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These Are Not The K-Mers You Are Looking For: Efficient Online K-Mer Counting Using A Probabilistic Data Structure, Qingpeng Zhang, Jason Pell, Rosangela Canino-Koning, Adina Chuang Howe, C. Titus Brown
These Are Not The K-Mers You Are Looking For: Efficient Online K-Mer Counting Using A Probabilistic Data Structure, Qingpeng Zhang, Jason Pell, Rosangela Canino-Koning, Adina Chuang Howe, C. Titus Brown
Adina Howe
K-mer abundance analysis is widely used for many purposes in nucleotide sequence analysis, including data preprocessing for de novo assembly, repeat detection, and sequencing coverage estimation. We present the khmer software package for fast and memory efficient online counting of k-mers in sequencing data sets. Unlike previous methods based on data structures such as hash tables, suffix arrays, and trie structures, khmer relies entirely on a simple probabilistic data structure, a Count-Min Sketch. The Count-Min Sketch permits online updating and retrieval of k-mer counts in memory which is necessary to support online k-mer analysis algorithms. On sparse data sets this …
Revealing The Bacterial Butyrate Synthesis Pathways By Analyzing (Meta)Genomic Data, Marius Vital, Adina Chuang Howe, James M. Tiedje
Revealing The Bacterial Butyrate Synthesis Pathways By Analyzing (Meta)Genomic Data, Marius Vital, Adina Chuang Howe, James M. Tiedje
Adina Howe
Butyrate-producing bacteria have recently gained attention, since they are important for a healthy colon and when altered contribute to emerging diseases, such as ulcerative colitis and type II diabetes. This guild is polyphyletic and cannot be accurately detected by 16S rRNA gene sequencing. Consequently, approaches targeting the terminal genes of the main butyrate-producing pathway have been developed. However, since additional pathways exist and alternative, newly recognized enzymes catalyzing the terminal reaction have been described, previous investigations are often incomplete. We undertook a broad analysis of butyrate-producing pathways and individual genes by screening 3,184 sequenced bacterial genomes from the Integrated Microbial …
The Genome And Developmental Transcriptome Of The Strongylid Nematode Haemonchus Contortus, Erich M. Schwarz, Pasi K. Korhonen, Bronwyn E. Campbell, Neil D. Young, Aaron R. Jex, Abdul Jabbar, Ross S. Hall, Alinda Mondal, Adina C. Howe, Jason Pell, Andreas Hofmann, Peter R. Boag, Xing-Quan Zhu, T. Ryan Gregory, Alex Loukas, Brian A. Williams, Igor Antoshechkin, C. Titus Brown, Paul W. Sternberg, Robin B. Gasser
The Genome And Developmental Transcriptome Of The Strongylid Nematode Haemonchus Contortus, Erich M. Schwarz, Pasi K. Korhonen, Bronwyn E. Campbell, Neil D. Young, Aaron R. Jex, Abdul Jabbar, Ross S. Hall, Alinda Mondal, Adina C. Howe, Jason Pell, Andreas Hofmann, Peter R. Boag, Xing-Quan Zhu, T. Ryan Gregory, Alex Loukas, Brian A. Williams, Igor Antoshechkin, C. Titus Brown, Paul W. Sternberg, Robin B. Gasser
Adina Howe
Background The barber's pole worm, Haemonchus contortus, is one of the most economically important parasites of small ruminants worldwide. Although this parasite can be controlled using anthelmintic drugs, resistance against most drugs in common use has become a widespread problem. We provide a draft of the genome and the transcriptomes of all key developmental stages of H. contortus to support biological and biotechnological research areas of this and related parasites. Results The draft genome of H. contortus is 320 Mb in size and encodes 23,610 protein-coding genes. On a fundamental level, we elucidate transcriptional alterations taking place throughout the life …
A Reference-Free Algorithm For Computational Normalization Of Shotgun Sequencing Data, C. Titus Brown, Adina Howe, Qingpeng Zhang, Alexis B. Pyrkosz, Timothy H. Brom
A Reference-Free Algorithm For Computational Normalization Of Shotgun Sequencing Data, C. Titus Brown, Adina Howe, Qingpeng Zhang, Alexis B. Pyrkosz, Timothy H. Brom
Adina Howe
Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and high sequencing error rates of modern sequencers present many new computational challenges in data interpretation. These challenges have led to the development of new classes of mapping tools and {\em de novo} assemblers. These algorithms are challenged by the continued improvement in sequencing throughput. We here describe digital normalization, a single-pass computational algorithm that systematizes coverage in shotgun sequencing data sets, thereby decreasing sampling variation, discarding redundant data, …
Illumina Sequencing Artifacts Revealed By Connectivity Analysis Of Metagenomic Datasets, Adina Chuang Howe, Jason Pell, Rosangela Canino-Koning, Rachel Mackelprang, Susanna Tringe, Janet Jansson, James M. Tiedje, C. Titus Brown
Illumina Sequencing Artifacts Revealed By Connectivity Analysis Of Metagenomic Datasets, Adina Chuang Howe, Jason Pell, Rosangela Canino-Koning, Rachel Mackelprang, Susanna Tringe, Janet Jansson, James M. Tiedje, C. Titus Brown
Adina Howe
Sequencing errors and biases in metagenomic datasets affect coverage-based assemblies and are often ignored during analysis. Here, we analyze read connectivity in metagenomes and identify the presence of problematic and likely a-biological connectivity within metagenome assembly graphs. Specifically, we identify highly connected sequences which join a large proportion of reads within each real metagenome. These sequences show position-specific bias in shotgun reads, suggestive of sequencing artifacts, and are only minimally incorporated into contigs by assembly. The removal of these sequences prior to assembly results in similar assembly content for most metagenomes and enables the use of graph partitioning to decrease …
Assembling Large, Complex Environmental Metagenomes, Adina Howe, Janet Jansson, Stephanie A. Malfatti, James M. Tiedje, C. Titus Brown
Assembling Large, Complex Environmental Metagenomes, Adina Howe, Janet Jansson, Stephanie A. Malfatti, James M. Tiedje, C. Titus Brown
Adina Howe
The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approaches, digital normalization and partitioning, to make large metagenome assemblies more comput\ ationaly tractable. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils. The predicted functional content and phylogenetic …
Potential For Nitrogen Fixation And Nitrification In The Granite-Hosted Subsurface At Henderson Mine, Co, Elizabeth D. Swanner, Alexis S. Templeton
Potential For Nitrogen Fixation And Nitrification In The Granite-Hosted Subsurface At Henderson Mine, Co, Elizabeth D. Swanner, Alexis S. Templeton
Elizabeth D. Swanner
The existence of life in the deep terrestrial subsurface is established, yet few studies have investigated the origin of nitrogen that supports deep life. Previously, 16S rRNA gene surveys cataloged a diverse microbial community in subsurface fluids draining from boreholes 3000 feet deep at Henderson Mine, CO, USA (Sahl et al., 2008). The prior characterization of the fluid chemistry and microbial community forms the basis for the further investigation here of the source of NH4+. The reported fluid chemistry included N2, NH4+ (5–112 μM), NO2− (27–48 μM), and NO3− (17–72 μM). In this study, the correlation between low NH4+ concentrations …
Jncml-Like, An Ef-Hand Motif-Containing Gene Seasonally Upregulated In The Transition Zone Of Black Walnut (Juglans Nigra L.), Priyanka Surana, Zhonglian Huang, Daisuke Kihara, Richard Meilan, Keith Woeste
Jncml-Like, An Ef-Hand Motif-Containing Gene Seasonally Upregulated In The Transition Zone Of Black Walnut (Juglans Nigra L.), Priyanka Surana, Zhonglian Huang, Daisuke Kihara, Richard Meilan, Keith Woeste
Priyanka Surana
The economic value of a black walnut (Juglans nigra L.) tree is strongly determined by the quality and quantity of darkly colored heartwood in its stem. To understand the regulation of heartwood formation, we analyzed the region of heartwood formation in walnut stems (i.e., the transition zone, TZ) for the expression of 80 ESTs. Semi-quantitative RT-PCR and real-time PCR was performed to detect expression changes of candidate genes in the TZ and sapwood of trees harvested in summer and fall. Results revealed that the transcript of a clone containing two presumed EF-hand motifs was expressed at higher levels in the …
Genetic Analysis Of The Federally Endangered Winged Mapleleaf Mussel To Aid Proposed Re-Introduction Efforts, Kevin J. Roe
Genetic Analysis Of The Federally Endangered Winged Mapleleaf Mussel To Aid Proposed Re-Introduction Efforts, Kevin J. Roe
Kevin J. Roe
The winged mapleleaf, Quadrula fragosa, historically occurred in the Mississippi, Tennessee, Ohio, and Cumberland river drainages, but has suffered severe population and range reductions. At the time that the species was federally listed as endangered, its range was thought to have been reduced to a stretch of the St. Croix River between northwestern Wisconsin and east-central Minnesota. Recently, morphologically “Q. fragosa-like” specimens were discovered at sites in Arkansas (Ouachita River and Saline River), Missouri (Bourbeuse River), and Oklahoma (Little River). Subsequently, a plan was proposed to re-introduce Q. fragosa into portions of its historic range where its been extirpated from …
Raman Multiplexers For Alternative Gene Splicing, Lan Sun, Chenxu Yu, Joseph Irudayaraj
Raman Multiplexers For Alternative Gene Splicing, Lan Sun, Chenxu Yu, Joseph Irudayaraj
Chenxu Yu
Nonfluorescent labels were used for an array-format multiplex detection of alternative splice junctions of breast cancer susceptibility gene 1 (BRCA1) by surface-enhanced Raman scattering (SERS). A four-plex detection scheme using nonfluorescent labels was demonstrated for DNA sequences specific to four BRCA1 alternative splice variants: Δ(11q) (the last 3309 nt deleted from exon 11), Δ(9, 10) (exon 9 and 10 deleted), Δ(5) (exon 5 deleted), and Δ(5q, 6) (the last 22 nt of exon 5 and the entire exon 6 is deleted). This is the first proof-of-concept study to apply SERS-based detection using nonfluorescent labels to investigate alternative gene splicing. Detection …
Mechanism Of High-Mobility Group Protein B Enhancement Of Progesterone Receptor Sequence-Specific Dna Binding, James S. Adelman, Sarah C. Roemer, Mair E.A. Churchill, Dean P. Edwards
Mechanism Of High-Mobility Group Protein B Enhancement Of Progesterone Receptor Sequence-Specific Dna Binding, James S. Adelman, Sarah C. Roemer, Mair E.A. Churchill, Dean P. Edwards
James S. Adelman
The DNA-binding domain (DBD) of progesterone receptor (PR) is bipartite containing a zinc module core that interacts with progesterone response elements (PRE), and a short flexible carboxyl terminal extension (CTE) that interacts with the minor groove flanking the PRE. The chromosomal high-mobility group B proteins (HMGB), defined as DNA architectural proteins capable of bending DNA, also function as auxiliary factors that increase the DNA-binding affinity of PR and other steroid receptors by mechanisms that are not well defined. Here we show that the CTE of PR contains a specific binding site for HMGB that is required for stimulation of PR-PRE …
Surface-Enhanced Raman Scattering Based Nonfluorescent Probe For Multiplex Dna Detection, Lan Sun, Chenxu Yu, Joseph Irudayaraj
Surface-Enhanced Raman Scattering Based Nonfluorescent Probe For Multiplex Dna Detection, Lan Sun, Chenxu Yu, Joseph Irudayaraj
Chenxu Yu
To provide rapid and accurate detection of DNA markers in a straightforward, inexpensive, and multiplex format, an alternative surface-enhanced Raman scattering based probe was designed and fabricated to covalently attach both DNA probing sequence and nonfluorescent Raman tags to the surface of gold nanoparticles (DNA-AuP-RTag). The intensity of Raman signal of the probes could be controlled through the surface coverage of the nonfluorescent Raman tags (RTags). Detection sensitivity of these probes could be optimized by fine-tuning the amount of DNA molecules and RTags on the probes. Long-term stability of the DNA-AuP-RTag probes was found to be good (over 3 months). …
Applications Of Transposable Elements In Fish For Transgenesis And Functional Genomics, Perry B. Hackett, Karl J. Clark, Stephen C. Ekker, Jeffrey J. Essner
Applications Of Transposable Elements In Fish For Transgenesis And Functional Genomics, Perry B. Hackett, Karl J. Clark, Stephen C. Ekker, Jeffrey J. Essner
Jeffrey J. Essner
Transgenic fish were first made more than 30 years ago. Since then a variety of methods and const ructs have been tested for introducing genetic sequences into fish for scientitlc investigations as well as commercial purposes. Here we review transposable clements and t heir applications in fish. Transposons can be used to deliver genes to chromosomes to confer new traits or as insertional agents and traps to uncover the functions and expression patterns of natural genes in chromosomes. Two DNA transposons have been characterized for transposon-based gene transfer and insertional mutagenesis. The t1rst is d1e Sleeping Beauty transposon system that …
Bifunctional Abietadiene Synthase: Mutual Structural Dependence Of The Active Sites For Protonation-Initiated And Ionization-Initiated Cyclizations, Reuben J. Peters, Ora A. Carter, Yan Zhang, Brian W. Matthews, Rodney B. Croteau
Bifunctional Abietadiene Synthase: Mutual Structural Dependence Of The Active Sites For Protonation-Initiated And Ionization-Initiated Cyclizations, Reuben J. Peters, Ora A. Carter, Yan Zhang, Brian W. Matthews, Rodney B. Croteau
Reuben J. Peters
Abietadiene synthase from grand fir catalyzes two sequential, mechanistically distinct cyclizations, of geranylgeranyl diphosphate and of copalyl diphosphate, in the formation of a mixture of abietadiene isomers as the committed step of diterpenoid resin acid biosynthesis. Each reaction is independently conducted at a separate active site residing in what were considered to be structurally distinct domains typical of terpene cyclases. Despite the presence of an unusual 250-residue N-terminal insertional element, a tandem pair of charged residues distal to the insertion was shown to form a functional part of the C-terminal active site. Because abietadiene synthase resembles the ancestral plant terpene …
Jun Dimerization Protein 2 Functions As A Progesterone Receptor N-Terminal Domain Coactivator, James S. Adelman, Suzanne E. Wardell, Viroj Boonyaratanakornkit, Ami Aronheim
Jun Dimerization Protein 2 Functions As A Progesterone Receptor N-Terminal Domain Coactivator, James S. Adelman, Suzanne E. Wardell, Viroj Boonyaratanakornkit, Ami Aronheim
James S. Adelman
The progesterone receptor (PR) contains two transcription activation function (AF) domains, constitutive AF-1 in the N terminus and AF-2 in the C terminus. AF-2 activity is mediated by a hormone-dependent interaction with a family of steroid receptor coactivators (SRCs). SRC-1 can also stimulate AF-1 activity through a secondary domain that interacts simultaneously with the primary AF-2 interaction site. Other protein interactions and mechanisms that mediate AF-1 activity are not well defined. By interaction cloning, we identified an AP-1 family member, Jun dimerization protein 2 (JDP-2), as a novel PR-interacting protein. JDP-2 was first defined as a c-Jun interacting protein that …
Mechanism Of Abietadiene Synthase Catalysis: Stereochemistry And Stabilization Of The Cryptic Pimarenyl Carbocation Intermediates, Reuben J. Peters, Matthew M. Ravn, Robert M. Coates, Rodney Croteau
Mechanism Of Abietadiene Synthase Catalysis: Stereochemistry And Stabilization Of The Cryptic Pimarenyl Carbocation Intermediates, Reuben J. Peters, Matthew M. Ravn, Robert M. Coates, Rodney Croteau
Reuben J. Peters
Abietadiene synthase (AS) catalyzes the complex cyclization-rearrangement of (E,E,E)-geranylgeranyl diphosphate (8, GGPP) to a mixture of abietadiene (1a), double bond isomers 2a-4a and pimaradienes 5a-7a as a key step in the biosynthesis of the abietane resin acid constituents (1b-4b) of conifer oleoresin. The reaction proceeds at two active sites by way of the intermediate, copalyl diphosphate (9). In the second site, a putative tricyclic pimaradiene or pimarenyl(+) carbocation intermediate of undefined C13 stereochemistry and annular double bond position is formed. Three 8-oxy-17-nor analogues of 9 (17 and 19a,b) and three isomeric 15,16-bisnorpimarenyl-N-methylamines (26a-c) were synthesized and evaluated as alternative substrates …
Molecular Systematics Of The Freshwater Mussel Genus Potamilu (Bivalvia: Unionidae), Kevin J. Roe, Charles Lydeard
Molecular Systematics Of The Freshwater Mussel Genus Potamilu (Bivalvia: Unionidae), Kevin J. Roe, Charles Lydeard
Kevin J. Roe
Few explicit hypotheses for the relationships of unionid mussels exist. The absence of explicit phylogenetic hypotheses is problematic and is in part responsible for the lack of taxonomic stability seen in this group. In this paper we examine the relationships of mussels in the genus Potamilus, based upon the DNA sequences of a 600 base pair portion of the first subunit of the mitochondrial cytochrome c oxidase (COI) gene. We also examine the genetic distinctiveness of populations of the inflated heelsplitter P. inflatus. The molecular phylogeny indicates that Potamilus is paraphyletic with Leptodea fragilis and Lampsilis ornata nested between P. …
Recombinant Soluble Epoxide Hydrolase, Bruce D. Hammock, David F. Grant, Jeffrey K. Beetham
Recombinant Soluble Epoxide Hydrolase, Bruce D. Hammock, David F. Grant, Jeffrey K. Beetham
Jeffrey K. Beetham
The present invention relates to nucleic acid sequences and methods useful for producing recombinant human soluble epoxide hydrolase (sEH).
Gene Evolution Of Epoxide Hydrolases And Recommended Nomenclature, Jeffrey K. Beetham, David Grant, Michael Arand, Joan Garbarino, Tomohiro Kiyosue, Franck Pinot, Franz Oesch, William R. Belknap, Kazuo Shinosaki, Bruce D. Hammock
Gene Evolution Of Epoxide Hydrolases And Recommended Nomenclature, Jeffrey K. Beetham, David Grant, Michael Arand, Joan Garbarino, Tomohiro Kiyosue, Franck Pinot, Franz Oesch, William R. Belknap, Kazuo Shinosaki, Bruce D. Hammock
Jeffrey K. Beetham
We have analyzed amino acid sequence relationships among soluble and microsomal epoxide hydrolases, haloacid dehalogenases, and a haloalkane dehalogenase. The amino-terminal residues (1-229) of mammalian soluble epoxide hydrolase are homologous to a haloacid dehalogenase. The carboxy-terminal residues (230-554) of mammalian soluble epoxide hydrolase are homologous to haloalkane dehalogenase, to plant soluble epoxide hydrolase, and to microsomal epoxide hydrolase. The shared identity between the haloacid and haloalkane dehalogenases does not indicate relatedness between these two types of dehalogenases. The amino-terminal and carboxy-terminal homologies of mammalian soluble epoxide hydrolase to. the respective dehalogenases suggests that this epoxide hydrolase, but not the soluble …
Identification And Prevalence Of A Genetic Defect That Causes Leukocyte Adhesion Deficiency In Holstein Cattle, Dale E. Shuster, Marcus E. Kehrli Jr., Mark R. Ackermann, R. O. Gilbert
Identification And Prevalence Of A Genetic Defect That Causes Leukocyte Adhesion Deficiency In Holstein Cattle, Dale E. Shuster, Marcus E. Kehrli Jr., Mark R. Ackermann, R. O. Gilbert
Mark R. Ackermann
Two point mutations were identified within the gene encoding bovine CD18 in a Holstein calf afflicted with leukocyte adhesion deficiency (LAD). One mutation causes an aspartic acid to glycine substitution at amino acid 128 (D128G) in the highly conserved extracellular region of this adhesion glycoprotein, a region where several mutations have been found to cause human LAD. The other mutation is silent. Twenty calves with clinical symptoms of LAD were tested, and all were homozygous for the D128G allele. In addition, two calves homozygous for the D128G allele were identified during widespread DNA testing, and both were subsequently found to …
Molecular-Marker-Facilitated Investigations Of Quantitative-Trait Loci In Maize. I. Numbers, Genomic Distribution And Types Of Gene Action, Jonathan F. Wendel, M. D. Edwards, Charles W. Stuber
Molecular-Marker-Facilitated Investigations Of Quantitative-Trait Loci In Maize. I. Numbers, Genomic Distribution And Types Of Gene Action, Jonathan F. Wendel, M. D. Edwards, Charles W. Stuber
Jonathan F. Wendel
Individual genetic factors which underlie variation in quantitative traits of maize were investigated in each of two F 2 populations by examining the mean trait expressions of genotypic classes at each of 17-20 segregating marker loci. It was demonstrated that the trait expression of marker locus classes could be interpreted in terms of genetic behavior at linked quantitative trait loci (QTLs). For each of 82 traits evaluated, QTLs were detected and located to genomic sites. The numbers of detected factors varied according to trait, with the average trait significantly influenced by almost two-thirds of the marked genomic sites. Most of …
Additional Mapping Of Isozyme Loci: Localization Of Acp4, Dia2, Adkl, Tpi3, And Sadl, Jonathan F. Wendel, Major M. Goodman, Charles W. Stuber
Additional Mapping Of Isozyme Loci: Localization Of Acp4, Dia2, Adkl, Tpi3, And Sadl, Jonathan F. Wendel, Major M. Goodman, Charles W. Stuber
Jonathan F. Wendel
We recently listed the isozyme loci being studied by starch gel electrophoresis in our laboratory and summarized the available mapping data in a series of reports (Wendel et al., MGCNL 59:87-90). Subsequent work has resulted in further clarification of the chromosomal locations of markers on chromosomes 1 (Acp4, Dia2), 6 (Adkl), 8 (Tpi3), and 10 (Sadl). Previously unreported information on these loci and their chromosomal locations follows.
Tpi4 Is Located Near The Centromere On The Long Arm Of Chromosome 3, Jonathan F. Wendel, J. B. Beckett
Tpi4 Is Located Near The Centromere On The Long Arm Of Chromosome 3, Jonathan F. Wendel, J. B. Beckett
Jonathan F. Wendel
Tpi4, one of the three genes encoding cytosolic triose phosphate isomerase isozymes, was earlier shown to be on 3L between Pgd2 (phosphogluconate dehydrogenase) and the centromere (Wendel et al., MNL 59:88). In an effort to better localize Tpi4, a series of crosses was made between Tpi4 testers and stocks carrying three B-A translocations believed to be near the centromere on 3L.
Comparison Of Africanized And European Queen-Mating Colonies In Venezuela, Richard L. Hellmich Ii, Robert G. Danka, Thomas E. Rinderer, Anita M. Collins
Comparison Of Africanized And European Queen-Mating Colonies In Venezuela, Richard L. Hellmich Ii, Robert G. Danka, Thomas E. Rinderer, Anita M. Collins
Richard L Hellmich
Africanized queen-mating colonies produced fewer mated queens (P < 0.05), absconded more (P < 0.001) and had more population dwindling (P < 0.03) when compared to European queenmating colonies. Africanized colonies most affected by these factors were 5-1 nuclei, the type of mating nuclei most commonly used by U.S. queen producers. Efficiency of queen production was increased by doubling bee populations and hive volume and by adding brood.
Male Reproductive Parasitism: A Factor In The Africanization Of European Honey-Bee Populations, Thomas E. Rinderer, Richard L. Hellmich Ii, Anita M. Collins, Robert G. Danka
Male Reproductive Parasitism: A Factor In The Africanization Of European Honey-Bee Populations, Thomas E. Rinderer, Richard L. Hellmich Ii, Anita M. Collins, Robert G. Danka
Richard L Hellmich
Africanized drone honey bees (Apis mellifera) migrate into European honey-bee colonies in large numbers, but Africanized colonies only rarely host drones from other colonies. This migration leads to a strong mating advantage for Africanized bees since it both inhibits European drone production and enhances Africanized drone production
Localization Of Two New Isozyme Loci, Hexl And Tpi4, To Chromosome 3, Jonathan F. Wendel, Charles W. Stuber, Major M. Goodman
Localization Of Two New Isozyme Loci, Hexl And Tpi4, To Chromosome 3, Jonathan F. Wendel, Charles W. Stuber, Major M. Goodman
Jonathan F. Wendel
Recent work with starch gel electrophoresis of coleoptile extracts has indicated that Hexl, the structural locus for the most anodal set of hexokinase isozymes, and Tpi4, which encodes the slowest migrating set of triose phosphate isomerase bands, are located on chromosome 3.
Mapping Data For 34 Isozyme Loci Currently Being Studied, Jonathan F. Wendel, Charles W. Stuber, Major M. Goodman
Mapping Data For 34 Isozyme Loci Currently Being Studied, Jonathan F. Wendel, Charles W. Stuber, Major M. Goodman
Jonathan F. Wendel
With the recent localization of several new loci, a composite listing of these loci and chromosomal locations has been compiled and is shown in Table 1. Although locations of some of the loci are tentative, many are very precisely located from studies involving 1600 to more than 1900 F2 plants.
Linkage Relationships Between A New Locus, Hex2, And Previously Assigned Loci On Chromosome 6, Jonathan F. Wendel, Charles W. Stuber, Major M. Goodman
Linkage Relationships Between A New Locus, Hex2, And Previously Assigned Loci On Chromosome 6, Jonathan F. Wendel, Charles W. Stuber, Major M. Goodman
Jonathan F. Wendel
Starch gel electrophoresis of maize coleoptile extracts in our laboratory has shown two zones of staining for isozymes of hexokinase. Genetic analyses 9 indicate that the slower migrating set of bands is encoded by the structural gene Hex2 and that the enzyme is monomeric. Recent linkage analyses and work with B-A translocation stocks (generously supplied by Jack Beckett) have allowed for the placement ofHex2 on the long arm of chromosome 6. Its location relative to other markers on 6L was determined from the analysis of two very large F2 populations generated for other reasons.
Twelve New Isozyme Loci In Maize: Progress Report On Chromosomal Locations, The Subunit Composition, And Subcellular Localization Of Their Products, Jonathan F. Wendel, Charles W. Stuber, Major M. Goodman
Twelve New Isozyme Loci In Maize: Progress Report On Chromosomal Locations, The Subunit Composition, And Subcellular Localization Of Their Products, Jonathan F. Wendel, Charles W. Stuber, Major M. Goodman
Jonathan F. Wendel
To improve the degree to which the com genome is biochemically marked, we have expanded the number of enzyme systems analyzed by starch gel electrophoresis. Seven new enzyme systems encoded by a minimum of 16 loci have been added to the 23 loci used for previous work in our laboratory. A wide range of domestic and exotic maize has been screened for variation at these new loci and genetic analysis of variant electromorphs is well under way. Crosses with B-A translocation stocks (kindly provided by Jack Beckett), previously mapped allozyme loci, and in a few cases morphological markers, are being …
Genetic Divergence Within The Genus Liriodendron (Magnoliaceae), Jonathan F. Wendel, Clifford R. Parks, Norton G. Miller, Karen M. Mcdougal
Genetic Divergence Within The Genus Liriodendron (Magnoliaceae), Jonathan F. Wendel, Clifford R. Parks, Norton G. Miller, Karen M. Mcdougal
Jonathan F. Wendel
The genus Liriodendron L. consists of a southeast Asian-eastern North American disjunct species pair, but the genus had a much wider distribution in the Northern Hemisphere during the late Cretaceous and the Tertiary. Although generally similar in morphology, the two extant species are measurably different. In 1973 and 1977 they were hybridized, and interspecific heterosis was observed in the progeny. After seven years, the interspecific hybrids synthesized in 1973 had a significantly greater biomass than intraspecific hybrids of L. tulipifera. The growth rate of interspecific and intraspecific F2 seedlings was approximately equal. A preliminary survey of flavonoid extracts in L. …