Personalized Gut Microbiome Analysis for Colorectal Cancer Classification with Explainable AI

Explainable AI offers a promising solution for finding links between diseases and certain species of gut bacteria, finds a research team at Tokyo Tech. Using a concept borrowed from game theory, the researchers developed a framework that reveals which bacterial species are closely associated with colorectal cancer in individual subjects, providing a more reliable way to find and characterize disease subgroups and identify biomarkers in the gut microbiome.

The gut microbiome comprises a complex population of different bacterial species that are essential to human health. In recent years, scientists across several fields have found that changes in the gut microbiome can be linked to a wide variety of diseases, notably colorectal cancer (CRC). Multiple studies have revealed that a higher abundance of certain bacteria, such as Fusobacterium nucleatum and Parvimonas micra, is typically associated with CRC progression.

Microscopic Syringes for Stressed Out Strep

Slide culture of a Streptomyces
Photo Credit: Public Domain 

Researchers from the University of Tsukuba find that Streptomyces phage tail-like particles are located intracellularly, unlike other contractile injections systems, and protect the bacterium against osmotic stress

Everyone can use a little stress relief, even bacteria. Now, researchers from Japan have found that a bacterial nanomachine with an unusual cellular location can protect cells from stressful environments.

In a study published recently in mSphere, researchers from the University of Tsukuba have revealed that a protein complex related to phage tail-like secretion systems is expressed intracellularly in a model Gram-positive organism and protects it from osmotic stress.

Many types of bacteria contain genes encoding phage tail-like nanomachines called contractile injection systems (CISs). These systems are essentially little syringes that the bacteria produce and release into their environment to contact other cells and inject their contents.

Hundreds of thousands of fungi are denied scientific names

Drying soil samples immediately upon collection under field conditions in Norway.
Photo Credit: Sten Anslan

Fungi that do not form fruiting bodies and that we can’t cultivate in the laboratory cannot be given scientific names. This has left them essentially ignored by science. In a study coordinated from the university of Gothenburg, researchers analyzed a large dataset of fungal DNA sequences from global soil samples and found that these intangible fungi seem to dominate the fungal kingdom.

The concept of dark biodiversity denotes species that are recovered through DNA sequencing of substrates such as soil and water – but where no individuals of those species have ever been observed.

It has been known for more than a decade that the fungal kingdom is home to dark biodiversity, but the magnitude of this dark fungal diversity has been the subject of much speculation. A new study from the University of Gothenburg, published in the journal MycoKeys, addresses the question based on 8 million fungal DNA sequences from global soil sampling. The study turns our understanding of the fungi on its head by showing that the fungal kingdom may be almost exclusively dark.

How a photon becomes four charge carriers

Illustration of exciton cleavage in the organic semiconductor pentacene consisting of five benzene rings. Instead of the usually two free charge carriers, four free charge carriers, represented by orange orbits, are generated by absorbing a photon in pentacene.
Photo Credit: Technical University of Berlin

Some materials convert photons into more charge carriers than would be expected. With an ultra-fast film, researchers have now been able to get an idea of this process. Physicists from the University of Würzburg were there.

Photovoltaics, i.e. The conversion of light into electricity is a key technology in the sustainable generation of energy. Since Max Planck and Albert Einstein, it has been known that both light and electricity occur in tiny, quantized packages: on the one hand in the form of photons and on the other hand as elementary charges in the form of electrons and holes.

Better solar cells thanks to exciton splitting

In the material of a conventional solar cell, the energy of a single photon is transferred to two free charges, nothing more. However, some molecular materials such as pentacene show an exception to this rule and instead convert a photon into four charges. This excitation doubling, which is referred to as exciton fission, is of great benefit for the highly efficient photovoltaics, in particular to improve the prevailing technologies based on silicon.

Ambrosia beetles can recognize their food fungi by their scents

Nest of a black stem borer (Xylosandrus germanus) in a hazelnut branch with adult females (large), a male (small) and individual larvae. The greyish fungal coating of the food fungus is visible on the walls of the tunnel system.
Photo Credit: Antonio Gugliuzzo

Experiments at the University of Freiburg provide evidence for the first time of the ability of ambrosia beetles to distinguish between food and harmful fungi

Certain ambrosia beetles species engage in active agriculture. As social communities, they breed and care for food fungi in the wood of trees and ensure that so-called weed fungi spread less. Researchers led by Prof. Dr. Peter Biedermann, professor of Forest Entomology and Forest Protection at the University of Freiburg, now demonstrates for the first time that ambrosia beetles can distinguish between different species of fungi by their scents. "The results can contribute to a better understanding of why beetles selectively colonize trees with conspecifics and how exactly their fungiculture works," says Biedermann. "In addition, the scents of the fungi could be used to develop attractants to control non-native ambrosia beetles."

Curtin researchers map genetic signature of precursor to liver cancer

Photo Credit: Julia Koblitz

Researchers at Curtin University have identified the genetic signature of pre-malignant liver cells, offering potentially significant implications for the almost 3,000 Australians diagnosed with the deadly cancer each year.

The study, published in the prestigious journal Cell Genomics, found that quantifying pre-malignant liver cells in patients with liver disease could help determine their future risk of developing liver cancer.

First author Dr Rodrigo Carlessi, from the Curtin Medical School and the Curtin Health Innovation Research Institute, said the discovery had the potential to save lives by changing how chronic liver disease patients are staged and monitored based on their cancer risk.

“The research used cutting-edge technology to identify the molecular fingerprint of thousands of genes, one cell at a time,” Dr Carlessi said.

“During this process, we discovered the genetic signature and its diagnostic value, which was subsequently confirmed in several hundred individual patient liver samples.

Private pools are a major cause of water scarcity

The researchers found that city elites over-consume water for their own leisure activities, such as filling their pools, watering their gardens or washing their cars.
Photo Credit: Joe Ciciarelli

Rich elites with large pools and well-kept lawns deprive poorer groups of basic access to water in cities around the world. Social inequality is a major cause of urban water scarcity than environmental factors such as climate change or urban population growth. This shows a new study, led by Uppsala University and now published in Nature Sustainability.

"Our study shows that the only way to preserve available water resources is to change privileged lifestyles, limit the amount of water used for recreational purposes and distribute income and water resources more evenly. Future strategies for secure water supply and drought resistance must be more proactive and be able to identify and counteract long-term inequality and unsustainable patterns that create the type of water crisis in cities we saw in Cape Town," says Dr. Elisa Savelli at Uppsala University who led the study.

The study was conducted with colleagues at Vrije Universiteit Amsterdam in the Netherlands and the University of Manchester and the University of Reading in the United Kingdom. They have developed a model that analyzes how water is used by households in Cape Town, which in turn gives an understanding of how different classes of society consume water. They found that city elites over-consume water for their own leisure activities, such as filling their pools, watering their gardens or washing their cars.

How rainforest fish adapt to habitat

Eastern rainbowfish from the Wet Tropics region of Australia.
Photo Credit: Keith Martin.

The future of freshwater fish species in Australia’s tropical rainforest areas, including the Daintree and Mosman Gorge, will increasingly be subject to the vagaries of climatic and other changes.

Flinders University molecular ecology researchers have led an in-depth study of the colorful eastern rainbowfish for clues about how their populations have adapted to local conditions in the creeks and rivers of the wet tropical areas of Far North Queensland.

Their study, published in the Nature journal Heredity, provides insights into what drives genetic diversity in Australian eastern rainbowfish (Melanotaenia splendida splendida) – highlighting the ways their biodiversity may be affected, and conserved, particularly with any increase in climate change rates.

“Tropical rainforests are home to a staggering variety of plants and animals, ranking them among Earth’s greatest biodiversity hotspots,” says postdoctoral research fellow Dr Katie Gates, first author on the new paper.

Benefits of “Zombie” Cells: Senescent Cells Aid Regeneration in Salamanders

The salamander species studied by the Yun group: a red spotted newt Notophthalmus viridescens.
Photo Credit: Dr. Maximina Yun

Scientists show that so-called senescent cells, i.e., cells that have permanently stopped dividing, boost production of new muscle cells to enhance regeneration of lost limbs in salamanders.

Senescent cells, often referred to as "zombie" cells, have long been associated with aging and disease. However, a new study from the Center for Regenerative Therapies Dresden (CRTD) at TU Dresden adds to a growing body of evidence that not all senescent cells are harmful. The study led by Dr. Maximina Yun shows that these cells can play a beneficial role in regeneration. Her team found that senescent cells boost muscle formation in regenerating salamander limbs. Their findings reveal a new role for senescent cells and expand the understanding of the early events in the regeneration process. The research was published in the journal Aging Cell.

Senescent cells are cells that have permanently stopped dividing in response to cellular stress but have not died. As organisms age, the number of senescent cells in the body increases. This accumulation is currently considered one of the hallmarks of aging and has been linked to a variety of diseases, including cancer. However, the true nature of these cells may be more complex and context-dependent.

Apes may have evolved upright stature for leaves, not fruit, in open woodland habitats

Artistic rendering of the open woodland habitat reconstruction at Moroto II with Morotopithecus bishopi vertically climbing with infant on back and juvenile below. Active volcano (Mount Moroto) is in background. Fossil relative of an elephant (Prodeinotherium) is foraging in center back.
Illustration Credit: Corbin Rainbolt

Anthropologists have long thought that our ape ancestors evolved an upright torso in order to pick fruit in forests, but new research from the University of Michigan suggests a life in open woodlands and a diet that included leaves drove apes’ upright stature.

The findings shed light on ape origins and push back the origin of grassy woodlands from between 7 million and 10 million years ago to 21 million years ago in equatorial Africa, during the Early Miocene.

Fruit grows on the spindly peripheries of trees. To reach it, large apes need to distribute their weight on branches stemming from the trunk, then reach out with their hands toward their prize. This is much easier if an ape is upright because it can more easily grab onto different branches with its hands and feet. If its back is horizontal, then its hands and feet are generally underneath the body, making it much harder to move outward to the smaller branches of a tree—especially if the ape is large bodied.