Life Sciences Commons^™

High Variance In Reproductive Success Generates A False Signature Of A Genetic Bottleneck In Populations Of Constant Size: A Simulation Study, Sean M. Hoban, Massimo Mezzavilla, Oscar E. Gaggiotti, Andrea Benazzo, Cock Van Oosterhout, Giorgio Bertorelle

Faculty Publications and Other Works -- General Biology

Background

Demographic bottlenecks can severely reduce the genetic variation of a population or a species. Establishing whether low genetic variation is caused by a bottleneck or a constantly low effective number of individuals is important to understand a species’ ecology and evolution, and it has implications for conservation management. Recent studies have evaluated the power of several statistical methods developed to identify bottlenecks. However, the false positive rate, i.e. the rate with which a bottleneck signal is misidentified in demographically stable populations, has received little attention. We analyse this type of error (type I) in forward computer simulations of stable …

Cellular And Population Plasticity Of Helper Cd4(+) T Cell Responses, G Magombedze, P B. Reddy, S Eda, V V. Ganusov

Faculty Publications and Other Works -- General Biology

Vertebrates are constantly exposed to pathogens, and the adaptive immunity has most likely evolved to control and clear such infectious agents. CD4(+) T cells are the major players in the adaptive immune response to pathogens. Following recognition of pathogen-derived antigens naïve CD4(+) T cells differentiate into effectors which then control pathogen replication either directly by killing pathogen-infected cells or by assisting with generation of cytotoxic T lymphocytes (CTLs) or pathogen-specific antibodies. Pathogen-specific effector CD4(+) T cells are highly heterogeneous in terms of cytokines they produce. Three major subtypes of effector CD4(+) T cells have been identified: T-helper 1 (Th1) cells …

Dynamical Basis For Drug Resistance Of Hiv-1 Protease, Yi Mao

Faculty Publications and Other Works -- General Biology

Background

Protease inhibitors designed to bind to protease have become major anti-AIDS drugs. Unfortunately, the emergence of viral mutations severely limits the long-term efficiency of the inhibitors. The resistance mechanism of these diversely located mutations remains unclear.

Results

Here I use an elastic network model to probe the connection between the global dynamics of HIV-1 protease and the structural distribution of drug-resistance mutations. The models for study are the crystal structures of unbounded and bound (with the substrate and nine FDA approved inhibitors) forms of HIV-1 protease. Coarse-grained modeling uncovers two groups that couple either with the active site or …

Prodigal: Prokaryotic Gene Recognition And Translation Initiation Site Identification, Doug Hyatt, Gwo-Liang Chen, Philip F. Locascio, Miriam L. Land, Frank W. Larimer, Loren J. Hauser

Faculty Publications and Other Works -- General Biology

Abstract

Background

The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals.

Results

With our years of experience in manually curating genomes for the Joint Genome Institute, we developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm). With Prodigal, we focused specifically on the three goals of improved gene structure prediction, improved translation …

Using A Literature-Based Nmf Model For Discovering Gene Functional Relationships, Elina Tjioe, Michael W. Berry, Ramin Homayouni, Kevin Heinrich

Faculty Publications and Other Works -- General Biology

No abstract provided.

Differential Transferrin Expression In Placentae From Normal And Abnormal Pregnancies: A Pilot Study, Alena Kralova, Marta Svetlikova, Jindrich Madar, Zdena Ulcova-Gallova, Antonin Bukovsky, Jana Peknicova

Faculty Publications and Other Works -- General Biology

Abstract

Background

The placenta is an important site for iron metabolism in humans. It transfers iron from the mother to the fetus. One of the major iron transport proteins is transferrin, which is a blood plasma protein crucial for iron uptake. Its localization and expression may be one of the markers to distinguish placental dysfunction.

Methods

In the experimental study we used antibody preparation, mass spectrometric analysis, biochemical and immunocytochemical methods for characterization of transferrin expression on the human choriocarcinoma cell line JAR (JAR cells), placental lysates, and cryostat sections. Newly designed monoclonal antibody TRO-tf-01 to human transferrin was applied …

Hybridization Produces Novelty When The Mapping Of Form To Function Is Many To One, Nicholas F. Parnell, C Darrin Hulsey, J. Todd Streelman

Faculty Publications and Other Works -- General Biology

Background

Evolutionary biologists want to explain the origin of novel features and functions. Two recent but separate lines of research address this question. The first describes one possible outcome of hybridization, called transgressive segregation, where hybrid offspring exhibit trait distributions outside of the parental range. The second considers the explicit mapping of form to function and illustrates manifold paths to similar function (called many to one mapping, MTOM) when the relationship between the two is complex. Under this scenario, functional novelty may be a product of the number of ways to elicit a functional outcome (i.e., the degree of MTOM). …

Nfu-Enabled Fasta: Moving Bioinformatics Applications Onto Wide Area Networks, Erich J. Baker, Guan N. Lin, Huadong Liu, Ravi Kosuri

Faculty Publications and Other Works -- General Biology

Abstract

Background

Advances in Internet technologies have allowed life science researchers to reach beyond the lab-centric research paradigm to create distributed collaborations. Of the existing technologies that support distributed collaborations, there are currently none that simultaneously support data storage and computation as a shared network resource, enabling computational burden to be wholly removed from participating clients. Software using computation-enable logistical networking components of the Internet Backplane Protocol provides a suitable means to accomplish these tasks. Here, we demonstrate software that enables this approach by distributing both the FASTA algorithm and appropriate data sets within the framework of a wide area …

Statistical Tools For Transgene Copy Number Estimation Based On Real-Time Pcr, Joshua S. Yuan, Jason N Burris, Nathan R. Stewart, Ayalew Mentewab, C. Neal Stewart

Faculty Publications and Other Works -- General Biology

Background

As compared with traditional transgene copy number detection technologies such as Southern blot analysis, real-time PCR provides a fast, inexpensive and high-throughput alternative. However, the real-time PCR based transgene copy number estimation tends to be ambiguous and subjective stemming from the lack of proper statistical analysis and data quality control to render a reliable estimation of copy number with a prediction value. Despite the recent progresses in statistical analysis of real-time PCR, few publications have integrated these advancements in real-time PCR based transgene copy number determination.

Results

Three experimental designs and four data quality control integrated statistical models are …

Modeling Sage Tag Formation And Its Effects On Data Interpretation Within A Bayesian Framework, Michael A. Gilchrist, Hong Qin, Russell Zaretzki

Faculty Publications and Other Works -- General Biology

Abstract

Background

Serial Analysis of Gene Expression (SAGE) is a high-throughput method for inferring mRNA expression levels from the experimentally generated sequence based tags. Standard analyses of SAGE data, however, ignore the fact that the probability of generating an observable tag varies across genes and between experiments. As a consequence, these analyses result in biased estimators and posterior probability intervals for gene expression levels in the transcriptome.

Results

Using the yeast Saccharomyces cerevisiae as an example, we introduce a new Bayesian method of data analysis which is based on a model of SAGE tag formation. Our approach incorporates the variation …

Genomic And Microarray Analysis Of Aromatics Degradation In Geobacter Metallireducens And Comparison To A Geobacter Isolate From A Contaminated Field Site, Jessica E. Butler, Qiang He, Kelly P. Nevin, Zhili He, Jizhong Zhou, Derek R. Lovley

Faculty Publications and Other Works -- General Biology

Background

Groundwater and subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species that couple oxidation of these compounds to reduction of Fe(III)-oxides. Geobacter metallireducens metabolizes many aromatic compounds, but the enzymes involved are not well known.

Results

The complete G. metallireducens genome contained a 300 kb island predicted to encode enzymes for the degradation of phenol, p-cresol, 4-hydroxybenzaldehyde, 4-hydroxybenzoate, benzyl alcohol, benzaldehyde, and benzoate. Toluene degradation genes were encoded in a separate region. None of these genes was found in closely related species that cannot degrade aromatic compounds. Abundant transposons and phage-like genes in …

Distinct Phospholipase A2 Enzymes Regulate Prostaglandin E2 And F2alpha Production By Bovine Endometrial Epithelial Cells, Patricia K. Tithof, Mary P. Roberts, Wei Guan, Mona Elgayyar, James D. Godkin

Faculty Publications and Other Works -- General Biology

Background

The rate-limiting step in prostaglandin (PG) biosynthesis is catalyzed by phospholipase A2 (PLA2) enzymes which hydrolyze arachidonic acid from membrane phospholipids. Despite their importance in uterine PG production, little is known concerning the specific PLA2 enzymes that regulate arachidonic acid liberation in the uterine endometrium. The objectives of this study were to evaluate the expression and activities of calcium-independent Group VI and Group IVC PLA2 (PLA2G6 and PLA2G4C) and calcium-dependent Group IVA PLA2 (PLA2G4A) enzymes in the regulation of bovine uterine endometrial epithelial cell PG production.

Methods

Bovine endometrial epithelial cells in culture were treated with oxytocin, interferon-tau and …

On The Functions Of The H Subunit Of Eukaryotic Initiation Factor 3 In Late Stages Of Translation Initiation, Byung-Hoon Kim, Xue Cai, Justin N. Vaughn, Albrecht G. Von Arnim

Faculty Publications and Other Works -- General Biology

Background

The eukaryotic translation initiation factor 3 (eIF3) has multiple roles during the initiation of translation of cytoplasmic mRNAs. How individual subunits of eIF3 contribute to the translation of specific mRNAs remains poorly understood, however. This is true in particular for those subunits that are not conserved in budding yeast, such as eIF3h.

Results

Working with stable reporter transgenes in Arabidopsis thaliana mutants, it was demonstrated that the h subunit of eIF3 contributes to the efficient translation initiation of mRNAs harboring upstream open reading frames (uORFs) in their 5' leader sequence. uORFs, which can function as devices for translational regulation, …

Rna:Protein Ratio Of The Unicellular Organism As A Characteristic Of Phosphorous And Nitrogen Stoichiometry And Of The Cellular Requirement Of Ribosomes For Protein Synthesis, Tatiana V. Karpinets, Duncan J. Greenwood, Carl E. Sams, John T. Ammons

Faculty Publications and Other Works -- General Biology

Background

Mean phosphorous:nitrogen (P:N) ratios and relationships of P:N ratios with the growth rate of organisms indicate a surprising similarity among and within microbial species, plants, and insect herbivores. To reveal the cellular mechanisms underling this similarity, the macromolecular composition of seven microorganisms and the effect of specific growth rate (SGR) on RNA:protein ratio, the number of ribosomes, and peptide elongation rate (PER) were analyzed under different conditions of exponential growth.

Results

It was found that P:N ratios calculated from RNA and protein contents in these particular organisms were in the same range as the mean ratios reported for diverse …

A Statistical Investigation Of Normal Regional Intra-Subject Heterogeneity Of Brain Metabolism And Perfusion By F-18 Fdg And O-15 H2o Pet Imaging, Ching-Yee O. Wong, Joseph Thie, Marianne Gaskill, Richard Ponto, Jack Hill, Hai-Yan Tian, Helena Balon, Dafang Wu, Darlene Fink-Bennett, Conrad Nagle

Faculty Publications and Other Works -- General Biology

Abstract

Background

The definite evaluation of the regional cerebral heterogeneity using perfusion and metabolism by a single modality of PET imaging has not been well addressed. Thus a statistical analysis of voxel variables from identical brain regions on metabolic and perfusion PET images was carried out to determine characteristics of the regional heterogeneity of F-18 FDG and O-15 H₂O cerebral uptake in normal subjects.

Methods

Fourteen normal subjects with normal CT and/or MRI and physical examination including MMSE were scanned by both F-18 FDG and O-15 H₂O PET within same day with head-holder and facemask. The …

Statistical Analysis Of Real-Time Pcr Data, Joshua S. Yuan, Ann Reed, Feng Chen, C. Neal Stewart

Faculty Publications and Other Works -- General Biology

Background

Even though real-time PCR has been broadly applied in biomedical sciences, data processing procedures for the analysis of quantitative real-time PCR are still lacking; specifically in the realm of appropriate statistical treatment. Confidence interval and statistical significance considerations are not explicit in many of the current data analysis approaches. Based on the standard curve method and other useful data analysis methods, we present and compare four statistical approaches and models for the analysis of real-time PCR data.

Results

In the first approach, a multiple regression analysis model was developed to derive ΔΔCt from estimation of interaction of gene and …

Efficient Gene-Driven Germ-Line Point Mutagenesis Of C57bl/6j Mice, Edward J. Michaud, Cymbeline T. Culiat, Mitchell L. Klebig, Paul E. Barker, Kt Cain, Debra J. Carpenter, Lori L. Easter, Carmen M. Foster, Alysyn W. Gardner, Zy Guo, Kay J. Houser, Lori A. Hughes, Marilyn K. Kerley, Zhaowei Liu, Robert E. Olszewski, Irina Pinn, Ginger D. Shaw, Sarah G. Shinpock, Ann M. Wymore, Eugene M. Rinchik, Dabney K. Johnson

Faculty Publications and Other Works -- General Biology

Background

Analysis of an allelic series of point mutations in a gene, generated by N-ethyl-N-nitrosourea (ENU) mutagenesis, is a valuable method for discovering the full scope of its biological function. Here we present an efficient gene-driven approach for identifying ENU-induced point mutations in any gene in C57BL/6J mice. The advantage of such an approach is that it allows one to select any gene of interest in the mouse genome and to go directly from DNA sequence to mutant mice.

Results

We produced the Cryopreserved Mutant Mouse Bank (CMMB), which is an archive of DNA, cDNA, tissues, and …

Oogenesis In Cultures Derived From Adult Human Ovaries, Antonin Bukovsky, Marta Svetlikova, Michael R. Caudle

Faculty Publications and Other Works -- General Biology

Ten years ago, we reported that in adult human females the ovarian surface epithelium (OSE) is a source of germ cells. Recently, we also demonstrated that new primary follicles are formed by assembly of oocytes with nests of primitive granulosa cells in the ovarian cortex. The components of the new primary follicles, primitive granulosa and germ cells, differentiated sequentially from the OSE, which arises from cytokeratin positive mesenchymal progenitor cells residing in the ovarian tunica albuginea. In the present study, we investigated the possibility that the oocytes and granulosa cells may differentiate in cultures derived from adult human ovaries. Cells …

An Svd-Based Comparison Of Nine Whole Eukaryotic Genomes Supports A Coelomate Rather Than Ecdysozoan Lineage, Gary W. Stuart, Michael W. Berry

Faculty Publications and Other Works -- General Biology

Background

Eukaryotic whole genome sequences are accumulating at an impressive rate. Effective methods for comparing multiple whole eukaryotic genomes on a large scale are needed. Most attempted solutions involve the production of large scale alignments, and many of these require a high stringency pre-screen for putative orthologs in order to reduce the effective size of the dataset and provide a reasonably high but unknown fraction of correctly aligned homologous sites for comparison. As an alternative, highly efficient methods that do not require the pre-alignment of operationally defined orthologs are also being explored.

Results

A non-alignment method based on the Singular …

Reproductive Biology And Endocrinology – First Year Anniversary, Antonin Bukovsky

Faculty Publications and Other Works -- General Biology

First paragraph (this article has no abstract)

One year after launch, Reproductive Biology and Endocrinology has been evaluated as one of the most successful BioMed Central Independent journals. Out of 185 submitted manuscripts, 146 articles have been published to date; 77 are Research articles, three Debates, two Editorials, two Hypotheses and 62 Reviews. An Open Access policy attracts both the authors and the readers.

Origin Of Germ Cells And Formation Of New Primary Follicles In Adult Human Ovaries, Antonin Bukovsky, Michael R. Caudle, Marta Svetlikova, Nirmala B. Upadhyaya

Faculty Publications and Other Works -- General Biology

Recent reports indicate that functional mouse oocytes and sperm can be derived in vitro from somatic cell lines. We hypothesize that in adult human ovaries, mesenchymal cells in the tunica albuginea (TA) are bipotent progenitors with a commitment for both primitive granulosa and germ cells. We investigated ovaries of twelve adult women (mean age 32.8 ± 4.1 SD, range 27–38 years) by single, double, and triple color immunohistochemistry. We show that cytokeratin (CK)+ mesenchymal cells in ovarian TA differentiate into surface epithelium (SE) cells by a mesenchymal-epithelial transition. Segments of SE directly associated with ovarian cortex are overgrown by TA, …

Publish In Reproductive Biology And Endocrinology – Article Processing Charges Are Only Paid By Those Who Can Afford It, Antonin Bukovsky, Fuller W. Bazer

Faculty Publications and Other Works -- General Biology

Editorial

Electronic journals are the basis of a world of purely electronic scientific communication. Just imagine, no more bookshelves and mountains of disorganized paperwork, no more late nights organizing and searching for articles of interest. For most active research-oriented students and scientists this is already a reality, or will be in the near future.

Although most 'top ranked' traditional journals now offer web access to recent publications, and to less or more of their archives, not everyone has the luxury of access through their university, or has his/her subscription paid for, or can afford to pay US $30–35 for an …

Multiple Luteinizing Hormone Receptor (Lhr) Protein Variants, Interspecies Reactivity Of Anti-Lhr Mab Clone 3b5, Subcellular Localization Of Lhr In Human Placenta, Pelvic Floor And Brain, And Possible Role For Lhr In The Development Of Abnormal Pregnancy, Pelvic Floor Disorders And Alzheimer's Disease, Antonin Bukovsky, Korakod Indrapichate, Hiroshi Fujiwara, Maria Cekanova, Maria E. Ayala, Roberto Dominguez, Michael R. Caudle, Jay Wimalsena, Robert F. Elder, Pleas Copas, James S. Foster, Romaine I. Fernando, Donald C. Henley, Nirmala B. Upadhyaya

Faculty Publications and Other Works -- General Biology

Distinct luteinizing hormone receptor (LHR) protein variants exist due to the posttranslational modifications. Besides ovaries, LHR immunoreactivity (LHRI) was also found in other tissues, such as the brain, fallopian tube, endometrium, trophoblast and resident tissue macrophages. The 3B5 mouse monoclonal antibody was raised against purified rat LHR. In rat, porcine and human ovaries, the 3B5 identified six distinct LHR bands migrating at ~92, 80, 68, 59, 52 and 48 kDa. Characteristic LHRI was detected in rat, human and porcine corpora lutea. During cellular differentiation, subcellular LHR distribution changed from none to granular cytoplasmic, perinuclear, surface, nuclear and no staining. There …

Placental Expression Of Estrogen Receptor Beta And Its Hormone Binding Variant – Comparison With Estrogen Receptor Alpha And A Role For Estrogen Receptors In Asymmetric Division And Differentiation Of Estrogen-Dependent Cells, Antonin Bukovsky, Michael R. Caudle, Maria Cekanova, Romaine I. Fernando, Jay Wimalasena, James S. Foster, Donald C. Henley, Robert F. Elder

Faculty Publications and Other Works -- General Biology

During human pregnancy, the production of 17-beta-estradiol (E2) rises steadily to eighty fold at term, and placenta has been found to specifically bind estrogens. We have recently demonstrated the expression of estrogen receptor alpha (ER-alpha) protein in human placenta and its localization in villous cytotrophoblast (CT), vascular pericytes, and amniotic fibroblasts. In vitro, E2 stimulated development of large syncytiotrophoblast (ST) aggregates. In the present study we utilized ER-beta affinity purified polyclonal (N19:sc6820) and ER-alpha monoclonal (clone h-151) antibodies. Western blot analysis revealed a single ~52 kDa ER-beta band in chorionic villi (CV) protein extracts. In CV, strong cytoplasmic ER-beta immunoreactivity …

Expression And Localization Of Estrogen Receptor-Alpha Protein In Normal And Abnormal Term Placentae And Stimulation Of Trophoblast Differentiation By Estradiol, Antonin Bukovsky, Maria Cekanova, Michael R. Caudle, Jay Wimalasena, James S. Foster, Donald C. Henley, Robert F. Elder

Faculty Publications and Other Works -- General Biology

Estrogens play an important role in the regulation of placental function, and 17-beta-estradiol (E2) production rises eighty fold during human pregnancy. Although term placenta has been found to specifically bind estrogens, cellular localization of estrogen receptor alpha (ER-alpha) in trophoblast remains unclear. We used western blot analysis and immunohistochemistry with h-151 and ID5 monoclonal antibodies to determine the expression and cellular localization of ER-alpha protein in human placentae and cultured trophoblast cells. Western blot analysis revealed a ~65 kDa ER-alpha band in MCF-7 breast carcinoma cells (positive control). A similar band was detected in five normal term placentae exhibiting strong …

Fine Mapping In Tomato Using Microsynteny With The Arabidopsis Genome: The Diageotropica (Dgt) Locus, Kwangchul Oh, Kristine Hardeman, Maria G. Ivanchenko, Mary Ellard-Ivey, Andreas Nebenfüh, Tj White, Terri L. Lomax

Faculty Publications and Other Works -- General Biology

Background

The Arabidopsis thaliana genome sequence provides a catalog of reference genes applicable to comparative microsynteny analysis of other species, facilitating map-based cloning in economically important crops. We have applied such an analysis to the tomato expressed sequence tag (EST) database to expedite high-resolution mapping of the Diageotropica (Dgt) gene within the distal end of chromosome 1 in tomato (Lycopersicon esculentum).

Results

A BLAST search of the Arabidopsis database with nucleotide sequences of markers that flank the tomato dgt locus revealed regions of microsynteny between the distal end of chromosome 1 in tomato, two regions of …

Association Of Mesenchymal Cells And Immunoglobulins With Differentiating Epithelial Cells, Antonin Bukovsky, Michael R. Caudle, Jeffrey A. Keenan, Nirmala B. Upadhyaya, Stuart E. Van Meter, Jay Wimalsena, Robert F. Elder

Faculty Publications and Other Works -- General Biology

Background

Mesenchymal-epithelial interactions play an important role in the physiology and pathology of epithelial tissues. Mesenchymal cells either associate with epithelium basement membrane [pericytes and perivascular monocyte-derived cells (MDC)] or reside within epithelium (MDC and T cells). Although intraepithelial mesenchymal cells were suggested to contribute to the epithelium physiology, their association with particular steps in differentiation of epithelial cells, interactions among themselves, and their fate remain unclear. We studied epitopes of mesenchymal cells and their products (immunoglobulins) in stratified epithelium of uterine ectocervix, which is one of the prototypes of complete cellular differentiation from stem into the aged cells.

Results …