Machine learning helps to determine the diverse conformations of RNA molecules
2024-12-18 - 2024-12
An innovative technique called HORNET uses atomic force microscopy and a machine-learning architecture called a deep neural network to recapitulate the 3D structures of individual RNA molecules. This method enables the study of the structure and dynamics of RNAs that adopt flexible and variable conformations under biologically relevant conditions.
New Software Unlocks Secrets of Cell Signaling
2024-12-19 - 2024-12
Researchers have developed innovative software that enhances our understanding of cell signaling pathways. This tool allows scientists to analyze complex cellular interactions more efficiently, potentially leading to breakthroughs in understanding diseases at the molecular level
Scientists Destroy 99% of Cancer Cells in Lab Using Vibrating Molecule
2024-12-25 - 2024-12
Scientists have discovered a remarkable way to destroy cancer cells. A study published last year found stimulating aminocyanine molecules with near-infrared light caused them to vibrate in sync, enough to break apart the membranes of cancer cells.
Aminocyanine molecules are already used in bioimaging as synthetic dyes. Commonly used in low doses to detect cancer, they stay stable in water and are very good at attaching themselves to the outside of cells.
The research team from Rice University, Texas A&M University, and the University of Texas, said their approach is a marked improvement over another kind of cancer-killing molecular machine previously developed, called Feringa-type motors, which could also break the structures of problematic cells.
"It is a whole new generation of molecular machines that we call molecular jackhammers," said chemist James Tour from Rice University, when the results were published in December 2023.
Gene Therapy Market Analysis,Growth, Insights and Future Outlook | Exactitude Consultancy
2024-12-26 - 2024-12
Luton, Bedfordshire, United Kingdom, Dec. 26, 2024 (GLOBE NEWSWIRE) -- Gene Therapy Market Analysis: A Paradigm Shift in Modern Medicine
Gene therapy, a transformative approach to treating diseases, involves altering, replacing, or supplementing faulty genetic material to combat various illnesses. This innovative method represents a significant milestone in addressing degenerative and chronic diseases. As the global burden of conditions like cancer and diabetes continues to rise, the demand for gene therapy is expected to surge, positioning it as a pivotal solution in modern medicine.
Advancements Driving Gene Therapy Adoption
Gene therapies work by modifying genetic information to treat or even cure diseases. Techniques include inactivating malfunctioning genes, replacing defective ones with healthy copies, or introducing new genes to aid in disease management. This cutting-edge treatment has shown remarkable promise against conditions such as cancer, diabetes, AIDS, and heart disease, underscoring its potential to replace traditional methods like chemotherapy, which often result in significant side effects.
Recent years have witnessed significant advancements in gene therapy research, supported by robust investments from both public and private entities. These investments aim to accelerate the approval of advanced gene therapies, fostering market growth. For instance, the adoption of viral vectors—known for their low toxicity and high immunological efficacy—has marked a shift towards safer, more efficient therapeutic solutions.
The Cell Division Challenge to Eukaryogenesis — And to Evolution
2024-12-24 - 2024-12
In a previous article, I discussed the irreducible complexity of the eukaryotic cell division machinery. What makes the origins of the eukaryotic cell cycle particularly resistant to evolutionary explanations is that a wide gulf exists between the mechanism of cell division by eukaryotes and that employed by prokaryotic cells — both in terms of the protein components involved, as well as the underlying logic. There is essentially nothing in common between the two systems. As I noted in my paper,
The invagination of the bacterial cell inner membrane is mediated by FtsZ and the other proteins that together comprise the divisome. In eukaryotic cells, by contrast, a contractile ring forms from actin filaments and myosin motor proteins, which pinches the cell’s membrane to form two daughter cells. The mechanisms of segregating DNA in prokaryotes are also significantly different from the manner of segregating genetic material in eukaryotes. During eukaryotic mitosis…the cell’s replicated DNA condenses into distinct chromosomes. These chromosomes are then equally divided and segregated into two daughter cells through a process guided by the spindle apparatus, ensuring each cell receives a complete and identical set of genetic information. The underlying apparatus of these processes, therefore, are quite distinct between prokaryotes and eukaryotes.
Table 1 in the paper (pages 9-10) highlights important differences in the mode of cell division between these two systems.
Bacterial Cell Division Is Irreducibly Complex
For a survey of the mechanisms involved in bacterial cell division, I refer readers to two articles I previously published at Evolution News — here and here. Various features of the prokaryotic cell division machinery, much like eukaryotic cell division, exhibit irreducible complexity. For example, in gram-negative organisms, a minimum of ten proteins (FtsA, B, I, K, L, N, Q, W, Z and ZipA) are indispensable for successful division, and therefore have been suggested as potential targets of antibiotic drugs.1,2,3 For economy of space, I refer readers to my previous articles on this for a more detailed discussion of the irreducible complexity of the prokaryotic cell division machinery.
LECA Possessed Modern-Like Cell Cycle Complexity
Phylostratigraphic analysis has revealed that most of the components found in the modern eukaryotic cell cycle were already present in the last eukaryotic common ancestor (LECA). For example, one study revealed that a minimum of 24 of 37 known subunits, co-activators and direct / indirect substrates of the APC/C were present in LECA.4 A similar analysis was carried out on the components of the mitotic checkpoint and their associated functional domains and motifs. They concluded that “most checkpoint components are ancient and were likely present in the last eukaryotic common ancestor.”5 Another study likewise confirmed that the dynactin complex (the activator of cytoplasmic dynein, which is crucial for
Aspartate promotes lung metastases by activating protein synthesis in cancer cells.
2025-01-03 - 2025-01
Researchers from the lab of Prof. Sarah-Maria Fendt (VIB-KU Leuven) and colleagues have uncovered that the availability of the amino acid aspartate is one reason why the lung is a frequent organ of metastasis. Their work appears in Nature and improves our understanding of cancer biology while providing the foundation for new therapeutic interventions in metastatic diseases.
A role for aspartate
More than half of cancer patients in whom the cancer spreads beyond the primary site have lung metastases. What makes the lungs such a tempting place for cancer cells?
To find out, the team of Prof. Sarah-Maria Fendt (VIB-KU Leuven Center for Cancer Biology) and colleagues investigated the gene expression in cells from aggressive lung metastases. They found evidence for an alternative ‘translation program.’ What does this mean? Translation is the process that uses our genetic code as a blueprint to make proteins in cells. A change in the translational program results in a set of different proteins that allow cancer cells to grow easier in the lung environment.
But what starts this alternative translational program in aggressive metastases?
Ginevra Doglioni, PhD student at the Fendt lab and first author of the study says “We found high levels of aspartate in the lungs of mice and patients with breast cancer compared to mice and patients without cancer, which suggests that aspartate may be important for lung metastasis”
Aspartate is an amino acid (a protein building block) that has very low concentrations in blood plasma but, surprisingly, very high concentrations in the lungs of mice with metastatic breast cancer.
Advancements in RNA Sequencing Enhance Cancer Research with MaCroDNA Platform
2024-12-31 - 2024-12
Recent advancements in RNA sequencing, particularly with the MaCroDNA platform, have set new standards for single-cell sequencing data integration in cancer research. Developed by researchers at Rice University, this platform facilitates a deeper understanding of cancer at the single-cell level, shedding light on the early stages of tumor development and progression
Bioreactor allows automated long-term culturing of stem cells
2025-01-02 - 2025-01
Human induced pluripotent stem cells (hiPSCs) are considered a promising tool in medicine, with the potential to unlock treatments for many health conditions such as neurodegenerative diseases and disorders. However, producing large amounts of hiPSCs remains a challenge.
Human induced pluripotent stem cells (hiPSCs) hold great potential for the development of cell therapies and drugs and for disease research. HiPSCs are very similar to embryonic stem cells, but they are cultured and reprogrammed in a lab from adult cells taken from the connective tissue of adult subjects.
The advantage is that pluripotent stem cells have the potential to produce almost any type of cell or tissue that the body requires for self-repair purposes. It is also possible to perform patient-specific tests of potential active ingredients directly on the cells affected by a certain health condition.
To meet the rising demand for hiPSCs and allow for standardized production in larger volumes, a team of researchers from Fraunhofer ISC in Würzburg has developed a dynamic incubator and suspension bioreactor that can be used for long-term culturing of hiPSCs as part of their work on the SUSI (short for "Suspension Incubator") project. It offers optimum conditions, such as a temperature of 37°C and an atmosphere saturated with 5% CO2, both of which are necessary to culture the cells.
One key component of the bioreactor is the impeller, a type of stirrer that performs the important tasks of mixing, aeration and heat and mass transfer inside the glass vessel to create homogeneous conditions within the cell suspension, thereby enabling robust and reproducible cell propagation.
"We focus on the good of the cells and designed and built all of the components of our bioreactor with that in mind," says Thomas Schwarz, a scientist at Fraunhofer TLC-RT. For example, one crucial factor is the shear forces that affect the cells during the process of stirring, or agitating, the culture.
Novel Technique May Accelerate Study of Gene Regulation
2025-01-02 - 2025-01
Investigators from the laboratory of Ali Shilatifard, PhD, the Robert Francis Furchgott Professor and chair of Biochemistry and Molecular Genetics, have developed a novel technique to efficiently and dynamically label chromatin-binding proteins at specific genomic sites in the mammalian genome, as detailed in a recent study published in Molecular Cell.
The technique, called TurboCas, may allow scientists to more precisely and efficiently study transcriptional regulation, which has the potential to contribute for the development of new therapeutic strategies targeting gene expression.
Ali Shilatifard, PhD, the Robert Francis Furchgott Professor and chair of Biochemistry and Molecular Genetics, was senior author of the study published in Molecular Cell.
“This revolutionary methodology, which we and the field have been trying to develop for the past 20 years, is going to change the way we define gene specific regulation of transcription. Now we can identify a region of the genome that is a diseased region and molecularly define what’s really going on in there,” said Shilatifard, who is also director of Feinberg’s Simpson Querrey Institute for Epigenetics and leader of the Cancer Epigenetics and Nuclear Dynamics Program at the Robert H. Lurie Comprehensive Cancer Center of Northwestern University.
The motivation behind developing TurboCas stemmed from a longstanding challenge of labeling proteins at a single point in the genome. The new technique allows scientists to map a complete set of proteins interacting with a specific genomic region in mammalian cells with higher specificity, sensitivity and temporal control than previous methods.
St. Jude scientists create scalable solution for analyzing single-cell data
2025-01-08 - 2025-01
Researchers have amassed vast single-cell gene expression databases to understand how the smallest details impact human biology. However, current analysis methods struggle with the large volume of data and, as a result, produce biased and contradictory findings. Scientists at St. Jude Children’s Research Hospital created a machine-learning algorithm capable of scaling with these single-cell data repositories to deliver more accurate results. The new method was published today in Cell Genomics.
Before single-cell analysis, bulk gene expression data gave high-level but unrefined results for many diseases. Single-cell analysis enables researchers to look at individual cells of interest, a difference akin to looking at an individual corn kernel instead of a field. These detailed insights have already made breakthroughs in understanding some diseases and treatments, but difficulty replicating and scaling analyses for data that keeps increasing in size has stymied progress.
Researchers uncover molecular mechanisms driving RNA processing defects in Huntington's disease
2025-01-09 - 2025-01
A University of California, Irvine-led research team has discovered intricate molecular mechanisms driving the RNA processing defects that lead to Huntington's disease and link HD with other neurodegenerative disorders such as amyotrophic lateral sclerosis, frontotemporal lobar dementia and Alzheimer's disease.
The findings may pave the way for neurodegenerative disorder researchers to collaborate and share therapeutic strategies across diseases, opening additional avenues for treatment.
While it's known that HD is caused by an abnormal expansion of cytosine, adenine and guanine nucleotide repeats in the DNA of the gene responsible for HD, how this mutation interferes with cellular functions is highly complex.
The study, recently published online in the journal Nature Neuroscience, reveals the interplay between two key regulators of RNA processing. Binding of both the RNA-binding protein TDP-43 and the m6A RNA modification chemical tag has been found to be altered on genes that are dysregulated in HD. Further, TDP-43 pathology, classically associated with ALS and FTLD, is found in diseased brains from HD patients.
RNA modifications and how they control RNA abundance to lead to disease is an emergent and challenging area of biological research. "Our findings offer new insights into the role of TDP-43 and m6A modifications in contributing to defective RNA processing in HD. This enhanced understanding highlights their potential as therapeutic targets, which are major areas of research for other neurological disorders. Drugs developed to interact with these pathways could offer new hope for slowing or even reversing neurodegeneration in HD, ALS and other diseases where TDP-43 dysregulation is significant. This research is very important because it uses clinically relevant model systems to understand and elucidate novel RNA-based mechanisms for aberrant gene regulation in HD," said co-corresponding author Leslie Thompson, Ph.D., UC Irvine Chancellor's Professor and Donald Bren Professor of psychiatry & human behavior as well as neurobiology & behavior.
A tiny anticancer weapon: Nano-sized particles trigger tumor cell self-destruction
2025-01-15 - 2025-01
A new twist on a decades-old anticancer strategy has shown powerful effects against multiple cancer types in a preclinical study from researchers in the Perelman School of Medicine at the University of Pennsylvania. The experimental approach, which uses tiny capsules called small extracellular vesicles (sEVs), could offer an innovative new type of immunotherapy treatment and is poised to move toward more advanced development and testing.Researchers have been trying for more than 20 years to develop successful DR5-targeting cancer treatments. The new approach, using engineered sEVs to target DR5, outperformed DR5-targeting antibodies, which have been considered a leading DR5-targeting strategy. The sEVs were efficient killers of multiple cancer cell types in lab-dish tests, and blocked tumor growth in mouse models, enabling much longer survival than DR5-targeting antibodies.
Women in Science: Bristol Academic Honored with 2025 Cell Biology Medal
2025-01-15 - 2025-01
Dr Helen Weavers, Associate Professor in Cell and Developmental Biology in the Faculty of Health and Life Sciences, has been awarded the Women in Cell Biology (WCIB) Early Career Medal 2025 by the British Society for Cell Biology (BSCB).
Dr Weavers and her interdisciplinary team in the School of Biochemistry focuses on the molecular mechanisms enabling cells and tissues to resist and recover from insult, with the aim of developing novel therapies for regenerative medicine. Her group uses a wide range of cutting-edge approaches, integrating in vivo live imaging, molecular cell biology, genetics and ‘omics with computational modelling and genetic epidemiology.
Dr Weavers and her group have harnessed their models to uncover the fundamental molecular adaptations that enable diverse cell types to resist and repair damage. These cytoprotective mechanisms are important within barrier tissues, such as the skin or airways, vulnerable to environmental damage but also within internal tissues (e.g. kidneys), to defend against endogenous threat. Such self-defence strategies – which include redox control and metabolic reprogramming – limit cellular damage, ageing and death, so tissues can quickly restore function.
Terumo Blood and Cell Technologies and FUJIFILM Irvine Scientific collaborate to accelerate T cell expansion for cell therapy developers
2025-01-15 - 2025-01
Terumo Blood and Cell Technologies (Terumo BCT) and FUJIFILM Irvine Scientific have announced a strategic collaboration to help accelerate T cell expansion using Fujifilm's PRIME-XV® T Cell Expansion Media on Terumo BCT’s Quantum Flex™ Cell Expansion System. By using systems that work together, this collaboration offers an optimized workflow solution with a ready-to-use process, aimed at reducing the barriers in scaling T cell expansion.
Cell therapy developers, especially early-stage companies, often face significant challenges scaling their manufacturing processes, requiring extensive investment in developing their own methods for T cell expansion. Terumo BCT’s protocols, tested with Fujifilm’s commercially available, chemically defined, GMP-compliant media, help reduce challenges associated with T cell expansion such as time, cost, and complexity of creating in-house processes.
