Doubling Down on Known Protein Families

Shedding light on the diversity of microbial communities by looking at protein function within them.
Illustration Credit: Samantha Trieu/Berkeley Lab

Imagine researchers exploring a dark room with a flashlight, only able to clearly identify what falls within that single beam. When it comes to microbial communities, scientists have historically been unable to see beyond the beam – worse, they didn’t even know how big the room is.

A new study published online October 11, 2023 in Nature highlights the vast array of functional diversity of microbes through a novel approach to better understand microbial communities by looking at protein function within them. The work was led by a team of scientists at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab), and collaborators across multiple other research centers around the world.

“We’ve more than doubled the number of protein families known up until now, and identified many novel structure predictions,” said lead author on the paper Georgios Pavlopoulos, now a research director at the Biomedical Sciences Research Center Alexander Fleming. “This was a massive analysis of 1.3 billion proteins with massively parallel computations.”

Removal of magnetic spacecraft contamination within extraterrestrial samples easily carried out

PhD student Ji-In Jung, left, and Assistant Professor Sonia Tikoo examine a collection of lunar samples.
 Photo Credit: Harry Gregory

By demonstrating that spaceflight doesn’t adversely affect the magnetism of moon rocks, Stanford researchers underscore the exciting potential of studying the magnetic histories stored in these samples.

For decades, scientists have pondered the mystery of the moon’s ancient magnetism. Based on analyses of lunar samples, its now-deceased magnetic field may have been active for more than 1.5 billion years – give or take a billion years. Scientists believe it was generated like the Earth’s via a dynamo process, whereby the spinning and churning of conductive liquid metal within a rocky planet’s core generates a magnetic field. However, researchers have grappled with how such a small planetary body could have sustained a long-lived magnetic field. Some have even questioned the legitimacy of return samples that point to the existence of an ancient dynamo, suggesting magnetism may have been acquired via exposure to strong magnetic fields onboard spacecraft during the return mission or from plasmas produced by massive impacts on the moon.

Stanford University scientists have now demonstrated that the magnetism in lunar samples is not adversely altered by the spacecraft journey back to Earth or certain laboratory procedures, disproving one of the two major oppositions to the ancient dynamo theory. The findings, published in Geophysical Research Letters Oct. 11, bode well for research stemming from other sample-return missions from space, since any magnetic contamination acquired during flight or on Earth can likely be easily removed.

A step towards AI-based precision medicine

Mika Gustafsson and David Martínez hope that AI-based models could eventually be used in precision medicine to develop treatments and preventive strategies tailored to the individual. 
Photo Credit: Thor Balkhed

Artificial intelligence, AI, which finds patterns in complex biological data could eventually contribute to the development of individually tailored healthcare. Researchers at LiU have developed an AI-based method applicable to various medical and biological issues. Their models can for instance accurately estimate people’s chronological age and determine whether they have been smokers or not.

There are many factors that can affect which out of all our genes are used at any given point in time. Smoking, dietary habits and environmental pollution are some such factors. This regulation of gene activity can be likened to a power switch determining which genes are switched on or off, without altering the actual genes, and is called epigenetics.

Researchers at Linköping University (LiU) have used data with epigenetic information from more than 75,000 human samples to train a large number of AI neural network models. They hope that such AI-based models could eventually be used in precision medicine to develop treatments and preventive strategies tailored to the individual. Their models are of the autoencoder type, that self-organizes the information and finds interrelation patterns in the large amount of data.

Antigen testing can reduce, but not eliminate, the risk of COVID-19 clusters according to mathematical model

Illustration Credit: Kojima Kyoko

A research group has created a new model to calculate the probability of the occurrence of localized clusters caused by novel coronavirus infections. Led by Shingo Iwami at Nagoya University with collaborators in the United Kingdom and South Korea model, they revealed that screening of infected persons by antigen testing is effective in significantly reducing the probability of cluster occurrence. However, their findings also suggest that it is not sufficient to prevent clusters caused by highly infectious mutant strains, such as Omicron.  

With the availability of COVID-19 vaccines and population immunity, countries around the world are seeking to resume social activities while also trying to prevent the spread of infection. However, outbreaks of new strains of the coronavirus, associated with increased infectiousness and evasion of existing immunity, continue to be a threat. In several countries, new infections are increasing as the northern hemisphere enters the autumn and winter months.

Rivers may not recover from drought for years

Low water levels in rivers
Photo Credit: Manh Tuan Nguyen

Lack of rainfall is not the only measure of drought. New UC Riverside research shows that despite a series of storms, the impact of drought can persist in streams and rivers for up to 3.5 years.

There are two measures of drought in streams. One measure is the total water level, which is impacted by snowmelt and rainfall. Many researchers examine this measurement. Another measure is baseflow, which is the portion of streamflow fed by groundwater.

Fewer researchers examine baseflow droughts, and there was not previously an accurate way to measure them. Because baseflow is strongly tied to groundwater, and because the lack of it has significant impacts on water management and ecosystem services, the UCR team decided to examine baseflow more closely.

“People often just use rain as an indicator of drought because it’s easier to measure. But there are other kinds of drought that each have their own impacts,” said Hoori Ajami, corresponding study author and associate professor of groundwater hydrology at UCR. “We needed a new way to see how long it takes for one form of drought to become another form.”

Tens of thousands of endangered sharks and rays caught off Congo

Shark catch from one boat after a week at sea.
Photo Credit: Phil Doherty

Tens of thousands of endangered sharks and rays are caught by small-scale fisheries off the Republic of the Congo each year, new research shows.

Scientists surveyed fish brought ashore at Songolo, which is home to more than 60% of the country’s “artisanal” fishers (small boats, small engines, hand-hauled lines and nets).

In three years, the team – led by the University of Exeter in partnership with the Wildlife Conservation Society (WCS) Congo Program and the Republic of the Congo’s fisheries department – recorded more than 73,000 sharks and rays landed.

Most were juveniles, and 98% of individuals were of species listed as vulnerable, endangered or critically endangered on the IUCN Red List.

The researchers highlighted good news from the study: it shows the area is rich in sharks and rays, including two species previously thought to be locally absent – the African wedgefish and the smoothback angelshark.

Making hydropower plants more environmentally friendly

Dr. Melanie Müller, Dr. Joachim Pander and Prof. Jürgen Geist (from left) investigated the ecological impact of eight hydropower plants.
Photo Credit: Andreas Heddergott / TUM 

A research team from the Chair of Aquatic Systems Biology at the Technical University of Munich (TUM) has analyzed the harm caused to fish, changes in their behavior and the impact on the aquatic habitat at the shaft power plant in the Loisach, a river in Bavaria. This study was part of a large-scale research project looking into the ecological impact of different types of hydroelectric power plant. It has highlighted a number of factors that should be considered in the construction of future shaft power plants to minimize the environmental impact as far as possible.

Developed in recent years, the shaft power plant is a novel type of hydropower installation. A shaft housing the turbine and generator is installed in the riverbed upstream of a weir. Water flows into the shaft, drives the turbine and is then directed back into the river by the weir. A smaller proportion of the water flows over the shaft and the weir. The weir features openings, which are designed to allow fish to migrate downstream. This design aims to ensure that, unlike in other types of hydropower plants, only a small number of fish are harmed by traveling into the turbine. Conventional fish ladders also allow fish to migrate upstream.

Land use: produce more food and store more carbon at the same time

Optimized land use could still significantly increase yields taking climatic conditions into account, keeping land use within limits.
Photo Credit: Anita Bayer

Double food production, save water and at the same time increase carbon storage - that sounds paradoxical, but would be theoretically possible, at least according to the biophysical potential of the earth. However, a radical spatial reorganization in land use would be necessary. Researchers from the Karlsruhe Institute of Technology (KIT) and the Heidelberg Institute for Geoinformation Technology (HeiGIT), an affiliated institute of Heidelberg University, found this out. They have their results in the Proceedings of the National Academy of Sciences.

How people use the surface of the earth, including for the production of food, has changed a lot in the past centuries. Today, more and more people live on earth, more food is needed and food can be transported around the world in a short time. However, as the study shows, the historically grown systems of food production do not reflect the biophysical potential of our ecosystems. Food is therefore not produced where there is area, water and CO2- would be the most efficient in terms of technology. Instead, according to the authors of the study, forests for arable and pasture land continue to be cleared and fields in arid areas irrigated - measures that have a massive negative impact on water availability and carbon storage.

Illuminating the dance of RNA with ultrabright X-rays

Researchers demonstrated the ability to observe fine details, right down to angstrom-scale features in RNA at SLAC’s Linac Coherent Light Source (LCLS).   
Photo Credit: Olivier Bonin/SLAC National Accelerator Laboratory

DNA, RNA, and proteins are three pillars of molecular biology. While DNA holds genetic instructions and proteins put these plans to action, RNA serves as the messenger and interpreter. DNA is transcribed to RNA, which then decodes those instructions to synthesize proteins. But large portions of RNA don't proceed to produce proteins, with a vast majority remaining just as RNA. What these molecules do or why they exist in such a state is still not fully understood.

Now, scientists have developed a promising method to uncover RNA’s secrets. Using X-ray free-electron laser sources such as the Linac Coherent Light Source at the Department of Energy’s SLAC National Accelerator Laboratory, researchers can now observe fine details, right down to angstrom-scale features, in RNA that is freely dispersed in solution so that large scale structural changes can occur – just as they would in our bodies. Not only does this research shed light on RNA's behavior, but the techniques developed can also be applied to other biological molecules. The implications are far-reaching, from better understanding diseases to designing new therapeutics. The results were published last week in Science Advances.

New Study Points to New Possibilities for Treating Lung Cancer Patients

Illustration Credit: Rawpixel

Currently, researchers from different institutions in the world are testing a drug against obesity and diabetes, and now a Danish research team reports that the same substance has had a beneficial effect on mice with experimental lung cancer.

The substance is the short-chain fatty acid propionate, which is naturally produced by bacteria in our gut. From there, it is distributed throughout the body, and this new research study shows that treating mice with lung cancer with propionate can reduce the occurrence of metastases.

The study also demonstrates a role for propionate in increasing the effectiveness of Cisplatin, a commonly used drug for lung cancer patients. This was shown by lab experiments carried out in cancer cells derived from patients.