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How can I get started in molecular biology?

How can I get started in molecular biology?


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I have a background in computer science and math and am interested in learning molecular / synthetic biology - what resources do people recommend?


First develop a background of basic highschool chemistry, basic biochemistry and basic genetics.

What is molecular biology: Molecular biology has 2 definitions. A broader definition is molecular basis of life. That is indistinguishable from biochemistry. The second definition is how does genetic information flows through molecular mechanism. The secod one is a more specific definition of molecular biology and how it differs from biochemistry.

Its good to develop some background in biochemistry and genetics because concepts of molecular biology comes from biochemistry and genetics.

A quick start through biochemistry:

  1. Lippincott's illustrated review on biochemistry.
  2. Harpers's illustrated review on biochemistry
  3. Organic chemistry by Solomons and Fryhle (especially stereochemistry portion).

then go through gradually more detailed book, such as biochemistry by Lubert Stryer.

Parallelly go through Genetics book such as

  1. Principle of genetics by Hartl and Jones
  2. Gene IX by Benjamin Lewin
  3. Principles of genetics by Snustad et al.
  4. iGenetics by peter J. Russell
  5. Concept of genetics by Benjamin pearce
  6. Genomes 3 by T A Brown
  7. Principles of gene manipulation and genomics by RM Twyman and Sandy B Primrose.

Each book has a different perspective. it will help a clearer picture of different concepts.

Some basic molecular biology books:

  1. Molecular bioloy- principle of Genome function: by Nancy Craig et al.
  2. Molecular biology by RF Weaver.
  3. Fundamental molecular biology - Lizabeth Allison
  4. Princiles of molecular biology by Barton and Tropp.

For a more cellular approach and bigger picture see cell biology based molecular biology books viz.

  1. Cell biology by Pollard, Earnshaw et al.
  2. Cell biology by Gerald Karp
  3. Lewins' CELL by Plopper et al.
  4. The Cell- a molecular approach- by Geoffrey M. Cooper.

How can I get started in molecular biology? - Biology

So I have been trying to make a construct. But I am seeing no insertion of my desired insert into the vector. So let me tell you guys some details

1. I am doing double digestion of my pET3a plasmid and my insert with Nde1 and BamH1-HF enzymes using cutsmart buffer. And then for both the cases, am gel purifying it.

2. For ligation, I am using quickligase, and have tried concentration ratios of 3:1, 5:1, for insert:vector. i also tried incubation times like 5mins, 15mins at room temperature.

3. I am transforming in E.cloni-10G cells using heat shock and am getting colonies on Amp resistant plates.

However, every time during colony PCR I am seeing no desired band, so the colonies I am observing are all having empty plasmid.

I did several controls, like doing single digestion with either of the enzyme and gel shows that they have been linearized everytime. So I thought the enzymes are good. Although for BamH1 the band is broadened.

I have been done controls during ligation step, like without the enzyme one time, or without the insert. But whatever colony I am seeing is of the empty plasmid.


Basics of Molecular Biology and Genetics

Molecular biology is the study of the molecular underpinnings of the processes of replication, transcription, translation, and cell function.

Genetics is the study of how genetic differences affect organisms. Genetics attempts to predict how mutations, individual genes and genetic interactions can affect the expression of a phenotype.

This DNA purification guide addresses general information on the basics of DNA extraction, plasmid preparation and DNA quantitation, as well as how optimized purification techniques can help increase your productivity, so you spend less time purifying DNA and more time developing experiments and analyzing data.

In today’s world of DNA analysis by multiplex and real-time PCR, the importance of high-quality, purified DNA cannot be underestimated. Finding a suitable DNA isolation system to satisfy your downstream application needs is vital for the successful completion of experiments.

This course is dedicated to learn the basics of Molecular Biology and understand the principle involved in DNA isolation and its process in details:

To know the various sources of DNA,

To understand the steps involved in DNA separation,

To review the techniques used for identification of isolated DNA,

To review the procedure for quantification of isolated DNA.

Understanding the basic Genetic markers

DNA isolation and purification are designed to deal with basic principles of molecular biology and genetics. After understanding the basic terminologies and processes in genetics

This course is very useful for Employees working in Laboratories, Hospitals, Pharmaceutical or Biotech companies, Doctors (Pathologists, Microbiologists, MBBS, BAMS, BHMS) or Medical Students, Life-Sciences graduates and Post Graduates.

Jehangir Centre for Learning (JCL) is a division of Jehangir Clinical Development Centre (JCDC) which is a leading clinical research centre in India. We bring to you specialized courses in Healthcare. Candidates interested in learning about Molecular Biology and Molecular Genetics can take up this course.


DESIGN A COURSE BACK TO FRONT

Backward design starts with course-level learning goals instead of a subject's content (Wiggins and McTighe, 2005 Allen and Tanner, 2007). What do we want students to be capable of when a course ends: Thinking critically? Evaluating primary literature? Understanding the energetics of biochemical reactions? Learning goals lead to specific objectives—what students do to demonstrate that they have achieved desired goals. For example, how would we know whether students can think critically? Perhaps because they can evaluate whether a data set supports a conclusion. How would we know whether students understand the energetics of biochemical reactions? Perhaps they can predict whether an enzyme is likely to play a regulatory role in metabolism according to the thermodynamics of the reaction it catalyzes. Objectives define the desired student performance. Students should practice that performance (e.g., analyzing data sets, predicting regulatory enzymes in a pathway) and get feedback from instructors, teaching assistants, or peers. As students practice, feedback helps them learn what they are doing correctly and incorrectly so that they can adjust.

Designing backward takes time and practice, so using a guide helps (Allen and Tanner, 2007). Instructional materials developed using a backward design are available in LSE or other journals (e.g., Advances in Physiology Education). CourseSource (www.coursesource.org) is a new journal of teaching resources that align with scientific society–approved learning goals. ASCB-approved goals for a cell biology course can be found here: www.coursesource.org/courses/cell-biology. It is not necessary to reinvent an entire course one goal, objective, or lesson at a time is a good start. Begin with a concept that students struggle most to learn Smith and Tanner (2010), that is most important, or that would be most troubling if students do not understand it after completing the course (Garvin-Doxas et al., 2007 Coley and Tanner, 2012). Also, make sure that learning goals, objectives, tasks (how students will practice), and assessments (how students will get feedback and be graded) align. If an assessment tests students' factual knowledge, was that the aim? If exams demand a higher level of thinking, did students have opportunities to practice that level of thinking and get feedback on their performance?


DESIGN AND METHODS

Context and Participants

All student recruitment and data collection for this study was approved through the institutional review board. All students in one section of an introductory biology course at a large midwestern university were recruited, and 85 students (88% of the class) consented to participate. Students in the class were primarily sophomores taking the second of two required introductory biology classes toward a life sciences major. The course consisted of three 50-minute meetings per week throughout the Fall semester, and four units respectively focused on the genetic basis of evolution, phylogeny and speciation, form and function, and ecology. In each unit, students completed three assignments (15 points each) and one exam (150 points each) for a total of 12 assignments worth 18% of the final grade and four unit exams worth 55% of the final grade. The assignments consisted of open-response questions that asked students to take concepts discussed in class and use them to interpret data, engage in scientific practices such as creating graphs to present data or models to explain connections between concepts, and apply concepts to new situations as presented to students in case studies. Exams consisted of multiple true/false, short-­answer, and essay questions that all focused on students’ ability to integrate concepts and transfer information from in-class and assignment work. See the Supplemental Material (Appendix A) for an example comparing how the assignments and exams evaluated similar topics but with different scenarios and questions.

As a normal part of the course, students had access to an instructor-designed, postassignment, enhanced answer key that was specific to each assignment or exam (example included in Appendix B in the Supplemental Material). These enhanced answer keys were used by instructors and learning assistants to grade the assignments and as feedback and examples of ideal answers for students after the graded assignments were returned. Instructors and learning assistants added explanations to the answer keys as they graded the assignments or exams and saw common issues in students’ responses. They also added information on how particular questions were graded if partial credit was awarded. Students received the regular enhanced answer key for the assignments in the first unit. As a part of this study, students then received a modified enhanced answer key for all assignments and exams from the second unit through the end of the semester. The modified enhanced answer key consisted of all components of the regular enhanced answer key with added reflection questions intended to support students in using the enhanced answer key to engage in metacognition to evaluate their work and reflect on their understanding. The questions included prompts to help students think about what they understood about a concept, what they needed to know to understand it better, what they did not understand, and whether or not they understood the idea well enough to apply the information to a different situation (Wood, 2009). Further, the questions challenged students to consider the intelligibility, plausibility, and wide applicability of the concepts that were relevant to the assignments (Grotzer and Mittlefehldt, 2012) and thus were explicitly embedded in the conceptual framework underlying the study (Figure 1). The reflection questions are included in the Supplemental Material (Appendix C).

Students who consented to be contacted were invited to participate in two interviews each, and the first 20 students who responded were selected. The group of interviewed students was found to be equivalent to the group of noninterviewed students based on no significant differences in grade point average (GPA t(77) = 1.66, p = 0.17) and ACT composite scores ( t(69) = 1.67, p = 0.08). The interview participants consisted of 11 females and nine males. Twelve of the students were sophomores, four were juniors, and four were seniors or returning postbaccalaureate students. Students received a $10 gift card for each interview they completed. The 20 participants were randomly assigned to one of two groups of 10 each (see Table 1). Group 1 (10 students) received the regular enhanced answer key during the first interview. Group 2 (10 students) received the modified enhanced answer key with the added reflection questions and instruction on their use in the first interview this was before any other students in the course had access to the reflection questions. Group 1 then received the reflection questions and instruction on their use in the second interview, at the same time those items were available to all other students in the course. For both groups, instruction on the enhanced answer key and reflection question use consisted of discussion of why the documents were created and the intention of their use for students’ reflection and consideration of their own ideas. The researcher conducting the interview then walked students through the various components of the enhanced answer keys and reflection questions to demonstrate how students might use them. Students were then asked to consider the ways in which the scaffolds might be useful in general and the ways in which they could see themselves using the scaffolds in practice.

TABLE 1. Data-collection summary

Data Collection

Data collection consisted of scores from all assignments and exams, three online surveys, and semistructured interviews (see Table 1). The assignments consisted of open-response questions that asked students to take concepts discussed in class and use them to interpret data, engage in scientific practices such as creating graphs or models, and apply concepts to new situations. Exams consisted of multiple true/false, short-­answer, and essay questions that focused on students’ abilities to integrate concepts and to transfer information from in-class and assignment work. The instructors and learning assistants graded the assignments and exams. Scores from all assignments and exams for the first two units were collected for research purposes.

All students in the course were asked to complete three surveys after the first, second, and third exams. The timing of the surveys allowed analysis of how students used the enhanced answer keys both before and after the reflection questions were added, and how they may have changed their usage of the enhanced answer keys and reflection questions over the course of the semester. The surveys consisted of 1) closed-response questions about enhanced answer key use 2) Likert-style statements focused on how students used the enhanced answer keys and reflection questions and the extent to which they used metacognitive skills and 3) open-response questions about studying, how they evaluated whether or not they understood a concept, and enhanced answer key and reflection question use. The surveys were conducted online through Qualtrics. Students were given 1 week to complete each survey and received a small amount of course credit for each survey. The survey questions are included in the Supplemental Material (Appendix D).

The interviews were semistructured (Miles et al., 2014) and consisted of questions about metacognitive skills the students used and connections they made between the content on the assignments and exam. The first interview occurred in the first unit before the first exam (interview protocol in Appendix E in the Supplemental Material). The second interview occurred after the second exam (interview protocol in Appendix F in the Supplemental Material). Group 1 students (see Table 1) were asked about the regular enhanced answer key in the first interview and about the modified enhanced answer key in the second interview. Group 2 students (see Table 1) were asked about both regular and modified enhanced answer keys in the first interview and about the ways the modified enhanced answer key affected the way they thought about the content and studying in the second interview. In both groups, the first interview also included a think-aloud task (Gall et al., 2007) that consisted of the students reading through the enhanced answer key and then using it to analyze their assignments. Following these tasks, students were asked follow-up questions, again in a semistructured format, to reflect on the metacognitive processes they used to complete the task. First interviews averaged 20 minutes long and ranged from 11 to 33 minutes. Second interviews averaged 17 minutes long and ranged from 11 to 34 minutes. All interviews were audio-recorded and transcribed. Interviewed students were given pseudonyms for dissemination of research results.

Data Analysis

The assignments and exams scores were used for statistical analysis. We used independent sample t tests and analysis of variance (ANOVA) to identify differences on mean assignment and exam scores between students who used the enhanced answer keys and those who did not, those who used the reflection questions and those who did not, and between students who received the directed instruction (interviewed students) and those who did not (all other students). We also used independent-sample t tests to examine GPA and ACT composite scores between the group of the students who were interviewed and the group of students who were not in order to determine the equivalency of the two groups. We found no significant difference between the scores in the two groups as reported above. The survey data were used to examine trends in how students reported using the enhanced answer keys and the extent to which they engaged in metacognitive strategies. The open-response survey questions were categorized into common categories and both open- and closed-response survey responses were examined for trends across the surveys based on scaffold use.

The transcribed interviews were imported into qualitative analysis software (QDAMiner). First-round analysis consisted of coding for discussion of 1) enhanced answer keys, 2) reflection questions, and 3) metacognition. All statements coded as metacognition then underwent second-round analysis, which consisted of coding for Grotzer and Mittlefehldt’s (2012) three dimensions of metacognition: 1) intelligibility, 2) plausibility, and 3) wide applicability (see Appendix G in the Supplemental Material for examples of codes). We used open coding to identify common segments of data and pattern coding to group segments into common themes across the data and between groups 1 and 2 (Miles et al., 2014). To ensure reliability of the findings, we cocoded a sample of the data to establish interrater reliability. Initial agreement was ∼70%, and reached 100% following discussion. Students’ answers to interview questions, closed-­response survey questions, and open-response survey questions were used to triangulate the data sources to ensure the findings were corroborated across sources (Miles et al., 2014).


Molecular Genetics

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Mycoplasma Detection

Mycoplasmas can contaminate cell cultures and cost biotechnology companies lost time and reduced profit. The presence of mycoplasmas in cellular lines may significantly influence the results of experiments because they may negatively affect many aspects of the cell lines, including growth rate.

We perform mycoplasma testing, as well as other safety testing procedures and molecular-based assays. We can help you identify the source of the contamination and help you implement corrective and preventative actions moving forward.


Getting Started with Molecular Cloning: Simple Tips to Improve your Cloning Efficiency

Molecular cloning has traditionally utilized restriction enzymes to excise a fragment of interest from source DNA, and to linearize a plasmid vector while creating compatible ends. After purification of the insert and vector, both are joined with the activity of a DNA ligase, and the newly-created recombinant vector is used to transform an E. coli host for propagation of the recombinant molecule. More recently, PCR has been used to generate both the vector and insert, which can be joined using a variety of techniques, ranging from standard DNA ligation or enzymatic joining using a recombinase or topoisomerase, to homologous recombination, or synthetic biology. These newly-fashioned recombinant constructions may then be used to transform an appropriate E. coli host.

Regardless of which cloning method is chosen, the process can be made more efficient and successful by following good practices in the lab. Use NEBcloner to find the right products and protocols for each cloning step.

1. Take the time to plan your experiments

Attention to detail when planning a cloning project is essential. Ensure that your design is sound with a complete understanding of the methods being used and the sequences being generated. Pay attention to the junction sequences and the effect on reading frames of any translated sequences. Check both the vector and insert for internal restriction sites (we recommend NEBcutter®) prior to designing PCR primers that contain similar sites to those used for cloning. Verify that the antibiotic selective marker in the vector is compatible with the chosen host strain.

2. Start with clean DNA at the right concentration

Ensuring that your source DNA is free of contaminants, including nucleases and unwanted enzymatic activities, is important. Using spin-column based kits like the Monarch PCR & DNA Cleanup Kits (5 µg) (#T1030) to purify starting DNA is good practice. Completely remove solvents, such as phenol, chloroform and ethanol, prior to manipulation of the DNA. Ensure that the final elution of DNA from the spin columns is made with salt-free buffer to prevent inhibition of the downstream steps, either restriction digestion or PCR amplification.

3. Perform your restriction digests carefully

It is important to set up digestion reactions properly when you are cutting your DNA. The volume of the reaction should be compatible with the downstream step, for instance, smaller than the volume of the well of an agarose gel used to resolve the fragments. For a typical cloning reaction, this is often between 20&ndash50 µl. The volume of restriction enzyme(s) added should be no more than 10% of the total reaction volume, to ensure that the glycerol concentration stays below 5% this is an important consideration to minimize star activity, or unwanted cleavage.

4. Mind your ends

DNA ends prepared for cloning by restriction digest are ready for ligation without further modification, assuming the ends to be joined are compatible (have complementary overhangs or are blunt). If the ends are non-compatible, modify them using the appropriate end-modification method (e.g., use of blunting reagents, phosphatases, etc.).

DNA ends prepared by PCR for cloning may have a 3´ addition of a single adenine (A) residue as a result of amplification using Taq DNA Polymerase (NEB #M0273). High-fidelity DNA polymerases, such as Q5® (NEB #M0491), leave blunt ends. PCR using standard commercial primers produces non-phosphorylated fragments, unless the primers were 5´ phosphorylated. The PCR product may need to be kinase treated to add a 5´ phosphate prior to ligation with a dephosphorylated vector.

5. Clean up your DNA prior to vector:insert joining

For low-throughput projects, such as single gene cloning, you&rsquoll want to clean up your digest, end modification or PCR reaction prior to proceeding. This can be achieved with gel electrophoresis or the Monarch PCR & DNA Cleanup Kits (5 µg) (#T1030). Isolating the desired DNA species and resolving it from unwanted parent vectors and/or other DNA fragments can dramatically improve your cloning results.

Confirm digested DNA on an agarose gel prior to ligation. For a single product, run a small amount of the digest, and then use the Monarch PCR & DNA Cleanup Kit (#T1030) to isolate the remainder. When there are multiple fragments produced and only one is to be used, resolving the fragments on a gel and excising the desired fragment under UV light is common. Using longwave (365nm) UV light will minimize any radiation-induced DNA damage to the fragment of interest. The DNA fragment may then be recovered from the agarose slice with the Monarch DNA Gel Extraction Kit (#T1020) or &beta Agarase I (NEB #M0392).

6. Quantitate your isolated material

Simple quantitation methods, such as gel electrophoresis with mass standards or spectroscopic quantitation on low-input spectrophotometers (such as a NanoSpec®), ensure that the proper amount of material is used for the downstream reactions.

7. Follow the manufacturer&rsquos guidelines for the joining/ligation reaction

For traditional cloning, follow the guidelines specified by the ligase supplier. If a 3:1 molar ratio of insert to vector is recommended, try this first for the best result. Using a 3:1 mass ratio is not the same thing (unless the insert and vector have the same mass). Ligation usually proceeds quickly and, unless your cloning project requires the generation of a high-complexity library that benefits from the absolute capture of every possible ligation product, long incubation times are not necessary. Follow the manufacturers&rsquo guidelines for the joining reactions in PCR cloning and seamless cloning. If you are performing a cloning protocol for the first time, adhere to the recommended protocol for optimal results. NEB recommends using NEBioCalculator to calculate ligation ratios.

8. Use competent cells that are suited to your needs

While some labs have traditionally prepared their own competent cells &ldquofrom scratch&rdquo for transformations, the levels of competence achieved rarely matches the high levels attained with commercially-available competent cells. Commercially-available competent cells save time and resources, and make cloning more reproducible.


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Career choice

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Studying computer science but more interested in 3d designing stuff or building things like using Autocad 360 to design things 3d printing etc

Is there any career that will allow me to align with something I like

Currently, I'm studying programming but I don't like it as much,

if there is anything on the CAD or 3dprinting design stuff, rendering, Vr experiences where I can land a job and have good future outlook just like programming and AI.

If I am a newbie without friends or relatives at the workplace, what are the first signs I should move on ASAP?

BDC Pay Plan - Car Dealership

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Therapists, do you still have to read a lot of scientific psychology papers/studies?

I have always been bad at reading scientific papers. Like, really bad. When it comes to writing them, I'm fine. I understand the process of creating them well, but every single time I read a complicated scientific study, its like I have ADHD or something, and I have trouble understanding what they are saying without taking forever to read them. So far, I am getting good grades and am almost done with my major, but part of me feels like I am BSing in order to make up for the fact that I am so bad at reading these, and it just happened to work. My question is, if I go on to grad school and ultimately become a therapist, will I need to read a lot of papers? Like more than in college? What is it like day to day working as a therapist? Do you need to read a lot of scientific studies in order to keep up to date on everything, or is that more on the research side of the field of psychology? Thanks in advance!


Cell analysis subtopics

Cell imaging information

Learn about imaging microscopy and high-content analysis including articles on new applications and techniques, webinars and videos covering controls, experiment design, and more. We cover topics including live- and fixed-cell imaging, high-content analysis for quantitative imaging, automated imaging platforms as well as transmitted light and colorimetric imaging applications.

Cell structure information

Find useful articles, videos and tools for studying cell structure using fluorescence microscopy and high-content analysis.

Cell viability and function information

Learn about assays and techniques for detecting and monitoring cell health and function by flow cytometry, imaging, high-content analysis and microplate assays. Topics include apoptosis, autophagy, cell counting, proliferation and viability as well as cell cycle, endocytosis, oxidative stress and more.

Cell counting information

Cell counting can be a critical step in any experiment that involves comparing different cell populations or responses. In this section you will find application notes, videos and technical guides to help you achieve more accurate cell counts and ultimately more accurate results.

Cell analysis antibodies information

Learn about a wide range of applications and techniques related to using primary and secondary antibodies in your cell biology research. Topics include immunocytochemistry, immunohistochemistry, immunofluorescence, using flow cytometry, and western blot analysis.

Labeling and detection information

Learn about strategies and techniques for labeling proteins and antibodies for cell biology research. Topics include traditional reactive chemistries like amine and thiol labeling, protein-protein crosslinking, general protein crosslinkers and more. Newer chemistries for labeling proteins include click chemistry–based protein and carbohydrate labeling reactions.

Flow cytometry information

Find the resources and tools that cover a wide range of techniques and applications for flow cytometry including functional assays and reagents for cell proliferation and viability, cell cycle, and apoptosis, flow cytometry antibodies and immunophenotyping, flow cytometer set-up and calibration, cell sorting, and more.

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Watch the video: Molecular Biology Basics Lesson 1 - What is DNA? (May 2022).


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