Population genetics reveals bidirectional fish movement across the Continental Divide via an interbasin water transfer

Interbasin water transfers are becoming an increasingly common tool to satisfy municipal and agricultural water demand, but their impacts on movement and gene flow of aquatic organisms are poorly understood. The Grand Ditch is an interbasin water transfer that diverts water from tributaries of the upper Colorado River on the west side of the Continental Divide to the upper Cache la Poudre River on the east side of the Continental Divide. We used single nucleotide polymorphisms to characterize population genetic structure in cutthroat trout (Oncorhynchus clarkii) and determine if fish utilize the Grand Ditch as a movement corridor. Samples were collected from two sites on the west side and three sites on the east side of the Continental Divide. We identified two or three genetic clusters, and relative migration rates and spatial distributions of admixed individuals indicated that the Grand Ditch facilitated bidirectional fish movement across the Continental Divide, a major biogeographic barrier. Previous studies have demonstrated ecological impacts of interbasin water transfers, but our study is one of the first to use genetics to understand how interbasin water transfers affect connectivity between previously isolated watersheds. We also discuss implications on native trout management and balancing water demand and biodiversity conservation.

     

Effects of nutrient (N,P, C) enrichment,grazing and depth upon littoral periphyton of a softwater lake

Three field experiments were performed in Lake Lacawac, PA to determine the importance of potentially limiting nutrients relative to other factors (grazing, depth) in structuring shallow water algal periphyton communities. All three experiments measured periphyton growth (as chlorophyll-a, AFDM or biovolumes of the algal taxa) on artificial clay flower pot substrates which released specified nutrients to their outer surfaces.Control of standing crop by nutrient supply rate vs. grazing was examined in Expt. I. Substrates releasing excess N and P, together with one of 4 levels of C (as bicarbonate) were placed either inside or outside exclosures designed to reduce grazer densities. Chlorophyll-a rose from 1.1–25.6 µg.cm^–2, and some dominant taxa (e.g., Oedogonium, Nostoc, Anacystis) were replaced by others (e.g., Scenedesmus, Cryptomonas) as bicarbonate supply increased. Reductions in invertebrate density did not significantly affect chlorophyll-a at any of the nutrient levels.Reasons for the species shift were further evaluated in Expt. II, using a minielectrode to measure the elevation of pH within the periphyton mat through photosynthetic utilization of bicarbonate. The pH adjacent to pots diffusing N, P and large quantities of bicarbonate, and supporting high chlorophyll-a densities of 32 µg cm^–2, averaged 10.0 compared to 6.3 in the water column. Pots diffusing only N and P supported 0.7 µg chlorophyll-a cm^–2 and elevated pH to 8.2. We suspect that bicarbonate addition favored efficient bicarbonate users (e.g., Scenedesmus), while inhibiting other taxa (e.g., Oedogonium) because of the attendant high pH.Expt. III was designed to test effects of depth (0.1 m vs. 0.5 m) and N (NH₄ ⁺ vs. NO₃ ^–) upon the growth response to bicarbonate observed in Expts. I and II. Similar standing crop and species composition were noted on pots at 0.1 m vs. 0.5 m. Enrichment with NH₄ ⁺ vs. NO₃ ^– also appeared to have little effect upon the periphyton community.Shallow water periphyton communities in Lake Lacawac, when supplied with sufficient N and P, appear to show a distinctive response to increasing bicarbonate concentration and pH which is robust to moderate variation in grazer densities, distance from the water surface, and the form of N enrichment.     

Patterns of divergence during evolution of alpha 1-proteinase inhibitors in mammals

alpha 1-Proteinase inhibitor (alpha 1-PI), a member of the serine proteinase inhibitor superfamily, has a primary role in controlling neutrophil elastase activity within the mammalian circulation. Several studies have indicated that the reactive center region of alpha 1-PI, the amino acid sequence of which is critical to recognition of and binding to target proteinases, is highly divergent within and among species. This appears to be a consequence of accelerated rates of evolution that may have been driven by positive Darwinian selection. In order to examine this and other features of alpha 1-PI evolution in more detail, we have isolated and sequenced cDNAs representing alpha 1- PI mRNAs of the mouse species Mus saxicola and Mus minutoides and have compared these with a number of other mammalian alpha 1-PI mRNAs. Relative to other mammalian mRNAs, the extent of nonsynonymous substitution is generally high throughout the alpha 1-PI mRNA molecule, indicating greater overall rates of amino acid substitution. Within and among mouse species, the 5'-half of the mRNA, but not the 3'-half, has been homogenized by concerted evolution. Finally, the reactive center is under diversifying or positive Darwinian selection in murid rodents (rats, mice) and guinea pigs yet is under purifying selection in primates and artiodactyls. The significance of these findings to alpha 1-PI function and the possible selective forces driving evolution of serpins in general are discussed.      

Phylogenetic utility of the nuclear gene arginine decarboxylase: an example from Brassicaceae

Arginine decarboxylase (ADC) is an important enzyme in the production of putrescine and polyamines in plants. It is encoded by a single or low-copy nuclear gene that lacks introns in sequences studied to date. The rate of Adc amino acid sequence evolution is similar to that of ndhF for the angiosperm family studied. Highly conserved regions provide several target sites for PCR priming and sequencing and aid in nucleotide and amino acid sequence alignment across a range of taxonomic levels, while a variable region provides an increased number of potentially informative characters relative to ndhF for the taxa surveyed. The utility of the Adc gene in plant molecular systematic studies is demonstrated by analysis of its partial nucleotide sequences obtained from 13 representatives of Brassicaceae and 3 outgroup taxa, 2 from the mustard oil clade (order Capparales) and 1 from the related order Malvales. Two copies of the Adc gene, Adc1 and Adc2, are found in all members of the Brassicaceae studied to data except the basal genus Aethionema. The resulting Adc gene tree provides robust phylogenetic data regarding relationships within the complex mustard family, as well as independent support for proposed tribal realignments based on other molecular data sets such as those from chloroplast DNA.      

Design,synthesis, functional and structural characterization of an inhibitor of N-acetylneuraminate-9-phosphate phosphatase: Observation of extensive dynamics in an enzyme/inhibitor complex

The design, synthesis and characterization of a phosphonate inhibitor of N-acetylneuraminate-9-phosphate phosphatase (HDHD4) is described. Compound 3, where the substrate C-9 oxygen was replaced with a nonlabile CH₂ group, inhibits HDHD4 with a binding affinity (IC₅₀ 11 μM) in the range of the native substrate Neu5Ac-9-P (compound 1, K_m 47 μM). Combined SAR, modeling and NMR studies are consistent with the phosphonate group in inhibitor 3 forming a stable complex with native Mg²⁺. In addition to this key interaction, the C-1 carboxylate of the sugar interacts with a cluster of basic residues, K141, R104 and R72. Comparative NMR studies of compounds 3 and 1 with Ca²⁺ and Mg²⁺ are indicative of a highly dynamic process in the active site for the HDHD4/Mg²⁺/3 complex. Possible explanations for this observation are discussed.     

A proposed nonpathogenic biological indicator for thermal inactivation of Listeria monocytogenes.

Listeria innocua M1 was developed as a thermal processing indicator organism for L. monocytogenes by selection of a rifampin- and streptomycin-resistant mutant. zetaD values were 5.6 and 5.8 degrees C, and D (68 degrees C) values were 3.8 and 4.9 s for L. monocytogenes and L. innocua, respectively, in skim milk. The advantages of easy selection, similar heat resistance, and nonpathogenicity make L. innocua M1 appropriate for challenge studies designed to evaluate process lethality with respect to L. monocytogenes.     

Altered Hemodynamic Activity in Conduct Disorder: A Resting-State fMRI Investigation

Background

Youth with conduct disorder (CD) not only inflict serious physical and psychological harm on others, but are also at greatly increased risk of sustaining injuries, developing depression or substance abuse, and engaging in criminal behaviors. The underlying neurobiological basis of CD remains unclear.

Objective

The present study investigated whether participants with CD have altered hemodynamic activity under resting-state conditions.

Methods

Eighteen medication-naïve boys with CD and 18 age- and sex- matched typically developing (TD) controls underwent functional magnetic resonance imaging (MRI) scans in the resting state. The amplitude of low-frequency fluctuations (ALFF) was measured and compared between the CD and TD groups.

Results

Compared with the TD participants, the CD participants showed lower ALFF in the bilateral amygdala/parahippocampus, right lingual gyrus, left cuneus and right insula. Higher ALFF was observed in the right fusiform gyrus and right thalamus in the CD participants compared to the TD group.

Conclusions

Youth with CD displayed widespread functional abnormalities in emotion-related and visual cortical regions in the resting state. These results suggest that deficits in the intrinsic activity of resting state networks may contribute to the etiology of CD.     

VX hydrolysis by human serum paraoxonase 1: a comparison of experimental and computational results

Human Serum paraoxonase 1 (HuPON1) is an enzyme that has been shown to hydrolyze a variety of chemicals including the nerve agent VX. While wildtype HuPON1 does not exhibit sufficient activity against VX to be used as an in vivo countermeasure, it has been suggested that increasing HuPON1's organophosphorous hydrolase activity by one or two orders of magnitude would make the enzyme suitable for this purpose. The binding interaction between HuPON1 and VX has recently been modeled, but the mechanism for VX hydrolysis is still unknown. In this study, we created a transition state model for VX hydrolysis (VX(ts)) in water using quantum mechanical/molecular mechanical simulations, and docked the transition state model to 22 experimentally characterized HuPON1 variants using AutoDock Vina. The HuPON1-VX(ts) complexes were grouped by reaction mechanism using a novel clustering procedure. The average Vina interaction energies for different clusters were compared to the experimentally determined activities of HuPON1 variants to determine which computational procedures best predict how well HuPON1 variants will hydrolyze VX. The analysis showed that only conformations which have the attacking hydroxyl group of VX(ts) coordinated by the sidechain oxygen of D269 have a significant correlation with experimental results. The results from this study can be used for further characterization of how HuPON1 hydrolyzes VX and design of HuPON1 variants with increased activity against VX.