Category: genomics

Sample pretreatment helps remove non-target DNA before DNA sequencing

May 21, 2024

DNA sequencing has become cheaper and more accessible to even common labs over the past ten years. More importantly, more types of samples are used for sequencing to detect and understand the genomic profile of more types of species. However, some of these samples contain large amount of DNA from different organisms that may interfere … More Sample pretreatment helps remove non-target DNA before DNA sequencing

Sample library preparation adds adaptor molecules to DNA fragments to make them compatible to the sequencing chemistry of the DNA sequencing instrument used

May 12, 2024

In modern DNA sequencing enabled by a variety of DNA sequencers using different sequencing chemistries, sample library preparation using a commercial kit compatible with the DNA sequencing instrument is a must. Why is this so? The key issue here is the need to modify the DNA fragments in your sample to enable them to ligate … More Sample library preparation adds adaptor molecules to DNA fragments to make them compatible to the sequencing chemistry of the DNA sequencing instrument used

Adaptor molecules replace primers in sample preparation for next-generation sequencing

May 10, 2024

In conventional Sanger sequencing, there is a need for a sequencing primer for the DNA polymerase to latch on, and continue the polymerisation cum sequencing of the DNA molecule. But such sequencing primer is mysteriously absent in many next-generation DNA sequencing applications. Why is that so? This comes about because the adaptor molecules that bind … More Adaptor molecules replace primers in sample preparation for next-generation sequencing

Long sequence reads are no longer less accurate than short reads with advances in third generation sequencing

April 2, 2024

Next generation sequencing technologies which have been at the forefront of genomics in the past decade benefits primarily from the accuracies of short sequence reads. But, short sequence reads suffer from deficiencies in enabling the deciphering of repeats or structural variation regions of the DNA. To this end, third generation sequencing come to the fore … More Long sequence reads are no longer less accurate than short reads with advances in third generation sequencing

Gene expression pattern analysis illuminates diverse aspects of biological function

February 14, 2024

It is common knowledge that the genetic repertoire of an organisms lends unique functions to the species. But, it is less well known that differential gene expression pattern can lead to different morphotypes and phenotypic traits in the same species. At the heart of differential gene expression pattern analysis is that not all genes are … More Gene expression pattern analysis illuminates diverse aspects of biological function

Large scientific collaborations are permeating biological research

February 9, 2024

Research is commonly thought to be performed in individual laboratories by small groups of researchers. However, the trend in physics research has been the forging of large collaborations that number in the thousands of researchers. More importantly, the trend is permeating the biological realm, where many large biological scientific collaborations tackling large complex challenges in … More Large scientific collaborations are permeating biological research

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

No endogenized phage gene in Helicobacter pylori genome

January 23, 2024

Bacteriophage attacks their corresponding host bacterial species in order to gain access to the host cell’s replication machinery and nutritional sources for building more phages, and thus, maintain the phage population in the environment. Hence, possibility exists that each bacterial species will have a corresponding phage that helps to control its population. Presence of the … More No endogenized phage gene in Helicobacter pylori genome

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