It’s possible that I shall make an ass of myself. But in that case one can always get out of it with a little dialectic. I have, of course, so worded my proposition as to be right either way (K.Marx, Letter to F.Engels on the Indian Mutiny)
Thursday, December 22, 2022
Climate change: evaluating CO2 emissions from land use with greater precision
Determining greenhouse gas emissions precisely and consistently is essential for mitigating climate change. Due to different methods and definitions, however, the land-use-related CO2 fluxes calculated from global models deviate from the data furnished to the UN in the country reports. In their reports, for example, the countries frequently combine natural and indirect, human-caused CO2 flows on managed land. This leads to a certain amount of double-counting of natural CO2 absorption by the ground and vegetation, causing an overestimation of the remaining carbon budget to limit global warming to 1.5°C or 2°C.
A team led by LMU geographers Clemens Schwingshackl and Julia Pongratz has now harmonized the various calculation methods at country level and determined possible reasons for outstanding differences. The researchers’ analysis allows country targets to reduce CO2 emissions from land use to be evaluated with greater precision, thereby supporting the fair distribution of climate mitigation goals.
The high mortality in the early stages of life is a common phenomenon in fish and other species, but it is little studied due to its complexity. A study by the University of Barcelona and the Centre for Advanced Studies of Blanes (CEAB-CSIC) has analysed whether this mortality in the sharpsnout seabream (Diplodus puntazzo), a species of the Mediterranean with an important commercial interest, occurs by chance or whether it is genetically determined. The results, published in the journal Scientific Reports, show that the survival of this fish in the first months has a genetic basis and it is associated with the time of birth.
The study is led by Marta Pascual, lecturer at the Faculty of Biology and member of the Biodiversity Research Institute (IRBio) of the UB and Enrique Machpherson, research professor at CEAB-CSIC. Among the participants of the study are Héctor Torrado (CEAB-CSIC and IRBio), Cinta Pegueroles (IRBio), Carlos Carreras (IRBio) and Nuria Raventós (CEAB-CSIC).
A species with an important ecological role
The sharpsnout seabream is an animal that lives in rocky coastal reefs and seagrass meadows in the Mediterranean and the eastern Atlantic, where it plays a key ecological role, since it is the only Mediterranean fish with a wide prey spectrum, including preys such as sponges, echinoderms and coelenterates. In order to find out the causes for its mortality during the early stages of life, the researchers compared genomic data to phenotypic and environmental data from recruits, individuals that only settled in October after being larvae in the plankton, and survivors, six-month-old fish that had survived the winter.
The researchers analysed a total of 105 individuals from three populations along a geographical gradient, in particular in the coastal areas of Blanes, Jávea and Agua Amarga. “Analysing in three different populations the individuals that settle for the first time and those that survive enabled us to identify parallel evolutionary processes associated with environmental and phenotypical variables”, the researchers note.
The information on the analysed fish and the environments was inferred using the analysis of its otoliths, bones in the inner part of the ear. “These are bone structures that show daily growth rings that allow us to see when it catches an individual, a series of variables like when it was born and its size, when it settled and what growth rate it will have or how many days it was in the plankton; they also allow us to record environmental variables of the temperature and the lunar cycles”, they say.
The individuals that survive are the ones who are born later
The results showed clear signs of selective mortality mostly associated with birth time, sea surface temperature and growth rate during the larval stage. "It is very interesting to see that in this species, which reproduces in late summer and early autumn, the individuals that survive best are those that are born later, in cooler conditions, and grow more slowly, and mostly, that genetics is important in that survival", they add.
Using sequencing techniques, 122 loci were found to be significantly associated with these phenotypic and environmental variables in parallel in the three populations analysed. Finding parallel genomic changes between these populations supports the idea of a genetic basis for this mortality during the first six months of life. "Our study is the first to do a genomic approach and in different localities. It is very important to have this sampling, as it shows that the results cannot be due to chance", they stress.
“Therefore —they continue—, we treat different populations as survival replicates and look mostly at changes in the same direction.
A pioneer methodology
The methodology used in this study offers a prototype for future genomic and ecological studies of this and other species which will enable the researchers to assess the causes that determine selective mortality in a wild state during this early stage. “To date, there were no studies that combined the methodologies and types of sampling we used. Our study sets the bases to analyse the survival in early stages in nature, to determine whether this process is by chance or whether it is genetically determined and to understand with long-term studies how polymorphisms are maintained in the populations in the presence of selection”, the researchers note.
Sequencing project for the genome of the sharpsnout seabream genome
Although there is a high number of identified loci associated with these features, most of them have not been localized in the closest available genome to the sharpsnout seabream, which suggests that they are in poorly conserved regions and that it is necessary to have phylogenetically closer genomes for comparison. In this sense, one of the co-authors of the study, IRBio researcher Carlos Carreras, has led a study by the Catalan Initiative for the Earth Biogenome Project to sequence the sharpsnout seabream and it is currently under the annotation phase. “We hope that in the future, this helps us to identify where the loci are and the role they can play in this species’ survival”, they say.
Studies to analyse interannual variation
The continuation of this study will be to see how selection can change within and between localities and years, as, according to the researchers, there is an interannual variation that can be very important. "The fact that we have found selective mortality has led us to want to know more. We are not only obtaining the genome of the sharpsnout seabream with the quality of international standards, but we are also analysing other years. We want to see parallel evolutionary processes, and how they vary over time, as well as to see if there is local adaptation in each population. And, with all of this, we want to identify candidate genes in which we can find out their function", they conclude.
The researchers compared genomic data to phenotypic and environmental data from recruits, individuals that only settled in October after being larvae in the plankton, and survivors, six-month-old fish that had survived the winter.
IMAGE: SPATIAL PATTERNS OF MULTI-YEAR MEAN BIASES IN (A) SURFACE DOWNWARD SOLAR RADIATION (RS, IN W•M-2), (B) TOTAL CLOUD COVER FRACTION (TCC, IN %) AND (C) CLEAR-SKY SURFACE DOWNWARD SOLAR RADIATION (RS-CLEAR, IN W•M-2) OF THE CMIP6 MMM AGAINST THE GROUND-BASED OBSERVATIONS AVERAGED FROM 1961 TO 2014. PHOTO CREDIT: YANYI HE AND KUN YANG.view more
This study is led by Prof. Kun Yang (Department of Earth System Science, Tsinghua University). Surface solar radiation (Rs) data is the essential information for the development of solar power usage to mitigate the ongoing climate change. To meet China’s carbon neutrality goal, China has invested and planned heavily in the solar photovoltaic systems. However, future projections of Rs based on climate models contain large uncertainties due to internal climate variability, model uncertainty, and scenario uncertainty, which have not been eliminated by previous studies. Moreover, the model biases in Rs and the underlying drivers have yet to be quantified.
By integrating the high-quality observations and the latest Coupled Model Intercomparison Project Phase 6 (CMIP6) model data of Rs, the research team explored the model bias of CMIP6 models in Rs and quantified the physical causes of the model bias in China. The systematic bias in Rs in CMIP6 models is revealed to be caused by clouds and aerosols, resulting in largely uncertain projections for future changes in Rs (No.1).
To correct this effect, the team used historical biases of models to constrain the future projections of Rs under three possible future scenarios based on emergent constraints, an approach with a solid physical basis for narrowing the uncertainties of future climate projections through the combination of an ensemble of climate simulations with contemporary measurements. The constrained results substantially reduce the projection uncertainties by about 56% in the mid-21st century (No.2). Moreover, they found that the constraints using the combined effect of the TCC and Rs-clear biases can account for about 81% of the projection uncertainties using R.
Moreover, the constrained projections of Rs show a spatial pattern significantly favorable for the future solar energy layout. They found that the mean Rs change during 2050-2069 relative to 1995-2014 is brightening. Particularly in North China and Southeast China with higher power demand, the constrained projections present more significant brightening (No.3).
With increased anthropogenic forcing, the constrained future changes become weaker brightening in eastern China and more dimming in western China (No.3). “Low anthropogenic emissions under the carbon neutrality actions would not only help to mitigate global warming but also increase solar energy potential, consequently creating positive feedback for building a climate-resilient society”, Yang says.
Better estimates and uncertainties of future Rs changes improves the reliability of climate projections to facilitate effective investment of solar power in China. Their results highlight the need to consider the change in spatial pattern of future Rs when making policies or decisions associated with future solar energy deployment.
(a) The relationship between the future Rs during 2050-2069 in SSP1-2.6 (a low-emission scenario) and the historical bias in Rs during 1961-2014 for the 24 models. (b) Comparisons of raw and constrained projections of Rs in SSP1-2.6. Rs projections are constrained by the historical bias in Rs (red bars) and the historical bias in TCC and Rs-clear, respectively (blue bars). Photo credit: Yanyi He and Kun Yang.
Future changes (shading; in W•m-2) in the 20-year mean of Rs during 2050-2069 relative to the 1995-2014 mean from constrained values in three possible future scenarios, i.e., SSP1-2.6 (a), SSP2-4.5 (b) and SSP5-8.5 (c), with the 66% confidence interval shown as contour. Photo credit: Yanyi He and Kun Yang.
The Earth's deep-sea trenches are some of the least explored places on Earth - as they are very difficult to access, are pitch black and the pressure is extremely high. Collecting samples and making reliable measurements of the processes that regulate the turnover of organic material in the deep is therefore difficult.
In recent years, however, researchers from the Danish Center for Hadal Research (HADAL) at University of Southern Denmark have carried out a number of expeditions to deep-sea trenches.
They have developed and applied sophisticated underwater robots, and they have demonstrated in several published studies that the steep deep-sea trenches accumulate various material including organic carbon that ends up at the bottom of the trenches.
The bottom of a deep-sea trench can therefore be a veritable deposition hotspot for microbial life forms that converts the material.
Carbon accumulates in the trenches
In three recent studies, the researchers report that hard-to-decompose organic carbon, including so-called black carbon, accumulates in large quantities at the bottom of the trenches. The studies can be found here, here and here.
Black carbon consists of particles formed during burning of fossil fuels, wood and forests; activities that also lead to the release of CO2. The occurrence of black carbon is thus an indicator of the extent of fossil burning. The particles themselves can also contribute to warming, as they are carried by wind and weather to ice-covered areas, e.g. polar regions, where they settle on ice and snow, increasing heat absorption and thus the melting.
- And now we see that large amounts of black carbon end up at the bottom of deep-sea trenches, says Ronnie N. Glud, professor and head of the Danish Center for Hadal Research.
Samples from more than six kilometers depth
More concretely, the research team has calculated that every year, somewhere between 500,000 and 1,500,000 tonnes of black carbon is stored in the hadal deep-sea; that is the part of the seabed that lies at a depth of more than six kilometers.
In comparison, 6,600,000 – 7,200,000 tonnes of black carbon are emitted annually from the burning of fossil fuels.
The researchers base their calculations on sediment samples that they have retrieved from various deep-sea trenches, exceeding six km deep and thus part of the hadal realm. The hadal zone covers 1% of the seabed.
Not only are disproportionately large amounts of black carbon being deposited in the deep; the same happens for other resilient, hard-to-decompose carbons. In fact, the studies show that every square meter in the central parts of a deep-sea trench buries 70 times more resilient carbon compared to the deep sea in general.
- Although the hadal zone only makes up a very small part of the seabed, disproportionately more carbon is stored here than in the deep sea in general, says Ronnie N. Glud and elaborates:
- So, despite the fact that the deep trenches have a relatively high microbial turnover, the hadal zone and the deep-sea trenches are overlooked reservoirs of stored carbon and thus represent a piece of the global carbon cycle and counteract the rate at which Co2 accumulates in the atmosphere.
The researchers cannot say with certainty where the deep-sea trenches' content of deposited carbon comes from; this work is still going on.
The sea as a landfill
But the black carbon can be the result from burning fossil fuels in nearby countries such as New Zealand, Australia and Chile, which sends black carbon out to sea with the wind.
This hypothesis aligns with the fact that the black carbon content is highest in trenches that are close to industrialized countries, while trenches that are close to less industrialized countries such as Papua New Guinea have a lower content of black carbon. However, factors such as wind direction, ocean currents are forest fires may confound such relations.
According to Ronnie N. Glud the deep-sea trenches act as deposit zones for organic material. The process is facilitated by frequent earthquakes, which are characteristic of the hadal systems.
The earthquakes carry large amounts of material down into the deepest parts of the trenches and bury it in oxygen-free sediments. Here, the material will accumulate over centuries and millennia.
Thus, one may want to ask whether the deep-sea trenches are suitable for carbon storage?
- Man has always used the sea and the deep sea as a dumping ground in the pretense of being "out of sight out of mind". But today we know this is not true. The ocean, rich in life, and its biological and biogeochemical processes are important for the function of the globe – this also applies to the hadal trenches, says Ronnie N. Glud.
Other materials end up in the deep-sea trenches
The fact that man-made, resilient, hard-to-decompose organic material (partly from our burning of fossil fuels), reaches the bottom of our deepest deep-sea trenches, does not surprise Ronnie N. Glud.
- In the past, it was believed that the deep-sea trenches were deserted and devoid of life, and that they were unaffected by what happened at the surface. Hence the name "hadal", which is derived from the name of the realm of Death in Greek mythology (HADES), he says, continuing:
- Today we know that the hadal trenches have a rich and diverse life, are dynamic and very diverse, and that material from land and the surface finds its way all the way to their interior – unfortunately this also includes plastic and pollutants. For example, we have previously demonstrated that hadal sediments contain surprisingly high levels of mercury.
IMAGE: ADVANCES IN RESEARCH AND DEVELOPMENT OF CARBON-BASED METAL-FREE ELECTROCATALYSTS (C-MFECS) HAVE PROVIDED POTENTIAL ALTERNATIVES TO PRECIOUS METAL CATALYSTS FOR VARIOUS REACTIONS IMPORTANT TO RENEWABLE ENERGY AND ENVIRONMENTAL REMEDIATION.view more
CREDIT: NANO RESEARCH ENERGY, TSINGHUA UNIVERSITY PRESS
The abundant carbon on Earth might offer a rich, renewable resource for clean, sustainable energy. The technology — called carbon-based electrochemical catalysis — that could make green energy conversion possible exists, according to an international collaboration investigating recent advancements, but is not ready for broad application.
While the catalysts have yet to hit the sweet spot of performance and cost-effectiveness needed for industrial deployment, the researchers said, there are clear pathways to advance the technology through the promise of carbon-based metal-free electrocatalysts (C-MFECs). The team published their review on December 15 in Nano Research Energy.
“It is imperative to develop sustainable and clear energy as well as related storage devices to alleviate the energy shortage and environmental pollution,” said co-corresponding author Liming Dai, Scientia Professor, Australian Research Council Laureate and funding director of the Australian Carbon Materials Centre, School of Chemical Engineering, University of New South Wales. “In this article, we provide a concise but critical review of recent progress in the development of rationally designed C-MFECs with high-performance activity sites for energy-related reactions and systems. We also discuss current challenges and future opportunities to provide forward-looking guidance for their potential application in various catalytic processes of practical significance.”
Electrochemical catalysts typically accelerate a reaction at an electrode, which often require a metal. The metals that work best, such as platinum, are scarce and expensive. More common metals, such as iron and copper, are cheaper but less efficient in accelerating a full reaction. According to co-corresponding author Chuangang Hu, corresponding author and a professor from the State Key Laboratory of Organic-Inorganic Composites, College of Chemical Engineering, Beijing University of Chemical Technology, C-MFECs offer a potential alternative to noble metal-based and transition metal-based electrocatalysts.
“Low-cost, high-activity and stable metal-free alternatives for renewable energy technologies are desperately desired,” Hu said. “After about a decade worldwide extensive research and development and with the availabilities of these newly developed strategies, C-MFECs show potential applications in renewable energy and environmental technologies of practical significance. Mainly since 2015, many strategies have been reported to improve electrochemical catalytic activity by designing C-MFECs through intrinsic catalytic structure adjustment and rational assembly.”
In their assessment of the last seven years, roughly, of scientific literature, the researchers found that the most recent work includes how to control focus on structure design and regulation of intrinsic catalytic active sites, or how efficiently and effectively the catalyst causes the desired reaction. The recent work also includes advancements in construction of 3D assembly and composite structures and investigations into the mechanisms underlying C-MFECs
“Recent years have witnessed tremendous progress in the field of C-MFECs,” Dai said. “Rational design and regulation of the configuration and structure of C-MFECs could be used for tailoring advanced catalysts with desired properties and performance, which could make C-MFECs overtake metal-based catalysts in the race to the renewable energy technological marketplace.”
To support the advancement of C-MFECs as a metal alternative for practical applications at a large scale, Dai said there is still an “urgent” need to develop efficient and controllable synthesis strategies. According to Dai and Hu, researchers should focus on overcoming key challenges to generate large-scale, reproducible C-MFECs with uniform and stable electrocatalytic active sites for specific reactions. These barriers include developing better synthesis and precise control of C-MFECs’ structure and properties; improving the characterization of the catalysts and their active sites to better inform theoretical modeling; developing multifunctional C-MFECs; and preparing C-MFECs for industrialization.
“Our goal is to provide a timely and concise, but critical review of recent progress in the development of C-MFECs as meaningful guidance for the design and synthesis of high-performance C-MFECs.” Hu said.
Other contributors include Jixin Yan, Fenghui Ye, Xinyue Ma and Zhihai Fang, State Key Laboratory of Organic-Inorganic Composites, College of Chemical Engineering, Beijing University of Chemical Technology; and Quanbin Dai, Department of Macromolecular Science and Engineering, Case School of Engineering, Case Western Reserve University in the United States.
The National Natural Science Foundation of China and the Fundamental Research Funds for the Central Universities financially supported this work in part.
Nano Research Energy is launched by Tsinghua University Press, aiming at being an international, open-access and interdisciplinary journal. We will publish research on cutting-edge advanced nanomaterials and nanotechnology for energy. It is dedicated to exploring various aspects of energy-related research that utilizes nanomaterials and nanotechnology, including but not limited to energy generation, conversion, storage, conservation, clean energy, etc. Nano Research Energy will publish four types of manuscripts, that is, Communications, Research Articles, Reviews, and Perspectives in an open-access form.
SciOpen is a professional open access resource for discovery of scientific and technical content published by the Tsinghua University Press and its publishing partners, providing the scholarly publishing community with innovative technology and market-leading capabilities. SciOpen provides end-to-end services across manuscript submission, peer review, content hosting, analytics, and identity management and expert advice to ensure each journal’s development by offering a range of options across all functions as Journal Layout, Production Services, Editorial Services, Marketing and Promotions, Online Functionality, etc. By digitalizing the publishing process, SciOpen widens the reach, deepens the impact, and accelerates the exchange of ideas.
Recent progress in carbon-based electrochemical catalysts: from structure design to potential applications
Brazilian model vaccination program reduced severe cases of COVID-19 and deaths even from variants
The dynamics of SARS-CoV-2 variant substitution in the town where a clinical trial of vaccination effectiveness was conducted matched the pattern seen elsewhere in the country, but most cases were mild
FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO
IMAGE: THE DYNAMICS OF SARS-COV-2 VARIANT SUBSTITUTION IN THE TOWN WHERE A CLINICAL TRIAL OF VACCINATION EFFECTIVENESS WAS CONDUCTED MATCHED THE PATTERN SEEN ELSEWHERE IN THE COUNTRY, BUT MOST CASES WERE MILD.view more
CREDIT: BUTANTAN INSTITUTE
A study conducted in Serrana, a small town in São Paulo state used as a model for COVID-19 vaccination in Brazil, shows that mass vaccination reduced the severe case and death rates even while the gamma and delta variants were circulating. Gamma and delta were considered alarming because they spread so much faster than previous variants.
Based on an analysis of the virus’s evolutionary history (phylogeny), the researchers showed that the dynamics of SARS-CoV-2 substitution in the town was similar to the pattern seen in the rest of Brazil. The ancestral strains (B.1.1.28 and B.1.1.33) were replaced by gamma, delta (first detected in India in 2020 and originally labeled B.1.617.2) and more recently omicron. In Serrana, however, the study showed that most cases caused by all three variants (88.9%, 98.1% and 99.1% respectively) were mild, thanks to immunization with CoronaVac (Sinovac Biotech-Butantan Institute). Coverage had then reached 80% of the target population.
The phylogenetic analysis was applied to 4,375 genomes obtained between June 2020 and April 2022, the period between the introduction of SARS-CoV-2 and completion of the double-dose vaccination process.
According to the authors, their genomic surveillance exercise not only monitored the spread of the key variants in the town but also helped identify some rare variants of interest, such as C.37, which circulated in the Andean countries but was under-represented in Brazil, and alpha, which was detected in Serrana but did not spread elsewhere. All told, the scientists detected 52 sublineages of SARS-CoV-2 in the town.
An article on the study is published in the journal Viruses. Codenamed Project S, the study was conducted by Butantan Institute with FAPESP’s support. The authors are researchers affiliated with Butantan Institute, the Ribeirão Preto Blood Center and the Center for Cell-Based Therapy (CTC), a Research, Innovation and Dissemination Center (RIDC) funded by FAPESP and hosted by the University of São Paulo’s Ribeirão Preto Blood Center and Medical School (FMRP-USP).
Serrana was a model for a clinical study of the first mass vaccination of a town’s entire adult population (over 18) using CoronaVac before the Ministry of Health began official vaccine rollout. A large-scale sequencing program was developed to analyze all SARS-CoV-2 positive samples obtained in the town in real time (read more at: revistapesquisa.fapesp.br/en/a-town-turned-laboratory/).
“Next-generation sequencing is increasingly affordable and widely used for genetic monitoring of infectious diseases and the viral variants involved. The technologies now available are applicable even in relatively remote areas with scant resources. This type of surveillance helps us prevent outbreaks, understand how novel viral genotypes spread and identify emerging viruses. Detection of novel agents and viral variants provides key input for public health decisions to avoid future pandemics or epidemics,” Svetoslav Nanev Slavov, first author of the article and a researcher at Butantan Institute, told Agência FAPESP.
Results
The 4,375 genomes analyzed in the study broke down as follows by variant: 1,653 delta (37.8%), 1,053 gamma (24.1%), 1,513 omicron (34.6%), 75 zeta (1.7%), and 81 other (1.9%). Most subjects were in the 21-50 age group, although there were participants of all ages.
According to the authors, based on the clinical scores of the subjects who tested positive, vaccination reduced morbidity and mortality in Serrana, especially during the gamma and delta waves. They compared the results with those of São José do Rio Preto, a medium-sized city about 200 km away, where mortality was higher during the gamma wave, especially among unvaccinated young people.
The beneficial effects of vaccination have been observed in other studies, showing that fully vaccinated people are less likely to contract symptomatic or asymptomatic infections. The conclusion is that vaccination reduces infection rates, numbers of severe cases and death rates due to SARS-CoV-2.
“In addition to genomic monitoring of patients who tested positive for SARS-CoV-2 in Serrana, the study demonstrated the benefits of early mass vaccination in significantly reducing morbidity and mortality due to this viral agent,” said Simone Kashima, last author of the article and a researcher at the Ribeirão Preto Blood Center.
The study serves as a basis for future research on the genetic monitoring of viral diseases and measures to combat them, she added.
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
IMAGE: A NEW DISCOVERY FROM THE UNIVERSITY OF VIRGINIA SCHOOL OF MEDICINE'S JASON PAPIN, PHD, AND COLLABORATORS COULD HELP DOCTORS IDENTIFY PATIENTS AT RISK FOR SEVERE C. DIFFICILE AND OPEN THE DOOR TO NEW TREATMENTS.view more
CREDIT: DAN ADDISON | UVA COMMUNICATIONS
New research from the University of Virginia School of Medicine and collaborators reveals how microorganisms found in our guts can worsen dangerous C. difficile infections. The discovery could help doctors identify patients at risk for severe illness and open the door to new treatments.
C. difficile is a bacterium that can cause potentially deadly infections, particularly among the elderly and people on long-term antibiotics. These infections are characterized by diarrhea, nausea and fever. C. diff, as it is commonly known, strikes more than 350,000 Americans a year. Once infected, patients are prone to suffer re-infections; among those who survive, one in six will develop another case within eight weeks, according to the federal Centers for Disease Control and Prevention. As such, C. diff can be a major problem for hospitals and nursing facilities.
UVA’s new findings help explain why certain patients are at particular risk. The researchers determined that a group of antibiotic-resistant “opportunistic pathogens” found in the gut called enterococci can make C. diffmore potent and dangerous.
“The interactions between C. diff, other microbes and the human gut are highly complex. This study leveraged expertise from a large, multidisciplinary team across several institutions to disentangle these complex interactions and discover key mechanisms that help C. diff cause disease,” said researcher Jason Papin, PhD, of UVA’s Department of Biomedical Engineering, a joint program of the School of Medicine and School of Engineering. “With this greater understanding, we have an opportunity to develop new therapeutic strategies to treat this dangerous infection.”
A More Dangerous C. difficile
Enterococci are bacteria that can, on their own, cause dangerous infections that are difficult to treat. For example, they can cause meningitis, urinary tract infections (which can be very serious in the elderly) and the painful gastrointestinal disease diverticulitis, as well as other illnesses. But the researchers found that the threat they pose does not end there.
The research team collected stool samples from patients with C. difficile infections at Vanderbilt University Medical Center, Children’s Hospital of Philadelphia and the Hospital of the University of Pennsylvania. They then used a combination of lab tests and advanced computer modeling to better understand how C. diffinteracts with other microorganisms in the gut.
They found that enterococci make for a dangerous ally for C. diff. Enterococci produce amino acids, including leucine and ornithine, which make C. difficile a more potent threat for patients whose gut compositions have been disrupted by antibiotics.
Papin and his team developed powerful computer models that helped the researchers understand and predict the complex changes in the gut. Their work, combined with lab research performed in other labs, showed that enterococci can dramatically reshape the “metabolome” – the collection of metabolites such as amino acids – in the gut. These changes, the researchers report, ultimately reprogram C. difficile and enhance its disease-causing behaviors.
“The computational modeling that Matthew Jenior [UVA postdoctoral fellow in the Papin lab] performed was instrumental in discovering the role of amino acids in the interaction between C. diff and enterococci,” Papin said. “The computational models that Matthew constructed will continue to help us better understand the molecular processes in C. diff that cause disease.”
By better understanding how C. diff interacts with enterococci and other microorganisms in the gut, doctors will be better positioned to battle this common and serious infection, the researchers say.
“Biology is a data-rich science and the power of computational models to use these data is only in its infancy,” Papin said. “ We’re excited about the innumerable opportunities to use data science and computer modeling to drive biological discovery.”
Findings Published
The researchers have published their findings in the prestigious scientific journal Nature. The team consisted of Alexander B. Smith, Matthew L. Jenior, Orlaith Keenan, Jessica L. Hart, Jonathan Specker, Arwa Abbas, Paula C. Rangel, Chao Di, Jamal Green, Katelyn A. Bustin, Jennifer A. Gaddy, Maribeth R. Nicholson, Clare Laut, Brendan J. Kelly, Megan L. Matthews, Daniel R. Evans, Daria Van Tyne, Emma E. Furth, Papin, Frederic D. Bushman, Jessi Erlichman, Robert N. Baldassano, Michael A. Silverman, Gary M. Dunny, Boone M. Prentice, Eric P. Skaar and Joseph P. Zackular.
The research was supported by the National Institutes of Health, grants K22AI7220, R35GM138369, R01AI138581, R01AI145992, R01HD090061, R01AT010253, UL1TR000445, K23 AI121485 and 1DP1DA051620; a Children’s Hospital of Philadelphia Junior Faculty Pilot Grant; a Cell and Molecular Biology Training Grant, T32GM07229; a UVA TransUniversity Microbiome Initiative Pilot Grant; Chemical and Biology Interface Training Grant 5T32GM071339-15; Centers for Disease Control and Prevention grant BAA 200-2016-91937; and Commonwealth Universal Research Enhancement programme grant SAP#4100068710.
