Lifeboat Foundation

Natural products collection reveals novel enzymes with surprising properties. Scientists have discovered two enzymes that enable bacteria to target and break up DNA. This chemical defense likely evolved to help the organism fight off germs. The chemical riches were found within the institute’s one-of-a-kind Natural Products Discovery Center collection.

Slumbering among thousands of bacterial strains in a collection of natural specimens at The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, several fragile vials held something unexpected, and possibly very useful.

Writing in the journal Nature Chemical Biology, a team led by chemist Ben Shen, Ph.D., described discovery of two new enzymes, ones with uniquely useful properties that could help in the fight against human diseases including cancer. The discovery, published last week, offers potentially easier ways to study and manufacture complex natural chemicals, including those that could become medicines.

To identify potential therapeutic targets and preclinical drug candidates for the treatment of ovarian cancer, researchers led by Tan Li from the Shanghai Institute of Organic Chemistry of the Chinese Academy of Sciences have developed novel small molecule inhibitors of CPSF3, a key module of the cleavage and polyadenylation specificity factor (CPSF) complex that catalyzes pre-mRNA splicing and regulates transcription termination.

This work was published in Science Advances on Nov. 22.

Ovarian cancer is the deadliest gynecological cancer and is often diagnosed at a late stage. In treating ovarian cancer, surgery and systemic chemotherapy can modestly improve the survival rate, while targeted therapies with PARP inhibitors are effective in a limited number of ovarian cancer patients.

Microbial sequence databases contain a wealth of information about enzymes and other molecules that could be adapted for biotechnology. But these databases have grown so large in recent years that they’ve become difficult to search efficiently for enzymes of interest.

Now, scientists at the Broad Institute of MIT and Harvard, the McGovern Institute for Brain Research at MIT, and the National Center for Biotechnology Information (NCBI) at the National Institutes of Health have developed a new search algorithm that has identified 188 kinds of new rare CRISPR systems in bacterial genomes, encompassing thousands of individual systems. The work appears in Science.

The algorithm, which comes from the lab of CRISPR pioneer Feng Zhang, uses big-data clustering approaches to rapidly search massive amounts of genomic data. The team used their algorithm, called Fast Locality-Sensitive Hashing-based clustering (FLSHclust) to mine three major public databases that contain data from a wide range of unusual bacteria, including ones found in coal mines, breweries, Antarctic lakes, and dog saliva.

Cell toxicity and genomic instability are potential side effects from the use of CRISPR-Cas9. The gene editing tool can also cause large rearrangements of DNA through retrotransposition to theoretically trigger tumor development.

While rare, the fact that CRISPR is used to edit millions of cells for some therapies means precautionary steps are warranted given the potential increase in cancer risk. However, retrotransposition is much rarer during base editing, a more precise technique that chemically changes just one “letter” of the genetic code without causing a double-strand break in DNA.

Although MHRA decided that the benefits of Casgevy outweigh its risks, the U.K. regulator granted a one-year conditional marketing authorization of the world-first gene therapy based on the findings of two global clinical trials, noting that no significant safety concerns were identified during the trials.

University of Missouri researchers’ conceptual design of a nanomaterial could potentially pave the way for new uses of nanotechnology in medicine and science.

In a recent study, scientists at the University of Missouri developed a proof of concept for a nanocapsule — a microscopic container — capable of delivering a specific “payload” to a targeted location.

While beyond the scope of this study, the discovery has the potential to revolutionize the delivery of drugs, nutrients, and other chemicals in humans and plants. The power of the forward-thinking idea for this tiny delivery mechanism comes from its inventive structure, said Gary Baker, an associate professor in the Department of Chemistry and study co-author.

In a recent study published in Nature Communications, researchers aimed to develop a model of rumination, a mental process characterized by persistent negative self-reflective thoughts that can lead to depression and anxiety. Using resting-state functional magnetic resonance imaging (rsfMRI) — a technique that captures brain activity when a person is at rest — they identified a specific region of the brain, the dorsal medial prefrontal cortex (dmPFC), as playing a pivotal role in these ruminative thoughts.

Recognizing that rumination can be an early risk factor for depression, the researchers aimed to develop methods for subclinical detection and intervention before clinical episodes of depression occur. Early detection and intervention can be crucial for preventing the development of more severe mental health conditions.

The default mode network (DMN), a large-scale resting-state network, had been consistently linked to rumination in previous research. But the precise brain regions responsible for variations in individual levels of rumination have remained elusive. The researchers wanted to investigate the specific role of the DMN and its subsystems in rumination, as it is involved in various processes related to self-referential thought, autobiographical memory, emotional experience, and more.

An algorithm that can analyse hundreds of millions of genetic sequences has identified DNA-cutting genes and enzymes that are extremely rare in nature.

Human chromosomes are long polymer chains that store genetic information. The nucleus of each cell contains the entire human genome (DNA) encoded on 46 chromosomes with a total length of about 2 meters. To fit into the microscopic cell nucleus and at the same time provide constant access to genetic information, chromosomes are folded in the nucleus in a special, predetermined way. DNA folding is an urgent task at the intersection of polymer physics and systems biology.

A few years ago, as one of the mechanisms of chromosome folding, researchers put forward a hypothesis of active extrusion of loops on chromosomes by molecular motors. Although the ability of motors to extrude DNA in vitro has been demonstrated, observing loops in a living cell experimentally is a technically very difficult, almost impossible, task.

A team of scientists from Skoltech, MIT, and other leading scientific organizations in Russia and the U.S. have presented a physical model of a polymer folded into loops. The analytical solution of this model allowed scientists to reproduce the universal features of chromosome packing based on the experimental data—the image shows the peak-dip derivative curve of the contact probability.

Biological computing machines, such as micro and nano-implants that can collect important information inside the human body, are transforming medicine. Yet, networking them for communication has proven challenging. Now, a global team, including EPFL researchers, has developed a protocol that enables a molecular network with multiple transmitters.

First, there was the Internet of Things (IoT) and now, at the interface of computer science and biology, the Internet of Bio-Nano Things (IoBNT) promises to revolutionize medicine and health care. The IoBNT refers to biosensors that collect and process data, nano-scale Labs-on-a-Chip that run medical tests inside the body, the use of bacteria to design biological nano-machines that can detect pathogens, and nano-robots that swim through the bloodstream to perform targeted drug delivery and treatment.

“Overall, this is a very, very exciting research field,” explained Assistant Professor Haitham Al Hassanieh, head of the Laboratory of Sensing and Networking Systems in EPFL’s School of Computer and Communication Sciences (IC). “With advances in bio-engineering, synthetic biology, and nanotechnology, the idea is that nano-biosensors will revolutionize medicine because they can reach places and do things that current devices or larger implants can’t,” he continued.