Lifeboat Foundation

The Human Genome Project (HGP), the world’s largest collaborative biological project, was a 13-year effort led by the U.S. government with the goal of generating the first full sequence of the human genome. In 2003, HGP produced a genome sequence that accounted for more than 90% of the human genome and was considered as close to complete as was possible with the technologies of the time. HGP unlocked the door to a vast but unannotated collection of genes.

In the following decades, via experimental studies, researchers painstakingly curated reannotations in the form of biochemical reaction graphs. Though gene set enrichment analysis considers groups within these annotation graphs, it disregards group dependencies.

Researchers from the University of Hawaii at Mānoa John A. Burns School of Medicine (JABSOM) are utilizing data from HGP and making advancements in biochemical reaction network analysis. Their work, published in the May 22, 2023 issue of Patterns, demonstrates their approach and may help predict the effects of rare or indistinct genetic variations and guide precision medicine (treatment that can use a patient’s own genes to help fight disease or guide specific therapy).

Imagine the possibility of life forms on other planets that don’t resemble any on Earth. What might they look like, and why would they be so different?

Juan Pérez-Mercader says it may be possible and the answer may be that they developed from a different type of chemistry. For more than 10 years, the senior research fellow in the Department of Earth & Planetary Sciences and the Origins of Life Initiative at Harvard has studied how to produce synthetic living systems—without relying on biochemistry, or the chemistry that has enabled life on Earth.

“We have been trying to build a non-biochemical system, which unaided is capable of executing the essential properties common to all natural living systems,” Pérez-Mercader explained.

Year 2019 😗😁

Hepatology and drug development for liver diseases require in vitro liver models. Typical models include 2D planar primary hepatocytes, hepatocyte spheroids, hepatocyte organoids, and liver-on-a-chip. Liver-on-a-chip has emerged as the mainstream model for drug development because it recapitulates the liver microenvironment and has good assay robustness such as reproducibility. Liver-on-a-chip with human primary cells can potentially correlate clinical testing. Liver-on-a-chip can not only predict drug hepatotoxicity and drug metabolism, but also connect other artificial organs on the chip for a human-on-a-chip, which can reflect the overall effect of a drug. Engineering an effective liver-on-a-chip device requires knowledge of multiple disciplines including chemistry, fluidic mechanics, cell biology, electrics, and optics.

The 2020 Nobel Prize for Chemistry was awarded to Dr. Jennifer Doudna and Dr. Emmanuelle Charpentier for their work on the gene editing technique known as CRISPR-Cas9. This gives us the ability to change the DNA of any living thing, from plants and animals to humans.

The applications are enormous, from improving farming to curing diseases. A decade or so from now, CRISPR will no doubt be taught in High Schools, and be a basic building block of medicine and agriculture. It is going to change everything.

Continue reading “Throw Forward Thursday: CRISPR” »

Sucralose, a widely used artificial sweetener, produces a DNA

DNA, or deoxyribonucleic acid, is a molecule composed of two long strands of nucleotides that coil around each other to form a double helix. It is the hereditary material in humans and almost all other organisms that carries genetic instructions for development, functioning, growth, and reproduction. Nearly every cell in a person’s body has the same DNA. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA).

A group of biochemical engineers, Siavash Ahrar, Manasi Raje, Irene Lee and Elliot Hui at the University of California, Irvine, has developed a finite state machine (FSM) implemented as a pneumatic circuit using microfluidic valves to build a lab-on-a-chip. Their work is published in the journal Science Advances.

Over the past several years, biochemical and mechanical engineers have been working toward the goal of automating many of the chemical process that are currently done by hand—trained lab technicians using pipettes to determine the concentration of a chemical dissolved in a liquid, for example. Automating such tasks would not only make them less expensive, it could speed things up, potentially offering medical lab results in minutes rather than hours. To that end, engineers have been working toward building what they call a lab-on-a-chip. In this new effort, the research team has applied pneumatics to the problem.

Many chemical processes involve the movement of liquids. The researchers sought to use water pressure instead of electricity when building circuits for use on a potential lab-on-a-chip. They created a tiny sandwich comprising panes of glass as the bread and a sheet of silicone as the interior. But before making their sandwich, they etched the glass panes to allow a liquid to pass through and poked holes in the silicone sheet to connect the channels in the glass panes.

Exhaled breath VOCs showed variations in concentration associated with the different clips, even though the relative change was less distinguishable compared to the genital response (Fig. 3). For female participants, breath levels of CO₂ and isoprene during the sex clip were significantly lower compared to the anxiety and sport clips (p 0.05, Table S2). For male participants, CO₂, C₂H₄O₂ and C₆H₆O were found to have a significantly lower, higher and higher breath level, respectively, for the sex clip comparing to the other two clips (p 0.05, Table S2). The relative change of CO₂ during the sex clip was in general only 3–4% lower than that during the anxiety and sport clips but was significant for both genders (p 0.05). The minute-by-minute box plot (Fig. 2c) also shows that breath CO₂ appears to lower slightly in concentration for both genders during the sex clip. Isoprene was significantly decreased during the sex clip compared to the sport clip for both genders (males:13%, females:15%, p ≤ 0.001). For women during the sex clip, the isoprene also had a significantly lower level compared to the anxiety clip (12%, p 0.01). For the 1-min data distribution shown in Fig. 2d, participants showed not only elevated isoprene concentration during the sport and anxiety clips but also larger variations among each other reflected by the length of the box representing 25–75% data distribution. Interestingly, isoprene level peaked at the beginning of the sex clip (the second minute) for both genders.

From Fig. 3, it can be seen that several other measured VOCs, C₁₀ H₁₄ O, C₇H₈O, C₈H₁₁ NO₂ and acetaldehyde for female participants, and C₈H₇N for male participants showed large relative changes during the sex clip compared to the anxiety clip and the sport clip. However, no significant difference was identified between the sex clip and the other two clips (Table S2) for these VOCs, indicating the mean values were largely affected by outliers. In such cases, the VOCs identified as having a distinguishable change during the sex clip might be specific to an individual rather than being representative of the whole group of participants. Among the female participants, one subject (No. 39) had substantial elevation of C₁₀ H₁₄ O, C₇H₈O, C₈H₁₁ NO₂ in her breath starting in the end of the sport clip until the end of the sex clip, which caused a significant deviation in terms of the mean values. While for acetaldehyde, subject No. 20 had a much higher relative increase compared to the first neutral clip in her breath than other participants, affecting the mean values. For male participants, two persons with a strong physiological response (No. 6 and 10) had substantial elevated breath levels of C₈H₇N, C₆H₆O and C₇H₈O during the sex clip.

Among all participants, several VOCs showed change according to the genital response of certain individual participants (1 female and 2 male participants). Although the data from those participants were considered as outliers in the previous section, as there were no experimental errors identified and the breath-genital related change occurred in different clip playing order, it is unlikely that those outliers coincidentally followed the genital response pattern. Furthermore, genital response and genital temperature data was rated highly in terms of quality for those individuals. Therefore, we may use these individuals to characterize the breath marker responses for each gender in real time.

Human influences have the potential to reduce the effectivity of communication in bees, adding further stress to struggling colonies, according to new analysis.

Scientists at the University of Bristol studying honeybees, bumblebees and stingless bees found that variations in communication strategies are explained by differences in the habitats that bees inhabit and differences in the social lifestyle such colony size and nesting habits.

The findings, published today in PNAS, reveal that anthropogenic changes, such as habitat conversion, climate change and the use of agrochemicals, are altering the world bees occupy, and it is becoming increasingly clearer that this affects communication both directly and indirectly; for example, by affecting food source availability, social interactions among nestmates and their cognitive functions.

Researchers have detected complex organic molecules in a galaxy more than 12 billion light-years away from Earth—the most distant galaxy in which these molecules are now known to exist. Thanks to the capabilities of the recently launched James Webb Space Telescope and careful analyses from the research team, a new study lends critical insight into the complex chemical interactions that occur in the first galaxies in the early universe.

University of Illinois Urbana-Champaign astronomy and physics professor Joaquin Vieira and graduate student Kedar Phadke collaborated with researchers at Texas A&M University and an international team of scientists to differentiate between infrared signals generated by some of the more massive and larger dust grains in the galaxy and those of the newly observed hydrocarbon molecules.

The study findings are published in the journal Nature.