...Mechanisms of epigenetic modifications The main mechanism of epigenetic modification is chromatin remodeling...in this study,epigenetic changes were statistically significantly associated with reduced life-span, but...methylation in living cells." Journal of the American Chemical Society 126.19 (2004): 5982-5983. PubMed PMID...literally means ‘on top of the genome’). Epigenetic modifications can result in phenotypic changes without any...any change in genotype. Epigenetic modifications play a large role in turning genes ‘off’ and ‘on’, signaling...becomes. This prevents the cellular machinery from physically interacting with the genes in the compacted region...two main mechanisms, either through histone modifications, which can influence the transcription of genes...

...arrows indicate a conversion directly catalyzed by the base editor. Dotted red arrows indicate the change... point modifications. CRISPR base editing persists through multiple cell divisions, indicating that this...target modification in primary T cells, making them a promising tool for cell therapy applications. Dual...Base editing publication highlights In the table below, you'll find a list of publications we've highlighted...Early CRISPR applications were often limited by the low editing efficiency of homology-directed repair...all. Base editing to the rescue! Base editors chemically modify DNA bases without breaking the DNA backbone...following base editing and DNA repair. Black arrows indicate natural cellular processes. BER = base excision...

...which provides the AAV replication (rep) and capsid (cap) genes. AAV replication uses the host’s polymerase...this AAV purification video! It didn’t exist when I did my first iodixanol gradient purification, but I ...margins of my protocol. While these tips weren’t critical to the experiment, they definitely made my life...In this post, I’ll share some AAV production, purification, and titration tips, while also summarizing ...adenovirus genes which help mediate AAV viral replication; and 3) the transfer plasmid which encodes a ... that aids in the homologous recombination of duplicated regions like the ITRs. Restriction digest screening...consider performing PEG precipitation. Instead of sonicating the cell pellet, I lyse the cells with this AAV...

...blogger Jessica Polka, a Postdoctoral Research Fellow with Pamela Silver.  Most types of biological motion...these applications, purified R bodies could also perform as actuators in microelectromechanical systems... with new ways to interact mechanically with their environment.   Jessica Polka is a Postdoctoral Research...Systems Biology at Harvard Medical School. Follow her on Twitter @jessicapolka.     References 1. Kanabrocki...it to suit our purposes? In search of simple biological machines R bodies can repeatedly extend and...R-bodies, check out this video. Most types of biological motion (whether endocytosis, vesicle trafficking...to pH changes without the need for ATP or other chemical fuel sources. Like an actin filament or a microtubule...

...3’ end binds template DNA for PCR amplification, while modifications and homologous sequences are encoded...multiple modifications A key feature of IVA cloning is the ability to combine multiple modifications. Any ...’ Check your amplification by gel electrophoresis. In our experience, good amplification after PCR means...gain traction? It is likely that both vector amplification with low fidelity polymerases and the cost of...this approach requires no special reagents or purification kits, it is low cost and can be immediately ...to produce the linear fragments, as desired modifications and homologous regions can be encoded in the...parental DNA (37 °C for 15 mins). This enzyme specifically cuts methylated DNA, so it will selectively ...

... ensure they bind their antigens specifically. Possible applications for validation include western blot...addgene.org Addgene's Antibody Purification Protocol Addgene's Video Antibody Purification Protocol Addgene's Antibody...cells can perform human-like post-translational modifications that bacterial and most yeast cells cannot. ...production system may depend on what downstream applications you are planning, cost, and the amount of protein...secretes fewer of its own proteins, making the purification process simpler. Due to its high yields, E. ...using a mammalian production system, cell lines typically used include Human Embryonic Kidney (HEK) cells...production (Schwarz et. al., 2020). Harvest and purification At its core, harvesting recombinant antibodies...

...next-gen sequencing. ChIP is an incredibly useful application for exploring these interactions, and can give... protein interactions, including epigenetic modifications. But it's not an approach for the faint of heart...your sample before moving on to the next step. Typically, this can be done by cutting the tissue sample...into random, small pieces of roughly equal size, typically between 200-1000 bp. This is to ensure that your...background information. Your options for this step are sonication, which uses high-frequency sound waves to break...break up the DNA, or enzymatic digestion. Sonication provides a truly random digestion, but is harsher ...to the selective nature of the cutting. While sonication is usually the preferred method, enzymatic digestion...

...2024 American Chemical Society. Both PILATeS (18 kDa) and STReTCh (11 kDa) are significantly smaller...cofactors or using significantly truncated forms that limit its functionality. To make biophysical and structural...Sensors for Bioluminescent Readout of Mechanical Forces in Biological Systems. ACS Sensors, 9(7), 3489–3495...disruption in M. abscessus  Bioluminescent reporter of mechanical forces   Epitope tag antibody collection grows...performs well in many different antibody-based applications.  IPI’s recombinant version is a fusion of mouse...properties, and is amenable to a wide range of biophysical assays (Kroupova et al., 2024). They were able... Cereblon construct for crystallographic and biophysical studies of protein degraders. Nat Commun., 15...

...eukaryotic secretory pathway."Biochemical and biophysical research communications 430.3 (2013): 1114-1119. ...referring to the evil side of a mystical "Force," this quote is equally applicable to many microscopy experiments...within these compartments undergo significant post-translational modifications including glycosylation, disulfide... the cytoplasm? Or more troubling, what if a significant fraction of the fusion protein molecules fail...time. Previously, we have described a number of practical considerations that should be taken into account...human (and most eukaryotic) proteins localize to chemically distinct subcellular environments, including ...are equally susceptible to these non-native modifications, which can all potentially affect function [...

...fluorescent genetically encoded voltage indicator Article contributed by Shreya Vedantam Genetically encoded... for its biotechnological applications including conversion of CO2 into water and electrical energy generation...can be reconstituted in vivo to form a protein identical in sequence to the unmodified enzyme. Each half...tested the base editors in vivo and achieved therapeutically relevant editing efficiencies in the mouse ... base editors at Addgene. Levy et al., Nature Biomedical Engineering, 2020. PubMed PMID: 31937940. Detection...encoded voltage indicators (GEVIs) are proteins that detect and output the voltage changes in neural activity...fluorescent optics. Existing red fluorescent voltage indicators, however, fall short compared to GFP-based sensors...

...HIV. A notable landmark study showed significant clinical efficacy against a form of blindness known as...patients with clinical diagnosis of LCA and mutations in RPE65 (n=3), showed significant improvements ...and other ongoing clinical trials support the utility of AAV as a broadly applicable gene delivery tool...Almost all patients have achieved persistent immunological reconstitution with a normally functioning T...translating gene therapies from conceptual design to clinical trials involve identifying a therapeutic gene,...carcinogenic profiles have limited their usability in clinical settings. On the other hand, vectors derived from...Unlike most naturally occurring viruses used in clinical trials, wild type AAV is not associated with any...

...calcium indicator (Shemetov et al., 2021). In addition to FRET, intensiometric calcium indicators NIR-GECOs...characteristics, performance, and applications of near-infrared calcium indicators in this recent review (Shcherbakova...expertise is development and applications of fluorescent proteins, genetically encoded biosensors, and optogenetic...Qian, Y. et al. A genetically encoded near-infrared fluorescent calcium ion indicator. Nat Methods 16, ...Shemetov, A.A. et al. A near-infrared genetically encoded calcium indicator for in vivo imaging. Nat Biotechnol...Shcherbakova, D.M. Near-infrared and far-red genetically encoded indicators of neuronal activity. J Neurosci Methods...information on NIR FPs, their properties and applications. At the end, there is a Table that summarizes...

...covered in detail here. Classical double-strand break repair (DSBR) In the classical DSBR pathway, the 3’...not be immediately applicable in DSB-induced genome engineering, it has biological importance for the ... PubMed. A Mouse Geneticist's practical guide to CRISPR applications. Singh P, et al. Genetics 114.169771...pathways of DSBs, with a focus on repair for genome modification purposes. How does homology directed repair...and Homology Directed Repair (HDR). NHEJ is the canonical homology-independent pathway as it involves the... provided the DNA template used for repair is identical to the original DNA sequence at the DSB, or it...specific mutations into the damaged DNA if these modifications exist in the template DNA. There are several...

...holding a physical model of the protein in your hand – you will understand the power of a physical model.... researchers use physical models of protein structure? We have been creating physical models of proteins... your hand? At 3D Molecular Designs, we create physical models of proteins using 3D printing technology...and I encourage you to hold one. Why do we need physical models of protein structure? Structural biologists...biologists have always struggled to effectively communicate the nuances of protein structure in a flat 2-D...problem with the development of Byron’s Bender – a mechanical device that could be used to bend 1/8th inch ... example, when Tom Steitz was presented with a physical model of his large ribosomal subunit, he kept ...

...like team building, collaborative critical thinking, and communication among others. They additionally ...therapeutic and pre-clinical problems! Who knows, perhaps the ideas spurred by this “gamification” will lead to...to develop strategies to make our classes more practical and hands-on. Students in these courses get plenty...playing a card game called “Magic”. There were complicated rules that governed how this game was played....upon who your challenger was, you might have to drastically alter your strategy. I realized that similar ... as I try being compelling, interactive, and application-driven to boost curiosity, I have never experienced...engineering and strategic knowledge to solve a clinical disease case. As a teacher, you explain the game...

...presented chronologically. With a resume however, most often people choose a reversed chronological style ... job asks for experience in “statistical analysis”, mention “statistical analysis” (word by word) in your...together a grant application? Are you familiar with the publishing or patent application processes? How ... pages in a Curricula Vitae to showcase your publications, academic performances, and research experiences... applying for. Also remember that a resume is typically no more than 2 pages long. Write your resume for...information. Think "skills," not just "research and publications” What are the skills you developed through your...handled large data sets and are familiar with statistical analysis. If you have done fluorescent imaging...

...detection is crucial for clinical diagnostics, genotyping, and biotechnological advancements. Many methods...method can be used for an array of applications including clinical diagnostics (e.g. pathogen or virus...population for an array of molecular and clinical diagnostic applications. The company Mammoth Biosciences has...activated” Cas13 produces a quantifiable signal that indicates the presence of your targeted nucleic acid. To...amplified using RPA (recombinase polymerase amplification) or reverse transcriptase (RT)-RPA, respectively...RNA for subsequent detection by Cas13. This amplification step in combination with the ssRNA reporter ... introduced in 2017 so the lab made further modifications to improve their detection system. They named...

...circle. Typically, a yellow check mark indicates that a particular parameter was automatically adjusted... The vertical black dotted line represents the cut site. Cutting and error-prone repair typically result...content. Many thanks to our guest blogger, Jessica Roginsky. Jessica Roginsky leads the scientific support ...This article was contributed by Jessica Roginsky, Scientific Support Lead at Synthego. Article source... of robust software tools. As a consequence, a critical step in the gene editing workflow - analyzing ...either one at a time or as a batch of hundreds, and indicate the guide RNA sequence you used. The ICE tool ...and interpret data about these types of edits is critical to the CRISPR workflow. For a multiplex sample...

...preference.   Historically, ICSS was done by implanting an electrode and non-specifically electrically stimulating...the steps and technical considerations are directly applicable to the rat [6]. Technical differences include...A high-light sensitivity optical neural silencer: development and application to optogenetic control of...[2]. Laser activation is usually controlled automatically using motion capture software such as EthoVision...EthoVision. Consult the literature to find all the applications of optogenetics relevant to your field. Ultimately..., regardless of the type of behavior, certain technical considerations still apply. Testing stimulation...Inhibition of neuronal activation is a little more complicated since basal neuronal activity in your brain region...

...intuitive, or logical to a biologist that are not at all obvious, intuitive, or logical to a layperson...from other sources. Mode of communication Different modes of communication take up different amounts of...your audience needs to understand what you’re communicating. While I’m sure that there are loads of ways...new languages!) Jargon has a place in science communication, but the more you use, the higher cognitive ...This can be obvious, in that a lot of science communication is helping people understand new concepts. You...layperson. When you’re communicating ideas that you think are clearly connected, step back and ask yourself, ...pick and choose what concepts and details to communicate. It’s okay (and encouraged) to leave blank spaces...