QuickBiology News

Cellular hypoxia (low oxygen) is a stress common in the pathological processes, such as cancers (tumor hypoxia), ischemia (ischemic hypoxia), and preeclampsia (placental hypoxia). It affects cell metabolism, apoptosis, proliferation, and differentiation. Importantly, hypoxia in the Tumor Microenvironment (TME) is the negative factor in the efficacy of radio- and chemotherapy, which becomes a big barrier in cancer treatment. Read More

Since the first case of COVID-19 was reported in Dec 2019, a large amount of SARS-CoV-2 strains have been fully sequenced, transcriptome is also being functionally annotated. Such an explosion of omics data of SARS-CoV2 has created a need for storing, analyzing, comparing these data. Read More

Countries across Europe especially France, the UK, and Poland are seeing a resurgence in COVID-19 cases, are likely dealing with the much-feared second wave of SARs-CoV2 recently. Quick Biology previously summarized three methods which used next generation sequencing, to do high throughput diagnostics.
Most of these amplicon NGS libraries are based on RNA extraction followed by PCR; LAMP-seq, although getting rid of RNA extractions, combining isothermal nucleic acid amplification, its dynamic range/quantitative measure is still under evaluation (see News in Quick Biology).
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The cell surface is the crucial interface between cell-cell and cell-environment interactions. These interactions involve extracellular signal sensing, extracellular matrix anchoring, or antigen presentation. The key bioactive molecules in these cell surface functions are transmembrane proteins, glycans, or lipids. In contrast, the contribution of RNAs to the cell functions is largely unknown.Read More

We previously introduced Oxford Nanopore sequencing, a third-generation sequencing that read the nucleotide sequences at a single-molecule level. It has many advantages than the current Illumina sequencing platform, however, its output and reads accuracy so far is far inferior to that of Illumina. Quick Biology believes the products of Illumina and Oxford Nanopore have different applications; both will occupy a certain share in the current high throughput sequencing market.Read More

Single-cell RNA sequencing is a great method to study cell heterogeneity, track cell lineages in developments, but it obscures spatial (location) and temporal resolution. To get spatial information, many other methods are developed such as (1)Geo-seq (Geographical position sequencing) through tissue staining and laser capture microdissection developed by Dr. Han and Dr.Jing’s group in CHINA (Ref1) ; (2) Slide-seq, whereby RNA was spatially resolved from tissue sections by transfer onto a surface covered with DNA-barcoded beads developed by Dr. Chen and Dr. Macosko in Broad Institute in the USA (Ref2).Read More

Extrachromosomal DNA (ecDNA) is any DNA that is found off the chromosomes. In early Feb, we discussed one research work led by UCSD and Stanford. By integrating RNA-Seq, ATAC-seq and 4C-seq etc, they revealed extrachromosomal circular DNA (eccDNA) is common in cancer cells, has a loose chromatin structure, genes encoded in eccDNA are most highly expressed. Read More

Ticks (Acari: Ixodidae) are obligate blood-feeding arthropods. They are the most versatile vectors, transmit the most diverse human and animal pathogens. Due to urbanization, deforestation, and climate change, tick-borne diseases (TBDs) have increased unpredictably, worsen the quality of human health.Read More

Decoding the genome of the species is a fundamental question in biology. Current short-read sequencing technology cannot cover the low complexity of simple repetitive regions such as centromeric or telomeric, and cannot assemble large structural variation. In plants, higher genomic rearrangement events, abundant repeat expansion, and plant polyploids make it much more challenging for uncovering their complete genomes.
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N6-methyladenosine (m6A) is the most abundant modification of mRNA. This modification has critical roles in stem cell proliferation, differentiation, mRNA splicing, RNA metabolism, etc. Previously, we described the DART-seq method developed by Dr. Kate D.Meyer, an antibody-free method for global m6A detection. In DART-seq, the researcher fused APOBEC1 to the m6A-binding YTH domain. Recruitment of APOBEC1 to m6A site will enable the deamination of cytidine immediately following m6A residue like C-to-U editing. Read More