Podcasts are perfect for busy, but intellectually curious people. It’s like reading, but instead of fixing your eyes to a page or screen, you can run or cook or simply relax while the podcast delivers fascinating, funny, new information straight to your brain. It’s basically like learning by osmosis! Whether you’re working in lab or you have these few months off to relax, I curated a list of science podcasts to keep you company both bench-side and poolside.
It’s no secret that scientific research is becoming less of a priority to the federal government. For two decades, research and development (R&D) funding has remained stagnant or dropping, despite increases to the overall federal budget. With a growing population of scientists entering the field, a lack of funding generates a hyper-competitive and stressful funding climate. For those looking to secure funding for the first time, or simply curious about how science is funded, this post serves as an introductory guide.
The G2/M cycle checkpoint prevents cells with genomic DNA damages from entering mitosis (M phase). The Cyclin B-CDK1 complex plays an important regulatory role during the G2 transition, at which time CDK1 is maintained inactivated by the tyrosine kinases Wee1 and Myt1. When the cells enter the M phase, the kinase Aurora A and the cofactor Bora act together to activate PLK1, which in turn activates the activity of phosphatase CDC25 and downstream CDC2, effectively driving the cells into mitosis. When the DNA is damaged, it activates the DNA-PK/ATM/ATR kinase and eventually inactivates the Cyclin B-CDK1 complex.
In some ways, the heart is quite a vulnerable organ. Cardiac complications such as heart attack, cardiac arrest, or heart failure are common. But interestingly, of the many diseases that may affect the heart, cancer is not one of them. For example, we often hear about cancer in the prostate, breast, colon, skin, etc., but rarely of the heart. How is this vital organ different?
The G1/S cell cycle checkpoints control whether eukaryotic cells enter the S phase (synthesis phase) of DNA synthesis through the G1 phase. Two cell cycle kinase complexes, CDK4/6-Cyclin D and CDK2- Cyclin E, work together to relieve the inhibition of dynamic transcriptional complexes containing retinoblastoma protein (Rb) and E2F. In cells undefined during the G1 phase, hypophosphorylated Rb binds to the E2F-DP1 transcription factor and forms an inhibitory complex with HDAC, thereby inhibiting downstream key transcriptional activities. Clear entry into the S phase is achieved by continuous phosphorylation of Rb by Cyclin D-CDK4/6 and Cyclin E-CDK2, which separates the transcription factor E2F from the inhibitory complex and allows transcription of the gene required for DNA replication. After the growth factor disappears, the expression level of cylin D is down-regulated by down-regulation of protein expression and phosphorylation-dependent degradation.
Proteins known as transcription factors play a crucial role in gene regulation by activating, enhancing, and even silencing a gene’s expression. Many textbooks and resources compare transcription factors (TFs) to something like an on/off switch for gene transcription. However, it is a bit more complicated than just turning gene expression on or off. Various properties (e.g. binding affinity, specificity, and genetic variance of binding sites) impact the binding of TFs to DNA, thereby altering gene expression. To study transcription and how it is regulated, scientists study TF-DNA interactions on a genome-wide level.
A healthy immune system requires a series of checkpoints to ensure self tolerance and prevent damage to other tissues during immune response. Binding of costimulatory signal transduction molecules (such as CD28, ICOS, GITR) on T cells to their receptors (such as CD80/CD86, ICOSL, GITRL) on antigen presenting cells (APCs) may contribute to T cell activation. However, in some states, inhibitory signals of T cell activation and response occur during the involvement of T cell receptors. These signals are generated by proteins involved in immune checkpoints (eg, PD-1, CTLA-4, TIM-3, and LAG3). Usually PD-1 and CTLA-4 immunological checkpoint proteins are upregulated in T cells infiltrating tumors and bind to their respective ligands, PD-L1 (ligand B7-H1)/PD-L2 (ligand B7- DC) and CD80/86, and down-regulate T cell responses. Immunological checkpoint ligands are often upregulated in cancer cells as a means of evading immune detection. Therefore, immunotherapy by blocking immunological checkpoint protein activation of anti-tumor immunity has become a popular research subject for cancer therapy.
The cliché of the pragmatic and lonely scientist gets old. Although scientists are highly analytical, their emotional range is not as limited as the media and stereotypes portray. In their work, scientists must be logical and methodical, but that doesn’t necessarily carry over to life and relationships.
Embryonic stem cells (ES cells) are pluripotent stem cells isolated from an inner cell mass of early-stage embryo-blastocysts. ES cells have a high differentiation potential. At the same time, while ES cells are undifferentiated, they have the potential to infinitely replicate, making them highly attractive subjects for cell therapy and regenerative medicine.
CD molecules are cell surface markers that appear or disappear when cells (leukocytes, red blood cells, platelets, and vascular endothelial cells, etc.) differentiate or become different lineages, different segments of cells, become active or diseased. Most CD molecules are transmembrane proteins or glycoproteins, including extracellular regions, transmembrane regions, and cytoplasmic regions. Some CD molecules are "anchored" on the cell membrane by means of inositol phospholipids. A few CD molecules are carbohydrate haptens. The study of CD molecules can be used in many basic immunology research fields, such as the relationship between CD antigen structure and function, cell activation pathway, signal transduction and cell differentiation, etc. It can be used clinically for disease mechanism research, clinical diagnosis, disease prognosis, efficacy tracking and treatment, and more.
The Literature Review
Literature reviews are some of the most widely read and highly cited papers in academia, but writing one can be a daunting task, requiring an expert understanding of the topic at hand. To write a review article is so much more than simply summarizing recent studies published in the field. The most valuable literature reviews, which I find myself going back to again and again, are those that:
The Problem with Cancer Models
Very few cancer drugs succeed in clinical trials, despite showing promise in the lab. Treatments that may work on animal models, cell lines, or even patient-derived xenografts often do not have the same efficacy in patients. The underlying reason is tumor environments within the human body are far more complex than in research models. For example, the tissue structure (histological complexity) and genetic heterogeneity of an animal model is different than that of humans. Even cell lines and patient-derived xenografts, which are human-derived, have their own pitfalls such as genetic mutations and animal-specific tumor evolution, respectively. Due to the inability to reproduce human tumor environments, many drugs fail clinical trials after lengthy and costly development.
The Hippo signal is very conservative in evolution. It regulates organ size and tissue stability by regulating cell proliferation, apoptosis, and stem cell renewal. The core process of Hippo signaling is a kinase tandem process, Mst1/2 and Sav1 form a complex, phosphorylate and activate Lats1/2; Lats1/2 kinase then phosphorylates and inhibits transcriptional coactivators Yap and Taz. Yap and Taz are the most important effectors downstream of the Hippo pathway. Upon dephosphorylation, Yap and Taz translocate to the nucleus and interact with TEAD1-4 or other transcription factors (such as CTGF) to induce gene expression, thereby initiating cell proliferation and inhibiting apoptosis.
As scientists, writing is a major component of the job, yet having “no time to write” is a common complaint echoed amongst PhD candidates, post-docs, and professors alike. On top of experiments, data analyses, and taking/teaching courses, writing can easily end up on the back burner. But publishing papers, like it or not, is critical for a career in science. Rather than setting intimidating goals like publishing some number of papers within a year or publishing in a high impact journal, it is more feasible and beneficial to first develop good writing habits, which will in the long run increase productivity.
Every year, scientists make fascinating breakthroughs which broaden, yet challenge, our understanding of life and the world around us. Just as we start to understand a biological process, like how heredity or aging works, a new discovery can flip it on its head or open a whole new avenue for research. As 2018 comes to an end, it’s the time for roundups of top products, gifts, movies, tech, etc. We decided to put our own spin on it with the top life science discoveries of the year.
These days major debates center around scientific information – from climate change, gene-editing to vaccinations – yet, despite the data-driven nature of science, there are deeply divided opinions regarding these hot topics. For researchers, it might be frustrating to witness scientific findings being misinterpreted or exaggerated. But it’s not surprising that so much science is misunderstood. Too many scientists still reside within their own research bubbles, which is counterproductive.
GAPDH is a constitutively expressed housekeeping protein, and GAPDH mRNA levels and protein levels are often used as controls in experiments that quantify target-specific expression changes. Recent studies have elucidated the role of GAPDH in apoptosis, gene expression, and nuclear transport. GAPDH may also play a role in neurodegenerative diseases such as Huntington's disease and Alzheimer's disease. ABclonal GAPDH recombinant rabbit monoclonal antibody is a human-specific antibody with a dilution ratio of 1:2560000.
In the last What’s Hot in Life blog post, we discussed how next generation sequencing (NGS) is used as a basis for understanding disease. This week I wanted to talk about DNA sequencing again, but in a completely different context. On November 1st, scientists launched an ambitious project to sequence all 1.5 million complex species on Earth. Their purpose? To save biodiversity.
As one of the most common reagents in biology and medical research, there are more than 350,000 commercially produced antibodies available for research and clinical applications. However, the quality of the commercially available antibodies varies from vendor to vendor. Different suppliers have different protocols for validating antibodies and some researchers might want to verify the product before using them on precious samples. Here are some of the factors to examine when it comes to antibody quality.
Long-interspersed nuclear elements (LINEs) are genetic components found in higher eukaryotes. They are retrotranposons, meaning that they are transcribed into mRNA and then translated into proteins that act as a reverse transcriptase. The reverse transcriptase makes a copy of the LINE DNA which can then be integrated into the genome at a new site. The only active LINE in humans is LINE-1. It has been associated with oncogenesis and Haemophilia A, a diseased caused by insertional mutagenesis.
We have previously explored the function of organelle markers USO1, GOLGA2, and GOLM1 but not how the corresponding antibodies can be applied in research. Organelle marker antibodies are common tools in cell biology research. They can be used with immunofluorescence technology to observe the morphological structure of organelles and understanding the subcellular localization of proteins. In turn, they help to explore the biological functions/role of organelle proteins in normal or disease models. These markers can also be used in Western blot (WB) experiments examining organelle extracts: as a positive control to determine whether the organelle is successfully extracted.
Pursuing a PhD is undoubtedly one of the most challenging chapters in a researcher's career. For the first time, as an early career scientist, you must juggle research, writing, teaching, and your own personal life (yes, you should still have one). A PhD is definitely exhausting, but given the right guidance and support it can be an enjoyable and exciting time too.
Organelle marker antibodies are common tools in cell biology research. They can be used with immunofluorescence technology to observe the morphological structure of organelles and understanding the subcellular localization of proteins. In turn, they help to explore the biological functions/role of organelle proteins in normal or disease models. These markers can also be used in Western blot (WB) experiments examining organelle extracts: as a positive control to determine whether the organelle is successfully extracted.
The scientific community operates on a self-correcting model that relies on repetition and replication. However, according to a 2016 survey by Nature, more than 70% reported to have failed to replicate experiments from another scientist, more than 50% reported failure in replicating his/her own experiment. Out of the 1,576 scientists surveyed, 906 were from biology or medicine disciplines.
Therapies targeting the function of a small intestinal protein, SGLT1, might have the potential to treat diseases like obesity, diabetes, heart failure, and associated death—and we have next generation sequencing to thank.
CREB1 is a bZIP transcription factor that activates a target gene through a cAMP response element. It regulates a variety of cellular responses by mediating a number of physiological stimuli. CREB1 is expressed in many tissues and plays an especially important regulatory role in the nervous system: promoting neuronal survival, precursor proliferation, neurite outgrowth, neuronal differentiation and more. In addition, CREB1 signaling is involved in the learning and memory of many organisms. CREB1 is capable of selectively activating many downstream genes through interaction with multiple dimerization partners. Phosphorylation of CREB1 at the Ser133 site involves multiple signaling pathways, such as Erk, Ca2+, and stress signaling. Some of the kinases involved in CREB1 phosphorylation include p90RSK, MSK, CaMKIV, and MAPKAPK-2.
Autophagy is a catabolic process in which autophagic lysosomes degrade most cytoplasmic contents. Autophagy is usually activated in the absence of nutrients and is associated with many physiological and pathological processes, including growth, differentiation, neurodegenerative diseases, infections and tumors. Light chain 3 (LC3) is a widely recognized autophagy marker. There are three isoforms of the LC3 protein (LC3A, LC3B, and LC3C) in mammals. They undergo post-translational modifications during autophagy. The LC3 protein is first cleaved by Atg4 at its carboxy terminus immediately after synthesis to produce LC3-I, which is localized in the cytoplasm. During autophagy, LC3-I is modified and processed by a ubiquitin-like system including Atg7 and Atg3 to produce LC3-II with a molecular weight of 14 kD and localized to autophagosomes. The magnitude of the LC3-II/I ratio can be used to assess the level of autophagy.
ABclonal Technology hosted its second lunch and learn at the Koch Institute for Integrative Cancer Research at MIT, the second event of its lecture series. The lunch and learn, led by ABclonal’s senior principal scientist, focused on rabbit monoclonal antibody technologies, its advantages and development.
RNA methyltransferases such as METTL3, METTL14, WTAP, and VIR can catalyze the methylation of the N6 position of adenylate (M6A) and demethylases include FTO and ALKBH5.
It’s a relatively new world for scientists. Up until the 2000s, research funding increased steadily before reaching a plateau and dropping with sequestration budget cuts. Nowadays, scientists spend a great deal of time fighting for grants, rather than actually doing research. It’s an interesting, but sobering reality: as you progress in your science career, you may (or already do), find yourself spending more and more time planning and writing grants.
The nucleosome consists of an octamer composed of four histones (H2A, H2B, H3, and H4) and a DNA entangled with 147 base pairs. The core of the histones constituting the nucleosome are roughly the same, but the free N-terminus can be subjected to various modifications.
Endoplasmic Reticulum Marker
The P4HB gene encodes a protein disulfide isomerase (PDI) that catalyzes both the formation of disulfide bonds and isomerization between or within molecules of secreted proteins. To achieve the natural conformation, this process takes place in the endoplasmic reticulum, so P4HB is often used as an ER marker. Studies on the oxidative folding mechanism indicate that molecular oxygen can oxidize the ER protein Ero1, and Ero1 can oxidize PDI through a disulfide bond. After this activity, PDI catalyzes the folding of proteins to form disulfide bonds.
Ebola outbreaks are considered rare, but they do emerge every several years and can be quite lethal. Although the first confirmed Ebola epidemic was in 1976, we still lack licensed therapeutics to prevent and control Ebola’s spread. Vaccine development is in the works, but the lack of an approved treatment is a chilling reminder that we may not know enough about the virus. With the recent outbreaks in mind, we sought to summarize everything you should know about Ebola, its biology, and the current progress of vaccine development.
ERK1/2 (MAPK1/MAPK3, p44/42MAPK) are members of the mitogen-activated protein kinase family (MAPKs) that are commonly located in the cytoplasm. They act as catalysts in the phosphorylation of serine/threonine and are negatively regulated by the bispecific (Thr/Tyr) MAPK phosphatase family (called DUSP or MKP) and MEK inhibitors (such as U0126 and PD98059).
The interest in using primary cells for cell-biology research has gained prominence in recent years due to factors such as cell line contamination (Kaur G, 2012). What made primary cells lose their popularity in the first place is partly due to the rigorous and arduous process associated with primary-cell cultivation. So why is primary-cell cultivation so difficult?
When I began my science journey as an undergrad, research seemed rigorous, but reassuringly straightforward in its tenets. Observe, question, hypothesize. Predict, test, analyze. And repeat. It made perfect sense to me that if you followed this protocol and remained unbiased in the process, great discoveries were sure to come.
But then I learned about the other steps in between. Steps like grant-writing, worrying about publishing and impact factors, getting your mentor to actually respond, and struggling to troubleshoot experiments. Twitter’s PhD community seems to relate.
DNA methyltransferase (DNMT) is an important family of enzymes that catalyze and maintain DNA methylation in epigenetics. The enzymes play a key role in the regulation of gene expression and genomic imprinting/development.
While the scientific community is enveloped in a reproducibility crisis (and debates as to whether there is one), there are certainly steps life science researchers can take to ensure more reproducible outcomes. We can start by limiting self-bias and improving reporting standards. But first, what is reproducibility and why is there a crisis?
Glial fibrillary acidic protein (GFAP) is an intermediate filament protein that is mainly found in astrocytes found in the central nervous system. It is also expressed in chondrocytes, fibroblasts, myoepithelial cells, lymphocytes, and hepatic stellate cells.
Epidermal growth factor receptor (EGFR, also known as ErbB-1 or HER1) is a member of the ErbB family. This family includes four tyrosine receptor kinases: HER1 (ErbB1, EGFR), HER2 (ErbB2, NEU), HER3 (ErbB3), and HER4 (ErbB4). The ErbB family plays an important regulatory role in the process of cell physiology.
EGFR is distributed along the surface of cells including mammalian epithelial cells, fibroblasts, glial cells, keratinocytes, and more. The EGFR signaling pathway plays an important role in physiological processes such as cell growth, proliferation and differentiation. The loss of function in tyrosine kinases such as EGFR, or the abnormal activity/cell localization of key factors in related signaling pathways can cause tumor, diabetes, immunodeficiency and cardiovascular diseases.
Part of the Golgi protein family, USO1 protein (also known as vesicle docking protein p115) is a peripheral membrane protein that can be used as a Golgi marker. It cycles between the cytoplasm and the Golgi apparatus during interphase. The position of the USO1 protein is regulated by phosphorylation -- dephosphorylated proteins bind to the Golgi membrane and dissociate from the membrane when phosphorylated. This regulated transportation plays an important role in protein localization, secretion, and signal transduction. USO1 protein acts as a vesicle anchor by interacting with the target membrane and keeping the vesicles close to the target membrane. In addition, the USO1 protein interacts with GOLGA2 (GM130) and Giantin to promote endoplasmic reticulum-Golgi transportation.
In a previous article, we explored the differences between rabbit and mouse antibodies as well as the biology behind rabbit antibody superiority. But after choosing the host, the type of technology used to produce the antibody is important too. Here, we explore some of the rabbit monoclonal antibody technologies available in the current market.
Nuclear lamina is a layer of cross-linked fibrin network that commonly exists in higher eukaryotic cells. It is interior to the nuclear envelope with a fiber diameter of about 10 nm. The nuclear lamina of higher animals are usually composed of three intermediate filament polypeptides – lamins A, B, and C. The nuclear lamina is closely related to the stability of nuclear envelopes, maintenance of nuclear pore location, stabilizing interphase chromatin morphology and spatial structure, chromatin construction, and nuclear assembly.
Golgi membrane protein 1 (GOLM1) is a type II Golgi membrane protein discovered in recent years. The protein expression level increases in a variety of diseases and cancerous tissues. It is especially closely related to liver diseases. Many studies have shown that GOLM1 is more sensitive and more specific than alpha-fetoprotein (AFP, the most specific marker for primary liver cancer and the main indicator for the diagnosis of liver cancer) in the serological diagnosis of liver cancer. GOLM1 is expected to be the serological marker for the early diagnosis of liver cancer. It has also been reported to be highly expressed in patients with viral hepatitis and cirrhosis.
Last week, ABclonal Technology set foot on the "Land of the Rising Sun" to attend the 17th International Biotech and Life Sciences Exhibition & Conference. One of our technical sales specialists from the Boston office, Giovanni Musto, joined our colleagues in Japan for the exhibition. Here are some highlights from his trip.
Antibodies are the most commonly used tools in biological research. They are used in various applications such as Western Blot (WB), Immunoprecipitation (IP), Immunofluorescence (IF), Immunohistochemistry (IHC) and enzyme-linked immunosorbent assays (ELISA). Two of the most common hosts for producing research antibodies are rabbits and mice, but what are the differences between rabbit and mouse antibodies? Which antibody would be best suited for your research?
Although exosomes were discovered over five decades ago, interest among the scientific community didn’t pique until much later. Specifically, in the last ten years, the number of annual publications about exosomes have almost increased by tenfold (from 1,570 published papers in 2007 to 14,000 in 2017). But what exactly are exosomes and what justifies the frenzy?
Epithelial-mesenchymal transition (EMT) plays an important role in the development of embryos and the maintenance of normal human tissue structure and function. Nowadays, more and more studies have shown that cellular plasticity is also regulated by this transition, and EMT is the most critical process in the initial phase of cancer metastasis.
Cell proliferation assays have a wide range of applications in scientific research – from testing drug reagents to the effect of growth factors, from testing cytotoxicity to analyzing cell activity. So, what are cell proliferation assays? Cell proliferation assays typically detect changes in the number of cells in a division or changes in a cell population.
Doesn’t everyone have that one friend or relative who always says “I know someone who will just be perfect for you”? Usually, the claim is based on knowledge of personality and common interests between you and the potential Mr./Mrs. Perfect. However, in the past two decades scientists have suggested a more innate predictor to attractiveness – genetics. More specifically, alleles in the human leukocyte antigens (HLA) genomic region.
One of the most important, most studied, yet still unresolved question in life science is “how can DNA (which unfolds to 2-3 meters in length) fit in the nuclei of eukaryotic cells (which is only a few microns in diameter) and regulate genome functions in an orderly fashion?”