Express yourself through your genes! See if you can generate and collect three types of protein, then move on to explore the factors that affect protein synthesis in a cell.

This exercise is designed to help students identify the parts of a gene and an mRNA. The exercise requires a synthesis of their understanding of the various steps of gene expression.

The Geniverse software is being developed as part of a five-year research project funded by the National Science Foundation. Still in its early stages, a Beta version of the software is currently being piloted in six schools throughout New England. We invite you to try the current Beta version, keeping in mind that you may encounter errors or pages that are not fully functional. If you encounter any problem, it may help to refresh or reload the web page.

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:

"Extracellular vesicles (EVs) function in many physiological events ranging from normal cellular activity to pathogenic processes. Some EVs prepared in vitro have exhibited therapeutic effects in preclinical models of immune or neurodegenerative disease. In a recent study, researchers generated EVs enriched with HSPB8 (small heat shock protein B8) in vitro from oligodendroglia (OLs). HSPB8 protects cells from oxidative stress-mediated cell death by supporting autophagic activity and could be carried by EVs. Both the native OL-EVs and the HSPB8-enriched OL-EVs were internalized by a microglial cell line and primary mixed neural cultures without inducing cell death. The HSPB8-enriched OL-EVs increased the endogenous production of HSPB8 mRNA. Both EV subsets helped maintain cellular homeostasis during chronic inflammation by increasing autophagic vesicle formation..."

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:

"Coral reefs are important ocean ecosystems. However, they have been declining in recent years due to human activities, including elevated nitrate in the water. Corals maintain complex relationships with numerous microbes, including the dinoflagellate algae Symbiodiniaceae and bacteria. To better understand the impact of nitrate on coral and their resident microbes, researchers recently examined coral and microbial gene expression changes in larval Pocillopora damicornis. Under elevated nitrate conditions, the Symbiodiniaceae algae generally hoarded more nutrients for its own growth. Normally Symbiodiniaceae share nutrients with the coral, so this was a shift from a mutualistic relationship to a parasitic one, which led to impaired development in the larval coral. However, the prokaryotic microbes might reduce this negative interaction by restraining Symbiodiniaceae growth, which partially restores coral larval development..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

In this activity, learners explore the "nuts and bolts" of gene chips. Learners construct a simple model of a DNA microarray (also known as gene chips) and learn how microarrays can be used to identify and treat disease--including cancer. This resource includes references and an explanation of microarrays.

Meiosis is the process by which gametes (eggs and sperm) are made. Gametes have only one set of chromosomes. Therefore, meiosis involves a reduction in the amount of genetic material. Each gamete has only half the chromosomes of the original germ cell. Explore meiosis with a computer model of dragons. Run meiosis, inspect the chromosomes, then choose gametes to fertilize. Predict the results of the dragon offspring and try to make a dragon without legs. Learn why all siblings do not look alike.

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:

"Amphibians are one of the most vulnerable animal groups on the planet, with over 40% of their species threatened with extinction. A major driver of that vulnerability is the fungal pathogen _Batrachochytrium dendrobatidis_ (Bd). Bd is linked to the decline of at least 500 amphibian species, the greatest loss in biodiversity due to a pathogen ever recorded. The amphibian skin microbiome community structure has been linked to health outcomes of Bd infection, but the functional importance of the microbiota is not yet fully understood. To close this gap and potentially discover biomarkers or disease control methods, researchers investigated the microbiome of midwife toads. They examined both wild populations with naturally occurring Bd infection and controlled laboratory exposure. Infection with Bd led to changes in the microbial community structure, gene profile, and metabolic function in laboratory and wild toad populations..."

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:

"Wastewater treatment plants are a critical piece of infrastructure that depend on microbes, both resident and incoming. Incoming microbes can be beneficial but may include parasites that need to be removed. Resident microbes, meanwhile, help break down organic waste. While much is known about bacteria in wastewater treatment plants, eukaryotes are frequently overlooked. Recently, researchers examined the whole microbiome of 10 wastewater treatment plants in Switzerland. They utilized metagenomics to measure which microbes were present and metatranscriptomics to analyze their activity. Bacteria were the most numerous— but eukaryotes, particularly protists, showed the most activity, and there was a surprising number and range of active parasites, which were particularly prevalent in the inflow. Network analysis suggested predation by resident microbes likely helped remove parasites..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This initial module from the GENIQUEST project introduces the dragons and the inheritance of their traits, then delves into meiosis and its relationship to inherited traits. Students examine the effects of choosing different gametes on dragon offspring, and learn about genetic recombination by creating recombination events to generate specific offspring from two given parent dragons. Students learn about inbred strains and breed an inbred strain of dragons themselves.

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:

"Human activity is driving an increase in the amount of atmospheric reactive nitrogen. California grassland growth is typically limited by the amount of available nitrogen. Thus, more available nitrogen leads to more plant biomass, which means more carbon is deposited in the soil. Both the increase in nitrogen itself and the increase in carbon affect soil microbes. To better understand these impacts, a recent study examined microbial metabolic functioning in experimental grassland plots in California. These plots had been maintained for 14 years with increased nitrogen deposition mimicking the predicted levels for the end of the 21st century. This increased deposition led to an increased abundance of fast-growing bacterial species, as well as an increased capacity to use easily accessible, or labile, carbon sources. In contrast, the community's capacity to degrade recalcitrant carbon sources was unchanged or even decreased by elevated nitrogen..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Looking at how regulatory DNA sequences can repress or promote gene transcription (particularly in bacteria operons).

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:

"It may be surprising to learn that drugs like morphine can actually make it harder to heal from injuries, including surgery. Researchers report that using opioids to manage this type of acute pain can make the pain last longer, potentially drawing out the need for pain relief. Although it’s unclear exactly why this happens, scientists are beginning to uncover some of the physiological causes of this delayed healing. And they think it has something to do with the brain’s immune system. That conclusion comes from an in-depth look at how morphine affects recovery in mice. Using a mouse model of orthopedic surgery, researchers looked at the consequences of postoperative morphine use. Mice were subjected to tibial fracture and repair and given a 7-day course of either morphine or an inactive vehicle. Some mice underwent a sham operation – they were anesthetized and received skin incisions, but no bone fracture – followed by the same treatment regimen..."

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:

"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 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.