Category: genetics

Hypothesis: SARS-CoV-2 may have spread worldwide as a mild infective virus prior to onset of pandemic in 2020

February 1, 2024

Questions remain on the origins of SARS-CoV-2 with different conceptual models awaiting verification. Here, I would like to propose a new hypothesis concerning the outbreak of COVID-19 in early 2020, which later morphed into a global pandemic. First, it may be the case that infective virus of global importance do not emerge overnight in its … More Hypothesis: SARS-CoV-2 may have spread worldwide as a mild infective virus prior to onset of pandemic in 2020

Thoughts on Sisyphean evolution in Darwin’s finches

December 28, 2023

The number of species is 1, for the 6 sub-species of Darwin’s Finches under consideration. Firstly, there are observations that the 6 sub-species still interbreed and produce fertile hybrid offsprings. Thus, according to the Biological species concept, the 6 sub-species cannot be considered as separate species as there is no reproductive isolation. Next, contention that … More Thoughts on Sisyphean evolution in Darwin’s finches

Possible speciation of Cyanoderma erythropterum

December 28, 2023

At the present time, morphological characteristics may divide the Bornean and western Sundaic populations of Cyanoderma erythropterum as two species due to speciation events between the allopatric populations in Borneo and western Sumatra during the past 20 to 200 kya. Two ice ages between 20 to 200 kya likely exposed vast swathe of land bridge … More Possible speciation of Cyanoderma erythropterum

Very difficult to assemble a genome based on short read sequencing data

January 2, 2023

Genome sequencing is commonly viewed to be routine now by lay people. But, this is not the case. Genome sequencing and downstream assembly remains an active area of research that can benefit from better, faster, and more efficient algorithms that can reduce the need for expensive computational power. In the contemporary era, short read sequencing … More Very difficult to assemble a genome based on short read sequencing data

Single cell RNA sequencing increasingly needs to be augmented by detection of protein product of RNA transcripts profiled

April 29, 2021

Current thinking in biological research posits that many phenomena is potentiated by events at the single cell level. This drove the desire to understand differential gene expression at the single cell level and its correlation with diseased phenotype at the cellular level. Advent of high throughput next-generation sequencing has brought forth technologies able to support … More Single cell RNA sequencing increasingly needs to be augmented by detection of protein product of RNA transcripts profiled

Stability of evolved traits in microbial species depends on a variety of factors

March 8, 2021

Mutations in DNA is the bedrock on which natural selection acts on and from which evolution build on. Evolved traits are thus based on mutations in genes and pathways, but are evolved traits stable? Would they revert back to the original state of the gene? Answering this question requires knowledge on the different factors that … More Stability of evolved traits in microbial species depends on a variety of factors

Promoter sequence is less well defined than gene sequence

November 16, 2020

With the advent of genome sequencing and the generation of large datasets, automated algorithms have been used to annotate whole genome sequences for coding sequences (genes). Such algorithms require identifiers to locate specific genes, which in the simplest case for coding sequence is the AUG start codon. On the other hand, promoters that control the … More Promoter sequence is less well defined than gene sequence

Plant genomes are more complex and larger than human genomes

October 7, 2020

Sequencing of human genome was a huge undertaking in its time and took approximately a decade. Progressive refinement in sequencing technologies and new innovations such as short-read sequencing followed by genome assembly have redefined whole genome sequencing. This has helped reduce the cost and time needed to sequence a full human genome. However, significant amount … More Plant genomes are more complex and larger than human genomes

Mutagenic source is needed to drive evolution experiment

September 28, 2020

Evolution is a common tool for developing new microbial strains able to perform new functions or existing functions more efficiently. But, what is the source of information for which evolution and natural selection is able to act upon? The answer is mutations. Without mutations and the diversity it engenders, natural selection would not be able … More Mutagenic source is needed to drive evolution experiment

Detection of differences in current characteristics as each nucleotide transits a single pore enable Nanopore sequencing

August 6, 2020

While short read next-generation sequencing provides large amount of data that could be bioinformatically assembled into genetic information useful for understanding genes and genome as well as understanding the relative abundance of different RNA transcripts, inability to detect single nucleotide polymorphism has driven the development of long read sequencing technologies known as third generation sequencing. … More Detection of differences in current characteristics as each nucleotide transits a single pore enable Nanopore sequencing