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PubMed2006

The role of the proteasomal ATPases and activator monoubiquitylation in regulating Gal4 binding to promoters.

Recent studies have shown that the intersection between transcription and proteins involved in the ubiquitin-proteasome pathway encompasses both proteolytic and nonproteolytic functions. Examples of the latter type include evidence that monoubiquitylation of some transcriptional activators stimulates their activity. In addition, the proteasomal ATPases are recruited to many active promoters through binding to activators and play an important, nonproteolytic role in promoter escape and elongation. In this study, we report the discovery of a new nonproteolytic activity of the proteasome (specifically the proteasomal ATPases): the active destabilization of activator-promoter complexes. This reaction depends on the presence of an activation domain and ATP. Destabilization is inhibited in vitro and in vivo if the protein is monoubiquitylated or if ubiquitin is genetically fused to the activator. The fact that monoubiquitylated activator is resistant to the "stripping" activity of the proteasomal ATPases may explain, in part, why some activators require this modification in order to function efficiently.

Adenosine Triphosphatases↗

PubMed2025

A neural network model enables worm tracking in challenging conditions and increases signal-to-noise ratio in phenotypic screens.

High-resolution posture tracking of C. elegans has applications in genetics, neuroscience, and drug screening. While classic methods can reliably track isolated worms on uniform backgrounds, they fail when worms overlap, coil, or move in complex environments. Model-based tracking and deep learning approaches have addressed these issues to an extent, but there is still significant room for improvement in tracking crawling worms. Here we train a version of the DeepTangle algorithm developed for swimming worms using a combination of data derived from Tierpsy tracker and hand-annotated data for more difficult cases. DeepTangleCrawl (DTC) outperforms existing methods, reducing failure rates and producing more continuous, gap-free worm trajectories that are less likely to be interrupted by collisions between worms or self-intersecting postures (coils). We show that DTC enables the analysis of previously inaccessible behaviours and increases the signal-to-noise ratio in phenotypic screens, even for data that was specifically collected to be compatible with legacy trackers including low worm density and thin bacterial lawns. DTC broadens the applicability of high-throughput worm imaging to more complex behaviours that involve worm-worm interactions and more naturalistic environments including thicker bacterial lawns.

Caenorhabditis elegans↗

PubMed2000

Replication and recombination intersect.

A bacterial housekeeping function, which requires both recombination and replication enzymes, has been identified that re-establishes inactivated replication forks under normal growth conditions. Some long-tract gene-conversion events initiated by double-strand breaks in yeast and mammalian cells can be attributed to recombination-directed DNA replication. Double-strand break repair in yeast has been shown to require both leading- and lagging-strand DNA synthesis. These observations suggest that the recombination and replication machinery cooperate to maintain genomic integrity.

Animals↗

PubMed1994

Interactions among regulators of RNA abundance characterized using RNA fingerprinting by arbitrarily primed PCR.

Using RNA fingerprinting by arbitrarily primed PCR it is possible to infer convergent transcript regulatory pathways from the coordinate behavior of subsets of anonymous transcripts without cloning any genes. The number of transcripts in each response category can be estimated. The same may be true for differential display. We demonstrate these claims by treating a cell line with two known modulators of RNA abundance, transforming growth factor-beta (TGF beta) and cycloheximide (CX), used together and alone. The responses of over 1700 anonymous transcripts were monitored under these three conditions and in an untreated control. Eight of the twenty-seven [3(3)] possible transcript response categories were observed among 86 differentially expressed transcripts. For example, CX stabilizes or induces as many as 2.7% of transcripts of which about one third do not accumulate when TGF beta is also present. This intersection may reflect CX stabilization or induction of an important class of RNAs that otherwise usually have short half-lives. We predict that RNAs in this class constitute the majority of transcripts targeted for rapid down regulation in response to TGF beta and perhaps most other natural transcriptional modulators.

Animals↗

PubMed1991

Expression of cDNA sequences encoding mature and precursor forms of human dihydrolipoamide dehydrogenase in Escherichia coli. Differences in kinetic mechanisms.

The cDNA sequences encoding mature and precursor forms of human dihydrolipoamide dehydrogenase (E3) were expressed in Escherichia coli using a lambda PL promoter-driven prokaryotic expression vector. The expressed proteins in total cell extracts were identified by Western blot analysis using anti-pig heart E3 antibody and also by measurement of E3 activity. Most of the expressed human E3 polypeptides (five bands) were found in the insoluble pellet while primarily full-length mature E3 was found in the soluble fraction. About 2% of the total soluble protein was mature human E3 when expressed in wild type E. coli AR120. Since wild type E. coli has its own endogenous E3 activity, the expression of human E3 was performed in a pyruvate dehydrogenase complex-deficient strain of E. coli, JRG1342. The expressed recombinant human E3s in JRG1342 were purified to near homogeneity. The amino-terminal amino acid sequence analysis revealed that the recombinant mature E3 had an expected sequence while the recombinant precursor E3 lost 19 amino acid residues of its 35-amino acid leader sequence presumably due to a proteolytic cleavage. The recombinant mature E3 displayed comparable kinetic properties to those reported for highly purified mammalian E3s. The truncated precursor E3 showed about half of the mature E3 activity. The double-reciprocal plot for the mature E3 in the direction of NAD+ reduction showed parallel lines (ping-pong mechanism) while that for the truncated precursor E3 displayed intersecting lines (sequential mechanism). In the direction of NADH oxidation, the kinetic mechanisms of both E3s were apparently a ping-pong mechanism. These kinetic results showed that the partial 16-amino acid extension in the leader sequence changed the kinetic mechanism of human E3 so that it resembled that of glutathione reductase.

Amino Acid Sequence↗

PubMed2004

Nutritional modulation of the cell cycle and breast cancer.

In the USA, breast cancer accounts for approximately 30% of all cancers diagnosed in women and is the second leading cause of cancer death in women. An understanding of the molecular genetic events governing breast cancer lead to both prevention and intervention strategies in an attempt to reduce mortality and morbidity from breast cancer. The last three decades of medical research examining the molecular pathogenesis of cancers have provided compelling evidence for the universal disruption of the cell cycle in human tumors. The importance of cell cycle control in human cancer was recognized by the recent award of the Nobel Prize to Drs Nurse and Hartwell for their discovery of the cyclins. More recent studies have demonstrated a critical interface between hormonal signaling and the cell cycle. In parallel, epidemiological studies have identified as being associated with breast cancer important dietary and environmental components that regulate hormonal signaling. This review describes the intersection of these two fields of study, which together imply a role for dietary prevention and intervention in human breast cancer perhaps through altering cell cycle components.

Androgens↗

PubMed2000

[Analysis of genealogical structure of populations. II. The use od numerical pedigrees for calculation of inbreeding coefficient].

A method for calculation of inbreeding coefficient F in a numerical pedigree with no reference to its graphic representation is suggested. For calculation of F, a formula that does not take into account inbreeding coefficients of common ancestors and admits intersections in a loop is used. An advantage of this method is that it automatically finds all loops formed by paths to common ancestors. Detecting these loops via their tracing in a graphic pedigree with intersecting lines of descent creates a possibility of errors. A criterion of existence of at least one common link for two numerical paths is presented. It enables one to exclude pairs of paths to common ancestors that do not form loops. The methods considered for computing F in a given pedigree give exact values of the inbreeding coefficient for autosomal and sex-linked loci and generalize the known approximate approaches. The methods are illustrated by examples.

Female↗

PubMed2006

Transcriptional regulation of perinatal lung maturation.

Respiration at birth depends on maturation changes in lung tissue architecture, cell differentiation, and gene expression. At the transcriptional level, maturation is controlled by the actions of a group of transcription factors mediating gene expression in the lung. A network of transcription factors regulates gene expression in the respiratory epithelium, which then influences cell maturation throughout the lung. Glucocorticoids (via the glucocorticoid receptor), acting primarily in the pulmonary mesenchyme, influence maturation in the respiratory epithelium. Elucidation of the intersecting pathways controlling perinatal lung function may provide opportunities to induce pulmonary maturation in preterm infants at risk for respiratory distress syndrome before birth, and will help identify genes and processes important for various aspects of lung function.

Animals↗

PubMed2001

Epidemiology and natural history of atrial fibrillation: clinical implications.

With a substantial impact on morbidity and mortality, the growing "epidemic" of atrial fibrillation (AF) intersects with a number of conditions, including aging, thromboembolism, hemorrhage, hypertension and left ventricular dysfunction. Currently, the epidemiology and natural history of AF govern all aspects of its clinical management. The ongoing global investigative efforts toward understanding AF are also driven by epidemiologic findings. New developments, by affecting the natural history of the disease, could eventually alter the nature of decision making in patients with AF. The crucial issue of rate versus rhythm control awaits completion of the AF Follow-up Investigation of Rhythm Management trial. The processes of electrical and structural remodeling that perpetuate AF appear to be reversible. In the era of functional genomics, the molecular basis of this ubiquitous arrhythmia is in the process of being defined. Unraveling the molecular genetics of AF might provide new insights into the structural and electrical phenotypes resulting from genetic mutations and, as such, new approaches to treatment of this arrhythmia at the ion channel and cellular levels. Thus, current adverse trends are superimposed on a background of a rapidly developing knowledge base and potentially exciting new therapeutic options. Consequently, an understanding of the epidemiology and natural history of AF is crucial to the future allocation of resources and the utilization of an expanding range of therapies aimed at reducing the impact of this disease on a changing patient population.

Atrial Fibrillation↗

PubMed2000

Molecules and morphology in concert: tests of some hypotheses in arctic Potentilla (Rosaceae).

We developed a combined molecular and morphological approach to unravel complex variation at low taxonomic levels, exemplified by some arctic members of Potentilla. Twenty-one populations from Svalbard were analyzed for random amplified polymorphic DNAs (RAPDs) and 64 morphological characters to test the hypotheses that (1) the P. nivea complex (section Niveae) consists of three taxa (P. chamissonis, P. insularis, and P. nivea), (2) three "eco-morphotypes" in P. pulchella (section Multifidae) should be considered different taxa, and (3) P. insularis originated as an intersectional hybrid (Niveae × Multifidae). Twenty-two RAPD multilocus phenotypes were observed in the 136 plants analyzed based on 35 markers. Three fairly distinct groups of RAPD phenotypes were identified in the P. nivea complex based on multivariate analyses and an analysis of molecular variance (AMOVA; 77.6% among-group variation). The variation within the P. nivea complex was more or less continuous in multivariate analyses of the morphological data. We identified, however, several individual morphological characters that separated unambiguously among the three groups of RAPD phenotypes, revealing that these groups correspond to the previously hypothesized taxa. Many identical RAPD multilocus phenotypes were observed in the "eco-morphotypes" of P. pulchella, suggesting that its conspicuous morphological variation is caused by plasticity or by genetic variation at a small number of loci. The hypothesis of the hybrid origin of P. insularis was not supported by the RAPD data. Overall, very little RAPD variation was observed within populations of the four taxa (2.1-16.7% in AMOVA analyses; average genotypic diversity, D, was 0.10-0.30). We conclude that detailed, concerted analysis of molecules and morphology is a powerful tool in low-level taxonomy.

Journal Article↗

PubMed1982

The mathematics of mosaic analysis III. Analysis of structures with extent in two dimensions.

This paper derives formulae for the use of mosaic analysis to determine the sizes, shapes and locations of structures that are not points but are extended areas on the blastoderm. We consider a male patch of any convex shape and size and a structure of any convex shape and size. The probability that these two intersect in a set of mosaics is simply one-quarter the product of their perimeters. From this perimeter formula we derive equations relating the frequency of mosaicism of a structure to its size and we derive a formula for the mapping of lethal foci. We then develop a method to locate the borders of a focus that covers an area on the blastoderm.

Animals↗

PubMed1983

[Autoradiographic analysis of transcription in sympathetic neurocyte nuclei following axonal injury].

One of the trunks of the inner carotid nerve of the cranial cervical sympathetic ganglion of the rabbit was intersected. The level of transcription in nervous cells at the height of the development of the morphological signs of the axonal reaction was determined by autoradiography. The method is based on the demonstration of the activity of RNA polymerases. Injury of the process causes a considerable decrease in the total and nucleoplasmic labeling of the nuclei of retrogradely changed neurocytes. The level of nucleolar labeling was not changed.

Animals↗

PubMed2004

Bone-specific transcription factor Runx2 interacts with the 1alpha,25-dihydroxyvitamin D3 receptor to up-regulate rat osteocalcin gene expression in osteoblastic cells.

Bone-specific transcription of the osteocalcin (OC) gene is regulated principally by the Runx2 transcription factor and is further stimulated in response to 1alpha,25-dihydroxyvitamin D3 via its specific receptor (VDR). The rat OC gene promoter contains three recognition sites for Runx2 (sites A, B, and C). Mutation of sites A and B, which flank the 1alpha,25-dihydroxyvitamin D3-responsive element (VDRE), abolishes 1alpha,25-dihydroxyvitamin D3-dependent enhancement of OC transcription, indicating a tight functional relationship between the VDR and Runx2 factors. In contrast to most of the members of the nuclear receptor family, VDR possesses a very short N-terminal A/B domain, which has led to the suggestion that its N-terminal region does not contribute to transcriptional enhancement. Here, we have combined transient-overexpression, coimmunoprecipitation, in situ colocalization, chromatin immunoprecipitation, and glutathione S-transferase pull-down analyses to demonstrate that in osteoblastic cells expressing OC, VDR interacts directly with Runx2 bound to site B, which is located immediately adjacent to the VDRE. This interaction contributes significantly to 1alpha,25-dihydroxyvitamin D3-dependent enhancement of the OC promoter and requires a region located C terminal to the runt homology DNA binding domain of Runx2 and the N-terminal region of VDR. Together, our results indicate that Runx2 plays a key role in the 1alpha,25-dihydroxyvitamin D3-dependent stimulation of the OC promoter in osteoblastic cells by further stabilizing the interaction of the VDR with the VDRE. These studies demonstrate a novel mechanism for combinatorial control of bone tissue-specific gene expression. This mechanism involves the intersection of two major pathways: Runx2, a "master" transcriptional regulator of osteoblast differentiation, and 1alpha,25-dihydroxyvitamin D3, a hormone that promotes expression of genes associated with these terminally differentiated bone cells.

Animals↗

PubMed2006

The mammary bud as a skin appendage: unique and shared aspects of development.

Like other skin appendages, the embryonic mammary gland develops via extensive epithelial-mesenchymal interactions. Early stages in embryonic mammary development strikingly resemble analogous steps in the development of hair follicles and teeth. In each case the first morphological sign of development is a localized thickening in the surface epithelium that subsequently invaginates to form a mammary, hair follicle or tooth bud. Similar sets of intersecting signaling pathways are involved in patterning the mammary, hair follicle and dental epithelium, directing placode formation, and controlling bud invagination. Despite these similarities, subsequent events in the formation of these appendages are diverse. The mammary bud extends to form a sprout that begins to branch upon contact with the mammary fat pad. Hair follicles also extend into the underlying mesenchyme, but instead of branching, hair follicle epithelium folds around a condensation of dermal cells. In contrast, teeth undergo a more complex folding morphogenesis. Here, we review what is known of the molecular and cellular mechanisms controlling early steps in the development of these organs, attempt to unravel both common themes and unique aspects that can begin to explain the diversity of appendage formation, and discuss human genetic diseases that affect appendage morphogenesis.

Animals↗

PubMed1997

Novel genes involved in endosomal traffic in yeast revealed by suppression of a targeting-defective plasma membrane ATPase mutant.

A novel genetic selection was used to identify genes regulating traffic in the yeast endosomal system. We took advantage of a temperature-sensitive mutant in PMA1, encoding the plasma membrane ATPase, in which newly synthesized Pma1 is mislocalized to the vacuole via the endosome. Diversion of mutant Pma1 from vacuolar delivery and rerouting to the plasma membrane is a major mechanism of suppression of pma1(ts). 16 independent suppressor of pma1 (sop) mutants were isolated. Identification of the corresponding genes reveals eight that are identical with VPS genes required for delivery of newly synthesized vacuolar proteins. A second group of SOP genes participates in vacuolar delivery of mutant Pma1 but is not essential for delivery of the vacuolar protease carboxypeptidase Y. Because the biosynthetic pathway to the vacuole intersects with the endocytic pathway, internalization of a bulk membrane endocytic marker FM 4-64 was assayed in the sop mutants. By this means, defective endosome-to-vacuole trafficking was revealed in a subset of sop mutants. Another subset of sop mutants displays perturbed trafficking between endosome and Golgi: impaired pro-alpha factor processing in these strains was found to be due to defective recycling of the trans-Golgi protease Kex2. One of these strains defective in Kex2 trafficking carries a mutation in SOP2, encoding a homologue of mammalian synaptojanin (implicated in synaptic vesicle endocytosis and recycling). Thus, cell surface delivery of mutant Pma1 can occur as a consequence of disturbances at several different sites in the endosomal system.

Biological Transport↗

PubMed1998

Rheumatoid arthritis in the Pima Indians: the intersection of epidemiologic, demographic, and genealogic data.

OBJECTIVE: To describe the clinical features and familial distribution of rheumatoid arthritis (RA) in the Pima Indians. METHODS: From 1965 through 1990, all cases of RA as defined by the American College of Rheumatology (formerly, the American Rheumatism Association) 1987 criteria or all cases of seropositive, erosive disease as defined by the Rome criteria were identified in individuals who were age 20 years and older and were of 50% or more Pima/Tohono-O'odham heritage. Radiographs were reviewed by 2 musculoskeletal radiologists who were blinded to case status. Kinship coefficients were used to evaluate familial aggregation. RESULTS: Eighty-eight RA cases were identified from this population-based sample. Over 66% of the cases had seropositive disease, over 60% had erosive disease, and over 40% had subcutaneous nodules. Of the 88 RA cases, 40 were members of families with more than 1 RA case. The remainder were simplex cases. CONCLUSION: In this population, clinical markers of severe RA were present in a majority of cases. The presence of familial aggregation for RA in the Pima Indians suggests underlying genetic factors in disease pathogenesis.

Adult↗

PubMed1991

HLA class I-restricted human cytotoxic T cells recognize endogenously synthesized hepatitis B virus nucleocapsid antigen.

Knowledge of the immune effector mechanisms responsible for clearance of hepatitis B virus (HBV)-infected cells has been severely limited by the absence of reproducible systems to selectively expand and to characterize HBV-specific cytotoxic T lymphocytes (CTLs) in the peripheral blood of patients with viral hepatitis. By using a strategy involving sequential stimulation with HBV nucleocapsid synthetic peptides followed by autologous, or HLA class I-matched, HBV nucleocapsid transfectants, we now report the existence of CTLs able to lyse target cells that express endogenously synthesized HBV nucleocapsid antigen in the peripheral blood of patients with acute viral hepatitis B. The CTL response is HLA-A2 restricted, mediated by CD8-positive T cells, and specific for a single epitope, located between amino acid residues 11 and 27 of HBV core protein; these residues are shared with the secretable precore-derived hepatitis B e antigen. Equivalent lysis of target cells that express each of these proteins suggests that their intracellular trafficking pathways may intersect. The current report provides definitive evidence that HLA class I-restricted, CD8-positive CTLs that recognize endogenously synthesized HBV nucleocapsid antigen are induced during acute HBV infection in humans and establishes a strategy that should permit a detailed analysis of the role played by HBV-specific CTLs in the immunopathogenesis of viral hepatitis.

B-Lymphocytes↗

PubMed2006

Sungear: interactive visualization and functional analysis of genomic datasets.

UNLABELLED: Sungear is a software system that supports a rapid, visually interactive and biologist-driven comparison of large datasets. The datasets can come from microarray experiments (e.g. genes induced in each experiment), from comparative genomics (e.g. genes present in each genome) or even from non-biological applications (e.g. demographics or baseball statistics). Sungear represents multiple datasets as vertices in a polygon. Each possible intersection among the sets is represented as a circle inside the polygon. The position of the circle is determined by the position of the vertices represented in the intersection and the area of the circle is determined by the number of elements in the intersection. Sungear shows which Gene Ontology terms are over-represented in a subset of circles or anchors. The intuitive Sungear interface has enabled biologists to determine quickly which dataset or groups of datasets play a role in a biological function of interest. AVAILABILITY: A live online version of Sungear can be found at http://virtualplant-prod.bio.nyu.edu/cgi-bin/sungear/index.cgi

Algorithms↗