Cover crop species influences soil fungal species richness and community structure.

Despite the well documented link between cover cropping and soil microbiology, the influence of specific cover crop species on soil microbes remains poorly understood. We evaluated how soil fungal communities in a no till system respond to four cover crop treatments: no cover crop (REF), cereal ryegrass (CRYE), wild pennycress (WPEN), and a mix of pea, clover, radish, and oat (PCRO). Soil samples were collected from experimental plots following termination of cover crops from depths of 0-2 cm and 2-4 cm where cover crops had significantly increased soil organic matter. There was no significant interaction between soil depth and cover crop treatment on either alpha diversity or beta diversity. All cover crop treatments (CRYE, PCRO, and WPEN) enhanced soil fungal richness but only CRYE enhanced soil fungal diversity and altered the fungal community structure. Soil depth altered the fungal community structure but had no effect on fungal diversity and richness. Genus Fusarium which includes some of the most economically destructive pathogens was more abundant in REF and PCRO treatments compared to CRYE and WPEN. In contrast, genus Mortierella which is known to promote plant health was more abundant in all cover crop treatments relative to the REF. These findings demonstrate that cover cropping can increase soil fungal species richness and alter fungal community structure, potentially promoting the abundance of beneficial fungi and reducing the abundance of some plant pathogens within the genus Fusarium. These effects are dependent on cover crop species, a factor that should be considered when selecting appropriate cover crops for a particular cropping system.

Human splicing factor SPF45 (RBM17) confers broad multidrug resistance to anticancer drugs when overexpressed--a phenotype partially reversed by selective estrogen receptor modulators.

The splicing factor SPF45 (RBM17) is frequently overexpressed in many solid tumors, and stable expression in HeLa cells confers resistance to doxorubicin and vincristine. In this study, we characterized stable transfectants of A2780 ovarian carcinoma cells. In a 3-day cytotoxicity assay, human SPF45 overexpression conferred 3- to 21-fold resistance to carboplatin, vinorelbine, doxorubicin, etoposide, mitoxantrone, and vincristine. In addition, resistance to gemcitabine and pemetrexed was observed at the highest drug concentrations tested. Knockdown of SPF45 in parental A2780 cells using a hammerhead ribozyme sensitized A2780 cells to etoposide by approximately 5-fold relative to a catalytically inactive ribozyme control and untransfected cells, suggesting a role for SPF45 in intrinsic resistance to some drugs. A2780-SPF45 cells accumulated similar levels of doxorubicin as vector-transfected and parental A2780 cells, indicating that drug resistance is not due to differences in drug accumulation. Efforts to identify small molecules that could block SPF45-mediated drug resistance revealed that the selective estrogen receptor (ER) modulators tamoxifen and LY117018 (a raloxifene analogue) partially reversed SPF45-mediated drug resistance to mitoxantrone in A2780-SPF45 cells from 21-fold to 8- and 5-fold, respectively, but did not significantly affect the mitoxantrone sensitivity of vector control cells. Quantitative PCR showed that ERbeta but not ERalpha was expressed in A2780 transfectants. Coimmunoprecipitation experiments suggest that SPF45 and ERbeta physically interact in vivo. Thus, SPF45-mediated drug resistance in A2780 cells may result in part from effects of SPF45 on the transcription or alternate splicing of ERbeta-regulated genes.

Adeno-Associated Virus (AAV) as a Vector for Gene Therapy.

There has been a resurgence in gene therapy efforts that is partly fueled by the identification and understanding of new gene delivery vectors. Adeno-associated virus (AAV) is a non-enveloped virus that can be engineered to deliver DNA to target cells, and has attracted a significant amount of attention in the field, especially in clinical-stage experimental therapeutic strategies. The ability to generate recombinant AAV particles lacking any viral genes and containing DNA sequences of interest for various therapeutic applications has thus far proven to be one of the safest strategies for gene therapies. This review will provide an overview of some important factors to consider in the use of AAV as a vector for gene therapy.

The role of C:N:P stoichiometry in affecting denitrification in sediments from agricultural surface and tile-water wetlands.

Nutrient stoichiometry within a wetland is affected by the surrounding land use, and may play a significant role in the removal of nitrate (NO3-N). Tile-drained, agricultural watersheds experience high seasonal inputs of NO3-N, but low phosphorus (PO4-P) and dissolved organic carbon (DOC) loads relative to surface water dominated systems. This difference may present stoichiometric conditions that limit denitrification within receiving waterways. We investigated how C:N:P ratios affected denitrification rates of sediments from tile-drained mitigation wetlands incubated for: 0, 5, 10, and 20 days. We then tested whether denitrification rates of sediments from surface-water and tile-drained wetlands responded differently to C:N ratios of 2:1 versus 4:1. Ratios of C:N:P (P < 0.05) and incubation length (P < 0.05) had a significant effect on denitrification in tile-drained wetland sediments. Carbon limitation of denitrification became evident at elevated NO3-N concentrations (20 mg L(-1)). Denitrification measured from tile water and surface water wetland sediments increased significantly (P < 0.05) at the 2:1 and 4:1 C:N treatments. The results from both experiments suggest wetland sediments provide a limiting pool of labile DOC to maintain prolonged NO3-N removal. Also, DOC limitation became more evident at elevated NO3-N concentrations (20 mg L(-1)). Irrespective of NO3-N concentrations, P did not limit denitrification rates. In addition to wetting period, residence time, and maintenance of anaerobic conditions, the availability of labile DOC is playing an important limiting role in sediment denitrification within mitigation wetlands.

The development of molecularly targeted anticancer therapies: an Eli Lilly and Company perspective.

The ability to identify activated pathways that drive the growth and progression of cancer and to develop specific and potent inhibitors of key proteins in these pathways promises to dramatically change the treatment of cancer: A patient's cancer could be characterized at the molecular level and the information used to select the best treatment options. The development of successful therapies not only requires extensive target validation, but also new approaches to evaluating drug efficacy in animal models and in the clinic compared to the development of traditional cytotoxic agents. This article highlights Eli Lilly and Company's approach to developing targeted therapies, from target identification and validation through evaluation in the clinic. A selection of drugs in the Lilly Oncology pipeline is also discussed.

Cloning and functional characterization of the multidrug resistance-associated protein (MRP1/ABCC1) from the cynomolgus monkey.

The multidrug resistance-associated protein 1 (ABCC1) gene from human (hMRP1), dog (canMRP1), and mouse (muMRP1) all encode proteins that efficiently transport the endogenous MRP1 substrate glutathione-S-leukotriene C(4) and confer resistance to anticancer agents, including vincristine and etoposide. hMRP1 also confers resistance to anthracyclines, whereas this is not true of canMRP1 or muMRP1. To determine whether MRP1 from another animal species used in toxicological studies would be more functionally similar to hMRP1, we cloned and characterized two alleles of the MRP1 homologue from the cynomolgus monkey Macaca fascicularis (monMRP1). The monMRP1 cDNAs encode proteins of 1531 residues that are 98, 90, and 88% identical to hMRP1, canMRP1, and muMRP1, respectively. Stable overexpression of both monMRP1 alleles and hMRP1 in transformed human embryonic kidney cells was achieved using an episomal expression vector. Transporters encoded by both monMRP1 alleles were functionally very similar to hMRP1. monMRP1 conferred an increased resistance to vincristine and etoposide and transported glutathione-S-leukotriene C(4) into membrane vesicles. In addition, MRP1-mediated drug resistance was effectively reversed in monMRP1 and hMRP1 transfectants by LY402913, a new MRP1-selective inhibitor in the class of tricyclic isoxazoles. However, monMRP1 transporters conferred a reduced level of resistance to the anthracyclines doxorubicin, daunorubicin, and epirubicin relative to hMRP1, although resistance levels were significant relative to vector control cells. These functional differences between human and monkey MRP1 transporters will need to be considered when designing pharmacokinetic and toxicological studies for the preclinical evaluation of MRP1 modulators.

JavaScript DNA translator: DNA-aligned protein translations.

There are many instances in molecular biology when it is necessary to identify ORFs in a DNA sequence. While programs exist for displaying protein translations in multiple ORFs in alignment with a DNA sequence, they are often expensive, exist as add-ons to software that must be purchased, or are only compatible with a particular operating system. JavaScript DNA Translator is a shareware application written in JavaScript, a scripting language interpreted by the Netscape Communicator and Internet Explorer Web browsers, which makes it compatible with several different operating systems. While the program uses a familiar Web page interface, it requires no connection to the Internet since calculations are performed on the user's own computer. The program analyzes one or multiple DNA sequences and generates translations in up to six reading frames aligned to a DNA sequence, in addition to displaying translations as separate sequences in FASTA format. ORFs within a reading frame can also be displayed as separate sequences. Flexible formatting options are provided, including the ability to hide ORFs below a minimum size specified by the user. The program is available free of charge at the BioTechniques Software Library (www.Biotechniques.com).

Evaluation of the binding of the tricyclic isoxazole photoaffinity label LY475776 to multidrug resistance associated protein 1 (MRP1) orthologs and several ATP- binding cassette (ABC) drug transporters.

Several of the ATP-binding cassette (ABC) transporters confer resistance to anticancer agents and/or antiviral agents when overexpressed in drug-sensitive cells. Recently a MRP1 (ABCC1) tricyclic isoxazole inhibitor, LY475776 was shown to be a glutathione-dependent photoaffinity label of human MRP1 and showed poor labeling of murine mrp1, an ortholog that does not confer anthracycline resistance. In the present study, the specificity of LY475776 was examined for its ability to modulate or photolabel orthologs of MRP1 and several other drug efflux transporters of the ABC transporter family. LY475776 modulated MRP1 and Pgp-mediated resistance (MDR, ABCB1) in, respectively, HeLa-T5 and CEM/VLB(100) cells to both vincristine and doxorubicin. LY475776 photolabeled 170kDa Pgp and was inhibited by the potent Pgp inhibitor LY335979 (Zosuquidar.3HCl). The labeling of the 190kDa MRP1 protein in membranes of HeLa-T5 cells was inhibited by substrates of MRP1 such as leukotriene C(4), vincrisine, and doxorubicin and by the inhibitor, MK571. LY475776 did not photolabel human MRP2 (ABCC2), MRP3 (ABCC3), MRP5 (ABCC5) or breast cancer resistance protein (ABCG2). Because LY475776 photolabels murine mrp1 less well than human MRP1 and binds to a region believed important for anthracycline binding, studies were conducted with monkey and canine MRP1 which also show a reduced ability to confer resistance to anthracyclines. Unlike murine mrp1, both orthologs were photolabeled well by LY475776. These studies indicate that the specificity of LY475776 is fairly limited to Pgp and MRP1 and further studies will help to define the binding regions.

The acyl coenzymeA:monoacylglycerol acyltransferase 3 (MGAT3) gene is a pseudogene in mice but encodes a functional enzyme in rats.

Triglyceride (TAG) absorption involves its initial hydrolysis to fatty acids and monoacylglycerol (MAG), which are resynthesized back to diacylglycerol (DAG) and TAG within enterocytes. The resynthesis of DAG is facilitated by fatty acyl-CoA dependent monoacylglycerol acyltransferases (MGATs). Three MGAT enzymes have been isolated in humans and the expression of MGAT2 and MGAT3 in the intestines suggests their functional role in the TAG absorption. In this paper, we report that the Mogat3 gene appears to be a pseudogene in mice while it is a functional gene in rats. Examination of the mouse genomic Mogat3 sequence revealed multiple changes that would result in a translational stop codon or frameshifts. The rat Mogat3 gene, however, is predicted to encode a functional enzyme of 362 amino acids. Expression of rat MGAT3 in human embryonic kidney 293 (HEK293) cells led to the formation of a 36-kDa protein that displayed significant MGAT but not DGAT activity. Tissue expression analysis of rat MGAT3 by real-time PCR analysis indicated that rat MGAT3 has a high level of expression in intestines and pancreas. Our results thus provide the molecular basis to understand the relative functional role of MGAT2 and MGAT3 and also for future exploration of MGAT3 function in animal models.

Importance of hybridization between indigenous and nonindigenous freshwater species: an overlooked threat to North American biodiversity.

Biodiversity of North American freshwaters is among the greatest in the world. However, due to extensive habitat degradation, pollution, and introductions of nonindigenous species, this biodiversity is also among the most endangered. Unlike habitat degradation and pollution, nonindigenous species represent a permanent loss of biodiversity because their removal or control is often impossible. Most species introduced into nonnative North American ranges, however, are not from Eurasia but have been introduced from geographically isolated regions within North America. Although the ecological effects of introduced species have been widely documented, the effects of hybridization, especially between closely related species, represents an equally serious mechanism of extinction but is much less studied. Identification of which species are likely to hybridize after contact is of critical importance to prevent the further loss of native species. Molecular phylogenetics serves as a powerful tool to identify freshwater species at risk of introgression, if we can assume that genetic distance is a good predictor of the potential for hybridization. Although not a thorough review of all cases of hybridization, this article documents the extent and effects of hybridization in fishes, crayfishes, mussels, and other invertebrates in light of the currently accepted phylogenetic relationships. We suggest this approach may be the first step in addressing the potential threat of hybridization between many of the closely related species in North American fresh waters.

Allopatric genetic origins for sympatric host-plant shifts and race formation in Rhagoletis.

Tephritid fruit flies belonging to the Rhagoletis pomonella sibling species complex are controversial because they have been proposed to diverge in sympatry (in the absence of geographic isolation) by shifting and adapting to new host plants. Here, we report evidence suggesting a surprising source of genetic variation contributing to sympatric host shifts for these flies. From DNA sequence data for three nuclear loci and mtDNA, we infer that an ancestral, hawthorn-infesting R. pomonella population became geographically subdivided into Mexican and North American isolates approximately 1.57 million years ago. Episodes of gene flow from Mexico subsequently infused the North American population with inversion polymorphism affecting key diapause traits, forming adaptive clines. Sometime later (perhaps +/-1 million years), diapause variation in the latitudinal clines appears to have aided North American flies in adapting to a variety of plants with differing fruiting times, helping to spawn several new taxa. Thus, important raw genetic material facilitating the adaptive radiation of R. pomonella originated in a different time and place than the proximate ecological host shifts triggering sympatric divergence.

Human SPF45, a splicing factor, has limited expression in normal tissues, is overexpressed in many tumors, and can confer a multidrug-resistant phenotype to cells.

Our effort to identify novel drug-resistant genes in cyclophosphamide-resistant EMT6 mouse mammary tumors led us to the identification of SPF45. Simultaneously, other groups identified SPF45 as a component of the spliceosome that is involved in alternative splicing. We isolated the human homologue and examined the normal human tissue expression, tumor expression, and the phenotype caused by overexpression of human SPF45. Our analyses revealed that SPF45 is expressed in many, but not all, normal tissues tested with predominant expression in normal ductal epithelial cells of the breast, liver, pancreas, and prostate. Our analyses using tissue microarrays and sausages of tumors indicated that SPF45 is highly expressed in numerous carcinomas including bladder, breast, colon, lung, ovarian, pancreatic, and prostate. Interestingly, this study revealed that overexpression of SPF45 in HeLa, a cervical carcinoma cell line, resulted in drug resistance to doxorubicin and vincristine, two chemotherapeutic drugs commonly used in cancer. To our knowledge, this is the first study showing tumor overexpression of an alternate splicing factor resulting in drug resistance.