Substrate binding in protein-tyrosine phosphatase-like inositol polyphosphatases

Protein-tyrosine phosphatase-like inositol polyphosphatases are microbial enzymes that catalyze the stepwise removal of one or more phosphates from highly phosphorylated myo-inositols via a relatively ordered pathway. To understand the substrate specificity and kinetic mechanism of these enzymes we have determined high resolution, single crystal, x-ray crystallographic structures of inactive Selenomonas ruminantium PhyA in complex with myo-inositol hexa- and pentakisphosphate. These structures provide the first glimpse of a myo-inositol polyphosphatase-ligand complex consistent with its known specificity and reveal novel features of the kinetic mechanism. To complement the structural studies, fluorescent binding assays have been developed and demonstrate that the K(d) for this enzyme is several orders of magnitude lower than the K(m). Together with rapid kinetics data, these results suggest that the protein tyrosine phosphatase-like inositol polyphosphatases have a two-step, substrate-binding mechanism that facilitates catalysis.     

Evidence for the late MMN as a neurophysiological endophenotype for dyslexia

Dyslexia affects 5-10% of school-aged children and is therefore one of the most common learning disorders. Research on auditory event related potentials (AERP), particularly the mismatch negativity (MMN) component, has revealed anomalies in individuals with dyslexia to speech stimuli. Furthermore, candidate genes for this disorder were found through molecular genetic studies. A current challenge for dyslexia research is to understand the interaction between molecular genetics and brain function, and to promote the identification of relevant endophenotypes for dyslexia. The present study examines MMN, a neurophysiological correlate of speech perception, and its potential as an endophenotype for dyslexia in three groups of children. The first group of children was clinically diagnosed with dyslexia, whereas the second group of children was comprised of their siblings who had average reading and spelling skills and were therefore "unaffected" despite having a genetic risk for dyslexia. The third group consisted of control children who were not related to the other groups and were also unaffected. In total, 225 children were included in the study. All children showed clear MMN activity to/da/-/ba/contrasts that could be separated into three distinct MMN components. Whilst the first two MMN components did not differentiate the groups, the late MMN component (300-700 ms) revealed significant group differences. The mean area of the late MMN was attenuated in both the dyslexic children and their unaffected siblings in comparison to the control children. This finding is indicative of analogous alterations of neurophysiological processes in children with dyslexia and those with a genetic risk for dyslexia, without a manifestation of the disorder. The present results therefore further suggest that the late MMN might be a potential endophenotype for dyslexia.     

Derivation and Expansion Using Only Small Molecules of Human Neural Progenitors for Neurodegenerative Disease Modeling

Phenotypic drug discovery requires billions of cells for high-throughput screening (HTS) campaigns. Because up to several million different small molecules will be tested in a single HTS campaign, even small variability within the cell populations for screening could easily invalidate an entire campaign. Neurodegenerative assays are particularly challenging because neurons are post-mitotic and cannot be expanded for implementation in HTS. Therefore, HTS for neuroprotective compounds requires a cell type that is robustly expandable and able to differentiate into all of the neuronal subtypes involved in disease pathogenesis. Here, we report the derivation and propagation using only small molecules of human neural progenitor cells (small molecule neural precursor cells; smNPCs). smNPCs are robust, exhibit immortal expansion, and do not require cumbersome manual culture and selection steps. We demonstrate that smNPCs have the potential to clonally and efficiently differentiate into neural tube lineages, including motor neurons (MNs) and midbrain dopaminergic neurons (mDANs) as well as neural crest lineages, including peripheral neurons and mesenchymal cells. These properties are so far only matched by pluripotent stem cells. Finally, to demonstrate the usefulness of smNPCs we show that mDANs differentiated from smNPCs with LRRK2 G2019S are more susceptible to apoptosis in the presence of oxidative stress compared to wild-type. Therefore, smNPCs are a powerful biological tool with properties that are optimal for large-scale disease modeling, phenotypic screening, and studies of early human development.     

Annual carbon fixation in terrestrial populations of Nostoc commune (Cyanobacteria) from an Antarctic dry valley is driven by temperature regime

Nostoc commune Vaucher (a cyanobacterium) is a very conspicuous terrestrial primary producer in Victoria Land, continental Antarctica. Because polar ecosystems are considered to be especially sensitive to environmental changes, understanding the environmental constraints on net carbon (C) fixation by N. commune is necessary to determine the effects of environmental changes on the ecological functioning of ice‐free areas of the continent. A model describing net C fixation in terrestrial populations of N. commune in an Antarctic dry valley was constructed using field and laboratory measurements in which N. commune colonies were exposed to different combinations of incident irradiance (400–700 nm), temperature, and degree of desiccation. For desiccated N. commune mats with water content ≤ 30% saturation, net C fixation was highly variable between replicates and could not be modelled. However, for colonies at > 30% saturation, rates of net C fixation and dark respiration depended strongly on irradiance and temperature. Net C fixation reached a maximum rate of 21.6 μg C m^{− 2} s^{− 1} at irradiance of approximately 250 μmol m^{− 2} s^{− 1} and the optimum temperature of 20.5 °C. Agreement between predicted short‐term net C fixation and field and laboratory measurements allowed estimation of total seasonal fixation, using previously published environmental data. Annual net C fixation was estimated in the range 14.5–21.0 g C fixed m^{− 2}Nostoc mat, depending on year/season. Estimates for different seasons correlated with thermal time (accumulated hours above 0 °C during the year) rather than irradiance, in contrast to communities in local lacustrine environments, where irradiance is the main driver of primary productivity. In the terrestrial habitat, N. commune appears to compromise between an ability to capitalize on short periods of higher temperature and efficient utilization of lower irradiance at low temperature. The relationship between thermal time and net annual C fixation by N. commune is strongly linear.     

Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles

The exploration of copy-number variation (CNV), notably of somatic cells, is an understudied aspect of genome biology. Any differences in the genetic makeup between twins derived from the same zygote represent an irrefutable example of somatic mosaicism. We studied 19 pairs of monozygotic twins with either concordant or discordant phenotype by using two platforms for genome-wide CNV analyses and showed that CNVs exist within pairs in both groups. These findings have an impact on our views of genotypic and phenotypic diversity in monozygotic twins and suggest that CNV analysis in phenotypically discordant monozygotic twins may provide a powerful tool for identifying disease-predisposition loci. Our results also imply that caution should be exercised when interpreting disease causality of de novo CNVs found in patients based on analysis of a single tissue in routine disease-related DNA diagnostics.     

Development of the ACTH and corticosterone response to acute hypoxia in the neonatal rat

Acute episodes of severe hypoxia are among the most common stressors in neonates. An understanding of the development of the physiological response to acute hypoxia will help improve clinical interventions. The present study measured ACTH and corticosterone responses to acute, severe hypoxia (8% inspired O(2) for 4 h) in neonatal rats at postnatal days (PD) 2, 5, and 8. Expression of specific hypothalamic, anterior pituitary, and adrenocortical mRNAs was assessed by real-time PCR, and expression of specific proteins in isolated adrenal mitochondria from adrenal zona fascisulata/reticularis was assessed by immunoblot analyses. Oxygen saturation, heart rate, and body temperature were also measured. Exposure to 8% O(2) for as little as 1 h elicited an increase in plasma corticosterone in all age groups studied, with PD2 pups showing the greatest response ( approximately 3 times greater than PD8 pups). Interestingly, the ACTH response to hypoxia was absent in PD2 pups, while plasma ACTH nearly tripled in PD8 pups. Analysis of adrenal mRNA expression revealed a hypoxia-induced increase in Ldlr mRNA at PD2, while both Ldlr and Star mRNA were increased at PD8. Acute hypoxia decreased arterial O(2) saturation (SPo(2)) to approximately 80% and also decreased body temperature by 5-6 degrees C. The hypoxic thermal response may contribute to the ACTH and corticosterone response to decreases in oxygen. The present data describe a developmentally regulated, differential corticosterone response to acute hypoxia, shifting from ACTH independence in early life (PD2) to ACTH dependence less than 1 wk later (PD8).     

The orchids of Timor: checklist and conservation status

A checklist of the Orchidaceae of Timor is presented, with emphasis on the eastern half of the island (East Timor), based on historical herbarium collections and recent botanical explorations. This list comprises 38 genera with 66 species, including 15 new genera and 32 new species records for this island. Moreover, four new species are described: Bulbophyllum sundaicum , Habenaria ankylocentron , Habenaria cauda‐porcelli , and Pterostylis timorensis . Of these, we consider the finding of a new species of Pterostylis to be especially noteworthy, because this species seems to be more closely related to certain Australian members of the genus than to the Malesian ones, suggesting earlier contacts of Timor with Australia. Four new synonyms are proposed: Calanthe veratrifolia var. timorensis J.J.Sm. (C. triplicata), Habenaria cornuta Span. (H. giriensis), H. grandis Benth. ex Ridl. (Peristylus goodyeroides), and H. mutica Span. (H. elongata). The best represented genus is Habenaria, with 13 species, followed by Dendrobium with four, and Bulbophyllum with three. Because of insufficient or sterile material, it was not possible to identify, or describe as new, 20 different taxa. The conservation status of the ten endemic species, plus six possible new undescribed species and two non‐endemic, but threatened, species, was assessed using the World Conservation Union (IUCN) criteria, and categories of threat were proposed. Seven endemic species are considered to be Critically Endangered and two Endangered. One of the nonendemic species is considered to be Critically Endangered, and the other Endangered. The survival of some of these species might be less insecure if an effective application of Regulation project N.2000/19 on protected areas (UNTAET/REG/2000/19) was implemented and maintained, because most of these species were collected in areas considered for protection under this Regulation. Further studies are required, however, in order to complete our knowledge of the diversity and population dynamics of this interesting part of Timor's biodiversity. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 157 , 197–215.     

Metabolomic analysis of adrenal lipids during hypoxia in the neonatal rat: implications in steroidogenesis

The nursing rat pup exposed to hypoxia from birth exhibits ACTH-independent increases in corticosterone and renin/ANG II-independent increases in aldosterone. These increases are accompanied by significant elevation of plasma lipid concentrations in the hypoxic neonates. The purpose of the present study was to compare changes in the concentrations of specific fatty acid metabolites and lipid classes in serum and adrenal tissue from normoxic and hypoxic rat pups. We hypothesized that lipid alterations resulting from hypoxia may partly explain increases in steroidogenesis. Rats were exposed to normoxia or hypoxia from birth, and pooled serum and adrenal tissue from 7-day-old pups were subjected to metabolomic analyses. Hypoxia resulted in specific and significant changes in a number of fatty acid metabolites in both serum and the adrenal. Hypoxia increased the concentrations of oleic (18:1 n-9), eicosapentaenoic (EPA; 20:5 n-3), and arachidonic (20:4 n-6) acids in the triacylglyceride fraction of serum and decreased oleic and EPA concentrations in the cholesterol ester fraction. In the adrenal, hypoxia caused an increase in several n-6 fatty acids in the triacylglyceride fraction, including linoleic (18:2 n-6) and arachidonic acid. There was also an increase in the concentration of alpha-linolenic acid (18:3 n-3) in the triacylglyceride fraction of the hypoxic adrenal, along with an increase in linoleic acid concentration in the diacylglyceride fraction. We propose that specific changes in lipid metabolism in the adrenal, as a result of hypoxia, may partly explain the increased steroidogenesis previously observed. The mechanism responsible may involve alterations in cellular signaling and/or mitochondrial function. These cellular changes may be a mechanism by which the neonate can increase circulating adrenal steroids necessary for survival, therefore bypassing a relative insensitivity to normal stimuli.     

An oxidized metabolite of linoleic acid stimulates corticosterone production by rat adrenal cells

Oxidized derivatives of linoleic acid have the potential to alter steroidogenesis. One such derivative is 12,13-epoxy-9- keto-10-(trans)-octadecenoic acid (EKODE). To evaluate the effect of EKODE on corticosterone production, dispersed rat zona fasciculata/reticularis (subcapsular) cells were incubated for 2 h with EKODE alone or together with rat ACTH (0, 0.2, or 2.0 ng/ml). In the absence of ACTH, EKODE (26 microM) increased corticosterone production from 5.3 +/- 2.3 to 14.7 +/- 5.0 ng. 10(6) cells. h(-1). The stimulatory effect of ACTH was increased threefold in the presence of EKODE (26.0 microM). Cholesterol transport/P-450scc activity was assessed by measuring basal and cAMP-stimulated pregnenolone production in the presence of cyanoketone (1.1 microM). EKODE (13.1 and 26.0 microM) significantly increased basal and cAMP-stimulated (0.1 mM) pregnenolone production. In contrast, EKODE decreased the effect of 1.0 mM cAMP. EKODE had no effect on early or late-pathway activity in isolated mitochondria. We conclude that EKODE stimulates corticosterone biosynthesis and amplifies the effect of ACTH. Increased levels of fatty acid metabolites may be involved in the increased glucocorticoid production observed in obese humans.