SPECIATIONAL HISTORY IN A DIVERSE CLADE OF HABITAT-SPECIALIZED SPIDERS (ARANEAE: NESTICIDAE: NESTICUS): INFERENCES FROM GEOGRAPHIC-BASED SAMPLING

This paper summarizes the results of an initial effort to reconstruct the speciational history of cave spiders (Nesticus) from the southern Appalachian Mountains of eastern North America. The Appalachian Nesticus fauna includes a large series of about 30 species distributed across islandlike cave and montane habitats. Many of the species are geographically restricted; all of the species are found in allopatry. Observed patterns of morphological variation and biogeographic evidence suggest that species diversification in this lineage may have occurred recently, perhaps in response to Pleistocene climatic fluctuations. To address questions about the spatial and temporal dynamics of Nesticus speciation, while accounting for potential phylogenetic difficulties, I have gathered nuclear and mitochondrial DNA sequences for a sample of individuals from 81 populations representing 28 Nesticus species. Analyses of these data indicate that considerable genetic divergence exists within and among currently recognized morphological species. Consistent with relatively deep species divergences, most of which likely predate the Pleistocene, is a prevailing pattern of phylogenetic concordance between taxonomic species and monophyletic gene tree lineages. The few deviations from monophyly detected can be tentatively attributed to a peripatric mode of speciation. Although species limits as inferred by the molecular data are generally concordant with patterns of morphological continuity and discontinuity in genitalia, there is evidence to suggest that cryptic phylogenetic lineages exist within some morphologically continuous units. This observation, in combination with the general depth of species lineages, makes any argument about rapid evolution in Nesticus genitalic characteristics unnecessary.     

Comparative performance of double‐digest RAD sequencing across divergent arachnid lineages

Next‐generation sequencing technologies now allow researchers of non‐model systems to perform genome‐based studies without the requirement of a (often unavailable) closely related genomic reference. We evaluated the role of restriction endonuclease (RE) selection in double‐digest restriction‐site‐associated DNA sequencing (ddRADseq) by generating reduced representation genome‐wide data using four different RE combinations. Our expectation was that RE selections targeting longer, more complex restriction sites would recover fewer loci than RE with shorter, less complex sites. We sequenced a diverse sample of non‐model arachnids, including five congeneric pairs of harvestmen (Opiliones) and four pairs of spiders (Araneae). Sample pairs consisted of either conspecifics or closely related congeneric taxa, and in total 26 sample pair analyses were tested. Sequence demultiplexing, read clustering and variant calling were performed in the pyRAD program. The 6‐base pair cutter EcoRI combined with methylated site‐specific 4‐base pair cutter MspI produced, on average, the greatest numbers of intra‐individual loci and shared loci per sample pair. As expected, the number of shared loci recovered for a sample pair covaried with the degree of genetic divergence, estimated with cytochrome oxidase I sequences, although this relationship was non‐linear. Our comparative results will prove useful in guiding protocol selection for ddRADseq experiments on many arachnid taxa where reference genomes, even from closely related species, are unavailable.     

Chitosan/polyaniline hybrid conducting biopolymer base impedimetric immunosensor to detect Ochratoxin-A

Chitosan (CS)-polyaniline (PANI) hybrid conducting biopolymer film was obtained on indium-tin-oxide (ITO) electrode using electrochemical polymerization process. Fourier transform infrared (FT-IR) spectra of PANI-CS had showed covalent and hydrogen binding between PANI and CS molecules. Electrochemical impedance spectroscopy (EIS) measurements had showed low charge transfer resistance (R(CT)) of PANI-CS and PANI. Successive rabbit antibody (IgGs) immobilization on PANI-CS, CS and PANI matrixes surface were confirmed with FT-IR and EIS measurements. Ochratoxin-A (OTA) interaction with IgGs had increased R(CT) values and showed linear response up to 10 ng/mL OTA concentration in electrolyte. Relative change in R(CT) was higher in PANI-CS due to higher proportion of carboxylic and hydroxyl functionalities at PANI-CS matrix surfaces. The absolute sensitivity of PANI, CS, and PANI-CS were 16+/-6, 22+/-9 and 53+/-8 Omega mL/ng, respectively derived from slope of linear response up to 10 ng/mL with 1 ng/mL minimum detection limit.     

Mining activity and habitat use by mountain sheep (<Emphasis Type="Italic">Ovis canadensis</Emphasis>)

We studied mountain sheep in the vicinity of three high-wall limestone mines in San Bernardino County, CA, USA to evaluate factors that influenced habitat use and, specifically, to investigate the influence of mining activity on distribution of those specialized ungulates. We used aerial telemetry data to estimate a resource selection function by fitting a logistic regression model and then comparing environmental characteristics at observed sheep locations to those at random locations. Distribution of mountain sheep was most influenced by a fire in 1999 that resulted in an area they avoided. Mountain sheep used steeper slopes, areas of lower terrain roughness, higher elevations, and areas closer to escape terrain than were random points. In contrast, sheep avoided areas near roads (federal and state highways, local roads, and off-road vehicle trails) but used areas near hiking trails and a railway. Water sources had the smallest effect of the factors considered, with sheep being associated with areas further from water points than were random locations. The disturbed area associated with the mines had a moderate influence on distribution, with sheep being associated with areas closer to the mine than were random points. Mining activities can alter terrain features and vegetation structure or composition in a way that promotes occupancy by sheep if they create steep slopes and rugged terrain (escape terrain) or reduce vegetation density or height (i.e., improve visibility). Whether increased occupancy reflects a benefit depends on the demographic responses of those sheep to the resources and conditions available on mine sites; information about those responses remains lacking.     

E-pharmacophore filtering and molecular dynamics simulation studies in the discovery of potent drug-like molecules for chronic kidney disease

Chronic kidney disease (CKD) is a prominent health issue reported globally. The level of the vitamin D receptor (VDR) and cytochrome P450 enzyme 24-hydroxylase (CYP24A1) are crucial in the pathogenesis of secondary hyperparathyroidism (sHPT) in CKD. An elevated expression of the CYP24A1 leads to the deficiency of vitamin D and resistance to vitamin D therapy. Hence, VDR agonists and CYP24A1 antagonists are suggested to CKD patients for the management of biochemical complications. CTA-018 is a recently reported analog and acts as a potent CYP24A1 inhibitor. It inhibits CYP24A1 with an IC₅₀ 27 ± 6 nM, about 10 times more potentially than the non-selective inhibitor ketoconazole (253 ± 20 nM), and it is also been reported to induce the VDR expression. Thus, CTA-018 is under clinical trial among CKD patients. In this study, combined molecular docking and pharmacophore filtering were employed to identify compounds better than CTA-018. A huge set of 9127 compounds from Sweet Lead database were docked into the active site of VDR using Glide XP program. E-pharmacophore was developed from both the targets along with CTA-018. The compounds retrieved from the two different pharmacophore-based screening were re-docked into the active site of CYP24A1. The hits that bind well at both the active sites and matched with the pharmacophore models were considered as possible dual functional molecules against VDR and CYP24A1. Further, molecular dynamics simulation and subsequent energy decomposition analyses were also performed to study the role of specific amino acids in the active site of both VDR and CYP24A1.     

Sequence diversity and molecular evolution of the merozoite surface antigen 2 of plasmodium falciparum

Eleven new alleles of the Plasmodium falciparum merozoite surface antigen 2 (MSA2) from Papua New Guinea were analyzed by direct sequencing of polymerase chain reaction (PCR) products. We have used the sequence information to trace the molecular evolution of MSA2. The repeats of ten alleles belonging to the 3D7 allelic family differed considerably in size, nucleotide sequence, and repeat copy number. In the repeat region of these new alleles, codon usage was extremely biased with an exclusive use of NNT codons. Another new allele sequenced belonged to the FC27 family and confirmed the family-specific conserved structure of 96 and 36 bp repeats. In order to assess sequence microheterogeneity within samples defined as the same genotype by restriction fragment length polymorphism (RFLP), we have analyzed single-strand conformation polymorphism (SSCP) of different samples of the most frequent allele (D10 of the FC27 family) in the study population. No sequence heterogeneity could be detected within the repeat region. Based on analysis of the repeat regions in both allelic families, we discuss the hypothesis of a different evolutionary strategy being represented by each of the allelic families. Received: 8 February 1995 / Accepted: 24 March 1997     

β-Amyloid gene is not present in three copies in autopsy-validated Alzheimer's disease

Recently, it has been suggested that Alzheimer's disease is associated with a duplication of the amyloid precursor protein gene localized to chromosome 21q21. In this study, a cloned DNA probe (B2.3), complementary to the sequence coding the β-amyloid peptide, and DNA polymorphisms adjacent to this sequence were used to determine the number of copies of the β-amyloid gene in DNA isolated from human blood and brain. Individuals with trisomy 21 (Down syndrome) who were heterozygous for the polymorphisms showed a gene-dosage effect, with one allele exhibiting twice the autoradiographic intensity as the other. Heterozygous individuals with Alzheimer's disease and controls showed equal intensities of the two allelic bands, suggesting that there are only two copies of the β-amyloid gene in these individuals. In individuals with Alzheimer's disease and in controls who were homozygous for these polymorphisms, the number of copies of the β-amyloid gene was determined by comparing the autoradiographic intensity of β-amyloid alleles to that of DNA fragments detected by a reference probe. No difference was detected between these two groups.     

Effects of dimethyl sulfoxide on the globally ischemic heart: Possible general relevance to hypothermic organ preservation

Isolated perfused rabbit hearts were made globally ischemic for 2 hr, then reperfused. For 5 min before and after ischemia hearts were perfused with hypothermic (20 or 27 °C), hypoxic, substrate-free cardioplegic solutions, some of which contained 70 mM dimethyl sulfoxide. Postischemic ventricular pressure development, spontaneous heart rate, coronary flow, lactate dehydrogenase release, tissue Ca²⁺ content, and in vitro mitochondrial oxidative phosphorylation were used to evaluate the protective effects of the various solutions. Aside from the expected observations that cold cardioplegia lessens ischemic damage, we found that dimethyl sulfoxide gave no indication that it exacerbated ischemic damage or lessened the protection afforded by cardioplegia. We also found that, compared to values measured in comparable drug-free treated hearts, dimethyl sulfoxide significantly improved mitochondrial State 3 respiratory rates, respiratory control, and oxidative phosphorylation rates, and essentially prevented mitochondrial changes due to ischemia and reperfusion. We propose that dimethyl sulfoxide may act as a “scavenger” of cytotoxic free radicals, many of which are known to be generated by mitochondria during reoxygenation. Since hypoxia, ischemia, and reoxygenation are common accompaniments of most organ preservation protocols, we suggest that low concentrations of dimethyl sulfoxide might serve as a useful adjunct to organ preservation in the nonfrozen state, when cryoprotective concentrations are not needed.     

Salinity adaptation of the invasive New Zealand mud snail (Potamopyrgus antipodarum) in the Columbia River estuary (Pacific Northwest, USA): physiological and molecular studies

In this study, we examine salinity stress tolerances of two populations of the invasive species New Zealand mud snail Potamopyrgus antipodarum, one population from a high salinity environment in the Columbia River estuary and the other from a fresh water lake. In 1996, New Zealand mud snails were discovered in the tidal reaches of the Columbia River estuary that is routinely exposed to salinity at near full seawater concentrations. In contrast, in their native habitat and throughout its spread in the western US, New Zealand mud snails are found only in fresh water ecosystems. Our aim was to determine whether the Columbia River snails have become salt water adapted. Using a modification of the standard amphipod sediment toxicity test, salinity tolerance was tested using a range of concentrations up to undiluted seawater, and the snails were sampled for mortality at daily time points. Our results show that the Columbia River snails were more tolerant of acute salinity stress with the LC₅₀ values averaging 38 and 22 Practical Salinity Units for the Columbia River and freshwater snails, respectively. DNA sequence analysis and morphological comparisons of individuals representing each population indicate that they were all P. antipodarum. These results suggest that this species is salt water adaptable and in addition, this investigation helps elucidate the potential of this aquatic invasive organism to adapt to adverse environmental conditions.