Biology Commons^™

Transcription And Rna Interference In The Formation Of Heterochromatin, Shiv Grewal, Sarah C.R. Elgin

Biology Faculty Research

Transcription in heterochromatin seems to be an oxymoron--surely the 'silenced' form of chromatin should not be transcribed. But there have been frequent reports of low-level transcription in heterochromatic regions, and several hundred genes are found in these regions in Drosophila. Most strikingly, recent investigations implicate RNA interference mechanisms in targeting and maintaining heterochromatin, and these mechanisms are inherently dependent on transcription. Silencing of chromatin might involve trans-acting sources of the crucial small RNAs that carry out RNA interference, but in some cases, transcription of the region to be silenced seems to be required--an apparent contradiction.

Genomic And Expression Analysis Of Multiple Sry Loci From A Single Rattus Norvegicus Y Chromosome, Monte E. Turner, Carey Martin, Almir S. Martins, Jeffrey Dunmire, Joel Farkas, Daniel L. Ely, Amy Milsted

Biology Faculty Research

Background: Sry is a gene known to be essential for testis determination but is also transcribed in adult male tissues. The laboratory rat, Rattus norvegicus, has multiple Y chromosome copies of Sry while most mammals have only a single copy. DNA sequence comparisons with other rodents with multiple Sry copies are inconsistent in divergence patterns and functionality of the multiple copies. To address hypotheses of divergence, gene conversion and functional constraints, we sequenced Sry loci from a single R. norvegicus Y chromosome from the Spontaneously Hypertensive Rat strain (SHR) and analyzed DNA sequences for homology among copies. Next, to determine …

Anatomy Of The Recurrent Coastal Sediment Plume In Lake Michigan And Its Impacts On Light Climate, Nutrients, And Plankton, Henry Vanderploeg, Thomas Johengen, Peter J. Lavrentyev, Changsheng Chen, G. A. Lang, M. A. Agy, M. H. Bundy, J. F. Cavaletto, B. J. Eadie, J. R. Liebig, G. S. Miller, S. A. Ruberg, M. J. Mccormick

Biology Faculty Research

As part of the Episodic Events Great Lakes Experiment, we sampled total suspended matter (TSM), light climate, nutrients, and plankton along cross-margin transects in southern Lake Michigan during February, March, and April 1998-2000 to capture conditions before, during, and after the occurrence of storm-driven recurrent coastal sediment plumes to define the anatomy of the resuspension events and get insights into their interactions with nutrients and plankton. Variability in timing and strength of winter storms among years led to different timing, intensity, and extent of plumes among years. TSM concentrations in the core of plumes varied between 15 and 30 mg …

Lack Of Melanized Keratin And Barbs That Fall Off: How The Racketed Tail Of The Turquoise-Browed Motmot Eumomota Superciliosa Is Formed, Troy G. Murphy

Biology Faculty Research

The racket-tipped tail of the motmots is uniquely shaped and its formation has attracted much attention. Barbs that grow along the wire of the motmot’s two central tail feathers are weakly attached and shed soon after development. The cause of the weak attachment of these barbs is unclear. I induced feather growth by plucking the central tail feathers from seven turquoise-browed motmots Eumomota superciliosa and then collected the regrown feathers before the barbs along the wire had fully shed. I compared the barb-rachis junction (petiole of the ramus) along the distal flag (the racket-tip of the tail) where barbs are …

Phylogenetic Analysis Of The Socioecology Of Neotomine-Peromyscine Rodents, M C. Kalcounis-Rueppell, David O. Ribble

Biology Faculty Research

This chapter focuses on the breeding systems of Neotomine-Peromyscine rodents. There are three specific objectives to this chapter. First, we describe the patterns for major Neotomine-Peromyscine clades using data collected from the literature (table 6.1). Second, we examine data from the literature on the following breeding behaviors: male spacing, female spacing, relative intersexual home range/territory size, paternal care, and juvenile dispersal patterns. We examine breeding behavior data in a phylogenetic framework to test if any phylogenetic patterns emerge in the observed variation in these breeding behaviors and if relationships occur among these behaviors. Third, we examine in a phylogenetic framework …

Dishonest ‘Preemptive’ Pursuit-Deterrent Signal? Why The Turquoise-Browed Motmot Wags Its Tail Before Feeding Nestlings, Troy G. Murphy

Biology Faculty Research

Both sexes of the turquoise-browed motmot, Eumomota superciliosa, display their long-racketed tail in an exaggerated side-to-side wag display in two contexts. In the first, the wag display is performed in the presence of predators (predator-elicited wag display), and evidence supports the hypothesis that the signal functions as a pursuit-deterrent signal (Murphy 2006, Behavioral Ecology, 17, 547e553). In the second, the wag display is performed in the apparent absence of predators immediately before feeding nestlings (prefeeding wag display). I tested four hypotheses on the adaptive significance of the prefeeding wag display: (1) a dishonest, preemptive, pursuit-deterrent signal given in case predators …

Racketed Tail Of The Male And Female Turquoise-Browed Motmot: Male But Not Female Tail Length Correlates With Pairing Success, Performance, And Reproductive Success, Troy G. Murphy

Biology Faculty Research

Both males and females of many avian species maintain elaborate plumage traits, and elaborate monomorphic plumage may convey adaptive benefits to one or both sexes as inter- or intraspecific signals. Both sexes of the turquoise-browed motmot (Eumomota superciliosa) are elaborately plumed with long racket-tipped tail. I investigated whether the racketed tail functions as a sexually selected signal in one or both sexes by testing the predictions that males and/or females with the largest tails have: (1) greater pairing success, (2) greater reproductive performance (clutch-initiation date, clutch size, and hatching success), and (3) greater reproductive success. Yearling males with …

Philornis Fasciventris (Wulp) (Diptera: Muscidae): Description Of The Male, Larva And Puparium, With Notes On Biology And Host Association, Marcia S. Couri, Troy G. Murphy, Richard Hoebeke

Biology Faculty Research

The male, larva and puparium of Philornis fasciventris (Wulp) are described for the first time, as well as the larval habit and host association. The material was collected in Yucatan, Mexico in a nest of the turquoise-browed motmot, Eumomota superciliosa (Sandbach) (Coraciformes: Momotidae), first host record for this species. E. superciliosa is also a new host record for Philornis.

Cadherin2 (N-Cadherin) Plays An Essential Role In Zebrafish Cardiovascular Development, Brian Bagatto, Jessie Francl, Bei Liu, Qin Liu

Biology Faculty Research

Background: Cadherins are cell surface adhesion molecules that play important roles in development of vertebrate tissues and organs. We studied cadherin2 expression in developing zebrafish heart using in situ hybridization and immunocytochemical methods, and we found that cadherin2 was strongly expressed by the myocardium of the embryonic zebrafish. To gain insight into cadherin2 role in the formation and function of the heart, we analyzed cardiac differentiation and performance in a cadherin2 mutant, glass onion (glo).

The Contradictory Definitions Of Heterochromatin: Transcription And Silencing, Kathryn Huisinga, Brent Brower-Toland, Sarah C.R. Elgin

Biology Faculty Research

Eukaryotic genomes are packaged in two general varieties of chromatin: gene-rich euchromatin and gene-poor heterochromatin. Each type of chromatin has been defined by the presence of distinct chromosomal proteins and posttranslational histone modifications. This review addresses recent findings that appear to blur the definitions of euchromatin and heterochromatin by pointing to the presence of typically heterochromatic modifications (including H3K9me) in euchromatin and typically euchromatic enzymes (including RNA polymerases) in heterochromatin. We discuss the implications of these new findings for the current definition of heterochromatin.

A Three-Dimensional Functional Assessment Of Heart And Vessel Development In The Larva Of The Zebrafish (Danio Rerio), Brian Bagatto, Warren Burggren

Biology Faculty Research

There has been considerable recent interest in the development of the circulation in the zebrafish. Optical techniques typically used to visualize changes in heart size allow measurement of stroke volume during early vertebrate development, but this approach is complicated in zebrafish larvae because of the heart's irregular shape and its significant change in morphology during the first 6 d of development. By use of a three-dimensional integration of the early zebrafish heart and vessels, we have greatly reduced measurement error of stroke volume and cardiac output and have determined the cross-sectional growth of major vessels in the developing zebrafish larvae. …

Predator-Elicited Visual Signal: Why The Turquoise-Browed Motmot Wag-Displays Its Racketed Tail, Troy G. Murphy

Biology Faculty Research

Both sexes of the turquoise-browed motmot (Eumomota superciliosa) perform a wag-display in the presence of predators, whereby their long racketed tail is repeatedly rocked side-to-side in a pendulous fashion. I tested 3 hypotheses for the function of the predator-elicited wag-display: 1) pursuit-deterrent signal, 2) warning alarm signal, and 3) self-preservation alarm signal. These hypotheses were evaluated by testing whether the presence of potential receivers (kin, conspecifics, mate) modified the way in which the wag-display was performed. Data on wag-display were collected when I experimentally presented predators to motmots and when naturally occurring predators were observed at nesting colonies. …

Establishment Of Polarity During Organization Of The Acentrosomal Plant Cortical Microtubule Array, Ram Dixit, Eric Chang, Richard Cyr

Biology Faculty Research

The plant cortical microtubule array is a unique acentrosomal array that is essential for plant morphogenesis. To understand how this array is organized, we exploited the microtubule (+)-end tracking activity of two Arabidopsis EB1 proteins in combination with FRAP (fluorescence recovery after photobleaching) experiments of GFP-tubulin to examine the relationship between cortical microtubule array organization and polarity. Significantly, our observations show that the majority of cortical microtubules in ordered arrays, within a particular cell, face the same direction in both Arabidopsis plants and cultured tobacco cells. We determined that this polar microtubule coalignment is at least partially due to a …

Comparison Of Dot Chromosome Sequences From D. Melanogaster And D. Virilis Reveals An Enrichment Of Dna Transposon Sequences In Heterochromatic Domains, Elizabeth Slawson, Christopher Shaffer, Colin Malone, Wilson Leung, Elmer Kellmann, Rachel Shevchek, Carolyn Craig, Seth Bloom, James Bogenpohl 2nd, James Dee, Emiko Morimoto, Jenny Myoung, Andrew Nett, Fatih Ozsolak, Mindy Tittiger, Andrea Zeug, Mary-Lou Pardue, Jeremy Buhler, Elaine Mardis, Sarah C.R. Elgin

Biology Faculty Research

Background: Chromosome four of Drosophila melanogaster, known as the dot chromosome, is largely heterochromatic, as shown by immunofluorescent staining with antibodies to heterochromatin protein 1 (HP1) and histone H3K9me. In contrast, the absence of HP1 and H3K9me from the dot chromosome in D. virilis suggests that this region is euchromatic. D. virilis diverged from D. melanogaster 40 to 60 million years ago. Results: Here we describe finished sequencing and analysis of 11 fosmids hybridizing to the dot chromosome of D. virilis (372,650 base-pairs) and seven fosmids from major euchromatic chromosome arms (273,110 base-pairs). Most genes from the dot chromosome of …

The Dot Chromosome Of Drosophila: Insights Into Chromatin States And Their Change Over Evolutionary Time, Nicole Riddle, Sarah C.R. Elgin

Biology Faculty Research

Historically, chromatin has been subdivided into heterochromatin, transcriptionally inactive regions that remain densely packaged throughout the cell cycle, and euchromatin, transcriptionally active regions that take on a diffuse appearance as the cell enters interphase. The banded portion of the small fourth chromosome (dot chromosome) of Drosophila melanogaster is unusual in exhibiting many characteristics of heterochromatic domains, and at the same time maintaining a gene density typical of euchromatin. Similar to genes embedded in pericentric heterochromatin, many of the dot chromosome genes have adapted to a heterochromatic environment. Little is known about the regulation of these genes and less about their …

Reductionism And Holism, Chance And Selection, Mechanism And Mind, Ursula Goodenough

Biology Faculty Research

Despite its rich and deepening panoply of empirical support, evolutionary theory continues to generate widespread concern. Some of this concern can be attributed to misunderstandings of the original concept, some to unfamiliarity with its current trajectories, and some to strongly held fears that it strips the human of cherished attributes. In this essay I seek to deconstruct such misunderstandings, lift up current concepts of what evolution entails, and address some of the existential issues it generates.

Density And Cover Preferences Of Black-And-Rufous Elephant-Shrews (Rhynchocyon Petersi) In Chome Forest Reserve, Tanzania, Stephanie Coster, David O. Ribble

Biology Faculty Research

The objective of this study was to determine the density and habitat preference of the Black-andrufous elephant-shrew (Rhynchocyon petersi) in Chome Forest Reserve, Tanzania. Chome Forest (143km²) is located in the South Pare Mountains and provides critical habitat for endangered R. petersi. Twelve 300m transects were cut through the centre of the forest in an east-west direction and the number of elephant-shrew nests within 2.5 meters on each side of the transects was recorded. The mean number of nests per 100m transect (0.39 ± 0.47 [1SE]) translated to a density estimate of 19 elephant-shrews per …

Social Organization Of The Eastern Rock Elephant-Shrew (Elephantulus Myurus): The Evidence For Mate Guarding, David O. Ribble, M. R. Perrin

Biology Faculty Research

Understanding the costs and benefits of defending solitary females, or mate guarding, may be the key to understanding the evolution of monogamy in most mammals. Elephant-shrews, or sengis, are a unique clade of small mammals that are particularly attractive for studies of mate guarding. We studied the spatial organization of Eastern Rock Sengis (Elephantulus myurus) in KwaZulu-Natal, South Africa, from August – December 2000. Our objectives were to describe the home ranges of males and females using radiotelemetry, noting the sizes and overlap of adjacent ranges and how the spatial organization changes through time. Males and females were …

Interspecific Competition For Pollination Lowers Seed Production And Outcrossing In Mimulus Ringens, John M. Bell, Jeffrey D. Karron, Randall J. Mitchell

Biology Faculty Research

Sympatric plant species with similar flowering phenologies and floral morphologies may compete for pollination, and as a consequence potentially influence each other's reproductive success and mating system. Two likely competitors are Mimulus ringens and Lobelia siphilitica, which co-occur in wet meadows of central and eastern North America, produce blue zygomorphic flowers, and share several species of bumble bee pollinators. To test for effects of competition for pollination, we planted experimental arrays of Mimulus ringens, each consisting of genets with unique combinations of homozygous marker genotypes. In two arrays we planted mixtures of Mimulus and Lobelia. and in two additional arrays …

Bergmann's Clines In Ectotherms: Illustrating A Life-History Perspective With Sceloporine Lizards, Michael J. Angilletta Jr., Peter H. Niewiarowski, Arthur E. Dunham, Adam D. Leache, Warren P. Porter

Biology Faculty Research

The generality and causes of Bergmann's rule have been debated vigorously in the last few years, but Bergmann's clines are rarely explained in the context of life-history theory. We used both traditional and phylogenetic comparative analyses to explore the causes of latitudinal and thermal clines in the body size of the eastern fence lizard (Sceloporus undulatus). The proximate mechanism for larger body sizes in colder environments is delayed maturation, which results in a greater fecundity but a lower survival to maturity. Life-history theory predicts that a higher survivorship of juveniles in colder environments can favor the evolution of a Bergmann's …

Pyruvate Formate Lyase And Acetate Kinase Are Essential For Anaerobic Growth Of Escherichia Coli On Xylose, A. Hansona, Y. Kim, Frank G. Healy, L. O. Ingram, K. T. Shanmugan

Biology Faculty Research

During anaerobic growth of bacteria, organic intermediates of metabolism, such as pyruvate or its derivatives, serve as electron acceptors to maintain the overall redox balance. Under these conditions, the ATP needed for cell growth is derived from substrate-level phosphorylation. In Escherichia coli, conversion of glucose to pyruvate yields 2 net ATPs, while metabolism of a pentose, such as xylose, to pyruvate only yields 0.67 net ATP per xylose due to the need for one (each) ATP for xylose transport and xylulose phosphorylation. During fermentative growth, E. coli produces equimolar amounts of acetate and ethanol from two pyruvates, and these …

A Modeling Study Of Benthic Detritus Flux's Impacts On Heterotrophic Processes In Lake Michigan, Changsheng Chen, Lixia Wang, Jianhua Qi, Hedong Liu, Judith Wells Budd, David J. Schwab, Dmitry Beletsky, Henry Vanderploeg, Brian Eadie, Thomas Johengen, James Cotner, Peter J. Lavrentyev

Biology Faculty Research

Effects of sediment resuspension-induced benthic detrital flux on the heterotrophic part of the microbial food web in Lake Michigan were examined using a three-dimensional (3-D) coupled biological and physical model. The model was driven by the realistic meteorological forcing observed in March 1999. Wind-induced surface wave dynamics were incorporated into the physical model to generate the bottom flux. The model-generated benthic detrital flux was assumed to be proportional to the difference between model-calculated and critical stresses at the bottom. The model results indicate that detrital flux at the bottom was a key factor causing a significant increase of phosphorus and …

Heritability Of Nectar Traits: Why Do We Know So Little?, Randall J. Mitchell

Biology Faculty Research

Although floral and extrafloral nectar traits are important for plant reproduction and defense, we know little about their genetic basis. Only a handful of studies have quantified heritable variation for nectar traits, primarily in controlled environments that minimize environmental variation. Most such studies have reported strong genetic influences, with heritabilities often >0.35. However, because nectar traits are often very responsive to environmental variation, even substantial amounts of genetic variation may be swamped out in the,field. Environmental variation deserves to be studied in its own right, including exploration of genotype X environment interaction for nectar traits . Most genetic studies of …

Distribution And Dynamics Of Nitrogen And Microbial Plankton In Southern Lake Michigan During Spring Transition 1999-2000, Wayne S. Gardner, Peter J. Lavrentyev, Joann F. Cavaletto, Mark J. Mccarthy, B. J. Eadie, Thomas Johengen, James Cotner

Biology Faculty Research

[ 1] Ammonium and amino acid fluxes were examined as indicators of N and microbial food web dynamics in southern Lake Michigan during spring. Either (NH4+)-N-15 or a mixture of N-15-labelled amino acids (both at 4 muM N final concentration) was added to Lake Michigan water. Net fluxes were measured over 24 h under natural light and dark conditions using deck-top incubators and compared to microbial food web characteristics. Isotope dilution experiments showed similar light and dark NH4+ regeneration rates at lake ( 6 versus 5 nM N h(-1)) and river-influenced ( 20 versus 24 nM N h(-1)) sites. Ammonium …

Maintenance Of Androdioecy In The Freshwater Shrimp, Eulimnadia Texana: Field Estimates Of Inbreeding Depression And Relative Male Survival, Stephen C. Weeks, Richard L. Bernhardt

Biology Faculty Research

Androdioecy is a rare form of reproduction, only found in a few plant and animal species, wherein males co-exist with hermaphrodites. This particular form of mixed mating (mixtures of outcrossing and self-fertilization) is predicted to be evolutionarily unstable, with most androdioecious populations thought to be in a transition from hermaphroditism to dioecy, or vice versa. One well-studied androdioecious species is the freshwater clam shrimp Eulimnadia texana. A model by Otto et al. (1993), exploring the stability of this androdioecious system, predicts that males can co-exist with hermaphrodites when males fertilize an average of over twice the number of offspring that …

The Cortical Microtubule Array: From Dynamics To Organization, Ram Dixit, Richard Cyr

Biology Faculty Research

Cortical microtubules (CMTs) are essential for normal plant morphogenesis because they affect the axes of cell elongation and predict the placement of cell division planes. The function of the CMTs is intimately linked to their organizational state, which is subject to spatial and temporal modifications by developmental and environmental cues. CMT assembly dynamics govern when, where, and how microtubules appear in a cell's cortex, and the regulation of these properties affects their organization. However, the principles that link microtubule assembly dynamics to cortical array organization and reconfiguration are not well understood. This essay focuses on recent advances in the understanding …

Encounters Between Dynamic Cortical Microtubules Promote Ordering Of The Cortical Array Through Angle-Dependent Modifications Of Microtubule Behavior, Ram Dixit, Richard Cyr

Biology Faculty Research

Ordered cortical microtubule arrays are essential for normal plant morphogenesis, but how these arrays form is unclear. The dynamics of individual cortical microtubules are stochastic and cannot fully account for the observed order; however, using tobacco (Nicotiana tabacum) cells expressing either the MBD-DsRed (microtubule binding domain of the mammalian MAP4 fused to the Discosoma sp red fluorescent protein) or YFP-TUA6 (yellow fluorescent protein fused to the Arabidopsis alpha-tubulin 6 isoform) microtubule markers, we identified intermicrotubule interactions that modify their stochastic behaviors. The intermicrotubule interactions occur when the growing plus-ends of cortical microtubules encounter previously existing cortical microtubules. Importantly, the outcome …

Heterochromatic Silencing And Hp1 Localization In Drosophila Are Dependent On The Rnai Machinery, Manika Pal-Bhadra, Boris Leibovitch, Sumit Gandhi, Madhusudana Rao Chikka, Utpal Bhadra, James Birchler, Sarah C.R. Elgin

Biology Faculty Research

Genes normally resident in euchromatic domains are silenced when packaged into heterochromatin, as exemplified in Drosophila melanogaster by position effect variegation (PEV). Loss-of-function mutations resulting in suppression of PEV have identified critical components of heterochromatin, including proteins HP1, HP2, and histone H3 lysine 9 methyltransferase. Here, we demonstrate that this silencing is dependent on the RNA interference machinery, using tandem mini-white arrays and white transgenes in heterochromatin to show loss of silencing as a result of mutations in piwi, aubergine, or spindle-E (homeless), which encode RNAi components. These mutations result in reduction of H3 Lys9 methylation and delocalization of HP1 …

From Biology To Consciousness To Morality, Ursula Goodenough, Terrence W. Deacon

Biology Faculty Research

Social animals are provisioned with prosocial orientations that operate to transcend self-interest. Morality, as used here, describes human versions of such orientations. We explore the evolutionary antecedents of morality in the context of emergentism, giving considerable attention to the biological traits that undergird awareness and our emergent human forms of mind. We suggest that our moral frames of mind emerge from our primate prosocial capacities, transfigured and valenced by our symbolic languages, cultures, and religions.

Portions of this article were given by Deacon in a paper at the forty-ninth annual conference of IRAS, “Is Nature Enough? The Thirst for …

The Capacity To Form H-Dna Cannot Substitute For Gaga Factor Binding To A (Ct)N*(Ga)N Regulatory Site, Quinn Lu, John Teare, Howard Granok, Marci Swede, Jenny Xu, Sarah C.R. Elgin

Biology Faculty Research

Previous studies of the Drosophila melanogaster hsp26 gene promoter have demonstrated the importance of a homopurine*homopyrimidine segment [primarily (CT)n*(GA)n] for chromatin structure formation and gene activation. (CT)n regions are known to bind GAGA factor, a dominant enhancer of PEV thought to play a role in generating an accessible chromatin structure. The (CT)n region can also form an H-DNA structure in vitro under acidic pH and negative supercoiling; a detailed map of that structure is reported here. To test whether the (CT)n sequence can function through H-DNA in vivo, we have analyzed a series of hsp26-lacZ transgenes with altered sequences in …