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At least 1,243 records · Page 69Linked to original sources
PubMed1994

Genomic diversity among Corynebacterium jeikeium strains and comparison with biochemical characteristics and antimicrobial susceptibilities.

Levels of DNA relatedness were determined by performing DNA-DNA hybridization experiments (S1 nuclease procedure) with 13 human isolates exhibiting various antimicrobial susceptibility patterns which had been identified as Corynebacterium jeikeium by classical tests and the API Coryne system and with reference strains of C. jeikeium and related taxa. Twelve of 13 isolates which formed three genomic groups showed between 22 and 75% relatedness with the type strain of C. jeikeium. One of these genomic groups included all the strains resistant to penicillin and gentamicin and is genomically related to the C. jeikeium type strain at the species level. In addition, the reference strain of "Corynebacterium genitalium" biotype II was found to belong to this genospecies and therefore can be considered as a synonym of C. jeikeium. In contrast, one isolate and the reference strains of "Corynebacterium pseudogenitalium" biotypes C-3 and C-4 which were assigned to C. jeikeium by the API Coryne system were less than 10% related to the C. jeikeium type strain. These nongenomically related strains can be differentiated from the jeikeium-related strains on the basis of positive acidification from fructose and growth under anaerobic conditions. Furthermore, these strains exhibited full susceptibility to penicillin whereas the strains related to the C. jeikeium type strain are resistant to or only moderately susceptible to penicillin. No genomic relationship was found between C. jeikeium-related strains and other lipophilic coryneforms, identified as Corynebacterium accolens or Corynebacterium group G or F. Our study demonstrates the necessity to perform the fructose fermentation test or respiratory-type test for the correct identification of lipophilic coryneforms as C. jeikeium. Although these strains show genomic diversity at the species level, in a practical aspect, biochemical properties as well as antimicrobial susceptibility may allow the classification of such isolates in this single taxon.

Bacterial Typing Techniques↗
PubMed2026

Genomic wastewater surveillance of human and animal influenza A viruses in California during the 2024-2025 flu season.

BACKGROUND: Wastewater genomic surveillance provides an opportunity to detect human and animal influenza A virus (IAV). We aimed to implement an IAV genomic surveillance framework agnostic to subtype, which enables recovery of IAV from multiple hosts and estimation of proportions across subtypes. METHODS: We conducted IAV genomic surveillance in wastewater during the 2024-2025 flu season at multiple sites in California and compared these data with available human clinical IAV sequences and test positivity. We applied a custom whole-genome, multi-host IAV probe enrichment panel and adapted our custom expectation-maximization (EM) algorithm to deconvolute IAV mixtures in wastewater and infer subtype relative abundances. Absolute IAV concentrations were quantified using RT-PCR-based assays. H5N1 wastewater and clinical sequences were further characterized by constructing a whole-genome maximum-likelihood phylogenetic tree. Finally, we performed variant analysis to examine amino acid substitutions detected in wastewater. FINDINGS: Our IAV probe enrichment method and EM algorithm successfully enriched all eight segments of three circulating IAV subtypes and accurately estimated subclade relative abundances for mixed IAV samples. Seasonal human H1N1pdm09 and H3N2 were detected throughout the study period from both wastewater and clinical sequencing data, with H1N1 subclades 6B.1A.5a.2a.1 and 6B.1A.5a.2a co-circulating, and H3N2 dominated by subclade 3C.2a1b.2a.2a.3a.1. Wastewater surveillance consistently detected H5N1 clade 2.3.4.4b across three monitored wastewater sites, while clinical H5N1 detections, from anywhere in CA, were sporadic and rare. Whole-genome phylogenetic analysis revealed that wastewater H5N1 sequences clustered with reference sequences associated with dairy cow and avian infections, while all human clinical H5N1 sequences clustered exclusively with reference sequences associated with dairy cow infections. Amino acid substitutions were identified across viral segments, and no mutations associated with mammalian adaptation were observed from wastewater samples. INTERPRETATION: When IAV concentrations were dominated by seasonal human subtypes rather than H5N1, subtype patterns aligned between wastewater and clinical data. While sequencing IAV in wastewater was unable to distinguish if H5N1 detections were due to human or animal infections, it was able to provide clade-level information about H5N1 found in wastewater that could be useful in the future. Wastewater genomic surveillance can complement clinical surveillance, increasing ability to detect all circulating IAV subtypes and enhancing public health preparedness from a One Health perspective.

Journal Article↗
PubMed1997

Analyses of brain tumor cell lines confirm a simple model of relationships among fluorescence in situ hybridization, DNA index, and comparative genomic hybridization.

Several techniques are commonly used for genetic analysis of interphase nuclei. Flow cytometry assays the distribution of DNA content in populations of nuclei stained with a DNA-specific fluorochrome. Fluorescence in situ hybridization (FISH) quantifies the number of copies of a specific DNA sequence in single nuclei. Comparative genomic hybridization (CGH) assesses the relative copy number of DNA sequences throughout a test genome by comparing the signal intensities of test and reference DNA samples hybridized to a template of normal metaphase chromosomes. In principle, there are specific relationship among data obtained from these measurements, and combined measurements should provide a more comprehensive view of the sample that is analyzed. We applied these three techniques to nine brain tumor cell lines and find that a model of CGH that includes unsuppressed repeat sequences describes the data well. We estimate that up to 35% of the fluorescence intensity in well-blocked CGH preparations may not represent unique sequences. Taking these factors into account, our results are, in general, mutually consistent, and highlight issues critical for interpreting CGH preparations.

Algorithms↗
PubMed1995

Detection of c-erbB-2/neu and fibroblast growth factor-3/INT-2 but not epidermal growth factor receptor gene amplification in endometrial cancer by differential polymerase chain reaction.

BACKGROUND: It currently is well established that the activation of protooncogenes could trigger uncontrolled cell growth and cancer development. Although this correlation already has been evidenced in several human tumors, no conclusive studies have related oncogene activation with the development of endometrial neoplasia. Nevertheless, few reports suggest that c-erbB-2/neu, which is a prognostic marker in breast cancer, epidermal growth factor receptor (EGFR), which is overexpressed in a variety of neoplasms, and fibroblast growth factor-3 (FGF-3/INT-2), which has been found to be amplified in breast and ovarian cancer, could be implicated in the development of endometrial adenocarcinoma. METHODS: Amplification of c-erbB-2/neu, EGFR, and FGF-3/INT-2 was examined in 50 endometrial carcinomas, 10 adenomatous hyperplasias, and 50 normal endometrial samples, using the genomic differential polymerase chain reaction with the single copy reference gene interferon-gamma. Quantitation of the ratios between the amplified bands was assessed by image analysis. RESULTS: c-erbB-2 and FGF-3/INT-2 were amplified in a first group of 7 (14%) and a further group of 7 (14%) patients, respectively, of a total of 50 in whom endometrial cancer had been studied. In the latter seven, a strong correlation between this genetic marker and an advanced disease stage (International Federation of Gynecology and Obstetrics Stage III) was found. In two patients, both genes were amplified. No EGFR gene amplification was detected in any case. CONCLUSION: c-erbB-2/neu but not EGFR gene amplification was detected and FGF-3/INT-2 amplification and advanced disease were correlated in endometrial cancer.

Adenocarcinoma↗
PubMed2002

MSI in endometrial carcinoma: absence of MLH1 promoter methylation is associated with increased familial risk for cancers.

Loss of DNA mismatch repair occurs in a variety of malignancies and is associated with genome-wide instability of microsatellite repeats, a molecular phenotype referred to as microsatellite instability (MSI). MSI is a consistent feature of colorectal and endometrial tumors from patients with hereditary non-polyposis colorectal cancer (HNPCC). Sporadic colorectal and endometrial cancers that exhibit MSI frequently have methylation of the MLH1 promoter. We undertook a detailed family and medical history study to compare family cancer risk for women with MSI-positive and -negative endometrial cancers. The MLH1 promoter methylation status was determined for all cancers. Family histories were developed for 80 probands (40 with MSI-positive and 40 with MSI-negative tumors). The numbers of reported cancers in first- and second-degree relatives of the 2 groups were similar. There was a modest increase in familial cancer clustering for MSI-positive probands. When MSI-positive tumors were subclassified according to MLH1 promoter methylation, a clear association between methylation status and familial cancer risk was evident. Women with MSI-positive endometrial cancers in which the MLH1 promoter was unmethylated had a 7-fold relative risk (RR) of demonstrating familial clustering of cancers [RR 7.07 (95% confidence interval 2.29-21.81)]. The women with MSI-positive, MLH1-unmethylated tumors were significantly younger than the rest of the study population (56.1 years vs. 65.4, p < or = 0.01). Age of onset and tumor MSI not associated with MLH1 promoter methylation may point to women with a genetic susceptibility to malignancies.

Adaptor Proteins, Signal Transducing↗
PubMed2006

Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis.

In the last decade, an increasing number of sequenced archaeal genomes have become available, opening up the possibility for functional genomic analyses. Here, we reconstructed the central carbon metabolism in the hyperthermophilic crenarchaeon Sulfolobus solfataricus (glycolysis, gluconeogenesis and tricarboxylic acid cycle) on the basis of genomic, proteomic, transcriptomic and biochemical data. A 2-DE reference map of S. solfataricus grown on glucose, consisting of 325 unique ORFs in 255 protein spots, was created to facilitate this study. The map was then used for a differential expression study based on (15)N metabolic labelling (yeast extract + tryptone-grown cells (YT) vs. glucose-grown cells (G)). In addition, the expression ratio of the genes involved in carbon metabolism was studied using DNA microarrays. Surprisingly, only 3 and 14% of the genes and proteins, respectively, involved in central carbon metabolism showed a greater than two-fold change in expression level. All results are discussed in the light of the current understanding of central carbon metabolism in S. solfataricus and will help to obtain a system-wide understanding of this organism.

Archaeal Proteins↗
PubMed2006

The proteome of Mannheimia succiniciproducens, a capnophilic rumen bacterium.

Mannheimia succiniciproducens MBEL55E isolated from bovine rumen is an industrially important bacterium as an efficient succinic acid producer. Recently, its full genome sequence was determined. In the present study, we analyzed the M. succiniciproducens proteome based on the genome information using 2-DE and MS. We established proteome reference map of M. succiniciproducens by analyzing whole cellular proteins, membrane proteins, and secreted proteins. More than 200 proteins were identified and characterized by MS/MS supported by various bioinformatic tools. The presence of proteins previously annotated as hypothetical proteins or proteins having putative functions were also confirmed. Based on the proteome reference map, cells in the different growth phases were analyzed at the proteome level. Comparative proteome profiling revealed valuable information to understand physiological changes during growth, and subsequently suggested target genes to be manipulated for the strain improvement.

Animals↗
PubMed1996

Chromosomal localization of the human genes, CPP32, Mch2, Mch3, and Ich-1, involved in cellular apoptosis.

Members of the ICE/CED-3 protease family appear to play an essential role in programmed cell death process. In this paper the chromosomal localization of the human genes CPP32, Mch2, Mch3 and Ich-1 is reported, obtained by Radiation Hybrid Mapping. CPP32 was assigned to chromosome 4q33-q35.1, Mch2 to chromosome 4q25-q26, Mch3 to chromosome 10q25.1-q25.2 and Ich-1 to chromosome 7q35. Ich-1 was found to map very close to the marker WI-9353. The possible overlapping of the two independent locus assignments is considered. The genomic distribution of these genes is discussed, with particular reference to the co-location with some human genetic diseases all characterized by autosomal dominant inheritance and by similar malformative features.

Animals↗
PubMed1997

Isolation and expression of rat interferon beta gene and growth-inhibitory effect of its expression on rat glioma cells.

Rat interferon beta (IFN beta) was cloned from a part of rat genomic DNA by the polymerase chain reaction (PCR) with reference to the nucleotide sequence data of a mouse IFN beta. The sequence result showed that the clone had 555 bp of open reading frame (ORF) which encoded a 184-amino acid polypeptide. Comparison of our data with those of mouse and human IFN beta revealed 86.7 and 67.6% homology at the nucleotide level, and 76.2 and 48.9% homology at the amino acid level, respectively. This ORF was inserted into an expression vector, pCAGGS, and COS-1 cells were then transfected with the plasmid encapsulated in cationic multilamellar liposomes. From the results of reverse transcription-PCR and cytopathic activity assay, this ORF expressed IFN beta in COS-1 cells. When the cultured cells of rat glioma cell line T9 were transfected with the plasmid, their growth was markedly suppressed due to the expression of rat IFN beta.

Amino Acid Sequence↗
PubMed1997

Gene homologs on human chromosome 15q21-q26 and a chicken microchromosome identify a new conserved segment.

The genes for insulin-like growth factor 1 receptor (IGF1R), aggrecan (AGC1), beta2-microglobulin (B2M), and an H6-related gene have been mapped to a single chicken microchromosome by genetic linkage analysis. In addition, a second H6-related gene was mapped to chicken macrochromosome 3. The Igf1r and Agc1 loci are syntenic on mouse Chr 7, together with Hmx3, an H6-like locus. This suggests that the H6-related locus, which maps to the chicken microchromosome in this study, is the homolog of mouse Hmx3. The IGF1R, AGC1, and B2M loci are located on human Chr 15, probably in the same order as found for this chicken microchromosome. This conserved segment, however, is not entirely conserved in the mouse and is split between Chr 7 (Igf1r-Agc) and 2 (B2m). This comparison also predicts that the HMX3 locus may map to the short arm of human Chr 15. The conserved segment defined by the IGF1R-AGC1-HMX3-B2M loci is approximately 21-35 Mb in length and probably covers the entire chicken microchromosome. These results suggest that a segment of human Chr 15 has been conserved as a chicken microchromosome. The significance of this result is discussed with reference to the evolution of the avian and mammalian genomes.

Aggrecans↗
PubMed2003

Genomic organization of the S core region and the S flanking regions of a class-II S haplotype in Brassica rapa.

The nucleotide sequence of an 86.4-kb region that includes the SP11, SRK, and SLG genes of Brassica rapa S-60 (a class-II S haplotype) was determined. In the sequenced region, 13 putative genes were found besides SP11-60, SRK-60, and SLG-60. Five of these sequences were isolated as cDNAs, five were homologues of known genes, cDNAs, or ORFs, and three are hypothetical ORFs. Based on their nucleotide sequences, however, some of them are thought to be non-functional. Two regions of colinearity between the class-II S-60 and Brassica class-I S haplotypes were identified, i.e., S flanking region 1 which shows partial colinearity of non-genic sequences and S flanking region 2 which shows a high level of colinearity. The observed colinearity made it possible to compare the order of SP-11, SRK, and SLG genes in the S locus between the five sequenced S haplotypes. It emerged that the order of SRK and SLG in class-II S-60 is the reverse of that in the four class-I S haplotypes reported so far, and the order of SP11, SRK and SLG is the opposite of that in the class-I haplotype S-910. The possible gene designated as SAN1 (S locus Anther-expressed Non-coding RNA like-1), which is located in the region between SP11-60 and SRK-60, has features reminiscent of genes for non-coding RNAs (ncRNAs), but no homologous sequences were found in the databases. This sequence is transcribed in anthers but not in stigmas or leaves. These features of the genomic structure of S-60 are discussed with special reference to the characteristics of class-II S haplotypes.

Amino Acid Sequence↗
PubMed2006

Easy and rapid method of zygosity determination in transgenic mice by SYBR Green real-time quantitative PCR with a simple data analysis.

Establishment and maintenance of transgenic mouse strains require being able to distinguish homozygous from heterozygous animals. To date, the developed real-time quantitative PCR techniques are often complicated, time-consuming and expensive. Here, we propose a very easy and rapid method with a simple data analysis to determine zygosity in transgenic mice. We show that the real-time quantitative PCR using SYBR Green fluorescent dye can be applied to discriminate two-fold differences in copy numbers of the transgene. Our procedure has to fit only three simple requirements: (1) to design primers capable of detecting one Ct difference for two-fold differences in DNA amounts (2) to measure genomic DNA concentrations accurately and (3) to have a reference animal of known zygosity in each run. Then, if the Ct values for the control gene are similar in all samples, we are able to compare directly the Ct values for the transgene in every sample, and so, to deduce the zygosity status of each mouse relative to the reference animal. This method is really simple and reliable, and it may be valuable as a rapid screening tool for zygosity status in transgenic animals.

Animals↗
PubMed1988

Extra-ribosomal spacer sequences in Triturus.

We show that, in Triturus vulgaris meridionalis, sequences homologous to the rDNA "non-transcribed" spacer (NTS) are clustered at chromosomal loci where they are not associated with 18 S or 28 S rDNA genes: these sequences are referred to as the extra-ribosomal spacer sequences. Genomic clones containing such extra-ribosomal spacer sequences have been isolated. As shown by restriction mapping, these clones appear to consist mostly of repetitive BamHI fragments that are, in turn, internally repetitious and highly homologous to each other. The structure of the clones was confirmed by nucleotide sequence analysis, which also demonstrates the high degree of conservation between the BamHI elements and the homologous NTS sequences. An intriguing 12 base-pair homology between the extra-ribosomal spacer sequences and a Xenopus NTS enhancer sequence is reported. The possibility that a repetitive octanucleotide motif found within the BamHI elements could act as a recombination hotspot by virtue of its similarity with the Escherichia coli chi sequence is discussed.

Animals↗
PubMed1979

Nucleotide sequence analysis of the leader segments in a cloned copy of adenovirus 2 fiber mRNA.

Fiber mRNA of adenovirus 2 has been used as a template for RNA-dependent DNA polymerase. The resulting cDNA/RNA hybrids have been inserted at the Pst I site of the plasmid vector pBR322 after A:T tailing. One recombinant plasmid, pJAW 43, has been characterized in detail and shown to contain sequences from the main body of fiber mRNA, the three leaders common to most late adenoviral mRNAs and a fourth leader found in some species of fiber mRNA. The complete DNA sequence of the leader region has been determined and does not contain the initiation codon AUG, although this codon does occur immediately downstream from the junction between the fourth leader and the main body of the fiber mRNA. The first leader (map coordinate 16.6) is 41 nucleotides long, the second (from 19.6) is 71 nucleotides, the third (from 26.6) is 88 nucleotides and the fourth (from 78.5) is 181 nucleotides. The location of junctions between viral leaders and intervening sequences has been determined by reference, where possible, to sequences of the adenovirus 2 genome. Although the presence of short repeated sequences at the boundaries of intervening sequences and leaders makes it impossible to locate the splice point unambiguously, all of the leader-intervening sequence junctions can be arranged to stress a common feature--the presence of the dinucleotides GT and AG at the 5' and 3' ends, respectively, of the intervening sequences. This prototype sequence, which has also been recognized at or near the splice points in other eucaryotic systems, is possibly part of a larger unit which serves as a recognition site for specific excision-ligation events that ultimately lead to the production of mature mRNAs.

Adenoviruses, Human↗
PubMed1996

FISH digital imaging microscopy in mosquito genomics.

The yellow fever mosquito, Aedes aegypti, transmits pathogens that affect both humans and livestock, and has been the focus of extensive research to identify genetic loci that may be useful in control strategies. Fluorescence in situ hybridization (FISH) and digital imaging microscopy have provided a rapid mechanism to populate the physical map with probes derived from genetic markers, cDNAs and recombinant genomic libraries. When the physical and genetic linkage maps are aligned, map-based cloning will allow the rapid isolation of target genomic sequences. The strategy of FISH mapping and the results of initial hybridization studies are reviewed here by Martin Ferguson, Susan Brown and Dennis Knudson. An Ae. aegypti-specific genomic database, which collates data from mapping studies, sequences, references and other relevant information, is also discussed.

Journal Article↗
PubMed2006

Entamoeba histolytica: computational identification of putative microRNA candidates.

MicroRNAs are an abundant class of approximately 20-24-nucleotide noncoding RNAs that control the expression of several genes at the post-transcriptional level, regulating several important biochemical pathways. MicroRNAs have been identified in many vertebrates including humans, and also in flies, nematodes, plants, and viruses. In the present work we have identified seventeen putative candidate microRNAs in the pathogenic parasite Entamoeba histolytica using a bioinformatic approach. Putative microRNA identification in E. histolytica may act as a starting reference for cloning and characterization of miRNAs in Entamoeba genome.

Animals↗
PubMed2026

Transcription regulation of cell fate plasticity - from embryonic development to tissue regeneration.

Cell fate plasticity refers to the capacity of cells sharing the same genome to alter, reverse, or reconfigure their identity under physiological, pathological, or experimental conditions. This property underlies embryonic development, cellular reprogramming, and tissue regeneration, but becomes progressively restricted as lineage identity is stabilized. Embryonic development represents an intrinsic process of fate transitions, whereas reprogramming and regeneration reveal how differentiated cells can dedifferentiate or transdifferentiate under specific conditions. Across these contexts, plasticity is governed by multilayered regulatory networks involving transcription factors, epigenetic regulators, cofactors, and the core transcription machinery. Robust regulatory programs stabilize cell identity, whereas stochastic fluctuations in gene expression and chromatin state can prime cells for fate transitions, adding a tunable dimension to plasticity control. In this review, we synthesize recent advances in the regulation of cell fate plasticity across development, reprogramming, and regeneration, highlighting how transcription factors, epigenetic modifications, transcriptional cofactors, and core transcription machinery cooperate to control cell fate decisions and plasticity.

Animals↗
PubMed2024

Meningioma transcriptomic landscape demonstrates novel subtypes with regional associated biology and patient outcome.

Meningiomas, although mostly benign, can be recurrent and fatal. World Health Organization (WHO) grading of the tumor does not always identify high-risk meningioma, and better characterizations of their aggressive biology are needed. To approach this problem, we combined 13 bulk RNA sequencing (RNA-seq) datasets to create a dimension-reduced reference landscape of 1,298 meningiomas. The clinical and genomic metadata effectively correlated with landscape regions, which led to the identification of meningioma subtypes with specific biological signatures. The time to recurrence also correlated with the map location. Further, we developed an algorithm that maps new patients onto this landscape, where the nearest neighbors predict outcome. This study highlights the utility of combining bulk transcriptomic datasets to visualize the complexity of tumor populations. Further, we provide an interactive tool for understanding the disease and predicting patient outcomes. This resource is accessible via the online tool Oncoscape, where the scientific community can explore the meningioma landscape.

Meningioma↗