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At least 469 records · Page 26Linked to original sources
PubMed2001

Site-directed mutations of human hemoglobin at residue 35beta: a residue at the intersection of the alpha1beta1, alpha1beta2, and alpha1alpha2 interfaces.

Because Tyr35beta is located at the convergence of the alpha1beta1, alpha1beta2, and alpha1alpha2 interfaces in deoxyhemoglobin, it can be argued that mutations at this position may result in large changes in the functional properties of hemoglobin. However, only small mutation-induced changes in functional and structural properties are found for the recombinant hemoglobins betaY35F and betaY35A. Oxygen equilibrium-binding studies in solution, which measure the overall oxygen affinity (the p50) and the overall cooperativity (the Hill coefficient) of a hemoglobin solution, show that removing the phenolic hydroxyl group of Tyr35beta results in small decreases in oxygen affinity and cooperativity. In contrast, removing the entire phenolic ring results in a fourfold increase in oxygen affinity and no significant change in cooperativity. The kinetics of carbon monoxide (CO) combination in solution and the oxygen-binding properties of these variants in deoxy crystals, which measure the oxygen affinity and cooperativity of just the T quaternary structure, show that the ligand affinity of the T quaternary structure decreases in betaY35F and increases in betaY35A. The kinetics of CO rebinding following flash photolysis, which provides a measure of the dissociation of the liganded hemoglobin tetramer, indicates that the stability of the liganded hemoglobin tetramer is not altered in betaY35F or betaY35A. X-ray crystal structures of deoxy betaY35F and betaY35A are highly isomorphous with the structure of wild-type deoxyhemoglobin. The betaY35F mutation repositions the carboxyl group of Asp126alpha1 so that it may form a more favorable interaction with the guanidinium group of Arg141alpha2. The betaY35A mutation results in increased mobility of the Arg141alpha side chain, implying that the interactions between Asp126alpha1 and Arg141alpha2 are weakened. Therefore, the changes in the functional properties of these 35beta mutants appear to correlate with subtle structural differences at the C terminus of the alpha-subunit.

Amino Acid Substitution↗
PubMed2005

Anatomics: the intersection of anatomy and bioinformatics.

Computational resources are now using the tissue names of the major model organisms so that tissue-associated data can be archived in and retrieved from databases on the basis of developing and adult anatomy. For this to be done, the set of tissues in that organism (its anatome) has to be organized in a way that is computer-comprehensible. Indeed, such formalization is a necessary part of what is becoming known as systems biology, in which explanations of high-level biological phenomena are not only sought in terms of lower-level events, but are articulated within a computational framework. Lists of tissue names alone, however, turn out to be inadequate for this formalization because tissue organization is essentially hierarchical and thus cannot easily be put into tables, the natural format of relational databases. The solution now adopted is to organize the anatomy of each organism as a hierarchy of tissue names and linking relationships (e.g. the tibia is PART OF the leg, the tibia IS-A bone) within what are known as ontologies. In these, a unique ID is assigned to each tissue and this can be used within, for example, gene-expression databases to link data to tissue organization, and also used to query other data sources (interoperability), while inferences about the anatomy can be made within the ontology on the basis of the relationships. There are now about 15 such anatomical ontologies, many of which are linked to organism databases; these ontologies are now publicly available at the Open Biological Ontologies website (http://obo.sourceforge.net) from where they can be freely downloaded and viewed using standard tools. This review considers how anatomy is formalized within ontologies, together with the problems that have had to be solved for this to be done. It is suggested that the appropriate term for the analysis, computer formulation and use of the anatome is anatomics.

Adult↗
PubMed2004

Peripheral B-cell maturation: the intersection of selection and homeostasis.

B cells complete maturation after migrating to the periphery, where they transit several intermediate developmental stages prior to recruitment into the long-lived primary pool. Because B-lineage commitment is not regulated by peripheral pool size and most peripheral B cells are quiescent, the primary factors governing steady-state numbers are the proportion of immature B cells surviving transit through later developmental stages and the longevity of mature B cells themselves. Substantial evidence indicates that the B-cell receptor (BCR) plays an essential role in all these processes, but recent findings suggest a central role for the recently described tumor necrosis factor (TNF) family member, B-lymphocyte stimulator (BLyS). Signaling through one of the BLyS receptors, BLyS receptor 3 (BR3), controls B-cell numbers in two ways: by varying the proportion of cells that complete transitional B-cell development and by serving as the primary determinant of mature B-cell longevity. The recent discovery that BCR signaling is selectively coupled to BR3 expression in a developmentally regulated fashion links BCR- and BLyS-mediated events, suggesting that specificity-based selection and survival may be mechanistically similar processes.

Animals↗
PubMed2005

Melanocyte and keratinocyte carcinogenesis: p53 family protein activities and intersecting mRNA expression profiles.

Melanocytes and keratinocytes were analyzed for potential roles of p53, p73, and p63 tumor suppressor family proteins and of malignancy-specific gene expression changes in the etiology of multi-step cancer. Melanocytes expressed deltaNp73alpha, two p63 isoforms and p53. Although p21 and Noxa mRNA levels increased following DNA damage, p53 family member binding to p21 and Noxa DNA probes was undetectable, suggesting p53 family-independent responses. In contrast, keratinocytes expressed multiple isoforms each of p73 and p63 that were induced to bind p21 and Noxa DNA probes after ionizing (IR) or after ultraviolet B (UVB) irradiation, correlating with p21 and Noxa mRNA induction and with apoptosis. Interestingly, IR-resistant malignant melanocytes and keratinocytes both exhibited Noxa mRNA induction after UVB treatment, correlating with DNA binding of p53 family proteins to the Noxa probe only in keratinocytes. To uncover other malignancy-specific events, we queried mouse initiated keratinocyte clones for early changes that were exacerbated in malignant derivatives and also differentially expressed in human advanced melanoma versus normal melanocytes. Using a new method for ranking and normalization of microarray data for 5000 probe sets, 27 upregulated and 13 downregulated genes satisfied our query. Of these, the majority was associated with late-stage human cancers and six were novel genes. Thus, clonal lineage mouse models representing early through late cancer progression stages may inform the focus on early, potentially causal events from microarray studies of human cancers, facilitating prognosis and molecular therapy.

Animals↗
PubMed2004

Autoimmunity gene expression portrait: specific signature that intersects or differentiates between multiple sclerosis and systemic lupus erythematosus.

Autoimmune diseases are either tissue-specific like multiple sclerosis (MS) or multisystemic like systemic lupus erythematosus (SLE), although clinically both exhibit common features. To gain insight into the properties of the genes involved in each disease we have investigated the gene expression signature of peripheral blood mononuclear cells (PBMC) in MS and SLE in comparison to healthy subjects. Total RNA was purified, hybridized to Genechip array and analysed in 36 subjects (13 relapsing-remitting MS patients, five SLE patients and 18 age-matched healthy subjects that served as controls). Additional blood samples from 15 relapsing-remitting MS patients, 8 SLE patients and 10 healthy subjects were used for confirmation of microarray gene expression findings by ELISA and RT-PCR. MS and SLE patients demonstrated a common gene expression autoimmune signature of 541 genes which differentiated them from healthy subjects. The autoimmune signature included genes that encode proteins involved in apoptosis, cell cycle, inflammation and regulation of matrix metalloproteinase pathways. Specifically, decreased TIMP1 gene expression in the autoimmunity signature suggests increased MMP activity in target tissues as a result of the lack of feedback mechanism. An additional different disease specific signature identified the gene expression pattern for MS (1031 genes), mainly associated with over-expression of adhesion molecules and down-expression of heat shock proteins; the SLE specific signature (1146 genes) mainly involved DNA damage/repair pathways that result in production of nuclear autoantibodies. These results provide insights into the genetic pathways underlying autoimmune diseases, and identify specific disease-associated signatures that may enable targetted disease-related specific therapies to be developed.

Adult↗
PubMed2006

The distribution of eggs per host in a herbivorous insect--intersection of oviposition, dispersal and population dynamics.

1. The dynamics of parasitic organisms depend critically upon the frequency distribution of parasite individuals per host. However, the processes giving rise to this frequency distribution have rarely been modelled and tested for organisms with complex host selection behaviour. 2. In this study Microrhopala vittata, a chrysomelid beetle, was used to investigate how oviposition behaviour, movement and density of host plants interact in shaping the frequency distribution of egg clusters per host in the field. 3. Enclosures were stocked with two different host species and different beetle densities and various stochastic process models were fitted to egg cluster count data obtained from these enclosures. The different models were derived considering different scenarios, in particular whether or not plant density limits oviposition rate, whether or not ovipositing females actively seek out the most attractive plant within their perception radius and whether a female's oviposition rate is determined by plant intrinsic factors, the plant's egg cluster load or the surrounding beetle density. 4. The model parameters fitted to cage data were used to describe the frequency distribution of egg cluster counts obtained in a release experiment in the field. A total of 220 beetle pairs were released at five locations in a field where this beetle was not observed previously. Each release point was at a border between the two host species. 5. One model predicted for the preferred host species the egg cluster count frequencies in the field from parameters estimated in the cages. This model assumed that egg clusters present on a plant increased subsequent oviposition on this plant. All other models could not describe the distribution of egg cluster counts for either of the two host species. 6. The results suggest that females seek out attractive hosts actively and the attractiveness of a plant increases with its egg cluster load. This behaviour creates a frequency distribution of egg clusters per host that depends only on beetle density but not on plant density. This conclusion has important implications for modelling insect-plant interactions.

Animals↗
PubMed2005

Bacillus subtilis ilvB operon: an intersection of global regulons.

The genes of the major Bacillus subtilis operon (ilvB) for biosynthesis of branched-chain amino acids are subject to multiple mechanisms of regulation. The global regulatory proteins CodY and TnrA bind upstream of the transcription start site and are likely to control transcription initiation, leucine-specific tRNA regulates transcriptional elongation, and unknown factors differentially cleave the full-length mRNA. Another global regulator, CcpA, known to be required for ilvB transcription, was shown here to act directly at the ilvB promoter by a novel mechanism. Although CcpA was able to bind to the ilvB promoter region, it stimulated transcription significantly only when CodY was present, suggesting that CcpA acts primarily by interfering with repression by CodY. Additionally, CcpA was shown to control indirectly the expression of other CodY-regulated target genes, apparently by altering the intracellular level of branched-chain amino acids.

Bacillus subtilis↗
PubMed2006

Intersections of 'sanitation, sexual coercion and girls' safety in schools'.

OBJECTIVE: To explore safety for girls in schools, particularly how girls perceive and negotiate dangers and risks associated with the use of toilets. METHODS: Participatory action research over a period of 3 days at three schools in South Africa. Informants were 81 girls 16 years and older, teachers and other relevant school personnel. Data were collected through focus group discussions, in-depth interviews, participant observation, mapping and photography. RESULTS: Toilets had inadequate or no sanitation. Both their use and their avoidance were risky for female students and discouraged hygienic practices. Experience of sexual violence from male students and teachers was a major theme, but unrelated to school toilets. Male teachers used various strategies and opportunities to gain sexual access to the girls and previous experience of victimization prevented the girls from reporting them. CONCLUSION: To ensure a healthy school environment that promotes gender equality, all threats to safety, including the physical and social environment, must be considered.

Adolescent↗
PubMed2006

Florivory: the intersection of pollination and herbivory.

Plants interact with many visitors who consume a variety of plant tissues. While the consequences of herbivory to leaves and shoots are well known, the implications of florivory, the consumption of flowers prior to seed coat formation, have received less attention. Herbivory and florivory can yield different plant, population and community outcomes; thus, it is critical to distinguish between these two types of consumption. Here, we consider the ecological and evolutionary consequences of florivory. A growing number of studies recognize that florivory is common in natural systems and in some cases surpasses leaf herbivory in magnitude and impact. Florivores can affect male and female plant fitness via direct trophic effects and through altered pathways of species interactions. In particular, florivory can affect pollination and have consequences for plant mating and floral sexual system evolution. Plants are not defenceless against florivore damage. Concepts of resistance and tolerance can be applied to plant-florivore interactions. Moreover, extant theories of plant chemical defence, including optimal defence theory, growth rate hypothesis and growth differentiation-balance hypothesis, can be used to make testable predictions about when and how plants should defend flowers against florivores. The majority of the predictions remain untested, but they provide a theoretical foundation on which to base future experiments. The approaches to studying florivory that we outline may yield novel insights into floral and defence traits not illuminated by studies of pollination or herbivory alone.

Biomass↗
PubMed2006

Stepwise enforcement of the notochord and its intersection with the myoseptum: an evolutionary path leading to development of the vertebra?

The notochord constitutes the main axial support during the embryonic and larval stages, and the arrangement of collagen fibrils within the notochord sheath is assumed to play a decisive role in determining its functional properties as a fibre-wound hydrostatic skeleton. We have found that during early ontogeny in Atlantic salmon stepwise changes occur in the configuration of the collagen fibre-winding of the notochord sheath. The sheath consists of a basal lamina, a layer of type II collagen, and an elastica externa that delimits the notochord; and these constituents are secreted in a specific order. Initially, the collagen fibrils are circumferentially arranged perpendicular to the longitudinal axis, and this specific spatial fibril configuration is maintained until hatching when the collagen becomes reorganized into distinct layers or lamellae. Within each lamella, fibrils are parallel to each other, forming helices around the longitudinal axis of the notochord, with a tangent angle of 75-80 degrees to the cranio-caudal axis. The helical geometry shifts between adjacent lamellae, forming enantiomorphous left- and right-handed coils, respectively, thus enforcing the sheath. The observed changes in the fibre-winding configuration may reflect adaptation of the notochord to functional demands related to stage in ontogeny. When the vertebral bodies initially form as chordacentra, the collagen lamellae of the sheath in the vertebral region are fixed by the deposition of minerals; in the intervertebral region, however, they represent a pre-adaptation providing torsional stability to the intervertebral joint. Hence, these modifications of the sheath transform the notochord per se into a functional vertebral column. The elastica externa, encasing the notochord, has serrated surfaces, connected inward to the type II collagen of the sheath, and outward to type I collagen of the mesenchymal connective tissue surrounding the notochord. In a similar manner, the collagen matrix of the neural and haemal arch cartilages is tightly anchored to the outward surface of the elastic membrane. Hence, the elastic membrane may serve as an interface between the notochord and the adjacent structures, with an essential function related to transmission of tensile forces from the musculature. The interconnection between the notochord and the myosepta is discussed in relation to function and to evolution of the arches and the vertebra. Contrary to current understanding, this study also shows that notochord vacuolization does not result in an increased elongation of the embryo, which agrees with the circular arrangement of type II collagen that probably only enables a restricted increase in girth upon vacuolization, not aiding elongation. As the vacuolization occurs during the egg stage, this type of collagen disposition, in combination with an elastica externa, also probably facilitates flexibility and curling of the embryo.

Animals↗
PubMed2005

Defining standard of care in the developing world: the intersection of international research ethics and health systems analysis.

In recent years there has been intense debate regarding the level of medical care provided to 'standard care' control groups in clinical trials in developing countries, particularly when the research sponsors come from wealthier countries. The debate revolves around the issue of how to define a standard of medical care in a country in which many people are not receiving the best methods of medical care available in other settings. In this paper, we argue that additional dimensions of the standard of care have been hitherto neglected, namely, the structure and efficiency of the national health system. The health system affects locally available medical care in two important ways: first, the system may be structured to provide different levels of care at different sites with referral mechanisms to direct patients to the appropriate level of care. Second, inefficiencies in this system may influence what care is available in a particular locale. As a result of these two factors locally available care cannot be equated with a national 'standard'. A reasonable approach is to define the national standard of care as the level of care that ought to be delivered under conditions of appropriate and efficient referral in a national system. This standard is the minimum level of care that ought to be provided to a control group. There may be additional moral arguments for higher levels of care in some circumstances. This health system analysis may be helpful to researchers and ethics committees in designing and reviewing research involving standard care control groups in developing country research.

Control Groups↗
PubMed2005

The intersection between geriatrics and palliative care: a call for a new research agenda.

Palliative care is interdisciplinary treatment focused on the relief of suffering and achieving the best possible quality of life for patients and their caregivers. It differs for geriatric patients from what is usually appropriate in a younger population because of the nature and duration of chronic illness during old age. In spite of the fact that death occurs far more commonly in older people than in any age group, the evidence base for palliative care in older adults is sparse. Over the coming years, the research foci in the field of geriatrics and palliative care that must be addressed include establishing the prevalence of symptoms in patients with chronic disease; evaluating the association between treatment of symptoms and outcomes; increasing the evidence base for treatment of symptoms; understanding psychological well-being, spiritual well-being, and quality of life of patients and elucidating and alleviating sources of caregiver burden; reevaluating service delivery; adapting research methodologies specifically for geriatric palliative care; and increasing the number of geriatricians trained as investigators in palliative care research. This article discusses specific methods to improve the current situation within each of these seven areas.

Caregivers↗
PubMed1995

Integrating self and system: an empty intersection?

Synthesizing individual and family therapies can founder if the underlying epistemological assumptions concerning "what is self" are not taken into account. Most individual therapies assume self "really" exists as a relatively stable internal entity, the repository of residues of experience where traits, memories, et cetera are organized via internal schemas. Such a view tends to treat self as a thing, and implies that psychological problems are the result of internal deficits or conflicts; this can lead to difficulties in therapy. In contrast, ecosystemic views employ constructivist and contextualist approaches that are more fluid. However, by basing autopoetic self-organization in language, ecosystemic epistemology still separates subject from object. Adopting a perspective in which self has no fixed, distinguishing characteristics can resolve many difficulties and create a dimensionless point where self and system, individual and family, therapist and client can meet without hindrance.

Family Therapy↗
PubMed2006

Intersection of fungal fitness and virulence in Cryptococcus neoformans.

The use of insertional mutagenesis to discover genes that impact laccase activity has resulted in the identification of multiple cellular processes that affect the fitness of Cryptococcus neoformans. Fitness has been defined as the ability of an organism to propagate and evolve within a given environment. Because the human host is an evolutionary dead-end for an opportunistic pathogen, we have defined pathogenic fitness here as the capability to successfully propagate within the stressful environment of the host, causing disease by expression of virulence traits that damage the host. In this review, laccase-deficient insertional mutants will be highlighted in terms of the basic biological processes in which they are involved. The impact of laccase-associated cellular functions on fitness and virulence will be discussed, as will the mutants' potential as therapeutic targets. Vacuolar function, copper homeostasis, mitochondrial function and carbon repression are covered.

Cryptococcosis↗
PubMed2005

Septins: traffic control at the cytokinesis intersection.

The physical division of one cell into two requires the highly orchestrated separation of genetic and cytoplasmic contents during M phase of the cell cycle. Mitosis, the physical segregation of the genetic material of a cell into two daughter cells, has traditionally received more attention than cytokinesis, the partitioning of the cytoplasmic contents, yet clearly the two processes must be intimately co-ordinated and tightly regulated. While plant cells divide by the formation of a membranous cell barrier called the phragmoplast, animal cell division is largely driven by contraction of an actomyosin ring. However, recent evidence has suggested that membranes derived from one or more intracellular compartments are also required to break the cytoplasmic bridge connecting two dividing cells during late telophase. In this review, we focus on studies of animal cell cytokinesis that support a requirement for specific endomembrane fusion during fission, define molecular components of the membrane fusion apparatus that may be involved and point to possible roles for an emerging family of cytoskeletal proteins, the septins, in this process.

Animals↗