Microbiology

Molecular and Cell Biology of Symbiosis

DK16469 — Tue, 04 Oct 2022 19:22:20 +0000

Molecular and Cell Biology of Symbiosis DK16469 Tue, 10/04/2022 - 15:22

Directors: Phillip Cleves, Carnegie Institute of Science

Course Description

The Molecular and Cell Biology of Symbiosis advanced research training course at the �� is an immersive research-based course designed to teach basic concepts, open research questions, and facilitate state-of-the-art experimental approaches in symbiosis research. This 4-week experience will give students a deep understanding of the field of symbiosis research through a combination of hands-on research projects, lectures from experts in the field, and interactive workshops.

The course focuses on how evolutionarily diverse symbiotic relationships form, are maintained, and are impacted by environmental stress. Course modules will consist of a combination of well-established model organisms with tractable imaging and genetic tools and emerging model organisms. In addition to working with a variety of evolutionarily diverse organisms, participants will learn to study symbiotic relationships across various scales of biology - from molecules to ecosystems - to gain an appreciation for the interdisciplinary nature and impacts of symbiotic relationships.

Specific topics include:

molecular mechanisms of microbe selection
live-cell imaging of host-microbe interactions
biochemistry and metabolic maintenance of microbiome communities
effects of stress on symbiotic relationships
development and application of genetic tools to study aquatic symbiosis
gene regulatory and signaling networks associated with symbiosis
experimental model organisms to study symbiosis
evolution of symbiosis across taxa

In addition to hands-on experiences, the participants will also build professional skills, such as scientific communication through research presentations, and a network of international collaborators and mentors through immersive, daily interactions.

Optical Microscopy & Imaging in the Biomedical Sciences

sandstormer — Mon, 22 Nov 2021 21:38:19 +0000

Optical Microscopy & Imaging in the Biomedical Sciences sandstormer Mon, 11/22/2021 - 16:38

Directors: Joerg Bewersdorf, Yale University; and Alison North, The Rockefeller University

Course Description

This course is designed primarily for research scientists, postdoctoral trainees, core facility directors/staff and graduate students working in the biological sciences. Non-biologists seeking a comprehensive introduction to microscopy and digital imaging in the biomedical sciences will also benefit greatly from this course. The 9-day course is limited to 24 participants to ensure a truly interactive, hands-on experience. It consists of interrelated lectures, laboratory exercises, demonstrations, and discussions that will enable the participants to obtain and interpret high quality microscope data, to understand and assess potential artifacts, to perform quantitative optical measurements, and to generate digital images for documentation and analysis that accurately present the data. The course also places a strong emphasis on appropriate sample preparation, including choice of fluorescent probes and fluorescent proteins, and tissue clearing and refractive index matching. Particular emphasis will be placed on ‘picking the right tool for the job’.

Topics to be covered include:

Fundamental principles of microscope design, image formation, resolution and contrast;
Transmitted light and fluorescence microscopy techniques;
Cameras, signal to noise ratio, digital image recording, processing and analysis, multispectral imaging;
Advanced fluorescence – fluorescent probes, fluorescent biosensors, TIRF, FRET, FLIM, FRAP, polarization of fluorescence, fluorescence correlation spectroscopy;
Digital image restoration/deconvolution, and 3-D imaging principles;
Confocal and multiphoton laser scanning microscopy and light-sheet microscopy;
Super-resolution techniques including localization microscopy, stimulated emission depletion microscopy (STED), structured illumination microscopy and expansion microscopy.

Course participants will have direct hands-on experience with state-of-the-art microscopes, a variety of digital cameras, and image processing software provided by major optical, electronics, and software companies. Instruction will be provided by experienced staff from universities and industry. Participants are encouraged to bring their own, fixed biological specimens, and to discuss individual research problems with the faculty.

Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS)

sandstormer — Mon, 22 Nov 2021 21:19:05 +0000

Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS) sandstormer Mon, 11/22/2021 - 16:19

Directors: C. Titus Brown, University of California, Davis and Amy Willis, University of Washington

Visit external STAMPS website

Course Description

Modern sequencing technologies enable comprehensive investigations of microbial communities, but generating large microbial datasets is often easier than analyzing them. STAMPS bridges the gap between data generation and knowledge generation, offering interdisciplinary training in bioinformatics and statistics to practitioners of molecular microbial ecology and genomics. Topics include: experimental design; processing raw data into genomic and functional units; annotation and reference databases; and statistical methods for analyzing microbiome data. Hands-on tutorials will focus on short-read shotgun sequencing and 16S data, but other approaches (such as long-read sequencing and ITS sequencing) will be discussed. The course covers some basics of the Unix command-line and R statistical computing environments, but prior experience is strongly recommended. STAMPS promotes respectful dialogue and the exchange of ideas between experts and learners, and participants will have many opportunities to try out different analysis techniques and discuss their data and analyses with faculty. This hands-on, interactive course is designed for advanced graduate students, postdoctoral fellows, and established investigators from diverse biological fields.

Molecular Mycology: Current Approaches to Fungal Pathogenesis

sandstormer — Mon, 22 Nov 2021 21:07:38 +0000

Molecular Mycology: Current Approaches to Fungal Pathogenesis sandstormer Mon, 11/22/2021 - 16:07

Directors: David Andes, University of Wisconsin-Madison and Robert Cramer, Geisel School of Medicine at Dartmouth

Course Description

Fungal diseases are significant causes of mortality and morbidity in both the developed and the developing world. The recent increases in the incidence and severity of invasive fungal infections are directly attributable to new susceptible patient populations. Examples of these large, at-risk populations include patients with AIDS; hospitalized patients being treated for cancer and autoimmune disorders; andthose receiving organ transplants. Despite this increasing threat, our understanding of the basic pathophysiology of fungal disease lags far behind our understanding of bacterial, parasitic and viral diseases. Furthermore, the number of antifungal therapies in clinical use is limited, and there is a paucity of novel antifungal strategies in the current drug pipeline. To address the need for more research in the area of fungal diseases, this course aims to:

a) increase students’ breadth of knowledge in fungal pathogenesis research

b) introduce and explore both standard and cutting edge model systems for the analysis of fungal virulence

c) create an environment that fosters interactions and idea-exchange among students, faculty, and the greater mycology research community.

Course material is suitable for advanced graduate students, post-doctoral fellows, research faculty, and clinician-scientists.

The specific objectives of the Molecular Mycology course:

To present the current conceptual models for the pathogenesis of medically important fungi, with a focus on the most frequently encountered pathogens – Candida, Cryptococcus, and Aspergillus
To train students in molecular manipulation of Candida, Cryptococcus, and Aspergillus
To provide hands on experience with mammalian, invertebrate, and cell culture models to assess virulence and analyze different types of host-pathogen interactions
To present a broad perspective on experimental issues pertinent to pathogenic fungi, such as the definition and determination of virulence, the determination of host responses relevant to infection, and the quantification of antifungal susceptibility
To instruct students in techniques relevant to the analysis of the function of fungal gene products such as determination of essentiality, microscopic analysis of morphology and fluorescent protein fusions, comparison of RNA expression profiles of wild-type and mutant strains, assessment of chromosome content
To provide insight into the clinical aspects of fungal diseases from the perspective of the host and the pathogen
To provide an introduction to tools for comparative genome and transcriptional analysis
To discuss research ethics, professional development (academic, industrial, or government careers), and issues specific to the medical mycology field.

Microbial Diversity

sandstormer — Mon, 22 Nov 2021 21:05:20 +0000

Microbial Diversity sandstormer Mon, 11/22/2021 - 16:05

Directors: Scott C. Dawson, University of California, Davis; and John Spear (Colorado School of Mines)

Course Description

Launched in 1971 by Holger Jannasch, the Microbial Diversity summer course at �� has trained generations of scientists from diverse backgrounds. The course is an intense immersion experience for 20 students that lasts 6.5 weeks. The goal of the course is to teach professors, postdocs and advanced graduate students how to discover, cultivate, and isolate diverse microorganisms catalyzing a breadth of chemical transformations, as well as how to perform molecular and computational analyses relevant to their study. While microbial isolation techniques form the essential core of the course, each new set of directors brings an additional focus that reflects their interests/expertise. We have introduced basic genetic methods to the course for the first time to enable students to study how microbes catalyze interesting reactions and exhibit interesting behaviors. In addition, we emphasize state-of-the-art imaging techniques and training in quantitative microscopy to study microbial cell biology and single-cell gene expression. Genetically-tractable strains isolated in the course are sequenced by Pacific Biosystems, and students learn how to annotate and analyze their genomes. Given the wealth of DNA, RNA and protein sequences now available from isolated microbes and environmental samples, these tools are important for students to master so they may understand what these sequences mean and in which context they are expressed—be it in the marine environment, soils, or plant and animal hosts. We also emphasize quantitative approaches to microbial diversity, including teaching students how to describe the energetic potential of diverse metabolisms. A dedicated team of resident course instructors as well as guest-lecturers participate in the course every summer, allowing students to be exposed to exciting current research. The opportunity to interact one-on-one with these individuals is a tremendous opportunity, often leading to future collaborations.

Physiology: Modern Cell Biology Using Microscopic, Biochemical and Computational Approaches

sandstormer — Mon, 22 Nov 2021 20:55:47 +0000

Physiology: Modern Cell Biology Using Microscopic, Biochemical and Computational Approaches sandstormer Mon, 11/22/2021 - 15:55

Directors: Cliff Brangwynne, Princeton University; and Amy Gladfelter, Duke University

Course Description

The �� Physiology Course was founded by Jacques Loeb in 1892 and is one of the oldest continually running biology courses in the world. This intensive seven-week laboratory course has educated generations of leading biologists and fostered groundbreaking biological discoveries, including the Nobel prize-winning discovery of cyclin B.

As physiology has evolved to embrace modern microscopy and computational methods and incorporate the latest biological techniques, so has the Physiology Course. Today, the course is at the forefront of new tools — molecular, computational, biophysical — as it prepares students to tackle emerging biological questions. To teach this modern approach to research, faculty from the biological sciences and physical sciences, including engineering and computational sciences, come together each summer with an equally diverse set of students to create a unique training environment that mixes cell biology, biophysics, and computational methods in biology.

Join us! Students with backgrounds in either the biological sciences or engineering/physical/computational sciences are strongly encouraged to apply. Admission to �� courses is “need-blind”, and we are committed to recruiting underrepresented minorities and women in both the students and faculty.

Biology of Parasitism: Modern Approaches

sandstormer — Mon, 22 Nov 2021 20:47:13 +0000

Biology of Parasitism: Modern Approaches sandstormer Mon, 11/22/2021 - 15:47

Directors: Vernon Carruthers, University of Michigan, Ann Arbor; Friedrich Frischknecht, Heidelberg University Medical School; and Melissa Lodoen, University of California, Irvine

Course Description

A unique 7-week course for advanced doctoral students and postdocs who are seeking in-depth training in modern approaches to the study of protozoan parasites and parasitic worms.

This course is focused on the cellular and molecular mechanisms by which human and animal parasites cause disease and the host responses to infection. The course consists of daily lectures by distinguished leaders in the field juxtaposed with intensive experimental work. The lectures cover most areas of active research in modern parasitology and are designed to complement the laboratory work. Ample opportunity is provided for students to interact informally with visiting lecturers and course faculty. In the laboratory, the students work together in small groups, gaining hands-on experience and working collaboratively with the faculty to explore new questions and discover new knowledge. Students will use advanced imaging, flow cytometry, biophysical methods, a variety of state-of-the-art molecular, bioinformatics and cell biological techniques, and in vivo infection models to study mechanisms of nutrient uptake, drug resistance, parasite motility, host-to-host transmission by insect vectors and immune responses to infection. Students will gain experience working with malaria parasites, Toxoplasma gondii, African trypanosomes, Entamoeba histolytica, parasitic worms and the mosquitoes that transmit malaria. The course is international by design, with students coming from around the world. Coming into the course, students should have a solid understanding of cellular and molecular biology and will complete the course with a new set of experimental tools to apply to their own research, a greatly expanded network of international colleagues, and a deep and broad appreciation for the remarkable interactions that occur at the host–parasite interface.