bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic evidence of paternal genome elimination in the globular springtailAllacma fusca
Authors: Jaron Kamil S. , Hodson Christina N. , Ellers Jacintha , Baird Stuart JE , Ross Laura
Published: November 2021

Abstract

Paternal genome elimination (PGE) - a type of reproduction in which males inherit but fail to pass on their father’s genome - evolved independently in six to eight arthropod clades. Thousands of species, including several important for agriculture, reproduce via this mode of reproduction. While PGE is well established in some of the clades, the evidence in globular springtails (Symphypleona) remains elusive, even though they represent the oldest and most species rich clade putatively reproducing via PGE. We sequenced genomic DNA from whole bodies of Allacma fusca males with high fractions (>27.5%) of sperm to conclusively confirm that all the sperm carry one parental haplotype only. Although it is suggestive that the single haplotype present in sperm is maternally inherited, definitive genetic proof of the parent of origin is still needed. The genomic approach we developed allows for detection of genotypic differences between germline and soma in all species with sufficiently high fraction of germline in their bodies. This opens new opportunities for scans of reproductive modes in small organisms.
Cellular and transcriptional diversity over the course of human lactation
Authors: Nyquist Sarah K. , Gao Patricia , Haining Tessa K. J. , Retchin Michael R. , Maor Yarden Golan , Drake Riley S. , Kolb Kellie , Mead Benjamin E. , Ahituv Nadav , Martinez Micaela E. , Berger Bonnie , Shalek Alex K. , Goods Brittany A.
Published: November 2021

Human breast milk is a dynamic fluid that contains millions of cells, but their identities and phenotypic properties are poorly understood. We used single-cell RNA-seq (scRNA-seq) to characterize the transcriptomes of cells from human breast milk (hBM) across lactational time from 3 to 632 days postpartum in 15 donors. We find that the majority of cells in human breast milk are lactocytes, a specialized epithelial subset, and cell type frequencies shift over the course of lactation yielding greater epithelial diversity at later points. Analysis of lactocytes reveals a continuum of cell states characterized by transcriptional changes in hormone, growth factor, and milk production related pathways. Generalized additive models suggest that one sub-cluster, LALBAlow epithelial cells, increase as a function of time postpartum, daycare attendance, and the use of hormonal birth control. We identify several sub-clusters of macrophages in hBM that are enriched for tolerogenic functions, possibly playing a role in protecting the mammary gland during lactation. Our description of the cellular components of breast milk, their association with maternal-infant dyad metadata and quantification of alterations at the gene and pathways levels provides the first detailed longitudinal picture of human breast milk cells across lactational time. This work paves the way for future investigations of how a potential division of cellular labor and differential hormone regulation might be leveraged therapeutically to support healthy lactation and potentially aid in milk production.
Introspective inference counteracts perceptual distortion
Authors: Mihali Andra , Broeker Marianne , Ragalmuto Florian DM , Horga Guillermo
Published: November 2021

Introspective agents can recognize the extent to which their internal perceptual experiences deviate from the actual states of the external world. This ability, also known as insight, is critically required for reality testing and is impaired in psychosis, yet very little is known about its cognitive underpinnings. We developed a Bayesian modeling framework and a novel psychophysics paradigm to quantitatively characterize this type of insight while participants experienced a motion after-effect illusion. Participants could incorporate knowledge about the illusion into their decisions when judging the actual direction of a motion stimulus, compensating for the illusion (and often overcompensating). Furthermore, confidence, reaction-time, and pupil-dilation data all showed signatures consistent with inferential adjustments in the Bayesian insight model. Our results suggest that people can question the veracity of what they see by making insightful inferences that incorporate introspective knowledge about internal distortions.
Numerous expansions in TRP ion channel diversity highlight widespread evolution of molecular sensors in animal diversification
Authors: Hsiao Jan , Deng Lola Chenxi , Chalasani Sreekanth , Edsinger Eric
Published: November 2021

Transient Potential Receptor (TRP) ion channels are a diverse superfamily of multimodal molecular sensors that respond to a wide variety of stimuli, including mechanical, chemical, and thermal. TRP channels are present in most eukaryotes but best understood in mammalian, worm, and fly genetic models, where they are expressed in diverse cell-types and commonly associated with the nervous system. Here, we characterized TRP superfamily gene and genome evolution to better understand origins and evolution of molecular sensors, brains, and behavior in animals and help advance development of novel genetic technologies, like sonogenetics. We developed a flexible push-button bioinformatic and phylogenomic pipeline, GIGANTIC, that generated genome-based gene and species trees and enabled phylogenetic characterization of challenging remote homologs and distantly-related organisms deep in evolution. We identified complete sets of TRP superfamily ion channels, with over 3000 genes in 22 animal phyla and 70 species having publicly-available sequenced genomes, including 3 unicellular outgroups. We then identified clusters of TRP family members in genomes, evaluated gene models per cluster, and repaired split gene models. We also produced whole-organism PacBio transcriptomes for five species to independently validate our gene model assessment and model repairs. We find that many TRP families exhibited numerous and often extensive expansions in different phyla. Some expansions represent local clusters on respective genomes, a trend that is likely undercounted due to varied quality in genome assemblies and annotations of non-model organisms. Our work expands known TRP diversity across animals, including addition of previously uncharacterized phyla and identification of unrecognized homologs in previously characterized species.
An Integrated Process Analytical Platform for Automated Monitoring of Monoclonal Antibody N-linked Glycosylation
Authors: Gyorgypal Aron , Chundawat Shishir P.S.
Published: November 2021

The biopharmaceutical industry is transitioning towards adoption of continuous biomanufacturing practices that are often more flexible and efficient than traditional batch processes. Regulatory agencies such as the Food and Drug Administration (FDA) are further urging use of advanced PAT to analyze the design space to increase process knowledge and enable high quality biologics production. Post-translational modification of proteins, such as N-linked glycosylation are often critical quality attributes known to affect biologics safety and efficacy hence requiring close monitoring during manufacturing. Here, we developed an online sequential-injection based PAT system, called N-GLYcanyzer, that can rapidly monitor mAb glycosylation during upstream biomanufacturing. The key innovation includes design of an integrated mAb sampling and derivation system for antibody titer and glycoform analysis in under 2 hours. The N-GLYcanyzer process includes mAb capture, deglycosylation, fluorescent glycan labeling, and glycan enrichment for direct injection and analysis on an integrated high performance liquid chromatography (HPLC) system. Different fluorescent tags and reductants were tested to maximize glycan labeling efficiency under aqueous conditions, while porous graphitized carbon (PGC) was studied for optimum glycan recovery and enrichment. We find that 2-AB labeling of glycans with 2-picoline borane as a reducing agent, using the N-GLYcanyzer workflow, gives higher glycan labeling efficiency under aqueous conditions leading to upwards of a 5-fold increase in fluorescent products intensity. Finally, we showcase how the N-GLYcanyzer platform can be implemented at/on-line to an upstream bioreactor for automated and near real-time glycosylation monitoring of a Trastuzumab biosimilar produced by Chinese Hamster Ovary (CHO) cells.

Graphical Abstract

N-GLYcanyzer is an automated PAT toolkit for rapid sample processing for mAb N-linked glycans analysis to enable advanced biologics manufacturing
Aerobic Bacteria Produce Nitric Oxide via Denitrification and Trigger Algal Population Collapse
Authors: Abada Adi , Sperfeld Martin , Carmieli Raanan , Ben-Dor Shifra , Zhang Irene Huang , Babbin Andrew R. , Segev Einat
Published: November 2021

Microbial interactions govern marine biogeochemistry. These interactions are generally considered to rely on exchange of organic molecules. Here we report on a novel inorganic route of microbial communication, showing that algal-bacterial interactions are mediated through inorganic nitrogen exchange. Under oxygen-rich conditions, aerobic bacteria reduce algal-secreted nitrite to nitric oxide (NO) through denitrification, a well-studied anaerobic respiration mechanism. Bacteria secrete NO, triggering a cascade in algae akin to programmed cell death. During death, algae further generate NO, thereby propagating the signal in the algal population. Eventually, the algal population collapses, similar to the sudden demise of oceanic algal blooms. Our study suggests that the exchange of denitrification intermediates, particularly in oxygenated environments, is an overlooked yet ecologically significant route of microbial communication within and across kingdoms.

One Sentence Summary

Aerobic bacteria activate denitrification in oxygenated conditions and produce nitric oxide that kills their algal partners
Word structure tunes electrophysiological and hemodynamic responses in the frontal cortex
Authors: Gao Fei , Hua Lin , He Yuwen , Yuan Zhen
Published: November 2021

To date, it is still unclear how word structure might impact lexical processing in the brain for morphological impoverished language like Chinese. In this study, concurrent EEG and fNIRS recordings were performed to inspect the temporal and spatial brain activity that are related to the morphological priming effect (compound/derivation constitute priming vs. non-morphological priming) and word structure (compound vs. derivation) modulation. Interestingly, it was discovered that the morphological priming effect was mainly detected by the behavioral performance and spatial brain activation in the left prefrontal cortex, while word structure effect was revealed by the behavioral data as well as the temporal and spatial brain activation patterns. In addition, Chinese derivations exhibited significantly enhanced brain activation in the frontal cortex and involved more brain networks as compared to lexicalized compounds. The results were interpreted by the differing connection patterns between constitute morphemes within a given word structure from spreading activation perspective. More importantly, we demonstrated that Chinese word structure effect showed a distinct brain activation pattern as compared to that from the dual-route mechanism in alphabetic languages. Therefore, this pilot work paves a new avenue for comprehensively understanding the underlying cognitive neural mechanism associated with Chinese derivations and coordinate compounds.
Ethylene signaling increases reactive oxygen species accumulation to drive root hair initiation in Arabidopsis
Authors: Martin R. Emily , Marzol Eliana , Estevez Jose M. , Muday Gloria K.
Published: November 2021

Root hair initiation is a highly regulated aspect of root development. The plant hormone, ethylene, and its precursor, 1-amino-cyclopropane-1-carboxylic acid (ACC), induce formation and elongation of root hairs. Using confocal microscopy paired with redox biosensors and dyes, we demonstrated that treatments that elevate ethylene levels led to increased hydrogen peroxide accumulation in hair cells prior to root hair formation. In two ethylene-insensitive mutants, etr1-3 and ein3/eil1, there was no increase in root hair number or ROS accumulation. Conversely, etr1-7, a constitutive ethylene signaling receptor mutant, has increased root hair formation and ROS accumulation like ethylene-treated Col-0 seedlings. The caprice and werewolf transcription factor mutants have decreased and elevated ROS levels, which are correlated with levels of root hair initiation. The rhd2-6 mutant, with a defect in the gene encoding a ROS synthesizing Respiratory Burst Oxidase Homolog C (RBOHC) and the prx44-2 mutant defective in a class III peroxidase, showed impaired ethylene-dependent ROS synthesis and root hair formation and EIN3/EIL1 dependent transcriptional regulation. Together, these results indicate that ethylene increases ROS accumulation through RBOHC and PRX44 to drive root hair formation.

SUMMARY STATEMENT

The gaseous hormone ethylene increases root hair initiation by elevating reactive oxygen species (ROS) in trichoblast cells. Genetic and biochemical approaches identified ethylene-regulated ROS producing enzymes that drive root hair initiation.
Effectiveness of BNT162b2 (Comirnaty, Pfizer-BioNTech) COVID-19 booster vaccine against covid-19 related symptoms in England: test negative case-control study
Authors: Andrews Nick , Stowe Julia , Kirsebom Freja , Gower Charlotte , Ramsay Mary , Bernal Jamie Lopez
Published: November 2021

Background

In September 2021, the UK Government introduced a booster programme targeting individuals over 50 and those in a clinical risk group. Individuals were offered either a full dose of the BNT162b2 (Comirnaty, Pfizer-BioNTech) vaccine or a half dose of the mRNA-1273 (Spikevax, Moderna) vaccine, irrespective of the vaccine received as the primary course

Methods

We used a test-negative case-control design to estimate the Vaccine Effectiveness (VE) of the booster dose BNT162b2 (Comirnaty, Pfizer-BioNTech) in those aged over 50 against symptomatic disease in post booster time intervals compared to individuals at least 140 days post a second dose with no booster dose recorded. In a secondary analysis, we also compared to unvaccinated individuals and to the 2 to 6 day period after a booster dose was received. Analyses were stratified by which primary doses had been received and any mixed primary courses were excluded.

Results

The relative VE estimate in the 14 days after the BNT162b2 (Comirnaty, Pfizer-BioNTech) booster dose, compared to individuals that received a two-dose primary course, was 87.4 (95% confidence interval 84.9-89.4) in those individuals who received two doses ChAdOx1-S (Vaxzevria, AstraZeneca) as a primary course and 84.4 (95% confidence interval 82.8-85.8) in those individuals who received two doses of BNT162b2 (Comirnaty, Pfizer-BioNTech) as a primary course. Using the 2-6 day period post the booster dose as the baseline gave similar results. The absolute VE from 14 days after the booster, using the unvaccinated baseline, was 93.1(95% confidence interval 91.7-94.3) in those with ChAdOx1-S (Vaxzevria, AstraZeneca) as their primary course and 94.0 (93.4-94.6) for BNT162b2 (Comirnaty, Pfizer-BioNTech) as their primary course.

Conclusions

Our study provides real world evidence of significant increased protection from the booster vaccine dose against symptomatic disease in those aged over 50 year of age irrespective of which primary course was received.
CLMB: deep contrastive learning for robust metagenomic binning
Authors: Zhang Pengfei , Jiang Zhengyuan , Wang Yixuan , Li Yu
Published: November 2021

The reconstruction of microbial genomes from large metagenomic datasets is a critical procedure for finding uncultivated microbial populations and defining their microbial functional roles. To achieve that, we need to perform metagenomic binning, clustering the assembled contigs into draft genomes. Despite the existing computational tools, most of them neglect one important property of the metagenomic data, that is, the noise. To further improve the metagenomic binning step and reconstruct better metagenomes, we propose a deep Contrastive Learning framework for Metagenome Binning (CLMB), which can efficiently eliminate the disturbance of noise and produce more stable and robust results. Essentially, instead of denoising the data explicitly, we add simulated noise to the training data and force the deep learning model to produce similar and stable representations for both the noise-free data and the distorted data. Consequently, the trained model will be robust to noise and handle it implicitly during usage. CLMB outperforms the previous state-of-the-art binning methods significantly, recovering the most near-complete genomes on almost all the benchmarking datasets (up to 17% more reconstructed genomes compared to the second-best method). It also improves the performance of bin refinement, reconstructing 8-22 more high-quality genomes and 15-32 more middle-quality genomes than the second-best result. Impressively, in addition to being compatible with the binning refiner, single CLMB even recovers on average 15 more HQ genomes than the refiner of VAMB and Maxbin on the benchmarking datasets. On a real mother-infant microbiome dataset with 110 samples, CLMB is scalable and practical to recover 365 high-quality and middle-quality genomes (including 21 new ones), providing insights into the microbiome transmission. CLMB is open-source and available at https://github.com/zpf0117b/CLMB/.
Error-prone bypass of certain DNA lesions by the human DNA polymerase κ
Authors: Ohashi Eiji , Ogi Tomoo , Kusumoto Rika , Iwai Shigenori , Masutani Chikahide , Hanaoka Fumio , Ohmori Haruo
Published: November 2021

The Escherichia coli protein DinB is a newly identified error-prone DNA polymerase. Recently, a human homolog of DinB was identified and named DINB1. We report that the DINB1gene encodes a DNA polymerase (designated polκ), which incorporates mismatched bases on a nondamaged template with a high frequency. Moreover, polκ bypasses an abasic site andN-2–acetylaminofluorene (AAF)-adduct in an error-prone manner but does not bypass a cis–syn or (6-4) thymine–thymine dimer or a cisplatin-adduct. Therefore, our results implicate an important role for polκ in the mutagenic bypass of certain types of DNA lesions.
Conditional biallelic Nf2 mutation in the mouse promotes manifestations of human neurofibromatosis type 2
Authors: Giovannini Marco , Robanus-Maandag Els , van der Valk Martin , Niwa-Kawakita Michiko , Abramowski Vincent , Goutebroze Laurence , Woodruff James M. , Berns Anton , Thomas Gilles
Published: November 2021

Hemizygosity for the NF2 gene in humans causes a syndromic susceptibility to schwannoma development. However, Nf2hemizygous mice do not develop schwannomas but mainly osteosarcomas. In the tumors of both species, the second Nf2 allele is inactivated. We report that conditional homozygous Nf2 knockout mice with Cre-mediated excision of Nf2 exon 2 in Schwann cells showed characteristics of neurofibromatosis type 2. These included schwannomas, Schwann cell hyperplasia, cataract, and osseous metaplasia. Thus, the tumor suppressor function of Nf2, here revealed in murine Schwann cells, was concealed in hemizygousNf2 mice because of insufficient rate of second allele inactivation in this cell compartment. The finding of this conserved function documents the relevance of the present approach to model the human disease.
polι, a remarkably error-prone human DNA polymerase
Authors: Tissier Agnès , McDonald John P. , Frank Ekaterina G. , Woodgate Roger
Published: November 2021

TheSaccharomyces cerevisiae RAD30gene encodes DNA polymerase η. Humans possess two Rad30 homologs. One (RAD30A/POLH) has previously been characterized and shown to be defective in humans with the Xeroderma pigmentosum variant phenotype. Here, we report experiments demonstrating that the second human homolog (RAD30B), also encodes a novel DNA polymerase that we designate polι. polι, is a distributive enzyme that is highly error-prone when replicating undamaged DNA. At template G or C, the average error frequency was ∼1 × 10−2. Our studies revealed, however, a striking asymmetry in misincorporation frequency at template A and T. For example, template A was replicated with the greatest accuracy, with misincorporation of G, A, or C occurring with a frequency of ∼1 × 10−4to 2 × 10−4. In dramatic contrast, most errors occurred at template T, where the misincorporation of G was, in fact, favored ∼3:1 over the correct nucleotide, A, and misincorporation of T occurred at a frequency of ∼6.7 × 10−1. These findings demonstrate that polι is one of the most error-prone eukaryotic polymerases reported to date and exhibits an unusual misincorporation spectrum in vitro.
Coregulation of anterior and posterior mesendodermal development by a hairy-related transcriptional repressor
Authors: Bally-Cuif Laure , Goutel Carole , Wassef Marion , Wurst Wolfgang , Rosa Frédéric
Published: November 2021

During embryonic development in vertebrates, the endoderm becomes patterned along the anteroposterior axis to produce distinct derivatives. How this regulation is controlled is not well understood. We report that the zebrafish hairy/enhancer of split [E(spl)]-related gene her5 plays a critical role in this process. At gastrulation, following endoderm induction and further cell interaction processes including a local release of Notch/Delta signaling, her5 expression is progressively excluded from the presumptive anterior- and posteriormost mesendodermal territories to become restricted to an adjacent subpopulation of dorsal endodermal precursors. Ectopic misexpressions of wild-type and mutant forms of her5 reveal that her5functions primarily within the endodermal/endmost mesendodermal germ layer to inhibit cell participation to the endmost-fated mesendoderm. In this process, her5 acts as an active transcriptional repressor. These features are strikingly reminiscent of the function of Drosophila Hairy/E(spl) factors in cell fate decisions. Our results provide the first model for vertebrate endoderm patterning where an early regulatory step at gastrulation, mediated by her5 controls cell contribution jointly to the anterior- and posteriormost mesendodermal regions.
Control of her1 expression during zebrafish somitogenesis by a Delta-dependent oscillator and an independent wave-front activity
Authors: Holley Scott A. , Geisler Robert , Nüsslein-Volhard Christiane
Published: November 2021

Somitogenesis has been linked both to a molecular clock that controls the oscillation of gene expression in the presomitic mesoderm (PSM) and to Notch pathway signaling. The oscillator, or clock, is thought to create a prepattern of stripes of gene expression that regulates the activity of the Notch pathway that subsequently directs somite border formation. Here, we report that the zebrafish gene after eight (aei) that is required for both somitogenesis and neurogenesis encodes the Notch ligand DeltaD. Additional analysis revealed that stripes of her1 expression oscillate within the PSM and that aei/DeltaDsignaling is required for this oscillation.aei/DeltaD expression does not oscillate, indicating that the activity of the Notch pathway upstream ofher1 may function within the oscillator itself. Moreover, we found that her1 stripes are expressed in the anlage of consecutive somites, indicating that its expression pattern is not pair-rule. Analysis of her1 expression inaei/DeltaD, fused somites (fss), and aei;fss embryos uncovered a wave-front activity that is capable of continually inducing her1 expression de novo in the anterior PSM in the absence of the oscillation of her1. The wave-front activity, in reference to the clock and wave-front model, is defined as such because it interacts with the oscillator-derived pattern in the anterior PSM and is required for somite morphogenesis. This wave-front activity is blocked in embryos mutant for fssbut not aei/DeltaD. Thus, our analysis indicates that the smooth sequence of formation, refinement, and fading ofher1 stripes in the PSM is governed by two separate activities.
Complete lack of NF-κB activity in IKK1 and IKK2 double-deficient mice: additional defect in neurulation
Authors: Li Qiutang , Estepa Gabriela , Memet Sylvie , Israel Alain , Verma Inder M.
Published: November 2021

NF-κB activity is induced by cytokines, stress, and pathogens. IKK1 and IKK2 are critical IκB kinases in NF-κB activation. In this study mice lacking IKK1 and IKK2 died at E12. Additional defect in neurulation associated with enhanced apoptosis in the neuroepithelium was also observed. MEF cells fromIKK1−/−/IKK2−/−embryos did not respond to NF-κB inducers. Upon crossing withκB–lacZ transgenic mice, double-deficient embryos also lost lacZ transgene expression in vascular endothelial cells during development. Our data suggest that IKK1 and IKK2 are essential for NF-κB activation in vivo and have an important role in protecting neurons against excessive apoptosis during development.
Inhibition of Wnt signaling by ICAT, a novel β-catenin-interacting protein
Authors: Tago Ken-ichi , Nakamura Tsutomu , Nishita Michiru , Hyodo Junko , Nagai Shin-ichi , Murata Yoji , Adachi Shungo , Ohwada Susumu , Morishita Yasuo , Shibuya Hiroshi , Akiyama Tetsu
Published: November 2021

Wnt signaling has an important role in both embryonic development and tumorigenesis. β-Catenin, a key component of the Wnt signaling pathway, interacts with the TCF/LEF family of transcription factors and activates transcription of Wnt target genes. Here, we identify a novel β-catenin-interacting protein, ICAT, that was found to inhibit the interaction of β-catenin with TCF-4 and represses β-catenin–TCF-4-mediated transactivation. Furthermore, ICAT inhibited Xenopus axis formation by interfering with Wnt signaling. These results suggest that ICAT negatively regulates Wnt signaling via inhibition of the interaction between β-catenin and TCF and is integral in development and cell proliferation.
BCoR, a novel corepressor involved in BCL-6 repression
Authors: Huynh Khanh D. , Fischle Wolfgang , Verdin Eric , Bardwell Vivian J.
Published: November 2021

BCL-6 encodes a POZ/zinc finger transcriptional repressor that is required for germinal center formation and may influence apoptosis. Aberrant expression ofBCL-6 due to chromosomal translocations is implicated in certain subtypes of non-Hodgkin's lymphoma. The POZ domains of BCL-6 and several other POZ proteins interact with corepressors N-CoR and SMRT. Here we identify and characterize a novel corepressor BCoR (BCL-6 interacting corepressor), which is expressed ubiquitously in human tissues. BCoR can function as a corepressor when tethered to DNA and, when overexpressed, can potentiate BCL-6 repression. Specific class I and II histone deacetylases (HDACs) interact in vivo with BCoR, suggesting that BCoR may functionally link these two classes of HDACs. Strikingly, BCoR interacts selectively with the POZ domain of BCL-6 but not with eight other POZ proteins tested, including PLZF. Additionally, interactions between the BCL-6 POZ domain and SMRT, N-CoR, and BCoR are mutually exclusive. The specificity of the BCL-6/BCoR interaction suggests that BCoR may have a role in BCL-6-associated lymphomas.
Activin receptor patterning of foregut organogenesis
Authors: Kim Seung K. , Hebrok Matthias , Li En , Oh S. Paul , Schrewe Heinrich , Harmon Erin B. , Lee Joon S. , Melton Douglas A.
Published: November 2021

Foregut development produces a characteristic sequence of gastrointestinal and respiratory organs, but the signaling pathways that ensure this developmental order remain largely unknown. Here, mutations of activin receptors ActRIIA and ActRIIB are shown to disrupt the development of posterior foregut-derived organs, including the stomach, pancreas, and spleen. Foregut expression of genes includingShh and Isl1 is shifted in mutant mice. The endocrine pancreas is particularly sensitive to the type and extent of receptor inactivation. ActRIIA+/−B+/−animals lack axial defects, but have hypoplastic pancreatic islets, hypoinsulinemia, and impaired glucose tolerance. Thus, activin receptor-mediated signaling regulates axial patterning, cell differentiation, and function of foregut-derived organs.
Sip2p and its partner Snf1p kinase affect aging in S. cerevisiae
Authors: Ashrafi Kaveh , Lin Stephen S. , Manchester Jill K. , Gordon Jeffrey I.
Published: November 2021

For a number of organisms, the ability to withstand periods of nutrient deprivation correlates directly with lifespan. However, the underlying molecular mechanisms are poorly understood. We show that deletion of the N-myristoylprotein, Sip2p, reduces resistance to nutrient deprivation and shortens lifespan in Saccharomyces cerevisiae. This reduced lifespan is due to accelerated aging, as defined by loss of silencing from telomeres and mating loci, nucleolar fragmentation, and accumulation of extrachromosomal rDNA. Genetic studies indicate that sip2Δ produces its effect on aging by increasing the activity of Snf1p, a serine/threonine kinase involved in regulating global cellular responses to glucose starvation. Biochemical analyses reveal that as yeast age, hexokinase activity increases as does cellular ATP and NAD+ content. The change in glucose metabolism represents a new correlate of aging in yeast and occurs to a greater degree, and at earlier generational ages in sip2Δ cells. Sip2p and Snf1p provide new molecular links between the regulation of cellular energy utilization and aging.
tBID, a membrane-targeted death ligand, oligomerizes BAK to release cytochrome c
Authors: Wei Michael C. , Lindsten Tullia , Mootha Vamsi K. , Weiler Solly , Gross Atan , Ashiya Mona , Thompson Craig B. , Korsmeyer Stanley J.
Published: November 2021

TNFR1/Fas engagement results in the cleavage of cytosolic BID to truncated tBID, which translocates to mitochondria. Immunodepletion and gene disruption indicate BID is required for cytochrome c release. Surprisingly, the three-dimensional structure of this BH3 domain-only molecule revealed two hydrophobic α-helices suggesting tBID itself might be a pore-forming protein. Instead, we demonstrate that tBID functions as a membrane-targeted death ligand in which an intact BH3 domain is required for cytochrome c release, but not for targeting.Bak-deficient mitochondria and blocking antibodies reveal tBID binds to its mitochondrial partner BAK to release cytochrome c, a process independent of permeability transition. Activated tBID results in an allosteric activation of BAK, inducing its intramembranous oligomerization into a proposed pore for cytochrome c efflux, integrating the pathway from death receptors to cell demise.
Hypersensitivity to DNA damage leads to increased apoptosis during early mouse development
Authors: Heyer Babette S. , MacAuley Alasdair , Behrendtsen Ole , Werb Zena
Published: November 2021

Gastrulation in mice is associated with the start of extreme proliferation and differentiation. The potential cost to the embryo of a very rapid proliferation rate is a high production of damaged cells. We demonstrate a novel surveillance mechanism for the elimination of cells damaged by ionizing radiation during mouse gastrulation. During this restricted developmental window, the embryo becomes hypersensitive to DNA damage induced by low dose irradiation (<0.5 Gy) and undergoes apoptosis without cell cycle arrest. Intriguingly, embryonic cells, including germ cell progenitors, but not extraembryonic cells, become hypersensitive to genotoxic stress and undergo Atm- and p53-dependent apoptosis. Thus, hypersensitivity to apoptosis in the early mouse embryo is a cell fate-dependent mechanism to ensure genomic integrity during a period of extreme proliferation and differentiation.
Analysis ofArabidopsisglucose insensitive mutants,gin5andgin6, reveals a central role of the plant hormone ABA in the regulation of plant vegetative development by sugar
Authors: Arenas-Huertero Francisco , Arroyo Analilia , Zhou Li , Sheen Jen , León Patricia
Published: November 2021

Sugars have signaling roles in a wide variety of developmental processes in plants. To elucidate the regulatory components that constitute the glucose signaling network governing plant growth and development, we have isolated and characterized twoArabidopsisglucose insensitive mutants,gin5andgin6, based on a glucose-induced developmental arrest during early seedling morphogenesis. The T-DNA-taggedgin6mutant abrogates the glucose-induced expression of a putative transcription factor, ABI4, previously shown to be involved in seed-specific abscisic acid (ABA) responses. Thus, ABI4 might be a regulator involved in both glucose- and seed-specific ABA signaling. The characterization of thegin5mutant, on the other hand, reveals that glucose-specific accumulation of ABA is essential for hexokinase-mediated glucose responses. Consistent with this result, we show that three ABA-deficient mutants (aba1-1, aba2-1, andaba3-2) are also glucose insensitive. Exogenous ABA can restore normal glucose responses ingin5andabamutants but not ingin6plants. Surprisingly, onlyabi4andabi5-1but not other ABA-insensitive signaling mutants (abi1-1, abi2-1, andabi3-1) exhibit glucose insensitivity, indicating the involvement of a distinct ABA signaling pathway in glucose responses. These results provide the first direct evidence to support a novel and central role of ABA in plant glucose responses mediated through glucose regulation of both ABA levels by GIN5 and ABA signaling by GIN6/ABI4.
Cell surface-localized matrix metalloproteinase-9 proteolytically activates TGF-β and promotes tumor invasion and angiogenesis
Authors: Yu Qin , Stamenkovic Ivan
Published: November 2021

We have uncovered a novel functional relationship between the hyaluronan receptor CD44, the matrix metalloproteinase-9 (MMP-9) and the multifunctional cytokine TGF-β in the control of tumor-associated tissue remodeling. CD44 provides a cell surface docking receptor for proteolytically active MMP-9 and we show here that localization of MMP-9 to cell surface is required for its ability to promote tumor invasion and angiogenesis. Our observations also indicate that MMP-9, as well as MMP-2, proteolytically cleaves latent TGF-β, providing a novel and potentially important mechanism for TGF-β activation. In addition, we show that MMP-9 localization to the surface of normal keratinocytes is CD44 dependent and can activate latent TGF-β. These observations suggest that coordinated CD44, MMP-9, and TGF-β function may provide a physiological mechanism of tissue remodeling that can be adopted by malignant cells to promote tumor growth and invasion.
Dynamic organization of chromosomal DNA in Escherichia coli
Authors: Niki Hironori , Yamaichi Yoshiharu , Hiraga Sota
Published: November 2021

We have revealed the subcellular localization of different DNA segments that are located at ∼230-kb intervals on theEscherichia coli chromosome using fluorescence in situ hybridization (FISH). The series of chromosome segments is localized within the cell in the same order as the chromosome map. The large chromosome region including oriC shows similar localization patterns, which we call the Ori domain. In addition, the localization pattern of the large segment including dif is characteristic of the replication terminus region. The segment also shows similar localization patterns, which we call the Ter domain. In newborn cells, Ori and Ter domains of the chromosome are differentially localized near opposite cell poles. Subsequently, in the B period, the Ori domain moves toward mid-cell before the initiation of replication, and the Ter domain tends to relocate at mid-cell. An inversion mutant, in which the Ter domain is located close to oriC, shows abnormal subcellular localization of ori and dif segments, resulting in frequent production of anucleate cells. These studies thus suggest that the E. coli chromosome is organized to form a compacted ring structure with the Ori and Ter domains; these domains participate in the cell cycle-dependent localization of the chromosome.
Relief of gene repression by Torso RTK signaling: role of capicua in Drosophila terminal and dorsoventral patterning
Authors: Jiménez Gerardo , Guichet Antoine , Ephrussi Anne , Casanova Jordi
Published: November 2021

Differentiation of the embryonic termini in Drosophiladepends on signaling by the Tor RTK, which induces terminal gene expression by inactivating at the embryonic poles a uniformly distributed repressor activity that involves the Gro corepressor. Here, we identify a new gene, cic, that acts as a repressor of terminal genes regulated by the Tor pathway. cic also mediates repression along the dorsoventral axis, a process that requires the Dorsal morphogen and Gro, and which is also inhibited by Tor signaling at the termini. cic encodes an HMG-box transcription factor that interacts with Gro in vitro. We present evidence that Tor signaling regulates terminal patterning by inactivating Cic at the embryo poles. cic has been evolutionarily conserved, suggesting that Cic-like proteins may act as repressors regulated by RTK signaling in other organisms.
The human homologs of checkpoint kinases Chk1 and Cds1 (Chk2) phosphorylate p53 at multiple DNA damage-inducible sites
Authors: Shieh Sheau-Yann , Ahn Jinwoo , Tamai Katsuyuki , Taya Yoichi , Prives Carol
Published: November 2021

Upon DNA damage, the amino terminus of p53 is phosphorylated at a number of serine residues including S20, a site that is particularly important in regulating stability and function of the protein. Because no known kinase has been identified that can modify this site, HeLa nuclear extracts were fractionated and S20 phosphorylation was followed. We discovered that a S20 kinase activity copurifies with the human homolog of theSchizosaccharomyces pombecheckpoint kinase, Chk1 (hCHK1). We confirmed that recombinant hCHK1, but not a kinase-defective version of hCHK1, can phosphorylate p53 in vitro at S20. Additional inducible amino- and carboxy-terminal sites in p53 are also phosphorylated by hCHK1, indicating that this is an unusually versatile protein kinase. It is interesting that hCHK1 strongly prefers tetrameric to monomeric p53 in vitro, consistent with our observation that phosphorylation of amino-terminal sites in vivo requires that p53 be oligomeric. Regulation of the levels and activity of hCHK1 in transfected cells is directly correlated with the levels of p53; expression of either a kinase-defective hCHK1 or antisense hCHK1 leads to reduced levels of cotransfected p53, whereas overexpression of wild-type hCHK1 or the kinase domain of hCHK1 results in increased levels of expressed p53 protein. The human homolog of the secondS. pombecheckpoint kinase, Cds1 (CHK2/hCds1), phosphorylates tetrameric p53 but not monomeric p53 in vitro at sites similar to those phosphorylated by hCHK1 kinase, suggesting that both checkpoint kinases can play roles in regulating p53 after DNA damage.
Loss of PTEN facilitates HIF-1-mediated gene expression
Authors: Zundel Wayne , Schindler Cornelia , Haas-Kogan Daphne , Koong Albert , Kaper Fiona , Chen Eunice , Gottschalk Alexander R. , Ryan Heather E. , Johnson Randall S. , Jefferson Anne B. , Stokoe David , Giaccia Amato J.
Published: November 2021

In glioblastoma-derived cell lines, PTEN does not significantly alter apoptotic sensitivity or cause complete inhibition of DNA synthesis. However, in these cell lines PTEN regulates hypoxia- and IGF-1-induced angiogenic gene expression by regulating Akt activation of HIF-1 activity. Restoration of wild-type PTEN to glioblastoma cell lines lacking functional PTEN ablates hypoxia and IGF-1 induction of HIF-1-regulated genes. In addition, Akt activation leads to HIF-1α stabilization, whereas PTEN attenuates hypoxia-mediated HIF-1α stabilization. We propose that loss ofPTEN during malignant progression contributes to tumor expansion through the deregulation of Akt activity and HIF-1-regulated gene expression.
The carboxyl terminus of vertebrate poly(A) polymerase interacts with U2AF 65 to couple 3′-end processing and splicing
Authors: Vagner Stéphan , Vagner Christine , Mattaj Iain W.
Published: November 2021

Although it has been established that the processing factors involved in pre-mRNA splicing and 3′-end formation can influence each other positively, the molecular basis of this coupling interaction was not known. Stimulation of pre-mRNA splicing by an adjacentcis-linked cleavage and polyadenylation site in HeLa cell nuclear extract is shown to occur at an early step in splicing, the binding of U2AF 65 to the pyrimidine tract of the intron 3′ splice site. The carboxyl terminus of poly(A) polymerase (PAP) previously has been implicated indirectly in the coupling process. We demonstrate that a fusion protein containing the 20 carboxy-terminal amino acids of PAP, when tethered downstream of an intron, increases splicing efficiency and, like the entire 3′-end formation machinery, stimulates U2AF 65 binding to the intron. The carboxy-terminal domain of PAP makes a direct and specific interaction with residues 17–47 of U2AF 65, implicating this interaction in the coupling of splicing and 3′-end formation.
A major surface glycoprotein of Trypanosoma brucei is expressed transiently during development and can be regulated post-transcriptionally by glycerol or hypoxia
Authors: Vassella Erik , Den Abbeele Jan Van , Bütikofer Peter , Renggli Christina Kunz , Furger André , Brun Reto , Roditi Isabel
Published: November 2021

Differentiation is a means by which unicellular parasites adapt to different environments. In some cases, the developmental program may be modulated by interactions with the host, but the mechanisms are largely unknown. Trypanosoma brucei is transmitted between mammals by tsetse flies. The development of the procyclic form in the tsetse midgut is marked by the synthesis of a new glycoprotein coat, composed of EP and GPEET procyclins, that is important for survival. Here we demonstrate that the composition of the coat changes in response to extracellular signals in vitro and during development in vivo. EP and GPEET are coinduced when differentiation is initiated. Subsequently, EP expression is maintained, whereas GPEET is repressed after 7–9 days. The timepoint at which GPEET is repressed coincides with the appearance of parasites in a new compartment of the fly midgut. In culture, down-regulation of GPEET can be prevented by exogenous glycerol or accelerated by hypoxia. Regulation is post-transcriptional, and is conferred by the GPEET 3′ untranslated region. The same sequence also regulates expression of a reporter gene in the fly. The finding that GPEET is expressed during a defined window during the establishment of infection suggests that it has a specific function in host-parasite interactions rather than a generalized role in shielding underlying membrane molecules.
The leucine-rich repeat protein SUR-8 enhances MAP kinase activation and forms a complex with Ras and Raf
Authors: Li Weiquan , Han Min , Guan Kun-Liang
Published: November 2021

Caenorhabditis elegans sur-8 encodes a positive regulator of Ras signaling. We investigated the mechanism by which the human Sur-8 homolog can positively regulate Ras–MAP kinase signaling in mammalian cells. Sur-8 expression enhances Ras- or EGF-induced Raf and ERK activation but has no effect on ERK activation induced by active Raf or MEK. Furthermore, Sur-8 expression does not increase AKT or JNK activation. Sur-8 interacts with Ras and Raf and is able to form a ternary complex with the two proteins. Thus, Sur-8 may function as a scaffold that enhances Ras–MAP kinase signal transduction by facilitating the interaction between Ras and Raf.
Proteolysis in Caenorhabditis elegans sex determination: cleavage of TRA-2A by TRA-3
Authors: Sokol Sharon B. , Kuwabara Patricia E.
Published: November 2021

The Caenorhabditis elegans tra-3 gene promotes female development in XX hermaphrodites and encodes an atypical calpain regulatory protease lacking calcium-binding EF hands. We report that despite the absence of EF hands, TRA-3 has calcium-dependent proteolytic activity and its proteolytic domain is essential for in vivo function. We show that the membrane protein TRA-2A, which promotes XX female development by repressing the masculinizing protein FEM-3, is a TRA-3 substrate. Cleavage of TRA-2A by TRA-3 generates a peptide predicted to have feminizing activity. These results indicate that proteolysis regulated by calcium may control some aspects of sexual cell fate in C. elegans.
Nuclear localization and histone acetylation: a pathway for chromatin opening and transcriptional activation of the human β-globin locus
Authors: Schübeler Dirk , Francastel Claire , Cimbora Daniel M. , Reik Andreas , Martin David I.K. , Groudine Mark
Published: November 2021

We have investigated the mechanism, structural correlates, andcis-acting elements involved in chromatin opening and gene activation, using the human β-globin locus as a model. Full transcriptional activity of the human β-globin locus requires the locus control region (LCR), composed of a series of nuclease hypersensitive sites located upstream of this globin gene cluster. Our previous analysis of naturally occurring and targeted LCR deletions revealed that chromatin opening and transcriptional activity in the endogenous β-globin locus are dissociable and dependent on distinctcis-acting elements. We now report that general histone H3/H4 acetylation and relocation of the locus away from centromeric heterochromatin in the interphase nucleus are correlated and do not require the LCR. In contrast, LCR-dependent promoter activation is associated with localized histone H3 hyperacetylation at the LCR and the transcribed β-globin-promoter and gene. On the basis of these results, we suggest a multistep model for gene activation; localization away from centromeric heterochromatin is required to achieve general hyperacetylation and an open chromatin structure of the locus, whereas a mechanism involving LCR/promoter histone H3 hyperacetylation is required for high-level transcription of the β-globin genes.
Bromodomain factor 1 corresponds to a missing piece of yeast TFIID
Authors: Matangkasombut Oranart , Buratowski Robin M. , Swilling Nathan W. , Buratowski Stephen
Published: November 2021

The basal transcription factor TFIID consists of the TATA-binding protein (TBP) and TBP-associated factors (TAFs). Yeast Taf67 is homologous to mammalian TAFII55. Using a yeast two-hybrid screen to identify proteins that interact with Taf67, we isolated Bromodomain factor 1 (Bdf1) and its homolog (Bdf2). The Bdf proteins are genetically redundant, as cells are inviable without at least one of the two BDF genes. Both proteins contain two bromodomains, a motif found in several proteins involved in transcription and chromatin modification. The BDF genes interact genetically withTAF67. Furthermore, Bdf1 associates with TFIID and is recruited to a TATA-containing promoter. Deletion of Bdf1 or the Taf67 Bdf-interacting domain leads to defects in gene expression. Interestingly, the higher eukaryotic TAFII250 has an acetyltransferase activity, two bromodomains, and an associated kinase activity. Its yeast homolog, Taf145, has acetyltransferase activity but lacks the bromodomains and kinase. Bdf1, like TAFII250, has a kinase activity that maps carboxy-terminal to the bromodomains. The structural and functional similarities suggest that Bdf1 corresponds to the carboxy-terminal region of higher eukaryotic TAFII250 and that the interaction between TFIID and Bdf1 is important for proper gene expression.
Deletion of MUD2, the yeast homolog of U2AF65, can bypass the requirement for Sub2, an essential spliceosomal ATPase
Authors: Kistler Amy L. , Guthrie Christine
Published: November 2021

Mammalian U2AF65 and UAP56 are required for prespliceosome (PS) formation. We tested the predictions that the yeast UAP56 homolog,SUB2, is required for the same step and functions collaboratively with MUD2, the yeast homolog of U2AF65. Unexpectedly, sub2-1 extracts accumulate PS-like complexes. Moreover, deletion of MUD2 exacerbates the cs phenotype ofsub2 alleles yet suppresses both the ts sub2-1and the lethal Δsub2 phenotypes. We propose that Sub2 functionally interacts with Mud2 both before and after PS formation. In the absence of Mud2, Sub2 function becomes dispensable.