Saturday, December 30, 2023

 


Safety of aquatic animals as human protein sources amid SARS-CoV-2 concerns



Peer-Reviewed Publication

KEAI COMMUNICATIONS CO., LTD.

Potential routes of virus transmission from aquatic animals to humans. 

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POTENTIAL ROUTES OF VIRUS TRANSMISSION FROM AQUATIC ANIMALS TO HUMANS.

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CREDIT: YUAN CHEN., ET AL.



Aquatic animals have historically constituted a vital and nutritious dietary component for humans, contributing to nearly 20% of animal protein intake for approximately 3.3 billion people. Unlike terrestrial animals, there has been no evidence indicating that aquatic animals serve as reservoirs for zoonotic viruses. However, multiple cases of SARS-CoV-2 from cold-chain aquatic food and environmental samples have evoked worldwide concerns, despite the incidence being notably lower than that associated with poultry and livestock.

In a recent study published in the KeAi journal Reproduction and Breeding, a team of researchers from China and Canada developed a virus-mining pipeline to evaluate the risk of infections by aquatic animals.

The initial phase involved screening publicly available databases to gather transcriptomic and genomic data from commonly consumed aquatic species. This effort resulted in the acquisition of RNA-seq libraries of 70 aquatic species and reference genomes of 55 aquatic species. Human respiratory and intestine-related virus genomic sequences, such as coronavirus and influenza virus. were download and used to build a virus reference genome pool. Two strategies were adopted to map the aquatic animals’ transcriptomes onto the genomes of human respiratory- and intestine-related viruses.

“Positive hints occurred in all positive control groups, which confirms the reliability of our pipeline,” explains senior and co-corresponding author Jing Luo, a professor in State Key Laboratory for Conservation and Utilization of Bio-resource at Yunnan University. “Besides, both mapping strategies identified fragments of Influenza A Virus from a salmon skin sample. This fragment could result from either contamination during sampling, or an IAV infection of fish, but no similar viral fragment exists in the transcriptomes of other tissues of the same S. salar sample.”

The researchers recovered and verified this human-associated viral fragment through de novo assembly and phylogenetic analysis. The results show high homology between the fragment and human IAV (H7N9).

“We believe that the fragment most likely came from sample contamination by human handling rather than viral infection,” adds Luo. “Apart from this false-positive result, analyses fail to find any human-associated viruses in the other aquatic animal transcriptomes.”

Multiple recent cases of SARS-CoV-2 have shown that cold-chain food and environmental contamination play a role in the spread of SARS-CoV-2, but through human contamination. In addressing that, the team concluded that aquatic animals are safe sources of protein for humans, albeit under the caveat of safe processing and storage. “Therefore, the processing of frozen aquatic animal products is critical to controlling the spread of the virus, and this should be carefully monitored,” said Luo.

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Contact the author:Jing Luo, State Key Laboratory for Conservation and Utilization of Bio-resource, School of Ecology and Environment and School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China. jingluo@ynu.edu.cn

The publisher KeAi was established by Elsevier and China Science Publishing & Media Ltd to unfold quality research globally. In 2013, our focus shifted to open access publishing. We now proudly publish more than 100 world-class, open access, English language journals, spanning all scientific disciplines. Many of these are titles we publish in partnership with prestigious societies and academic institutions, such as the National Natural Science Foundation of China (NSFC).

 

Acellular players in the high cryosphere: diversity, function and activity of the global supraglacial DNA viruses


Peer-Reviewed Publication

SCIENCE CHINA PRESS

Composition, classification and specificity of global supraglacial DNA viruses 

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(A) SPECIFICITY OF SUPRAGLACIAL VIRUS POPULATIONS (VOTUS). (B) SHARED AND UNIQUE VOTUS ACROSS DIFFERENT REGIONS. (C) PROPORTION OF CLASSIFIED VOTUS. (D) COMPOSITIONS OF CLASSIFIED VOTUS. (E) RELATIVE ABUNDANCE OF CLASSIFIED AND UNCLASSIFIED VOTUS. HERE, RELATIVE ABUNDANCE REPRESENTS THE AVERAGE RELATIVE ABUNDANCE OF EACH TAXONOMIC GROUP’S SAMPLES FROM EACH REGION. PANELS (E) AND (F) SHARE THE SAME LEGEND. HOSTS OF EACH VIRAL GROUP (E.G., EUKARYOTES AND PROKARYOTES) ARE ALSO INCLUDED.

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CREDIT: ©SCIENCE CHINA PRESS




Supraglacial environments mainly consist of four main types of habitats for microbes and viruses, including snow, ice, meltwater, and cryoconites (the granular sediment on glacier surfaces). The paper revealed that there were more than 10,000 viral species in global supraglacial environments. This is a 15-fold expansion of DNA viral genomic inventory ever known. These viruses mainly belong to bacteriophages, viruses infecting bacteria. Liu et al., also found the viral communities showed a clear regional and habitat distribution pattern, with polar glacier samples separated from mountain glaciers of the Tibetan Plateau and cryoconites samples separated from snow and ice.

In addition, this work revealed a vigorous viral host interaction in supraglacial environments.

They found that supraglacial viruses could be linked to ~83% of obtained prokaryotic phyla/classes and possessed the genetic potential to promote metabolism and increase cold adaptation, cell mobility, and phenolic carbon use of hosts in hostile environmental conditions using diverse auxiliary metabolic genes. The on-site measurements carried out by Liu et al. showed that the virus production rate could reach 2×108 VLPs g−1 h−1, which is similar to global ocean and freshwater lakes.

Finally, a thorough analysis of viral genomic content revealed that supraglacial DNA viruses as shuttles for Antibiotic resistance genes (ARGs) and virulence factors (VFs). Liu et al. detected 122 (1.1% of total viral species) and 924 unique viral species (8.6% of total viral species) carrying 31 unique ARG types and 1405 VFs coding genes. Hence, supraglacial DNA viruses might serve as mobile genetic elements for ARGs and VFs in glacier ecosystems.

In conclusion, this study provides a systematic view of the diversity and function of mountain and polar supraglacial DNA viruses. It emphasized the importance of viruses in supraglacial biogeochemical cycling and their potential impacts on downstream ecosystem sustainability. This study expands our knowledge of the diversity, function, and adaptability of supraglacial viruses, and provides a basis for future research on the world’s glaciers.

 

Can we trust students to collect data ready to use in scientific research?


Peer-Reviewed Publication

THE POLISH ASSOCIATION OF SOCIAL PSYCHOLOGY

Army mentors students and educators 

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ARMY MENTORS STUDENTS AND EDUCATORS

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CREDIT: U.S. ARMY RESEARCH LABORATORY




Recent efforts to improve on the openness and transparency in science have already begun paying off towards greater integrity in the way researchers do and report science. It is now common practice for scientists to pre-register their studies and share openly their materials and data, so that their research is easily available to scientific scrutiny and collaborations.

However, behaviors during data collection are still somewhat of a “black box”, especially when done by students. In fact, there are plenty of questionable and even fraudulent behaviors, such as telling participants the specific hypotheses of interest before starting the study or even instructing them to answer in a certain way, which are almost impossible to detect. 

The major problem is that current practices and regulations are mostly ineffective in preventing or checking for problematic behaviors in the data collection process. Furthermore, detailed knowledge about the prevalence of such behaviors is relatively scarce. Past research has predominantly focused on questionable practices and misconduct in other stages of the research process like data analysis and reporting. 

Importantly, questionable or even fraudulent behaviors might not only be problematic among researchers but also highly relevant in student projects. If public, the data collected from students may be reused by other students, supervisors and other researchers as part of their own work, including research articles published in journals. Yet, there is no way for those reusers to fully be aware of what has been going during the data collection.

This is how a joint team of psychology students and researchers from LMU Munich decided to investigate students’ questionable practices and research misconduct during data collection. 

“We wondered: Can we trust student data?”

says Dr. Marlene Altenmüller, corresponding author of the article. 

“We wanted to know whether and how students actually engage in questionable and even fraudulent practices when collecting data for their projects. And, we were interested in situational factors potentially amplifying or alleviating students’ engagement in such behaviors,” she further explains.

The research team surveyed 473 psychology students and 199 supervisors at German-speaking universities. They asked them about 17 behaviors, ranging from questionable to fraudulent, to figure out whether and which of those the students had engaged in in previous projects. Examples include knowingly letting participants take part in the study while being aware they know the hypotheses; taking part in one’s own survey; and deleting or creating data from scratch. 

The researchers also sought to assess the students’ experiences during their projects. For example, they inquired what kind of expectations and future data use their supervisor had communicated to them. The research team then also asked supervisors about their perceptions of students’ data collection behaviors and what they thought about how their students experienced their projects and their supervision. 

The survey results reveal some reassuring, as well as some troubling insights into ‘the black box’ of student data collection. While 64% of students did not report any problematic data collection practices, some behaviors were not uncommon: 4% admitted to having deleted data; 8% had participated in their own study; and 26% had let participants take part despite them knowing the hypothesis. 

On average, supervisors had similar impressions of students’ questionable and fraudulent behaviors. Among the notable differences were that supervisors assumed a much lower prevalence for students to have taken part in their own survey and a lower prevalence for them to have deleted data. 

Thus, the research team concluded, supervisors might be underestimating some highly problematic behaviors among students.

To reduce the prevalence of problematic data collection behaviors among students, and therefore prompt better quality of data, the researchers recommend addressing students’ perceptions of pressures, opportunities and rationalizations for engaging in these behaviours. Additionally, it would be helpful to make Open Science a central element of teaching.

Particularly, transparent and clear communication between students and supervisors might be one of the most important keys to high-quality, research-ready student data. Those students who knew their data would be used by others, also reported lower prevalence rates of problematic behaviors. 

“Supervisors should maybe consider how empirical student projects may not only be an opportunity for teaching, but also for research,” conclude the authors with a positive outlook.

Research article:

Ludwig, T., Altenmüller, M. S., Schramm, L. F. F., & Twardawski, M. (2023). Evading Open Science: The Black Box of Student Data Collection. Social Psychological Bulletin, 18, 1-31. https://doi.org/10.32872/spb.9411

 

Blood poisoning keeping many people out of work


Peer-Reviewed Publication

NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY





A few years ago, the World Health Organization estimated that blood poisoning, or sepsis, is involved in one in five deaths in the world. 11 million people die from sepsis each year, of which nearly 3 million are children.

This is also a problem in Norway, with thousands of people affected every year.

“Sepsis is a severe immunological overreaction to an infection. It causes the body’s organs to fail,” says Nina Vibeche Skei. She is a doctoral research fellow at the Norwegian University of Science and Technology (NTNU) and a senior anaesthetist at Levanger Hospital.

In Norway, 3000 people die every year from sepsis.

“Many people believe that sepsis only affects the elderly, but a third of those who survive are between the ages of 18 and 60, and this has many consequences,” says doctoral research fellow Skei.

Many years of diminished health

Patients who survive sepsis may have health problems and reduced quality of life for years after they are discharged. Many develop a new chronic disorder or exacerbation of existing chronic conditions, or ailments due to organ failure and intensive care.

“Even everyday activities can become a challenge,” says Skei.

As a result, many people do not return to work after having sepsis, but until now, we have not known how many.

“We investigated the percentage of sepsis patients who returned to work in Norway,” says Lise Tuset Gustad. She is a researcher at the Faculty of Nursing and Health Sciences at Nord University and Levanger Hospital.

High levels of occupational disability among people with sepsis

The research group they were part of retrieved figures from the Norwegian Patient Registry and from the Norwegian Labour and Welfare Administration’s information on absence due to illness. The figures included 36,000 sepsis patients aged 18 to 60. The researchers looked at whether they had returned to work six months, one year and two years after they had been discharged from hospital.

After six months, less than 59 percent of the patients had returned to work. After one year, just over 67 percent were back at work. However, after two years, the number was down to just over 63 percent.

In other words, almost four out of ten of those who had had sepsis were out of work two years after contracting the illness.

Several determining factors

Several factors come into play regarding who is able to return to work after having sepsis.

“Those who fared best were young people with few additional chronic diagnoses and less extensive organ failure,” says Skei.

50- to 60-year-olds were 31 percent less likely to return to work than people aged 18 to 30. People with a chronic illness were 54 percent less likely to return to work, compared with those without a chronic illness. People who had two organs that failed were 40 percent less likely to return to work than those who suffered only one organ failure.

“In addition, people who required intensive care had almost a 50 percent reduced chance of returning to work, compared with those who were admitted to a ward,” says Gustad.

This is because the individuals who require intensive care often have more severe sepsis. Only 52 percent of those admitted to an intensive care unit, compared with 64 percent of those admitted to a ward, were back at work 2 years after discharge.

The researchers also investigated people who contracted sepsis as a result of COVID-19. This group was 31 percent more likely to return to work than the rest of the patients with sepsis.

No improvement

“The main finding of this study is that sepsis greatly reduces the chances of returning to work,” says Skei.

Unfortunately, there is nothing to indicate that we have become better in Norway at getting sepsis patients back to work. The figures were from the period 2010 to 2021, enabling the researchers to document changes.

“Developments over the past decade show no improvement. In fact, the percentage of people who were in work two years after discharge from a hospital ward fell from 70 percent in 2016 to 57 percent in 2019. The reasons for this should be investigated further. We can then implement targeted measures to improve the consequences of sepsis,” says Gustad.

Reference: Skei, N.V., Moe, K., Nilsen, T.I.L. et al. Return to work after hospitalization for sepsis: a nationwide, registry-based cohort study. Crit Care 27, 443 (2023). https://doi.org/10.1186/s13054-023-04737-7

 

KRISS develops world’s first coffee bean CRM for component analysis


New CRM enables accurate measurement of nutritional and harmful components in coffee beans; Expected to enhance quality control of coffee beans and contribute to related basic studies through international cooperation


Peer-Reviewed Publication

NATIONAL RESEARCH COUNCIL OF SCIENCE & TECHNOLOGY

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COFFEE BEAN CRM FOR ELEMENTAL ANALYSIS

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CREDIT: KOREA RESEARCH INSTITUTE OF STANDARDS AND SCIENCE (KRISS)





Coffee is an indispensable beverage in the daily lives of Koreans. In Korea, the per capita coffee consumption of the adult population is 2.7 times higher than the global average, and coffee imports (raw and roasted beans) reached a record high of 200,000 tons, amounting to approximately 1.7 trillion won last year. For food items like coffee, which are closely tied to daily routines, stringent quality control is crucial because they are highly sensitive to the reliability. The key to rigorous food quality management lies in the development of reference materials that assist in accurate component analysis.

The Korea Research Institute of Standards and Science (KRISS, President Dr. Ho Seong Lee) has developed the world’s first CRM(Certified Reference Material) capable of accurate measurement of the nutritional and harmful elements in coffee beans.

A CRM, which provides accurate measurement values certified by an authoritative body, serves as a standard providing a reference for verifying the accuracy of measurement results and analysis methods. The newly developed coffee bean CRM allows for the accurate measurement of five nutritional elements (calcium, magnesium, iron, zinc, copper) and three harmful elements (lead, mercury, cadmium) within coffee beans.

According to domestic regulations, the permissible limit for the total lead content in roasted coffee, instant coffee, and other coffee products is 2 mg/kg or less. In Europe, the cadmium content in dried edible coffee beans is regulated to be 0.05 mg/kg or less, and the lead content is restricted to 1 mg/kg or less. The lead, mercury, and cadmium content in this CRM are all approximately 0.1 mg/kg, which meets the standards for both domestic and European regulations.

To develop this CRM, the Inorganic Metrology Group at KRISS freeze-dried a large quantity of raw coffee beans and obtained a homogeneous sample through multiple grinding and mixing processes. The sample was then sterilized through irradiation, producing a CRM with outstanding stability and homogeneity.

To provide certified measurement values with the world’s highest level of accuracy, this CRM employs isotope dilution mass spectrometry for measurement, one of the most reliable measurement methods in the field of chemistry. With this method, KRISS achieved an accuracy which is more than three times better than that of the conventional measurement methods used by food testing institutions.

While coffee is widely favored with a substantial volume of international trade, a CRM for elemental analysis of coffee beans, allowing their quality control, has been absent. The newly developed coffee bean CRM by KRISS, however, is expected not only to enhance the measurement reliability and evaluation system of domestic food testing institutions but also to contribute to various fundamental coffee-related research through international collaboration such as overseas distribution.

Dr. Kyoung Seok Lee, the director of Division of Chemical and Biological Metrology, said, “This achievement represents a technological advancement that can significantly improve the quality control level of coffee, a popular beverage as well as heavily imported product. KRISS will continue to develop CRMs for foods such as Korean cabbage, blueberry, and pork, so as to make healthy and safe dining table for the nation.

As a national metrology institute (NMI) of Korea founded in 1975, KRISS (Korea Research Institute of Standards and Science) has developed measurement standards technology and played a pivotal role in upgrading Korea’s main industries to the global level.

The coffee bean CRM, developed with support from the fundamental project of KRISS, is currently available on the KRISS Measurement Service website (eshop.kriss.re.kr).

 

Cadmium and particulate matter toxicity


Peer-Reviewed Publication

PNAS NEXUS

Engels et al. supplemental fig 2 

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HIGH RESOLUTION MICROSCOPY IMAGES OF CELLS FROM THE (A) CONTROL, (B) URBAN 125ΜG/ML, OR (C) URBAN 500ΜG/ML EXPOSURE CONDITIONS CAPTURED USING A 60X OBJECTIVE. ACTIN (RED), NUCLEI (BLUE), AND THE HISTONE PHOSPHORYLATION ΓH2AX (GREEN). EACH IMAGE IS DISPLAYED WITH THE SAME BIT RANGE TO SHOW THE INCREASE IN INTENSITY OF ΓH2AX AS PM EXPOSURE CONCENTRATION INCREASES.

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CREDIT: ENGELS ET AL.




Particulate matter causes health problems for those who inhale the fine droplets and particles, but the chemical composition of the mixture matters—and can vary widely across space and time. Lydia Contreras and colleagues characterize the consequences of varying levels of exposure to three chemically distinct particulate matter mixes, sourced from the National Institutes of Standards and Technology (NIST), in a human bronchial epithelial cell model. Following exposures, the authors measured changes in gene expression and cell morphology. NIST’s “Urban” and “Fine” particulate matter mixes, which were collected in St. Louis, Missouri and Prague, Czech Republic, respectively, induced significant changes in gene expression. Particulate matter collected from a diesel engine produced fewer changes. Higher exposures caused more significant changes. Different particulate matter mixes also induced different morphological changes, with exposure to the “Urban” and “Fine” mixtures causing cells to become smaller and more rounded than exposure to the “Diesel” mix. These small rounded cells had signs of significant DNA damage. Next, the authors worked to identify which chemicals were responsible for these changes. Cadmium levels varied between the three mixes tested. Further, when the “Diesel” mix was supplemented with cadmium, it induced changes similar to that of the “Urban” and “Fine” mixes. This indicated that cadmium is at least partially responsible for differences in DNA damage and toxicity between the mixtures, according to the authors.