Nanobody & RANbody; a new techniqe to make antibody from plasmid expressin

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When a heavy chain variable domain of antibody is expressed in a plasmid, it is called Nanobody.

” Problems with Antibodies

  • Conventional antibodies are a non-renewable reagent – Their production requires animal sacrifice and because they are an animal derived product, there can be lot-to-lot variability in activity.
  • No Genetic Tagging – Since antibodies are produced in animals instead of via recombinant DNA, they can’t be genetically tagged and instead are conjugated to reporters (i.e. fluorescent dyes, HRP, etc. ) after purification.
  • Antibodies are difficult for an individual lab to produce – Hybridomas offer an alternative and renewable source of monoclonal antibodies, but they are laborious to generate and costly to share.”
  • From:http://blog.addgene.org/ranbodies-reporter-nanobody-fusions

 

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ChIC&ChEC ChIP and CUT&RUN ChIP

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ChIC&ChEC ChIP (2004)

https://www.ncbi.nlm.nih.gov/pubmed/15469830

CUT&RUN ChIP (2017)

https://www.ncbi.nlm.nih.gov/pubmed/28079019

 

Data visualization, bar naked: A free tool for creating interactive graphics

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“Abstract

Although bar graphs are designed for categorical data, they are routinely used to present continuous data in studies that have small sample sizes. This presentation is problematic, as many data distributions can lead to the same bar graph, and the actual data may suggest different conclusions from the summary statistics. To address this problem, many journals have implemented new policies that require authors to show the data distribution. This paper introduces a free, web-based tool for creating an interactive alternative to the bar graph

http://statistika.mfub.bg.ac.rs/interactive-dotplot/

This tool allows authors with no programming expertise to create customized interactive graphics, including univariate scatterplots, box plots, and violin plots, for comparing values of a continuous variable across different study groups. Individual data points may be overlaid on the graphs. Additional features facilitate visualization of subgroups or clusters of non-independent data. A second tool enables authors to create interactive graphics from data obtained with repeated independent experiments

http://statistika.mfub.bg.ac.rs/interactive-repeated-experiments-dotplot

These tools are designed to encourage exploration and critical evaluation of the data behind the summary statistics and may be valuable for promoting transparency, reproducibility, and open science in basic biomedical research.”

ARB Project; rRNA phylogenetic treeing

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http://www.arb-home.de  (rRNA sequence data phylogenetic treeing for rRNA and protein)

https://www.arb-silva.de    (A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data.)


16s sequencing:

Primers for microbial detection by sequencing.

Primer Sequence
For bacteria 10F 5′-GTTTGATCCTGGCTCA
800R 5′-TACCAGGGTATCTAATCC
For fungi ITS1F 5′-GTAACAAGGT(T/C)TCCGT
ITS1R 5′-CGTTCTTCATCGATG
For full-length sequencing(only for bacteria
27F 5′-AGAGTTTGATCCTGGCTCAG
1492R 5′-GGCTACCTTGTTACGACTT

From:

http://www.bexnet.co.jp/english/product/trust/gene-analysis/microbial.html

 

pPSU Plasmids for DNA Markers (Ladder)

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http://www.personal.psu.edu/sxt30/projects_DNA_ladders.html

https://www.addgene.org/89439

https://www.addgene.org/89566

 

 

Cytopathic Effects in Cell Culture

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https://www.kullabs.com/classes/subjects/units/lessons/notes/note-detail/7302

Or here: Cytopathic Effects in Cell Culture-www-kullabs-com

https://web.archive.org/web/20120602171845/http://microbelibrary.org/component/resource/laboratory-test/2875-cytopathic-effects-of-viruses-protocols

Protein Secondary Structure predictions online

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https://molbiol-tools.ca/Protein_secondary_structure.htm

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