From Fins to Genes: DNA Barcoding Unlocks Marine Diversity Along Mozambique’s Coast

DNA Barcding unlocks marine diversity along Mozambique's coast

The Mozambique Channel, which is located between the Madagascar and Mozambique on the African coast, is an important hot spot for biodiversity because its many coastal ecosystems provide a range of habitats that support diverse plant and animal species. Understanding the biodiversity of an ecosystem, particularly biodiversity hot spots, is important for many reasons. For marine systems, accurate classification and reporting of fish species supports fisheries research, natural resource surveys, forensic studies, conservation studies, and enables discovery of new or under-reported species. Studies have been limited along the west coast of Africa and are only now in their early stages.

A 2024 research study by Muhala and colleagues applied DNA barcoding to evaluate the composition of marine and coastal fish diversity from the Mozambican coast. In the study, the Wizard® Genomic DNA Purification Kit was used to extract DNA from both teleost (ray-finned) and elasmobranch (sharks, rays and skates) fish classes, with a total of 143 species sampled from local artisanal fisheries along the Mozambican coast. The samples were primarily composed of muscle or fin tissues, which are ideal for genetic analysis due to their higher DNA yield. These tissue samples were collected from various fish species captured along the coast of Mozambique, stored in ethanol (96%) to preserve DNA integrity, and then processed using the Wizard kit. Total genomic DNA was extracted from the muscle or fin tissues, as per the manufacturer’s protocol. This method ensures the isolation of high-quality genomic DNA, which is crucial for subsequent polymerase chain reaction (PCR) amplification and sequencing. The COI gene (cytochrome c oxidase subunit I) was targeted for DNA barcoding, enabling species identification and assessment of genetic diversity.

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The Buzz on Biodiversity: Exploring Pollinator Diversity Through Mitochondrial DNA Analysis

Almost three-quarters of the major crop plants across the globe depend on some kind of pollinator activity, and over one-third of the worldwide crop production is affected by bees, birds, bats, and other pollinators such as beetles, moths and butterflies (1). The economic impact of pollinators is tremendous: Between $235–577 billion dollars of global annual food production relies on the activity of pollinators (2).  Nearly 200,000 species of animals act as pollinators, including some 20,000 species of bees (1). Some of the relationships between pollinators and their target plants are highly specific, like that between fig plants and the wasps that pollinate them. Female fig wasps pollinate the flowers of fig plants while laying their eggs in the flower. The hatched wasp larvae feed on some, but not all, of the seeds produced by fertilization. Most of the 700 fig plants known are each pollinated by only one or a few specific wasp species (3). These complex relationships are one reason pollinator diversity is critical.

Measuring the Success of Conservation Legislation

A bee pollinates flowers in a field. Pollinator diversity is a critical aspect of ecosystems.
A bee pollinates the lavender flowers.

We are now beginning to recognize how critical pollinator diversity is to our own survival, and many governments, from the local level to the national level are enacting policies and legislation to help protect endangered or threatened pollinator species. However, ecosystems and biodiversity are complex subjects that make measuring and attributing meaningful progress on conservation difficult. Not only are there multiple variables in every instance, but determining the baseline starting point before the legislation is difficult. However, there are dramatic examples of success in saving species through legislative and regulatory action. The recovery of the bald eagle and other raptor populations in the United States after banning the use of DDT is one such example (4).

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Understanding Persistent Digestive Disorders With Multiplex PCR

Digestive disorders are a leading cause of mortality worldwide, with diarrhea being particularly deadly. Despite declining mortality rates, diarrhea still causes an estimated 1.65 million deaths annually, with the highest burden in low- and middle-income countries, largely due to poor sanitation and lack of clean water. While acute diarrhea has been extensively studied, less is known about the pathogens responsible for long-lasting digestive issues, including diarrhea and abdominal pain that persist for 14 days or more. A recent study in Scientific Reports offers valuable insights into the prevalence of these pathogens and highlights the importance of advanced molecular diagnostics in addressing this issue.

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Ancient Retroviruses and Modern Cancer: Role of Endogenous Retroviruses in Transcriptional Changes in Tumor Cells 

Approximately 30 million years ago, a retrovirus integrated into the germline of a common ancestor of baboons, gorillas, chimpanzees and humans. That endogenous retrovirus, now known as gammaretrovirus human endogenous retrovirus 1 (HERV-1), may provide clues about the aberrant regulation of gene transcription that enables tumor cells to grow and survive.  

Understanding the Mechanism Behind Cancer Gene Expression 

Scientists have long described the striking differences in gene expression, signaling activity and metabolism between cancer cells and normal cells, but the underlying mechanisms that cause these differences are not fully understood. In a recent Science Advances article, published by Ivancevic et al., researchers from the University of Colorado, Boulder; the University of Colorado Anschutz Medical Campus, and the University of Colorado School of Medicine report their efforts to identify endogenous retrovirus elements that might be part of the answer to the complex question of what biological events are responsible for the changes in gene expression in cancer cells.  

The researchers hypothesized that transposable elements (TEs), specifically those associated with endogenous retroviruses could be involved in cancer-specific gene regulation.  Endogenous retroviruses (ERVs) are the remnants of ancient retroviral infections that have integrated into the germline of the host. 

The transposable element LTR10, derived from an endogenous retrovirus, can alter gene expression in a number of cancers. Artist's conception of an invasive cancer cell.

Identifying Endogenous Retrovirus Elements That Affect Cancer Gene Expression 

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Can AI Replace High-Throughput Screens for Drug Discovery?

This image was created with the assistance of AI

For decades, pharmaceutical companies have relied on high-throughput screening (HTS) as the first step in the drug discovery process. After an initial screening of thousands of compounds, scientists select a smaller list of candidate drugs that is then used for further downstream testing. A major limitation to HTS, however, is the need to synthesize all compounds used in the screen—the compounds need to physically exist to be tested. This significantly limits the number of compounds that can be tested, hindering the discovery of new drugs.

What if we could test compounds even before they are synthesized?

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Silencing the Immunogenicity of AAV Vectors 

Recombinant adeno-associated viral (AAV) vectors are an appealing delivery strategy for in vivo gene therapy but face a formidable challenge: avoiding detection by an ever-watchful immune system (1,2). Efforts to compensate for the immune response to these virus particles have included immunosuppressive drugs and engineering the AAV vector to be especially potent to minimize its effective dosage. These methods, however, come with their own challenges and do not directly solve for the propensity of AAV vectors to induce immune responses.  

A recent study introduced a new approach to reduce the inherent immunogenicity of AAV vectors (2). Researchers strategically swapped out amino acids in the AAV capsid to remove the specific sequences recognized by T-cells that elicit the most pronounced immune response. As a result, they significantly reduced T-cell mediated immunogenicity and toxicity of the AAV vector without compromising its performance.  

Read on to get more of the study details, which include the use of NanoLuc® luciferase and Nano-Glo® Fluorofurimazine In Vivo Substrate for in vivo bioluminescent imaging of the AAV variants’ distribution and transduction efficiency in mice. 

A teal colored ribbon model of a AAV virus capsid floats against a black background.
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Connecting Synaptic Gene Polymorphisms to Parkinson’s Disease

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Neurodegenerative disorders represent a significant and growing concern in the realm of public health, particularly as global populations age. Among these, Parkinson’s disease (PD) stands out due to its increasing prevalence and profound impact on individuals. Characterized by the progressive degeneration of motor functions, PD is not just a health challenge but also poses substantial socio-economic burdens. While the etiology of Parkinson’s disease is far from simple, current research efforts elucidating its causes, mechanisms, and potential treatments illustrate the critical nature of this neurodegenerative disorder in today’s healthcare landscape.

In the clinic, Parkinson’s disease is often diagnosed as either sporadic or familial. Familial PD has a clear genetic basis, typically passed down through families, while sporadic PD, comprising about 90% of cases, occurs in individuals without a known family history of the disease. The exact cause of sporadic PD is not fully understood but is believed to be due to a combination of genetic predispositions and environmental factors. In contrast, the factors involved in familial PD are more thoroughly understood, offering insights into the molecular mechanisms underlying PD pathogenesis.

Polymorphisms and Parkinson’s Disease Susceptibility

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How Avian Influenza Crosses Species

Avian influenza, commonly known as bird flu, has become an increasingly severe public health issue. According to the CDC, the frequency of avian influenza outbreaks and diversity of virus subtypes have increased significantly in the past decade. In 2022, there were reports of sporadic H5 virus infections in mammals across several U.S. states, Canada, and other countries. Affected animals included fox kits, bobcats, coyote pups, raccoons, skunks, mink, and even seals. Human cases of H5N6 and other subtypes following poultry exposures were reported in China, with several cases resulting in severe or critical illness and death.

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Dynein Motor Proteins Could Be the Moving Power Behind Cancer Metastasis

3D Cancer Cell

“The cancer has spread.” are perhaps some of the most frightening words for anyone touched by cancer. It means that cancer cells have migrated away from the primary tumor, invaded health tissues and firmed secondary tumors. Called metastasis, this event is the deadliest feature of any type of cancer (1). The cellular mechanisms that play a role in metastasis could serve as powerful therapeutic targets. Unfortunately, understanding of these mechanisms is limited. However, some studies have suggested a link between the dysregulation of microtubule motors and cancer progression. A new study by a team from Penn State has revealed that the motor protein dynein plays a pivotal role in the movement of metastatic breast cancer cells through two model systems simulating soft tissues (1).

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The Tiniest Test Tube: Studying Cell-Specific Protein Secretion

Free floating single cells, blue
Researchers explore an innovative method for single-cell analysis

Cells produce proteins that serve different purposes in maintaining human health. These bioactive secretions range from growth factors to antibodies to cytokines and vary between different types of cells. Even within a certain cell type, however, there are individual cells that produce more secretions than others, a phenomenon that especially interests scientists studying cell-based therapies. In contrast to molecular therapies, which typically involve specific genes or proteins, a primary challenge to crafting cell therapies is the wide range of functional outputs seen in cells that have the same genetic template. This leads to the question of what molecular properties, from a genomic and transcriptomic perspective, would lead one cell to produce more of a protein than its companions. 

There have been few investigative strategies put forth that allow scientists to connect a cell’s characteristics and genetic coding with its secretions. In July 2023 a team of scientists published a paper in Nature Communications outlining an innovative solution: little hydrogel particles, or “nanovials”, that essentially serve as tiny test tubes and can be used to measure protein secretion, track transcriptome data, and identify relevant surface markers in a single cell.

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