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Results for “functional inference”

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PubMed2000

Conservation among HSP60 sequences in relation to structure, function, and evolution.

The chaperonin HSP60 (GroEL) proteins are essential in eubacterial genomes and in eukaryotic organelles. Functional regions inferred from mutation studies and the Escherichia coli GroEL 3D crystal complexes are evaluated in a multiple alignment across 43 diverse HSP60 sequences, centering on ATP/ADP and Mg2+ binding sites, on residues interacting with substrate, on GroES contact positions, on interface regions between monomers and domains, and on residues important in allosteric conformational changes. The most evolutionary conserved residues relate to the ATP/ADP and Mg2+ binding sites. Hydrophobic residues that contribute in substrate binding are also significantly conserved. A large number of charged residues line the central cavity of the GroEL-GroES complex in the substrate-releasing conformation. These span statistically significant intra- and inter-monomer three-dimensional (3D) charge clusters that are highly conserved among sequences and presumably play an important role interacting with the substrate. Unaligned short segments between blocks of alignment are generally exposed at the outside wall of the Anfinsen cage complex. The multiple alignment reveals regions of divergence common to specific evolutionary groups. For example, rickettsial sequences diverge in the ATP/ADP binding domain and gram-positive sequences diverge in the allosteric transition domain. The evolutionary information of the multiple alignment proffers attractive sites for mutational studies.

Adenosine Triphosphate↗

PubMed2004

Does gene flow constrain adaptive divergence or vice versa? A test using ecomorphology and sexual isolation in Timema cristinae walking-sticks.

Population differentiation often reflects a balance between divergent natural selection and the opportunity for homogenizing gene flow to erode the effects of selection. However, during ecological speciation, trait divergence results in reproductive isolation and becomes a cause, rather than a consequence, of reductions in gene flow. To assess both the causes and the reproductive consequences of morphological differentiation, we examined morphological divergence and sexual isolation among 17 populations of Timema cristinae walking-sticks. Individuals from populations adapted to using Adenostoma as a host plant tended to exhibit smaller overall body size, wide heads, and short legs relative to individuals using Ceonothus as a host. However, there was also significant variation in morphology among populations within host-plant species. Mean trait values for each single population could be reliably predicted based upon host-plant used and the potential for homogenizing gene flow, inferred from the size of the neighboring population using the alternate host and mitochondrial DNA estimates of gene flow. Morphology did not influence the probability of copulation in between-population mating trials. Thus, morphological divergence is facilitated by reductions in gene flow, but does not cause reductions in gene flow via the evolution of sexual isolation. Combined with rearing data indicating that size and shape have a partial genetic basis, evidence for parallel origins of the host-associated forms, and inferences from functional morphology, these results indicate that morphological divergence in T. cristinae reflects a balance between the effects of host-specific natural selection and gene flow. Our findings illustrate how data on mating preferences can help determine the causal associations between trait divergence and levels of gene flow.

Adaptation, Biological↗

PubMed1985

On the role of microfilaments in cell-shape-mediated growth control of lens epithelial cells.

With regard to the fact that, in anchorage-dependent lens epithelial cells, DNA synthesis can be switched on and off by cell flattening and cell rounding, respectively, the state of the microfilaments has been followed by labelling actin with FL-phalloidin during cell-shape alterations. Cell flattening proved to be accompanied by both a structural organization of actin filaments into stress fibres and an enlargement of the area of the cell nucleus. Cell rounding, on the other hand, caused the microfilament bundles to disappear and the area of the nucleus to become smaller. From the time course of the inhibition of DNA synthesis by cytochalasin B, it was inferred that functionally intact microfilaments are required for the entrance of the cells into DNA synthesis but not for the maintenance of ongoing DNA synthesis. The assumption has been made that the tension, generated by microfilaments during cell spreading, will affect the state of the plasma membrane as well as the shape and the structure of the nucleus, which in turn seems to be preparatory for cells to enter the cycle.

Actins↗

PubMed2005

Transcript profiling of Eucalyptus xylem genes during tension wood formation.

Tension wood formed in response to gravitational force is a striking example of the plasticity of angiosperm wood. In this study our goal was to characterize the early changes in gene expression during tension wood formation in Eucalyptus. Using cDNA array technology, transcript profiling of 231 genes preferentially expressed in differentiating Eucalyptus xylem was followed from 6 h to 1 wk of a tension time course of artificially bent Eucalyptus trees. 196 genes were differentially regulated between control and bent trees, some exhibiting distinctive expression patterns related to changes in secondary cell wall structure and composition. For instance, expression of a cellulose synthase gene was well correlated with the appearance of the G-layers. Cluster correlation analysis revealed differential regulation of lignin biosynthetic genes and may also be used to help infer the function of unknown gene products. Eucalyptus wood transcriptome analysis during tension wood formation not only provided new clues into the transcriptional regulatory network of genes preferentially expressed in xylem, but also highlighted candidate genes responsible for the genetic and environmentally induced variation of wood quality traits.

Biomechanical Phenomena↗

PubMed2006

Stresses and strains in the medial meniscus of an ACL deficient knee under anterior loading: a finite element analysis with image-based experimental validation.

The menisci are believed to play a stabilizing role in the ACL-deficient knee, and are known to be at risk for degradation in the chronically unstable knee. Much of our understanding of this behavior is based on ex vivo experiments or clinical studies in which we must infer the function of the menisci from external measures of knee motion. More recently, studies using magnetic resonance (MR) imaging have provided more clear visualization of the motion and deformation of the menisci within the tibio-femoral articulation. In this study, we used such images to generate a finite element model of the medial compartment of an ACL-deficient knee to reproduce the meniscal position under anterior loads of 45, 76, and 107 N. Comparisons of the model predictions to boundaries digitized from images acquired in the loaded states demonstrated general agreement, with errors localized to the anterior and posterior regions of the meniscus, areas in which large shear stresses were present. Our model results suggest that further attention is needed to characterize material properties of the peripheral and horn attachments. Although overall translation of the meniscus was predicted well, the changes in curvature and distortion of the meniscus in the posterior region were not captured by the model, suggesting the need for refinement of meniscal tissue properties.

Aged↗

PubMed2004

Inferred basilar-membrane response functions for listeners with mild to moderate sensorineural hearing loss.

Psychophysical estimates of cochlear function suggest that normal-hearing listeners exhibit a compressive basilar-membrane (BM) response. Listeners with moderate to severe sensorineural hearing loss may exhibit a linearized BM response along with reduced gain, suggesting the loss of an active cochlear mechanism. This study investigated how the BM response changes with increasing hearing loss by comparing psychophysical measures of BM compression and gain for normal-hearing listeners with those for listeners who have mild to moderate sensorineural hearing loss. Data were collected from 16 normal-hearing listeners and 12 ears from 9 hearing-impaired listeners. The forward masker level required to mask a fixed low-level, 4000-Hz signal was measured as a function of the masker-signal interval using a masker frequency of either 2200 or 4000 Hz. These plots are known as temporal masking curves (TMCs). BM response functions derived from the TMCs showed a systematic reduction in gain with degree of hearing loss. Contrary to current thinking, however, no clear relationship was found between maximum compression and absolute threshold.

Adult↗

PubMed2000

Crystal structure of a gammadelta T cell receptor ligand T22: a truncated MHC-like fold.

Murine T10 and T22 are highly related nonclassical major histocompatibility complex (MHC) class Ib proteins that bind to certain gammadelta T cell receptors (TCRs) in the absence of other components. The crystal structure of T22b at 3.1 angstroms reveals similarities to MHC class I molecules, but one side of the normal peptide-binding groove is severely truncated, which allows direct access to the beta-sheet floor. Potential gammadelta TCR-binding sites can be inferred from functional mapping of T10 and T22 point mutants and allelic variants. Thus, T22 represents an unusual variant of the MHC-like fold and indicates that gammadelta and alphabeta TCRs interact differently with their respective MHC ligands.

Alleles↗

PubMed2003

Patch-clamp fluorometry recording of conformational rearrangements of ion channels.

Conformational rearrangements are commonly observed in membrane proteins and constitute the molecular mechanisms through which they contribute to signal transduction. Information on structural changes in membrane proteins has mostly been inferred from functional studies. Recently, site-specific fluorescence recordings have made it possible to directly observe such molecular events in real time within the membrane environment. Here, we describe the patch-clamp fluorometry (PCF) technique that records simultaneously the local structural changes and the functional states of ion channels in isolated cell membranes. Combined with fluorescence resonance energy transfer (FRET), the technique should shed new light on ion channel activation, regulation, and interaction with other membrane proteins.

Animals↗

PubMed1985

Isotype commitment of B cells and dissemination of the primed state after mucosal stimulation with Mycoplasma pulmonis.

Live Mycoplasma pulmonis organisms were used to examine the immune response in the bronchus-associated lymphoid tissue after primary and secondary challenge with M. pulmonis, to study the dissemination of the primed state to distal tissues (i.e., spleen, peripheral blood, and Peyer's patches), and to determine whether the chronic antigenic stimulation accompanying infection influences the isotype potential and commitment of the primed B cells recovered from the various tissues. We have shown that exposure to M. pulmonis by a variety of routes results in a generalized rise in frequency of T-dependent, antigen-sensitive B cells in all lymphoid tissues. The route of secondary exposure to M. pulmonis was found to markedly increase the frequency of M. pulmonis-specific B cells in the bronchus-associated lymphoid tissue relative to that in the Peyer's patches after intraduodenal but not intratracheal challenge. A substantial rise in the number of M. pulmonis-sensitive B cells in the peripheral blood suggests that the dissemination of the primed state, at least in part, is due to B-cell migration via lymph and blood from local sites exposed to M. pulmonis. The majority of T-dependent clones generated by M. pulmonis-specific B cells secrete exclusively immunoglobulin G1 (IgG1). We have demonstrated that the exaggerated IgG1 response was not due to the accompanying viable donor T cells in the inoculum. The predominance of IgG1 was also demonstrated in clones from the bronchus-associated lymphoid tissue of athymic BALB/c mice that were primed with M. pulmonis. Thus, we can infer that functional T cells are not required for the development of specific B cells with the potential for IgG1 expression at the time of in vivo priming. When anti-trinitrophenyl- and anti-M. pulmonis-specific clones were generated in the same splenic fragment cultures stimulated by trinitrophenylated M. pulmonis, only the M. pulmonis-specific clones showed exaggerated IgG1 expression. Therefore, we conclude that the exaggerated IgG1 response accompanying M. pulmonis infection of euthymic mice seems to be dependent, at least in part, on an intrinsic property of the B cells that develop during this antigenic stimulation.

Animals↗

PubMed2001

Kaposi's sarcoma-associated herpesvirus latent and lytic gene expression as revealed by DNA arrays.

Kaposi's sarcoma-associated herpesvirus (KSHV; human herpesvirus 8) is associated with three human tumors, Kaposi's sarcoma, primary effusion lymphoma (PEL), and multicentric Castleman's disease. KSHV encodes a number of homologs of cellular proteins involved in the cell cycle, signal transduction, and modulation of the host immune response. Of the virus complement of over 85 open reading frames (ORFs), the expression of only a minority has been characterized individually. We have constructed a nylon membrane-based DNA array which allows the expression of almost every ORF of KSHV to be measured simultaneously. A PEL-derived cell line, BC-3, was used to study the expression of KSHV during latency and after the induction of lytic replication. Cluster analysis, which arranges genes according to their expression profile, revealed a correlation between expression and assigned gene function that is consistent with the known stages of the herpesvirus life cycle. Furthermore, latent and lytic genes thought to be functionally related cluster into groups. The correlation between gene expression and function also infers possible roles for KSHV genes yet to be characterized.

Amino Acid Sequence↗

PubMed1999

MDL and the statistical mechanics of protein potentials.

The combination of a wealth of structural data and impressive computational power provides detailed information pertaining to the structure and dynamics of biomacromolecules. A natural inclination is to incorporate this information into models to gain added predictive power on protein folding and stability. There has been considerable recent interest in developing "knowledge-based" potentials to describe internal interactions in proteins. In these approaches, probability distribution functions are inferred from existing knowledge. A common assumption has been the "quasi-chemical approximation" or "Boltzmann device". This method relates statistical mechanical probabilities to observed frequencies. The validity of this approach is discussed in detail from a statistical mechanics perspective. Because statistical mechanics is a form of statistical inference based on a lack of knowledge of the system, the "Boltzmann device" does not have a rigorous theoretical justification. In the present work, a statistical mechanics based on partial knowledge of the system is employed. This statistical mechanical scheme uses the minimum description length (MDL) of phase space as its main tool. With this approach, "knowledge-based" potentials can be derived in a rigorous fashion. In practical calculations, these potentials are best obtained using Bayesian inference methods similar to those used in image reconstruction.

Algorithms↗

PubMed2005

Disease gene discovery through integrative genomics.

The availability of complete genome sequences and the wealth of large-scale biological data sets now provide an unprecedented opportunity to elucidate the genetic basis of rare and common human diseases. Here we review some of the emerging genomics technologies and data resources that can be used to infer gene function to prioritize candidate genes. We then describe some computational strategies for integrating these large-scale data sets to provide more faithful descriptions of gene function, and how such approaches have recently been applied to discover genes underlying Mendelian disorders. Finally, we discuss future prospects and challenges for using integrative genomics to systematically discover not only single genes but also entire gene networks that underlie and modify human disease.

Databases, Genetic↗

PubMed1999

Loss of IA expression and increased excitability in postnatal rat Cajal-Retzius cells.

Although an important secretory function of Cajal-Retzius (CR) cells has been discovered recently, the precise electrical status of these cells among other layer I neurons in particular and in cortical function in general is still unclear. In this paper, early postnatal CR cells from rat neocortex were found to express an inactivating K current whose molecular substrate is likely to be the Kv1.4 channel. Both electrophysiological and immunocytochemical experiments revealed that expression of this A-type current is down-regulated in vivo and virtually disappears by the end of the second postnatal week. At this time, CR cells have become capable of evoked repetitive firing, and their action potentials are larger and faster, yet these electrical properties still appear incompatible with a role in cortical network function, as inferred from comparisons with other cortical neurons. Also at this time, a large proportion of CR cells display spontaneous spiking activity, which suggests the possibility of additional roles for these cells. We conclude that the loss of A channels along with an increase in Na channel density shape the changes in excitability of postnatal CR cells, in terms of both the patterns of evoked firing and the emergence of spontaneous spiking.

Action Potentials↗

PubMed2001

Oxidative stress and renal dysfunction in salt-sensitive hypertension.

Hypertension is a risk factor for the development of end-stage renal disease. The mechanisms underlying hypertensive nephropathy are poorly understood. There is evidence, however, that in hypertension there is an accumulation of partially reduced oxygen and its derivatives, known collectively as reactive oxygen species, which may contribute to progressive renal dysfunction. In the present study, we assess the contribution of oxidative stress in the development of salt-dependent hypertensive nephrosclerosis. Going beyond previous end point studies, which inferred renal function either indirectly or only qualitatively, we have determined oxidative stress concurrently with direct and quantitative measurements of renal function (via inulin and p-aminohippuric acid clearances). Moreover, in this time-dependent study, the measurements have been taken under low- as well as high-salt diets. As was expected from previous studies, in the Dahl salt-sensitive rat, a high-salt diet (8% NaCl) resulted in the development of hypertension, in a decreased glomerular filtration rate, and in a decreased renal plasma flow as compared with the normotensive control, the Dahl salt-resistant rat. In addition, however, we found clear evidence for the accumulation of reactive oxygen species in renal tissue homogenates of Dahl salt-sensitive rats on the high-salt diet. Our time-dependent protocol also indicated that renal oxidative stress follows, in time, the development of hypertension. We also found that after 2 weeks of increased salt loading, Dahl salt-sensitive rats excreted less cyclic guanosine monophosphate and NO(x) than Dahl salt-resistant rats on the same diet. It is known that urinary cyclic guanosine monophosphate and NO(x) represent the activity and stable derivatives of renal NO., respectively, and that they closely correlate with renal vascular resistance. Therefore, our results suggest that, in the Dahl salt-sensitive rat, increased oxidative stress is associated with salt-dependent hypertensive nephrosclerosis and that decreased NO. bioavailability may represent a common factor responsible for the vascular and glomerular dysfunction.

Animals↗

PubMed2001

Transformation of interleukin-3-dependent cells without participation of Stat5/bcl-xL: cooperation of akt with raf/erk leads to p65 nuclear factor kappaB-mediated antiapoptosis involving c-IAP2.

Tyrosine kinase oncogenes such as p210BCR-ABL activate multiple signal pathways. As a result, it is difficult to infer the functional relevance of a pathway acting alone or in cooperation with another. One or 2 second-tier kinases represented in the p21ras and phosphatidylinositol-3-kinase (PI-3-kinase) pathways (activated RafCAAX and gag-akt, respectively) were expressed in parental H7 interleukin-3 (IL-3)-dependent myeloid cells. IL-3-dependent cells served, independently, as recipients of p210BCR-ABL, which activated p21ras and PI-3-kinase pathways, including raf/erk and akt, respectively, en route to transformation. By contrast, neither RafCAAX nor gag-akt when expressed in parental cells in isolation produced factor-independent cells. On the other hand, H7 cells expressing both RafCAAX and gag-akt (H7gag-akt/RafCAAX) were transformed. Such transformation in H7gag-akt/RafCAAX was accomplished in the absence of active versions of Shc or cbl, and there was no evidence of Stat activity and only modest amounts of bcl-xL, a Stat5 transcriptional target protein, all of which characterized the cells transformed by BCR-ABL. However, H7gag-akt/RafCAAX cells and H7BCR-ABL cells cultured in the absence of IL-3 shared strikingly increased p65 nuclear factor kappaB (NFkappaB) activity. Treatment of cells with a specific NFkappaB inhibitor, parthenolide, led to loss of NFkappaB activity and down-regulation of antiapoptotic c-IAP2. In cells with only gag-akt/RafCAAX, this was sufficient to allow polyADP ribosyltransferase (PARP)-degradative apoptosis, but in cells with p210BCR-ABL, apoptosis was blocked, possibly by a Stat5/bcl-xL-dependent mechanism. Therefore, one hematopoietic antiapoptotic program, among others, available to certain tyrosine kinase oncogenes involves a cooperative response between raf/erk and akt, unambiguous components of p21ras and PI-3-kinase pathways, to induce p65 NFkappaB and c-IAP2.

Animals↗

PubMed2006

A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database.

BACKGROUND: We present here the PhIGs database, a phylogenomic resource for sequenced genomes. Although many methods exist for clustering gene families, very few attempt to create truly orthologous clusters sharing descent from a single ancestral gene across a range of evolutionary depths. Although these non-phylogenetic gene family clusters have been used broadly for gene annotation, errors are known to be introduced by the artifactual association of slowly evolving paralogs and lack of annotation for those more rapidly evolving. A full phylogenetic framework is necessary for accurate inference of function and for many studies that address pattern and mechanism of the evolution of the genome. The automated generation of evolutionary gene clusters, creation of gene trees, determination of orthology and paralogy relationships, and the correlation of this information with gene annotations, expression information, and genomic context is an important resource to the scientific community. DISCUSSION: The PhIGs database currently contains 23 completely sequenced genomes of fungi and metazoans, containing 409,653 genes that have been grouped into 42,645 gene clusters. Each gene cluster is built such that the gene sequence distances are consistent with the known organismal relationships and in so doing, maximizing the likelihood for the clusters to represent truly orthologous genes. The PhIGs website contains tools that allow the study of genes within their phylogenetic framework through keyword searches on annotations, such as GO and InterPro assignments, and sequence similarity searches by BLAST and HMM. In addition to displaying the evolutionary relationships of the genes in each cluster, the website also allows users to view the relative physical positions of homologous genes in specified sets of genomes. SUMMARY: Accurate analyses of genes and genomes can only be done within their full phylogenetic context. The PhIGs database and corresponding website http://phigs.org address this problem for the scientific community. Our goal is to expand the content as more genomes are sequenced and use this framework to incorporate more analyses.

Base Sequence↗

PubMed2005

Connecting the dots in Huntington's disease with protein interaction networks.

Analysis of protein-protein interaction networks is becoming important for inferring the function of uncharacterized proteins. A recent study using this approach has identified new proteins and interactions that might be involved in the pathogenesis of the neurodegenerative disorder Huntington's disease, including a GTPase-activating protein that co-localizes with protein aggregates in Huntington's disease patients.

Adaptor Proteins, Signal Transducing↗

PubMed2026

Spatial proteomics reveals four-stage molecular evolution in cancer immunotherapy-related gastritis.

BACKGROUND: Immune checkpoint inhibitors (ICIs) have transformed cancer treatment, yet immune-related adverse events (irAEs) including immunotherapy-related gastritis (IRAEG) pose significant clinical challenges-often necessitating treatment interruption that may compromise antitumor efficacy. IRAEG presents with atypical symptoms, lacks specific biomarkers, and shows histopathological overlap with other forms of gastritis, complicating diagnosis and management. Despite increasing clinical recognition, a systematic understanding of spatial molecular alterations across the full disease course remains limited. Here, we used spatial proteomics to map the molecular landscape of IRAEG during disease progression and to define stage-specific patterns of molecular evolution relevant to cancer immunotherapy management. METHODS: We analyzed tissue samples from seven patients, including four non-immunotherapy-related gastritis controls and three cancer patients who developed IRAEG following ICI therapy for solid tumors, sampled longitudinally across four disease stages: baseline (G1), acute severe inflammation (G2), early recovery (G3), and complete recovery (G4). Using laser capture microdissection coupled with data-independent acquisition mass spectrometry, we profiled 177 spatially resolved gastric tissue regions. Multiplex immunohistochemistry and immunofluorescence characterized features of the immune microenvironment, while Gene Ontology, KEGG pathway analysis, Gene Set Variation Analysis, and xCell inference enabled functional, metabolic, and immune profiling. Key immune and NET-related findings were further validated by multiplex immunofluorescence in an independent, expanded cohort of IRAEG and non-immunotherapy-related gastritis samples. RESULTS: IRAEG was characterized by widespread HLA molecule activation and enhanced antigen processing, resembling the immune phenotype observed in organ transplant rejection. The acute G2 stage exhibited excessive neutrophil extracellular trap formation, profound metabolic suppression, and collapse of immune homeostasis-features that may inform early intervention strategies to preserve ICI treatment continuity. During early recovery (G3), inflammatory injury transitioned toward repair, marked by activation of fatty acid metabolism and PPAR signaling. Notably, even at complete clinical recovery (G4), more than 1,000 proteins remained differentially expressed, reflecting sustained enhancement of metabolic and immune functions and establishing a distinct molecular "memory" state with implications for ICI rechallenge decisions. CONCLUSIONS: These findings define four molecularly distinct stages of IRAEG progression and recovery. The stage-specific signatures identified here serve as candidate biomarkers for diagnosis, disease staging, and therapeutic response assessment, and may guide clinical decisions regarding irAE management, treatment modification, and safe ICI rechallenge to support continued antitumor therapy.

Humans↗