as well as a promising prognostic biomarker and therapeutic target in osteosarcoma.

Humans↗
PubMed2005

Patterns of surveillance practices after curative surgery for colorectal cancer in a French population.

PURPOSE: Despite controversies, postoperative surveillance of colorectal cancer is generally recommended. This registry-based study was designed to assess the adherence of surveillance practices to French guidelines and identify three-year surveillance patterns and their demographic and clinical determinants. METHODS: All patients (N = 409) diagnosed with first colorectal cancer in 1998 and alive without recurrence at least six months after curative surgery were identified from a population-based registry. Medical charts from multiple sources were reviewed to collect exhaustive information on follow-up procedures used during a three-year period. Multiple correspondence and cluster analyses were used to identify surveillance patterns. RESULTS: The proportion of patients with a lower surveillance than that recommended was 35 percent for clinical examination, 65 percent for abdominal ultrasound, 52 percent for chest x-ray, and 20 percent for colonoscopy. Cluster analysis identified three patterns called minimal, moderate, and intensive surveillance patterns, which included 47, 24, and 29 percent of the patients respectively. The main independent predictors of both moderate and intensive surveillance patterns vs. minimal pattern were advanced tumor stage, chemotherapy, and radiation therapy. Younger age also was strongly associated with the intensive surveillance pattern, and the presence of symptoms with the moderate surveillance pattern. CONCLUSIONS: Adherence of surveillance practices to French guidelines seems relatively poor. Surveillance patterns are mainly explained by patient age, tumor stage, and treatment modalities.

Aged↗
PubMed2005

Aliphatic amidase from Rhodococcus rhodochrous M8 is related to the nitrilase/cyanide hydratase family.

A comparative study of amino acid sequence and physicochemical properties indicates the affiliation of an amidase from Rhodococcus rhodochrous M8 (EC 3.5.1.4) to the nitrilase/cyanide hydratase family. Cluster analysis and multiple alignments show that Cys166 is an active site nucleophile. The enzyme has been shown to be a typical aliphatic amidase, being the most active toward short-chain linear amides. Small polar molecules such as hydroxylamine and O-methyl hydroxylamine can serve as effective external nucleophiles in acyl transfer reactions. The kinetics of the industrially important amidase-catalyzed acrylamide hydrolysis has been studied over a wide range of substrate concentrations; inhibition during enzymatic hydrolysis by the substrate and product (acrylic acid) has been observed; an adequate kinetic scheme has been evaluated and the corresponding kinetic parameters have been determined.

Amidohydrolases↗
PubMed1994

Hyperlipidemia in the hypertensive patient.

Hypertension is known to be strongly associated with multiple metabolic abnormalities. A recent population survey carried out in Italy (the Gubbio study) involving 5,376 individuals showed that, up to the age of 64 years, hypertensive men were more markedly overweight (body mass index > or = 30) than normotensive men, whereas in women the prevalence of obesity was higher in hypertensive women at all ages. The prevalence of marked hypercholesterolemia (> or = 250 mg/dL) was uniformly higher in hypertensive compared with normotensive men except in the oldest age group; it was also higher in hypertensive women in the age 45-74 years group. Postabsorptive hyperglycemia and hyperuricemia were also more prevalent in hypertensive men and women, especially in the older age groups. Furthermore, the Tecumseh Blood Pressure Study indicated that not only patients with "sustained" hypertension but also those with so-called "white-coat" hypertension are, as a group, overweight and have elevated levels of cholesterol, insulin, and triglycerides and decreased levels of high-density lipoprotein. The multiple metabolic abnormalities clustered in hypertensives are important in relation to prognosis and therapy. The most recent World Health Organization/International Society of Hypertension guidelines for management of mild hypertension give considerable attention to the global assessment of cardiovascular risk in patients with hypertension and stress that, among individuals with mild hypertension, the risk of serious cardiovascular disease is also determined by a variety of risk factors other than blood pressure. The higher the absolute risk, the greater is the absolute benefit brought about by lowering blood pressure and correcting other risk factors, such as dyslipidemia.

Adult↗
PubMed1994

Anoxic injury of rat optic nerve: ultrastructural evidence for coupling between Na+ influx and Ca(2+)-mediated injury in myelinated CNS axons.

Physiological studies in the anoxic rat optic nerve indicate that irreversible loss of function, measured by the compound action potential, is due to depolarization and run-down of the transmembrane Na+ gradient which triggers Ca2+ entry through reverse Na(+)-Ca2+ exchange. EM studies in the anoxic optic nerve have demonstrated characteristic changes, including mitochondrial swelling and dissolution of cristae, submyelinic vacuoles, detachment of perinodal oligodendrocyte-axon loops, and severe cytoskeletal damage with loss of microtubules and neurofilaments within the axoplasm. To further examine the coupling between Na+ influx and Ca(2+)-mediated injury in myelinated axons within anoxic white matter, we have examined the ultrastructural effects of tetrodotoxin (TTX), in the anoxic optic nerve. Optic nerves, maintained in an interface brain slice chamber, were exposed to a 60-min period of anoxia. TTX (1 microM) was introduced 10 min before the onset of anoxia. Nerves were examined at the end of the anoxic period, or after 80 min in 1 microM TTX for normoxic controls. Under normoxic conditions, optic nerve axons exposed to TTX exhibited a normal ultrastructure. In optic nerves exposed to TTX studied at the end of a 60-min period of anoxia, mitochondria showed swelling and loss of cristae, and terminal oligodendroglial loops were detached from the nodal axon membrane. Cytoskeletal architecture was preserved in anoxic optic nerve axons treated with TTX, and axonal microtubules and neurofilaments maintained their continuity. Submyelinic empty spaces were not present. Perinodal astrocyte processes often appeared to be replaced by cellular remnants containing multiple membranous profiles; clusters of shrunken astrocytic processes were present between myelinated axons.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1992

Electrophoresis and chromatography of wheat proteins: available methods, and procedures for statistical evaluation of the data.

Analysis of gluten proteins from the wheat grain endosperm has long challenged the analytical chemist. Several hundred unique polypeptides are present, many in large polymers. This complexity, plus useful relationships of composition to genotype and quality, encouraged development and application of electrophoresis and chromatography for gluten analysis. We review the methods of polyacrylamide gel electrophoresis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, isoelectric focusing and high-performance liquid chromatography available for study of wheat proteins. Singly and in combination, they provide rapid, reproducible, high-resolution separations based on size, charge, or surface hydrophobicity. As challenging and important as the analyses themselves, however, is interpretation of data. Subjective evaluation is sometimes possible, but statistical methods such as similarity scores, clustering, principal components, multiple linear regression, and partial least squares now are increasingly used for data analysis. We review the use of these procedures, and precautions necessary to avoid misinterpretation of data. Optimal evaluation of protein analytical data will enhance the value of such analyses in wheat breeding, marketing, and processing.

Chromatography↗
PubMed1987

Base substitution mutagenesis by terminal transferase: its role in somatic mutagenesis.

We have addressed the possibility of terminal transferase involvement in somatic mutagenesis and the creation of N-region diversity, by measuring the ability of TdT to enhance single-base substitution mutagenesis during in vitro DNA synthesis. Using 3 independent assays we find that terminal transferase produces only a small increase in base-substitution mutagenesis when assayed in the presence of DNA polymerase-beta. In the presence of either polymerase-alpha or E. coli polymerase-I, however, no detectable increase in TdT-induced mutagenesis is seen. Furthermore, in an assay capable of detecting a variety of mutational events, terminal transferase primarily produces complex addition/deletion mutations, as well as a few multiple, tightly-clustered, single-base mutations. We conclude that the majority of the scattered single-base changes that occur during antibody gene differentiation are not catalyzed by terminal transferase, but instead result from another error-prone DNA synthetic process (possibly utilizing DNA polymerase-beta).

Bacteriophage phi X 174↗
PubMed1987

Somatic cell mutagenicity in Drosophila melanogaster in comparison with genetic damage in early germ-cell stages.

With the intention of assessing the general performance, sensitivity and the underlying mechanisms of somatic cell mutagenicity assays in Drosophila, a study was undertaken to compare the effectiveness of 5 procarcinogens and 4 direct-acting agents in the white/white-coral eye mosaic assay (SMART) with their activity in early (premeiotic) male and female germ-cell stages, after exposure of Drosophila larvae. The outcome indicated a lack of agreement in the results from recessive lethal assays (SLRL) in comparison with the somatic mutation and recombination test (SMART). The procarcinogens 2-naphthylamine (NA), 3-methylcholanthrene (MC), 9,10-dimethylanthracene (DA) and 7,12-dimethylbenz[a]anthracene (DMBA), and the direct-acting mutagens bleomycin (BM), methyl methanesulfonate (MMS) and ethyl methanesulfonate (EMS), were quite efficient in producing somatic recombination and mutations in white/white-coral larvae, as opposed to only weak effects in early germ-cell stages. 2-Acetylaminofluorene (2AAF) showed marginal effects in both germ cells and somatic tissue after exposure of female larvae, but was inactive in testis. The discrepancy in mutational response between somatic cells and premeiotic germ cells is most impressive for MMS and BM. There is sufficient evidence for attributing a good sized proportion of the encountered variation to efficient error-free DNA repair of premutational damage and to segregational elimination during meiosis of deleterious mutations: (1) The efficient point mutagen ENU was the but one agent producing high levels of viable genetic alterations in early germ cells and in somatic cells. A similar behaviour was previously described for diethylnitrosamine, which ethylates DNA in the same fashion as ENU. (2) In early germ-cell stages of mei-9L1 male larvae, MMS induced multiple mutations (putative clusters) at a low dose differing by a factor 20-40 from those needed to produce an equivalent response in repair-competent strains. This is consistent with the concept of an active excision repair in premeiotic cells. (3) In the case of EMS, next to DNA repair, germinal selection seems to restrict the realization of EMS-induced genetic damage in premeiotic cells. (4) Bleomycin-induced chromosome aberrations caused high mortality rates in males (hemizygous for an X-chromosome) but not in females. MMS and BM, agents known to show preference for chromosome aberration induction, produced 3-6-fold higher rates of somatic mutational events (SME) in female genotypes as compared with the other sex.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1988

Properties of synaptic transmission at the neuromuscular junction of the squid, Loligo opalescens.

1. Spontaneous and evoked synaptic activity were recorded from the muscles of squid fin and mantle. These spontaneous synaptic potentials were large (up to 30 mV) and pleomorphic. Their amplitudes were not normally distributed, nor did they appear to be clustered in integral multiples of some "unit" event size. 2. Electrical stimulation of the nerve resulted in muscle twitches when the bath calcium concentration was a third normal or higher. The frequency of spontaneous synaptic events was unaffected by low calcium. 3. The large size of spontaneous events may mean that the synchronized release of only a few such "quanta" are sufficient to cause muscle action potentials and contraction. 4. The shapes of spontaneous events correlated poorly with their amplitudes, which is consistent with release from multiple synaptic sites with distinct properties.

Animals↗
PubMed1989

Spectral characteristics of the responses of primary auditory-nerve fibers to amplitude-modulated signals.

The spectral responses of cat single primary auditory nerve fibers to sinusoidal amplitude-modulated (AM) and double-sideband (DSB) acoustic signals applied to the ear were examined. DSB is an amplitude-modulated signal with a suppressed carrier. Period histograms were compiled from the neural spike-train data, and the frequency spectrum was determined by Fourier transforming these histograms. For DSB signals, spectral components were found to be present at the frequencies of the stimulus as well as at certain combination frequencies. For AM signals, several clusters of spectral components were present. The lowest-frequency cluster consisted of components at DC, at the modulation frequency, and at its harmonics. A higher frequency cluster occurs around a component with the frequency of the carrier. The components of cluster are separated from the carrier by the modulation frequency and its harmonics. Yet higher-frequency clusters appear around multiples of the carrier frequency with components at frequencies separated from these multiples by the modulation frequency and its harmonics. The magnitudes of these spectral components were determined for carrier frequencies located below, at, and above the characteristic frequency of the units, and for different stimulus levels, modulation frequencies, and modulation depths. The low-frequency components present in the neural spike train appear to be the result of demodulation taking place in the inner ear. The demodulated components are strong and are present over a wide range of sound levels, carrier frequencies, modulation frequencies, and nerve-fiber characteristics. This demodulation may be significant for speech recognition.

Acoustic Stimulation↗
PubMed2006

Blurring cis and trans in gene regulation.

In this issue of Cell, Axel and colleagues (Lomvardas et al., 2006) report that a single enhancer of an odorant receptor (OR) gene cluster interacts with multiple OR gene promoters on different chromosomes. This study suggests a mechanism that allows olfactory sensory neurons to choose randomly and express only one out of more than 1000 OR genes.

Alleles↗
PubMed2006

Concurrent use of methamphetamine, MDMA, LSD, ketamine, GHB, and flunitrazepam among American youths.

BACKGROUND: The magnitude and the characteristics of the use of methamphetamine, MDMA (Ecstasy), LSD (d-lysergic acid diethylamide), ketamine, GHB (gamma-hydroxybutyrate), and flunitrazepam (Rohypnol) were examined in a probability sample of the U.S. civilian population that included multiethnic urban, suburban, and rural youths aged 16-23 (N=19,084). METHODS: Data were drawn from the National Survey on Drug Use and Health (NSDUH). Logistic regression analyses were conducted to identify the characteristics associated with the use of each of these drugs and of multiple drugs. RESULTS: Approximately 20% of youths aged 16-23 reported having ever used one or more of these drugs. Less than 1% of club drug users used club drugs only, and 82% of them had ever used three or more drug classes. Females were more likely than males to report using multiple club drugs. Recent users of methamphetamine were most likely to be females and adolescents aged 16 or 17. Recent users of MDMA tended to be young adults aged 18-21 and residents of metropolitan areas. Most recent users of LSD were adolescents aged 16-19 and those in low-income families. Ketamine users were primarily employed youths. Staying in school and getting married were associated with decreased odds of club drug use. Club drug use was highly associated with the presence of criminal behaviors and recent alcohol abuse or dependence. CONCLUSIONS: Adolescents are more likely than young adults to use multiple drugs. The clustering of multidrug use and alcohol use disorder is a cause of concern.

Adolescent↗
PubMed2006

Volumetric reduction of the corpus callosum in Alzheimer's disease in vivo as assessed with voxel-based morphometry.

Several recent magnetic resonance imaging studies have employed voxel-based morphometry (VBM) to detect regional gray matter volume abnormalities in Alzheimer's disease (AD). However, investigations of corpus callosum (CC) abnormalities in AD using this automated methodology have been scarce, and no VBM study investigated correlations between regional CC atrophy and cognitive measurements in AD subjects at mild disease stages. We used VBM to compare the topography of CC volume differences between 14 AD subjects (MMSE 14-25) and 14 healthy volunteers. Images were acquired using a 1.5-Telsa scanner, and were spatially normalized and segmented using optimized VBM. Statistical comparisons were performed using the general linear model. Significant CC atrophy was detected in the antero-superior portion of the splenium, the isthmus, the anterior and posterior portions of the CC body, and the rostral portion of the genu. Voxels showing peak statistical difference were all left-sided (P<0.001, uncorrected for multiple comparisons). A cluster of significant positive correlation with MMSE scores was seen on the left anterior CC body. Our results confirm previous findings of diffuse volumetric CC reductions early in the course of AD, and warrant further evaluation of the relevance of atrophic changes in anterior CC portions to the cognitive impairments that characterize the disorder.

Aged↗