This course provides a foundation in the following four areas: evolutionary and population genetics; comparative genomics; structural genomics and proteomics; and functional genomics and regulation.
This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:
"Does skeletal muscle have a memory? That’s the question researchers from the UK set out to answer in one of their most recent studies. Their finding: Yes, muscle memory is real. But it’s not quite the same type of memory you might be thinking of. This is memory of previous muscle growth—even after a period of muscle loss. The implications for athletes looking to bulk up is clear. But the results could also clue clinicians in on how to help patients retain muscle mass into older age. The researchers analyzed more than 850,000 sites on human DNA, discovering distinct patterns in how genes in these regions were chemically marked or unmarked during periods of exercise or no exercise. One cluster of genes lost its tags during muscle growth following exercise, kept them off after a period of no exercise, and lost even more during a second exercise period. Known as an epigenetic modification, this “untagging of DNA” is associated with switching gene expression on..."
The rest of the transcript, along with a link to the research itself, is available on the resource itself.
This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:
"Type 2 diabetes mellitus often leads to muscle atrophy driven by diminished differentiation capacity in myoblasts. Myogenesis is complex, and while many involved pathways have been described, there may still be yet undiscovered therapeutic targets. With this goal in mind, a recent study combined experiments in diabetic mice and cultured myoblasts to identify key proteins in diabetes-induced atrophy. The gene for the relatively undescribed solute carrier Slc2a6, also known as glut6, was up-regulated during myogenic differentiation and down-regulated during diabetes-induced myopathy. Silencing Slc2a6 with RNAi in cell culture impaired differentiation and myotube formation. Transcriptomics and metabolomics revealed that Slc2a6 silencing disproportionally impacted the glycolysis pathway . Further experiments and analysis determined that Slc2a6 regulates myogenic differentiation in cultured myoblasts and that this regulation was partly through the glycolysis pathway..."
The rest of the transcript, along with a link to the research itself, is available on the resource itself.
This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:
"TRF2 is a protein in charge of protecting the endcaps of chromosomes known as telomeres. But increasing evidence suggests that TRF2 also carries out important non-telomere-related functions, including DNA repair and transcription regulation. To better understand these functions, researchers recently mapped out where else TRF2 sites might exist. ChIP-Seq assays of fibrosarcoma cells revealed extra-telomeric TRF2 sites throughout the genome, which were highly enriched in DNA sequences with the potential to form G-quadruplexes, a DNA structure formed by G-rich sequences with a specific pattern, known to play a critical role in gene expression. TRF2 bound tightly to these sites, and further experiments revealed that TRF2 occupancy resulted in altered mRNA expression in nine target genes. Because naturally occurring intracellular G-quadruplexes are difficult to detect, TRF2 binding may serve as a new tool to specifically detect these regions..."
The rest of the transcript, along with a link to the research itself, is available on the resource itself.
This is a seminar based on research literature. Papers covered are selected to illustrate important problems and approaches in the field of computational and systems biology, and provide students a framework from which to evaluate new developments.
The MIT Initiative in Computational and Systems Biology (CSBi) is a campus-wide research and education program that links biology, engineering, and computer science in a multidisciplinary approach to the systematic analysis and modeling of complex biological phenomena. This course is one of a series of core subjects offered through the CSB Ph.D. program, for students with an interest in interdisciplinary training and research in the area of computational and systems biology.
This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:
"In cancer cells, even seemingly small gene expression changes can have a devastating impact, but for some molecules, like the enzyme USP22, researchers don’t know how their expression is regulated. High expression of USP22 is associated with poor prognosis in many human cancers. But the gene for USP22 is rarely mutated, suggesting that the expression changes happen at the transcription step. So, researchers set out to find transcription factors, which are transcription-modulating proteins, that regulate USP22. After identifying several that modulate USP22 expression, they focused on two related factors that increased USP22 expression, AP2α, and AP2β. Overexpressing AP2α/β in cultured non-small cell lung cancer (NSCLC) cells increased the expression of USP22 and the protein it targets, Cyclin D1, while also increasing the cancer cell behaviors proliferation, migration, and invasion..."
The rest of the transcript, along with a link to the research itself, is available on the resource itself.
This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:
"A new study shows that a novel embryonic cleavage pattern can evolve without affecting other developmental traits. But let’s start at the beginning. The earliest stages of animal development – the moments following fertilization of the egg – involve a sequence of cell divisions that will eventually turn a zygote into a multicellular embryo. This process is termed _cleavage_. Two cells become four. Four cells become eight. Etcetera. But it’s not just the addition of new cells that is important in this process – it’s also their orientation. Just as there are all shapes and sizes of animals, the pattern of early cell division varies across different organisms. In some animals, these cleavage patterns play the crucial role of precisely positioning early embryonic cells in just the right way. A single misplaced cell can have catastrophic consequences for the growing embryo..."
The rest of the transcript, along with a link to the research itself, is available on the resource itself.
Open data is a vital pillar of open science and a key enabler for reproducibility, data reuse, and novel discoveries. Enforcement of open-data policies, however, largely relies on manual efforts, which invariably lag behind the increasingly automated generation of biological data. To address this problem, we developed a general approach to automatically identify datasets overdue for public release by applying text mining to identify dataset references in published articles and parse query results from repositories to determine if the datasets remain private. We demonstrate the effectiveness of this approach on 2 popular National Center for Biotechnology Information (NCBI) repositories: Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA). Our Wide-Open system identified a large number of overdue datasets, which spurred administrators to respond directly by releasing 400 datasets in one week.
This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:
"A fundamental law of genetics states that offspring do not inherit traits from their parents that were acquired in response to environmental conditions. Recent research in the field of epigenetics, however, is turning this principle on its head. Several recent studies have come to the remarkable conclusion that unhealthy diets in males can contribute to the development of metabolic diseases in their offspring. Even when those offspring are raised with healthy diets_._ Now, a study has identified small RNAs as the molecules responsible for the transmission of these disorders. For a long time scientists thought that inheritance of traits only occurred via DNA being passed from parent to offspring. It is now clear, however, that the experiences of one generation can have an effect on the next. When parents have a high-stress lifestyle or an unhealthy diet, for example, chemical modifications can occur on genes that are then passed to their children. This is termed ‘epigenetic inheritance..."
The rest of the transcript, along with a link to the research itself, is available on the resource itself.
This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:
"Of the 20 standard amino acids, 18 can be coded by two to six synonymous codons. The preference for certain synonymous codons over others is a phenomenon known as “codon usage bias,” and it's been found in all genomes examined to date. Growing evidence suggests that codon usage regulates protein structure and gene expression through translation-dependent and translation-independent mechanisms. In fact, codon usage has been discovered to play an important role in controlling the speed of translation elongation during mRNA translation, as well as in regulating protein folding and function in both prokaryotes and eukaryotes. Additionally, studies show that intrinsically disordered domain structures are sensitive to codon usage. These disordered structures play a critical role in many biological processes and are sites for important post-translational modifications..."
The rest of the transcript, along with a link to the research itself, is available on the resource itself.
This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:
"Our microbiome plays a key role in our health and contains bacteria, fungi, viruses, and archaea. However, due to several factors, the bacterial residents get the most attention. Consequently, our understanding of fungi and their interactions with other microbiome residents remains limited. A recent study addressed this by collecting data on the nasal cavity and oropharynx microbiome of healthy newborn infants. The fungal and bacterial species composition was most strongly influenced by location in the airway. However, breastfeeding status also significantly shaped both the bacterial and fungal communities in the oropharynx. Multi-kingdom microbial networks inference analysis suggested potential interactions between the fungi and bacteria. To examine potential impacts on the infants, the gene expression in their nasal cavity was also evaluated..."
The rest of the transcript, along with a link to the research itself, is available on the resource itself.
This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:
"The rumen is the largest compartment of the ruminant forestomach and houses a complex microbiome. That microbiome greatly influences gut energy harvesting capacity. Improving our understanding of the mechanisms that influence energy harvesting capacity could be used to optimize ruminant feed efficiency and management. Thus, researchers recently examined temporal ecological interactions at the plant-biofilm interface by incubating fresh perennial ryegrass in cattle rumens and analyzing the bacterial diversity and gene expression at several time points. Network analysis identified two sub-microbiomes. They represented the primary (<4h) and secondary (>4h) colonization phases. Several of the most transcriptionally active microbial families didn't interact with either sub-microbiome, which suggests non-cooperative behavior. Conversely, the putative keystone families of each sub-microbiome had low transcriptional activity..."
The rest of the transcript, along with a link to the research itself, is available on the resource itself.
This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:
"Epithelial-mesenchymal transition (EMT) is a cellular process critical to the spread of breast cancer. EMT leads to stem-cell like behavior, or stemness, and is largely responsible for distal lung metastasis. Many oncogenic pathways, including Fzd/Wnt-mediated pathways, contribute to this process. A new study explored the role of Fzd7 in EMT, stemness, and metastasis. Database searches found that Fzd7 expression was correlated with mesenchymal phenotypes and mesenchymal-associated genes. Fzd7 knockdown in vitro reduced the expression of mesenchymal-associated genes induced epithelial-like morphology and inhibited cell motility, impaired mammosphere formation, and decreased the Lgr5+ subpopulation. In mice, Fzd7 knockdown reduced lung metastasis of xenograft tumors while also delaying their formation and suppressing growth. To explore the mechanisms behind this, the researchers identified correlations between expression levels of Fzd7, Wnt5a/b, and Col6a1 in expression databases..."
The rest of the transcript, along with a link to the research itself, is available on the resource itself.