Yellow perch genetic structure and habitat use among connected habitats in eastern Lake Michigan

Maintenance of genetic and phenotypic diversity is widely recognized as an important conservation priority, yet managers often lack basic information about spatial patterns of population structure and its relationship with habitat heterogeneity and species movement within it. To address this knowledge gap, we focused on the economically and ecologically prominent yellow perch (Perca flavescens). In the Lake Michigan basin, yellow perch reside in nearshore Lake Michigan, including drowned river mouths (DRMs)—protected, lake‐like habitats that link tributaries to Lake Michigan. The goal of this study was to examine the extent that population structure is associated with Great Lakes connected habitats (i.e., DRMs) in a mobile fish species using yellow perch as a model. Specifically, we tested whether DRMs and eastern Lake Michigan constitute distinct genetic stocks of yellow perch, and if so, whether those stocks migrate between the two connected habitats throughout the year. To do so, we genotyped yellow perch at 14 microsatellite loci collected from 10 DRMs in both deep and littoral habitats during spring, summer, and autumn and two nearshore sites in Lake Michigan (spring and autumn) during 2015–2016 and supplemented our sampling with fish collected in 2013. We found that yellow perch from littoral‐DRM habitats were genetically distinct from fish captured in nearshore Lake Michigan. Our data also suggested that Lake Michigan yellow perch likely use deep‐DRM habitats during autumn. Further, we found genetic structuring among DRMs. These patterns support hypotheses of fishery managers that yellow perch seasonally migrate to and from Lake Michigan, yet, interestingly, these fish do not appear to interbreed with littoral fish despite occupying the same DRM. We recommend that fisheries managers account for this complex population structure and movement when setting fishing regulations and assessing the effects of harvest in Lake Michigan.     

Accurate quantification of dimethylamine (DMA) in human urine by gas chromatography-mass spectrometry as pentafluorobenzamide derivative: evaluation of the relationship between DMA and its precursor asymmetric dimethylarginine (ADMA) in health and disease

Dimethylamine [DMA, (CH(3))(2)NH)] is abundantly present in human urine. Main sources of urinary DMA have been reported to include trimethylamine N-oxide, a common food component, and asymmetric dimethylarginine (ADMA), an endogenous inhibitor of nitric oxide (NO) synthesis. ADMA is excreted in the urine in part unmetabolized and in part after hydrolysis to DMA by dimethylarginine dimethylaminohydrolase (DDAH). Here we describe a GC-MS method for the accurate and rapid quantification of DMA in human urine. The method involves use of (CD(3))(2)NH as internal standard, simultaneous derivatization with pentafluorobenzoyl chloride and extraction in toluene, and selected-ion monitoring of m/z 239 for DMA and m/z 245 for (CD(3))(2)NH in the electron ionization mode. GC-MS analysis of urine samples from 10 healthy volunteers revealed a DMA concentration of 264+/-173 microM equivalent to 10.1+/-1.64 micromol/mmol creatinine. GC-tandem MS analysis of the same urine samples revealed an ADMA concentration of 27.3+/-15.3 microM corresponding to 1.35+/-1.2 micromol/mmol creatinine. In these volunteers, a positive correlation (R=0.83919, P=0.0024) was found between urinary DMA and ADMA, with the DMA/ADMA molar ratio being 10.8+/-6.2. Elevated excretion rates of DMA (52.9+/-18.5 micromol/mmol creatinine) and ADMA (3.85+/-1.65 micromol/mmol creatinine) were found by the method in 49 patients suffering from coronary artery disease, with the DMA/ADMA molar ratio also being elevated (16.8+/-12.8). In 12 patients suffering from end-stage liver disease, excretion rates of DMA (47.8+/-19.7 micromol/mmol creatinine) and ADMA (5.6+/-1.5 micromol/mmol creatinine) were found to be elevated, with the DMA/ADMA molar ratio (9.17+/-4.2) being insignificantly lower (P=0.46). Between urinary DMA and ADMA there was a positive correlation (R=0.6655, P<0.0001) in coronary artery disease, but no correlation (R=0.27339) was found in end-stage liver disease.     

Light- and carbon-signaling pathways. Modeling circuits of interactions

Here, we report the systematic exploration and modeling of interactions between light and sugar signaling. The data set analyzed explores the interactions of sugar (sucrose) with distinct light qualities (white, blue, red, and far-red) used at different fluence rates (low or high) in etiolated seedlings and mature green plants. Boolean logic was used to model the effect of these carbon/light interactions on three target genes involved in nitrogen assimilation: asparagine synthetase (ASN1 and ASN2) and glutamine synthetase (GLN2). This analysis enabled us to assess the effects of carbon on light-induced genes (GLN2/ASN2) versus light-repressed genes (ASN1) in this pathway. New interactions between carbon and blue-light signaling were discovered, and further connections between red/far-red light and carbon were modeled. Overall, light was able to override carbon as a major regulator of ASN1 and GLN2 in etiolated seedlings. By contrast, carbon overrides light as the major regulator of GLN2 and ASN2 in light-grown plants. Specific examples include the following: Carbon attenuated the blue-light induction of GLN2 in etiolated seedlings and also attenuated the white-, blue-, and red-light induction of GLN2 and ASN2 in light-grown plants. By contrast, carbon potentiated far-red-light induction of GLN2 and ASN2 in light-grown plants. Depending on the fluence rate of far-red light, carbon either attenuated or potentiated light repression of ASN1 in light-grown plants. These studies indicate the interaction of carbon with blue, red, and far-red-light signaling and set the stage for further investigation into modeling this complex web of interacting pathways using systems biology approaches.     

Engineering of Candida antarctica lipase B for hydrolysis of bulky carboxylic acid esters

Candida antarctica lipase B (CALB) is a widely used biocatalyst with high activity and specificity for a wide range of primary and secondary alcohols. However, the range of converted carboxylic acids is more narrow and mainly limited to unbranched fatty acids. To further broaden the biotechnological applications of CALB it is of interest to expand the range of converted carboxylic acid and extend it to carboxylic acids that are branched or substituted in close proximity of the carboxyl group. An in silico library of 2400 CALB variants was built and screened in silico by substrate-imprinted docking, a four step docking procedure. First, reaction intermediates of putative substrates are covalently docked into enzyme active sites. Second, the geometry of the resulting enzyme-substrate complex is optimized. Third, the substrate is removed from the complex and then docked again into the optimized structure. Fourth, the resulting substrate poses are rated by geometric filter criteria as productive or non-productive poses. Eleven enzyme variants resulting from the in silico screening were expressed in Escherichia coli BL21 and measured in the hydrolysis of two branched fatty acid esters, isononanoic acid ethyl ester and 2-ethyl hexanoic acid ethyl esters. Five variants showed an initial increase in activity. The variant with the highest wet mass activity (T138S) was purified and further characterized. It showed a 5-fold increase in hydrolysis of isononanoic acid ethyl ester, but not toward sterically more demanding 2-ethyl hexanoic acid ethyl ester.     

Molecular markers reconstruct the invasion history of variable leaf watermilfoil (<Emphasis Type="Italic">Myriophyllum heterophyllum</Emphasis>) and distinguish it from closely related species

Genetic variation is increasingly recognized as an important factor influencing the establishment and spread of introduced species, and depends on both the introduction history and partitioning of genetic variation within and among potential source populations. We examine patterns of genetic variation in native and introduced populations of variable leaf watermilfoil, Myriophyllum heterophyllum, using chloroplast (trnL-F) and ribosomal (ITS) DNA sequences, as well as amplified fragment length polymorphisms (AFLPs). We identify a strong phylogeographic break distinguishing populations located on the Atlantic Coastal Plain (ACP) versus other (“Continental”) portions of the native range. Within these distinct biogeographic regions, we also find genetic variation to be strongly partitioned among populations as analysis of molecular variance (AMOVA) partitioned 91 and 75% of cpDNA and ITS diversity among populations, respectively. We demonstrate that the introduced ranges of variable leaf watermilfoil (northeastern and western US) result from multiple independent introductions from a variety of source populations, including lineages from both the ACP and Continental portions of the native range. In addition, we used our molecular markers to demonstrate that variable leaf watermilfoil is genetically distinct from three closely-related species that it is morphologically similar to. In particular, we demonstrate that M. heterophyllum is clearly distinct from a morphologically similar native species in the western US, M. hippuroides—whose distinctiveness from M. heterophyllum has been questioned—and therefore confirm the introduction of M. heterophyllum in the western US. Furthermore, we provide the first evidence for hybridization between these two species. Finally, our molecular markers identify previously unrecognized genetic variation in these four species, and therefore demonstrate the need for further taxonomic investigation.     

Is Hybridization Responsible for Invasive Growth of Non-indigenous Water-milfoils?

Heterosis, or hybrid vigor, has recently been proposed as a factor promoting invasive growth of some non-indigenous aquatic plant species, particularly those capable of spreading rapidly within and among lakes through clonal reproduction. We tested this hypothesis for variable-leaf water milfoil (Myriophyllum heterophyllum), a non-indigenous aquatic plant that has become a major management and conservation concern in New England. Using nuclear ribosomal DNA, we looked for F₁ hybrid populations of invasive M. heterophyllum in 25 New Hampshire (NH) lakes. In contrast to a previous study that found F₁ hybrid lineages of invasive M. heterophyllum in Connecticut, we did not find hybrids in our study lakes. This result has two implications: (1) pure lineages of M. heterophyllum are also capable of invasive growth, and (2) the distribution of invasive M. heterophyllum lineages (hybrid vs. pure) may be spatially structured across New England. We stress the importance of more detailed distributional and ecological studies for understanding the invasive potential of this species.     

Loopholes in the regulation of invasive species: genetic identifications identify mislabeling of prohibited aquarium plants

Numerous invasive aquatic species introductions can be traced to the aquarium trade. Many potentially harmful aquarium species may be difficult to identify based on morphology alone. As such, some prohibited or invasive species may be available for purchase if they are mislabeled as species without restrictions. Here we compare molecular identifications to internet vendors’ identifications for accessions of a popular genus of aquarium plants that are difficult to distinguish morphologically (Myriophyllum; watermilfoils). Specifically, we identified the extensive mislabeling of M. heterophyllum—an invasive species in the northeastern and western US. Furthermore, genotypes of M. heterophyllum found in our aquarium survey have also been found in invasive populations, suggesting their potential introduction through escape from aquaria, water gardens, or nurseries. Two additional taxa were sold under incorrect names. Finally, our survey revealed that Myriophyllum taxa present in the aquarium trade generally have poorly known distributions and ecologies, and therefore their invasive potential is unknown. Our study confirms that molecular identification methods can provide a valuable tool to survey commercial pathways for potentially harmful species that are otherwise difficult to identify.     

Practical application of different enzymes immobilized on sepabeads

The immobilization of an endoglucanase, benzoylformate decarboxylase (BFD) from Pseudomonas putida, as well as of lipase B from Candida antarctica (CALB) onto the carrier supports Sepabeads EC-EP, Sepabeads EC-EA, and Sepabeads EC-BU was accomplished. It is shown that via these immobilized biocatalysts the synthesis of both fine and bulk chemicals is possible. This is illustrated by the syntheses of polyglycerol esters and (S)-hydroxy phenyl propanone. The benefit of immobilization is illustrated by repetitive use in a bubble column reactor as well as in a stirred tank reactor. High stability of two biocatalysts was achieved and reusability up to eight times was demonstrated. The comparison of CALB immobilized on Sepabeads EC-EP to Novozym 435 shows similar activity. Dedicated to Prof. Dr. Christian Wandrey on the occasion of his 65th birthday.     

Scalable preparation of silCoat‐biocatalysts by use of a fluidized‐bed reactor

SilCoat‐biocatalysts are immobilized enzyme preparations with an outstanding robustness against leaching and mechanical stress and therefore promising tools for technical synthesis. They consist of a composite material made from a solid enzyme carrier and silicone. In this study, a method has been found to enable provision of these catalysts in large scale. It makes use of easily scalable fluidized‐bed technology and, in contrast to the original method, works in almost complete absence of organic solvent. Thus, it is both a fast and safe method. When the Pt‐catalyst required for silicone formation is cast on the solid enzyme carrier before coating, resulting composites resemble the original preparations in morphology, catalytic activity, and stability against leaching and mechanical forces. Only the maximum total content of silicone in the composites lies about 10% w/w lower resulting in an overall leaching stability below the theoretical maximum. When the Pt‐catalyst is mixed with cooled siloxane solution before coating, surficial coating of the enzyme carriers is achieved, which provides maximum leaching stability at very low silicone consumption. Thus, the technology offers the possibility to produce both composite and for the first time also core‐shell silCoat‐particles, and optimize leaching stability over mechanical strength according to process requirements.