Getting dynamic information from static snapshots

In a new paper, UChicago researchers use machine learning insights to provide a better way for cancer and immunology researchers to study transcriptional dynamics of genes and cell-state transitions

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UNIVERSITY OF CHICAGO

 

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PART OF AN INTERDISCIPLINARY UNIVERSITY OF CHICAGO TEAM BEHIND A NEW METHOD OF USING STATIC DATA FROM SINGLE-CELL RNA SEQUENCING TO STUDY HOW CELLS AND GENES CHANGE OVER TIME. FROM LEFT, BIOPHYSICS GRADUATE STUDENT HANNA HIEROMNIMON, PRITZKER SCHOOL OF MOLECULAR ENGINEERING GRADUATE STUDENT JOEY FEDERICO, COMPUTER SCIENCE GRADUATE STUDENT RYAN ROBINETT, PME ASST. PROF. SAMANTHA RIESENFELD, CHEMISTRY GRADUATE STUDENT AND PAPER FIRST AUTHOR CHENG FRANK GAO, CHEMISTRY GRADUATE STUDENT JOSEPH SIFAKIS AND BIOPHYSICS GRADUATE STUDENT HOPE ANDERSON.

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CREDIT: PHOTO BY LORENZO ORECCHIA

Imagine predicting the exact finishing order of the Kentucky Derby from a still photograph taken 10 seconds into the race.

That challenge pales in comparison to what researchers face when using single-cell RNA-sequencing (scRNA-seq) to study how embryos develop, cells differentiate, cancers form, and the immune system reacts.

In a paper published today in Proceedings of the National Academy of Sciences, researchers from the UChicago Pritzker School of Molecular Engineering and the Chemistry Department have created TopicVelo, a powerful new method of using the static snapshots from scRNA-seq to study how cells and genes change over time.

The team took an interdisciplinary, collaborative approach, incorporating concepts from classical machine learning, computational biology, and chemistry.

“In terms of unsupervised machine learning, we use a very simple, well-established idea. And in terms of the transcriptional model we use, it's also a very simple, old idea. But when you put them together, they do something more powerful than you might expect,” said PME Assistant Professor of Molecular Engineering and Medicine Samantha Riesenfeld, who wrote the paper with Chemistry Department Prof. Suriyanarayanan Vaikuntanathan and their joint student, UChicago Chemistry PhD candidate Cheng Frank Gao.

The trouble with pseudotime

Researchers use scRNA-seq to get measurements that are powerful and detailed, but by nature are static.

“We developed TopicVelo to infer cell-state transitions from scRNA-seq data,” Riesenfeld said. “It's hard to do that from this kind of data because scRNA-seq is destructive. When you measure the cell this way, you destroy the cell.”

This leaves researchers a snapshot of the moment the cell was measured/destroyed. While scRNA-seq gives the best available transcriptome-wide snapshot, the information many researchers need, however, is how the cells transition over time. They need to know how a cell becomes cancerous or how a particular gene program behaves during an immune response.

To help figure out dynamic processes from a static snapshot, researchers traditionally use what’s called “pseudotime.” It’s impossible to watch an individual cell or gene’s expression change and grow in a still image, but that image also captured other cells and genes of the same type that might be a little further on in the same process. If the scientists connect the dots correctly, they can gain powerful insights into how the process looks over time.

Connecting those dots is difficult guesswork, based on the assumption that similar-looking cells are just at different points along the same path. Biology is much more complicated, with false starts, stops, bursts, and multiple chemical forces tugging on each gene.

Instead of traditional pseudotime approaches, which look at the expression similarity among the transcriptional profiles of cells, RNA velocity approaches look at the dynamics of transcription, splicing and degradation of the mRNA within those cells.

It’s a promising but early technology.

“The persistent gap between the promise and reality of RNA velocity has largely restricted its application,” the authors wrote in the paper.

To bridge this gap, TopicVelo puts aside deterministic models, embracing—and gleaning insights from—a far more difficult stochastic model that reflects biology’s inescapable randomness.

“Cells, when you think about them, are intrinsically random,” said Gao, the first author on the paper. “You can have twins or genetically identical cells that will grow up to be very different. TopicVelo introduces the use of a stochastic model. We're able to better capture the underlying biophysics in the transcription processes that are important for mRNA transcription.”

Machine learning shows the way

The team also realized that another assumption limits standard RNA velocity. “Most methods assume that all cells are basically expressing the same big gene program, but you can imagine that cells have to do different kinds of processes simultaneously, to varying degrees,” Riesenfeld said. Disentangling these processes is a challenge.

Probabilistic topic modeling—a machine learning tool traditionally used to identify themes from written documents—provided the UChicago team with a strategy. TopicVelo groups scRNA-seq data not by the types of cell or gene, but by the processes those cells and genes are involved in. The processes are inferred from the data, rather than imposed by external knowledge.

“If you look at a science magazine, it will be organized along topics like ‘physics,’ ‘chemistry’ and ‘astrophysics,’ these kinds of things,” Gao said. “We applied this organizing principle to single-cell RNA-sequencing data. So now, we can organize our data by topics, like ‘ribosomal synthesis,’ ‘differentiation,’ ‘immune response,’ and ‘cell cycle’. And we can fit stochastic transcriptional models specific to each process.”

After TopicVelo disentangles this kludge of processes and organizes them by topic, it applies topic weights back onto the cells, to account for what percentage of each cell’s transcriptional profile is involved in which activity.

According to Riesenfeld, “This approach helps us look at the dynamics of different processes and understand their importance in different cells. And that's especially useful when there are branch points, or when a cell is pulled in different directions.”

The results of combining the stochastic model with the topic model are striking. For example, TopicVelo was able to reconstruct trajectories that previously required special experimental techniques to recover. These improvements greatly broaden potential applications.

Gao compared the paper’s findings to the paper itself—the product of many areas of study and expertise.

“At PME, if you have a chemistry project, chances are there’s a physics or engineering student working on it,” he said. “It’s never just chemistry.”

Citation: “Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems,” Gao et al., Proceedings of the National Academy of Sciences, April 26, 2024. DOI: 10.1073/pnas.2306901121

Funding: This work was supported by the NIH NIGMS Award R35GM147400.

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JOURNAL

Proceedings of the National Academy of Sciences

DOI

10.1073/pnas.2306901121 

METHOD OF RESEARCH

Observational study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Dissection and integration of bursty transcriptional dynamics for complex systems

ARTICLE PUBLICATION DATE

26-Apr-2024

 

Component of keto diet plus immunotherapy may reduce prostate cancer

UNIVERSITY OF NOTRE DAME

 

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XIN LU, THE JOHN M. AND MARY JO BOLER COLLEGIATE ASSOCIATE PROFESSOR IN THE DEPARTMENT OF BIOLOGICAL SCIENCES AT THE UNIVERSITY OF NOTRE DAME

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CREDIT: PHOTO BY BARBARA JOHNSTON/UNIVERSITY OF NOTRE DAME

Adding a pre-ketone supplement — a component of a high-fat, low-carb ketogenic diet — to a type of cancer therapy in a laboratory setting was highly effective for treating prostate cancer, researchers from the University of Notre Dame found.

Recently published online in the journal Cancer Research, the study from Xin Lu, the John M. and Mary Jo Boler Collegiate Associate Professor in the Department of Biological Sciences, and collaborators tackled a problem oncologists have battled: Prostate cancer is resistant to a type of immunotherapy called immune checkpoint blockade (ICB) therapy. ICB therapy blocks certain proteins from binding with other proteins and paves the way for our body’s fighter cells, T cells, to kill the cancer.

“Prostate cancer is the most common cancer for American men, and immunotherapy has been really influential in some other cancers, like melanoma or lung cancer, but it hasn’t been working almost at all for prostate cancer,” said Lu, who is affiliated with the Boler-Parseghian Center for Rare and Neglected Diseases. Adding a dietary supplement might overcome this resistance, the lead author in the study, Sean Murphy, suggested.

Murphy, a ’24 alumnus who was a doctoral student in Lu’s lab, had been following a keto diet himself. Knowing that cancer cells feed off of sugar, he decided that depriving mouse models of carbohydrates — a key component of the keto diet — might prevent cancer growth.

He divided the models into different groups: immunotherapy alone, ketogenic diet alone, a pre-ketone supplement alone, the ketogenic diet with the immunotherapy, the supplement with the immunotherapy, and the control. While the immunotherapy alone had almost no effect on the tumors (just like what happens to most patients with prostate cancer), both the ketogenic diet with the immunotherapy and the pre-ketone supplement with the immunotherapy reduced the cancer and extended the lives of the mouse models.

The supplement with the immunotherapy worked best.

“It turned out this combination worked really well,” Lu said. “It made the tumor become very sensitive to the immunotherapy, with 23 percent of the mice cured — they were tumor-free; in the rest, the tumors were shrinking really dramatically.”

The evidence points to the possibility that a supplement providing ketones, which are what is produced in the body when people eat a keto diet, might prevent the prostate cancer cells from being resistant to immunotherapy. This may lead to future clinical studies that examine how ketogenic diets or keto supplements could enhance cancer therapy.

While keto diets allow for minimal carbohydrates, the success of this study is not about the lack of carbohydrates, Murphy and Lu stressed. It is about the presence of the ketone body, a substance produced by the liver and used as an energy source when glucose is not available. The ketones disrupt the cycle of the cancer cells, allowing the T cells to do their job to destroy them.

The discovery was also exciting on a molecular level, Lu said. Any type of dietary study can suffer from the potential issue of causation: Are the results from the diet or other changes made because of the diet? But Lu and his collaborators confirmed their results using single-cell RNA sequencing, which examines the gene expression of single cells within the tumor.

“We found that this combination of the supplement and the immunotherapy reprogrammed the whole immune profile of the tumors and recruited many T cells into the tumors to kill prostate cancer cells,” Lu said.

The successful therapy also reduced the number of a type of immune cell called neutrophils. Once in the tumor microenvironment, neutrophils’ natural properties become greatly distorted, and they become largely responsible for inhibiting T cell activities and allowing more tumor progression. Dysregulation of neutrophils is also associated with many other diseases.

“With the main ketone body depleting neutrophils, it opens the door for investigating the effects of the keto diet and the ketone supplement on diseases ranging from inflammatory bowel disease to arthritis,” Murphy said.

Lu agreed.

“What’s exciting is that we’re getting closer to the mechanism, backed up by genetic models and what we’re seeing in the tumors themselves, of why this works,” he said.

Co-authors include Sharif Rahmy, Dailin Gan, Guoqiang Liu, Yini Zhu, Maxim Manyak, Loan Duong, Jianping He, James H. Schofield, Zachary T. Schafer, Jun Li and Xuemin Lu, all from the University of Notre Dame.

The research was supported by a grant from the American Institute for Cancer Research, funding from the National Institutes of Health and a core facility grant from Indiana Clinical and Translational Sciences Institute. Other support included the Department of Defense and the Boler Family Foundation at the University of Notre Dame. A provisional patent application has been filed based on this study by the IDEA Center at Notre Dame.

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JOURNAL

Cancer Research

DOI

10.1158/0008-5472.CAN-23-2742 

ARTICLE TITLE

Ketogenic diet alters the epigenetic and immune landscape of prostate cancer to overcome resistance to immune checkpoint blockade therapy

 

Computer scientists unveil novel attacks on cybersecurity

Intel and AMD will issue security alerts today based on the findings

Reports and Proceedings

UNIVERSITY OF CALIFORNIA - SAN DIEGO

 

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THE NEW PAPER, "PATHFINDER: HIGH-RESOLUTION CONTROL-FLOW ATTACKS EXPLOITING THE CONDITIONAL BRANCH PREDICTOR,"  DETAILS TWO NOVEL ATTACKS THAT COULD COMPROMISE THE BILLIONS OF INTEL PROCESSORS IN USE. 

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CREDIT: HOSEIN YAVARZADEH

Researchers have found two novel types of attacks that target the conditional branch predictor found in high-end Intel processors, which could be exploited to compromise billions of processors currently in use. 

The multi-university and industry research team led by computer scientists at University of California San Diego will present their work at the 2024 ACM ASPLOS Conference that begins tomorrow. The paper, "Pathfinder: High-Resolution Control-Flow Attacks Exploiting the Conditional Branch Predictor," is based on findings from scientists from UC San Diego, Purdue University, Georgia Tech, the University of North Carolina Chapel Hill and Google.

They discover a unique attack that is the first to target a feature in the branch predictor called the Path History Register, which tracks both branch order and branch addresses. As a result, more information with more precision is exposed than with prior attacks that lacked insight into the exact structure of the branch predictor.

Their research has resulted in Intel and Advanced Micro Devices (AMD) addressing the concerns raised by the researchers and advising users about the security issues. Today, Intel is set to issue a Security Announcement, while AMD will release a Security Bulletin.

In software, frequent branching occurs as programs navigate different paths based on varying data values. The direction of these branches, whether "taken" or "not taken," provides crucial insights into the executed program data. Given the significant impact of branches on modern processor performance, a crucial optimization known as the "branch predictor" is employed. This predictor anticipates future branch outcomes by referencing past histories stored within prediction tables. Previous attacks have exploited this mechanism by analyzing entries in these tables to discern recent branch tendencies at specific addresses.

In this new study, researchers leverage modern predictors' utilization of a Path History Register (PHR) to index prediction tables. The PHR records the addresses and precise order of the last 194 taken branches in recent Intel architectures. With innovative techniques for capturing the PHR, the researchers demonstrate the ability to not only capture the most recent outcomes but also every branch outcome in sequential order. Remarkably, they uncover the global ordering of all branches. Despite the PHR typically retaining the most recent 194 branches, the researchers present an advanced technique to recover a significantly longer history.

“We successfully captured sequences of tens of thousands of branches in precise order, utilizing this method to leak secret images during processing by the widely used image library, libjpeg,” said Hosein Yavarzadeh, a UC San Diego Computer Science and Engineering Department PhD student and lead author of the paper.

The researchers also introduce an exceptionally precise Spectre-style poisoning attack, enabling attackers to induce intricate patterns of branch mispredictions within victim code. “This manipulation leads the victim to execute unintended code paths, inadvertently exposing its confidential data,” said UC San Diego computer science Professor Dean Tullsen.

"While prior attacks could misdirect a single branch or the first instance of a branch executed multiple times, we now have such precise control that we could misdirect the 732nd instance of a branch taken thousands of times,” said Tullsen.

The team presents a proof-of-concept where they force an encryption algorithm to transiently exit earlier, resulting in the exposure of reduced-round ciphertext. Through this demonstration, they illustrate the ability to extract the secret AES encryption key.

"Pathfinder can reveal the outcome of almost any branch in almost any victim program, making it the most precise and powerful microarchitectural control-flow extraction attack that we have seen so far," said Kazem Taram, an assistant professor of computer science at Purdue University and a UC San Diego computer science PhD graduate. 

In addition to Dean Tullsen and Hosein Yavarzadeh, other UC San Diego coauthors are. Archit Agarwal and Deian Stefan. Other coauthors include Christina Garman and Kazem Taram, Purdue University; Daniel Moghimi, Google; Daniel Genkin, Georgia Tech; Max Christman and Andrew Kwong, University of North Carolina Chapel Hill. 

This work was partially supported by the Air Force Office of Scientific Research (FA9550- 20-1-0425); the Defense Advanced Research Projects Agency (W912CG-23-C-0022 and HR00112390029); the National Science Foundation (CNS-2155235, CNS-1954712, and CAREER CNS-2048262); the Alfred P. Sloan Research Fellowship; and gifts from Intel, Qualcomm, and Cisco.

Responsible disclosure 

Researchers communicated the security findings outlined in the paper to both Intel and AMD in November 2023. Intel has informed other affected hardware/software vendors about the issues. Both Intel and AMD plan to address the concerns raised in the paper today through a Security Announcement and a Security Bulletin (AMD-SB-7015), respectively. The findings have been shared with the Vulnerability Information and Coordination Environment (VINCE), Case VU#157097: Class of Attack Primitives Enable Data Exposure on High End Intel CPUs.

 

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ARTICLE TITLE

Pathfinder: High-Resolution Control-Flow Attacks Exploiting the Conditional Branch Predictor

ARTICLE PUBLICATION DATE

27-Apr-2024

 

Ancient Maya blessed their ballcourts

Researchers find evidence of ceremonial offerings beneath ballcourt in Mexico

UNIVERSITY OF CINCINNATI

 

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UNIVERSITY OF CINCINNATI PROFESSOR DAVID LENTZ HOLDS UP A REPRODUCTION TILE FEATURING ANCIENT MAYA GLYPHS. RESEARCHERS DISCOVERED EVIDENCE OF CEREMONIAL OFFERINGS AT THE SITE OF AN ANCIENT MAYA BALLCOURT IN YAXNOHCAH, MEXICO.

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CREDIT: ANDREW HIGLEY

For sports fans, places like Fenway Park, Wembley Stadium or Wimbledon's Centre Court are practically hallowed ground.

Archaeologists at the University of Cincinnati found evidence of similar reverence at ballcourts built by the ancient Maya in Mexico.

Using environmental DNA analysis, researchers were able to identify a collection of plants used in ceremonial rituals in the ancient Maya city of Yaxnohcah. The plants, known for their religious associations and medicinal properties, were discovered beneath a plaza floor upon which a ballcourt was built.

Researchers said the ancient Maya likely made a ceremonial offering during the ballcourt’s construction.

“When they erected a new building, they asked the goodwill of the gods to protect the people inhabiting it,” UC Professor David Lentz said. “Some people call it an ensouling ritual, to get a blessing from and appease the gods.”

The study was published in the journal PLOS ONE.

The research was carried out through Mexico's National Institute of Anthropology and History in collaboration with researchers from the University of Calgary, the Autonomous University of Campeche and the National Autonomous University of Mexico.

Researchers from 2016 to 2022 worked at Yaxnohcah in Campeche about 9 miles north of the border of Guatemala, where they excavated a small area of a ballcourt.

The ancient Maya played several ball games, including pok-a-tok, which has rules similar to soccer and basketball. Players tried to get a ball through a ring or hoop on a wall.

UC Professor Emeritus Nicholas Dunning said when buildings were expanded or repurposed, as with the ballcourt, the ancient Maya made offerings to bless the site. Archaeologists sometimes find ceramics or jewelry in these offerings along with plants of cultural significance.

“We have known for years from ethnohistorical sources that the Maya also used perishable materials in these offerings, but it is almost impossible to find them archaeologically, which is what makes this discovery using eDNA so extraordinary,” Dunning said.

Ancient plant remains are rarely discovered in tropical climates, where they decompose quickly. But using environmental DNA, researchers were able to identify several types known for their ritual significance.

They discovered evidence of a morning glory called xtabentun, known for its hallucinogenic properties, lancewood, chili peppers and jool, the leaves of which were used to wrap ceremonial offerings.

Botanist and UC Associate Professor Eric Tepe said finding evidence of these plants together in the same tiny sediment sample is telling. He has studied modern plants in the same forests once traveled by the ancient Maya.

“I think the fact that these four plants which have a known cultural importance to the Maya were found in a concentrated sample tells us it was an intentional and purposeful collection under this platform,” Tepe said.

Researchers noted the challenge of trying to interpret a collection of plants through the opaque lens of 2,000 years of prehistory. But Lentz said the findings help add to the story of this sophisticated culture.

Researchers believe the ancient Maya devised water filtration systems and employed conservation-minded forestry practices. But they were helpless against years-long droughts and also are believed to have deforested vast tracts for agriculture.

“We see the yin and yang of human existence in the ancient Maya,” Lentz said. “To me that’s why they’re so fascinating.”

UNIVERSITY OF CINCINNATI PROFESSOR DAVID LENTZ, PICTURED HERE AT TIKAL, DISCOVERED EVIDENCE OF CEREMONIAL OFFERINGS AT THE SITE OF AN ANCIENT MAYA BALLCOURT IN YAXNOHCAH, MEXICO.

CREDIT

Liwy Grazioso Sierra

JOURNAL

PLoS ONE

DOI

10.1371/journal.pone.0301497 

METHOD OF RESEARCH

Imaging analysis

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Psychoactive and other ceremonial plants from a 2,000-year-old Maya ritual deposit at Yaxnohcah, Mexico

ARTICLE PUBLICATION DATE

26-Apr-2024

 

CRISPR is promising to tackle antimicrobial resistance, but remember bacteria can fight back

Experts looking to use the Nobel winning technology to target resistance genes and make bacteria sensitive to first line antibiotics again; but the bacteria have ways to fight back

EUROPEAN SOCIETY OF CLINICAL MICROBIOLOGY AND INFECTIOUS DISEASES

In the second new research review on this subject, Assistant Prof. Ibrahim Bitar, Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University in Prague, Plzen, Czech Republic, will give an overview of the molecular biology of CRISPR technology in explaining how it can used to tackle antimicrobial resistance.

Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR associated genes (cas) are widespread in the genome of many bacteria and are a defence mechanism against foreign invaders such as plasmids and viruses.  The CRISPR arrays are composed of a repeated array of short sequences, each originating from and exactly matching a nucleic acid sequence that once invaded the host.

Accompanying CRISPR sequences, there are 4-10 CRISPR-associated genes (cas), which are highly conserved and encode the Cas proteins. Cas proteins conduct adaptive immunity in prokaryotes (bacteria) based on immunological memories stored in the CRISPR array. The CRISPR/Cas system integrates a small piece of foreign DNA from invaders such as plasmids and viruses into their direct repeat sequences and will recognise and degrade the same external DNA elements during future invasions.

As the CRISPR/Cas systems integrate DNA from invading pathogens in chronical order, genotyping can be used to trace the clonality and the origin of the isolates and define them as a population of strains that were subjected to the same environmental conditions including geographic location (region) and community/hospital settings and eventually further extended to track pathogenic bacteria around human society.

CRISPR/Cas systems can also be employed for developing antimicrobial agents: introduction of self-targeting crRNAs will effectively and selectively kill target bacterial populations. Due to the shortage of available effective antimicrobial agents in treating multidrug-resistant (MDR) infections, researchers started to search for alternative methods to fight MDR infections rather than going through the process of developing new antimicrobial agents which can go on for decades. As a result, the concept of CRISPR/Cas-based selective antimicrobials was first developed and demonstrated in 2014. Vectors coding Cas9 and guide RNAs targeting genomic loci of a specific bacterial strain/species can be delivered to the target strain via bacteriophages or conjugative bacterial strains. In theory, delivery of the engineered CRISPR/Cas systems specifically eliminates target strains from the bacterial population, yet it is not that simple.

While these systems can seem a target for manipulation/intervention, all bacteria are regulated by multiple pathways to ensure the bacteria retains control over the process. Therefore, there remain several major challenges in using this system as an antimicrobial agent.

Most methods require delivery of the re-sensitised system by conjugation; the vector is carried by a non-virulent lab strain bacteria that is supposed to go and share the vector/plasmid through conjugation. The conjugation process is a natural process that the bacteria do which results in sharing plasmids among each other (even with other species). The percentage of conjugated (successfully delivered) bacteria in the total bacterial population is critical to the re-sensitised efficiency. This process is governed by several complicated pathways.

Bacteria also possess built-in anti-CRISPR systems, that can repair any damage caused by CRISPR-Cas systems. Defence systems that the bacteria uses to protect itself from foreign DNA often co-localise within defence islands (genomic segments that contain genes with similar function in protecting the host from invaders)  in bacterial genomes; for example: acr (a gene that acts, with other similar variants, as a repressor of plasmid conjugative systems) often cluster with antagonists of other host defence functions (e.g., anti-restriction modification systems) and experts hypothesise that MGEs (mobile genetic elements) organise their counter defence strategies in “anti-defence” islands.

Assistant Professor Bitar concludes: “In summary, this method seems very promising as an alternative way of fighting antimicrobial resistance. The method uses the concept of re-sensitising the bacteria in order to make use of already available antibiotics – in other words, removing their resistance and making them vulnerable again to first-line antibiotics. Nevertheless, the bacterial pathways are always complicated and such systems are always heavily regulated by multiple pathways. These regulated pathways must be studied in depth in order to avoid selective pressure favoring anti-CRISPR systems activation, hence prevalence of resistance in a more aggressive manner.”

 

Experts developing way to harness Nobel Prize winning CRISPR technology to deal with antimicrobial resistance (AMR)

EUROPEAN SOCIETY OF CLINICAL MICROBIOLOGY AND INFECTIOUS DISEASES

Antimicrobial resistance (AMR) is continuing to increase globally, with rates of AMR in most pathogens increasing and threatening a future in which every day medical procedures may no longer be possible and infections thought long dealt with could kill regularly again. As such, new tools to battle AMR are vitally needed.

In a new research review at this year’s ESCMID Global Congress (formerly ECCMID – Barcelona 27-30 April) shows how the latest CRISPR-Cas gene editing technology can be used to help modify and attack AMR bacteria. The presentation is by Dr Rodrigo Ibarra-Chávez, Department of Biology, University of Copenhagen, Denmark.

CRISPR-Cas gene editing technology is a groundbreaking method in molecular biology that allows for precise alterations to the genomes of living organisms. This revolutionary technique, which brought its inventors, Jennifer Doudna and Emmanuelle Charpentier, the Nobel Prize in Chemistry in 2020, enables scientists to accurately target and modify specific segments of an organism's DNA (genetic code). Functioning like molecular ‘scissors’ with the guidance of guide RNA (gRNA), CRISPR-Cas can cut the DNA at designated spots. This action facilitates either the deletion of unwanted genes or the introduction of new genetic material into an organism's cells, paving the way for advanced therapies.

Dr Ibarra-Chávez says: “Fighting fire with fire, we are using CRISPR-Cas systems (a bacterial immunity system) as an innovative strategy to induce bacterial cell-death or interfere with antibiotic resistance expression – both hold promise as novel sequence-specific targeted ‘antimicrobials’.”

One line of their work involves creating guided systems against antimicrobial resistance genes could treat infections and prevent dissemination of resistance genes.

Mobile genetic elements (MGEs) are parts of the bacterial genome that can move about to other host cells or also transfer to another species. These elements drive bacterial evolution via horizontal gene transfer.  Dr Ibarra-Chávez explains how repurposing mobile genetic elements (MGEs) and choosing the delivery mechanism involved in the antimicrobial strategy is important for reaching the target bacterium.

A phage is a virus that infects bacteria, and it is also considered MGE, as some can remain dormant in the host cell and transfer vertically. The MGEs his team is using are phage satellites, which are parasites of phages. He says: “These ‘phage satellites’ hijack parts of the viral particles of phages to ensure their transfer to host cells. In contrast to phages, satellites can infect bacteria without destroying them, offering a step-change over existing methods involving phages and thus developing an arsenal of viral particles that are safe to use for applications such as detection and modification via gene delivery. Phage particles are very stable and easy to transport and apply in medical settings. It is our task to develop safe guidelines for their application and understand the resistance mechanisms that bacteria can develop.”

Bacteria can evolve mechanisms to evade the action of the CRISPR-Cas system and delivery vectors can be vulnerable to anti-MGE defences. Thus Dr Ibarra-Chávez’s team and others are developing the use of anti-CRISPRs and defence inhibitors in the delivery payloads to counter these defences, to enable the CRISPR to arrive and attack the AMR genes in the cell.

Dr Ibarra-Chávez will also discuss how combination strategies employing CRISPR-Cas systems could promote antibiotic susceptibility in a target bacterial population. Phages have a particular selective pressure on AMR cells, which can improve the effect of some antibiotics. Similarly, using CRISPR-Cas in combination with phages and/or antibiotics, it is possible to suppress the mechanisms of resistance that infectious bacteria may develop by targeting such virulence/resistance genes, making these therapies safer.

He explains: “Bacteria are particularly good at adapting and becoming resistance. I believe we need to be cautious and try using combinatorial strategies to avoid the development of resistance, while monitoring and creating guidelines of new technologies.”

Dr Ibarra-Chávez has primarily focused on tackling resistance in Staphylococcus aureus and Escherichia coli. Now, in collaboration with Prof. Martha Clokie and Prof. Thomas Sicheritz-Pontén, his team will treat group A Streptococci necrotising soft tissue infection (flesh eating bacteria) using the combination approaches described above.

 

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ARTICLE PUBLICATION DATE

26-Apr-2024

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Food insecurity is significant among inhabitants of the region affected by the Belo Monte dam in Brazil

A study of 500 households in Altamira, a city near the dam in Pará state, showed that 61% experienced food insecurity

FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO

 

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A PARTIAL VIEW OF THE CITY OF ALTAMIRA, PARÁ, IN AUGUST 2022, WITH THE XINGU RIVER IN THE BACKGROUND 

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CREDIT: IGOR CAVALLINI JOHANSEN

The social and environmental impact of the Belo Monte dam and hydroelectric power plant in Pará state, Brazil, has been called a “disaster” by researchers, environmentalists and several media outlets. The damage has again been highlighted recently in an inspection report issued by the Brazilian Institute for the Environment and Renewable Natural Resources (IBAMA), an agency of the Ministry for the Environment and Climate Change. The inspectors detected silting and erosion of the Xingu River, obstacles to river navigation, a significant increase in tree mortality, and the impossibility of reproduction for several fish species, as well as disruptions to the way of life of Indigenous and river-dwelling communities.

A new study conducted with FAPESP’s support focuses specifically on food insecurity in Altamira, which is the city with the largest population in the region and has been dramatically affected by the construction of Belo Monte. Because of the megaproject, Altamira became a hub for the distribution of goods, services and the logistics essential to the construction process, with a significant impact on its population. 

Construction took place between 2011 and 2015, causing the city’s population to grow without adequate planning to assure the provision of services to residents and migrants looking for work. The shock made Altamira one of Brazil’s most violent cities. Although its population has declined since the dam was completed, the 2022 census recorded 126,279 inhabitants, 27.46% more than in 2010, when the previous census was conducted. This growth rate compares with 6.46% for Brazil’s total population growth in the same period.

The study, published in the International Journal of Environmental Research and Public Health, shows that 61% of Altamira’s households experienced some level of food insecurity and malnutrition in 2022, when the data was collected. 

“We conducted the survey in July 2022, seven years after construction ended, visiting 500 households selected as representative of the city’s socioeconomic strata and geographic areas. The scale used to measure household food insecurity is divided into three categories. We found the worst food insecurity in the poorest group, where heads of household had low levels of educational attainment and unemployment was high. In addition, the households with severe food insecurity had more members. Families displaced by the dam and resettled elsewhere also experienced severe food insecurity,” said Igor Cavallini Johansen, first author of the article. Johansen is a demographer and a postdoctoral researcher affiliated with the State University of Campinas’s Center for Environmental Studies (NEPAM-UNICAMP) in São Paulo state.

Unlike other studies of food insecurity in the context of hydroelectric developments in Brazil, this one used the Brazilian Household Food Insecurity Scale, known by the Portuguese-language acronym EBIA, Johansen said, explaining that the scale is based on a scientifically validated methodology for measuring access to sufficient food of adequate quality. 

“The survey included a questionnaire with eight standardized items. The responses were scored using the EBIA scale to arrive at a classification of food insecurity for each household in the sample,” he said.

The households were classified into the following categories: (1) food security (adequate food quantity and quality); (2) mild food insecurity (food quality impaired and uncertainty regarding future food availability; (3) moderate food insecurity (inadequate diet, food becoming scarce within the household, children prioritized over adults); (4) severe food insecurity (insufficient food for all household members).

“We formulated three hypotheses: (1) households were affected by a range of factors that together produced food insecurity; (2) poverty played a key role, and the most affected groups were those who had been forced to leave their homes and had been resettled in purpose-built housing projects, known as RUCs; and (3) besides the impact of the dam, the problem was made worse by the COVID-19 pandemic,” Johansen said.

The survey also took into account several socioeconomic variables as correlates of food insecurity, such as a wealth index (poorest, intermediate, least poor) considering the characteristics of the home, ownership of vehicles and appliances, etc.; whether respondents were monthly handouts from the Bolsa Família conditional cash transfer program; whether they had officially declared themselves affected by the dam; whether they lived in an RUC; the number of household members and over-sixties; and the head of household’s gender, skin color, age, marital status, educational attainment and employment status. 

“All three hypotheses were confirmed. Predictably, the various factors correlated with each other: the impact of the dam’s construction significantly increased the probability that household members lived in an RUC, and this increased the likelihood that a family was poor, which in turn entailed a risk of food insecurity,” Johansen said. “Access to food of the desired quantity and quality became more difficult for 69.7% of the households after construction of the dam was completed in 2015.” About half of these households (52.5%) said it had already been difficult before the pandemic, and the rest blamed the pandemic for the worsening of food insecurity since then.

“We also found that households with one or more members aged 60 and over experienced less food insecurity. This can be attributed to the contribution of old-age pensions to the household income, potentially reducing their exposure to poverty and hence to food insecurity,” he noted.

The lack of a survey conducted before the dam’s construction and based on the EBIA scale was unfortunate, Johansen added, as this could have been compared with the results obtained after its construction. “In any event, it was a shock to find that 61% of the households experienced food insecurity when the consortium that built the dam claimed to have invested BRL 6.5 billion, or about USD 1.3 billion, in social, environmental and sustainability-related measures in the region between 2016 and 2022. What was all that money used for?” he said.

The negative impact of Belo Monte is not an isolated case. Several other megaprojects implemented in the Amazon have also had significant social and environmental side effects. Another study conducted by the same research group and led by Caroline Arantes, a professor at West Virginia University in the United States showed that fishing communities lost production and income after construction of the Santo Antônio and Jirau hydroelectric projects in Porto Velho, Rondônia state. The communities were forced to adapt their fishing strategies and find other ways to earn a living in response to the impact of the dams. Household consumption of fish diminished significantly as a result. “These communities had always had fish meals every day, but after the dams were built they were able to do so only once or twice a week, if not less often,” Johansen said. The study in question is published in the Journal of Environmental Management.

Another prior study, in this case focusing on a fishing community on the Xingu River after construction of Belo Monte, showed that fish became scarce and food in general became more expensive in the region. An article on this study is published in the journal Human Ecology.

All these studies involved contributions by Professor Emilio F. Moran, principal investigator for the project “After hydropower dams: social and environmental processes that occur after the construction of Belo Monte, Jirau and Santo Antônio in Brazilian Amazon”, and supported by FAPESP via the São Paulo Excellence Chair program (SPEC). 

In addition to this grant, the study was supported by a postdoctoral scholarship awarded to Johansen, and a postdoctoral scholarship awarded to Vanessa Cristine e Souza Reis, also a member of the research group.

About São Paulo Research Foundation (FAPESP)

The São Paulo Research Foundation (FAPESP) is a public institution with the mission of supporting scientific research in all fields of knowledge by awarding scholarships, fellowships and grants to investigators linked with higher education and research institutions in the State of São Paulo, Brazil. FAPESP is aware that the very best research can only be done by working with the best researchers internationally. Therefore, it has established partnerships with funding agencies, higher education, private companies, and research organizations in other countries known for the quality of their research and has been encouraging scientists funded by its grants to further develop their international collaboration. You can learn more about FAPESP at www.fapesp.br/en and visit FAPESP news agency at www.agencia.fapesp.br/en to keep updated with the latest scientific breakthroughs FAPESP helps achieve through its many programs, awards and research centers. You may also subscribe to FAPESP news agency at http://agencia.fapesp.br/subscribe.

 

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JOURNAL

International Journal of Environmental Research and Public Health

DOI

10.3390/ijerph21020155 

ARTICLE TITLE

Poverty–Food Insecurity Nexus in the Post-Construction Context of a Large Hydropower Dam in the Brazilian Amazon