Mechanistic insights into the role of vitamin D and computational identification of potential lead compounds for Parkinson's disease

Parkinson's disease (PD) is the second most common neurodegenerative disorder that affects dopaminergic neurons in the midbrain. A recent study suggests that Orphan Nuclear Receptor 1 (NURR1) impairment may contribute to PD pathogenesis. Our study found three potent agonists for NURR1 protein based on structural and ligand-based screening methods. The pharmacophore is comprised of a hydrogen bond donor, a hydrophobic group, and two aromatic rings (DHRR). The Pharmacophore screening method screened 3142 compounds, of which 3 were screened using structure-based screening. An analysis of the molecules using Molecular Mechanics-Generalized Born Surface Area (binding free energy) revealed a range of −46.77 to −59.06 Kcal/mol. After that, chemical reactivity was investigated by density functional theory, and molecular dynamics simulation was performed (protein-ligand stability). Based on the computational studies, Lifechemical_16901310, Maybridge_2815310, and NPACT_392450 are promising agonists with respect to NURR1. To confirm the potency of the identified compounds, further validation and experiments must be conducted.     

Original Articles: Nitrogen Mineralization in Two Unpolluted Old-Growth Forests of Contrasting Biodiversity and Dynamics

Studies in unpolluted, old-growth forests in the coastal range of southern Chile (42°30′S) can provide a baseline for understanding how forest ecosystems are changing due to the acceleration of nitrogen (N) inputs that has taken place over the last century. Chilean temperate forests, in contrast to their northern hemisphere counterparts, exhibit extremely low losses of inorganic N to stream waters. The objectives of this study were (a) to determine whether low inorganic N outputs in these forests were due to low rates of N mineralization or nitrification, and (b) to examine how biodiversity (defined as number of dominant tree species) and forest structure influence N mineralization and overall patterns of N cycling. Studies were conducted in a species-poor, conifer-dominated (Fitzroya cupressoides) forest with an even-aged canopy, and in a mixed-angiosperm (Nothofagus nitida) forest with a floristically more diverse and unstable canopy. Nitrogen mineralization rates measured in laboratory assays varied seasonally, reaching 6.0 μg N/g DW/day in both forests during late summer. Higher values were related to higher microbial activity, larger pools of labile inorganic N, and increased fine litter inputs. Field assays, conducted monthly, indicated positive net flux from N mineralization mainly from December to January in both forests. Annual net flux of N from mineralization varied from 20 to 23 kg/ha/year for the Fitzroya forest and from 31 to 37 kg/ha/year for the Nothofagus forest. Despite low losses of inorganic N to streams, N mineralization and nitrification are not inhibited in these forests, implying the existence of strong sinks for NO₃ ⁻ in the ecosystem. Field N mineralization rates were two times higher in the Nothofagus forest than in the Fitzroya forest, and correlated with greater N input via litterfall, slightly higher soil pH, and narrower carbon (C)–nitrogen ratios of soils and litter in the former. Differences in N mineralization between the two forest types are attributed to differences in biotic structure, stand dynamics, and site factors. Median values of net N mineralization rates in these southern hemisphere forests were lower than median rates for forests in industrialized regions of North America, such as the eastern and central USA. We suggest that these high N mineralization rates may be a consequence of enhanced atmospheric N deposition.     

Stimulatory effects of bradykinin on the ovulatory process in the in vitro-perfused rat ovary

The role of bradykinin in the ovulatory process was investigated using an in vitro-perfused rat ovary model. Stimulation with LH (0.1 micrograms/ml) resulted in 2.6 +/- 0.5 (mean +/- SEM) ovulations per ovary, whereas no ovulations occurred in the nonstimulated control group. Bradykinin (5 microM) added to the perfusion system hourly for 10 h induced 2 of 5 ovaries to ovulate, with 2 and 3 ovulations, respectively. When bradykinin (5 microM) was given as a single dose at 5 or 10 h after LH, the ovulation rate was significantly increased to 11.0 +/- 2.8 and 8.6 +/- 2.0 ovulations per ovary, respectively. A competitive bradykinin antagonist, phenylalanine bradykinin, inhibited the bradykinin-induced increase in LH-stimulated ovulations. The addition of LH, but not of bradykinin, increased the levels of prostaglandin endoperoxide synthase in granulosa cells, but the levels of the enzyme in the residual ovarian tissue were negligible. In contrast, prostacyclin synthase was predominantly located in the residual ovarian tissue. This enzyme was not affected by LH or bradykinin. LH increased the tissue levels of prostaglandins, predominantly prostaglandin E2 (PGE2), at 7 h, whereas the stimulatory effect of bradykinin was smaller, with a preferential increase in prostacyclin (prostaglandin I2) levels. This study indicates a modulatory role of bradykinin, possibly involving prostacyclin late in the ovulatory process, in the rat.     

The effect of heterochromatin on synapsis of the sex chromosomes of Peromyscus (Rodentia, Cricetidae)

The pairing behavior of the sex chromosomes in male and female individuals representing seven species of Peromyscus was analyzed by electron microscopy of silver-stained zygotene and pachytene configurations. Six species possess submetacentric or metacentric X chromosomes with heterochromatic short arms. Sex-chromosome pairing in these species is initiated during early pachynema at an interstitial position on the X and Y axes. Homologous synapsis then progresses in a unidirectional fashion towards the telomeres of the X short arm and the corresponding arm of the heterochromatic Y chromosome. The distinctive pattern of synaptic initiation allowed a late-synapsing bivalent in fetal oocytes to be tentatively identified as that of the X chromosomes. In contrast to the other species, Peromyscus megalops possesses an acrocentric X chromosome and a very small Y chromosome. Sex-chromosome pairing in this species is initiated at the proximal telomeric region during late zygonema, and then proceeds interstitially towards the distal end of the Y chromosome. These observations suggest that the presence of X short-arm heterochromatin and corresponding Y heterochromatin interferes with late-zygotene alignment of the pairing initiation sites, thereby delaying XY synaptic initiation until early pachynema. The pairing initiation sites are conserved in the vicinity of the X and Y centromeres in Peromyscus, and consequently the addition of heterochromatin during sex-chromosome evolution essentially displaces these sites to an interstitial position.     

Regulation of prostaglandin biosynthesis by luteinizing hormone and bradykinin in rat preovulatory follicles in vitro.

Luteinizing hormone (LH) stimulates prostaglandin biosynthesis and steroidogenesis in preovulatory (PO) follicles prior to ovulation. Since the ovulatory process shares many similarities with an inflammatory reaction, mediators of the inflammatory response, such as bradykinin (BK) have been suggested to modulate the effects of LH. In the present study the effect of BK (5 microM) on: 1) prostaglandin biosynthesis (PGE2, PGF2 alpha and 6-keto-PGF1 alpha), 2) the levels of two enzymes in the cyclo-oxygenase pathway, prostaglandin endoperoxide synthase (PGS) and prostacyclin synthase (PCS), and 3) cyclic adenosine 3'5'-monophosphate (cAMP) and progesterone response of PO follicles incubated in vitro were examined. LH (0.1 microgram/ml) stimulated the accumulation of cAMP and progesterone in the medium, while BK had no effect on these parameters. BK exerted a slight stimulatory effect on PGE2, and PGF2 alpha, (p less than or equal to 0.01) but not on 6-keto-PGF1 alpha synthesis, but no changes in PGS or PCS levels could be detected. The effect of LH on prostaglandin biosynthesis was much more pronounced, with an increase of PGE2, PGF2 alpha and 6-keto-PGF1 alpha. LH also induced PGS. The combination of LH and BK did not alter these responses compared to that of LH alone. This study demonstrates that BK stimulates prostaglandin biosynthesis in PO follicles. In contrast to LH, this effect of BK does not seem to involve the adenylate cyclase system, since BK did not stimulate cAMP production. BK did not affect the levels of PGS or PCS, and the stimulatory effect of BK is suggested to involve an increase in the availability of substrate for the cyclo-oxygenase pathway.     

Nucleotide composition of the RNA from RD-114 virions

The 70S and 4S RNA components of a C-type oncornavirus, RD-114, released from a human rhabdomyosarcoma cell line (RD) after transplantation in a kitten, were analyzed for nucleotide constituents. Minor nucleotides were detected only in the 4S RNA populations, and two of these nucleotides were identified as 5,6-dihydro-UMP and pseudo-UMP. The base composition of the RD-114 70S RNA differs from that of the 70S RNA from RD-FeLV (the virus released from the RD cell line after deliberate infection with a feline leukemia virus).     

Population genomic evidence for multiple Pliocene refugia in a montane‐restricted harvestman (Arachnida,Opiliones, Sclerobunus robustus) from the southwestern United States

The integration of ecological niche modelling into phylogeographic analyses has allowed for the identification and testing of potential refugia under a hypothesis‐based framework, where the expected patterns of higher genetic diversity in refugial populations and evidence of range expansion of nonrefugial populations are corroborated with empirical data. In this study, we focus on a montane‐restricted cryophilic harvestman, Sclerobunus robustus, distributed throughout the heterogeneous Southern Rocky Mountains and Intermontane Plateau of southwestern North America. We identified hypothetical refugia using ecological niche models (ENMs) across three time periods, corroborated these refugia with population genetic methods using double‐digest RAD‐seq data and conducted population‐level phylogenetic and divergence dating analyses. ENMs identify two large temporally persistent regions in the mid‐latitude highlands. Genetic patterns support these two hypothesized refugia with higher genetic diversity within refugial populations and evidence for range expansion in populations found outside hypothesized refugia. Phylogenetic analyses identify five to six genetically divergent, geographically cohesive clades of S. robustus. Divergence dating analyses suggest that these separate refugia date to the Pliocene and that divergence between clades pre‐dates the late Pleistocene glacial cycles, while diversification within clades was likely driven by these cycles. Population genetic analyses reveal effects of both isolation by distance (IBD) and isolation by environment (IBE), with IBD more important in the continuous mountainous portion of the distribution, while IBE was stronger in the populations inhabiting the isolated sky islands of the south. Using model‐based coalescent approaches, we find support for postdivergence migration between clades from separate refugia.     

Multilocus genealogies reveal multiple cryptic species and biogeographical complexity in the California turret spider Antrodiaetus riversi (Mygalomorphae, Antrodiaetidae)

Antrodiaetus riversi (Araneae, Antrodiaetidae) is a dispersal-limited, habitat specialized mygalomorph spider species endemic to mesic woodlands of northern and central California. This species occupies a disjunct distribution, with populations in the Sierra Nevada and Coast Ranges, separated by the inhospitable Central Valley. Previous studies of morphological and allozyme variation have suggested that these populations may constitute cryptic species. We investigated the phylogeography of A. riversi using both nuclear and mitochondrial DNA sequences, collected for a comprehensive population sample. These data reveal the presence of at least five species in the A. riversi complex - these species are deeply diverged, and genealogically exclusive in both nuclear and mitochondrial genomes. Each of these species is characterized by extreme population subdivision and deep phylogeographical structuring, consistent with minimal gene flow across the dissected Californian landscape. Three species are restricted to the Coast Ranges, one to high altitudes of the central Sierran Nevada, and one species is found in both ranges. These species have allopatric distributions, although species parapatry is hypothesized to occur in several areas. Species diversification appears to have pulsed in the Late Miocene/Early Pliocene, a timing consistent with biogeographical reconstructions for many Californian taxa, and a time of turbulent geological activity in the region.     

Quantitative assessment of the structural bias in protein-protein interaction assays

With recent publications of several large-scale protein-protein interaction (PPI) studies, the realization of the full yeast interaction network is getting closer. Here, we have analysed several yeast protein interaction datasets to understand their strengths and weaknesses. In particular, we investigate the effect of experimental biases on some of the protein properties suggested to be enriched in highly connected proteins. Finally, we use support vector machines (SVM) to assess the contribution of these properties to protein interactivity. We find that protein abundance is the most important factor for detecting interactions in tandem affinity purifications (TAP), while it is of less importance for Yeast Two Hybrid (Y2H) screens. Consequently, sequence conservation and/or essentiality of hubs may be related to their high abundance. Further, proteins with disordered structure are over-represented in Y2H screens and in one, but not the other, large-scale TAP assay. Hence, disordered regions may be important both in transient interactions and interactions in complexes. Finally, a few domain families seem to be responsible for a large part of all interactions. Most importantly, we show that there are method-specific biases in PPI experiments. Thus, care should be taken before drawing strong conclusions based on a single dataset.