Understanding the source of METTL3-independent m6A in mRNA

N6-methyladenosine (m6A) is a highly prevalent mRNA modification which promotes degradation of transcripts encoding proteins that have roles in cell development, differentiation, and other pathways. METTL3 is the major methyltransferase that catalyzes the formation of m6A in mRNA. As 30—80% of m6A can remain in mRNA after METTL3 depletion by CRISPR/Cas9-based methods, other enzymes are thought to catalyze a sizable fraction of m6A. Here, we re-examined the source of m6A in the mRNA transcriptome. We characterized mouse embryonic stem cell lines which continue to have m6A in their mRNA after Mettl3 knockout. We show that these cells express alternatively spliced Mettl3 transcript isoforms that bypass the CRISPR/Cas9 mutations and produce functionally active methyltransferases. We similarly show that other reported METTL3 knockout cell lines express altered METTL3 proteins. We find that gene dependency datasets show that most cell lines fail to proliferate after METTL3 deletion, suggesting that reported METTL3 knockout cell lines express altered METTL3 proteins rather than have full knockout. Finally, we reassessed METTL3's role in synthesizing m6A using a genomic deletion of Mettl3, and found that METTL3 is responsible for >95% of m6A in mRNA. Overall, these studies suggest that METTL3 is responsible for the vast majority of m6A in the transcriptome, and that remaining m6A in putative METTL3 knockout cell lines is due to the expression of altered but functional METTL3 isoforms.

Implantation Failures and Miscarriages in Frozen Embryo Transfers Timed in Hormone Replacement Cycles (HRT): A Narrative Review

The recent advent of embryo vitrification and its remarkable efficacy has focused interest on the quality of hormone administration for priming frozen embryo transfers (FETs). Products available for progesterone administration have only been tested in fresh assisted reproduction technologies (ARTs) and not in FET. Recently, there have been numerous concordant reports pointing at the inefficacy of vaginal preparations at delivering sufficient progesterone levels in a sizable fraction of FET patients. The options available for coping with these shortcomings of vaginal progesterone include (i) rescue options with the addition of injectable subcutaneous (SC) progesterone at the dose of 25 mg/day administered either solely to women whose circulating progesterone is <10 ng/mL or to all in a combo option and (ii) the exclusive administration of SC progesterone at the dose of 25 mg BID. The wider use of segmented ART accompanied with FET forces hormone replacement regimens used for priming endometrial receptivity to be adjusted in order to optimize ART outcomes.

Rationalizing the irrational: Making sense of (in)consistency among union members and non-members

Focusing on 13 OECD countries over 25 years, we examine the factors that explain why a sizable fraction of wage-earners exhibit an inconsistency between their union membership status and their confidence in unions by being either confident non-members or non-confident members. While structural factors associated with joining constraints generate inconsistency in specific labour market categories, wage-earners who have extreme ideological orientations and are highly interested in politics are much less likely to exhibit inconsistency across time and countries. For individuals who have intermediate ideological orientations and are not very interested in politics, differences in terms of non-member and member inconsistency between countries are explainable through contextual variables such as economic conditions, the level of employment protection, and historical legacies. Implications for union membership research and union strategies are discussed.

TOWARD A THEORY OF SYSTEMS ENGINEERING

The derivation of a theory of systems engineering has long been complicated by the fact that there is little consensus within the systems engineering community regarding precisely what systems engineering is, what systems engineers do, and what might constitute reasonable systems engineering practices. To date, attempts at theories fail to accommodate even a sizable fraction of the current systems engineering community, and they fail to present a test of validity of systems theories, analytical methods, procedures or practices. This paper presents a more theoretical and more abstract approach to the derivation of a theory of systems engineering that has the potential to accommodate a broad segment of the systems engineering community and present a validity test. It is based on a simple preference statement: “I want the best system I can get.” From this statement, it is argued that a very rich theory can be obtained. Whereas most engineering disciplines are framed around a core set of widely accepted physical laws, to the authors' knowledge, this is the first attempt to frame an engineering discipline around a preference.

Presence of Unabsorbed Free Amino Acids at the End of the Small Intestine of Humans and Pigs: Potential Implications for Amino Acid Bioavailability

Objectives The protein quality digestible indispensable amino acid scores (DIAAS) require determination of amino acid (AA) bioavailability, which is often quantified as the net disappearance of dietary AAs at the end of the small intestine, so-called true ileal digestibility. It is often assumed that bioavailability is mainly influenced by protein breakdown and that free AAs are completely absorbed by the small intestine. However, some studies report substantial amounts of free AAs in the unabsorbed protein fraction present in terminal ileal digesta. This study quantified free AAs in ileal digesta of humans and pigs and estimated their impact on AA bioavailability. Methods Two studies were performed with 3 diets, i.e., zein, whey or protein-free. In study 1, ileal digesta of 8 human ileostomates was collected over 9 hours after ingestion of a single meal. In study 2, 12 pigs were fed 7 days with one of the 3 diets and ileal digesta was collected over 9 h on the last 2 days according to a standardized digestibility protocol. Total and free AA content were analyzed in ileal digesta. Results All ileal digesta contained free AAs. If the analyzed free AAs would have been absorbed in the small intestine the bioavailability for whey, which was &gt; 95%, would only increase 0.4%-unit on average for the different AAs in humans and 0.1%-unit in pigs. For zein protein, which is ∼70% bioavailable, the impact of unabsorbed free AAs on bioavailability was on average 2.3 ± 1.2%-unit in humans and 3.5 ± 5.1%-unit in pigs. In both species, the biggest impact was seen for the free essential AA threonine; its potential absorption could increase threonine bioavailability of zein by 6.6 ± 4.0%-units for humans and 6.6 ± 8.6%-units for pigs. Moreover, for both species the proportion of threonine in free form, relative to total threonine, was significantly higher in ileal digesta after ingestion of zein compared to whey or the protein-free condition (p &lt; 0.05). Conclusions Our results show that not all free AAs are fully absorbed by the end of the small intestine. When the AA bioavailability of a protein is low, these unabsorbed AAs can be a quantitatively sizable fraction of ingested AAs. Funding Sources Proteos project, funded by a consortium of food companies and food sectors, coordinated by Global Dairy Platform, USA.

Wnt/ß-catenin-mediated p53 suppression is indispensable for osteogenesis of mesenchymal progenitor cells

The developmental origins of mesenchymal progenitor cells (MPCs) and molecular machineries regulating their fate and differentiation are far from defined owing to their complexity. Osteoblasts and adipocytes are descended from common MPCs. Their fates are collectively determined by an orchestra of pathways in response to physiological and external cues. The canonical Wnt pathway signals MPCs to commit to osteogenic differentiation at the expense of adipogenic fate. In contrast to ß-catenin, p53’s anti-osteogenic function is much less understood. Both activities are thought to be achieved through targeting Runx2 and/or Osterix (Osx, Sp7) transcription. Precisely, how Osx activity is dictated by ß-catenin or p53 is not clarified and represents a knowledge gap that, until now, has largely been taken for granted. Using conditional lineage-tracing mice, we demonstrated that chondrocytes gave rise to a sizable fraction of MPCs, which served as progenitors of chondrocyte-derived osteoblasts (Chon-ob). Wnt/ß-catenin activity was only required at the stage of chondrocyte-derived mesenchymal progenitor (C-MPC) to Chon-ob differentiation. ß-catenin– C-MPCs lost osteogenic ability and favored adipogenesis. Mechanistically, we discovered that p53 activity was elevated in ß-catenin– MPCs including ß-catenin– C-MPCs and deleting p53 from the ß-catenin– MPCs fully restored osteogenesis. While high levels of p53 were present in the nuclei of ß-catenin– MPCs, Osx was confined to the cytoplasm, implying a mechanism that did not involve direct p53-Osx interaction. Furthermore, we found that p53’s anti-osteogenic activity was dependent on its DNA-binding ability. Our findings identify chondrocytes as an additional source for MPCs and indicate that Wnt/ß-catenin discretely regulates chondrocyte to C-MPC and the subsequent C-MPC to osteoblast developments. Most of all we unveil a previously unrecognized functional link between ß-catenin and p53, placing p53’s negative role in the context of Wnt/ß-catenin signaling-induced MPC osteogenic differentiation.

The Effects of Foreign Multinationals on Workers and Firms in the United States*

Governments go to great lengths to attract foreign multinationals because they are thought to raise the wages paid to their employees (direct effects) and to improve outcomes at local domestic firms (indirect effects). We construct the first U.S. employer-employee dataset with foreign ownership information from tax records to measure these direct and indirect effects. We find the average direct effect of a foreign multinational firm on its U.S. workers is a 7 percent increase in wages. This premium is larger for higher-skilled workers and for the employees of firms from high GDP per capita countries. We find evidence that it is membership in a multinational production network—instead of foreignness—that generates the foreign-firm premium. We leverage the past spatial clustering of foreign-owned firms by country of ownership to identify the indirect effects. An expansion in the foreign-multinational share of commuting-zone employment substantially increases the employment, value added, and—for higher-earning workers—wages at local domestic-owned firms. Per job created by a foreign multinational, our estimates suggest annual gains of 13,400 USD to the aggregate wages of local incumbents, two-thirds of which are from indirect effects. Our estimates suggest that—via mega-deals for subsidies from local governments—foreign multinationals are able to extract a sizable fraction of the local surplus they generate.

Evolution of Brightness and Color of the Night Sky in Madrid

Major schemes to replace other streetlight technologies with Light-Emitting Diode (LED) lamps are being undertaken across much of the world. This is predicted to have important consequences for nighttime sky brightness and color. Here, we report the results of a long-term study of these characteristics focused on the skies above Madrid. The sky brightness and color monitoring station at Universidad Complutense de Madrid (inside the city) collected Johnson B, V, and R sky brightness data, Sky Quality Meter (SQM), and Telescope Encoder Sky Sensor-WiFi (TESS-W) broadband photometry throughout the night, every night between 2010–2020. Our analysis includes a data filtering process that can be used with other similar sky brightness monitoring data. Major changes in sky brightness and color took place during 2015–2016, when a sizable fraction of the streetlamps in Madrid changed from High-Pressure Sodium (HPS) to LEDs. The sky brightness detected in the Johnson B band darkened by 14% from 2011 to 2015 and brightened by 32% from 2015 to 2019.

Plant Pan-Genomics Comes of Age

A pan-genome is the nonredundant collection of genes and/or DNA sequences in a species. Numerous studies have shown that plant pan-genomes are typically much larger than the genome of any individual and that a sizable fraction of the genes in any individual are present in only some genomes. The construction and interpretation of plant pan-genomes are challenging due to the large size and repetitive content of plant genomes. Most pan-genomes are largely focused on nontransposable element protein coding genes because they are more easily analyzed and defined than noncoding and repetitive sequences. Nevertheless, noncoding and repetitive DNA play important roles in determining the phenotype and genome evolution. Fortunately, it is now feasible to make multiple high-quality genomes that can be used to construct high-resolution pan-genomes that capture all the variation. However, assembling, displaying, and interacting with such high-resolution pan-genomes will require the development of new tools. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

SARS-CoV-2 infection and COVID-19 severity in individuals with prior seasonal coronavirus infection

A sizable fraction of healthy blood donors have cross-reactive T cells to SARS-CoV-2 peptides due to prior infection with seasonal coronavirus. Understanding the role of cross-reactive T cells in immunity to SARS-CoV-2 has implications for managing the COVID-19 pandemic. We show that individuals with documented history of seasonal coronavirus have a similar SARS-CoV-2 infection rate and COVID-19 severity as those with no prior history of seasonal coronavirus. Our findings suggest prior infection with seasonal coronavirus does not provide immunity to subsequent infection with SARS-CoV-2.