Nanopore sequencing devices read individual RNA strands directly. This facilitates identification of exon linkages and nucleotide modifications; however, using conventional direct RNA nanopore ...sequencing, the 5' and 3' ends of poly(A) RNA cannot be identified unambiguously. This is due in part to RNA degradation in vivo and in vitro that can obscure transcription start and end sites. In this study, we aimed to identify individual full-length human RNA isoforms among ∼4 million nanopore poly(A)-selected RNA reads. First, to identify RNA strands bearing 5' m
G caps, we exchanged the biological cap for a modified cap attached to a 45-nt oligomer. This oligomer adaptation method improved 5' end sequencing and ensured correct identification of the 5' m
G capped ends. Second, among these 5'-capped nanopore reads, we screened for features consistent with a 3' polyadenylation site. Combining these two steps, we identified 294,107 individual high-confidence full-length RNA scaffolds from human GM12878 cells, most of which (257,721) aligned to protein-coding genes. Of these, 4876 scaffolds indicated unannotated isoforms that were often internal to longer, previously identified RNA isoforms. Orthogonal data for m
G caps and open chromatin, such as CAGE and DNase-HS seq, confirmed the validity of these high-confidence RNA scaffolds.
Non-alcoholic fatty liver disease (NAFLD) affects over 30% of adults in the United States. Bone morphogenetic protein (BMP) signaling is known to contribute to hepatic fibrosis, but the role of BMP ...signaling in the development of NAFLD is unclear. In this study, treatment with either of two BMP inhibitors reduced hepatic triglyceride content in diabetic (db/db) mice. BMP inhibitor-induced decrease in hepatic triglyceride levels was associated with decreased mRNA encoding Dgat2, an enzyme integral to triglyceride synthesis. Treatment of hepatoma cells with BMP2 induced DGAT2 expression and activity via intracellular SMAD signaling. In humans we identified a rare missense single nucleotide polymorphism in the BMP type 1 receptor ALK6 (rs34970181;R371Q) associated with a 2.1-fold increase in the prevalence of NAFLD. In vitro analyses revealed R371Q:ALK6 is a previously unknown constitutively active receptor. These data show that BMP signaling is an important determinant of NAFLD in a murine model and is associated with NAFLD in humans.
Aortic calcification is an important independent predictor of future cardiovascular events. We performed a genome-wide association meta-analysis to determine SNPs associated with the extent of ...abdominal aortic calcification (n = 9,417) or descending thoracic aortic calcification (n = 8,422). Two genetic loci, HDAC9 and RAP1GAP, were associated with abdominal aortic calcification at a genome-wide level (P < 5.0 × 10
). No SNPs were associated with thoracic aortic calcification at the genome-wide threshold. Increased expression of HDAC9 in human aortic smooth muscle cells promoted calcification and reduced contractility, while inhibition of HDAC9 in human aortic smooth muscle cells inhibited calcification and enhanced cell contractility. In matrix Gla protein-deficient mice, a model of human vascular calcification, mice lacking HDAC9 had a 40% reduction in aortic calcification and improved survival. This translational genomic study identifies the first genetic risk locus associated with calcification of the abdominal aorta and describes a previously unknown role for HDAC9 in the development of vascular calcification.
Zen Evangelist McRae, John R; Robson, James; Sharf, Robert H ...
08/2023, Volume:
12
eBook
Huineng (638-713), author and hero of the Platform Sutra, is
often credited with founding the Southern school of Chan Buddhism
and its radical doctrine of "sudden enlightenment." However,
manuscripts ...discovered at Dunhuang at the beginning of the
twentieth century reveal that the real architect of the Southern
school was Huineng's student Shenhui (684-758). An ardent
evangelist for his master's teaching and a sharp critic of rival
meditation teachers of his day, Shenhui was responsible for
Huineng's recognition as the "sixth patriarch," for the promotion
and eventual triumph of the sudden teaching, and for a somewhat
combative style of Chan discourse that came to be known as
"encounter dialogue." Shenhui's historical importance in the rise
and success of Chan is beyond dispute, yet until now there has been
no complete translation of his corpus into English. This volume
brings together John McRae's lifetime of work on the Shenhui
corpus, including extensively annotated translations of all five of
Shenhui's texts discovered at Dunhuang as well as McRae's seminal
studies of Shenhui's life, teachings, and legacy. McRae's research
explores the degree to which the received view of the Northern
school teachings is a fiction created by Shenhui to score
rhetorical points and that Northern and Southern teachings may have
been closer to one another than the canonical narrative depicts.
McRae explains Shenhui's critical role in shaping what would later
emerge as "classical Chan," while remaining skeptical about the
glowing image of Shenhui as an effective mentor and inspired
revolutionary. This posthumously published book is the fulfillment
of McRae's wish to make Shenhui's surviving writings accessible
through carefully annotated English translations, allowing readers
to form their own opinions.
Some introduced populations thrive and evolve despite the presumed loss of diversity at introduction. We aimed to quantify the amount of genetic diversity retained at introduction in species that ...have shown evidence of adaptation to their introduced environments. Samples were taken from native and introduced ranges of Arctotheca populifolia and Petrorhagia nanteuilii. Using microsatellite data, we identified the source for each introduction, estimated genetic diversity in native and introduced populations, and calculated the amount of diversity retained in introduced populations. These values were compared to those from a literature review of diversity in native, confamilial populations and to estimates of genetic diversity retained at introduction. Gene diversity in the native range of both species was significantly lower than for confamilials. We found that, on average, introduced populations showing evidence of adaptation to their new environments retained 81% of the genetic diversity from the native range. Introduced populations of P. nanteuilii had higher genetic diversity than found in the native source populations, whereas introduced populations of A. populifolia retained only 14% of its native diversity in one introduction and 1% in another. Our literature review has shown that most introductions demonstrating adaptive ability have lost diversity upon introduction. The two species studied here had exceptionally low native range genetic diversity. Further, the two introductions of A. populifolia represent the largest percentage loss of genetic diversity in a species showing evidence of substantial morphological change in the introduced range. While high genetic diversity may increase the likelihood of invasion success, the species examined here adapted to their new environments with very little neutral genetic diversity. This finding suggests that even introductions founded by small numbers of individuals have the potential to become invasive.
A review of introduced populations showing evidence of adaptation to their new environments indicated that these introductions retained 81% of the genetic diversity from the native range. Although the two species studied here had exceptionally low native range genetic diversity, introductions of A. populifolia represent a larger percentage loss of genetic diversity than found in any introduction identified in our review. While high genetic diversity may increase the likelihood of invasion success, these species adapted to their new environments with very little neutral genetic diversity, suggesting that even introductions founded by small numbers of individuals have the potential to become invasive.
Eukaryotic mRNAs are modified at their 5' end early during transcription by the addition of N7-methylguanosine (m
G), which forms the "cap" on the first 5' nucleotide. Identification of the 5' ...nucleotide on mRNA is necessary for determination of the Transcription Start Site (TSS). We explored the effect of various reaction conditions on the activity of the yeast scavenger mRNA decapping enzyme DcpS and examined decapping of 30 chemically distinct cap structures varying the state of methylation, sugar, phosphate linkage, and base composition on 25mer RNA oligonucleotides. Contrary to the generally accepted belief that DcpS enzymes only decap short oligonucleotides, we found that the yeast scavenger decapping enzyme decaps RNA transcripts as long as 1400 nucleotides. Further, we validated the application of yDcpS for enriching capped RNA using a strategy of specifically tagging the 5' end of capped RNA by first decapping and then recapping it with an affinity-tagged guanosine nucleotide.
Background: With communication skills deemed increasingly important for engineering graduates, we wanted to understand how writing is currently included in engineering classes, what challenges are ...caused by including writing in such classes, and what resources would be most useful to help engineering instructors more easily include writing in engineering classes. Literature review: Writing is a necessary skill for engineering graduates and has received increased attention in engineering classes. However, despite many instructors' beliefs that writing is an important skill for engineers, it is not typically taught in a systematic and comprehensive way across the engineering curriculum. Research questions: 1. What perceptions of writing, and specifically writing in engineering, do engineering instructors hold? 2. To what extent do engineering instructors report incorporation of writing activities and assignments in their classes? 3. What barriers do engineering instructors perceive as inhibiting the inclusion of more writing in engineering courses? 4. What resources do engineering instructors desire to expand and improve the inclusion of writing in engineering courses? Research methods: A survey was completed by engineering instructional staff (n = 190 respondents, 10.7% response rate) from seven institutions as well as by some members of the Big10+ Engineering Deans Mailing List. Instructors were asked about their general perceptions about writing in engineering and were also asked to consider the most recent engineering course that they taught and reflect on how they included (or did not include) writing in their course. Findings and conclusions: As expected, we found that most engineering instructional staff agree that writing skills are very important in engineering. Yet, we found that constraints on time and resources kept instructors from including more writing in their courses. This paper concludes with a discussion of our efforts to develop resources, such as rubrics, graded writing examples, and strategies for developing writing prompts, to help instructors include more writing in their engineering courses .
IntroductionOlder people with multimorbidities frequently access 999 ambulance services. When multimorbidities include dementia, the risk of ambulance use, accident and emergency (A&E) attendance and ...hospital admission are all increased, even when a condition is treatable in the community. People with dementia tend to do poorly in the acute hospital setting and hospital admission can result in adverse outcomes. This study aims to provide an evidence-based understanding of how older people living with dementia and other multimorbidities are using emergency ambulance services. It will also provide evidence of how paramedics make decisions about taking this group of patients to hospital, and what resources would allow them to make more person-focused decisions to enable optimal patient care.Methods and analysisPhase 1: retrospective data analysis: quantitative analysis of ambulance service data will investigate: how often paramedics are called to older people with dementia; the amount of time paramedics spend on scene and the frequency with which these patients are transported to hospital. Phase 2: observational case studies: detailed case studies will be compiled using qualitative methods, including non-participant observation of paramedic decision-making, to understand why older people with multimorbidities including dementia are conveyed to A&E when they could be treated at home or in the community. Phase 3: needs analysis: nominal groups with paramedics will investigate and prioritise the resources that would allow emergency, urgent and out of hours care to be effectively delivered to these patients at home or in a community setting.Ethics and disseminationApproval for the study has been obtained from the Health Research Authority (HRA) with National Health Service (NHS) Research Ethics Committee approval for phase 2 (16/NW/0803). The dissemination strategy will include publishing findings in appropriate journals, at conferences and in newsletters. We will pay particular attention to dissemination to the public, dementia organisations and ambulance services.
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