QuickBiology News

The COVID-19 pandemic has already greatly disrupted all our life and society since the outbreak about seven months ago. As of July 13th, SARs-CoV2 has already resulted in over 3.4 million confirmed cases and 137,786 deaths in the USA (https://coronavirus.jhu.edu/map.html). Something worse is happening, at the beginning of June 2020, as more and more states are moving to reopen their economies. Such ease of coronavirus restrictions planning for the economic and society reopening, many of the states, especially states especially Florida, Arizona, and Alabama are experiencing a surge in cases. To adequately combat the COVID-19 pandemic and reopen society safely, comprehensive, and reliable SARs-CoV2 screening is essential to guide the community to contain the spread. Read More

The CRISPR-Cas system is adapted from a naturally occurring genome editing system in bacteria and archaea, it is a prokaryotic immune system that confers resistance to foreign genetic elements. This CRISPR-associated system is highly expanded and developed by Dr. Jennifer Doudna in UC, Berkeley (https://doudnalab.org/) and Dr. Feng Zhang at Broad Institute (https://zlab.bio/). Currently, the CRISPR-Cas system offers the eukaryotic genome (DNA level) and epigenome editing (RNA level), which can be repurposed in gene activation or repression via CRISPR-Cas or variants fusion to other modifiers. Read More

Orchestrated gene expression is critical in cell differentiation and organ development. Gene transcripts can be controlled in different layers including but not limited to: a) Temporal and spatial expressed transcription factor can binding to certain genes’ promoter region, trigger their expression; b) mRNA-alternative splicing coupled to nonsense-mediated decay of transcripts ensure no toxic truncated protein product; c) 5’ UTR (Untranslated Region) of transcript contains various regulatory elements, play a major role in translation initiation; d) 3’ UTR carrying lots of miRNA binding sites plays a role in mRNAs’ half-life, mRNA stability, in final protein production.Read More

Quantitative trait locus (QTL) analysis is to identify which molecular markers correlate with an observed trait, bridging the gap between genes and the phenotypic traits. Genome-wide association studies using DNA level variants (e.g. single nucleotide polymorphism) is a powerful tool for QTL mapping. However, DNA level variants may not be the causal variants, they might just hitchhike with causal variants, or they function as trans factors, indirectly regulate in a distal genome region. Message RNA is the intermediate level between genetic materials (DNA) and phenotypic traits (protein). Using RNA level variants (i.e. transcript expression level, eQTL) has its unique advantage: they are more associated with traits. One vivid example is that our body has tissue-specific transcript patterns while sharing the same genome sequences. Read More

In June, all 50 states in the USA have begun to reopen in some way. Some companies or institutes are providing employee coronavirus testing for returning to the office. Diagnostic capability is always challenging in such a SARS-CoV2 pandemic. We summarized here of three strategies, which used next-generation sequencing, to do high throughput diagnostics of SARs-CoV2. Read More

Personal Health Information Management (PHIM) is to stay healthy and combat illness, and it includes sleep, diet, and exercise management. Wearable devices such as a smartwatch, wristband, have been popular as they track our sleeping, heart rate, and activity, provide wearers with health and fitness recommendations. Today, we are going to talk about molecular dynamics (not heart rate, not calories burned) in our acute physical activity.Read More

Quick Biology has been posting lots of eukaryotic single cell profiling methods and their applications in biomedical, stem cell field. Bacterial cells, however, have lagged a lot due to the presence of thick prokaryotic cell (lysis challenge) and lack of poly(A) tails mRNA (capture efficiency in reverse transcription). In current Nature Microbiology, Scientists in Columbia University borrow two concepts i) single cell combinatorial indexing ii) cells are themselves as compartments for barcoding, developed prokaryotic expression-profiling by tagging RNA in situ and sequencing (PETRI-seq). Read More

Circulating tumor DNA (ctDNA) is an accessible biomarker for cancer detection, molecular stratification, therapeutic monitoring, and post-treatment surveillance. Compared to traditional tissue biopsy, ctDNA as liquid biopsy is minimally invasive and can be performed serially to monitor tumor evolution or response to any drug therapy.  Due to these advantages, ctDNA is being rapidly adopted in precision medicine.  However, ctDNA sequencing assays face major challenges such as cell-free DNA exists as small fragments, and only a small fraction (< 0.01-0.1 %) of cell-free DNA is tumor-derived as we call ctDNA. In addition, ctDNA sequencing assays are also affected by a range of experimental variables and artifacts.Read More

T cell receptor (TCR) diversity or heterogeneity is a great measure of immune response to pathogens, cancer, and therapeutic interventions. Identification of exact pair of TCR-alpha and TCR-beta chain interacting with an antigen provides a potential vaccination therapy for cancer. Multiplex PCR amplicon sequencing is a straightforward strategy for analyzing TCR alpha and beta variables. However, non-specific amplification, primer dimers caused by multiple primers in PCR generate lots of NGS reads useless finally.Read More

CRISPR-Cas9 endonuclease is a powerful gene-editing technology. Direct editing of cells by delivering Cas9 gene typically triggers an immune response, a big challenge for CRISPR gene editing therapies. While in ex vivo, cells are treated in a dish before transplantation, Cas9 immune response can be circumvented as Cas9 transiently expresses, Cas9 is cleaned up before corrected cells are administered into patients (ref1).Read More