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PubMed2004

Ambiguity, logic, simplicity, and dynamics: Wittgensteinian evaluative criteria in peer review of quantitative research on categorization.

Research on categorization has changed over time, and some of these changes resemble how Wittgenstein's views changed from his Tractatus Logico-Philosophicus to his Philosophical Investigations. Wittgenstein initially focused on unambiguous, abstract, parsimonious, logical propositions and rules, and on independent, static, "atomic facts." This approach subsequently influenced the development of logical positivism and thereby may have indirectly influenced method and theory in research on categorization: much animal research on categorization has focused on learning simple, static, logical rules unambiguously interrelating small numbers of independent features. He later rejected logical simplicity and rigor and focused instead on Gestalt ideas about figure-ground reversals and context, the ambiguity of family resemblance, and the function of details of everyday language. Contemporary contextualism has been influenced by this latter position, some features of which appear in contemporary empirical research on categorization. These developmental changes are illustrated by research on avian local and global levels of visual perceptual analysis, categorization of rectangles and moving objects, and artificial grammar learning. Implications are described for peer review of quantitative theory in which ambiguity, logical rigor, simplicity, or dynamics are designed to play important roles.

Artificial Intelligence↗
PubMed2004

Developmental analyses reveal early arrests of the spore-bearing parts of reproductive organs in unisexual flowers of cucumber (Cucumis sativus L.).

To understand the regulatory mechanisms governing unisexual flower development in cucumber, we conducted a systematic morphogenetic analysis of male and female flower development, examined the dynamic changes in expression of the C-class floral organ identity gene CUM1, and assessed the extent of DNA damage in inappropriate carpels of male flowers. Accordingly, based on the occurrence of distinct morphological events, we divided the floral development into 12 stages ranging from floral meristem initiation to anthesis. As a result of our investigation we found that the arrest of stamen development in female flowers, which occurs just after the differentiation between the anther and filament, is mainly restricted to the primordial anther, and that it is coincident with down-regulation of CUM1 gene expression. In contrast, the arrest of carpel development in the male flowers occurs prior to the differentiation between the stigma and ovary, given that no indication of ovary differentiation was observed even though CUM1 gene expression remained detectable throughout the development of the stigma-like structures. Although the male and female reproductive organs have distinctive characteristics in terms of organ differentiation, there are two common features regarding organ arrest. The first is that the arrest of the inappropriate organ does not affect the entirety of the organ uniformly but occurs only in portions of the organs. The second feature is that all the arrested portions in both reproductive organs are spore-bearing parts.

Cucumis sativus↗
PubMed2005

Thinking clockwise.

Throughout the Animal Kingdom, the time of embryonic development is maintained and strictly controlled. Each step of the process is successful only when it occurs at the right time and place. This raises the question: how is time controlled during embryonic development? Time control is particularly crucial during embryo segmentation processes, where the number of generated segments, as well as the time of formation of each segment, is extraordinarily constant and specific for each species. Somitogenesis is the process through which the vertebrate presomitic mesoderm is segmented along its anterior-posterior axis into round-shaped masses of epithelial cells, named somites. In the chick embryo, a new pair of somites is formed every 90 min. The discovery that this clock-like precision is dictated by the somitogenesis molecular clock constituted a landmark in the Developmental Biology field. Several genes exhibit cyclic gene expression in the embryo presomitic mesoderm from which the somites arise, presenting a 90 min oscillation period, the time required to form a pair of somites. The combined levels of dynamic gene expression throughout the presomitic mesoderm enable cells to acquire positional information, thus giving them a notion of time. Anterior-posterior patterning of the vertebrate nervous system also involves partition into discrete territories. This is particularly evident in the hindbrain where overt segmentation occurs. Nevertheless, little is known about the segmentation genes and mechanisms that may be involved. This paper intends to describe the molecular clock associated with vertebrate somitogenesis, suggesting that it may be operating in many other patterning processes.

Animals↗
PubMed1995

Dynamic model comparing the bionomics of two isolated Culex tarsalis (Diptera: Culicidae) populations: model development.

The population dynamics of Culex tarsalis in the Coachella and southern San Joaquin valleys of California were studied using Monte Carlo simulations. Multiple years of abundance data were averaged to extract a generalized seasonal pattern for each site. These patterns were used to establish qualitative goodness-of-fit criteria to assess model output and to evaluate the importance of model parameters in simulating mosquito population trends. The parameters associated with the degree of temperature and density dependency on larval mortality were found to be important components in determining whether or not the output was classified as having passed or failed on the basis of our criteria, whereas autogeny and the heterogeneity of developmental time were found not to be important.

Animals↗
PubMed1997

Developmental expression of the GIRK family of inward rectifying potassium channels: implications for abnormalities in the weaver mutant mouse.

G-protein-gated inward rectifying potassium channels (GIRKs) are a newly identified gene family. These gene products are thought to form functional channels through the assembly of heteromeric subunits. Recently, it has been demonstrated that a point mutation in the GIRK2 gene, one of the GIRK family members, is the cause of the neurological and reproductive defects observed in the weaver (wv) mutant mouse. The mechanism(s) by which a single amino acid substitution in GIRK2 protein leads to the severe phenotypes in the wv / wv mouse is not fully understood. However, it implicates the importance of GIRK channels in neuronal development. To characterize the mRNA expression patterns of GIRK1-3 during mouse brain development we have used in situ hybridization analyses. We found that the expression of all three genes showed developmental regulation. In most areas that showed expression, the levels of GIRK1-3 transcripts reached their peak at around postnatal day 10 (P10). In general, GIRK1 showed the least fluctuation in its levels of expression during development, while dynamic changes were found with the levels of GIRK2 and GIRK3 transcripts. GIRK3 becomes the predominant inward rectifying K+-channel in the brain at later postnatal ages. In the CNS regions affected in the wv / wv mouse, GIRK2 is the predominant inward rectifying channel that is expressed. This suggests that the presence of the other subtypes are able to compensate for the mutated GIRK2 channel in weaver neurons that survive.

Animals↗
PubMed2000

Tissue-specific developmental expression of OAX, a Xenopus repetitive element.

Approximately 1% of the Xenopus laevis genome consists of highly repetitive DNA known alternatively as OAX (for Oocyte Activation in Xenopus), Satellite I, or Repetitive HindIII Monomer 2. Present as tandemly repeated units of approximately 750 base pairs, OAX encodes a family of small RNA species transcribed by RNA polymerase III. Although the subject of many of the classic studies on early embryonic gene regulation, reports on OAX expression remain contradictory and incomplete. Using whole-mount in situ hybridization and RNase protection assays, we have therefore examined in detail the expression pattern of OAX in Xenopus embryos of various stages. OAX is initially expressed during gastrula stages; by tailbud stages embryos display discrete zones of expression at the dorsal boundary of the cement gland, in the developing somites and differentiating skeletal muscle, as well as in the dorsal aspect of the neural tube. These data demonstrate that OAX is expressed in a dynamic pattern under tight spatial and temporal regulation.

Animals↗
PubMed2000

Regulatory mutations of the Drosophila Sox gene Dichaete reveal new functions in embryonic brain and hindgut development.

Sox domain proteins encompass a conserved family of transcriptional regulators that are implicated in a variety of developmental processes in eukaryotes from worm to man. The Dichaete gene of Drosophila encodes a group B Sox protein related to mammalian Sox1, -2, and -3 and, like these proteins, it is widely and dynamically expressed throughout embryogenesis. In order to unravel new Dichaete functions, we characterized the organization of the Dichaete gene using a combination of regulatory mutant alleles and reporter gene constructs. Dichaete expression is tightly controlled during embryonic development by a complex of regulatory elements distributed over 25 kb downstream and 3 kb upstream of the transcription unit. A series of regulatory alleles which affect tissue-specific domains of Dichaete were used to demonstrate that Dichaete has functions in addition to those during segmentation and midline development previously described. First, Dichaete has functions in the developing brain. A specific group of neural cells in the tritocerebrum fails to develop correctly in the absence of Dichaete, as revealed by reduced expression of labial, zfh-2, wingless, and engrailed. Second, Dichaete is required for the correct differentiation of the hindgut. The Dichaete requirement in hindgut morphogenesis is, in part, via regulation of dpp, since ectopically supplied dpp can rescue Dichaete phenotypes in the hindgut. Taken together, there are now four distinct in vivo functions described for Dichaete that can be used as models for context-dependent comparative studies of Sox function.

Alleles↗
PubMed2006

Chromosomal distribution of PcG proteins during Drosophila development.

Polycomb group (PcG) proteins are able to maintain the memory of silent transcriptional states of homeotic genes throughout development. In Drosophila, they form multimeric complexes that bind to specific DNA regulatory elements named PcG response elements (PREs). To date, few PREs have been identified and the chromosomal distribution of PcG proteins during development is unknown. We used chromatin immunoprecipitation (ChIP) with genomic tiling path microarrays to analyze the binding profile of the PcG proteins Polycomb (PC) and Polyhomeotic (PH) across 10 Mb of euchromatin. We also analyzed the distribution of GAGA factor (GAF), a sequence-specific DNA binding protein that is found at most previously identified PREs. Our data show that PC and PH often bind to clustered regions within large loci that encode transcription factors which play multiple roles in developmental patterning and in the regulation of cell proliferation. GAF co-localizes with PC and PH to a limited extent, suggesting that GAF is not a necessary component of chromatin at PREs. Finally, the chromosome-association profile of PC and PH changes during development, suggesting that the function of these proteins in the regulation of some of their target genes might be more dynamic than previously anticipated.

Animals↗
PubMed2006

Population developmental stage determines the recovery potential of Daphnia magna populations after fenvalerate application.

This study investigated the responses of Daphnia magna populations to pulsed exposures of the pyrethroid insecticide Fenvalerate applied during an early and a late stage of population development, and analyzed the dynamics of the subsequent recovery. A novel digital observation technique was used to describe the size and numbers of animals. High Fenvalerate concentrations caused high mortality rates during exponential population growth as well as during the food-limited stationary phase. However, recovery of populations took considerably longer in the stationary phase than in populations growing exponentially. The poor nutritional and reproductive state of food-deprived adults was indicated as the main cause of the slow recovery of populations. It is argued that populations operating at the carrying capacity of their environment are vulnerable to toxicant-induced disturbances to an extent not predictable from observations on exponentially growing populations such as are commonly used in ecotoxicology.

Animals↗
PubMed1998

Selective treatment program for developmental dysplasia of the hip in an epidemiologic prospective study.

Over 1 year of ultrasound (US) mass screening, 4,568 newborns were examined consecutively at age 3-4 weeks using both clinical and ultrasonographic examination methods. The US examination involved both the static and dynamic scanning. In total, 25 babies were treated early (5.5 per 1,000), and 6 babies were given late treatment for postnatally developing acetabular dysplasia (1.3 per 1,000). Early treatment was instituted only for hips remarkably distorted anatomically, as could be seen from their shape on the static scan, and for those that were sonographically unstable with an apparent stress displacement. Clinical examination at age 3-4 weeks failed in more than half of all sonographically abnormal cases. In one case, the postnatal development of the hip joint was associated with the worsening of its formation and a developing subluxation despite its primary normal characteristics.

Czech Republic↗
PubMed2006

Developmental appearance of cyclic guanosine monophosphate (cGMP) production and nitric oxide responsiveness in embryonic mouse cortex and striatum.

The second messenger cyclic guanosine monophosphate (cGMP) regulates multiple aspects of both structural development and physiological function in the developing nervous system. Recent in vitro experiments have shown that cGMP also modulates the response of developing vertebrate neurons to guidance molecules. This has led to the proposal that in vivo cGMP plays a critical role in directing the outgrowth of the apical dendrites of developing neurons in the cerebral cortex. Despite this proposed role, the onset, localization, and dynamics of cGMP production in the embryonic cortex are unknown. To investigate the potential contribution of cGMP in the embryo, we have used a pharmacological and immunohistochemical approach to test whether the endogenous production of cGMP, and the capacity to produce cGMP in response to nitric oxide (NO), in the cerebral cortex is compatible with the proposed developmental roles for cGMP. We find that cortical cGMP production and NO sensitivity are regionally and developmentally regulated. Cortical cGMP production begins at E15, later than in the ganglionic eminences, becomes high in the cortical plate but not the ventricular zone, and is dependent on nitric oxide synthase activity. Furthermore, although radially migrating neurons were not NO responsive until they reached the cortical plate, NO exposure revealed an additional population of tangentially migrating presumptive interneurons from the ganglionic eminences with the capacity to produce cGMP. These results provide a new level of understanding of the stage and cell type specific regulation of the NO/cGMP pathway during embryonic development.

Animals↗
PubMedDate not supplied

The scale independence of evolution.

In this paper, I argue that the ultimate causes of morphological, and hence developmental, evolution are scale independent. In other words, micro- and macroevolutionary patterns show fundamental similarities and therefore are most simply explained as being caused by the same kinds of evolutionary forces. I begin by examining the evolution of single lineages and argue that dynamics of adaptive evolution are the same for bacteria in test-tube evolution experiments and fossil lineages. Similarly, I argue that the essential features of adaptive radiations large and small can be attributed to conventional forces such as mutation and diversifying natural selection due to competition. I then address recent claims that the molecular features of metazoan development are the result of clade-level selection for evolvability, and suggest that these features can be more easily explained by conventional individual-level selection for the suppression of deleterious pleiotropic effects. Finally, I ask what must be known if we are to understand the ultimate causes of molecular and developmental diversity.

Biological Evolution↗
PubMed2006

Cytoskeletal organization during xylem cell differentiation.

The water and mineral conductive tube, the xylem vessel and tracheid, is a highly conspicuous tissue due to its elaborately patterned secondary-wall deposition. One constituent of the xylem vessel and tracheid, the tracheary element, is an empty dead cell that develops secondary walls in the elaborate patterns. The wall pattern is appropriately regulated according to the developmental stage of the plant. The cytoskeleton is an essential component of this regulation. In fact, the cortical microtubule is well known to participate in patterned secondary cell wall formation. The dynamic rearrangement of the microtubules and actin filaments have also been recognized in the cultured cells differentiating into tracheary elements in vitro. There has recently been considerable progress in our understanding of the dynamics and regulation of cortical microtubules, and several plant microtubule associated proteins have been identified and characterized. The microtubules have been observed during tracheary element differentiation in living Arabidopsis thaliana cells. Based on this recently acquired information on the plant cytoskeleton and tracheary element differentiation, this review discusses the role of the cytoskeleton in secondary cell wall formation.

Cell Differentiation↗
PubMed1992

Spatial and temporal transcellular current patterns during oogenesis.

We have used the two-dimensional vibrating probe to examine spatial and temporal patterns in the transcellular current flow around telotrophic ovarioles of the insect Rhodnius prolixus. We demonstrate a dynamic pattern of currents which correlates with various stages of vitellogenesis. Asymmetries exist in the radial current pattern around intact ovarioles, particularly around the terminal follicle, and may correlate with early developmental axes. The extra-cellular current pattern is largely reflected by a similar, though weaker pattern of currents over the germ cell membranes, indicating that both germ cell and somatic cell membranes are involved in current generation. Current enters previtellogenic oocytes and leaves oocytes entering vitellogenesis. We speculate that current reversal and loss of trophic cord contact may represent an electrophysiological feedback control mechanism during oogenesis.

Animals↗
PubMed2003

Do 'clumsy' children have visual deficits.

Visual processing by 10-year-old children diagnosed on the basis of standardised tests as having developmental 'clumsiness' syndrome, and by a control group of children without motor difficulties, was tested using three different psychophysical tasks. The tasks comprised a measure of global motion processing using a dynamic random dot kinematogram, a measure of static global pattern processing where the position of the target was randomised, and a measure of static global pattern processing in which the target position was fixed. The most striking finding was that the group of clumsy children, who were diagnosed solely on the basis of their motor difficulties, were significantly less sensitive than the control group on all three tasks of visual sensitivity. Clumsy children may have impaired visual sensitivity in both the dorsal and ventral streams in addition to their obvious problems with motor control. These results support the existence of generalised visual anomalies associated with impairments of cerebellar function.

Case-Control Studies↗
PubMed1991

Dynamic space codes in the superior colliculus.

Space coding in the superior colliculus has traditionally been viewed as a static representation by multiple, aligned, sensory and motor maps. Recent evidence has revealed that the maps are dynamic, shaped by sensory experience in developing animals, and by eye and head position signals in adults. The superior colliculus thus provides an ideal model for studying the neural mechanisms underlying developmental and real-time modifications of information representation in the brain.

Animals↗
PubMed2005

Towards the application of proteomics in renal disease diagnosis.

Proteomics is widely envisioned as playing a significant role in the translation of genomics to clinically useful applications, especially in the areas of diagnostics and prognostics. In the diagnosis and treatment of kidney disease, a major priority is the identification of disease-associated biomarkers. Proteomics, with its high-throughput and unbiased approach to the analysis of variations in protein expression patterns (actual phenotypic expression of genetic variation), promises to be the most suitable platform for biomarker discovery. Combining such classic analytical techniques as two-dimensional gel electrophoresis with more sophisticated techniques, such as MS, has enabled considerable progress to be made in cataloguing and quantifying proteins present in urine and various kidney tissue compartments in both normal and diseased physiological states. Despite these accomplishments, there remain a number of important challenges that will need to be addressed in order to pave the way for the universal acceptance of proteomics as a clinically relevant diagnostic tool. We discuss issues related to three such critical developmental tasks as follows: (i) completely defining the proteome in the various biological compartments (e.g. tissues, serum and urine) in both health and disease, which presents a major challenge given the dynamic range and complexity of such proteomes; (ii) achieving the routine ability to accurately and reproducibly quantify proteomic expression profiles; and (iii) developing diagnostic platforms that are readily applicable and technically feasible for use in the clinical setting that depend on the fruits of the preceding two tasks to profile multiple disease biomarkers.

Animals↗
PubMed1999

Endogenous activation of metabotropic glutamate receptors in neocortical development causes neuronal calcium oscillations.

Oscillations in intracellular free calcium concentration ([Ca(2+)](i)) occur spontaneously in immature neurons of the developing cerebral cortex. Here, we show that developing murine cortical neurons exhibit calcium oscillations in response to direct activation of the mGluR5 subtype of the group I metabotropic glutamate receptor (mGluR). In contrast, other manipulations that elicit [Ca(2+)](i) increases produce simple, nonoscillatory changes. Furthermore, we find that spontaneous oscillatory [Ca(2+)](i) activity is blocked by antagonists of group I mGluRs, suggesting a specific role for mGluR activation in the promotion of oscillatory [Ca(2+)](i) dynamics in immature cortical neurons. The oscillatory pattern of [Ca(2+)](i) increases produced by mGluR activation might play a role in the regulation of gene expression and the control of developmental events.

Animals↗