Skeletal Muscle Degeneration and Regeneration in Mice and Flies

Many aspects of skeletal muscle biology are remarkably similar between mammals and tiny insects, and experimental models of mice and flies (Drosophila) provide powerful tools to understand factors controlling the growth, maintenance, degeneration (atrophy and necrosis), and regeneration of normal and diseased muscles, with potential applications to the human condition. This review compares the limb muscles of mice and the indirect flight muscles of flies, with respect to the mechanisms of adult myofiber formation, homeostasis, atrophy, hypertrophy, and the response to muscle degeneration, with some comment on myogenic precursor cells and common gene regulatory pathways. There is a striking similarity between the species for events related to muscle atrophy and hypertrophy, without contribution of any myoblast fusion. Since the flight muscles of adult flies lack a population of reserve myogenic cells (equivalent to satellite cells), this indicates that such cells are not required for maintenance of normal muscle function. However, since satellite cells are essential in postnatal mammals for myogenesis and regeneration in response to myofiber necrosis, the extent to which such regeneration might be possible in flight muscles of adult flies remains unclear. Common cellular and molecular pathways for both species are outlined related to neuromuscular disorders and to age-related loss of skeletal muscle mass and function (sarcopenia). The commonality of events related to skeletal muscles in these disparate species (with vast differences in size, growth duration, longevity, and muscle activities) emphasizes the combined value and power of these experimental animal models.

Skeletal Muscle Degeneration and Regeneration in Mice and Flies

Many aspects of skeletal muscle biology are remarkably similar between mammals and tiny insects, and experimental models of mice and flies (Drosophila) provide powerful tools to understand factors controlling the growth, maintenance, degeneration (atrophy and necrosis), and regeneration of normal and diseased muscles, with potential applications to the human condition. This review compares the limb muscles of mice and the indirect flight muscles of flies, with respect to the mechanisms of adult myofiber formation, homeostasis, atrophy, hypertrophy, and the response to muscle degeneration, with some comment on myogenic precursor cells and common gene regulatory pathways. There is a striking similarity between the species for events related to muscle atrophy and hypertrophy, without contribution of any myoblast fusion. Since the flight muscles of adult flies lack a population of reserve myogenic cells (equivalent to satellite cells), this indicates that such cells are not required for maintenance of normal muscle function. However, since satellite cells are essential in postnatal mammals for myogenesis and regeneration in response to myofiber necrosis, the extent to which such regeneration might be possible in flight muscles of adult flies remains unclear. Common cellular and molecular pathways for both species are outlined related to neuromuscular disorders and to age-related loss of skeletal muscle mass and function (sarcopenia). The commonality of events related to skeletal muscles in these disparate species (with vast differences in size, growth duration, longevity, and muscle activities) emphasizes the combined value and power of these experimental animal models.

A non-resonant mass sensor to eliminate the ``missing mass'' effect during mass measurement of biological materials

Resonant sensors and crystal oscillators for mass detection need to be excited at very high natural frequencies (MHz). Use of such systems to measure mass of biological materials affects the accuracy of mass measurement due to their viscous and/or viscoelastic properties. The measurement limitation of such sensor system is the difficulty in accounting for the ``missing mass'' of the biological specimen in question. A sensor system has been developed in this work, to be operated in the stiffness controlled region at very low frequencies as compared to its fundamental natural frequency. The resulting reduction in the sensitivity due to non-resonant mode of operation of this sensor is compensated by the high resolution of the sensor. The mass of different aged drosophila melanogaster (fruit fly) is measured. The difference in its mass measurement during resonant mode of operation is also presented. That, viscosity effects do not affect the working of this non-resonant mass sensor is clearly established by direct comparison. (C) 2014 AIP Publishing LLC.

Raman Spectroscopic Studies on Screening of Myopathies

Myopathies are among the major causes of mortality in the world. There is no complete cure for this heterogeneous group of diseases, but a sensitive, specific, and fast diagnostic tool may improve therapy effectiveness. In this study, Raman spectroscopy is applied to discriminate between muscle mutants in Drosophila on the basis of associated changes at the molecular level. Raman spectra were collected from indirect flight muscles of mutants, upheld1 (up1), heldup(2) (hdp(2)), myosin heavy chain7 (Mhc7), actin88F(KM88) (Act88F(KM88)), upheld101 (up101), and Canton-S (CS) control group, for both 2 and 12 days old flies. Difference spectra (mutant minus control) of all the mutants showed an increase in nucleic acid and beta-sheet and/or random coil protein content along with a decrease in a-helix protein. Interestingly, the 12th day samples of up1 and Act88F(KM88) showed significantly higher levels of glycogen and carotenoids than CS. A principal components based linear discriminant analysis classification model was developed based on multidimensional Raman spectra, which classified the mutants according to their pathophysiology and yielded an overall accuracy of 97% and 93% for 2 and 12 days old flies, respectively. The up1 and Act88F(KM88) (nemaline-myopathy) mutants form a group that is clearly separated in a linear discriminant plane from up101 and hdp2 (cardiomyopathy) mutants. Notably, Raman spectra from a human sample with nemaline-myopathy formed a cluster with the corresponding Drosophila mutant (up1). In conclusion, this is the first demonstration in which myopathies, despite their heterogeneity, were screened on the basis of biochemical differences using Raman spectroscopy.

Colored polydimethylsiloxane micropillar arrays for high throughput measurements of forces applied by genetic model organisms

Measuring forces applied by multi-cellular organisms is valuable in investigating biomechanics of their locomotion. Several technologies have been developed to measure such forces, for example, strain gauges, micro-machined sensors, and calibrated cantilevers. We introduce an innovative combination of techniques as a high throughput screening tool to assess forces applied by multiple genetic model organisms. First, we fabricated colored Polydimethylsiloxane (PDMS) micropillars where the color enhances contrast making it easier to detect and track pillar displacement driven by the organism. Second, we developed a semiautomated graphical user interface to analyze the images for pillar displacement, thus reducing the analysis time for each animal to minutes. The addition of color reduced the Young's modulus of PDMS. Therefore, the dye-PDMS composite was characterized using Yeoh's hyperelastic model and the pillars were calibrated using a silicon based force sensor. We used our device to measure forces exerted by wild type and mutant Caenorhabditis elegans moving on an agarose surface. Wild type C. elegans exert an average force of similar to 1 mu N on an individual pillar and a total average force of similar to 7.68 mu N. We show that the middle of C. elegans exerts more force than its extremities. We find that C. elegans mutants with defective body wall muscles apply significantly lower force on individual pillars, while mutants defective in sensing externally applied mechanical forces still apply the same average force per pillar compared to wild type animals. Average forces applied per pillar are independent of the length, diameter, or cuticle stiffness of the animal. We also used the device to measure, for the first time, forces applied by Drosophila melanogaster larvae. Peristaltic waves occurred at 0.4Hz applying an average force of similar to 1.58 mu N on a single pillar. Our colored microfluidic device along with its displacement tracking software allows us to measure forces applied by multiple model organisms that crawl or slither to travel through their environment. (C) 2015 AIP Publishing LLC.

Experimental and theoretical studies of Notch signaling-mediated spatial pattern

Notch signaling acts in many diverse developmental spatial patterning processes. To better understand why this particular pathway is employed where it is and how downstream feedbacks interact with the signaling system to drive patterning, we have pursued three aims: (i) to quantitatively measure the Notch system's signal input/output (I/O) relationship in cell culture, (ii) to use the quantitative I/O relationship to computationally predict patterning outcomes of downstream feedbacks, and (iii) to reconstitute a Notch-mediated lateral induction feedback (in which Notch signaling upregulates the expression of Delta) in cell culture. The quantitative Notch I/O relationship revealed that in addition to the trans-activation between Notch and Delta on neighboring cells there is also a strong, mutual cis-inactivation between Notch and Delta on the same cell. This feature tends to amplify small differences between cells. Incorporating our improved understanding of the signaling system into simulations of different types of downstream feedbacks and boundary conditions lent us several insights into their function. The Notch system converts a shallow gradient of Delta expression into a sharp band of Notch signaling without any sort of feedback at all, in a system motivated by the Drosophila wing vein. It also improves the robustness of lateral inhibition patterning, where signal downregulates ligand expression, by removing the requirement for explicit cooperativity in the feedback and permitting an exceptionally simple mechanism for the pattern. When coupled to a downstream lateral induction feedback, the Notch system supports the propagation of a signaling front across a tissue to convert a large area from one state to another with only a local source of initial stimulation. It is also capable of converting a slowly-varying gradient in parameters into a sharp delineation between high- and low-ligand populations of cells, a pattern reminiscent of smooth muscle specification around artery walls. Finally, by implementing a version of the lateral induction feedback architecture modified with the addition of an autoregulatory positive feedback loop, we were able to generate cells that produce enough cis ligand when stimulated by trans ligand to themselves transmit signal to neighboring cells, which is the hallmark of lateral induction.

Functional genomic studies of the structure and regulation of eukaryotic transcriptomes

The main focus of this thesis is the use of high-throughput sequencing technologies in functional genomics (in particular in the form of ChIP-seq, chromatin immunoprecipitation coupled with sequencing, and RNA-seq) and the study of the structure and regulation of transcriptomes. Some parts of it are of a more methodological nature while others describe the application of these functional genomic tools to address various biological problems. A significant part of the research presented here was conducted as part of the ENCODE (ENCyclopedia Of DNA Elements) Project.

The first part of the thesis focuses on the structure and diversity of the human transcriptome. Chapter 1 contains an analysis of the diversity of the human polyadenylated transcriptome based on RNA-seq data generated for the ENCODE Project. Chapter 2 presents a simulation-based examination of the performance of some of the most popular computational tools used to assemble and quantify transcriptomes. Chapter 3 includes a study of variation in gene expression, alternative splicing and allelic expression bias on the single-cell level and on a genome-wide scale in human lymphoblastoid cells; it also brings forward a number of critical to the practice of single-cell RNA-seq measurements methodological considerations.

The second part presents several studies applying functional genomic tools to the study of the regulatory biology of organellar genomes, primarily in mammals but also in plants. Chapter 5 contains an analysis of the occupancy of the human mitochondrial genome by TFAM, an important structural and regulatory protein in mitochondria, using ChIP-seq. In Chapter 6, the mitochondrial DNA occupancy of the TFB2M transcriptional regulator, the MTERF termination factor, and the mitochondrial RNA and DNA polymerases is characterized. Chapter 7 consists of an investigation into the curious phenomenon of the physical association of nuclear transcription factors with mitochondrial DNA, based on the diverse collections of transcription factor ChIP-seq datasets generated by the ENCODE, mouseENCODE and modENCODE consortia. In Chapter 8 this line of research is further extended to existing publicly available ChIP-seq datasets in plants and their mitochondrial and plastid genomes.

The third part is dedicated to the analytical and experimental practice of ChIP-seq. As part of the ENCODE Project, a set of metrics for assessing the quality of ChIP-seq experiments was developed, and the results of this activity are presented in Chapter 9. These metrics were later used to carry out a global analysis of ChIP-seq quality in the published literature (Chapter 10). In Chapter 11, the development and initial application of an automated robotic ChIP-seq (in which these metrics also played a major role) is presented.

The fourth part presents the results of some additional projects the author has been involved in, including the study of the role of the Piwi protein in the transcriptional regulation of transposon expression in Drosophila (Chapter 12), and the use of single-cell RNA-seq to characterize the heterogeneity of gene expression during cellular reprogramming (Chapter 13).

The last part of the thesis provides a review of the results of the ENCODE Project and the interpretation of the complexity of the biochemical activity exhibited by mammalian genomes that they have revealed (Chapters 15 and 16), an overview of the expected in the near future technical developments and their impact on the field of functional genomics (Chapter 14), and a discussion of some so far insufficiently explored research areas, the future study of which will, in the opinion of the author, provide deep insights into many fundamental but not yet completely answered questions about the transcriptional biology of eukaryotes and its regulation.

Engineered underdominance as a method of insect population replacement and reproductive isolation

Insect vector-borne diseases, such as malaria and dengue fever (both spread by mosquito vectors), continue to significantly impact health worldwide, despite the efforts put forth to eradicate them. Suppression strategies utilizing genetically modified disease-refractory insects have surfaced as an attractive means of disease control, and progress has been made on engineering disease-resistant insect vectors. However, laboratory-engineered disease refractory genes would probably not spread in the wild, and would most likely need to be linked to a gene drive system in order to proliferate in native insect populations. Underdominant systems like translocations and engineered underdominance have been proposed as potential mechanisms for spreading disease refractory genes. Not only do these threshold-dependent systems have certain advantages over other potential gene drive mechanisms, such as localization of gene drive and removability, extreme engineered underdominance can also be used to bring about reproductive isolation, which may be of interest in controlling the spread of GMO crops. Proof-of-principle establishment of such drive mechanisms in a well-understood and studied insect, such as Drosophila melanogaster, is essential before more applied systems can be developed for the less characterized vector species of interest, such as mosquitoes. This work details the development of several distinct types of engineered underdominance and of translocations in Drosophila, including ones capable of bringing about reproductive isolation and population replacement, as a proof of concept study that can inform efforts to construct such systems in insect disease vectors.

Molecular genetic studies on voltage-gated ion channels

Several different methods have been employed in the study of voltage-gated ion channels. Electrophysiological studies on excitable cells in vertebrates and molluscs have shown that many different voltage-gated potassium (K⁺) channels and sodium channels may coexist in the same organism. Parallel genetic studies in Drosophila have identified mutations in several genes that alter the properties of specific subsets of physiologically identified ion channels. Chapter 2 describes molecular studies that identify two Drosophila homologs of vertebrate sodium-channel genes. Mutations in one of these Drosophila sodium-channel genes are shown to be responsible for the temperature-dependent paralysis of a behavioural mutant para^ts. Evolutionary arguments, based on the partial sequences of the two Drosophila genes, suggest that subfamilies of voltage-gated sodium channels in vertebrates remain to be identified.

In Drosophila, diverse voltage-gated K⁺ channels arise from alternatively spliced mRNAs generated at the Shaker locus. Chapter 3 and the Appendices describe the isolation and characterization of several human K⁺-channel genes, similar in sequence to Shaker. Each of these human genes has a highly conserved homolog in rodents; thus, this K⁺-channel gene family probably diversified prior to the mammalian radiation. Functional K⁺ channels encoded by these genes have been expressed in Xenopus oocytes and their properties have been analyzed by electrophysiological methods. These studies demonstrate that both transient and noninactivating voltage-gated K⁺ channels may be encoded by mammalian genes closely related to Shaker. In addition, results presented in Appendix 3 clearly demonstrate that independent gene products from two K⁺-channel genes may efficiently co-assemble into heterooligomeric K⁺ channels with properties distinct from either homomultimeric channel. This finding suggests yet another molecular mechanism for the generation of K⁺-channel diversity.

四川黄龙杓兰属植物的传粉生物学

兰科植物传粉生物学的研究以往多集中于单个物种上，很少对两个以上的物种同时进行研究。但后一类研究对于理解一个地区或一个代表类群的传粉适应是大有裨益和非常必要的，毕竟单一种植物与其传粉者在一个居群或是一年中的相互关系所提供的有效信息是非常有限的。杓兰属Cypripedium L.是兰科植物中比较原始的类群，全世界约有50种;中国是杓兰属植物的分布中心，有30多种。但是，有关该属植物的传粉生物学研究集中在欧、美的种类，中国绝大部分物种尚未进行这方面的研究。本文通过对分布于四川省黄龙寺自然保护区的8种杓兰属植物的传粉生物学研究，探讨了该属植物的传粉机制、适应进化及生殖隔离等问题。 1． 杓兰属植物的繁育系统 虽然所研究的8种杓兰人工自交授粉均可以成功结实，但在自然条件下都必须依赖于昆虫才能结实成功，表明杓兰属植物的繁殖系统以异交授粉为主。 2． 杓兰属植物的传粉系统以及传粉系统的进化趋势 杓兰属植物一向被认为是典型的蜂类传粉物种，本文所包括的西藏杓兰C. tibeticum King ex Rolfe、离萼杓兰C. plectrochilum Franch.、绿花杓兰C. henryi Rolfe与褐花杓兰C. smithii Schltr.的传粉生物学研究也证明了这一点。但研究发现最进化的“无苞组”的3种杓兰，即无苞杓兰C. bardolphianum W. W. Smith et Farrer、小花杓兰C. micranthum Franch.与四川杓兰C. sichuanense Perner都是由蝇类传粉的，而黄花杓兰C. flavum P. F. Hunt et Summerh.则可由蜂类和蝇类共同传粉。结合杓兰的种间系统关系，本文认为杓兰属中存在从蜂类传粉系统向蝇类传粉系统的进化趋势。 3．杓兰属植物传粉系统的特化机制 传粉观察表明8种杓兰均有多种多样的访花昆虫，但只有1种或1类具有相同功能的昆虫能成为其传粉者。这说明杓兰属植物是具备特化传粉系统的种类。以离萼杓兰为例进行的花色、花香及花结构的分析表明，杓兰拥有特化的传粉者几乎完全是由于受到花结构的限制，特别是雄蕊到唇瓣底高度（AL）、柱头到唇瓣底高度（SL）、唇瓣入口直径（DL）与唇瓣出口宽度（EL）的大小。这些因素决定了昆虫是否能进入唇瓣，是否能碰触到柱头和花粉，是否能从出口挤出来。因此，杓兰的唇瓣的主要功能不仅是象原来所认为的作为“陷阱”来诱捕昆虫，而且同样作为一种促进产生“特化传粉”的机制而存在。 4． 杓兰属植物吸引昆虫的机制 杓兰属植物具有复杂的吸引昆虫的机制。离萼杓兰、黄花杓兰主要以泛化的食源性欺骗机制来吸引昆虫，绿花杓兰能通过其唇瓣和退化雄蕊的光滑特性诱使其传粉昆虫被动进入唇瓣中，西藏杓兰可以通过“筑巢式欺骗”来吸引昆虫，无苞杓兰则可通过模拟成熟果实来吸引其特化的传粉者—果蝇Drosophila spp.。 5． 杓兰属植物的花部特征与传粉系统的适应 在整个杓兰属内，不同种类植物的花色与花香和传粉者种类间没有统一的规律。但是，杓兰属植物的唇瓣大小与其传粉者大小之间存在比较明显的适应关系。体积最大的西藏杓兰、褐花杓兰与黄花杓兰由体型最大的熊蜂Bombus spp.传粉，体积中等的离萼杓兰、绿花杓兰、四川杓兰由中等大小的蜂或蝇传粉，而体积最小的无苞杓兰与小花杓兰由体型很小的果蝇传粉。 在杓兰属中，大部分种类的花粉只是粘性的团状，只有一部分能在一次访问中被昆虫带出，如黄花杓兰、西藏杓兰、离萼杓兰及绿花杓兰的花粉团。与此不同，在2个“无苞组”的杓兰，即无苞杓兰、小花杓兰中，它们的花粉凝聚成块状，而且它们的传粉昆虫(果蝇)的一次访问可带出一侧雄蕊的全部花粉。它们的花粉成块可能是对果蝇这类小昆虫传粉的一种适应。 6． 杓兰属植物的生殖隔离机制 本文的研究表明，杓兰属植物之间人工杂交授粉可以成功结实，它们主要是通过受精前隔离机制保持物种界限的。它们的受精前隔离机制多种多样。具有相同传粉者—果蝇的无苞杓兰与小花杓兰通过地理隔离机制保持物种界限; 同域的西藏杓兰与黄花杓兰通过利用不同大小的熊蜂作为传粉者来保持生殖隔离;同域的离萼杓兰与绿花杓兰可能通过花香成分的不同特化吸引同一属中不同种的传粉昆虫;而同域的西藏杓兰与褐花杓兰之间并不具备完善的生殖隔离机制。

横断山地区果蝇三新种(双翅目: 果蝇科)

分述了横断山地区果蝇新种叉茎果蝇Drosophila (D.) furcapenis、拟叉茎果 蝇D. (D.) furcapenisoides和长叉茎果蝇D. (D.) longifurcapenis的形态特征及其与近似种的区别。

黑色拱背果蝇种组三新种记述 (双翅目: 果蝇科)

该文记述果蝇属拱背果蝇亚属黑色拱背果蝇种组三新种: 锚形拱背果蝇 Drosophila (Lordiphosa) archoroides sp. nov, 毛拱背果蝇 Drosophila (Lordiphosa) penicilla sp. nov. 和钳拱背果蝇 Drosophila (Lordiphosa) forcipata sp. nov.. 附中国10个种的检索表。

Murine MyaK, a member of a family of yeast YAK1-related genes, is highly expressed in hormonally modulated epithelia in the reproductive system and in the embryonic central nervous system

We have cloned a mouse homologue (designated Myak) of the yeast protein kinase YAK1. The 1210 aa open reading frame contains a putative protein kinase domain, nuclear localization sequences and PEST sequences. Myak appears to be a member of a growing family of YAK1-related genes that include Drosophila and human Minibrain as well as a recently identified rat gene ANPK that encode a steroid hormone receptor interacting protein. RNA blot analysis revealed that Myak is expressed at low levels ubiquitously but at high levels in reproductive tissues, including testis, epididymis, ovary, uterus, and mammary gland, as well as in brain and kidney. In situ hybridization analysis on selected tissues revealed that Myak is particularly abundant in the hormonally modulated epithelia of the epididymis, mammary gland, and uterus, in round spermatids in the testis, and in the corpora lutea in the ovary, Myak is also highly expressed in the aqueduct of the adult brain and in the brain and spinal cord of day 12.5 embryos, Mol. Reprod. Dev. 55:372-378, 2000. (C) 2000 Wiley-Liss, Inc.

Electric times in olfaction.

Recent work established the spread of interglomerular excitation in the Drosophila antennal lobe. Two papers in this issue of Neuron, by Huang et al. and Yaksi and Wilson, show that cholinergic krasavietz local interneurons are a major substrate for this spread of excitation, predominantly via electrical coupling.

Comparative Expression of Zebrafish Lats1 and Lats2 and Their Implication in Gastrulation Movements

Large tumor suppressor (Lats) is a Ser/Thr kinase, and it presents an important function in tumor suppression. lats was originally identified in Drosophila and recently in mammals. In mammals, it contains two homologues, lats1 and lats2. In the present study, lats1 and lats2 were characterized from zebrafish (Danio rerio), which is the first report of lats in a nonmammalian vertebrate. The primary structure, genomic organization, and phylogenesis of lats from different species were studied, and the results suggest that lats1 is the direct descendant of invertebrate lats, whereas lats2 is formed by genome duplication. In zebrafish, both lats genes are maternally expressed, while they show distinctly different expression profiles during gastrulation. lats1 is almost ubiquitously expressed through development, and lats2 is more prominently expressed in the non-neural ectoderm region of zebrafish gastrula. Most intriguingly, as revealed by cell tracing and gene expression analysis, morpholino-mediated knockdown of either lats1 or lats2 led to obvious defects of cell migration in gastrulation, indicating the functional significance of lats in gastrulation movements. Developmental Dynamics 238:28502859, 2009. (C) 2009 Wiley-Liss, Inc.