Development and Reproduction

Gene Regulatory Networks for Development

sandstormer — Mon, 22 Nov 2021 19:52:33 +0000

Gene Regulatory Networks for Development sandstormer Mon, 11/22/2021 - 14:52

Directors: Titus Brown, University of California, Davis and Veronica Hinman, Carnegie Mellon University

Course Description

Gene regulatory networks (GRNs) are key to the genomic control of development in animals and plants. To study GRNs requires insights from various research fields, including systems biology, developmental and evolutionary biology, as well as functional genomics, and provides an integrative approach to fundamental research questions in biology. This course introduces the concepts of GRNs, and teaches experimental and computational methods used to study them, through highly interactive lectures, discussions, group projects, and practical tutorials. We will cover a broad range of topics, including transcriptional control systems, the structural organization of hierarchical networks, developmental functions of GRN circuit modules, GRN evolution, and computational modeling using BioTapestry as well as Boolean and quantitative mathematical approaches. Students will learn how to generate GRN models based on data extracted from the literature, and will generate computational models to analyze dynamic circuit behavior. We will present and discuss a broad range of experimental approaches and how they are effectively used for studying gene regulation and developmental GRNs. Examples of experimentally solved developmental GRNs from a variety of organisms, such as flies, sea urchins, frogs, chicken, and mice, will be explored. Students are encouraged to share their research projects in a poster session, and to discuss with course faculty how to apply the approaches taught in the course to their own research questions. The course is intended for advanced graduate students, postdoctoral scholars, and faculty.

Frontiers in Stem Cells & Regeneration

sandstormer — Mon, 22 Nov 2021 19:49:31 +0000

Frontiers in Stem Cells & Regeneration sandstormer Mon, 11/22/2021 - 14:49

Directors: Ina Dobrinski, University of Calgary; and Charles Easley, University of Georgia

Course Description

The Frontiers in Stem Cells and Regeneration Course is a laboratory and lecture based course that includes a complete array of biological and medical perspectives from fundamental basic biology of “stemness” and mechanisms of regeneration through evaluation of pluripotent stem cells for therapeutic benefit. This dynamic, evolving course features world class lectures from experts in stem cells and regeneration biology, including a keynote Pioneer Lecture delivered by a leading expert. The laboratories explore a variety of timely topics including stem cell derivation, pluripotency, directed differentiation, and spinal cord and limb regeneration, using an array of experimental models ranging from planarians to human stem cells.

The NIH sponsored course is designed for graduate students, postdoctoral fellows, newly independent scientists, and established investigators seeking comprehensive and sophisticated training in research strategies and state-of-the-art cellular, molecular and genetic approaches for advancing stem cell and regeneration research.

The course also features bioethics seminars, career coaching, and ongoing one-on-one mentoring by course faculty participants.

The Stem Cells and Regeneration Course will exclusively use human embryonic stem cell lines on the NIH Human Embryonic Stem Cell Registry and being routinely cultured at the Pittsburgh Development Center.

Zebrafish Development and Genetics

sandstormer — Mon, 22 Nov 2021 19:07:32 +0000

Zebrafish Development and Genetics sandstormer Mon, 11/22/2021 - 14:07

Directors: Thomas Schilling, University of California, Irvine; and Deborah Yelon, University of California, San Diego

Course Description

Over the past 25 years, the zebrafish has emerged as a powerful model system for the study of vertebrate development and disease. This intensive two-week course for advanced graduate students, postdoctoral fellows, and independent investigators will focus on the development and genetics of zebrafish. The course will cover time proven as well as novel technologies geared towards their application in zebrafish. Mornings and afternoons will be devoted mainly to laboratory exercises and the evenings to lectures and discussion. Limited to 22 students.

Lectures and labs in the first week will introduce students to early development of the zebrafish and to methods for manipulating and studying gene function, including genetic and small molecule screening, mRNA overexpression, optogenetics, and functional knockdown approaches. In addition, students will gain experience in relevant bioinformatics tools, cell fate mapping, regeneration experiments, and mounting and imaging of antibody and in situ samples for publication ready documentation. In the second week, students will be introduced to imaging of live cells and intracellular signaling events, biophysical manipulations, cell transplantation/chimera analysis, and behavioral testing of live animals. Informal ‘roundtable’ discussions held periodically during the course include topics such as reverse genetics, transgenesis, and zebrafish breeding and husbandry.

Each laboratory exercise will be under the supervision of a senior faculty member who will be assisted by one or two junior faculty members. Senior faculty will give research lectures about their work, in addition to leading discussions on topics covered in the course.

Workshop on Molecular Evolution

sandstormer — Mon, 22 Nov 2021 18:15:56 +0000

Workshop on Molecular Evolution sandstormer Mon, 11/22/2021 - 13:15

Directors: Tracy Heath, Iowa State University; and Laura Kubatko, The Ohio State University

View the external website for the Workshop on Molecular Evolution course.

Course Description

MBL’s Workshop on Molecular Evolution is the most prestigious workshop serving the field of evolutionary studies. Founded in 1988, it is the longest-running workshop if its kind, and it has earned worldwide recognition for its rich and intensive learning experience. Students work closely with internationally-recognized scientists, receiving (i) high-level instruction in the principles of molecular evolution and evolutionary genomics, (ii) advanced training in statistical methods best suited to modern datasets, and (iii) hands-on experience with the latest software tools (often from the authors of the programs they are using). The material is delivered via lectures, discussions, and bioinformatic exercises motivated by contemporary topics in molecular evolution. A hallmark of this workshop is the direct interaction between students and field-leading scientists. The workshop serves graduate students, postdocs, and established faculty from around the world seeking to apply the principles of molecular evolution to questions of anthropology, conservation genetics, development, behavior, physiology, and ecology. The workshop also welcomes participants from federal agencies and science journalists. A priority of this workshop is to foster an environment where students can learn from each other as well from the course faculty.

Content has been carefully selected to provide participants with the background and practical skills required by modern molecular datasets. The schedule addresses the following subject areas, with each subject having one or more exercises focused on practical data analysis and interpretation skills.

An evolutionary perspective on molecular data: sequence matching; homology, orthology and parology; mathematical, statistical, and theoretical aspects of sequence database searches; multiple alignment; information resources
Foundations of phylogenetic analysis: theoretical, mathematical, and statistical principles; sampling properties of sequence data; Maximum likelihood theory and practice; Bayesian analysis; hypothesis testing
Species-level phylogenomics: species trees from gene trees; species delimitation; multi locus and SNP data; empirical examples
Deep phylogenomics: deep evolutionary relationships; lateral gene transfer; modeling approaches; sequencing strategies; interfacing with phylogenomic databases
Foundations of population genetic analysis: neutral theory; coalescence theory; maximum likelihood and Bayesian estimation of population genetic parameters; empirical examples
Population genomics: phylogeography; molecular ecology; next-generation population genetics; signatures of natural selection; natural populations of non-model organisms; machine learning methods
Comparative genomics: genome content; genome structure; gene and genome evolutionary dynamics
Molecular evolution integrated at organism and higher levels: population biology and ecology; natural selection; systematics and conservation

As the course progresses, participants learn how to use the following software to address questions concerning the origins, maintenance, and function of molecular variation: ASTRAL, FigTree, MIGRATE, IQ-Tree, RevBayes, PAML, PAUP*, Phybase, PhyloNetworks, SnaQ, SVD Quartets, and Open Tree of Life. Students will have the opportunity to work with software on their own laptops as well receive training on how to use the same programs on a high performance computer cluster.

Endocrine-Disrupting Chemicals: Hazards and Opportunities (ECHO)

sandstormer — Mon, 22 Nov 2021 18:13:46 +0000

Endocrine-Disrupting Chemicals: Hazards and Opportunities (ECHO) sandstormer Mon, 11/22/2021 - 13:13

Directors: Patricia Hunt, Washington State University; Joan Ruderman, Princeton University

Course Description

Numerous chemicals invented for agricultural, industrial and consumer products are now known to interfere with hormone-regulated events in development, reproduction, metabolism, and behavior. Exposures to many of these endocrine-disrupting chemicals (EDCs) have pronounced adverse effects in animals (including transgenerational effects), and increasing evidence suggests human populations also are affected. The field has attracted increasing scrutiny, bringing EDC researchers into contact with the press, regulatory agencies, industry, and consumer groups. Thus, expertise across a wide range of disciplines is required to understand and deal with the full impacts of EDCs. The course focuses on the chemical, biological, and societal challenges of EDCs and new opportunities for moving forward. It provides an immersion experience designed to foster deeper understanding of key questions, state-of-the-art approaches, and intersecting needs of the biologists from many sub-disciplines, chemists, public health researchers, epidemiologists, clinicians, industry, and federal regulatory agencies involved in the field.

This course is designed for advanced graduate students, postdoctoral researchers, clinicians, and established investigators transitioning into the EDC field. It incorporates lectures and labs that focus on chemical, cellular and organismal screening of chemicals for endocrine-disrupting effects; analysis of specific EDC effects on the placenta, brain, and mammary gland in mice; EDC effects on chromosome segregation in C. elegans and early development in zebrafish; mass spec approaches for environmental biomonitoring; using epidemiology to discover connections between EDC exposures and adverse effects on human health; designing chemicals that lack EDC effects; epigenetics and transgenerational effects. Several sessions will be devoted to hazard and risk assessment, and to science policy, regulation, and implementation. Students will also receive communications training, prepare for interactions with the media, and then be interviewed by science journalists.

The ultimate goal of the course is to bring together individuals across the entire field to broaden their understanding and forge cross-disciplinary collaborations with the goal of advancing the field and training future leaders. For a quick look at the first year (2022) of this course, see "New ��ϲ�appCourse Targets Hormone-Disrupting Pollutants".

Embryology: Concepts and Techniques in Modern Developmental Biology

sandstormer — Mon, 22 Nov 2021 17:52:57 +0000

Embryology: Concepts and Techniques in Modern Developmental Biology sandstormer Mon, 11/22/2021 - 12:52

Directors: Tatjana Piotrowski, Stowers Institute; and Athula Wikramanayake, University of Miami

Course Description

The Embryology Course is an intensive six-week laboratory and lecture course for advanced graduate students, postdoctoral fellows, and more senior researchers who seek a broad and balanced view of modern issues in developmental biology. Enrollment is limited to 24 students.

Established in 1893, the Embryology Course offers integrated lectures and laboratories that comprehensively cover the paradigms, problems, and technologies of modern developmental biology cast within a comparative framework of metazoan evolution. This course has a rich history of shaping the field: six students and eight faculty have become Nobel Laureates, and numerous others have emerged as prominent leaders and pioneers. The over 40 teaching faculty members, all leaders in their respective fields, deliver lectures, lead discussions, and oversee laboratory sections.

The course introduces students to a wide variety of embryonic systems. These include established models such as fruit flies, nematodes, zebrafish, mice, chickens, sea urchins, frogs, ascidians, and planaria, as well as emerging marine invertebrate models like cnidarians, nemerteans, acoels, crustaceans, cephalopods, annelids, hemichordates, and ctenophores. This extensive coverage of metazoan phylogeny allows for a thorough examination of developmental strategies and mechanisms that drive evolutionary change. The hands-on analytical and experimental techniques employed to explore invertebrate and vertebrate development include embryological manipulation (e.g., cell ablation, tissue grafting) and molecular genetic (e.g., CRISPR/Cas9, RNAi, electroporation) and cell biological approaches (e.g., analysis of cell lineage and migratory behavior). As a result, students receive training in applying cutting-edge microscopy and imaging technologies using the latest instrumentation, reagents, and methods. The curriculum encompasses molecular, genetic, and cellular approaches to studying animal development, stem cell biology, regenerative biology, quantitative biophysical methods, and genomics, all taught within a comparative framework of animal evolution.

Frontiers in Reproduction: Molecular and Cellular Concepts and Applications

sandstormer — Tue, 16 Nov 2021 19:18:35 +0000

Frontiers in Reproduction: Molecular and Cellular Concepts and Applications sandstormer Tue, 11/16/2021 - 14:18

Directors: Rafael Fissore, University of Massachusetts, Amherst; and Daniel Bernard (McGill University)

Course Description

Frontiers in Reproduction (FIR) is an intensive six-week laboratory and lecture course designed for advanced graduate students, post-doctoral fellows, newly independent scientists and physicians who seek training in modern state-of-the-art methods and a broad view of current concepts in all areas of reproductive biology.

The FIR course is divided into three sections of two weeks’ duration and covers the following broad themes:

Section 1 – Signal Transduction and Gene Regulation in the Hypothalamic-Pituitary-Gonadal Axis (Djurdjica Coss, Director)

Section 2 – Stem cells, Gametogenesis, Fertilization, and Preimplantation Embryo Development (Karen Schindler, Director)

Section 3 – Male and Female Reproductive Tract Development, Function and Disease (Peggy Petroff, Director)

Each section consists of lectures from faculty and world-renowned scientists in the field of reproductive science. Discussions, informal seminars, laboratory exercises, demonstrations, and one-on-one tutorials comprise a typical day in the FIR course.

Section 1 emphasizes signal transduction and gene regulation in the hypothalamic-pituitary-gonadal axis and its impact on reproductive function, development, and fertility. Lectures cover physiologic to molecular actions of peptide, protein and steroid hormones and the intracellular signaling as well as the transcriptional gene regulatory mechanisms that drive reproductive biology. Section 1 laboratories teach methods key to studying hormone action and cell biology. Techniques include quantification of second messengers and transcriptional activity; cell culture and transient transfection; western blot analysis; ELISAs; quantitative RT-PCR; chromatin immunoprecipitation; immunofluorescence; tissue dissection.

Section 2 is focused on stem cells, gametogenesis, fertilization, and preimplantation embryo development. The lectures focus on germline stem cells and their differentiation into functional gametes through the processes of spermatogenesis and folliculogenesis, maturation of gametes and acquisition of fertilization and developmental competence, sperm-egg interaction, egg activation and preimplantation embryo development. Epigenetic mechanisms are examined, including discussion of imprinting and transgenerational inheritance. Additional lectures explore how the environment impacts reproduction, the genetic basis of infertility, including animal models and assisted reproductive technologies used in the clinic. Ethical issues concerning the use of technology in human reproduction are also discussed. The labs in Section 2 focus on stem cell transplantation and meiotic staging of germ cells, follicular culture and in vitro techniques related to maturation of oocytes, sperm physiology, fertilization of various animal models, intracytoplasmic sperm injection, and other micromanipulation procedures. Commonly used methods in bioinformatics and their applicability are discussed and illustrated.

Section 3 focuses on the examination of the developing and adult male and female reproductive tracts under normal and pathological conditions. Lectures cover transgenic technology including microinjection, gene editing, and embryo transfer; development of the male and female reproductive tracts, mammary gland and gonads; maternal-fetal interactions including implantation, uterine decidualization, comparative placentation, placental function and immunological adaptations to pregnancy. Additional lectures cover topics of clinical relevance to the reproductive tract, such as implantation failure, endometriosis, breast cancer and functions of the oviduct. The use of non-traditional species in advancing reproductive sciences such as domestic animals and wild animals will be discussed. The labs in Section 3 focus on techniques associated with the lecture topics, including generation and characterization of transgenic embryos, the use of laser capture microdissection, in vitro models including cell and organ culture, flow cytometry, and reporter assays to evaluate function of the reproductive tract.

Spread throughout the course are discussions on professional development such as publishing, grant preparation and review, and ethics. The Frontiers in Reproduction course concludes with a two-day symposium featuring seminars by distinguished speakers and short research presentations by current and previous participants.