SEARCH · PubMed Health

Results for “Next generation sequencing”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 919 records · Page 51Linked to original sources

PubMed1996

Microheterogeneity of the hydrophobic and hydrophilic part of the glycosylphosphatidylinositol anchor of alkaline phosphatase from calf intestine.

Digestion of calf intestine alkaline phosphatase with pronase and subsequent dephosphorylation of the released peptidyl-(Etn-P)2-glycosyl-PtdIns with HF generated 8 glycosyl-Ins species the largest of which (G1 and G2) have the following proposed structures: [sequence: see text] G3 and G5 are lower homologues of G1 and G2, respectively, being one alpha 1-2 linked mannopyranosyl residue shorter. G4 is analogous to G2 lacking the N-acetylgalactosaminyl residue and G6 is the next lower homologue of G4. Most of G4 and G6 occur substituted with a palmitoyl (G4, G6) or a myristoyl residue (G6) probably attached to the inositol moiety. Thus, the basic ManxGlc-Ins species are either substituted with an N-acetylgalactosaminyl residue or a fatty acid ester. The structures were deduced from compositional analysis, molecular-mass determination by matrix-assisted laser desorption MS, sequential hydrolysis with appropriate exoglycosidases and treatment with CrO3. Purification of the glycosylinositol species was achieved by a novel reverse-phase HPLC technique using fluorescent fluoren-9-yl-methoxy-carbonyl (Fmoc) derivatives. These stable derivatives were susceptible to hydrolysis with exoglycosidases which allowed sequential cleavages to be carried out and kinetics to be followed at the picomole level. We observed recently that native alkaline phosphatase separates on octyl-Sepharose into four distinct fractions of increasing hydrophobicity (F1-F4). Here we show that all four fractions contain G1-G6. The acylated species G4 and G6 were restricted to F2 and F4 which had been shown earlier to contain, on average, 2.5 and 3 fatty acid residues/subunit, respectively. In all four fractions the diradylglycerol moiety was predominantly diacylglycerol, alkylacylglycerol being less than 10% which is in contrast to most glycosyl-PtdIns--anchored proteins of mammalian origin.

Acetylgalactosamine↗

PubMed2005

DNA sequencing by indexer walking.

BACKGROUND: There is a need for DNA sequencing methods that are faster, more accurate, and less expensive than existing techniques. Here we present a new method for DNA analysis by means of indexer walking. METHODS: For DNA sequencing by indexer walking, we ligated double-stranded synthetic oligonucleotides (indexers) to DNA fragments that were produced by type IIS restriction endonucleases, which generate nonidentical 4-nucleotide 5' overhangs. The subsequent amplification (30 thermal cycles) of indexed DNA provided a template for automated DNA sequencing with fluorescent dideoxy terminators. The data gathered in the first sequencing reaction permitted further movement into the unknown nucleotide sequence by digestion of analyzed DNA with selected type IIS restriction endonuclease followed by ligation of the next indexer. A library of presynthesized indexers consisting of 256 oligonucleotides was used for bidirectional analysis of DNA molecules and provided universal primers for sequencing. RESULTS: The proposed protocol was successfully applied to sequencing of cryptic plasmids isolated from pathogenic strains of Escherichia coli. The overall error rate for base-calling was 0.5%, with a mean read length of 550 nucleotides. Approximately 1000 nucleotides of high-quality sequence could be obtained per day from a single clone. CONCLUSIONS: Indexer walking can be used as a low-cost procedure for nucleotide sequence determination of DNA molecules, such as natural plasmids, cDNA clones, and longer DNA fragments. It can also serve as an alternative method for gap filling at the final stage of genome sequencing projects.

DNA Primers↗

PubMed2025

Advancing the fight against tuberculosis: integrating innovation and public health in diagnosis, treatment, vaccine development, and implementation science.

Tuberculosis (TB) remains one of the leading causes of infectious disease mortality worldwide, increasingly complicated by the emergence of drug-resistant strains and limitations in existing diagnostic and therapeutic strategies. Despite decades of global efforts, the disease continues to impose a significant burden, particularly in low- and middle-income countries (LMICs) where health system weaknesses hinder progress. This comprehensive review explores recent advancements in TB diagnostics, antimicrobial resistance (AMR surveillance), treatment strategies, and vaccine development. It critically evaluates cutting-edge technologies including CRISPR-based diagnostics, whole-genome sequencing, and digital adherence tools, alongside therapeutic innovations such as shorter multidrug-resistant TB regimens and host-directed therapies. Special emphasis is placed on the translational gap-highlighting barriers to real-world implementation such as cost, infrastructure, and policy fragmentation. While innovations like the Xpert MTB/RIF Ultra, BPaLM regimen, and next-generation vaccines such as M72/AS01E represent pivotal progress, their deployment remains uneven. Implementation science, cost-effectiveness analyses, and health equity considerations are vital to scaling up these tools. Moreover, the expansion of the TB vaccine pipeline and integration of AI in diagnostics signal a transformative period in TB control. Eliminating TB demands more than biomedical breakthroughs-it requires a unified strategy that aligns innovation with access, equity, and sustainability. By bridging science with implementation, and integrating diagnostics, treatment, and prevention within robust health systems, the global community can accelerate the path toward ending TB.

diagnostic innovation↗

PubMed2005

EEG analysis with nonlinear excitable media.

The detection of patterns embedded within a complex, nonstationary, and noisy background activity is a crucial and important task in EEG analysis. The authors present a biologically inspired, analog approach to EEG analysis that is conceptually different from a variety of statistical approaches currently used. A nonlinear, excitable, spatially extended medium that is composed of diffusively coupled model neurons is considered. When EEG recordings are applied as local perturbations to such an excitable neural tissue, the induced transient changes in the dynamics of the perturbed system can be regarded as an instantaneous characterization of transient processes in the brain reflected by the EEG, e.g., in the form of a sequence of correlated dynamical events (patterns). Nonlinear excitable media can be implemented in form of an array of locally coupled integrated analog nonlinear electrical circuits called cellular neural networks, which represent a next evolutionary step in the parallel analog computer architecture. Using cellular neural networks, the authors show that the concept of signal-induced pattern generation allows an almost instantaneous and unsupervised detection of seizure onsets in EEG recordings. In addition, they show that a cellular neural network can be trained in a supervised way to approximate the degree of synchronization in EEG recordings. The resulting pattern-recognition device may be suitable for the prediction of epileptic seizures.

Animals↗

PubMed2004

The Anopheles gambiae genome: next steps for malaria vector control.

Malaria remains a major public health problem that is made worse by poor implementation of control measures, and by the spread of drug- and insecticide-resistant parasites and vectors, respectively. Availability of the Anopheles gambiae genome sequence will accelerate identification and exploitation of new target genes in this insect vector. This provides unique opportunities to improve on existing vector control tools and to generate new tools within a global partnership. However, significant capacity needs to be built for investigators in disease-endemic countries to exploit the genome data. When integrated with existing strategies, the new tools will form an effective package for selective vector control in an effort to prevent mortality and morbidity due to malaria.

Animals↗

PubMed1992

Induction of DNA amplification in the Bacillus subtilis chromosome.

A system allowing the induction of DNA amplification in Bacillus subtilis was developed, based on a thermosensitive plasmid, pE194, stably integrated in the bacterial chromosome. An amplification unit, comprising an antibiotic resistance marker flanked by directly repeated sequences, was placed next to the integrated plasmid. Activation of pE194 replication led to DNA amplification. Two different amplification processes appeared to take place: one increased the copy number of all sequences in the vicinity of the integrated plasmid and was possibly of the onion skin type, while the other increased the copy number of the amplification unit only and generated long arrays of amplification units. These arrays were purified and shown to consist mainly of directly repeated amplification units but to also contain non-linear regions, such as replication forks and recombination intermediates. They were attached to the chromosome at one end only, and were, in general, not stably inherited, which suggests that they are early amplification intermediates. Longer arrays were detected before the shorter ones during amplification. When the parental amplification unit contained repeats which differed by a restriction site the arrays which derived thereof contained in a majority of cases only a single type of repeat. We propose that the amplified DNA is generated by rolling circle replication, and that such a process might underlie a number of amplification events.

Bacillus subtilis↗

PubMed1989

Spectrum of spontaneous mutations in a cDNA of the human hprt gene integrated in chromosomal DNA.

Altered sequences were determined of 52 independent spontaneous mutations occurring in a cDNA of the human hypoxanthine phosphoribosyltransferase (hprt) gene, which was integrated into chromosomal DNA of the mouse cell as a part of the retroviral shuttle vector. Spontaneous mutations comprised a variety of events: base substitutions, frameshifts, deletions, duplications, and complex mutational events, and were distributed randomly over the coding region of the gene. Frameshifts were the most frequent mutational event (38%), and base substitutions were the next most frequent (25%), followed by deletions (19%). Frameshift and deletion mutations commonly occurred preferentially at sites flanked by short direct repeats. Short inverted repeats were frequently found to be associated with duplication and complex mutational events. Analysis of the sequence alterations in the mutant genes suggests that misalignment mutagenesis represents an important molecular mechanism for the generation of spontaneous mutations in eukaryotic cells.

Animals↗

PubMed2006

Environmental and nutritional effects on the epigenetic regulation of genes.

Major efforts have been directed towards the identification of genetic mutations, their use as biomarkers, and the understanding of their consequences on human health and well-being. There is an emerging interest, however, in the possibility that environmentally-induced changes at levels other than the genetic information could have long-lasting consequences as well. This review summarises our current knowledge of how the environment, nutrition, and ageing affect the way mammalian genes are organised and transcribed, without changes in the underlying DNA sequence. Admittedly, the link between environment and epigenetics remains largely to be explored. However, recent studies indicate that environmental factors and diet can perturb the way genes are controlled by DNA methylation and covalent histone modifications. Unexpectedly, and not unlike genetic mutations, aberrant epigenetic alterations and their phenotypic effects can sometimes be passed on to the next generation.

Aging↗

PubMed2005

Role of oxyR from Sinorhizobium meliloti in regulating the expression of catalases.

The process of symbiotic nitrogen fixation results in the generation of reactive oxygen species such as the superoxide anion (O2-) and hydrogen peroxide (H2O2). The response of rhizobia to these toxic oxygen species is an important factor in nodulation and nitrogen fixation. In Sinorhizobium meliloti, one oxyR homologue and three catalase genes, katA, katB, and katC were detected by sequence analysis. This oxyR gene is located next to and divergently from katA on the chromosome. To investigate the possible roles of oxyR in regulating the expression of catalases at the transcriptional level in S. meliloti, an insertion mutant of this gene was constructed. The mutant was more sensitive and less adaptive to H2O2 than the wild type strain, and total catalase/peroxidase activity was reduced approximately fourfold with the OxyR mutation relative to controls. The activities of KatA and KatB and the expression of katA::lacZ and katB::lacZ promoter fusions were increased in the mutant strain compared with the parental strain grown in the absence of H2O2, indicating that katA and katB are repressed by OxyR. However, when exposed to H2O2, katA expression was also increased in both S. meliloti and Escherichia coli. When exposed to H2O2, OxyR is converted from a reduced to an oxidized form in E. coli. We concluded that the reduced form of OxyR functions as a repressor of katA and katB expression. Thus, in the presence of H2O2, reduced OxyR is converted to the oxidized form of OxyR that then results in increased katA expression. We further showed that oxyR expression is autoregulated via negative feedback.

Catalase↗

PubMed1994

Conditional ablation of dendritic cells in transgenic mice.

Dendritic cells (DC) are professional Ag-presenting cells that play a major role in T cell-mediated immune responses and in thymocyte differentiation. To better analyze their physiological importance, we sought to generate transgenic mice presenting a conditional DC deficiency. We used a strategy based on the cell-specific expression of a suicide gene. The DC-targeted expression is obtained using HIV regulatory sequences; indirect evidence has suggested that these sequences control a preferential expression in DC. The suicide gene is the herpes simplex virus type 1 thymidine kinase (HSV1-TK) which allows conditional ablation of dividing HSV1-TK-expressing cells by converting nucleoside analogs such as ganciclovir (GCV) into toxic molecules. We generated transgenic mice expressing an HSV1-TK gene transcribed from HIV regulatory sequences. A low but significant HSV1-TK expression was observed in mature DC and DC precursors grown from granulocyte-macrophage colony-stimulating factor-supplemented bone marrow cultures. These HSV1-TK-expressing DC precursors are specifically killed by GCV. We next treated transgenic mice with GCV, and obtained a specific ablation of DC in spleen and thymus. Ninety percent of spleen DC could be depleted within a week, indicating a turnover rate of approximately 15% per day. Interestingly, this DC depletion always correlated with a major thymic atrophy and disappearance of CD4+CD8+ thymocytes. This animal model should help to assess the physiological role of DC in the immune response and in thymocyte differentiation. It should also help to appreciate the consequences of DC dysfunction in pathological situations, such as HIV-infection or allograft rejection.

Animals↗

PubMed1993

Can a protein influence the fate of its own coding sequence?: the amino- and carboxyl-terminal regions of H1 histone.

The amino- and carboxyl-terminal regions of H1 histone are afforded an opportunity to bind to their own coding segments. While such binding is of no consequence to the type of H1 histone that is expressed only in terminally differentiated cells (here referred to as H5), the same binding occurring in H1 of proliferating cells might affect the course of evolution of its amino- and carboxyl-terminal regions. With the above in mind, amino acid sequences of H5 from three species were compared with those of H1 from five species. The spherical core was more conserved in H1 than in H5, whereas the amino- and carboxyl-terminal regions of both were hypervariable. A distinct evolutionary pattern, however, was observed only in these regions of H1 but not of H5. Tandem repeats of short palindromes often generated nearly identical long palindromes in distantly related species. Thus, as far as the 37-residue-long amino-terminal region was concerned, the greatest homology was between the rat and human rather than between the rat and the mouse. With regard to the last 25 residues in the carboxyl-terminal region, the greatest homology was between the chicken and the rainbow trout; the next was between the mouse and the trout. Successions of long palindromes populating the amino- and carboxyl-terminal regions of H1 might be the direct consequence of the autologous binding between peptides and their coding sequence.

Amino Acid Sequence↗

PubMed2005

The effects of total sleep deprivation on the generation of random sequences of key-presses, numbers and nouns.

According to a recent hypothesis, executive functions should be particularly vulnerable to the effects of total sleep deprivation. Random generation is a task that taps executive functions. In three experiments we examined the effects of total sleep deprivation on random generation of key-presses, numbers, and nouns, in particular on the suppression of prepotent responses and the selection of next responses by way of applying a local-representativeness heuristic. With random key-presses suppression of prepotent responses did not suffer from lack of sleep, but it became poorer at a sufficiently high pacing rate. In contrast, suppression of prepotent responses suffered when numbers and nouns were generated. According to these findings different types of random generation tasks involve different types of inhibitory process. With only four response alternatives, but not with larger response sets, application of the local-representativeness heuristic was impaired after a night without sleep. In terms of a simple formal model, serial-order representations of the preceding responses are used in selecting the next response only for the small response set, and not for larger response sets. Thus, serial-order representations are likely to suffer from loss of sleep. These findings strongly suggest that random generation involves multiple processes and that total sleep deprivation does not impair all sorts of executive functions, but only some.

Adult↗

PubMed2000

DNAssist, a C++ program for editing and analysis of nucleic acid and protein sequences on PC-compatible computers running Windows 95, 98, NT4.0 or 2000.

The size of sequence databases, the rapid rate of generating sequence data and the need to routinely construct recombinant DNA molecules in molecular biological research necessitate the frequent handling and analysis of nucleotide and protein sequences on a computer. Although several console or Web-based utility programs are available, the application of these programs generally requires reformatting the data when proceeding from one such program to the next. The acquisition of elaborate, integrated program suites is financially prohibitive to smaller laboratories. Here, we report the development of DNAssist, a shareware program for editing and analysis of nucleic acid and protein sequences. It was developed as a multiple-document interface program--similar to a word processor--where sequences are entered, edited and analyzed in a single integrated environment. DNAssist can calculate the physicochemical properties of a sequence, convert between nucleic acid and protein sequences, translate DNA in multiple frames, identify open reading frames and locate ambiguous sequence patterns allowing gaps and mismatches. DNAssist also performs restriction enzyme and transcription factor-binding site analyses of DNA sequences, the multiple alignment of nucleic acid and protein sequences and the analysis of DNA sequences for nucleosome positioning sites.

Amino Acid Sequence↗

PubMedDate not supplied

Fight against cancer in countries with limited resources: the post-genomic era scenario.

The enormous advances in science and technology in the 20th century have facilitated the process of globalization with the aim of a better quality of life for all. Paradoxically, the gap between the rich and the poor, for both nations and people, is constantly widening. The actual trends in human genome research are leading towards promising genomic medicine, but it will be expensive and inaccessible for many. Also, it may not offer a quick fix "cure" for various types of cancers. The biggest challenge before the clinicians now is the management of the rising incidence of cancer in developing countries, with little prospect of more resources becoming available to fight the disease. The death rate from cancer in the developing countries is set to rise at least 3-fold by the year 2025 largely due to the increased life expectancy, containment of infectious diseases and changing lifestyles. It is estimated that about 50% of cancers are curable if they are detected early and treated appropriately. Screening has a major role in early diagnosis. However, in the developing world around 80% of cancer patients have late stage incurable disease when they are diagnosed. Moreover, in a developing country like India, about 70% of the population obtain medical help from private practitioners. Nearly half of those who seek medical help utilize alternative and traditional systems of medicine. Appalling poverty, poor hygiene and complex social dynamics, pose major hurdles in this regard. Many in the private sector who call themselves doctors have no medical degree. By 2030 tobacco is expected to kill 10 million people worldwide, out of which 70% of the deaths will occur in the developing countries. Control of usage of tobacco has still not achieved a conducive atmosphere. It is now realized that the research information and knowledge generated in the west may neither be relevant nor applicable to developing countries, due to differences in social and cultural attitudes, lifestyles and lack of sophisticated technologies. Though the sequencing of the human genome will have a major impact on the prevention, diagnosis, treatment, monitoring, and outcome of cancer, the cancer scenario in the developing countries for the next 20 years is likely to be more or less the same, rather than presenting a radically different picture. Cancer awareness and screening programs for early detection thus should be continue to be given utmost attention.

Antineoplastic Agents↗

PubMed1997

Cytoplasmically anchored plakoglobin induces a WNT-like phenotype in Xenopus.

Plakoglobin is one of two vertebrate proteins closely related to the Drosophila segment polarity gene product armadillo. Overexpression of plakoglobin induces neural axis duplication in Xenopus and the exogenous plakoglobin is localized to nuclei (Karnovsky, A., and Klymkowsky, M. W., Proc. Natl. Acad. Sci. USA 92, 4255, 1995; Rubenstein, A., et al., Dev. Genet., 1997, in press). We have carried out a series of experiments to test whether the nuclear localization of plakoglobin is required for its inductive effects. Prior to the midblastula transition exogenous plakoglobin is cytoplasmic and concentrated in the cortical regions of blastomeres; after the midblastula transition exogenous plakoglobin accumulates in embryonic nuclei. The addition of a "nuclear localization sequence" does not change the timing of plakoglobin's nuclear localization, suggesting that it is anchored in the cytoplasm prior to the midblastula transition. Next, we constructed two "membrane-anchored" forms of plakoglobin. These are exclusively cytoplasmic; yet both were as effective at producing a "Wnt-like" axis duplication as were "free," unfettered forms of plakoglobin. Moreover, expression of anchored plakoglobins had no apparent effect on the cytoplasmic or nuclear levels of beta-catenin. These data indicate that plakoglobin can act cytoplasmically to generate a WNT-like phenotype. Taken together with the ventralizing effects of a mutant from of the XTcf-3 transcription factor, described by Molenaar et al. Cell 86, 391, 1996, we speculate that in the early Xenopus embryo, activation of plakoglobin (or beta-catenin) inhibits the activity of XTcf-3 or a XTcf-3-like factor.

Amino Acid Sequence↗

PubMed2004

Conservation, duplication and divergence of the zebrafish stat5 genes.

There are seven mammalian signal transducer and activator of transcription (Stat) proteins that act downstream of cytokine and growth factor receptors to mediate rapid changes in gene expression. The mammalian Stat5a and Stat5b genes show high sequence identity and lie adjacent in a head-to-head configuration next to the Stat3 gene, apparently the result of a relatively recent mammal-specific gene duplication event. We have identified and characterized two stat5 homologues that are expressed in zebrafish, named stat5.1 and stat5.2. The stat5.1 gene shows a high level of conservation with the single stat5 gene found in other teleosts and lies next to the stat3 gene, in the same relative orientation as the mammalian Stat5b gene. In contrast, the stat5.2 gene lies on a different chromosome to stat5.1 and stat3, and has diverged from the stat5 genes of other teleosts, with no apparent orthologue. Together, these data suggest that the ancestral Stat5 gene has undergone two independent gene duplication events to generate a stat5.2 paralogue in zebrafish and a Stat5a paralogue in mammals.

Amino Acid Sequence↗

PubMed1993

DNA profiling.

Although some concerns still remain in standard DNA profiling technology over the assumptions from population genetics used to calculate expected match frequencies, forensic scientists are preparing for the introduction of the next generation of DNA profiling techniques based on the polymerase chain reaction. These new techniques offer the prospect of dramatically increasing the speed and sensitivity of DNA profiling and have already been applied in some casework studies.

Base Sequence↗

PubMed2001

[Perspectives on postgenome medicine: Cancer].

Carcinogenesis is a multistep process which is the outcome of the accumulation of genetic and epigenetic events. However, characteristics of cancers, such as drug sensitivity, abilities in invasion and metastasis, are different in each patients, and reliable prediction of those characteristics is not available. DNA microarray and SNP have become the most widely used functional genomics tools. Microarray technology has provided the ability to analyse the expression profiles for thousands of genes, and a wealth of new information that should aid in cancer diagnosis and ultimately in therapy. The SNP project also will generate very variable resources for cancer therapy. The medicine in the next century will be so called 'personalized medicine' based on the new information of patients and diseases.

Gene Expression Profiling↗