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PubMed2026

Farming reshapes the gut resistome, virulome, and mobilome of Cervidae.

The rapid expansion of cervid farming raises concerns about antimicrobial resistance (AMR) dissemination, yet its impact on the Cervidae gut microbiome remains poorly characterized. We integrated 89 newly sequenced fecal metagenomes with 599 publicly available datasets, comprising 285 metagenomes from farmed cervids and 370 from wild cervids, to construct a catalog of 15,494 non-redundant metagenome-assembled genomes (MAGs) representing 2,401 species. Our analysis demonstrates that farming profoundly reshapes the gut microbiome's functional composition. Specifically, farmed cervids exhibited significantly higher relative abundance, diversity, and heterogeneity of antimicrobial resistance genes (ARGs) compared to wild counterparts. We observed a robust synergistic relationship between ARGs, virulence factor genes, and mobile genetic element (MGE)-associated genes, identifying 70 ARG-MGE combinations as evidence of potential horizontal gene transfer. Plasmid profiling further suggested that a subset of ARGs may be associated with conjugative plasmids, with plasmid-associated ARGs being significantly more abundant in farmed than in wild cervids. Virome analyses indicated that bacteriophages, particularly Siphoviridae, may serve as mobile reservoirs for ARGs. Notably, Cervidae shared 268 ARG types with humans, including 23 high-risk genes associated with resistance to clinically important antibiotics (e.g. tetX1, vanRD, and bla-CTX-M-178), with Escherichia coli as a key cross-host carrier. These findings highlight that human-impacted cervid gut microbiomes are significant environmental reservoirs of clinically relevant AMR, underscoring the necessity for enhanced antibiotic stewardship and resistance surveillance in managed wildlife within a One Health framework.

Animals↗
PubMedDate not supplied

Classification and naming of dyes, stains and fluorochromes.

A classification of dyes and other colorants is proposed, based on the chemical features responsible for their visibility and generally consonant with the writings of modern color chemists. The scheme differs in several respects from that of the Colour Index (CI), but it retains some traditional small groups of dyes that include biological stains. Natural dyes, recognized as a group in the CI, are placed with or near synthetic dyes with identical or similar chromophores. The new scheme also provides categories for dyes and fluorochromes that do not have places in the CI classification. Some CI categories, including lactones, aminoketones and hydroxyketones, are not recognized in this new scheme, which is adopted in the forthcoming 10th edition of Conn's Biological Stains: a Handbook of Dyes and Fluorochromes for Use in Biology and Medicine. Some rules are also set out for the spelling of trivial names, which has long been inconsistent in scientific literature. The ending '-ine' is used for compounds derived from organic bases (e.g., fuchsine and thionine, not fuchsin or thionin), and names ending in '-in' are for compounds that are not bases or their derivatives (e.g., eosin and phloxin, not eosine or phloxine). Initial capital letters are used only for words that are names of people or places (e.g., Nile blue or Congo red) and for the 'generic' components of CI application names (as in Acid yellow 36). Other words, including trade names that have fallen into common usage are not capitalized (e.g., alcian blue, biebrich scarlet, coomassie blue). The recommended spellings of some dyes differ from those commonly seen in vendors' catalogs and in biological publications, but they are generally consistent with English and American dictionaries, with recent writings in English by color chemists, and with the trivial names of other organic compounds.

Coloring Agents↗
PubMed1999

Environmental Dependence of the Fundamental Plane of Galaxy Clusters.

Galaxy clusters approximate a planar distribution in a three-dimensional parameter space that can be characterized, for example, by an optical luminosity, half-light radius, and X-ray luminosity. We find the nearest neighbor clusters for those common to either of two previous fundamental-plane studies and a high-quality cluster redshift catalog. Examining scatter about one plane in parameter space, we find a 2 sigma result that it is dependent on the nearest neighbor distance. Study of another sample of X-ray clusters shows that those with high central gas densities are systematically (2.5 sigma) closer to neighbor clusters. These results suggest a possible explanation for recent evidence that X-ray cooling flow clusters reside in crowded environments.

Journal Article↗
PubMed1999

The Contribution of Normal, Dim, and Dwarf Galaxies to the Local Luminosity Density.

From the Hubble Deep Field catalog recently presented by Driver et al., we derive the local (0.3<z<0.5) bivariate brightness distribution of field galaxies within a 326 Mpc3 volume-limited sample. The sample contains 47 galaxies which uniformly sample the underlying galaxy population within the specified redshift, magnitude, and surface brightness limits (0.3<z<0.5, -21.3<MB<-13.7 mag, 18.0<µB<24.55 mag arcsec-2). We conclude that (1) a luminosity-surface brightness relation exists for both the field and cluster galaxy populations, MB approximately &sqbl0;&parl0;1.5+/-0.2&parr0;µe-&parl0;50+/-2&parr0;&sqbr0;, (2) luminous low surface brightness galaxies account for less than 10% of the L* population, and (3) low-luminosity low surface brightness galaxies outnumber Hubble types by a factor of approximately 1.4; however, their space density is not sufficient to explain the faint blue excess either by themselves or as faded remnants. In terms of the local luminosity density and galaxy dynamical mass budget, normal galaxies (i.e., the Hubble tuning fork) contribute 88% and 72%, respectively. This compares to 7% and 12% for dim galaxies and 5% and 16% for dwarf galaxies (within the above specified limits).

Journal Article↗
PubMed2000

The Space Density of Primordial Gas Clouds near Galaxies and Groups and their Relation to Galactic High-Velocity Clouds.

The Arecibo H i Strip Survey probed the halos of approximately 300 cataloged galaxies and the environments of approximately 14 groups with sensitivity to neutral hydrogen masses >/=107 M middle dot in circle. The survey detected no objects with properties resembling the high-velocity clouds (HVCs) associated with the Milky Way or Local Group. If the HVCs were typically MHi=107.5 M middle dot in circle objects distributed throughout groups and galaxy halos at distances of approximately 1 Mpc, the survey should have made approximately 70 HVC detections in groups and approximately 250 detections around galaxies. The null detection implies that HVCs are deployed at typical distances of </=200 kpc from the galaxies or group barycenters. If the clouds are in virial equilibrium, their average dark matter fraction must be 98% or higher.

Journal Article↗
PubMed2000

Comparing the Evolution of the Galaxy Disk Sizes with Cold Dark Matter Models: The Hubble Deep Field.

The intrinsic sizes of the field galaxies with I</=26 in the Hubble and ESO New Technology Telescope (NTT) Deep Fields are shown as a function of their redshifts and absolute magnitudes using photometric redshifts derived from the multicolor catalogs and are compared with the cold dark matter (CDM) predictions. Extending to the lower luminosities and to the higher z that our previous analysis performed on the NTT field alone, we find the distribution of the galaxy disk sizes at different cosmic epochs is within the range predicted by typical CDM models. However, the observed size distribution of faint (MB>-19) galaxies is skewed with respect to the CDM predictions, and an excess of small-size disks (Rd<2 kpc) is already present at z approximately 0.5. The excess persists up to z approximately 3 and involves brighter galaxies. Such an excess may be reduced if luminosity-dependent effects, like starburst activity in interacting galaxies, are included in the physical mechanisms governing the star formation history in CDM models.

Journal Article↗
PubMed2000

A Comparison of Estimators for the Two-Point Correlation Function.

Nine of the most important estimators known for the two-point correlation function are compared using a predetermined, rigorous criterion. The indicators were extracted from over 500 subsamples of the Virgo Hubble volume simulation cluster catalog. The "real" correlation function was determined from the full survey in a 3000 h(-1) Mpc periodic cube. The estimators were ranked by the cumulative probability of returning a value within a certain tolerance of the real correlation function. This criterion takes into account bias and variance, and it is independent of the possibly non-Gaussian nature of the error statistics. As a result, for astrophysical applications, a clear recommendation has emerged: the Landy & Szalay estimator, in its original or grid version (Szapudi & Szalay), is preferred in comparison with the other indicators examined, with a performance almost indistinguishable from the Hamilton estimator.

Journal Article↗
PubMed2000

Age Difference between the Populations of Binary and Single F Stars Revealed from Hipparcos Data.

We have compared the kinematics and metallicity of the main-sequence binary and single uvby F stars from the Hipparcos catalog to see if the populations of these stars originate from the same statistical ensemble. The velocity dispersions of the known unresolved binary F stars have been found to be dramatically smaller than those of the single F stars. This suggests that the population of these binaries is, in fact, younger than that of the single stars, which is further supported by the difference in metal abundance: the binaries turn out to be, on average, more metal rich than the single stars. So, we conclude that the population of these binaries is indeed younger than that of the single F stars. Comparison of the single F stars with the C binaries (binary candidates identified in Suchkov & McMaster) has shown, on the other hand, that the latter stars are, on average, older than the single F stars. We suggest that the age difference between the single F stars, known unresolved binaries, and C binaries is associated with the fact that stellar evolution in a binary systems depends on the binary components' mass ratio and separation, with these parameters being statistically very different for the known binaries and C binaries (e.g., mostly substellar secondaries in C binaries vs. stellar secondaries in known binaries). In general we conclude that the populations of known binaries, C binaries, and single F stars do not belong to the same statistical ensemble. The implications of the discovered age difference between these populations along with the corresponding differences in kinematics and metallicity should be important not only for understanding the evolution of stars but also for the history of star formation and the evolution of the local Galactic disk.

Journal Article↗
PubMed2000

Measuring Cosmological Bulk Flows via the Kinematic Sunyaev-Zeldovich Effect in the Upcoming Cosmic Microwave Background Maps.

We propose a new method for measuring the possible large-scale bulk flows in the universe from the cosmic microwave background (CMB) maps from the upcoming missions of the Microwave Anistropy Probe (MAP) and Planck. This can be done by studying the statistical properties of the CMB temperature field at many X-ray cluster positions. At each cluster position, the CMB temperature fluctuation will be a combination of the Sunyaev-Zeldovich (SZ) kinematic and thermal components, the cosmological fluctuations, and the instrument noise term. When averaged over many such clusters, the last three will integrate down, whereas the first one will be dominated by a possible bulk flow component. In particular, we propose to use all-sky X-ray cluster catalogs that should (or could) be available soon from X-ray satellites and then to evaluate the dipole component of the CMB field at the cluster positions. We show that for the MAP and Planck mission parameters, the dominant contributions to the dipole will be from the terms that are due to the SZ kinematic effect produced by the bulk flow (the signal we seek) and the instrument noise (the noise in our signal). Then, by computing the expected signal-to-noise ratio for such measurement, we find that at the 95% confidence level, the bulk flows on scales >/=100 h(-1) Mpc can be probed down to the amplitude of less than 200 km s(-1) with the MAP data and down to only approximately 30 km s(-1) with the Planck mission.

Journal Article↗
PubMed2005

Single-gene disorders: what role could moonlighting enzymes play?

Single-gene disorders with "simple" Mendelian inheritance do not always imply that there will be an easy prediction of the phenotype from the genotype, which has been shown for a number of metabolic disorders. We propose that moonlighting enzymes (i.e., metabolic enzymes with additional functional activities) could contribute to the complexity of such disorders. The lack of knowledge about the additional functional activities of proteins could result in a lack of correlation between genotype and phenotype. In this review, we highlight some notable and recent examples of moonlighting enzymes and their possible contributions to human disease. Because knowledge and cataloging of the moonlighting activities of proteins are essential for the study of cellular function and human physiology, we also review recently reported and recommended methods for the discovery of moonlighting activities.

Animals↗
PubMed2002

Characterization of T-DNA insertion sites in Arabidopsis thaliana and the implications for saturation mutagenesis.

A key component of a sound functional genomics infrastructure is the availability of a knockout mutant for every gene in the genome. A fruitful approach to systematically knockingout genes in the plant Arabidopsis thaliana has been the use of transferred-DNA (T-DNA) from Agrobacterium tumefaciens as an insertional mutagen. One of the assumptions underlying the use of T-DNA as a mutagen is that the insertion of these DNA elements into the Arabidopsis genome occurs at randomly selected locations. We have directly investigated the distribution of T-DNA insertions sites in populations of transformed Arabidopsis using two different approaches. To begin with, we utilized a polymerase chain reaction (PCR) procedure to systematically catalog the precise locations of all the T-DNA elements inserted within a 65 kb segment of chromosome IV. Of the 47 T-DNA insertions identified, 30% were found within the coding regions of genes. We also documented the insertion of T-DNA elements within the centromeric region of chromosome IV. In addition to these targeted T-DNA screens, we also mapped the genomic locations of 583 randomly chosen T-DNA elements by sequencing the genomic DNA flanking the insertion sites from individual T-DNA-transformed lines. 35% of these randomly chosen T-DNA insertions were located within the coding regions of genes. For comparison, coding sequences account for 44% of the Arabidopsis genome. Our results demonstrate that there is a small bias towards recovering T-DNA insertions within intergenic regions. However, this bias does not limit the utility of T-DNA as an effective insertional mutagen for use in reverse-genetic strategies.

Arabidopsis↗
PubMed2003

A sense of life: computational and experimental investigations with models of biochemical and evolutionary processes.

We collaborate in a research program aimed at creating a rigorous framework, experimental infrastructure, and computational environment for understanding, experimenting with, manipulating, and modifying a diverse set of fundamental biological processes at multiple scales and spatio-temporal modes. The novelty of our research is based on an approach that (i) requires coevolution of experimental science and theoretical techniques and (ii) exploits a certain universality in biology guided by a parsimonious model of evolutionary mechanisms operating at the genomic level and manifesting at the proteomic, transcriptomic, phylogenic, and other higher levels. Our current program in "systems biology" endeavors to marry large-scale biological experiments with the tools to ponder and reason about large, complex, and subtle natural systems. To achieve this ambitious goal, ideas and concepts are combined from many different fields: biological experimentation, applied mathematical modeling, computational reasoning schemes, and large-scale numerical and symbolic simulations. From a biological viewpoint, the basic issues are many: (i) understanding common and shared structural motifs among biological processes; (ii) modeling biological noise due to interactions among a small number of key molecules or loss of synchrony; (iii) explaining the robustness of these systems in spite of such noise; and (iv) cataloging multistatic behavior and adaptation exhibited by many biological processes.

Animals↗
PubMed1996

Ginkgo biloba L.: history, current status, and future prospects.

In this paper, we describe the status of the exploration and use of the Ginkgo biloba leaves in China. We emphasize the need for careful studies of the intra-specific genetic diversity of Ginkgo biloba since genetic variation within this species may result in significant differences between the chemical and pharmacological properties of the different sub-species. It is therefore imperative that we catalog the intraspecific diversity of Ginkgo biloba L., and we stress that it is important to conserve this diversity since different subspecies may have different pharmacochemical properties resulting in differential medical usages.

Cycadopsida↗
PubMedDate not supplied

The uses of computer-aided signal peptide selection and polymerase chain reaction in gene construction and expression of secreted proteins.

The computer program, SIGSEQ2, was used to select heterologous signal peptides from a catalog of published sequences to express the echistatin gene in insect (Sf9) cells. S-values for each amino acid were determined to select empirically the site of cleavage between the signal peptide and mature echistatin. Five gene fragments encoding the signal peptides for human immunoglobulin kappa (Ig kappa), Drosophila 68C glue, antistasin, bovine growth hormone (bGH), and human apolipoprotein E (Apo E) were constructed by the use of long synthetic oligonucleotides or polymerase chain reaction (PCR). Echistatin expression vectors then were constructed using the baculovirus polyhedrin promoter. Following transient transfection, the media were assayed for echistatin activity. The results indicate that the computer program greatly facilitated the selection and design of five different signal peptides and accurately predicted their relative functionality in the expression and secretion of echistatin in insect cell cultures.

Animals↗
PubMed2004

Genomic and proteomic expression patterns in HPV-16 E6 gene transfected stable human carcinoma cell lines.

cDNA microarray and proteomics studies were performed to analyze the genomic and proteomic expression patterns in HPV-16 E6 gene transfected stable human carcinoma cell lines. Among 1024 known genes and ESTs tested by cDNA microarray, we found 50 upregulated and 35 downregulated genes in RC10.1 HPV-16 E6 transfected human colon adenocarcinoma cells compared to RKO cells, and 27 upregulated and 43 downregulated genes in A549E6 HPV-16 E6 transfected human lung adenocarcinoma cells compared to A549 cells. Employing two dimensional gel electrophoresis and MALDI-TOF-MS, the global pattern of protein expressions in RC10.1 human colon adenocarcinoma and A549E6 human lung adenocarcinoma cell lines stably expressing the HPV 16-E6 gene were compared with those of RKO and A549 cell lines to generate a differential protein expression catalog. We found 13 upregulated and 13 downregulated proteins in RC10.1 (E6-expressing RKO) cells compared to RKO cells and 12 upregulated and 14 downregulated proteins in A549E6 (E6-expressing A549) cells compared to A549 cells. The identified genes and proteins were classified into several groups according to the subcellular function. Expressing pattern of three genes and proteins (CDK5, Bak, and I-TRAF) were matched in both analyses of cDNA microarray and proteomics. These powerful approaches using cDNA microarray and proteomics could provide in-depth information on the impact of HPV-16 E6-related genes and proteins. Differential gene and protein expression patterns by transfection of HPV-16 E6 will provide the nucleus of valuable resource for investigation of the biochemical basis of cervical carcinogenesis. Further understanding of this data base may provide valuable resources for developing novel diagnostic markers and therapeutic targets of cervical cancer.

Adenocarcinoma↗
PubMed2006

Murine ortholog of the novel glycosyltransferase, B3GTL: primary structure, characterization of the gene and transcripts, and expression in tissues.

Glycosylation of proteins and lipids is important in cellular communication and maintenance of tissues. B3GTL (beta3-glycosyltransferase-like) is a novel glycosyltransferase that is found in multicellular animals ranging from mammals to insects and nematodes. The aim of this work was to identify and characterize the B3GTL gene in the mouse and to study its expression in various tissues. The murine gene codes for a protein which shares 84% amino acid sequence identity with its human ortholog, and contains all the primary structural features that characterize B3GTL proteins. The murine and human B3GTL genes share an identical exon/intron organization, and both genes utilize multiple polyadenylation signals. Their promoter regions show extensive conservation, implying that the two genes also share regulatory similarities. This notion was reinforced by Northern hybridization analysis of mouse tissues, which showed the tissue distribution of B3GTL mRNA to be similar to that previously found in human tissues, with the heart, kidney, and brain being major sites of expression in both species. The localization of B3GTL mRNA was studied by in situ hybridization in an extensive collection of mouse tissues, of which the granular cells of the olfactory bulb and the epithelium of the seminal vesicle displayed particularly strong signals. Together, these analyses indicate that the B3GTL mRNA is subject to strong tissue-specific and developmental regulation. The findings reported here make possible the design of a B3GTL "knock-out" mouse, provide a framework for analyzing the regulation of the gene, and provide an extensive catalog of tissues in which this novel protein acts.

Amino Acid Sequence↗
PubMed2002

Identification of genes periodically expressed in the human cell cycle and their expression in tumors.

The genome-wide program of gene expression during the cell division cycle in a human cancer cell line (HeLa) was characterized using cDNA microarrays. Transcripts of >850 genes showed periodic variation during the cell cycle. Hierarchical clustering of the expression patterns revealed coexpressed groups of previously well-characterized genes involved in essential cell cycle processes such as DNA replication, chromosome segregation, and cell adhesion along with genes of uncharacterized function. Most of the genes whose expression had previously been reported to correlate with the proliferative state of tumors were found herein also to be periodically expressed during the HeLa cell cycle. However, some of the genes periodically expressed in the HeLa cell cycle do not have a consistent correlation with tumor proliferation. Cell cycle-regulated transcripts of genes involved in fundamental processes such as DNA replication and chromosome segregation seem to be more highly expressed in proliferative tumors simply because they contain more cycling cells. The data in this report provide a comprehensive catalog of cell cycle regulated genes that can serve as a starting point for functional discovery. The full dataset is available at http://genome-www.stanford.edu/Human-CellCycle/HeLa/.

Cell Cycle↗
PubMed1998

Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.

We sought to create a comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle. To this end, we used DNA microarrays and samples from yeast cultures synchronized by three independent methods: alpha factor arrest, elutriation, and arrest of a cdc15 temperature-sensitive mutant. Using periodicity and correlation algorithms, we identified 800 genes that meet an objective minimum criterion for cell cycle regulation. In separate experiments, designed to examine the effects of inducing either the G1 cyclin Cln3p or the B-type cyclin Clb2p, we found that the mRNA levels of more than half of these 800 genes respond to one or both of these cyclins. Furthermore, we analyzed our set of cell cycle-regulated genes for known and new promoter elements and show that several known elements (or variations thereof) contain information predictive of cell cycle regulation. A full description and complete data sets are available at http://cellcycle-www.stanford.edu

Base Sequence↗