The University of Pretoria Genomics Laboratory (UPGL), in the Faculty of Natural and
Agricultural Sciences, hosted a successful introductory workshop on quantitative
Polymerase Chain Reaction (qPCR) from March 25-26, 2024. This event, held at UP’s Bio-
Laboratories, was made possible with the support of DIstributed PLatform in OMICS
(DIPLOMICS) and the African Centre for Gene Technologies (ACGT). Renowned experts
from Whitehead Scientific presented the course, which covered various aspects of qPCR,
from experimental design to result interpretation, over the span of two days.

Workshop Overview

The UPGL, known for its high-throughput sequencing and coordinated molecular biology
capabilities, is dedicated to advancing genetic and genomic technologies. The laboratory
also emphasizes training in the latter, laboratory automation systems, data analysis, and
related information management tools. This particular workshop aimed to equip students
and staff with essential qPCR techniques, focusing specifically on SYBR green.

The two-day program included:

• Introduction to PCR and qPCR: Understanding the basics and differences between
  PCR and qPCR.
• Primer Design using the IDT Portal: Learning how to design primers effectively.
• Planning a qPCR Experiment: Setting up a qPCR workspace for optimal results.
• qPCR Application Examples: Real-world applications and data analysis techniques.
• Basic Pipetting Skills: Ensuring accuracy and precision in pipetting.
• Overview of the qPCR Protocol: Detailed walk-through of the qPCR process.
• Introduction to qPCR Instrument Software: Familiarization with the software used in
  qPCR.
• Setting up qPCR Reactions: Practical setup and execution of qPCR protocols.
• Analysing and Interpreting qPCR Run Data: Methods for accurate data analysis and
  interpretation.

Participants and Attendance
The course attracted numerous staff and students from various institutions, including
Historically Disadvantaged Institutions (HDIs). The workshop attracted 23 participants from
various institutions, including:

• University of Venda
• University of Limpopo
• University of the Witwatersrand
• University of Johannesburg
• University of South Africa
• Tshwane University of Technology
• Council for Scientific and Industrial Research.

 

 

 

These participants, selected based on their need for skills development and their potential to
benefit from enhanced qPCR capabilities, included many from HDI’s, ensuring a diverse and
inclusive learning environment that supports equitable access to advanced genomic
technologies.

Participant Feedback: Experiences and suggestions for improvement

At the conclusion of the workshop, participants were invited to share their thoughts on the
training. The feedback highlighted a range of positive experiences as well as constructive
suggestions for future improvements.

“The introductory lectures were well-structured and covered essential aspects of qPCR, making complex concepts easier to understand.”

“This was a basic workshop, yet I learned different types of PCR and qPCR. I believe
this is the knowledge I have been looking for and more. I can confidently say I know how to perform qPCR. It was very informative.”

“I appreciated the detail and effort that went into the workshop. The presenters were knowledgeable and answered questions thoroughly.”

In the spirit of continuous improvement, the participants also shared their constructive
feedback aimed at enhancing the quality and effectiveness of future workshops. These
improvement areas were noted and will be taken into consideration when organizing future
workshops.

The feedback underscored several significant benefits and takeaways from the workshop,
highlighting both the immediate impact on participants and the long-term value for their
respective institutions/colleagues/fellow-students.

The feedback underscored several significant benefits and takeaways from the workshop,
highlighting both the immediate impact on participants and the long-term value for their
respective institutions/colleagues/fellow-students.

Key Takeaways

The workshop provided several significant benefits:

• Learning and capacity building: created an enriching environment for participants.
• Research collaborations: fostered opportunities for collaborative research efforts.
• Enhanced access to -omics technology: empowered participants to enhance access
  to -omics technologies at their institutions.
• Equitable access for HDIs: contributed to equitable access to -omics infrastructure
  and technology for HDI’s.

Acknowledgements

Special thanks to the University of Pretoria Genomics Laboratory, DIPLOMICS, Whitehead
Scientific, the ACGT, and the participants from various universities for making this workshop
a tremendous success.

Research in nonhuman primates is opening the possibility of testing treatments for the early stages of Alzheimer’s and similar diseases, before extensive brain cell death and dementia set in. A study published in Alzheimer’s & Dementia shows up to a six-month window in which disease progress could be tracked and treatments tested in rhesus macaques.

“This is a very powerful translational model to test interventions that target the tau protein,” said John H. Morrison, professor of neurology at the University of California, Davis and California National Primate Research Center and corresponding author on the paper.

The tau protein is found in neurons in the brain. The spread of misfolded tau through the brain is implicated in Alzheimer’s disease, frontotemporal dementia and other dementias. In Alzheimer’s, misfolded tau disrupts multiple processes essential for normal brain cell functioning. As the misfolded proteins spread, they affect neurons throughout the connected regions of the cortex that are crucial for memory and cognition.

The sick neurons then cause an inflammatory response mediated early on by microglial cells. Eventually, neurons die, leaving neurofibrillary tangles of tau protein, one of the key markers of Alzheimer’s and other dementing illnesses.

Thanks to advances in brain imaging, the discovery of biomarkers in human serum and cerebrospinal fluid, and work in rodent models, we now know more about the early stages of Alzheimer’s. But it is still difficult to figure out how tau, inflammation and disease progression relate to each other.

 

 

 

 

By UC Davis

Article can be accessed on: MedicalXpress

Synthetic chromosomes are ideal delivery systems for ferrying large sections of human DNA into cells. In contrast to viral vectors, human artificial chromosomes (HAC) carry more genetic material and are less likely to trigger an immune response. So far, however, technical problems have prevented HAC from reaching their full potential. Now, in a paper published in Science, researchers described an improved technique for engineering HAC that sidesteps previous barriers.

Earlier methods to synthesize HAC relied on linking shorter DNA constructs into a larger chromosome within the cell in a process called multimerization. However, the genetic fragments tended to connect in unpredictable sequences of varying lengths, making it difficult to anticipate how the genes would behave. Furthermore, the constructs often attached to natural chromosomes, potentially disrupting the host cell’s genome.

In the new study, researchers at the University of Pennsylvania circumvented this problem, known as uncontrolled multimerization, by synthesizing larger strands of DNA so that HAC could be formed from a single construct. Instead of creating 200 kilobase pair sequences, the researchers increased the size of the DNA construct to approximately 750 kilobases, removing the need for multimerization.

“We hypothesized that to [avoid] multimerization, we would have to start big,” said University of Pennsylvania biochemist Ben Black, who led the research.

Within each HAC, the researchers designed sequences to bind centromeric proteins, which ensured that daughter cells would inherit the chromosome when the original cell divided. Specifically, they added hundreds of DNA binding sites for the bacterial Lac repressor protein (LacI). By engineering the host cells to express a fusion protein—LacI fused to another protein that binds to a key centromeric protein—the team recruited proteins to form the centromere on the DNA construct.

 

 

 

By Holly Barker, PhD

Article can be accessed on: The Scientist

When one cell becomes two, it must divide its chromosomes equally. To accomplish this feat, each chromosome comes equipped with a centromere. As a chromosome duplicates, the centromeres connect the old and new copies in an X shape. This union provides the mitotic spindle a place to latch onto so that it can tug the two chromosomes apart during cell division. Without centromeres, cells would fail to evenly separate their chromosomes. This could lead to aneuploidy conditions, such as Down syndrome, in which people are born with an unbalanced set of chromosomes.

Six years ago, when Glennis Logsdon was a graduate student, everyone assumed that centromeres had conserved sequences and structures given their essential role in divvying up genetic material. “We had one consensus sequence that we used for all centromeres, and we thought, ‘this is all we need to know,’” said Logsdon, a geneticist at the University of Pennsylvania. Now, in a paper published in Nature, Logsdon and her colleagues reported that centromeres differ greatly between people. Their findings could allow researchers to explore which centromere characteristics predispose humans to aneuploidy.

One reason scientists remained unaware of the rich diversity of centromeres was because of how tough they are to sequence. “In fact, most people just throw it out because it’s the only part of the genome you couldn’t touch,” said Yamini Dalal, a molecular biologist at the National Institutes of Health (NIH) who was not involved with the study. Normally, researchers decode a chromosome by sequencing short segments and piecing them into a single string at points where their sequences overlap, just as someone completing a jigsaw puzzle might use objects in the image to guide them. Centromeres, however, are mostly made up of repeating sequences. Just as one might struggle to solve a jigsaw puzzle of a recurring pattern, scientists fail to string together short reads collected from the chromosome’s repetitive core.

 

By Kamal Nahas, PhD

Article can be accessed on: The Scientist