Association genetics of carbon isotope discrimination, height and foliar nitrogen in a natural population of Pinus taeda L

Loblolly pine, Pinus taeda L., is one of the most widely planted, commercially and ecologically important tree species in North America. We took an association genetics approach, using an unimproved population of 380 clonally replicated unrelated trees, to test 3,938 single nucleotide polymorphisms (SNPs) in as many genes for association with phenotypic variation in carbon isotope discrimination, foliar nitrogen concentration and total tree height after two growing seasons. Best linear unbiased prediction (BLUP) was used with a spatial adjustment to remove environmental variation from phenotypic data derived from a common garden experiment. After correction for multiple testing, a total of 14 SNPs were associated with the traits of carbon isotope discrimination (n = 7), height (n = 1) and foliar nitrogen concentration (n = 6) using 380 clones. Tails of the population phenotypic distribution were compared for allele frequency differences, revealing 10 SNPs with allele frequency in at least one tail significantly different from the overall population. Eight associated SNPs were in sequences similar to known genes, such as an AP2 transcription factor related to carbon isotope discrimination and glutamate decarboxylase associated with foliar nitrogen concentration, and others were from unknown genes without homologs in Arabidopsis.

A laccase associated with lignification in loblolly pine xylem

Peroxidase has been thought to be the only enzyme that oxidizes monolignol precursors to initiate lignin formation in plants. A laccase was purified from cell walls of differentiating xylem of loblolly pine and shown to coincide in time and place with lignin formation and to oxidize monolignols to dehydrogenation products in vitro. These results suggest that laccase participates in lignin biosynthesis and therefore could be an important target for genetic engineering to modify wood properties or to improve the digestibility of forage crops.

Does distance affect utilization of substance abuse and mental health services in the presence of transportation services?

Long travel times have been identified as a significant barrier to accessing mental health and other critical services. This study examines whether distance to treatment was a barrier to receiving outpatient mental health and substance abuse care for HIV-positive persons when transportation was provided. Data from a cohort of HIV-positive persons who participated in a year-long substance abuse and mental health treatment programme were examined longitudinally. Transportation, which included buses, taxis, and mileage reimbursement for private transportation, was provided free of charge for participants who needed this assistance. Nearly three-quarters (74%) of participants utilized the transportation services. No statistically significant differences in retention in, or utilization of, the mental health and substance abuse treatment programme were identified by distance to the treatment site. This analysis demonstrated that increased distance to care did not decrease utilization of the treatment programme when transportation was provided to the client when necessary. These results provide preliminary evidence that distance to substance abuse and mental health services need not be a barrier to care for HIV-positive individuals when transportation is provided. Such options may need to be considered when trying to treat geographically dispersed individuals so that efficiencies in treatment can be attained.

Improving health outcomes among individuals with HIV, mental illness, and substance use disorders in the Southeast

Providing behavioral treatment for mental health and substance use disorders among HIV-infected individuals is critical because these disorders have been associated with negative outcomes such as poorer medication adherence. This study examines the effectiveness of an integrated treatment model for HIV-infected individuals who have both substance use and mental disorders. Study participants (n = 141) were recruited through routine mental health and substance abuse screening at tertiary Infectious Disease clinics in North Carolina. The study participants received integrated mental health and substance abuse treatment for one year and were interviewed at three-month intervals. Using linear regression analyses, we detected statistically significant decreases in participants' psychiatric symptomatology, illicit substance use, alcohol use, and inpatient hospital days. Participants also reported fewer emergency room visits and were more likely to be receiving antiretroviral medications and adequate psychotropic medication regimens at follow-up. No changes in sexual risk, physical health, or medical adherence were detected after treatment participation. This integrated treatment model offers an option for treating HIV-infected individuals with mental health and substance use disorders that can be adapted for use in a variety of psychiatric and medical treatment settings.

Gene expression during formation of earlywood and latewood in loblolly pine: expression profiles of 350 genes

The natural variability of wood formation in trees affords opportunities to correlate transcript profiles with the resulting wood properties. We have used cDNA microarrays to study transcript abundance in developing secondary xylem of loblolly pine (Pinus taeda) over a growing season. The cDNAs were selected from a collection of 75 000 ESTs that have been sequenced and annotated (http://web.ahc.umn.edu/biodata/nsfpine/). Cell wall thickness and climatic data were related to earlywood and latewood formation at different time points during the growing season. Seventy-one ESTs showed preferential expression in earlywood or latewood, including 23 genes with no significant similarity to genes in GenBank. Seven genes involved in lignin synthesis were preferentially expressed in latewood. The studies have provided initial insights into the variation of expression patterns of some of the genes related to the wood formation process.

Regeneration of transgenic loblolly pine (Pinus taeda L.) from zygotic embryos transformed with Agrobacterium tumefaciens

Embryos of 24 open-pollinated families of loblolly pine (Pinus teade L.) were used as explants to conduct in vitro regeneration. Then, Agrobacterium tumefaciens strain GV3101 harboring the plasmid pPCV6NFHygGUSINT was used to transform mature zygotic embryos of seven families of loblolly pine. The frequency of transformation varied among families infected with A. tumefaciens. The highest frequency (100%) of transient beta-glucuronidase (GUS)-expressing embryos was obtained from family 11-1029 with over 300 blue spots per embryo. Expression of the GUS reporter gene was observed in cotyledons, hypocotyls, and radicles of co-cultivated mature zygotic embryos, as well as in callus and shoots derived from co-cultivated mature zygotic embryos. Ninety transgenic plants were regenerated from hygromycin-resistant callus derived from families W03. 8-1082 and 11-1029. and 19 transgenic plantlets were established in soil. The presence of the GUS gene in the plant genome was confirmed by polymerase chain reaction. Southern blot, and plant DNA/T-DNA junction analysis. These results suggest that an efficient A. tumefaciens-mediated transformation protocol for stable integration of foreign genes into loblolly pine has been developed and that this transformation system could be useful for future studies on transferring economically important genes to loblolly pine.

Functional genomics and cell wall biosynthesis in loblolly pine

Loblolly pine (Pinus taeda L.) is the most widely planted tree species in the USA and an important tree in commercial forestry world-wide. The large genome size and long generation time of this species present obstacles to both breeding and molecular genetic analysis. Gene discovery by partial DNA sequence determination of cDNA clones is an effective means of building a knowledge base for molecular investigations of mechanisms governing aspects of pine growth and development, including the commercially relevant properties of secondary cell walls in wood. Microarray experiments utilizing pine cDNA clones can be used to gain additional information about the potential roles of expressed genes in wood formation. Different methods have been used to analyze data from first-generation pine microarrays, with differing degrees of success. Disparities in predictions of differential gene expression between cDNA sequencing experiments and microarray experiments arise from differences in the nature of the respective analyses, but both approaches provide lists of candidate genes which should be further investigated for potential roles in cell wall formation in differentiating pine secondary xylem. Some of these genes seem to be specific to pine, while others also occur in model plants such as Arabidopsis, where they could be more efficiently investigated.

Genotypic control of high-frequency adventitious shoot regeneration via somatic organogenesis in loblolly pine

Mature zygotic embryos of 24 genotypes of loblolly pine (Pinus taeda L.) were used as explants to establish an adventitious shoot regeneration system through somatic organogenesis. Callus formation frequencies of 18.2 (genotype 11-1103) -77.7% (genotype 7-100) have been induced from mature zygotic embryos of all genotypes tested on callus induction medium (basal salts) containing 2,4-dichlorophenoxyacetic acid (2,4-D) or alpha-naphthaleneacetic acid (NAA), 6-benzyladenine (BA), and kinetin. Adventitious shoot regeneration via organogenesis with the frequency of 5.4 (genotype 11-1103 and 7-2) -77.2% (genotype 8-1082) was obtained from callus and tissue cultures derived from mature zygotic embryos of 24 genotypes of loblolly pine. The highest mean number of 18 adventitious buds per piece of callus 0.5x0.5 cm(2) in size was obtained from genotype 8-1082. Elongation of adventitious buds was achieved on TE medium supplemented with 0.5 mg/l indole-3-butyric acid (IBA) and 1 mg/l BA. After rooting, regenerated plantlets were established in soil. These results suggested that adventitious shoot regeneration via somatic organogenesis was influenced by the genotypes. The in vitro regeneration procedure established in this investigation could be used for clonal micropropagation of some genotypes of loblolly pine, as well as for establishing a transformation system in coniferous species.

Genetic analysis of cinnamyl alcohol dehydrogenase in loblolly pine: single gene inheritance, molecular characterization and evolution

The gene encoding the monolignol biosynthetic enzyme cinnamyl alcohol dehydrogenase (CAD, E.C. 1.1.1.195) can be expressed in response to different developmental and environmental cues. Control of Cad gene expression could involve either differential regulation of more than one Cad gene or, alternatively combinatorial regulation of a single Cad gene. In loblolly pine (Pinus taeda L.), we found several electrophoretic variants (allozymes) of CAD and a high level of heterozygosity (he = 0.46). Analysis of inheritance patterns of pine CAD allozymes gave segregation ratios that were consistent with Mendelian expectations for a single functional gene. The identity of the full-length Cad cDNA sequence was confirmed by alignment with peptide sequences obtained from purified active enzyme and by extensive similarity to Cad sequences from other species. Southern blot analysis of genomic DNA using the Cad cDNA as a hybridization probe gave simple patterns, consistent with our interpretation that pine Cad is a single-copy gene. Phylogenetic analysis and evolution rate estimates showed that Cad sequences are diverging less rapidly in the gymnosperms than in the angiosperms. The Cad mRNA was present in both lignifying tissues and a non lignifying tissue (the megagametophyte) of pine. The presence of a single gene suggests that different regulatory mechanisms for a single Cad gene, rather than differential regulation of several genes, can account for its expression in response to different cues.

Molecular structure and transformation of the glucose dehydrogenase gene in Drosophila melanogaster

We have precisely mapped and sequenced the three 5' exons of the Drosophila melanogaster Gld gene and have identified the start sites for transcription and translation. The first exon is composed of 335 nucleotides and does not contain any putative translation start codons. The second exon is separated from the first exon by 8 kb and contains the Gld translation start codon. The inferred amino acid sequence of the amino terminus contains two unusual features: three tandem repeats of serine-alanine, and a relatively high density of cysteine residues. P element-mediated transformation experiments demonstrated that a 17.5-kb genomic fragment contains the functional and regulatory components of the Gld gene.

Isolation of the eclosion gene cluster and the developmental expression of the Gld gene in Drosophila melanogaster

During the development of Drosophila melanogaster the expression of glucose dehydrogenase (GLD) changes from non sex-limited to male limited. We have isolated the Gld gene and three other functionally related genes in the eclosion gene cluster by the method of chromosome walking. The Gld gene has been identified by two deletions and a translocation which genetically define the gene. A 2.8-kb RNA has been identified as the putative GLD mRNA. The temporal and spatial expression of this RNA is correlated with the expression of the GLD enzyme and levels of the steroid hormone ecdysterone. Using single-strand antisense probes we have detected three RNA species. However these three transcripts are not derived from the Gld locus. One of these RNAs is weakly detected by the multiple cloning site of the pSP65 vector. The level of detection of this latter RNA is greatly increased by the insertion of a specific Gld gene fragment in the pSP65 vector.