bluuebunny/crossref_metadata_2025 huggingface dataset:
Constitutionalizing Reproductive Rights (and Justice)
Authors: Murray Melissa , Meyers Hilarie
Published: November 2021

In Griswold v. Connecticut and Roe v. Wade, the U.S. Supreme Court framed constitutional protections for reproductive rights around the right to privacy. But the Court’s emphasis on privacy was not inevitable. Rather, in the 1960s and 1970s, advocates challenging laws prohibiting contraception and abortion offered a wide range of constitutional grounds in which to root reproductive freedom, including claims of race, class, and sex inequality. Nevertheless, mainstream reproductive rights groups reiterated Griswold and Roe’s privacy logic in their advocacy efforts, further entrenching the rhetoric of privacy, individual choice, and negative rights. However, advocates on the ground sought to recuperate the concerns of race, sex, and class inequality that had previously marked reproductive rights advocacy, and by the 1990s, the reproductive justice movement had emerged as a counterpoint to the traditional reproductive rights framework. Over time, the intersectional elements of the reproductive justice movement have infiltrated mainstream reproductive rights advocacy, widening the range and scope of reproductive rights discourse. But critically, as aspects of reproductive justice have been integrated into mainstream reproductive rights discourse, those opposed to reproductive rights—from antiabortion groups to members of the Supreme Court—have sought to coopt the reproductive justice movement’s rhetoric for their own purposes. Rather than viewing access to abortion and contraception as essential to women’s equality, this new conservative discourse argues that reproductive rights are rooted in, and function as, tools of, race, sex, class, and disability-based inequality and injustice.
Feminism’s Transformation of Legal Education and Unfinished Agenda
Authors: Abrams Jamie R.
Published: November 2021

Feminism has had a broad influence in legal education. Feminist critiques have challenged the substance of legal rules, the methods of law teaching, and the culture of legal education. Following decades of advocacy, feminist pedagogical reforms have generated new fields, new courses, new laws, new leaders, and new feminist spaces. There are many reasons to celebrate the accomplishments of our feminist pioneers and champions. Yet, COVID-19 has also exposed all the vulnerabilities and tenuousness of feminist gains too. Critical work remains for faculty, administrators, and students to carry the work forward with a vigilant purpose and determination.
Changes in TMS measures induced by repetitive TMS
Authors: Classen Joseph , Huang Ying-Zu , Zrenner Christoph
Published: November 2021

Commonly used repetitive transcranial magnetic stimulation (rTMS) protocols, including regular rTMS, intermittent and continuous theta-burst stimulation (TBS) and quadripulse stimulation (QPS) are presented with respect to their induced neuromodulatory after-effects and the underlying cellular and synaptic neurophysiological mechanisms. The anatomical target is typically primary motor cortex since motor evoked potentials (MEPs) before and after the intervention can be used to assess effects of the respective rTMS protocol. High-frequency regular rTMS and intermittent TBS protocols tend to increase corticospinal excitability as indexed by MEP amplitude, whereas low-frequency regular rTMS and continuous TBS protocols tend to reduce corticospinal excitability. These effects are primarily due to LTP-like and LTD-like synaptic changes mediated by GABA and NMDA receptors. Changes in the balance between excitatory and inhibitory cortical microcircuits play a secondary role, with inconsistent effects as determined by paired-pulse TMS protocols. Finally, the challenge of large inter-subject response variability, and current directions of research to optimize rTMS effects through EEG-dependent personalized TMS are discussed.
rTMS and NONDECLARATIVE learning
Authors: Freedberg Michael V. , Wassermann Eric M.
Published: November 2021

Nondeclarative learning and memory involve acquiring and retaining skills or habits and include subtypes, such as procedural learning, priming, and classical conditioning. Animal studies, lesion, and functional imaging studies in humans have implicated a range of brain areas, including frontal and parietal cortical regions, basal ganglia, cerebellum in these functions. Repetitive transcranial magnetic stimulation (rTMS) can modulate functional connectivity in brain networks and provide causal evidence for their involvement in behavior. In this chapter, we review the use of rTMS to investigate the brain networks underlying nondeclarative learning by stimulating their cortical nodes and examining the effects of these interventions on behavior and imaging measures of brain activity and connectivity, with emphasis on how the timing of stimulation (before, during, or after learning) affects these measures.
Extreme Speech, Democratic Deliberation, and Social Media
Authors: Howard Jeffrey W.
Published: November 2021

Social media are now central sites of democratic discourse among citizens. But are some contributions to social media too extreme to be permitted? This entry considers the permissibility of suppressing extreme speech on social media, such as terrorist propaganda and racist hate speech. It begins by considering the argument that such restrictions on speech would wrong democratic citizens, violating their freedom of expression. It proceeds to investigate the moral responsibilities of social media companies to suppress extreme speech, and whether these ought to be enforced through the law. Finally, it explores an alternative mechanism for combatting extreme speech on social media—counter-speech—and evaluates its prospects.
Price Discrimination in the Digital Age
Authors: Lippert-Rasmussen Kasper , Aastrup Munch Lauritz
Published: November 2021

This chapter discusses the morality of online price discrimination. Price discrimination is a widespread type of market behaviour and it occurs, roughly, when a seller systematically charges different prices for the same product when it is offered to different groups of customers. Price discrimination occurs both online and offline, but some find the practice particularly suspicious when deployed in online markets. This asymmetry, we argue, calls for an explanation. In the chapter, we define price discrimination and review a number of explanations of why, and when, price discrimination is morally objectionable. We argue that online price discrimination will often prove more problematic than its offline counterpart, but also that neither practice is necessarily morally wrong.
Privacy in Social Media
Authors: Marmor Andrei
Published: November 2021

Most people’s immediate concern about privacy in social media, and about the internet more generally, relates to data protection. People fear that information they post on various platforms is potentially abused by corporate entities, governments, or even criminals, in all sorts of nefarious ways. The main premise of this chapter is that concerns about data protection, legitimate and serious as they may be, are not, mostly, about the right to privacy. Privacy is about control over the presentation of the self, not about protection of property rights. From the perspective of privacy as self-presentation, I argue that social media is, generally, very conducive to privacy—in fact, often too much so. Social media enables a great deal of privacy at the expense of truth and authenticity. But the medium also comes with dangers of exposure that carry serious risks to privacy, potentially undermining peoples’ ability to control what aspects of themselves they present to others. Privacy in social media is a mixed bag, containing different goods and dangers pulling in opposite directions.
Fake News
Authors: Levy Neil
Published: November 2021

The blame for fake news obviously lies with the producers. It is plausible, nevertheless, that consumers have a responsibility to avoid fake news, to engage in fact-checking, or to seek multiple sources, including sources with different ideologies. This chapter argues that these strategies have limited utility and if the problem of fake news is to be effectively addressed, we need responses at the supply end, not the consumption end. Since suppliers, who are often ill motivated, cannot be expected to offer or consent to these responses, we need effective regulation or control of sources. The author sketches proposals compatible with maintaining the rights of everyone to free speech.
Is There Collective Responsibility for Misogyny Perpetrated on Social Media?
Authors: Lawford-Smith Holly , Megarry Jessica
Published: November 2021

Women, particularly those who work in public positions (such as journalists, politicians, celebrities, activists) are subject to disproportionate amounts of abuse on social media platforms such as Twitter. This abuse occurs in a landscape that those platforms designed and that they maintain. Focusing in particular on Twitter, as typical of the kind of platform we are interested in, this chapter argues that it is the platform, not (usually) the individuals who use it, that bears collective responsibility as a corporate agent for misogyny. Social media platforms, however, should not overstep the prevention of misogyny into interference in open political debates.
Global 4-group symmetry and ’t Hooft anomalies in topological axion electrodynamics
Authors: Hidaka Yoshimasa , Nitta Muneto , Yokokura Ryo
Published: November 2021

We study higher-form global symmetries and a higher-group structure of a low-energy limit of (3 + 1)-dimensional axion electrodynamics in a gapped phase described by a topological action. We argue that the higher-form symmetries should have a semi-strict 4-group (3-crossed module) structure by consistency conditions of couplings of the topological action to background gauge fields for the higher-form symmetries. We find possible ’t Hooft anomalies for the 4-group global symmetry, and discuss physical consequences.
Advances in artificial intelligence and deep learning systems in ICU-related acute kidney injury
Authors: Ozrazgat-Baslanti Tezcan , Loftus Tyler J. , Ren Yuanfang , Ruppert Matthew M. , Bihorac Azra
Published: November 2021

Purpose of review

Acute kidney injury (AKI) affects nearly 60% of all patients admitted to ICUs. Large volumes of clinical, monitoring and laboratory data produced in ICUs allow the application of artificial intelligence analytics. The purpose of this article is to assimilate and critically evaluate recently published literature regarding artificial intelligence applications for predicting, diagnosing and subphenotyping AKI among critically ill patients.

Recent findings

Among recent studies regarding artificial intelligence implementations for predicting, diagnosing and subphenotyping AKI among critically ill patients, there are many promising models, but few had external validation, clinical interpretability and high predictive performance. Deep learning techniques leveraging multimodal clinical data show great potential to provide continuous, accurate, early predictions of AKI risk, which could be implemented clinically to optimize preventive and early therapeutic management strategies.

Use of consensus criteria, standard definitions and common data models could facilitate access to machine learning-ready data sets for external validation. The lack of interpretability, explainability, fairness and transparency of artificial intelligence models hinder their entrustment and clinical implementation; compliance with standardized reporting guidelines can mitigate these challenges.
How Hypertension Guidelines Address Social Determinants of Health
Authors: Razon Na’amah , Hessler Danielle , Bibbins-Domingo Kirsten , Gottlieb Laura
Published: November 2021

Background:

Patient-level and community-level social and economic conditions impact hypertension risk and control. We examined adult hypertension management guidelines to explore whether and how existing guidelines refer to social care activities.

Objective:

The objective of this study was to explore how hypertension guidelines reference social care activities.

Research Design:

A systematic scoping review of clinical guidelines for adult hypertension management. We employed a PubMed search strategy to identify all hypertension guidelines published in the United States between 1977 and 2019. We reviewed all titles to identify the most updated versions focused on nonpregnant adults with hypertension. We extracted instances where guidelines referred to social determinants of health (SDH) or social care activities. The primary outcome was how guidelines covered social care activities, defined using a framework adapted from the National Academies of Sciences, Engineering, and Medicine (NASEM).

Results:

Search terms yielded 126 guidelines. Thirty-six guidelines met the inclusion criteria. Of those, 72% (26/36) recommended social care activities as part of hypertension management; 58% recommended clinicians change clinical practice based on social risk information. These recommendations often lacked specific guidance around how to directly address social risk factors or reduce the impact of these risks on hypertension management. When guidelines referred to specific social factors, patient financial security was the most common. Over time, hypertension guidelines have included more references to SDH.

Conclusion:

Information about SDH is included in many hypertension guidelines, but few guidelines provide clear guidance for clinicians or health systems on how to identify and address social risk factors in the context of care delivery.
Sphingobacterium micropteri sp. nov. and Sphingobacterium litopenaei sp. nov., isolated from aquaculture water
Authors: Zhang Mingxia , Li Anzhang , Xu Shuaishuai , Chen Meng , Yao Qing , Xiao Botao , Zhu Honghui
Published: November 2021

Two novel bacterial strains, designated as DN00404T and DN04309T, were isolated from aquaculture water and characterized by using a polyphasic taxonomic approach. Cells of strains DN00404T and DN04309T were Gram-stain-negative, aerobic, non-motile, oxidase-positive and catalase-positive. Cells of DN00404T were short rod-shaped and those of DN04309T were long rod-shaped. Strain DN00404T was found to grow at 15–37 °C (optimum, 25–30 °C), at pH 6.0–11.0 (optimum, pH 7.5) and in 0–2.0 % (w/v) NaCl (optimum, 1.0 %). Strain DN04309T was found to grow at 15–45 °C (optimum, 20–37 °C), at pH 5.5–11.0 (optimum, 7.5) and in 0–4.0 % (w/v) NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that the two strains belonged to the genus

Sphingobacterium

and were distinct from all known species of this genus. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the two strains and between each of the two strains and related type strains of this genus were well below the recognized thresholds of 95.0–96.0 % ANI and 70.0 % dDDH for species delineation. The genomic DNA G+C contents of strains DN00404T and DN04309T were 41.6 and 36.0 mol%, respectively. The respiratory quinone in both strains was identified as MK-7, and their major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1
 ω6c and/or C16 : 1
 ω7c), which were similar to those of other species of this genus. The two major fatty acids C16 : 0 and iso-C17 : 0 3-OH were also found in strain DN00404T. Based on genotypic and phenotypic characteristics, two novel species of the genus

Sphingobacterium

are proposed: Sphingobacterium micropteri sp. nov. with DN00404T (=GDMCC 1.1865T=KACC 21924T) as the type strain and Sphingobacterium litopenaei sp. nov. with DN04309T (=GDMCC 1.1984T=KCTC 82348T) as the type strain.
Antimicrobial resistance genes and genetic characteristics of multidrug-resistant Escherichia coli in a veterinary hospital in Taiwan
Authors: Wu Lii-Tzu , Wu Xin-Xia , Ke Se-Chin , Lin Yi-Pei , Wu Ying-Chen , Chen Ter-Hsin , Chen Chih-Ming
Published: November 2021

Introduction. Antimicrobial resistance associated with animal hosts is easily transmitted to humans either by direct contact with resistant organisms or by transferring resistance genes into human pathogens.

Gap statement. There are limited studies on antimicrobial resistance genes and genetic elements of multidrug-resistant (MDR)

Escherichia coli

in veterinary hospitals in Taiwan.

Aim. The aim of this study was to investigate antimicrobial resistance genes in multidrug-resistant

Escherichia coli

from animals.

Methodology. Between January 2014 and August 2015, 95 multidrug-resistant

Escherichia coli

isolates were obtained from pigs (n=66), avians (n=18), and other animals (n=11) in a veterinary hospital in Taiwan. Susceptibility testing to 24 antimicrobial agents of 14 antimicrobial classes was performed. Antimicrobial resistance genes, integrons, and insertion sequences were analysed by polymerase chain reaction and nucleotide sequencing. Pulsed-field gel electrophoresis (PFGE), and multi-locus sequence typing were used to explore the clonal relatedness of the study isolates.

Results. Different antimicrobial resistance genes found in these isolates were associated with resistance to β-lactams, tetracycline, phenicols, sulfonamides, and aminoglycosides. Fifty-five of 95

E. coli

isolates (55/95, 57.9 %) were not susceptible to extended-spectrum cephalosporins, and bla
CTX-M-55 (11/55, 20.0 %) and bla
CMY-2 (40/55, 72.7 %) were the most common extended-spectrum β-lactamase (ESBL) and AmpC genes, respectively. Both bla
CTX-M and bla
CMY-2 were present on conjugative plasmids that contained the insertion sequence ISEcp1 upstream of the bla genes. Plasmid-mediated FOX-3 β-lactamase-producing

E. coli

was first identified in Taiwan. Forty isolates (40/95, 42 %) with class 1 integrons showed seven resistance phenotypes. Genotyping of 95

E. coli

isolates revealed 91 different XbaI pulsotypes and 52 different sequence types. PFGE analysis revealed no clonal outbreaks in our study isolates.

Conclusion. This study showed a high diversity of antimicrobial resistance genes and genotypes among MDR

E. coli

isolated from diseased livestock in Taiwan. To our knowledge, this is the first report of plasmid-mediated ESBL in FOX-3 β-lactamase-producing

E. coli

isolates in Taiwan. MDR

E. coli

isolates from animal origins may contaminate the environment, resulting in public health concerns, indicating that MDR isolates from animals need to be continuously investigated.
Early and rapid identification of COVID-19 patients with neutralizing type I-interferon auto-antibodies by an easily implementable algorithm
Authors: Akbil Bengisu , Meyer Tim , Stubbemann Paula , Thibeault Charlotte , Staudacher Olga , Niemeyer Daniela , Jansen Jenny , Mühlemann Barbara , Doehn Jan , Tabeling Christoph , Nusshag Christian , Hirzel Cédric , Sanchez David Sökler , Nieters Alexandra , Lother Achim , Duerschmied Daniel , Schallner Nils , Lieberum Jan Nikolaus , August Dietrich , Rieg Siegbert , Falcone Valeria , Hengel Hartmut , Kölsch Uwe , Unterwalder Nadine , Hübner Ralf-Harto , Jones Terry C. , Suttorp Norbert , Drosten Christian , Warnatz Klaus , Spinetti Thibaud , Schefold Joerg C. , Dörner Thomas , Sander Leif , Corman Victor M. , Merle Uta ,   Pa-COVID study Group, Kurth Florian , von Bernuth Horst , Meisel Christian , Goffinet Christine
Published: November 2021

Purpose

Six-19% of critically ill COVID-19 patients display circulating auto-antibodies against type I interferons (IFN-AABs). Here, we establish a clinically applicable strategy for early identification of IFN-AAB-positive patients for potential subsequent clinical interventions.

Methods

We analysed sera of 430 COVID-19 patients with severe and critical disease from four hospitals for presence of IFN-AABs by ELISA. Binding specificity and neutralizing activity were evaluated via competition assay and virus-infection-based neutralization assay. We defined clinical parameters associated with IFN-AAB positivity. In a subgroup of critically ill patients, we analyzed effects of therapeutic plasma exchange (TPE) on the levels of IFN-AABs, SARS-CoV-2 antibodies and clinical outcome.

Results

The prevalence of neutralizing AABs to IFN-α and IFN-ω in COVID-19 patients was 4.2% (18/430), while being undetectable in an uninfected control cohort. Neutralizing IFN-AABs were detectable exclusively in critically affected, predominantly male (83%) patients (7.6% IFN-α and 4.6% IFN-ω in 207 patients with critical COVID-19). IFN-AABs were present early post-symptom onset and at the peak of disease. Fever and oxygen requirement at hospital admission co-presented with neutralizing IFN-AAB positivity. IFN-AABs were associated with higher mortality (92.3% versus 19.1 % in patients without IFN-AABs). TPE reduced levels of IFN-AABs in three of five patients and may increase survival of IFN-AAB-positive patients compared to those not undergoing TPE.

Conclusion

IFN-AABs may serve as early biomarker for development of severe COVID-19. We propose to implement routine screening of hospitalized COVID-19 patients according to our algorithm for rapid identification of patients with IFN-AABs who most likely benefit from specific therapies.
Crowd-sourced observations of a polyphagous moth reveal evidence of allochronic speciation varying along a latitudinal gradient
Authors: Black Emily N. , Blair Jarrett D. , van der Burg Karin R.L. , Marshall Katie E.
Published: November 2021

Allochronic speciation, where reproductive isolation between populations of a species is facilitated by a difference in reproductive timing, depends on abiotic factors such as seasonality and biotic factors such as diapause intensity. These factors are strongly influenced by latitudinal trends in climate, so we hypothesized that there is a relationship between latitude and divergence among populations separated by life history timing.

Hyphantria cunea(the fall webworm), a Lepidopteran defoliator with red and black colour morphs, is hypothesized to be undergoing an incipient allochronic speciation. However, given their broad geographic range, the strength of allochronic speciation may vary across latitude. We annotated >11,000 crowd-sourced observations of fall webworm to model geographic distribution, phenology, and differences in colour phenotype between morphs across North America.

We found that red and black morph life history timing differs across North America, and the phenology of morphs diverges more in warmer climates at lower latitudes. We also found some evidence that the colour phenotype of morphs also diverges at lower latitudes, suggesting reduced gene flow between colour morphs.

Our results demonstrate that seasonality in lower latitudes may increase the strength of allochronic speciation in insects, and that the strength of sympatric speciation can vary along a latitudinal gradient. This has implications for our understanding of broad-scale speciation events and trends in global biodiversity.
Effect of COVID-19 vaccination on menstrual periods in a retrospectively recruited cohort
Authors: Male Victoria
Published: November 2021

Surveillance schemes are receiving increasing numbers of reports from people who have noticed a change to their period following COVID-19 vaccination. In order to investigate this, we retrospectively recruited 1273 people who have a record of their menstrual cycle and vaccination dates and used their reports to explore hypotheses about how COVID-19 vaccination and menstrual changes could be linked. In this dataset, we were unable to detect strong signals to support the idea that COVID-19 vaccination is linked to menstrual changes. However, larger, prospectively recruited studies may be able to find associations that we were not powered to detect.
Role of the rasGAP-associated docking protein p62dokin negative regulation of B cell receptor-mediated signaling
Authors: Yamanashi Yuji , Tamura Toshiki , Kanamori Toshihide , Yamane Hidehiro , Nariuchi Hideo , Yamamoto Tadashi , Baltimore David
Published: November 2021

Antigenic stimulation of the B-cell receptor (BCR) is a central event in the immune response. In contrast, antigen bound to IgG negatively regulates signals from the BCR by cross-linking it to the inhibitory receptor FcγRIIB. Here we show that upon cross-linking of BCR or BCR with FcγRIIB, the rasGAP-associated protein p62dokis prominently tyrosine phosphorylated in a Lyn-dependent manner. Inactivation of thedokgene by homologous recombination has shown that upon BCR cross-linking, p62doksuppresses MAP kinase and is indispensable for FcγRIIB-mediated negative regulation of cell proliferation. We propose that p62dok, a downstream target of many PTKs, plays a negative role in various signaling situations.
Identification and disruption of an Arabidopsis zinc finger gene controlling seed germination
Authors: Papi Maura , Sabatini Sabrina , Bouchez David , Camilleri Christine , Costantino Paolo , Vittorioso Paola
Published: November 2021

We describe here the Arabidopsis gene DAG1, encoding a zinc finger transcription factor of the Dof family, and show that it is involved in the control of seed germination. By a reverse genetics approach, we isolated an Arabidopsis mutant line with one T-DNA insertion in DAG1. Seeds from homozygous knockoutdag1-1 plants do not develop dormancy and germinate also in the absence of light. Segregation analysis indicates that the effect of the mutation is maternal. Accordingly, in situ mRNA hybridizations reveal expression of DAG1 in the vascular tissue of the flower and maturing fruit but not in the seed.
The yeast Sgs1p helicase acts upstream of Rad53p in the DNA replication checkpoint and colocalizes with Rad53p in S-phase-specific foci
Authors: Frei Christian , Gasser Susan M.
Published: November 2021

We have examined the cellular function of Sgs1p, a nonessential yeast DNA helicase, homologs of which are implicated in two highly debilitating hereditary human diseases (Werner's and Bloom's syndromes). We show that Sgs1p is an integral component of the S-phase checkpoint response in yeast, which arrests cells due to DNA damage or blocked fork progression during DNA replication. DNA polε and Sgs1p are found in the same epistasis group and act upstream of Rad53p to signal cell cycle arrest when DNA replication is perturbed. Sgs1p is tightly regulated through the cell cycle, accumulates in S phase and colocalizes with Rad53p in S-phase-specific foci, even in the absence of fork arrest. The association of Rad53p with a chromatin subfraction is Sgs1p dependent, suggesting an important role for the helicase in the signal-transducing pathway that monitors replication fork progression.
H19 and Igf2 monoallelic expression is regulated in two distinct ways by a shared cis acting regulatory region upstream of H19
Authors: Srivastava Madhulika , Hsieh Sandra , Grinberg Alexander , Williams-Simons Lisa , Huang Sing-Ping , Pfeifer Karl
Published: November 2021

H19 and Igf2 are expressed in a monoallelic fashion from the maternal and paternal chromosomes, respectively. A region upstream of H19 has been shown to regulate such imprinted expression of both genes in cis. We have taken advantage of aloxP/cre recombinase-based strategy to delete this region in mice in a conditional manner to determine the temporal requirement of the upstream region in initiating and maintaining the imprinted expression of H19 and Igf2. Analysis of allele-specific expression of H19 and Igf2 and DNA methylation at the H19 promoter demonstrates that this region controls the monoallelic expression of the two genes in different ways, suggesting that it harbors two functionally distinct regulatory elements. Continued presence of the region is required to silence maternal Igf2 in accordance with its proposed role as an insulator. However, it does not have a direct role in keeping the paternal H19 promoter silenced. Instead, on the paternal chromosome, the upstream element mediates epigenetic modifications of the H19 promoter region during development, leading to transcriptional silencing of H19. Thereafter, its presence is redundant for preventing transcription. Presently, this temporal requirement of the silencing element appears to be a unique cisactivity in the mammalian system. However, it is likely that othercis-acting elements, positive and negative, have the ability to effect stable changes in the chromatin structure and are not constantly required to give signals to the transcriptional machinery.
The zebrafish bonnie and clyde gene encodes a Mix family homeodomain protein that regulates the generation of endodermal precursors
Authors: Kikuchi Yutaka , Trinh Le A. , Reiter Jeremy F. , Alexander Jonathan , Yelon Deborah , Stainier Didier Y.R.
Published: November 2021

Vertebrate endoderm development has recently become the focus of intense investigation. In this report, we first show that the zebrafishbonnie and clyde (bon) gene plays a critical early role in endoderm formation. bon mutants exhibit a profound reduction in the number of sox17-expressing endodermal precursors formed during gastrulation, and, consequently, a profound reduction in gut tissue at later stages. The endodermal precursors that do form inbon mutants, however, appear to differentiate normally indicating that bon is not required at later steps of endoderm development. We further demonstrate that bon encodes a paired-class homeodomain protein of the Mix family that is expressed transiently before and during early gastrulation in both mesodermal and endodermal progenitors. Overexpression of bon can rescue endodermal gene expression and the formation of a gut tube inbon mutants. Analysis of a newly identified mutant allele reveals that a single amino acid substitution in the DNA recognition helix of the homeodomain creates a dominant interfering form of Bon when overexpressed. We also show through loss- and gain-of-function analyses that Bon functions exclusively downstream of cyclopsand squint signaling. Together, our data demonstrate that Bon is a critical transcriptional regulator of early endoderm formation.
N-myc can functionally replace c-myc in murine development, cellular growth, and differentiation
Authors: Malynn Barbara A. , de Alboran Ignacio Moreno , O'Hagan Rónán C. , Bronson Roderick , Davidson Laurie , DePinho Ronald A. , Alt Frederick W.
Published: November 2021

Members of the myc family of cellular oncogenes have been implicated as transcriptional regulators in pathways that govern cellular proliferation and death. In addition, N-myc andc-myc are essential for completion of murine embryonic development. However, the basis for the evolutionary conservation ofmyc gene family has remained unclear. To elucidate this issue, we have generated mice in which the endogenous c-myccoding sequences have been replaced with N-myc coding sequences. Strikingly, mice homozygous for this replacement mutation can survive into adulthood and reproduce. Moreover, when expressed from the c-myc locus, N-myc is similarly regulated and functionally complementary to c-myc in the context of various cellular growth and differentiation processes. Therefore, themyc gene family must have evolved, to a large extent, to facilitate differential patterns of expression.
FACKEL is a sterol C-14 reductase required for organized cell division and expansion in Arabidopsis embryogenesis
Authors: Schrick Kathrin , Mayer Ulrike , Horrichs Andrea , Kuhnt Christine , Bellini Catherine , Dangl Jeff , Schmidt Jürgen , Jürgens Gerd
Published: November 2021

In flowering plants, the developing embryo consists of growing populations of cells whose fates are determined in a position-dependent manner to form the adult organism. Mutations in the FACKEL(FK) gene affect body organization of theArabidopsis seedling. We report that FK is required for cell division and expansion and is involved in proper organization of the embryo. We isolated FK by positional cloning. Expression analysis in embryos revealed that FK mRNA becomes localized to meristematic zones. FK encodes a predicted integral membrane protein related to the vertebrate lamin B receptor and sterol reductases across species, including yeast sterol C-14 reductase ERG24. We provide functional evidence that FK encodes a sterol C-14 reductase by complementation of erg24. GC/MS analysis confirmed that fk mutations lead to accumulation of intermediates in the biosynthetic pathway preceding the C-14 reductase step. Although fk represents a sterol biosynthetic mutant, the phenotype was not rescued by feeding with brassinosteroids (BRs), the only plant sterol signaling molecules known so far. We propose that synthesis of sterol signals in addition to BRs is important in mediating regulated cell growth and organization during embryonic development. Our results indicate a novel role for sterols in the embryogenesis of plants.
A critical role of sterols in embryonic patterning and meristem programming revealed by thefackelmutants ofArabidopsis thaliana
Authors: Jang Jyan-Chyun , Fujioka Shozo , Tasaka Masao , Seto Hideharu , Takatsuto Suguru , Ishii Akira , Aida Mitsuhiro , Yoshida Shigeo , Sheen Jen
Published: November 2021

Here we report a novelArabidopsisdwarf mutant,fackel-J79, whose adult morphology resembles that of brassinosteroid-deficient mutants but also displays distorted embryos, supernumerary cotyledons, multiple shoot meristems, and stunted roots. We cloned theFACKELgene and found that it encodes a protein with sequence similarity to both the human sterol reductase family and yeast C-14 sterol reductase and is preferentially expressed in actively growing cells. Biochemical analysis indicates that thefk-J79mutation results in deficient C-14 sterol reductase activity, abnormal sterol composition, and reduction of brassinosteroids (BRs). Unlike other BR-deficient mutants, the defect of hypocotyl elongation infk-J79cannot be corrected by exogenous BRs. The unique phenotypes and sterol composition infk-J79indicate crucial roles of sterol regulation and signaling in cell division and cell expansion in embryonic and post-embryonic development in plants.
Transgene-mediated cosuppression in the C. elegans germ line
Authors: Dernburg Abby F. , Zalevsky Jonathan , Colaiácovo Mónica P. , Villeneuve Anne M.
Published: November 2021

Functional silencing of chromosomal loci can be induced by transgenes (cosuppression) or by introduction of double-stranded RNA (RNAi). Here, we demonstrate the generality of and define rules for a transgene-mediated cosuppression phenomenon in the Caenorhabditis elegans germ line. Functional repression is not a consequence of persistent physical association between transgenes and endogenous genes or of mutations in affected genes. The cosuppression mechanism likely involves an RNA mediator that defines its target specificity, reminiscent of RNAi. Cosuppression is strongly abrogated inrde-2 and mut-7 mutants, but is not blocked in anrde-1 mutant, indicating that cosuppression and RNAi have overlapping but distinct genetic requirements.
A family of rhomboid-like genes: Drosophila rhomboid-1 and roughoid/rhomboid-3 cooperate to activate EGF receptor signaling
Authors: Wasserman Jonathan D. , Urban Sinisa , Freeman Matthew
Published: November 2021

As in mammals, the Drosophila EGF receptor controls many aspects of growth and development. The rate limiting component ofDrosophila Egfr signaling is Rhomboid, a seven transmembrane domain protein, whose expression prefigures Egfr signaling. Little is known about the molecular mechanism of Rhomboid function but genetic evidence suggests that it controls the activation of the ligand Spitz, a TGFα-like factor. Spitz/Egfr signaling regulates cell determination in the eye but here there is no apparent function for Rhomboid, an observation that casts doubt on this prevailing model of Rhomboid function. We describe our identification of six newrhomboid-like genes in Drosophila, and a large family of related genes present in organisms as diverse as bacteria and mammals; a human rhomboid homolog has also recently been described. Drosophila rhomboid-3 corresponds to theroughoid mutation; it cooperates with rhomboid-1 to control Egfr signaling in the eye, thereby solving the puzzle of the apparent lack of Rhomboid-1 function there. Rhomboid-1 and Roughoid/Rhomboid-3 act in the signal-emitting not signal-receiving cell, supporting the idea that Spitz activation is regulated by Rhomboid-like molecules.
Inactivation of mouse Hus1 results in genomic instability and impaired responses to genotoxic stress
Authors: Weiss Robert S. , Enoch Tamar , Leder Philip
Published: November 2021

The eukaryotic cell cycle is overseen by regulatory mechanisms, termed checkpoints, that respond to DNA damage, mitotic spindle defects, and errors in the ordering of cell cycle events. The DNA replication and DNA damage cell cycle checkpoints of the fission yeastSchizosaccharomyces pombe require the hus1+(hydroxyurea sensitive) gene. To determine the role of the mouse homolog of hus1+ in murine development and cell cycle checkpoint function, we produced a targeted disruption of mouse Hus1. Inactivation of Hus1results in mid-gestational embryonic lethality due to widespread apoptosis and defective development of essential extra-embryonic tissues. DNA damage-inducible genes are up-regulated inHus1-deficient embryos, and primary cells fromHus1-null embryos contain increased spontaneous chromosomal abnormalities, suggesting that loss of Hus1 leads to an accumulation of genome damage. Embryonic fibroblasts lackingHus1 fail to proliferate in vitro, but inactivation ofp21 allows for the continued growth of Hus1-deficient cells.Hus1−/−p21−/−cells display a unique profile of significantly heightened sensitivity to hydroxyurea, a DNA replication inhibitor, and ultraviolet light, but only slightly increased sensitivity to ionizing radiation. Taken together, these results indicate that mouse Hus1 functions in the maintenance of genomic stability and additionally identify an evolutionarily-conserved role for Hus1 in mediating cellular responses to genotoxins.
members only encodes a Drosophila nucleoporin required for Rel protein import and immune response activation
Authors: Uv Anne E. , Roth Peggy , Xylourgidis Nikos , Wickberg Anna , Cantera Rafael , Samakovlis Christos
Published: November 2021

Many developmental and physiological responses rely on the selective translocation of transcriptional regulators in and out of the nucleus through the nuclear pores. Here we describe the Drosophila genemembers only (mbo) encoding a nucleoporin homologous to the mammalian Nup88. The phenotypes of mbo mutants andmbo expression during development are cell specific, indicating that the nuclear import capacity of cells is differentially regulated. Using inducible assays for nucleocytoplasmic trafficking we show that mRNA export and classic NLS-mediated protein import are unaffected inmbo mutants. Instead, mbo is selectively required for the nuclear import of the yeast transcription factor GAL4 in a subset of the larval tissues. We have identified the first endogenous targets of the mbo nuclear import pathway in the Rel proteins Dorsal and Dif. In mbo mutants the upstream signaling events leading to the degradation of the IκB homolog Cactus are functional, but Dorsal and Dif remain cytoplasmic and the larval immune response is not activated in response to infection. Our results demonstrate that distinct nuclear import events require different nucleoporins in vivo and suggest a regulatory role for mbo in signal transduction.
Yeast heterochromatin is a dynamic structure that requires silencers continuously
Authors: Cheng Tzu-Hao , Gartenberg Marc R.
Published: November 2021

Transcriptional silencing of the HM loci in yeast requirescis-acting elements, termed silencers, that function during S-phase passage to establish the silent state. To study the role of the regulatory elements in maintenance of repression, site-specific recombination was used to uncouple preassembled silent chromatin fragments from silencers. DNA rings excised from HMR were initially silent but ultimately reactivated, even in G1- or G2/M-arrested cells. In contrast, DNA rings bearing HML-derived sequence were stably repressed due to the presence of a protosilencing element. These data show that silencers (or protosilencers) are required continuously for maintenance of silent chromatin. Reactivation of unstably repressed rings was blocked by overexpression of silencing proteins Sir3p and Sir4p, and chromatin immunoprecipitation studies showed that overexpressed Sir3p was incorporated into silent chromatin. Importantly, the protein was incorporated even when expressed outside of S phase, during G1 arrest. That silencing factors can associate with and stabilize preassembled silent chromatin in non-S-phase cells demonstrates that heterochromatin in yeast is dynamic.
The stringent response in Myxococcus xanthus is regulated by SocE and the CsgA C-signaling protein
Authors: Crawford Eugene W. , Shimkets Lawrence J.
Published: November 2021

Myxococcus xanthus fruiting body development is induced by amino acid limitation. The decision to grow or develop is established by the RelA-dependent stringent response and A-signaling. We identified two new members of this regulatory hierarchy, socE and the C-signaling gene csgA. SocE depletion arrests growth and induces sporulation under conditions that normally favor growth as well as curtailing DNA and stable RNA synthesis, inhibiting cell elongation, and inducing accumulations of the stringent nucleotides ppGpp and pppGpp [(p)ppGpp]. This system separates C-signaling, which does not occur under these conditions, from CsgA enzyme activity. Amino acid substitutions in the CsgA coenzyme binding pocket or catalytic site eliminate growth arrest. relA mutation also eliminates growth arrest. Eleven pseudorevertants selected for growth following SocE depletion contained mutations in csgA or relA. These results suggest that CsgA induces the stringent response and while SocE inhibits it. Unlike the csgA mutant, wild-type and socE csgA cells maintained high levels of (p)ppGpp throughout development. We suggest that CsgA maintains growth arrest throughout development to divert carbon from A-signaling and other sources into developmental macromolecular synthesis.
The zinc ribbon domains of the general transcription factors TFIIB and Brf: conserved functional surfaces but different roles in transcription initiation
Authors: Hahn Steven , Roberts Sadia
Published: November 2021

The function of the conserved zinc-binding domains in the related Pol II- and Pol III-specific factors TFIIB and Brf was investigated. Three-dimensional structure modeling and mutagenesis studies indicated that for both factors, the functional surface of the zinc ribbon fold consists of a small conserved patch of residues located on one face of the domain comprised mainly of the second and third antiparallel β strands. Previous studies have shown that the TFIIB zinc ribbon is essential for recruitment of Pol II into the preinitiation complex. In contrast, Pol III recruitment assays and in vitro transcription demonstrate that the disruption of the Brf zinc ribbon does not lead to a defect in Pol III recruitment but, rather, a defect in open complex formation. Therefore, the same conserved surface of the zinc ribbon domain has been adapted to serve distinct roles in the Pol II and Pol III transcription machinery.
Analysis of promoter binding by the E2F and pRB families in vivo: distinct E2F proteins mediate activation and repression
Authors: Takahashi Yasuhiko , Rayman Joseph B. , Dynlacht Brian David
Published: November 2021

The E2F transcription factor plays a pivotal role in the timely activation of gene expression during mammalian cell cycle progression, whereas pRB and related proteins control cell growth in part through the ability to block the action of E2F. To identify physiologically important E2F-responsive promoters and to study their occupancy and histone acetylation state in vivo, we have taken advantage of a cross-linking approach in synchronized, living cells. We find that the pattern of E2F and pRB-related polypeptides recruited to these promoters changes in a strikingly dynamic fashion as cells progress from quiescence into G1 and S phase: Repression of each promoter in quiescent cells is associated with recruitment of E2F-4 and p130 and low levels of histone acetylation, but by late G1, these proteins are replaced largely by E2F-1 and E2F-3, in concert with acetylation of histones H3 and H4 and gene activation. These findings suggest that repression and activation of E2F-responsive genes may occur through distinct E2F heterodimers that direct the sequential recruitment of enzymes able to deacetylate and then acetylate core histones.
The mouse homolog of Drosophila Vasa is required for the development of male germ cells
Authors: Tanaka Satomi S. , Toyooka Yayoi , Akasu Ryuko , Katoh-Fukui Yuko , Nakahara Yoko , Suzuki Rika , Yokoyama Minesuke , Noce Toshiaki
Published: November 2021

Restricted expression of a mouse Vasa homolog gene (Mvh) expression is first detected in primordial germ cells (PGCs) after colonization of the genital ridges. Subsequently,Mvh is maintained until postmeiotic germ cells are formed. Here, we demonstrate that male mice homozygous for a targeted mutation of Mvh exhibit a reproductive deficiency. Male homozygotes produce no sperm in the testes, where premeiotic germ cells cease differentiation by the zygotene stage and undergo apoptotic death. In addition, the proliferation of PGCs that colonize homozygous male gonads is significantly hampered, and OCT-3/4 expression appears to be reduced. These results indicate that the loss ofMvh function causes a deficiency in the proliferation and differentiation of mouse male germ cells.
Severe liver degeneration and lack of NF-κB activation in NEMO/IKKγ-deficient mice
Authors: Rudolph Dorothea , Yeh Wen-Chen , Wakeham Andrew , Rudolph Bettina , Nallainathan Dhani , Potter Julia , Elia Andrew J. , Mak Tak W.
Published: November 2021

Phosphorylation of IκB, an inhibitor ofNF-κB, is an important step in the activation of the transcription factor NF-κB. Phosphorylation is mediated by the IκB kinase (IKK) complex, known to contain two catalytic subunits: IKKα andIKKβ. A novel, noncatalytic component of this kinase complex called NEMO(NF-κBessentialmodulator)/IKKγ was identified recently. We have generatedNEMO/IKKγ-deficient mice by gene targeting. Mutant embryos die at E12.5–E13.0 from severe liver damage due to apoptosis.NEMO/IKKγ-deficient primary murine embryonic fibroblasts (MEFs) lack detectableNF-κB DNA-binding activity in response to TNFα, IL-1, LPS, and Poly(IC) and do not show stimulus-dependent IκB kinase activity, which correlates with a lack of phosphorylation and degradation of IκBα. Consistent with these data, mutant MEFs show increased sensitivity to TNFα-induced apoptosis. Our data provide in vivo evidence that NEMO/IKKγ is the first essential, noncatalytic component of the IKK complex.