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Category Archives: Transhuman News

Genome editing attitudes of medical students and doctors | JMDH – Dove Medical Press

Posted: May 4, 2021 at 8:25 pm

Introduction

DNA mutations are a major contributor to the development of diseases. Research into targeted therapies, as part of precision or personalized medicine, continues to expand and to include more mutations causing diseases.1 Two strategies for targeted therapy involving genetic mutation are gene therapy and genome editing, which have been applied to several diseases. In principle, gene therapy works by introducing DNA/RNA into the cells, removing or changing defective genes to drive the correct protein production. Genome editing in particular, which is one of the gene therapy techniques, is to remove, to disrupt or to correct faulty elements of DNA within the gene and leads to change sequence of the gene.2 Up to now, the approved gene therapies do not alter the genomic sequences, for instance Zynteglo for -thalassemia,3 Luxturna for Leber congenital amaurosis or retinitis pigmentosa4 and Zolgensma for spinal muscular atrophy,5 whilst the genome editing approach is still under clinical trials such as for lung cancer6 and blood disorder.7

Genome editing has become a rising star since the investigation of CRISPR/Cas9 found a defensive system from phage in bacteria.8,9 Currently, editing diseases caused by mutations and introducing the correct donor template have become much simpler and more affordable. Several components are required for CRISPR/Cas9 gene editing, including a gRNA designed to target a particular PAM sequence, the Cas9 enzyme to cut DNA and potentially a donor template.10 CRISPR/Cas9 recognizes a specific sequence, creates a double-strand break on the DNA and the cell automatically performs DNA repair, constituting an effective tool for genome editing.

CRISPR/Cas9 has been widely used for its simplicity and affordability.11 In fact, in 2020, CRISPR/Cas9 technology was awarded the Nobel Prize for its broad possible applications, simple handling and affordable price. However, low efficiency and off-targeting remain a concern in its application.10,12,13 Since the discovery of CRISPR/Cas9, many studies have been performed in vitro in human cells and in vivo in a range of animal models to correct disease-caused mutations and to create mutations for gene inactivation.13,14 Mostly, this powerful method has been applied to somatic cells, but concerns have been expressed by scientists regarding its application to germline cells that allows inheritance of the edited gene.15 Unfortunately, a red alert was raised in 2018 when one group of Chinese scientists announced the birth of twin babies for whom the CCR5 gene had been edited. Inactivation of this gene made the babies resistant to HIV invasion.16,17 Moreover, ethical concerns has been raised on the application of this technology to enhance human ability such as memory or intelligence.18

Despite the controversies, medical doctors and students need to understand the latest technology, which could potentially affect their future practice since this technology rapidly develops toward its clinical application.19 Acceptance and attitude of general public, medical doctors and students on gene therapy and genome editing have been extensively investigated and reviewed, with acceptance of this technology being affected by the education, religion, gender, age, economic status and trust to the scientist and government.20 Respondents with medical background are more likely to accept genome editing than are the general public.21 Moreover, due to the CCR5 babies scandal, public awareness of genome editing technology application, risk, safety and ethical problems increased, while the acceptance of this technology reduced.22 In Indonesia, genome editing is not part of a focus in Indonesian medical education,23 and as it is a country with a big religious population, the controversy regarding the ethics of some health approaches is unavoidable.24 Therefore, we conducted this study to explore the attitudes of Indonesian medical doctors and students toward human genome editing and the sociodemographic factors that might affect their attitude.

This cross-sectional study was part of a gene therapy and genome editing study in Indonesia which was conducted from May to December 2020, and ethics approval was obtained from the Faculty of Medicine, Universitas Airlangga No. 156/EC/KEPK/FKUA/2020. Before the start of the questionnaire, a page explaining the aim and content of the survey was provided, and informed consent, including for publication of anonymized responses, was obtained if the respondent clicked the BEGIN button to start the survey.

Primary data were collected from online questionnaires distributed through the researchers network, email and social media of medical doctors and students. Research staff shared and guided the respondents to access the online questionnaire, and the respondents completed and submitted the questionnaires independently. Respondents of this study comprised only Indonesian medical doctors and medical students, over 18 years of age, that were Indonesian citizens and who had studied in a medical program or graduated from an Indonesian Medical Faculty. Fifteen respondents were then contacted based on their answers to the online questionnaire; among these, only 10 respondents replied, and an in-depth email interview was performed by SNI, DS and AdA.25

The attitudes of respondents to genome editing were measured using a set of questionnaires. The questionnaire consisted of two sections, which comprised basic information of respondents and questions regarding their attitudes on genome editing. The questionnaire was adapted and translated by two native Indonesians from A Global Social Media Survey of Attitudes to Human Genome Editing.26 The translated questionnaire was further piloted among 20 Indonesian medical doctors to ensure the understanding of the respondents. The survey was divided into seven sections: (1) respondents characteristics (gender, age, place of residence, marital status, childbearing, education, work experience, religion and experience abroad); (2) general attitudes toward genome editing; (3) attitudes toward genome editing in somatic cells for fatal and debilitating diseases; (4) attitudes toward genome editing in embryos for fatal and debilitating diseases; (5) attitudes toward genome editing in the embryo to change individual characteristics, such as physical, intelligence quotient (IQ) and strength; (6) factors affecting the attitudes toward genome editing; and (7) their agreement in genome editing implementation in Indonesia. Finally, respondents were asked to answer an open-ended question regarding their concerns toward genome editing. The in-depth interview questions were developed based on each respondents answer, focusing on their concerns on genome editing.

Respondents were divided into two groups: doctors and students. The religion, place of residence and economic status were simplified into two categories each, ie, majority and minority; inside or outside the main islands; and lower and higher economic status, respectively. The attitudes toward genome editing in somatic cells and in embryos as well as its application in Indonesia were measured using a 5-point Likert scale, rated from strongly disagree to strongly agree, which was aggregated to disagree, neutral and agree, while attitudes toward genome editing in embryos to change individual characteristics were measured using yes/no answers. Additionally, participants chose from a list the factors that affected their attitudes toward genome editing, and the number of respondents per factor was calculated and divided by the total respondents; respondents could also write in their concerns regarding genome editing technology.

Data were processed using Microsoft Excel and analyzed using SPSS 25.0 (IBM, Chicago, IL, USA), and graphs were visualized using GraphPad Prism version 5.00 (La Jolla, California, USA). Descriptive statistical analyses were performed, and response rates were calculated as percentages on every item related to categorical variables. Differences between groups were measured using the t-test or MannWhitney U and KruskalWallis H-test to determine the sociodemographic factors influencing the respondents attitudes toward genome editing; significance was defined as a p-value < 0.05. The effect size further performed to measure the strength of the differences between two groups, with the interpretations for effect size g being: g=0.20 as small, g=0.5 as medium and g=0.8 as large, following the criteria proposed by Hedges (1985).27,28

Of the 1076 responses received, 1055 questionnaires were valid and used in the final analysis, corresponding to an effective rate of 98.05%. Four returned responses were excluded because they were incomplete, and 17 responses were excluded due to unmet the eligibility criteria. The ratio between doctors and students was almost 1:1, with females as the majority. A discrepancy of age was observed between the two groups: all the respondents in the student group were between 18 and 30 years old, while young doctors (18 to 40 years old) were the majority in the medical doctor group. As expected, the majority of respondents were located in Java and Bali, which are the most developed provinces in Indonesia and have more doctors and medical schools compared with other provinces. Moreover, as Indonesia is a Muslim majority country, two-thirds of the respondents in each group were Muslim. Based on their self-proclaimed economic status, the majority of respondents in the two groups had lower economic status. As expected, the education between the two groups differed; only 35.8% of the medical doctors pursued specialization/post-graduate studies. However, no significant difference was found between doctor and student respondents participating in mobility programs in other countries (20% vs 15.9%, respectively). The difference between the two groups also could be observed concerning their work experience. The majority of doctors had more than 5 years of working in their field, while the majority of students still studied in their fifth year. Nearly all respondents in the student group were unmarried and without children, while two-thirds of respondents in the doctor group were married and with children. Characteristics of the respondents are summarized in Table 1.

Table 1 Characteristics of Respondents

Fifteen questions assessed attitudes toward genome editing applications in humans (Table S1). The results showed very low familiarity with genome editing in the doctor and student groups (12.2% and 13.1%, respectively) even though more of the respondents had heard of this technology (21.3% and 28%, respectively, Figure 1A). The respondents were more familiar with genetically modified food (27.1% and 20.4%, respectively) or at least had heard of this issue (38.8% and 28.2%, respectively, Figure 1B). Despite genome editing technology being in the spotlight in these past 3 years with the CCR5 edited babies scandal and Nobel Prize winners, the respondents' knowledge was significantly lower compared with GMO and the more common issues in gene technology which have attracted more media coverage (p < 0.01). This was an unexpected finding, because medical doctors' and students' knowledge on this technology was lower than the US publics knowledge (31%).29

Figure 1 Knowledges and attitudes of Indonesian medical doctorsand medical studentstoward genome editing. (A) Knowledge on genome editing . (B) Knowledge on genetically modified food. The knowledge was divided into never heard, ever heard but not familiar and know which meansthe respondents were familiar with the technology including superficial knowledge to deep knowledge. (C) Attitudes of all respondents on GM food and genome editing application in health and non-health-relatedmatter, including application in Indonesia.

Although respondents had little knowledge of this field, no specialty terms were used in the questionnaire, allowing them to complete the survey. The majority of respondents (60.76%) supported the application of genome editing as therapy for fatal diseases in somatic cells, which prohibits inheritance in the next generation. Regarding its application in alleviating the burden of debilitating diseases in somatic cells, an almost similar number was obtained: 61.33% supported this aim. The respondents in the doctor group were more likely to support the applications in somatic cells for fatal and debilitating diseases compared to the student group (p = 0.000 and p = 0.000, respectively). Meanwhile, the support for the application of this technology in the embryo stage was not significantly different between the two groups (Table 2). However, the values of effect size g were 0.22 for both questions or had small effect, although the results were statistically significant.

Table 2 Knowledge and Attitude Toward Genome Editing Application

Overall, the number of respondents who agreed was slightly reduced when the application was to embryos, meaning the edited gene could be inherited by the next generation, both for fatal and debilitating diseases. Interestingly, their support of genome editing application concerning the embryo was higher compared with the application for genetically modified food (28.25%, Figure 1C). This might be caused by a lower acceptance of genetically modified food in this study compared with other studies (3057%).30,31 Nevertheless, similar to other countries, the support for human enhancement at the embryo stage was lower than that for treatment of health-related matters, with only 26.07% respondents. Moreover, the majority of respondents did not have any view or were neutral regarding the use of genome editing in Indonesia (Figure 1C).

We further explored the respondents' preference regarding enhancing individual characteristics at the embryonic stage. If the technology was safe, the respondents prefer to enhance the intelligence (40.53%) compared to sport ability/strength (28.69%) and physical appearance (17.52%). Factors of concern regarding genome editing included the possibility of inheritance (14.19%), expense (21.93%), side effects (22.24%), violation of privacy (9.5%), violation of fate (15.37%), violation of religious values (15.71%) and others such as misconduct, lack of evidence and less expertise (1.07%) (Table S2 C1-C5).

To determine the sociodemographic factors affecting the respondents' attitudes on genome editing, MannWhitney U and KruskalWallis H-test were performed. Our study supported that males were more likely to support genome editing application at somatic cells (p = 0.000) and embryo stages, both for health (p = 0.004) and non-health (p = 0.001) related matter, including its application in Indonesia (p = 0.000), similar with other studies (Table 3). This trend might be caused by males tending to follow the logic, while females tend to accept and find a supporting reason (Table S2, C6 and C7).

Table 3 Influence of Sociodemographic Factors on Respondents Attitudes

Age was also a contributing factor affecting Indonesian medical doctors attitude toward genome editing technology. The older respondents were more likely to support genome editing at somatic cells for treating fatal diseases (p = 0.049), and respondents aged 1830 years and >50 years were more likely to support the human enhancement ability (p = 0.003). Moreover, respondents residing outside of the main islands were more likely to support the latter application (p = 0.028); however, respondents from the main islands were more likely to support the application of this technology in Indonesia (p = 0.014) (Table 3). In the main island, the developments, the facilities and the transfer of knowledge can be performed more easily than in the outer parts of Indonesia.

Religion greatly influenced respondents' attitudes because the respondents with the majority religious affiliation in Indonesia were less permissive concerning applying genome editing application to treat fatal diseases (p = 0.016), debilitating diseases (p = 0.000) and human enhancement (p = 0.012), whether it could or could not be inherited to the next generation (Table 3, S2 C8 and C9). Moreover, they also were more likely to oppose its application in Indonesia (p = 0.001) when compared with other religions.

Respondents with higher education levels were more likely to support the application at somatic cells for fatal (p = 0.000) and debilitating diseases (p = 0.001) but tended to oppose this technology application when used to enhance human ability or performance (p = 0.001). This might relate to the ease of access to new information, such as journals, seminars and exchange/internship to developed countries (Table S2 C5 and C6). The exposure to broader society was also associated with respondents being more permissive on implementation in Indonesia (p = 0.014); however, this exposure did not significantly influence their view on genome editing technology in health and non-health-related matter.

Moreover, in line with other studies, respondents with higher self-proclaimed economic status were more likely to support the use of this technology on somatic cells for fatal and debilitating diseases (p = 0.005 and p = 0.003), implying that the changes were unable to be inherited in the next generation (Table S2).

To our knowledge, this constitutes the first study to measure Indonesian medical doctors' and students' attitudes toward genome editing. Our study found that the knowledge of Indonesian medical doctors and medical students on genome editing was lower compared to similar studies in various countries.22,26 Moreover, 60.76% of respondents agreed with the application of genome editing in somatic cells and embryos to improve health conditions. This acceptance reduced to only a quarter when applied to non-health-related aspects. This finding is similar to the public acceptance rate in the United States, where approximately 64% of the respondents accepted genome editing to cure diseases, while only 33% respondents accepted its application in enhancing human ability.32 Moreover, a study of 1004 Australians demonstrated a similar conclusion.33 This finding slightly differs with a study of geneticists in US, in which the majority support the use of genome editing on somatic cells and for research purposes, but not in embryos/germline cells.34

As reviewed by Delhove et al, sociodemographic factors influenced the acceptance by the general public toward gene therapy and genome editing.20 Our study found that gender, age, economic status, religion, education and place of residence influenced the attitude of the respondents on genome editing technology. Similar to the findings of a study conducted in the US on 1600 adult citizens,32 a study on 12,000 persons of the general public (mainly the US, UK and China),26 a study on 1004 Australians33 and 12,716 persons of the general public of 10 European countries and US citizens, our study found that males were more likely to approve genome editing application, both for disease treatment and human enhancement ability, and its application in Indonesia. This finding differs from that of a study in 13,201 Chinese persons of the general public, with 2165 clinicians, that concluded that females were more likely to accept the application of gene therapy for genetic disease treatments, including genome alterations approach.21

A relationship between age and the attitude on genome editing has been shown in many studies. Some studies reported that older respondents were less permissive regarding the usage of genome editing,22,33,35 especially on non-health-related matters.26 However, a study on 10 European countries and US citizens found no significant contribution of age on the application at the somatic cells or the embryos.36 In contrast with other studies, here we demonstrated that older respondents were more supportive of genome editing applications to treat fatal diseases at the somatic cells. Additionally, respondents less than 30 years old and more than 50 years old were more likely to permit the usage on non-health-related matters.

Moreover, economic status also might contribute to respondents acceptance of this technology, especially on its application to the somatic cells. This result was similar to a study from Australia that found the respondents from a country with high economic levels/GDP more likely to accept the implementation of genome editing26 and a study from US that showed respondents with higher family income more likely to support the human genome editing technology.32 This also might be related with the place of residence, as our study found that respondents who resided at more developed islands were more likely to support the application of genome editing technology in Indonesia, while respondents who resided at less developed islands were more likely to support this technology for enhancing human ability which might bring more benefit. A study in Europe suggested that less support from the lower-income respondents and less developed countries might relate to the lower benefit that they will get from this technology and to trust issues with the regulation and the government.37

Another factor that might influence the attitude toward genome editing is religion. As a country with a Muslim majority population, religious value is embedded in many aspects, including the medical field. Our study found that the minority were more likely to agree to its use in health and non-health-related matters, including its application in Indonesia. It was in line with studies in religious individuals who consistently rejected changes to the genome because they conflicted with religious teachings.26,37 It might also be related with less trust of the scientific community to guide this technology in a responsible way.32 However, a study in the general public, university students and high school teachers from various countries in Asia, Australia, New Zealand, Russia and China found no significant effect of religion on the application of gene therapy that included gene correction.38,39

Education was one of the influencing factors on the attitudes of the respondents to this rising technology. Our study found that respondents with higher education had more favorable attitude toward genome editing as treatment for fatal and debilitating diseases on somatic cells, but they were more likely to oppose its application for increasing human ability. Moreover, education did not affect the respondents attitude toward genome editing application on the embryo, both for fatal and debilitating diseases. A study by McCaughey showed that respondents with tertiary education were more likely to support this technology application as treatment for a fatal or life-threatening condition, either on somatic cells or embryo stage; in addition, they were also more likely to support their usage to prevents debilitating diseases at the embryonic stage, indicating that the edited gene was inheritable to the next generation.26 Similar with our results, studies in Australian, European and US citizens found no significant association between education and prenatal application of this technology.33,36 Nevertheless, even though those with experience abroad had increased knowledge regarding genome editing and the CCR5 edited infants, their views of its application did not differ from the respondents who did not have any experience in other countries. Respondents with experience abroad were also more likely to support the implementation of this technology in Indonesia.

Furthermore, even though the cost of CRISPR/Cas is lower than other genome editing technology, Indonesian medical doctors and students still emphasized the high costs that might become a burden on the application, and same reason applies to the reluctance to do genetic testing.40 Major side effects or safety of this technology were also a concern, as this technology is still in the development stage, with lack of supportive evidence, and less expertise in the Indonesian medical field. Increasing attention is also given by the Japanese general public, especially after the announcement of twins born with the edited CCR5 gene, mostly regarding the safety and ethical issues.22

Unfortunately, even though this technology raised controversial issues in 2018 and received the Nobel Prize in 2020, the majority of Indonesian medical doctors were still unaware of this issue. This implied that more effort was needed to broaden the knowledge of Indonesian medical doctors regarding this new technology approach, so that they will be more aware of and prepared for the upcoming treatment technologies. Consultation to the public before its application is necessary before implementation in Indonesia to avoid public negative sentiment and rejection.

We recognized the limitation of our study was the utilization of an online questionnaire; thus, there is a possibility for bias since respondents unfamiliar with the internet or residing in remote areas were unable to access the questionnaire. However, the sociodemographic distribution of our respondents was in line with that of Indonesian citizens. Moreover, without face-to-face interaction, lower engagement with the question might affect the results obtained in this study.

This study revealed that even though the majority of Indonesian medical doctors and students were unfamiliar with genome editing, they agreed with the use of genome editing to treat fatal and debilitating diseases, but fewer agreed with applying the method to improve non-health-related aspects. However, some concerns remain regarding the safety, misuse, ethics, religious values and cost of this treatment in Indonesia. Expanding the horizons and increasing the awareness of Indonesian medical doctors and students regarding new technologies that might affect the future of the medical field and humankind are important.

We would like to thank Dr. Zakiyatul Faizah, MD for valuable comments and suggestions.

This study was funded by RKAT Faculty of Medicine Universitas Airlangga as Rector's Decree No. 346/UN3/2020.

The authors report no conflicts of interest in this work.

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Six Faculty: Election to American Academy of Arts & Sciences – UPENN Almanac

Posted: at 8:25 pm

Six Faculty: Election to American Academy of Arts & Sciences

Six members of the University of Pennsylvania faculty have been elected to the American Academy of Arts & Sciences. They join more than 250 new members honored in 2021, recognized for their work to help solve the worlds most urgent challenges, create meaning through art, and contribute to the common good.

Cristina Bicchieri is the S. J. Patterson Harvie Professor of Social Thought and Comparative Ethics in the School of Arts & Sciences. She is also a professor of legal studies at the Wharton School. She is the director of the Center for Social Norms & Behavioral Dynamics and founding director of the Master of Behavioral and Decision Sciences program. Her research sits at the intersection of philosophy, game theory, and psychology, with a primary research focus on judgment and decision-making, as well as on how expectations affect behavior. Dr. Bicchieris work also examines the nature and evolution of social norms, how to measure them, and what strategies are necessary to foster social change.

Michael Hanchard is the Gustav C. Kuemmerle Professor of Africana Studies and professor of political science in the School of Arts & Sciences. He also serves as director of the Marginalized Populations Project, a collaborative research initiative designed to explore political dynamics between populations with unequal, minimal, or non-existent state protections and national governments. His research and teaching interests combine a specialization in comparative politics with an interest in contemporary political theory, encompassing themes of nationalism, racism, xenophobia, and citizenship.

Vijay Kumar is the Nemirovsky Family Dean of Penn Engineering with appointments in the departments of mechanical engineering & applied mechanics, computer & information science, and electrical & systems engineering. He is an internationally recognized robotics expert who specializes in multi-agent systems, teams of robots that can cooperate to complete a task. Dr. Kumars research on new ways for these teams to sense their environments and communicate will help them collaborate on tasks that no single robot could do on its own, whether splitting up to count oranges in an orchard or coming together to lift a heavy payload.

Stanley Plotkin is an emeritus professor of pediatrics and microbiology at the Perelman School of Medicine, an emeritus professor of virology at the Wistar Institute, and former director of infectious diseases at the Childrens Hospital of Philadelphia (CHOP). Dr. Plotkin has spent his career focused on developing vaccines for diseases like rubella, polio, rabies, varicella, and cytomegalovirus. He is also a founding member of the Pediatric Infectious Diseases Society.

Sarah Tishkoff is the David and Lyn Silfen University Professor in Genetics and Biology, holding appointments in the Perelman School of Medicine and School of Arts & Sciences. She is also director of the Penn Center for Global Genomics and Health Equity. Dr. Tishkoff studies human genetic diversity, specifically that of African populations, blending field, lab, and computational approaches. Her work has not only elucidated African population history but also how genetic variation affects traits such as disease susceptibility or ability to metabolize drugs.

Kenneth Zaret is the Joseph Leidy Professor in the department of cell and developmental biology at the Perelman School of Medicine. He is also the director of Penns Institute for Regenerative Medicine (IRM). Dr. Zaret joined Penn in 2009 as associate director of IRM and co-director of the epigenetics program, where he served until 2014. He is also a member of the Cell and Molecular Biology Graduate Group. The Zaret Lab focuses on understanding how genes are regulated to allow one type of cell to change into another type, cell type control that occurs in embryonic development and tissue regeneration.

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Six Faculty: Election to American Academy of Arts & Sciences - UPENN Almanac

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First Major Discoveries Reported From Project to Read Complete Genetic Sequences of All 70,000 Vertebrate Species – SciTechDaily

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New DNA sequencing technologies and assembly methods let researchers read the entire genomes of 25 species: pale spear-nosed bat, greater horseshoe bat, Egyptian fruit bat, greater mouse-eared bat, Kuhls pipistrelle bat, velvety free-tailed bat, Canada lynx, marmoset, vaquita, platypus, echidna, zebra finch, kkp, Annas hummingbird, domestic duck, emu, Goodes thornscrub tortoise, two-lined caecilian, zig-zag eel, climbing perch, flier cichlid, eastern happy cichlid, channel bull blenny, blunt-snouted clingfish, and thorny skate. The animals span all major classes of vertebrates. Credit: Irving Geis/HHMI

A bold project to read the complete genetic sequences of every known vertebrate species reaches its first milestone by publishing new methods and the first 25 high-quality genomes.

Its one of the most audacious projects in biology today reading the entire genome of every bird, mammal, lizard, fish, and all other creatures with backbones.

And now comes the first major payoff from the Vertebrate Genomes Project (VGP): near complete, high-quality genomes of 25 species, Howard Hughes Medical Institute (HHMI) Investigator Erich Jarvis with scores of coauthors report April 28, 2021, in the journal Nature. These species include the greater horseshoe bat, the Canada lynx, the platypus, and the kkp parrot one of the first high-quality genomes of an endangered vertebrate species.

The paper also lays out the technical advances that let scientists achieve a new level of accuracy and completeness and paves the way for decoding the genomes of the roughly 70,000 vertebrate species living today, says HHMI Investigator and study coauthor David Haussler, a computational geneticist at the University of California, Santa Cruz (UCSC). We will get a spectacular picture of how nature actually filled out all the ecosystems with this unbelievably diverse array of animals.

Together with a slew of accompanying papers, the work is beginning to deliver on that promise. The project team has discovered previously unknown chromosomes in the zebra finch genome, for example, and a surprise finding about genetic differences between marmoset and human brains. The new research also offers hope for saving the kkp and the endangered vaquita dolphin from extinction.

These 25 genomes represent a key milestone, explains Jarvis, VGP chair and a neurogeneticist at The Rockefeller University. We are learning a lot more than we expected, he says. The work is a proof of principle for whats to come.

The marmoset genome reveals that several brain genes have pathogenic differences to those in humans. The finding highlights why its important for scientists to consider genomic context when developing animal models.

The VGP milestone has been years in the making. The projects origins date back to the late-2000s, when Haussler, geneticist Stephen OBrien, and Oliver Ryder, director of conservation genetics at the San Diego Zoo, figured it was time to think big.

Instead of sequencing just a few species, such as humans and model organisms like fruit flies, why not read the complete genomes of ten thousand animals in a bold Genome 10K effort? At the time, though, the price tag was hundreds of millions of dollars, and the plan never really got off the ground. Everyone knew it was a great idea, but nobody wanted to pay for it, recalls HHMI Investigator and HHMI Professor Beth Shapiro, an evolutionary biologist at UCSC and a coauthor of the Nature paper.

Plus, scientists early efforts at spelling out, or sequencing, all the DNA letters in an animals genome were riddled with errors. In the original approach used to complete the first rough human genome in 2003, scientists chopped up DNA into short pieces a few hundred letters long and read those letters. Then came the fiendishly difficult job of assembling the fragments in the right order. The methods werent up to task, resulting in misassemblies, major gaps, and other mistakes. Often it wasnt even possible to map genes to individual chromosomes.

Canada Lynx (lynx canadensis) in Winter.

The introduction of new sequencing technologies with shorter reads helped make the idea of reading thousands of genomes possible.These rapidly developing technologies slashed costs but also reduced quality in genome assembly structure. Then in 2015, Haussler and colleagues brought in Jarvis, a pioneer in deciphering the intricate neural circuits that let birds trill new tunes after listening to others songs. Jarvis had already shown a knack for managing big, complex efforts. In 2014, he and more than a hundred colleagues sequenced the genomes of 48 bird species, which turned up new genes involved in vocal learning. David and others asked me to take on leadership of the Genome 10K project, Jarvis recalls. They felt I had the personality for it. Or, as Shapiro puts it: Erich is a very pushy leader, in a nice way. What he wants to happen, he will make happen.

Jarvis expanded and rebranded the Genome 10K idea to include all vertebrate genomes. He also helped launch a new sequencing center at Rockefeller that, together with one at the Max Planck Institute in Germany led by former HHMI Janelia Research Campus Group Leader Gene Myers, and another at the Sanger Institute in the UK led by Richard Durbin and Mark Blaxter, is currently producing most of the VGP genome data. He asked Adam Phillippy, a leading genome expert at the National Human Genome Research Institute (NHGRI), to chair the VGP assembly team. Then, he found about 60 top scientists willing to use their own grant money to pay for the sequencing costs at the centers to tackle the genomes they were most interested in. The team also negotiated with the Mori in New Zealand and officials in Mexico to get kkp and vaquita samples in a beautiful example of international collaboration, says Sadye Paez, program director of the VGP at Rockefeller.

The massive team of researchers pulled off a series of technological advances. The new sequencing machines let them read DNA chunks 10,000 or more letters long, instead of just a few hundred. The researchers also devised clever methods for assembling those segments into individual chromosomes. They have been able to tease out which genes were inherited from the mother and the father. This solves a particularly thorny problem known as false duplication, where scientists mistakenly label maternal and paternal copies of the same gene as two separate sister genes.

I think this work opens a set of really important doors, since the technical aspects of assembly have been the bottleneck for sequencing genomes in the past, says Jenny Tung, a geneticist at Duke University, who was not directly involved with the research. Having high-quality sequencing data will transform the types of question that people can ask, she says.

The teams improved accuracy shows that previous genome sequences are seriously incomplete. In the zebra finch, for example, the team found eight new chromosomes and about 900 genes that had been thought to be missing. Previously unknown chromosomes popped up in the platypus as well, as members of the team reported online in Nature earlier this year. The researchers also plowed through, and correctly assembled, long stretches of repetitive DNA, much of which contain just two of the four genetic letters. Some scientists considered these stretches to be non-functional junk or dark matter. Wrong. Many of the repeats occur in regions of the genome that code for proteins, says Jarvis, suggesting that the DNA plays a surprisingly crucial role in turning genes on or off.

Thats just the start of what the Nature paper envisions as a new era of discovery across the life sciences. With every new genome sequence, Jarvis and his collaborators uncover new and often unexpected findings. Jarviss lab, for example, has finally nabbed the regulatory region of a key gene parrots and songbirds need to learn tunes; next, his team will try to figure out how it works. The marmoset genome yielded several surprises. While marmoset and human brain genes are largely conserved, the marmoset has several genes for human pathogenic amino acids. That highlights the need to consider genomic context when developing animal models, the team reports in a companion paper in Nature. And in findings published last year in Nature, a group led by Professor Emma Teeling at University College Dublin in Ireland discovered that some bats have lost immunity-related genes, which could help explain their ability to tolerate viruses like SARS-CoV-2, which causes COVID-19.

The highly endangered kkp parrot lacks genetic diversity but has apparently been able to purge deleterious mutations, a new analysis of its genome suggests.

The new information also may boost efforts to save rare species. It is a critically important moral duty to help species that are going extinct, Jarvis says. Thats why the team collected samples from a kkp named Jane, part of a captive breeding program that has brought the parrot back from the brink of extinction. In a paper published in the new journal Cell Genomics, of the Cell family of journals, Nicolas Dussex at the University of Otago and colleagues described their studies of Janes genes along with other individuals. The work revealed that the last surviving kkp population, isolated on an island off New Zealand for the last 10,000 years, has somehow purged deleterious mutations, despite the species low genetic diversity. A similar finding was seen for the vaquita, with an estimated 10-20 individuals left on the planet, in a study published in Molecular Ecology Resources, led by Phil Morin at the National Oceanic and Atmospheric Administration Fisheries in La Jolla, California. That means there is hope for conserving the species, Jarvis concludes.

High-quality gene sequences show previously unknown chromosomes in the platypus.

The VGP is now focused on sequencing even more species. The project teams next goal is finishing 260 genomes, representing all vertebrate orders, and then snaring enough funding to tackle thousands more, representing all families. That work wont be easy, and it will inevitably bring new technical and logistical challenges, Tung says. Once hundreds or even thousands of animals readily found in zoos or labs have been sequenced, scientists may face ethical hurdles obtaining samples from other species, especially when the animals are rare or endangered.

But with the new paper, the path ahead looks clearer than it has in years. The VGP model is even inspiring other large sequencing efforts, including the Earth Biogenome Project, which aims to decode the genomes of all eukaryotic species within 10 years. Perhaps for the first time, it seems possible to realize the dream that Haussler and many others share of reading every letter of every organisms genome. Darwin saw the enormous diversity of life on Earth as endless forms most beautiful, Haussler observes. Now, we have an incredible opportunity to see how those forms came about.

Reference: Towards complete and error-free genome assemblies of all vertebrate species by Arang Rhie, Shane A. McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim, Chul Lee, Byung June Ko, Mark Chaisson, Gregory L. Gedman, Lindsey J. Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C. Vernes, Tanya M. Lama, Frank Grutzner, Wesley C. Warren, Christopher N. Balakrishnan, Dave Burt, Julia M. George, Matthew T. Biegler, David Iorns, Andrew Digby, Daryl Eason, Bruce Robertson, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F. Kautt, Paolo Franchini, H. William Detrich III, Hannes Svardal, Maximilian Wagner, Gavin J. P. Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B. Kingan, Richard Hall, Zev Kronenberg, Ivan Sovi, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E. Green, Nicholas H. Putnam, Ivo Gut, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Robel E. Dagnew, Dengfeng Guan, Sarah E. London, David F. Clayton, Claudio V. Mello, Samantha R. Friedrich, Peter V. Lovell, Ekaterina Osipova, Farooq O. Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Michael Hiller, Yang Zhou, Robert S. Harris, Kateryna D. Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kevin Howe, Paul Flicek, Brian P. Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert H. S. Kraus, Andrew J. Crawford, M. Thomas P. Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert W. Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E. Johnson, Federica Di Palma, Tomas Marques-Bonet, Emma C. Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A. Ryder, David Haussler, Stephen J. OBrien, Jonas Korlach, Harris A. Lewin, Kerstin Howe, Eugene W. Myers, Richard Durbin, Adam M. Phillippy and Erich D. Jarvis, 28 April 2021, Nature.DOI: 10.1038/s41586-021-03451-0

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First Major Discoveries Reported From Project to Read Complete Genetic Sequences of All 70,000 Vertebrate Species - SciTechDaily

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The origin of reproductive organs | Penn Today – Penn Today

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Early in human development, during the first trimester of gestation, a fetus may have XX or XY chromosomes that indicate its sex. Yet at this stage a mass of cells known as the bipotential gonad that ultimately develops into either ovaries or testes has yet to commit to its final destiny.

While researchers had studied the steps that go into the later stages of this process, little has been known about the precursors of the bipotential gonad. In a new study published in Cell Reports and co-led by Kotaro Sasaki of Penns School of Veterinary Medicine, an international team lays out the detailed development of this key facet of sexual determination in two mammalian models.

Using single-cell transcriptome data, we can get a lot of information about gene expression at each developmental stage, says Sasaki. We can define what the default process is and how it might go awry in some cases. This has never been done in traditional developmental biology. Now we can understand development in molecular terms.

Disorders of sex development (DSD) occur when internal and external reproductive structures develop differently from what would be expected based on an individuals genetics. For example someone with XY chromosomes might develop ovaries. These conditions often affect fertility and are associated with an increased risk of germ cell tumors.

These disorders oftentimes create psychological and physical distress for patients, Sasaki says. Thats why understanding gonadal development is important.

To understand atypical development, Sasaki and colleagues in the current study sought to layout the steps of typical development, working with a mouse model and a monkey model.

The researchers began by examining mouse embryos throughout embryonic development, using molecular markers to track the location of different proteins suspected to be involved in the formation of reproductive structures. They noticed that by day nine of a mouses embryonic development, a structure called the posterior intermediate mesoderm (PIM) lit up brightly with the marker for a gene critical to the development of gonads, kidneys, and the hormone-producing adrenal glands, which are located adjacent to the kidneys.

Zeroing in on the PIM and its progeny cells, the team found that, by day 10.5, these also expressed a marker known to be associated with the bipotential gonad.

People have previously studied the origin of the urogenital organs and the kidney and based on that believed that their origins were very close, Sasaki says. So our hypothesis was that the PIM was the origin of the gonads as well as the kidneys.

To identify the origin of the gonad, they performed lineage tracing, in which scientists label cells in order to track their descendents, which indeed supported the connection between the PIM and the gonads.

To further confirm that the PIM played a similar role in an organism closer to humans in reproductive biology, the researchers made similar observations in embryos from cynomolgus monkeys. Though the developmental timing was different from the mouse, as was expected, the PIM again appeared to give rise to the bipotential gonad.

Digging even deeper into the molecular mechanism of the transition between the PIM and bipotential gonad, the researchers used a cutting-edge technique: single-cell sequencing analysis, whereby they can identify which genes are being turned on during each developmental stage.

Not only were they able to identify genes that were turned onmany of which had never before been associated with reproductive developmentbut they observed a transition state between the PIM and bipotential gonad, called the coelomic epithelium. Comparing the mice and monkey embryos, the researchers came up with a group of genes that were conserved, or shared between the species. Some of these genes are already known to be important for the development of mouse and human ovaries and testes, Sasaki says, and some have been implicated in the development of DSDs.

He notes that in roughly half of patients with DSDs, however, the genetic cause is unknown. So this database were assembling may now be used to predict some additional genes that are important in DSD and could be used for screening and diagnosis of DSDs, or even treatment and prevention.

The study also illuminated the relationship between the origin of the kidneys, adrenal glands, and gonads. They all originate from the PIM, but the timing and positioning is different, Sasaki says.

The adrenal glands, he says, develop from the anterior portion of the PIM, or that section closer to the head and arise early, while the kidney arises later from the posterior portion of the PIM. The gonadal glands span the PIM, with some regions developing earlier and others later.

In future studies, Sasaki and colleagues would like to continue teasing out the details and stages of gonadal development. Sasakis ultimate goal is to coax a patients own stem cells to grow into reproductive organs in the lab.

Some patients with DSDs dont have ovaries and testes, and some cancer patients undergo chemotherapy and completely lose their ovary function, Sasaki says. If you could induce a stem cell to grow into an ovary in the lab, you could provide a replacement therapy for these patients, allowing them to regain normal hormone levels and even fertility. With a precise molecular map to the developing gonad in hand, we are now one step closer to the this goal.

Kotaro Sasaki is an assistant professor in the Department of Biomedical Sciences in the University of Pennsylvania School of Veterinary Medicine.

Sasakis coauthors on the study were Penns Keren Cheng and Yasunari Seita; Kyoto Universitys Akiko Oguchi, Yasuhiro Murakawa, Ikuhiro Okamoto, Hiroshi Ohta, Yukihiro Yabuta, Takuya Yamamoto, and Mitinori Saitou; and Shiga University of Medical Sciences Chizuru Iwatani and Hideaki Tsuchiya. Sasaki and Saitou were corresponding authors.

The study was supported by a JST-ERATO Grant (JPMJER1104), Grant-in-Aid for Specially Promoted Research from JSPS (17H06098), the Pythias Fund, and the Open Philanthropy Fund from Silicon Valley Community Foundation (2019-197906).

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The origin of reproductive organs | Penn Today - Penn Today

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Project to Read Genomes of All 70000 Vertebrate Species Reports First Discoveries – Howard Hughes Medical Institute

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HHMI Investigator Erich Jarvis and dozens of colleagues have launched an ambitious project to read the genomes of every vertebrate species. Credit: Peter Ross

Its one of the most audacious projects in biology today reading the entire genome of every bird, mammal, lizard, fish, and all other creatures with backbones.

###

Citation

Arang Rhie et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. Published online April 28, 2021. doi: 10.1038/s41586-021-03451-0

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Project to Read Genomes of All 70000 Vertebrate Species Reports First Discoveries - Howard Hughes Medical Institute

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ProQR Therapeutics and Yarrow Biotechnology, an RTW Investments, LP Incubated Company, Announce Exclusive Worldwide License and Discovery…

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NEW YORK, New York, LEIDEN, Netherlands & CAMBRIDGE, Mass., May 04, 2021 (GLOBE NEWSWIRE) -- RTW Investments, LP (RTW), a global, full life-cycle investment firm that focuses on identifying transformational and disruptive innovations across the biopharmaceutical and medical technologies sectors, and ProQR Therapeutics N.V. (Nasdaq: PRQR) (ProQR), a company dedicated to changing lives through the creation of transformative RNA therapies for genetic eye diseases, today announced that Yarrow Biotechnology, Inc. (Yarrow) , a company newly created by RTW, has in-licensed exclusive rights to ProQRs antisense oligonucleotide technology (ASO) to develop and commercialize potential therapies for an undisclosed non-ophthalmic target. Yarrow is focused on developing ASO-based therapeutics for disorders with high unmet need.

Roderick Wong, MD, Managing Partner and Chief Investment Officer of RTW, said: We believe RNA-based therapies hold great promise to treat genetically-defined diseases. We are excited to partner with ProQR to in-license the first target to be developed in Yarrows pipeline.

Under the terms of the agreement, ProQR is eligible to receive up to $115 million of upfront and milestone payments, plus single digit percentage royalties on the net sales of any resulting products during the royalty term. ProQR will also have the right to receive an undisclosed percentage of equity in the form of shares of common stock of Yarrow. ProQR will be responsible for certain preclinical activities with reimbursement for the research costs by Yarrow, while Yarrow will be responsible for continuing development of the program and commercialization activities.

Gerard Platenburg, Chief Innovation Officer at ProQR, will join Yarrows board of directors.

Peter Fong, PhD, Head of Company Creation at RTW, said: Our partnership with ProQR fits perfectly into Yarrows mission to develop first-in-class ASO-based therapies for genetically-defined diseases. We look forward to a long and productive partnership.

Daniel A. De Boer, Founder and CEO of ProQR, said: As we focus ProQR on our core genetic eye disease strategy, we are pleased to partner with Yarrow to advance our technology in applications outside the eye, while generating value from this partnership and the broad applicability of our platform.

About RTW Investments, LP

RTW Investments, LP (RTW) is a New York-based, global, full life-cycle investment firm that focuses on identifying transformational and disruptive innovations across the biopharmaceutical and medical technologies sectors. As a leading partner of industry and academia, RTW combines deep scientific expertise with a solution-oriented investment approach to support emerging medical therapies and the companies and academics developing them.

About Yarrow Biotechnology, Inc.

Yarrow Biotechnology, Inc. (Yarrow) is a newly formed biotechnology company developing antisense oligonucleotide-based therapeutics for disorders with high unmet need. Yarrow has established a proprietary target discovery engine leveraging large-scale human genetics studies to uncover novel targets where there is a significant unmet need.

Yarrow is the latest new company created and backed by RTW Investments, LP.

About ProQR

ProQR Therapeutics is dedicated to changing lives through the creation of transformative RNA therapies for the treatment of severe genetic rare diseases such as Leber congenital amaurosis 10, Usher syndrome and retinitis pigmentosa. Based on our unique proprietary RNA repair platform technologies we are growing our pipeline with patients and loved ones in mind. Learn more about ProQR at http://www.proqr.com.

Forward Looking Statements for ProQR

This press release contains forward-looking statements. All statements other than statements of historical fact are forward-looking statements, which are often indicated by terms such as "anticipate," "believe," "could," "estimate," "expect," "goal," "intend," "look forward to", "may," "plan," "potential," "predict," "project," "should," "will," "would" and similar expressions. Such forward-looking statements include, but are not limited to, statements regarding the collaboration with RTW and Yarrow and the intended benefits thereof, including milestone and royalty payments from commercial product sales, if any, from the products covered by the collaboration and the issuance of equity in Yarrow to ProQR, as well as the potential of our technologies and product candidates. Forward-looking statements are based on management's beliefs and assumptions and on information available to management only as of the date of this press release. Our actual results could differ materially from those anticipated in these forward-looking statements for many reasons, including, without limitation, the risks, uncertainties and other factors in our filings made with the Securities and Exchange Commission, including certain sections of our annual report filed on Form 20-F. These risks and uncertainties include, among others, the cost, timing and results of preclinical studies and clinical trials and other development activities by us and our collaborative partners whose operations and activities may be slowed or halted by the COVID-19 pandemic; the likelihood of our clinical programs being executed on timelines provided and reliance on our contract research organizations and predictability of timely enrollment of subjects and patients to advance our clinical trials and maintain their own operations; our reliance on contract manufacturers to supply materials for research and development and the risk of supply interruption from a contract manufacturer; the potential for future data to alter initial and preliminary results of early-stage clinical trials; the unpredictability of the duration and results of the regulatory review of applications or clearances that are necessary to initiate and continue to advance and progress our clinical programs; the ability to secure, maintain and realize the intended benefits of collaborations with partners; the possible impairment of, inability to obtain, and costs to obtain intellectual property rights; possible safety or efficacy concerns that could emerge as new data are generated in research and development; and general business, operational, financial and accounting risks, and risks related to litigation and disputes with third parties. Given these risks, uncertainties and other factors, you should not place undue reliance on these forward-looking statements, and we assume no obligation to update these forward-looking statements, even if new information becomes available in the future, except as required by law.

For ProQR Therapeutics N.V.

Investor Contact:Sarah KielyProQR Therapeutics N.V.T: +1 617 599 6228skiely@proqr.comorHans VitzthumLifeSci AdvisorsT: +1 617 430 7578hans@lifesciadvisors.com

Media Contact:Cherilyn Cecchini, MDLifeSci CommunicationsT: +1 646 876 5196ccecchini@lifesciadvisors.com

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Global Genes and Orphan Disease Center of the University of Pennsylvania to Convene Patient Group Leaders, Researchers, Clinicians and Industry for…

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ALISO VIEJO, Calif.--(BUSINESS WIRE)--The international rare disease patient advocacy organization, Global Genes, is pleased to announce the 6th Annual RARE Drug Development Symposium (RDDS) in partnership with the Orphan Disease Center of the University of Pennsylvania. The June 9-11 virtual event will connect and educate hundreds of advocates, clinicians, and academic and industry researchers to explore the latest science, opportunities, and challenges to the advancement of therapies for more than 7,000 rare diseases.

New to this year's event is an optional preconference workshop targeted to attendees who are in the earlier stages of their research efforts or careers and looking to build knowledge in core competencies that will be expanded upon in the main RDDS program. The main program will address the current landscape of rare drug development and allow attendees to interact with subject matter experts and other rare disease stakeholders to help them better understand and develop their impact and role in advancing potential treatments.

This year, the RDDS keynote speaker will be David Fajgenbaum, M.D., MBA, MSc, co-founder and executive director of the Castleman Disease Collaborative Network (CDCN), assistant professor of medicine in Translational Medicine & Human Genetics at the University of Pennsylvania, associate director, Patient Impact for the Orphan Disease Center of the University of Pennsylvania, and author of the national bestselling book, Chasing My Cure: A Doctors Race to Turn Hope Into Action.

Dr. Fajgenbaum has been a leader in helping researchers to prioritize treatments for COVID-19 clinical trials and inform patient care through the CORONA (COvid19 Registry of Off-label & New Agents) Project. Were thrilled to have him share his insights during this critical time in health care and understand how we can apply these approaches to accelerate progress in rare disease research and treatments, said Craig Martin, CEO at Global Genes. The rare disease leaders who will be featured during the RDDS have tremendous depth of knowledge to share, and we look forward to sharing it with members of the rare community during this event.

RDDS will continue to host the CureAccelerator Live! For Rare Diseases 2021 event on June 10 in partnership with Cures Within Reach, a not-for-profit organization exclusively dedicated to using the speed, safety, and cost-effectiveness of already approved drugs, devices, diagnostics, nutraceuticals, and combination products to impact patients with unmet medical needs driving more treatments to more patients more quickly.

The emergence of therapeutic platforms creates unprecedented opportunities for treatments to improve the lives of those living with rare diseases, said Jim Wilson, M.D., Ph.D., director, Gene Therapy Program, and Rose H. Weiss, professor and director at the Orphan Disease Center of the University of Pennsylvania. We are delighted to collaborate with Global Genes to educate the rare disease community on research directed to these treatments.

Thank you to our gold sponsors, Horizon Therapeutics and Greenwich Biosciences, and silver sponsor, Pfizer, Inc., for their generous support of this important event.

For more information, visit http://www.globalgenes.org/rdds.

About Global Genes

Global Genes is a 501(c)(3) nonprofit organization dedicated to eliminating the burdens and challenges of rare diseases for patients and families globally. In pursuit of our mission, we connect, empower, and inspire the rare disease community to stand up, stand out, and become more effective on their own behalf helping to spur innovation, meet essential needs, build capacity and knowledge, and drive progress within and across rare diseases. We serve the more than 400 million people around the globe and nearly one in 10 Americans affected by rare diseases. If you or someone you love has a rare disease or are searching for a diagnosis, contact Global Genes at 949-248-RARE, or visit our resource hub.

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Global Genes and Orphan Disease Center of the University of Pennsylvania to Convene Patient Group Leaders, Researchers, Clinicians and Industry for...

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Should scientists be allowed to grow human embryos in a dish beyond 14 days? Is it scientifically important or morally wrong? – USA TODAY

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For more than 30years, scientists have followed a rule they imposed on themselves to avoid growing a human embryo in a lab dish for more than 14 days.

Until recently, the "14-day rule" was largely academic. Scientists couldn't grow themfor that long if they wanted to.

But in 2016, two teams of researchers reached 12days, and in 2019, another group grew monkey embryos for 19 days.

These advances have spurredsome scientists to argue in two recent papersthat the 14-day rule should bemodified or dropped. There's a lot to be learned by pushing embryos out to 28 days, they say.

The regulatory committee of theInternational Society for Stem Cell Research, which lays down guidelines for the scientificfield,has been debating the issuefor months and is expected to issue its final decision this month.

Some ethicists and scientistsare concerned that revising the rule just asit becomes technologically feasible to break it is ridiculous and morally repugnant.

"If you abandoned every rule or law that inhibits you as soon as it inhibits you, we'd live in a lawless world," said Ben Hurlbut, a historian of science at Arizona State University.

And somepeople consider human embryo researchto be unethical at any stage.

"Whether 14 days, 14 months, or anywhere in between, such 'rules'remain contrivances to justify the most unethical kinds of science and to allow for the exploitation of our own vulnerable human offspring," said Tadeusz Pacholczyk, a neuroscientist and director of education at the National Catholic Bioethics Center in Philadelphia.

A single cell is removed from a human embryo to be used in generating embryonic stem cells for scientific research.Advanced Cell Technology via AP

Countries are free to ignore rules set by the society, but scientists for decades have generally abided by them. (In the U.S., there's no national law about the 14-day rule, though some states have their own regulations.)

Some cultures and religions believe that human life begins at conception, or that the human embryo carries a special status from conception onward. Other cultures believe that life starts later in fetal development, or even at birth.

Biologists routinely grow amphibian and mammal embryos in petri dishes, but human embryos are different.

Until about 14 days after conception, the human embryo looks likean undifferentiated blob of cells, which is one of the reasons the two week timeframemade sense, several scientists said.

Robin Lovell-Badge, who sits on the International Stem Cell Society committee that's considering overturning the rule, said scientists will take any changes seriously.

"We've stuck with that rule for over 30 years," he said.

Lovell-Badgefavors extending the limit, as long as the research is scientifically justified and has public support.

Not everyone in the scientific community shares this position.

"It's been a difficult part of the guidelines to get agreement on," Lovell-Badge said. "You have very wide-ranging views."

Some scientists argue there's a lot to be learned by pushing the 14-day rule out another two weeks.

Right now the second two weeks after fertilization is considered a "black box" because so little is known about it, said Insoo Hyun, a professor of bioethics atCase Western and Harvard universities. Heco-wrote a March 5 opinion piece arguing for a careful, stepwiseextension of the 14-day rule.

"You have to really make your case for it,"Hyun said."You have to explain what you want to do and why, have a very clear picture of where the next stopping point is."

Women generally don't know they're pregnant before 28 days, so historically, there has not been tissue from aborted or miscarried fetuses available for research.

The central nervous system, heart and other organs begin to develop during this crucial two-week period. The body plan is established. Cells that will become eggs and sperm start to form. Aspects of theplacenta are set up.

In many ways,days 14 through28 are the most interesting period of human development, Lovell-Badge said. "You can do a whole lot of incredibly valuable research," in that timeframe, he said.

And it's in that window that many things can go wrong in a pregnancy, such as miscarriage or abnormalities.

Perhaps there are treatments that could be developed to fix these problems, if they are better understood,Hyunsaid, just as pregnant women now take vitamin supplements to prevent spina bifida, in which the spine doesn't developproperly.

Do you think scientists should be allowed to grow embryos in a dish beyond 14 days? Share this story.

Developing embryos for another week "will thus illuminate this poorly understood period of our development and bring greater understanding of pregnancy loss and developmental disease,"saidMagdalenaZernicka-Goetz,theBritish scientist who developed the technique for growing human embryos for nearly two weeks.Zernicka-Goetz,author of a 2020 book on human development called "The Dance of Life,"would like to extend the 14-day rule out one week to 21 days.

"This will enable thescientiststo study a period of development that are highly susceptible to developmental failure, something that happens quite frequently in human pregnancy," she wrote in an email, stressing work should be closely regulated"to achieve these potential biomedical advances within an appropriate bi-ethical framework."

Despite their differences, most scientists seem to agreethere's no reason to push development past 28 days.

By onemonth after conception, embryonic tissue is easier to obtain and study and theorgans have formed, leaving fewer questions to answer.

"You wouldn't need to take them much beyond that point anyway," Lovell-Badgesaid.

Pacholczyk, of the Catholic Bioethics Center, said there's simply no justification for 14 days or any other time limit.

"Researchers have been feigning for a long time that the 14-day rule was somehow an ethical tenet grounded in biological facts while in reality it has been little more than a ceremonial 'line in the sand' and it should come as little surprise that they are now seeking to move that line beyond 14 days," he wrote in an email.

Even some who strongly supportscientific research are uncomfortable extending the 14-day rule.

HenryGreely, who directs the Stanford Center for Law and the Biosciences at Stanford University in California, saidthere should be a hard-stop endpointfor embryo research.

"Even though I do not personally give strong moral status to embryos, the idea of doing research on 18-day-oldhuman embryos is disturbing," said Greely, author of the new book "CRISPR People: The Science and Ethics of Editing Humans."

This sequence of images shows the development of embryos after correcting for a genetic error that would otherwise cause a type of inherited heart disease.OHSU

"I'd like to see an endpoint that had some rationale that would make it likely to stick," he said.

Growing an embryo in a lab dish instead of a woman's womb is necessarily different, Greely said, and may not represent a "real" embryo anyway.

"Does a 14-day embryo that is not implanted deep in a woman's uterus tell us anything meaningful about a 14-day embryo that is?" he asked.

Marcy Darnovsky, executive director of the Center for Genetics and Society, a nonprofit advocacy group,said efforts to overturn the 14-day rule are another example of scientific over-reach.

"There's a real problem with scientists who are jumping ahead of the public," she said.

Scientists should not be the ones who get to decide where society's moral boundaries lie,she and Hurlbut said.

"If moves are made to usurp these questions from wider society," Hurlbut said, "it's to the detriment of democracy and to the detriment of sciencecertainly in the long run, and probably in the short run."

Contact Karen Weintraub at kweintraub@usatoday.

Health and patient safety coverage at USA TODAY is made possible in part by a grant from the Masimo Foundation for Ethics, Innovation and Competition in Healthcare. The Masimo Foundation does not provide editorial input.

Published10:13 am UTC May. 2, 2021Updated10:13 am UTC May. 2, 2021

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Should scientists be allowed to grow human embryos in a dish beyond 14 days? Is it scientifically important or morally wrong? - USA TODAY

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New pandemic advice from the New York Times: Practicing good hygiene may be worse than COVID-19 – WSWS

Posted: at 8:25 pm

The title of a puzzling opinion piece published recently in the New York Times, written by author Markham Heid, asks: Can we learn to live with germs again? The subtitle proceeds to answer the curious question by suggesting that our health depends on resuming our pre-pandemic lifestyles that expose us to bacteria, despite the risks posed by the coronavirus. In short, the entire article promotes, in a virulent form of the not-so-subtle and unscientific construct, the cure cant be worse than the disease, taken to its extreme and bizarre conclusions that good hygiene is worse than COVID-19.

The author of this piece, Markham Heid, who the Times describes as a longtime health and science journalist who has written extensively about the microbiome, is, in fact, no such expert. He received his bachelors degree from the University of Michigan in English (2005), and his masters in journalism from Northwestern University (2009). He is a freelance writer, a title that in this case signifies that he writes about many things about which he does not know very much.

In his LinkedIn profile, he wrote, Im a regular contributor at TIME, Medium, and Food & Wine. My work has appeared in Playboy, Popular Mechanics, Everyday Health, Sports Illustrated, and elsewhere. Ive received reporting awards from the Society of Professional Journalists and the Maryland, Delaware, and D.C. Press Association. Im always open to new opportunities.

Armed with these dubious credentials, Heid sets outwith the endorsement of the New York Timesto mislead and miseducate his readers.

After introducing a video commissioned by United Airlines that demonstrates how breakthrough technology was being employed to clean air cabins, Heid questions these drastic measures. He claims that a century of accumulated scientific understanding of germs and disease has led to the misconception that only sterile environments are safe ones. The deception lies entirely with Mr. Heid and the Times in their attempt to pawn off their pseudo-scientific rationale. In short, they are attempting to assert that the measures employed to mitigate community transmission are doing more harm than good.

The article, which received a significant showing in the Times, provocatively opens with disgusting glossy close-up photos of filthy fingernails caressing the brow of a child with reddened eyes, a grime-ridden door handle clasped with dirty hands, and another showing snot dripping into a childs saliva-soaked open mouth whose face is covered with crayon markings.

Later in the piece, another photo shows macaroni and cheese splattered onto a childs hands and sleeves. And still another, a near-empty bottle of milk clasped with filthy hands, presumably being drunk directly out of the container.

Aside from their shock value, the images are intended to browbeat the reader into accepting the conclusions that these unhygienic practices are essential for enhancing our immunity and well-being. Exposure to these friendly pathogens, the article asserts, is vital to boost the immune system appropriately, and our obsession with cleanliness and sterility, avoidance of hugging and kissing each other during the pandemic could hazardously impact our bodies microbiomes and subsequent health.

Heid goes on to add, Despite the now consensus recognition that air transmission, not surface spread, is more important, most pandemic sanitation practices have continued. We continue to annihilate every microbe in our midst, even though most are harmless. After citing New York Citys efforts to keep subways clean, as well as surveys that indicate commuters were appreciative of these measures, he added, But some health experts are watching this ongoing onslaught with a mounting sense of dread. They fear that many of the measures weve employed to stop the virus, even some that are helpful and necessary, may pose a threat to human health in the long run if they continue.

Heid then enters the discussion in the barely understood world of human microbiomes, the microscopic environments of our guts, skin and oral membranes, where trillions of bacteria live in a symbiotic relationship with all living animals, including humans. Allusions are then made to recent associations between the changes in a persons microbiome and diseases such as asthma or obesity to defend this stance.

It is understood that some diseases of gynecologic (bacterial vaginosis) or gastrointestinal (Clostridium difficile colitis) origin have been linked to bacterial overgrowth. It has also become clear that misuse of antibiotics can promote the development of antibiotic-resistant strains of bacteria. Some researchers have hypothesized that there may be correlations between the development of early-onset autoimmune diseases and the dominance of certain bacteria in the gut microbiome. However, these assertions have far from been established. Heids equating these diseases to hygienic practices and the field of microbiomes is an attempt to mislead.

In a 2018 article published in Nature Medicine, Dr. Jack Gilbert and colleagues, after reviewing the current understanding of the human microbiome, conclude, There remains much that we do not understand about human microbiomes. The sources of bacteria that colonize an infant include the mother and other caregivers (even one-day-old pre-term infants have unique microbiomes that differ from each other and from the mother but possibly derived from their mothers), and human genetics shapes microbiome-immune interaction.

They added, The human microbiome is highly personalized. Understanding the relevance of the differing microbiota between individuals is confounded by the uniqueness of an individuals microbiome. The microbiome of every individual is unique to the person, making a generalization about their impact on the promotion of disease difficult.

Indeed, the study of human microbiomes is fascinating and novel, and over time may provide important insight into the dynamics of human diseases and health. However, as the authors note, present investigations have failed to establish firm conclusions and instead only raise critical questions. Many of these studies have been broad-based observational studies or animal models that lack sufficient context to justify shifts in public health practices.

However, with regards to the COVID-19 pandemic, which has, in a short period, infected over 150 million people worldwide, killing, at a minimum, 3.2 million people, how does the concern raised over the impact of hygienic standards and the impact of the microbiome even compare to the scale of this global crisis? This is a preposterous and dangerous insinuation on the part of Mr. Heid and the Times.

He attempts to defend this position by citing a paper published in the Proceedings of the National Academy of Sciences (PNAS) in January, titled, The hygiene hypothesis, the COVID pandemic, and consequences for the humane microbiome. What becomes immediately clear upon reading the PNAS paper is that the position being forwarded by Heid and the Times is incongruent with the subject of the article he cites.

In no uncertain terms, the authors wrote, We want to be clear: Preventing COVID-19 transmission is necessary, and the hygienic transformations of the past 100 years have resulted in major reductions in mortality from infectious diseases. Their foray into the world of microbiomes and COVID-19 is posed as a question: What microbial functions might we lose as a result of COVID-19 prevention efforts? What are the consequences as humans continue to encounter nutritional and immune challenges in future generations, and what can be done to mitigate them? They respond to their query, This pandemic presents a significant opportunity to study, in real-time, the relationship between an infectious agent, the microbiome, precipitous and uneven social and economic changes, and their combined effects on health and disease.

The hygiene hypothesis, first put forth by Dr. David Strachan in the late 1980s, states that early childhood exposure to various microorganisms, specifically from the gut flora and parasites, possibly aid in bolstering a young persons immune system. More precisely, the lack of exposure is thought to lead to a deficiency in immune tolerance, which predisposes environmental allergies.

However, this hypothesis has been erroneously interpreted as an attack on personal cleanliness, although there is no indication that any excesses on that score have impacted allergies and immune disorders and they have not been known to increase the risks of infections. On the contrary, hygienic standards have been critical for protecting vulnerable populations and have been the first line of defense in preventing the spread of antibiotic-resistant organisms and emerging infectious diseases such as COVID-19.

The authors of the PNAS article explained that the loss of microbial diversity, which has accelerated over the last century, is a byproduct of increased urbanization, overuse of antibiotics, and other medications. Additionally, they cite changes in birth and infant feeding practices, intensified hygienic practices, and the reduced diversity of global diet, specifically the decreased intake of dietary fiber and increased consumption of processed foods, to the development of disease. Compounding these have been the widespread use of tobacco, alcohol and other drugs.

They theorized that the decline in these essential healthy microbes, a result of a shift in the globalization of food manufacturing to higher caloric and cheaper sources, has led to the rise in rates of chronic diseases such as obesity, diabetes, asthma and autoimmune disease. They write, This process of microbial diversity loss is occurring unevenly across the planet. Clean water, soap, and sanitation are not equally distributed to all people; access to and use of antibiotics is widespread in low- and middle-income countries, constituting a quick fix infrastructure, even for the poorest population. Moreover, multiple vulnerable populationsurban residents, racial and ethnic minorities, migrants, low-income earnersdisproportionately suffer from certain chronic diseases linked to altered microbial functionality.

Though they acknowledge up front that there is little direct evidence of interactions between human microbiomes and COVID-19 disease, the fundamental purpose of their perspective was to recognize the observations that susceptibility to the SARS-CoV-2 is linked to biological determinants that are impacted by demographic and socioeconomic factors that render the elderly, racial and ethnic minorities, and those with lower socioeconomic status more likely to suffer worse outcomes from COVID-19 infection; these same groups have existing pathologies that correlate with dysbiosis [imbalance between the types of organisms present in a persons natural microflora] of gut microbiota.

The concerns raised by the PNAS article are far more urgent than those being discussed by Heids article, which is entirely out of touch with the lives of millions of people whose lives and livelihoods have been upended by the economic upheaval and health ramifications created by the COVID-19 pandemic.

It is worth noting that the coupling of hand washing to disease prevention is only a recent observation in the annals of medical history. In 1848, a Hungarian doctor, Ignaz Semmelweis, while working at a Viennese hospital, observed that the high maternal deaths they were encountering were a byproduct of a potential pathogen acquired when training physicians were called away during cadaver dissections to deliver an expecting mother without washing their hands. At the time, there was no clear understanding of bacterial or viral infections.

To test his hypothesis, he ordered physicians to wash their hands and instruments in a chlorine solution. After implementing a hand hygiene protocol, there was a dramatic decline in maternal mortality from 18 to 1 percent. However, Dr. Semmelweis met with resistance from his colleagues, offended by the notion that they were the source of the maternal infections. Dr. Nancy Tomes, a professor of history at Stony Brook University, New York, explained, The majority of doctors in Vienna at this time were from middle- or upper-class families, and they thought of themselves as very clean people compared with the working-class poor. He was insulting them when he said their hands could be dirty.

Dr. Semmelweis would lose his position and eventually was committed to a psychiatric institution, where he died at 47. Still, the following decades proved to be decisive in the field of infectious disease. Louise Pasteur brought awareness to pathogens and how to kill them using heat. Joseph Lister, a British surgeon, introduced antiseptic surgery, which included hand washing, which, Tomes noted, moved from being something doctors did to something everybody had been told to do. Potentially, a breakthrough in the study of microbiomes can provide critical links between social determinants of health and disease. These discoveries in the 19th century were crucial to the advancement of medicine and public health disciplines.

Despite our appreciation of the relationship between unsanitary conditions and disease, these basics in maintaining community hygienic practices are impossible for most countries. According to the World Health Organization and UNICEFs Joint Monitoring Program for Water Supply, Sanitation, and Hygiene, over 60 percent of the worlds population, or 4.5 billion people, lack access to safe sanitation. One in three people on the planet cannot receive safe drinking water. Two billion people use water sources that have been contaminated with feces.

In 2007, the readers of the British Medical Journal voted sanitation as the most important medical milestone since 1840. Ten percent of the global burden of disease is associated with poor sanitation conditions. These predominate in the densely populated urban centers of Africa, Asia and Latin America. Diarrheal disease caused by fecal-oral contamination kills 1.6 million to 2.5 million each year, many under the age of five years, living in developing countries. Adequate sanitation, well-maintained sewage systems and water treatment plants can dramatically reduce the burden of such diseases.

The Times article is an exercise in obfuscation and deceit. Heid deliberately attempts to equate the problem created by issues such as excessive use of antibiotics with hygienic measures essential to stop the spread of COVID-19. To imply that cleaning subways, washing hands, etc., will deprive humans of necessary contact with microbes (such as those we have in our gut) is absurd. One might just as well make the same argument about sanitizing hospitals. But as is well known, the transmission of bacteria and other germs is among the most significant problems confronting doctors and their patients in health facilities.

Heids commentary is aimed at delegitimizing hygienic measures whose implementation might subtract from the corporate bottom line. This is a variant of the dont let the cure be worse than the disease.

Moreover, the article completely ignores the fact that lack of adequate sanitation is, on a global scale, very possibly the greatest threat to health.

If the ignorant Heid is taken seriously, the conclusion to be drawn from his unappetizing piece is: Whenever you enter an office or store, make a point of licking the doorknobs.

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New pandemic advice from the New York Times: Practicing good hygiene may be worse than COVID-19 - WSWS

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Probiotics: Could they help treat IBD? – Medical News Today

Posted: at 8:25 pm

In inflammatory bowel disease (IBD), inflammation of the digestive tract can cause abdominal pain, diarrhea, fatigue, and weight loss, among other symptoms.

Crohns disease and ulcerative colitis are the two main types of IBD.

The Centers for Disease Control and Prevention (CDC) estimates that around 3 million adults in the United States have IBD.

One of the characteristics of the disease is increased permeability of the walls of the intestine sometimes known as a leaky gut which can provoke inflammation of the gut lining.

Protein complexes called tight junctions (TJs) act similarly to rivets to bind together adjacent cells in the guts lining to prevent microorganisms and other contents from seeping out.

The intestines TJ barrier is defective in IBD and other inflammatory conditions of the gut, including celiac disease and necrotizing enterocolitis.

Currently, there are no effective treatments to tighten the TJ barrier and reduce the permeability of the gut.

However, several studies have found that friendly bacteria in the gut help strengthen the intestinal barrier.

Scientists know that people with IBD have an imbalance in their gut bacteria, with reduced overall diversity of species and larger numbers of bacteria that provoke inflammation.

Researchers have tried to identify particular species of probiotic bacteria that enhance the TJ barrier and that could make effective treatments for IBD, but with inconclusive results.

However, in a new study, scientists have discovered a strain of Lactobacillus acidophilus that strengthens the TJ barrier in human cell cultures.

The strain, known as LA1, also reduced colitis, or inflammation of the inner lining of the colon, in a mouse model of IBD.

Our data indicate that LA1 is able to prevent colonic inflammation formation and promote colitis healing, says lead investigator Dr. Thomas Ma, Ph.D., of Penn State College of Medicine, Hershey Medical Center, in Hershey.

He says the findings suggest that the strain could have applications in a wide range of disorders involving chronic inflammation associated with a leaky gut, in addition to IBD.

These conditions include celiac disease, an autoimmune reaction to gluten in food, and necrotizing enterocolitis, where bacteria invade the intestine wall of premature infants.

The results of the study appear in The American Journal of Pathology.

The researchers screened more than 20 different probiotic species for their ability to tighten the TJ barrier.

They tested the bacteria in cultures of a human cell line called Caco-2, which scientists often use to model the intestinal epithelium.

Only LA1 caused a rapid, strong tightening of the TJ barrier.

The bacteria appeared to achieve this by activating a protein in the membrane of the cells, called a Toll-like receptor.

Toll-like receptors, part of the bodys immune defenses, recognize patterns on the surface of microbes.

Similar to ringing an intruder alarm, when the bacterium bound to the receptors, it triggered a train of events inside the cells that tightened the TJ barrier.

To test whether LA1 would have the same effect in a live animal, the researchers administered it orally to mice.

LA1 rapidly enhanced the TJ barrier in the animals, which then protected them against chemically induced colitis.

The bacterium also promoted healing of the intestinal barrier in mice with colitis.

In mice, the same Toll-like receptors mediated these enhancements of the TJ barrier.

Food manufacturers include L. acidophilus in a range of commercial brands of probiotic yogurt.

Medical News Today asked Dr. Ma whether any of these products contain the specific bacterial strain, LA1, that appears to protect the gut lining from inflammation.

Unfortunately, most probiotic companies do not list the specific strains contained in their probiotic product, Dr. Ma explained.

The Lactobacillus acidophilus strain that we referred to as LA1 is available in some of the commercial products, but it is not clear which do and do not, he said.

He added that the amount of probiotic bacteria in a product is also crucial to their biological effect, with quantities in excess of 1 billion colony-forming units per dose working best.

Dr. Ma went on to say that L. acidophilus is a component of healthy adults gut flora, but not necessarily LA1.

Because the bacterium undergoes constant genetic change, every individual will have different and often unique strains of the bacterium.

A persons diet helps determine the makeup of their gut microbiota, as recent research reported by MNT discovered.

The principal limitation of the current lab-based study was that its findings might not apply to people with inflammatory bowel conditions.

However, Dr. Ma and his colleagues hope to extend their investigation to include human volunteers, with possible clinical trials on the horizon.

The future direction of research in our laboratory is to test this in humans to see if [the bacteria] tighten the intestinal barrier and prevent or treat diseases associated with a leaky gut, said Dr. Ma.

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Should scientists be allowed to grow human embryos in a dish beyond 14 days? Is it scientifically important or morally wrong? – USA TODAY

New pandemic advice from the New York Times: Practicing good hygiene may be worse than COVID-19 – WSWS

Probiotics: Could they help treat IBD? – Medical News Today

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