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Lab Statistics & Math

Understanding gum diseases by integrating multiplexed-technologies in the microbiome and immunological analysis

Understanding gum diseases by integrating multiplexed-technologies in the microbiome and immunological analysis Date: Monday September 13th 2021Time: 8am Los Angeles, 11am New York, 4pm London, 5pm Berlin Speakers Dr. Renato Corrêa Viana Casarin Unicamp Dr. Casarin has a MSc and Ph.D. in Periodontics from the Piracicaba Dental School, State University of Campinas – UNICAMP. He is…

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Use ddRAD-seq to Study Non-Model Organisms

Reduced-representation genome sequencing has been one of the most important advances in the last several years for enabling massively parallel genotyping of organisms for which there is no reference-grade genome assembly. An implementation of the approach known as ddRAD-seq, first conceived in the Hoekstra lab at Harvard, has been widely adopted by the plant and…

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What to Expect When Working with a Scientific Recruiter

Have you ever wondered what it would be like if someone helped you step-by-step through your job search? A good recruiter does exactly that! Recruiters provide value to job-seekers by reviewing resumes, finding jobs that may be a good fit, and providing interview tips. But how does that process work? In this article we’ll cover…

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Nine Tips for Clinicians Starting a Scientific Career

There are many examples of the impact of physician-scientists on translational research. Dr Barry Marshall swallowed a steaming culture of Helicobacter pylori which eventually resulted in antibiotics curing peptic ulcer disease. However, the process of training these individuals is as effortless as training fish to ride bicycles. Our journeys into the laboratory have been equally…

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Cre-loxP Recombination Essentials Part 2

The Cre-loxP recombination system is routinely used for the generation of mouse knockouts. In part 1 of this mini-series, I introduced the concept and applications of Cre-loxP. As with any other technology or research tool, it has limitations and pitfalls that need to be considered while planning experiments or interpreting results. This article will take…

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How to perform cell synchronization in specific cell cycle phases

The cell cycle has been very well documented over the years because of its dysregulation in diseases such as cancer. Many different processes contribute to cell growth and replication, which is ultimately controlled by a series of tightly controlled cell cycle phases. For some areas of research, especially within drug discovery and cancer research, cell synchronization in…

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Analyze Immunostained Slides with Semiquantitative Scoring

A  routine task in the lab is to investigate the presence of your favorite protein in a range of histological samples. No doubt, staining your tissue sections using good old immunohistochemistry (IHC) would be your first choice. You just got to love a technique that has celebrated its 70th birthday, and is still used in…

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Size-Selection Is Essential for Cell-Free DNA Studies

Advances in using cell-free DNA (cfDNA) to glean clinically meaningful information for a patient have been stunning. For the most part, these research studies (or downstream diagnostic tests) isolate fetal DNA in the mother’s blood or tumor-derived DNA from the background of healthy DNA in the bloodstream. Typically known as liquid biopsies, these minimally invasive…

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Troubleshooting Surface Plasmon Resonance: Resolving Non-Specific Binding, Regeneration and Other Problems

Surface plasmon resonance (SPR), a label-free, real-time way to examine protein binding and other molecular interactions, is getting easier as manufacturers have streamlined SPR instruments and supporting software. But problems can still arise. Troubleshooting Your SPR Assay Here are some common issues and suggestions to solve them: Inactive Targets Your target protein may have become…

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Mysterious miRNA: Identifying miRNAs and Their Targets

In my first article on this topic we delved into what miRNAs are, how they are generated, and their function. Now, we are going to discuss how to identify miRNAs and their targets. Why Do You Want to Look at Something So Small Anyhow? miRNAs play a crucial role in most physiological processes. It’s not…

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How Many Data Points Do I Need For My Experiment?

To draw a convincing conclusion from your data, you cannot simply shoot for the standard significance cutoff. You also need to consider the statistical power, which is determined in part by the sample size in your experiment.

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Choose the Statistical Package that Will Make Your Data Talk

In the last years, the need for using statistical testing in bioscience has grown exponentially and so has the development of statistical software. It is now common that everyone is using some sort of stats in their basic research. Among the skillful biostatisticians, R is the most popular software for data analysis, but not all…

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How to Choose a PhD Topic

Choosing a PhD topic can be very hard. There are a lot of things to consider from the subject to the supervisor. Here are some tips to help you choose. Find out what you really like This is the first topic because it is the most important. My first advice would be to get some…

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Brushing Up On Your Excel Skills: Part Two

Last time we brushed up on cell referencing and constructing formulae to use Excel for some basic and some slightly more advanced calculations. This time we’re going to move on to using some built-in Excel functions and go through how to apply all that we’ve done so far to a worked example that is relevant…

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Brushing Up On Your Excel Skills: Part One

Microsoft Excel can be a really powerful, useful tool for certain kinds of data processing and record keeping, and the chances are you probably don’t even know how to use half of the functions it comes with! That’s OK, personally, I find Excel a bit less user-friendly than Word, but also it’s a programme I…

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Problems amplifying GC-rich regions? Problem Solved!

No, it isn’t you that’s the problem, and you’re certainly not alone if you’re having trouble amplifying GC-rich sequence and/or understanding why GC-rich sequences are causing such problems in the first place! Amplification of GC-rich sequences by PCR has been an irritant for scientists for decades! When we say “GC-rich” we mean ?60% of the…

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A Beginners Guide to Studying Exosomes

In this webinar you will learn: Biology of extracellular vesicle biogenesis and secretion. Extracellular vesicle composition and contents. Functional activity of extracellular vesicles. Abstract: Extracellular vesicles (EVs) are a heterogeneous group of vesicles that include exosomes, microvesicles, and apoptotic bodies.  There has been increasing interest in EVs in recent years not only as possible biomarkers for…

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Polymerase Incomplete Primer Extension (PIPE) Cloning Method

PIPE PCR is a ligase-independent, restriction enzyme-free cloning strategy like SLIC (link to my SLIC article), SLiCE and CPEC. The PIPE method eliminates sequence constraints and reduces cloning and site mutagenesis to a single PCR step followed by product treatment. It is fast, cost-effective and highly efficient. The key step is designing the primers; one…

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Analyzing Apoptosis – A Review of Analytical Techniques

Now that we’ve learned about the role of apoptosis in good health and disease, it will be useful to know how we can detect apoptosis in cells or organisms. A variety of apoptosis detection kits are commercially available, and here is a roundup of how they work: TUNEL and DNA damage assays The TUNEL assay…

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Beginners Introduction to R Statistical Software

In this webinar you will learn how to import data from Microsoft Excel into R how to use R to perform statistical analyses how get a beautifully formatted figure from your data   Summary: This webinar will take the case study approach to introduce R to biologists with little or no previous knowledge of the…

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Ten Non-Chemical Lab Hazards and What They Do to You!

Your lab is full of non-chemical hazards that can explode, stab, kill, and – as if that wasn’t enough – bite.  Here’s a list of those hazards to remind you why Environmental Health & Safety exists! 1.  Centrifuges Centrifuges are dangerous, especially when not cared for!  An unmaintained ultracentrifuge imploded in an American lab in…

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The Establishment of the Nobel Prize

Let’s play a game. I’ll say a word and you say what comes to your mind. Ready? Go! Cat… Kitchen… Doctor… Airplane… Nobel… I have no idea what you said when I said cat but I’d say most of you said “prize” when I said Nobel. Alfred Nobel’s name is most often remembered because of…

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R You Ready? Using R for Statistical Tests

We’ve been slowly coaxing you along in our R tutorials.  We’ve introduced what R is, gave you a basic tutorial into how to use R and also spent some time learning how to explore your data with R. By now you are probably itching to use R for more complicated analyses.  To indulge you, I…

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An Easy Way to Start Using R in Your Research: Exploratory Data Analysis

As you’ve probably kind of guessed from our previous articles Introducng R and the Basic R Tutorial, we think R programming language and R-studio are great tools for data analysis and figure production.  And now we are about to prove it! So, you’ve collected some data and are pretty sure you know what statistical test…

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You did a Co-IP…now what?

You spent the last few weeks tweaking your Co-immunoprecipitation conditions, testing different antibody/bead combinations, and sampling a panaply of solutions and FINALLY! You have your Co-immunoprecipitation (Co-IP) elution… Now what? Well, you have a few choices. It really all depends on what you need know about the proteins in your elution. Do you need to identify…

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Let’s Talk About Stats: Comparing Multiple Datasets

Last week I focused on the left-hand side of this diagram and talked about statistical tests for comparing only two datasets.  Unfortunately, many experiments are more complicated and have three or more datasets.  Different statistical tests are used for comparing multiple data sets. Today I will focus on the right side of the diagram and…

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Let’s Talk About Stats: Comparing Two Sets of Data

There are so may statistical tests out there it can be difficult to determine which is the right test to use. Below is a simple diagram to help you quickly determine which test is right for you. Although this is by no means a comprehensive guide, it includes some of the most common tests and…

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Let’s Talk About Stats: Understanding the Lingo

The first hurdle in learning about statistics is the language.  It’s terrible to be reading about a particular statistical test and have to be looking up the meaning of every third word. The type of data you have, the number of measurements, the range of your data values and how your data cluster are all…

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How to Deal With a Failed Experiment

Scientific success is often defined by how well your experiments progress and the results you produce. However, scientific research is driven by a curiosity about the unknown, and you cannot always be prepared for the unknown. Inevitably there will come a time when your experiments fail. In this article I give you some of the…

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Beneath the Lab Coat Part 2: What is lurking under our readers’ lab coats?

Recently, we wrote an article highlighting the prevalence of science-themed tattoos among scientists, and the particular significance these tattoos have among those who choose to get them (https://bitesizebio.com/articles/beneath-the-lab-coat-why-do-scientists-get-inked/). As a follow-up, we reached out to our readers to collect images and stories about their unique, science-themed tattoos. Some of you were kind enough to share…

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The Ten Lab Commandments: Or the Guide to a Happy Lab

I was lucky enough to do my PhD in an extremely friendly and well-organised lab.  In my opinion, these two key traits are required for a successful research experience. This environment, while appearing effortless, was due in part to the hard work of the senior postdoc who kept the lab, and all of us, in…

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A Guide for Solving Your Lab Math Problems

Math is an important part of lab life, from making solutions to calculating protein concentrations, and miscalculations can cause mayhem for your experiments. Therefore it is important that your math is right, or you could spend weeks trying to figure out what’s going wrong in your experiments. I was hopeless at remembering how to do…

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Show Us Your Moves: Making an MSD Plot

In the previous article, I showed you how to interpret mean-squared displacement (MSD) and showed four easy things you can learn from an MSD graph at a quick glance. Now let’s turn from analyzing an MSD plot to making one. I am going to use the programming language R to generate simulated data and then…

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