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1.  A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time 
Shaffer, Christopher D. | Alvarez, Consuelo J. | Bednarski, April E. | Dunbar, David | Goodman, Anya L. | Reinke, Catherine | Rosenwald, Anne G. | Wolyniak, Michael J. | Bailey, Cheryl | Barnard, Daron | Bazinet, Christopher | Beach, Dale L. | Bedard, James E. J. | Bhalla, Satish | Braverman, John | Burg, Martin | Chandrasekaran, Vidya | Chung, Hui-Min | Clase, Kari | DeJong, Randall J. | DiAngelo, Justin R. | Du, Chunguang | Eckdahl, Todd T. | Eisler, Heather | Emerson, Julia A. | Frary, Amy | Frohlich, Donald | Gosser, Yuying | Govind, Shubha | Haberman, Adam | Hark, Amy T. | Hauser, Charles | Hoogewerf, Arlene | Hoopes, Laura L. M. | Howell, Carina E. | Johnson, Diana | Jones, Christopher J. | Kadlec, Lisa | Kaehler, Marian | Silver Key, S. Catherine | Kleinschmit, Adam | Kokan, Nighat P. | Kopp, Olga | Kuleck, Gary | Leatherman, Judith | Lopilato, Jane | MacKinnon, Christy | Martinez-Cruzado, Juan Carlos | McNeil, Gerard | Mel, Stephanie | Mistry, Hemlata | Nagengast, Alexis | Overvoorde, Paul | Paetkau, Don W. | Parrish, Susan | Peterson, Celeste N. | Preuss, Mary | Reed, Laura K. | Revie, Dennis | Robic, Srebrenka | Roecklein-Canfield, Jennifer | Rubin, Michael R. | Saville, Kenneth | Schroeder, Stephanie | Sharif, Karim | Shaw, Mary | Skuse, Gary | Smith, Christopher D. | Smith, Mary A. | Smith, Sheryl T. | Spana, Eric | Spratt, Mary | Sreenivasan, Aparna | Stamm, Joyce | Szauter, Paul | Thompson, Jeffrey S. | Wawersik, Matthew | Youngblom, James | Zhou, Leming | Mardis, Elaine R. | Buhler, Jeremy | Leung, Wilson | Lopatto, David | Elgin, Sarah C. R.
CBE Life Sciences Education  2014;13(1):111-130.
While course-based research in genomics can generate both knowledge gains and a greater appreciation for how science is done, a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. Nonetheless, this is a very cost-effective way to reach larger numbers of students.
There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.
PMCID: PMC3940452  PMID: 24591510
2.  Zinc Mediated Azide–Alkyne Ligation to 1,5- and 1,4,5-Substituted 1,2,3-Triazoles 
Organic Letters  2013;15(18):4826-4829.
A mild method for regioselective formation of 1,5-substituted 1,2,3-triazoles is described. The zinc-mediated reaction works at room temperature and is successful across a wide range of azido/alkynyl substrates. Additionally, the triazole 4-position can be further functionalized through the intermediate aryl-zinc to accommodate a diverse three-component coupling strategy.
PMCID: PMC4331842  PMID: 24001177
3.  Identification and expression of maebl, an erythrocyte-binding gene, in Plasmodium gallinaceum 
Parasitology research  2012;112(3):945-954.
Avian malaria is of significant ecological importance and serves as a model system to study broad patterns of host switching and host-specificity. The erythrocyte invasion mechanism of the malaria parasite Plasmodium is mediated, in large part, by proteins of the erythrocyte binding-like (ebl) family of genes. However, little is known about how these genes are conserved across different species of Plasmodium, especially those that infect birds. Using bioinformatical methods in conjunction with PCR and genetic sequencing, we identified and annotated one member of the ebl family, maebl (merozoite apical erythrocyte binding ligand) from the chicken parasite Plasmodium gallinaceum. We then detected the expression of maebl in P. gallinaceum by PCR analysis of cDNA isolated from the blood of infected chickens. We found that maebl is a conserved orthologous gene in avian, mammalian, and rodent Plasmodium species. The duplicate extracellular binding domains of MAEBL, responsible for erythrocyte binding, are the most conserved regions. Our combined data corroborate the conservation of maebl throughout the Plasmodium genus, and may help elucidate the mechanisms of erythrocyte invasion in P. gallinaceum and the host specificity of Plasmodium parasites.
PMCID: PMC3581715  PMID: 23224610
Plasmodium gallinaceum; MAEBL; EBL; EBA-175; Avian Malaria
4.  Directional interactions between current and prior saccades 
One way to explore how prior sensory and motor events impact eye movements is to ask someone to look to targets located about a central point, returning gaze to the central point after each eye movement. Concerned about the contribution of this return to center movement, Anderson et al. (2008) used a sequential saccade paradigm in which participants made a continuous series of saccades to peripheral targets that appeared to the left or right of the currently fixated location in a random sequence (the next eye movement began from the last target location). Examining the effects of previous saccades (n−x) on current saccade latency (n), they found that saccadic reaction times (RT) were reduced when the direction of the current saccade matched that of a preceding saccade (e.g., two left saccades), even when the two saccades in question were separated by multiple saccades in any direction. We examined if this pattern extends to conditions in which targets appear inside continuously marked locations that provide stable visual features (i.e., target “placeholders”) and when saccades are prompted by central arrows. Participants completed 3 conditions: peripheral targets (PT; continuous, sequential saccades to peripherally presented targets) without placeholders; PT with placeholders; and centrally presented arrows (CA; left or right pointing arrows at the currently fixated location instructing participants to saccade to the left or right). We found reduced saccadic RT when the immediately preceding saccade (n−1) was in the same (vs. opposite) direction in the PT without placeholders and CA conditions. This effect varied when considering the effect of the previous 2–5 (n−x) saccades on current saccade latency (n). The effects of previous eye movements on current saccade latency may be determined by multiple, time-varying mechanisms related to sensory (i.e., retinotopic location), motor (i.e., saccade direction), and environmental (i.e., persistent visual objects) factors.
PMCID: PMC4211295  PMID: 25389401
saccade latency; peripheral cue; central cue; random walk paradigm; sequential saccades
5.  Spatial Interactions between Successive Eye and Arm Movements: Signal Type Matters 
PLoS ONE  2013;8(3):e58850.
Spatial interactions between consecutive movements are often attributed to inhibition of return (IOR), a phenomenon in which responses to previously signalled locations are slower than responses to unsignalled locations. In two experiments using peripheral target signals offset by 0°, 90°, or 180°, we show that consecutive saccadic (Experiment 1) and reaching (Experiment 3) responses exhibit a monotonic pattern of reaction times consistent with the currently established spatial distribution of IOR. In contrast, in two experiments with central target signals (i.e., arrowheads pointing at target locations), we find a non-monotonic pattern of reaction times for saccades (Experiment 2) and reaching movements (Experiment 4). The difference in the patterns of results observed demonstrates different behavioral effects that depend on signal type. The pattern of results observed for central stimuli are consistent with a model in which neural adaptation is occurring within motor networks encoding movement direction in a distributed manner.
PMCID: PMC3602592  PMID: 23527038
6.  The genomic impact of 100 million years of social evolution in seven ant species 
Trends in Genetics  2011;28(1):14-21.
Ants (Hymenoptera, Formicidae) represent one of the most successful eusocial taxa in terms of both their geographic distribution and species number. The publication of seven ant genomes within the past year was a quantum leap for socio- and ant genomics. The diversity of social organization in ants makes them excellent model organisms to study the evolution of social systems. Comparing the ant genomes with those of the honeybee, a lineage that evolved eusociality independently from ants, and solitary insects suggests that there are significant differences in key aspects of genome organization between social and solitary insects, as well as among ant species. Altogether, these seven ant genomes open exciting new research avenues and opportunities for understanding the genetic basis and regulation of social species, and adaptive complex systems in general.
PMCID: PMC3314025  PMID: 21982512
7.  Patterns of DNA Methylation in Development, Division of Labor and Hybridization in an Ant with Genetic Caste Determination 
PLoS ONE  2012;7(8):e42433.
DNA methylation is a common regulator of gene expression, including acting as a regulator of developmental events and behavioral changes in adults. Using the unique system of genetic caste determination in Pogonomyrmex barbatus, we were able to document changes in DNA methylation during development, and also across both ancient and contemporary hybridization events.
Methodology/Principal Findings
Sodium bisulfite sequencing demonstrated in vivo methylation of symmetric CG dinucleotides in P. barbatus. We also found methylation of non-CpG sequences. This validated two bioinformatics methods for predicting gene methylation, the bias in observed to expected ratio of CpG dinucleotides and the density of CpG/TpG single nucleotide polymorphisms (SNP). Frequencies of genomic DNA methylation were determined for different developmental stages and castes using ms-AFLP assays. The genetic caste determination system (GCD) is probably the product of an ancestral hybridization event between P. barbatus and P. rugosus. Two lineages obligately co-occur within a GCD population, and queens are derived from intra-lineage matings whereas workers are produced from inter-lineage matings. Relative DNA methylation levels of queens and workers from GCD lineages (contemporary hybrids) were not significantly different until adulthood. Virgin queens had significantly higher relative levels of DNA methylation compared to workers. Worker DNA methylation did not vary among developmental stages within each lineage, but was significantly different between the currently hybridizing lineages. Finally, workers of the two genetic caste determination lineages had half as many methylated cytosines as workers from the putative parental species, which have environmental caste determination.
These results suggest that DNA methylation may be a conserved regulatory mechanism moderating division of labor in both bees and ants. Current and historic hybridization appear to have altered genomic methylation levels suggesting a possible link between changes in overall DNA methylation and the origin and regulation of genetic caste determination in P. barbatus.
PMCID: PMC3411777  PMID: 22879983
8.  An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference 
Genome Biology and Evolution  2012;4(9):937-953.
Vertebrates have experienced two rounds of whole-genome duplication (WGD) in the stem lineages of deep nodes within the group and a subsequent duplication event in the stem lineage of the teleosts—a highly diverse group of ray-finned fishes. Here, we present the first full Hox gene sequences for any member of the Acipenseriformes, the American paddlefish, and confirm that an independent WGD occurred in the paddlefish lineage, approximately 42 Ma based on sequences spanning the entire HoxA cluster and eight genes on the HoxD gene cluster. These clusters comprise different HOX loci and maintain conserved synteny relative to bichir, zebrafish, stickleback, and pufferfish, as well as human, mouse, and chick. We also provide a gene genealogy for the duplicated fzd8 gene in paddlefish and present evidence for the first Hox14 gene in any ray-finned fish. Taken together, these data demonstrate that the American paddlefish has an independently duplicated genome. Substitution patterns of the “alpha” paralogs on both the HoxA and HoxD gene clusters suggest transcriptional inactivation consistent with functional diploidization. Further, there are similarities in the pattern of sequence divergence among duplicated Hox genes in paddlefish and teleost lineages, even though they occurred independently approximately 200 Myr apart. We highlight implications on comparative analyses in the study of the “fin-limb transition” as well as gene and genome duplication in bony fishes, which includes all ray-finned fishes as well as the lobe-finned fishes and tetrapod vertebrates.
PMCID: PMC3509897  PMID: 22851613
Polyodon spathula; whole-genome duplication; WGD; rate asymmetry; paralog retention; fin-limb transition
9.  A New Threat to Honey Bees, the Parasitic Phorid Fly Apocephalus borealis 
PLoS ONE  2012;7(1):e29639.
Honey bee colonies are subject to numerous pathogens and parasites. Interaction among multiple pathogens and parasites is the proposed cause for Colony Collapse Disorder (CCD), a syndrome characterized by worker bees abandoning their hive. Here we provide the first documentation that the phorid fly Apocephalus borealis, previously known to parasitize bumble bees, also infects and eventually kills honey bees and may pose an emerging threat to North American apiculture. Parasitized honey bees show hive abandonment behavior, leaving their hives at night and dying shortly thereafter. On average, seven days later up to 13 phorid larvae emerge from each dead bee and pupate away from the bee. Using DNA barcoding, we confirmed that phorids that emerged from honey bees and bumble bees were the same species. Microarray analyses of honey bees from infected hives revealed that these bees are often infected with deformed wing virus and Nosema ceranae. Larvae and adult phorids also tested positive for these pathogens, implicating the fly as a potential vector or reservoir of these honey bee pathogens. Phorid parasitism may affect hive viability since 77% of sites sampled in the San Francisco Bay Area were infected by the fly and microarray analyses detected phorids in commercial hives in South Dakota and California's Central Valley. Understanding details of phorid infection may shed light on similar hive abandonment behaviors seen in CCD.
PMCID: PMC3250467  PMID: 22235317
10.  Partial-thickness articular surface rotator cuff tears in patients over the age of 35: Etiology and intra-articular associations 
Partial-thickness articular-sided rotator cuff tears have a multifactorial etiology and are associated with degeneration of the tendon. They are often described as an injury of the young athlete, although they are also found in the older population. The aim of this study was to investigate the frequency and associations of partial-thickness articular-sided tears in patients over the age of 35 years.
Materials and Methods:
A retrospective study of all arthroscopic procedures for rotator cuff pathology in patients over the age of 35 years over a 2-year period by a single surgeon was performed. The included patients were divided into two groups based on the arthroscopic findings: those with a partial-thickness articular-sided rotator cuff tear and those with pure tendinopathy. The groups were then compared to identify the associated pathology with the rotator cuff lesions. 2×2 contingency table analysis and unpaired Student's t-test were used for statistical analysis.
One hundred patients were included in the study of whom 62 had a partial articular-sided tear. Those with a partial articular-sided tear were older (P=0.0001), were more commonly associated with a documented injury (P=0.03), and more commonly had biceps degeneration (P=0.001) and synovitis (P=0.02) within the joint.
Partial-thickness articular-sided tears are a common occurrence in patients requiring arthroscopic surgery for rotator cuff pathology over the age of 35 years. This probably reflects an injury in an already degenerate cuff. This would support the theory of intrinsic degeneration of the tendon in this age group and probably represent a different etiology to those seen in the young athletes.
Level of Evidence:
Level 3
PMCID: PMC3326750  PMID: 22518075
Associated pathology; etiology; partial-thickness; rotator cuff tears
11.  The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle 
PLoS Genetics  2011;7(2):e1002007.
Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. Mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldiers, resulting in one of the most complex polymorphic caste systems within ants. To begin uncovering the genomic underpinnings of this system, we sequenced the genome of Atta cephalotes using 454 pyrosequencing. One prediction from this ant's lifestyle is that it has undergone genetic modifications that reflect its obligate dependence on the fungus for nutrients. Analysis of this genome sequence is consistent with this hypothesis, as we find evidence for reductions in genes related to nutrient acquisition. These include extensive reductions in serine proteases (which are likely unnecessary because proteolysis is not a primary mechanism used to process nutrients obtained from the fungus), a loss of genes involved in arginine biosynthesis (suggesting that this amino acid is obtained from the fungus), and the absence of a hexamerin (which sequesters amino acids during larval development in other insects). Following recent reports of genome sequences from other insects that engage in symbioses with beneficial microbes, the A. cephalotes genome provides new insights into the symbiotic lifestyle of this ant and advances our understanding of host–microbe symbioses.
Author Summary
Leaf-cutter ant workers forage for and cut leaves that they use to support the growth of a specialized fungus, which serves as the colony's primary food source. The ability of these ants to grow their own food likely facilitated their emergence as one of the most dominant herbivores in New World tropical ecosystems, where leaf-cutter ants harvest more plant biomass than any other herbivore species. These ants have also evolved one of the most complex forms of division of labor, with colonies composed of different-sized workers specialized for different tasks. To gain insight into the biology of these ants, we sequenced the first genome of a leaf-cutter ant, Atta cephalotes. Our analysis of this genome reveals characteristics reflecting the obligate nutritional dependency of these ants on their fungus. These findings represent the first genetic evidence of a reduced capacity for nutrient acquisition in leaf-cutter ants, which is likely compensated for by their fungal symbiont. These findings parallel other nutritional host–microbe symbioses, suggesting convergent genomic modifications in these types of associations.
PMCID: PMC3037820  PMID: 21347285
12.  Neural Coding of Movement Direction in the Healthy Human Brain 
PLoS ONE  2010;5(10):e13330.
Neurophysiological studies in monkeys show that activity of neurons in primary cortex (M1), pre-motor cortex (PMC), and cerebellum varies systematically with the direction of reaching movements. These neurons exhibit preferred direction tuning, where the level of neural activity is highest when movements are made in the preferred direction (PD), and gets progressively lower as movements are made at increasing degrees of offset from the PD. Using a functional magnetic resonance imaging adaptation (fMRI-A) paradigm, we show that PD coding does exist in regions of the human motor system that are homologous to those observed in non-human primates. Consistent with predictions of the PD model, we show adaptation (i.e., a lower level) of the blood oxygen level dependent (BOLD) time-course signal in M1, PMC, SMA, and cerebellum when consecutive wrist movements were made in the same direction (0° offset) relative to movements offset by 90° or 180°. The BOLD signal in dorsolateral prefrontal cortex adapted equally in all movement offset conditions, mitigating against the possibility that the present results are the consequence of differential task complexity or attention to action in each movement offset condition.
PMCID: PMC2954155  PMID: 20967197
13.  Genome mapping and characterization of the Anopheles gambiae heterochromatin 
BMC Genomics  2010;11:459.
Heterochromatin plays an important role in chromosome function and gene regulation. Despite the availability of polytene chromosomes and genome sequence, the heterochromatin of the major malaria vector Anopheles gambiae has not been mapped and characterized.
To determine the extent of heterochromatin within the An. gambiae genome, genes were physically mapped to the euchromatin-heterochromatin transition zone of polytene chromosomes. The study found that a minimum of 232 genes reside in 16.6 Mb of mapped heterochromatin. Gene ontology analysis revealed that heterochromatin is enriched in genes with DNA-binding and regulatory activities. Immunostaining of the An. gambiae chromosomes with antibodies against Drosophila melanogaster heterochromatin protein 1 (HP1) and the nuclear envelope protein lamin Dm0 identified the major invariable sites of the proteins' localization in all regions of pericentric heterochromatin, diffuse intercalary heterochromatin, and euchromatic region 9C of the 2R arm, but not in the compact intercalary heterochromatin. To better understand the molecular differences among chromatin types, novel Bayesian statistical models were developed to analyze genome features. The study found that heterochromatin and euchromatin differ in gene density and the coverage of retroelements and segmental duplications. The pericentric heterochromatin had the highest coverage of retroelements and tandem repeats, while intercalary heterochromatin was enriched with segmental duplications. We also provide evidence that the diffuse intercalary heterochromatin has a higher coverage of DNA transposable elements, minisatellites, and satellites than does the compact intercalary heterochromatin. The investigation of 42-Mb assembly of unmapped genomic scaffolds showed that it has molecular characteristics similar to cytologically mapped heterochromatin.
Our results demonstrate that Anopheles polytene chromosomes and whole-genome shotgun assembly render the mapping and characterization of a significant part of heterochromatic scaffolds a possibility. These results reveal the strong association between characteristics of the genome features and morphological types of chromatin. Initial analysis of the An. gambiae heterochromatin provides a framework for its functional characterization and comparative genomic analyses with other organisms.
PMCID: PMC3091655  PMID: 20684766
14.  Genome Landscape and Evolutionary Plasticity of Chromosomes in Malaria Mosquitoes 
PLoS ONE  2010;5(5):e10592.
Nonrandom distribution of rearrangements is a common feature of eukaryotic chromosomes that is not well understood in terms of genome organization and evolution. In the major African malaria vector Anopheles gambiae, polymorphic inversions are highly nonuniformly distributed among five chromosomal arms and are associated with epidemiologically important adaptations. However, it is not clear whether the genomic content of the chromosomal arms is associated with inversion polymorphism and fixation rates.
Methodology/Principal Findings
To better understand the evolutionary dynamics of chromosomal inversions, we created a physical map for an Asian malaria mosquito, Anopheles stephensi, and compared it with the genome of An. gambiae. We also developed and deployed novel Bayesian statistical models to analyze genome landscapes in individual chromosomal arms An. gambiae. Here, we demonstrate that, despite the paucity of inversion polymorphisms on the X chromosome, this chromosome has the fastest rate of inversion fixation and the highest density of transposable elements, simple DNA repeats, and GC content. The highly polymorphic and rapidly evolving autosomal 2R arm had overrepresentation of genes involved in cellular response to stress supporting the role of natural selection in maintaining adaptive polymorphic inversions. In addition, the 2R arm had the highest density of regions involved in segmental duplications that clustered in the breakpoint-rich zone of the arm. In contrast, the slower evolving 2L, 3R, and 3L, arms were enriched with matrix-attachment regions that potentially contribute to chromosome stability in the cell nucleus.
These results highlight fundamental differences in evolutionary dynamics of the sex chromosome and autosomes and revealed the strong association between characteristics of the genome landscape and rates of chromosomal evolution. We conclude that a unique combination of various classes of genes and repetitive DNA in each arm, rather than a single type of repetitive element, is likely responsible for arm-specific rates of rearrangements.
PMCID: PMC2868863  PMID: 20485676
15.  The Release 5.1 Annotation of Drosophila melanogaster Heterochromatin 
Science (New York, N.Y.)  2007;316(5831):1586.
The repetitive DNA that constitutes most of the heterochromatic regions of metazoan genomes has hindered the comprehensive analysis of gene content and other functions. We have generated a detailed computational and manual annotation of 24 megabases of heterochromatic sequence in the Release 5 Drosophila melanogaster genome sequence. The heterochromatin contains a minimum of 230 to 254 protein-coding genes, which are conserved in other Drosophilids and more diverged species, as well as 32 pseudogenes and 13 noncoding RNAs. Improved methods revealed that more than 77% of this heterochromatin sequence, including introns and intergenic regions, is composed of fragmented and nested transposable elements and other repeated DNAs. Drosophila heterochromatin contains “islands” of highly conserved genes embedded in these “oceans” of complex repeats, which may require special expression and splicing mechanisms.
PMCID: PMC2819280  PMID: 17569856
16.  Improved repeat identification and masking in Dipterans 
Gene  2006;389(1):1-9.
PMCID: PMC1945102  PMID: 17137733
Heterochromatin; Drosophila; A. gambiae; PILER; transposable element; RepeatRunner
17.  Heterochromatic sequences in a Drosophila whole-genome shotgun assembly 
Genome Biology  2002;3(12):research0085.1-85.16.
Annotation of an improved whole-genome shotgun assembly of the Drosophila melanogaster genome predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Fluorescence in situ hybridization was used to correlate the genomic sequence with the cytogenetic map; the annotated euchromatic sequence extends into the centric heterochromatin on each chromosome arm.
Most eukaryotic genomes include a substantial repeat-rich fraction termed heterochromatin, which is concentrated in centric and telomeric regions. The repetitive nature of heterochromatic sequence makes it difficult to assemble and analyze. To better understand the heterochromatic component of the Drosophila melanogaster genome, we characterized and annotated portions of a whole-genome shotgun sequence assembly.
WGS3, an improved whole-genome shotgun assembly, includes 20.7 Mb of draft-quality sequence not represented in the Release 3 sequence spanning the euchromatin. We annotated this sequence using the methods employed in the re-annotation of the Release 3 euchromatic sequence. This analysis predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Bacterial artificial chromosome (BAC)-based fluorescence in situ hybridization analysis was used to correlate the genomic sequence with the cytogenetic map in order to refine the genomic definition of the centric heterochromatin; on the basis of our cytological definition, the annotated Release 3 euchromatic sequence extends into the centric heterochromatin on each chromosome arm.
Whole-genome shotgun assembly produced a reliable draft-quality sequence of a significant part of the Drosophila heterochromatin. Annotation of this sequence defined the intron-exon structures of 30 known protein-coding genes and 267 protein-coding gene models. The cytogenetic mapping suggests that an additional 150 predicted genes are located in heterochromatin at the base of the Release 3 euchromatic sequence. Our analysis suggests strategies for improving the sequence and annotation of the heterochromatic portions of the Drosophila and other complex genomes.
PMCID: PMC151187  PMID: 12537574
18.  Annotation of the Drosophila melanogaster euchromatic genome: a systematic review 
Genome Biology  2002;3(12):research0083.1-83.22.
The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to significantly improve genomic annotations.
The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences.
Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes.
Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations.
PMCID: PMC151185  PMID: 12537572
19.  Uncapping and Deregulation of Telomeres Lead to Detrimental Cellular Consequences in Yeast  
The Journal of Cell Biology  1999;145(2):203-214.
Telomeres are the protein–nucleic acid structures at the ends of eukaryote chromosomes. Tandem repeats of telomeric DNA are templated by the RNA component (TER1) of the ribonucleoprotein telomerase. These repeats are bound by telomere binding proteins, which are thought to interact with other factors to create a higher-order cap complex that stabilizes the chromosome end. In the budding yeast Kluyveromyces lactis, the incorporation of certain mutant DNA sequences into telomeres leads to uncapping of telomeres, manifested by dramatic telomere elongation and increased length heterogeneity (telomere deregulation). Here we show that telomere deregulation leads to enlarged, misshapen “monster” cells with increased DNA content and apparent defects in cell division. However, such deregulated telomeres became stabilized at their elongated lengths upon addition of only a few functionally wild-type telomeric repeats to their ends, after which the frequency of monster cells decreased to wild-type levels. These results provide evidence for the importance of the most terminal repeats at the telomere in maintaining the cap complex essential for normal telomere function. Analysis of uncapped and capped telomeres also show that it is the deregulation resulting from telomere uncapping, rather than excessive telomere length per se, that is associated with DNA aberrations and morphological defects.
PMCID: PMC2133106  PMID: 10209018
telomere; telomerase; chromosome aberrations; cell division; Kluyveromyces lactis
20.  Transposable element islands facilitate adaptation to novel environments in an invasive species 
Nature Communications  2014;5:5495.
Adaptation requires genetic variation, but founder populations are generally genetically depleted. Here we sequence two populations of an inbred ant that diverge in phenotype to determine how variability is generated. Cardiocondyla obscurior has the smallest of the sequenced ant genomes and its structure suggests a fundamental role of transposable elements (TEs) in adaptive evolution. Accumulations of TEs (TE islands) comprising 7.18% of the genome evolve faster than other regions with regard to single-nucleotide variants, gene/exon duplications and deletions and gene homology. A non-random distribution of gene families, larvae/adult specific gene expression and signs of differential methylation in TE islands indicate intragenomic differences in regulation, evolutionary rates and coalescent effective population size. Our study reveals a tripartite interplay between TEs, life history and adaptation in an invasive species.
Genetic variation is key to species evolution. Here the authors sequence two phenotypically distinct populations of the ant Cardiocondyla obscurior, and find accumulations of transposable elements correlating with genetic variation that may have a role in differentiation, adaptation and speciation.
PMCID: PMC4284661  PMID: 25510865

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