bluuebunny/crossref_metadata_2025 huggingface dataset:
Sensory processing sensitivity and axonal microarchitecture: Identifying brain structural characteristics for behavior
Authors: David Szabolcs , Brown Lucy L. , Heemskerk Anneriet M. , Aron Elaine , Leemans Alexander , Aron Arthur
Published: November 2021

Previously, researchers used functional MRI to identify regional brain activations associated with sensory processing sensitivity (SPS), a proposed normal phenotype trait. To further validate SPS as a behavioral entity, to characterize it anatomically, and to test the usefulness in psychology of methodologies that assess axonal properties, the present study correlated SPS proxy questionnaire scores (adjusted for neuroticism) with diffusion tensor imaging measures. Participants (n=408) from the Young Adult Human Connectome Project that are free of neurologic and psychiatric disorders were investigated. We computed mean diffusivity (MD), radial diffusivity (RD), axial diffusivity (AD) and fractional anisotropy (FA). A voxelwise, exploratory analysis showed that MD and RD correlated positively with SPS proxy scores in the right and left subcallosal and anterior ventral cingulum bundle, and the right forceps minor of the corpus callosum (peak Cohen’s D effect size = 0.269). Further analyses showed correlations throughout the entire right and left ventromedial prefrontal cortex, including the superior longitudinal fasciculus, inferior fronto-occipital fasciculus, uncinate and arcuate fasciculus. These prefrontal regions are generally involved in emotion, reward and social processing. FA was negatively correlated with SPS proxy scores in white matter of the right premotor/motor/somatosensory/supramarginal gyrus regions, which are associated with empathy, theory of mind, primary and secondary somatosensory processing. Region of interest (ROI) analysis, based-on previous fMRI results and Freesurfer atlas-defined areas, showed small effect sizes, (+0.151 to -0.165) in white matter of the precuneus and inferior frontal gyrus. Other ROI effects were found in regions of the dorsal and ventral visual pathways and primary auditory cortex. The results reveal that in a large, diverse group of participants axonal microarchitectural differences can be identified with SPS traits that are subtle and in the range of typical behavior. The results suggest that the heightened sensory processing in people who show SPS may be influenced by the microstructure of white matter in specific neocortical regions. Although previous fMRI studies had identified most of these general neocortical regions, the DTI results put a new focus on brain areas related to attention and cognitive flexibility, empathy, emotion and low-level sensory processing, as in the primary sensory cortex. Psychological trait characterization may benefit from diffusion tensor imaging methodology by identifying influential brain systems for traits.
Sustained effects of Short-term Adalimumab biosimilar (ZRC-3197) therapy on outcome measures in Ankylosing Spondylitis
Authors: Arvind Chopra , Khadke N , Saluja M , Kianifard T , Gharia Mihir , Venugopalan A
Published: November 2021

Introduction

Cost and drug toxicity often deter prolonged therapeutic use of anti-TNF agents in ankylosing spondylitis (AS). A planned study was completed to endorse our clinic-based observation of long-term relief following short-term administration of an anti-TNF agent.

Methods

50 consenting patients with symptomatic active chronic AS under rheumatology care in a community clinic were enrolled; naïve for anti-TNF. 40 mg standard biosimilar Adalimumab (Bs-ADA, Exemptia™) was injected subcutaneously every fortnight for six injections (10 weeks). Patients were monitored at several predetermined time points. Improvement was assessed with standard indices (Assessment Spondyloarthritis International Society/ASAS and Bath). An intention to treat analysis was performed: significant p <0·05

Results

Patients showed early and substantial significant improvement in pain, NSAID requirement, function, and in several indices (ASAS 20 & 40, ASAS partial remission, BASDAI, BASFI, ASDAS) which persisted after stopping injections. 84% and 52 % of patients respectively showed ASAS 20 improvement at weeks 12 and 48: corresponding to ASAS partial remission at 34% and 24%. Over 50% of patients maintained prolonged improvement and provided proof of concept (defined apriori). Serum Interleukin-6 assay showed a sharp reduction at 24 weeks. None developed TB or serious drug toxicity. 11 patients withdrew (mostly inadequate response). The absence of control was a limitation.

Conclusion

A ten-week administration of biosimilar adalimumab in difficult-to-treat AS showed early substantial improvement which often persisted for 24 weeks. This unconventional strategy was socioeconomically appealing. It merits further validation and acceptance, especially in resource strained settings.
Exploring the kinetic selectivity of antipsychotics for dopamine D2 and 5-HT2A receptors: implications for the prevalence of EPS and receptor occupancy
Authors: Sykes David A. , Lochray Jack , Comfort Hannah M.F. , Jain Palash , Charlton Steven J.
Published: November 2021

Certain atypical antipsychotic drugs (APDs) used in the treatment of schizophrenia have been hypothesized to show reduced extrapyramidal side effects (EPS), due to their ability to promote nigrostriatal dopamine release through 5-HT2A receptor (5-HT2AR) blockade. The strength of this hypothesis is currently limited to a consideration of the relative receptor affinities of APDs for the 5-HT2AR and dopamine D2 receptor (D2R). Here we measure the 5-HT2AR kinetic binding properties of a series of typical and atypical APDs in a novel time-resolved fluorescence resonance energy transfer assay and correlate these properties with their observed EPS at therapeutic doses. For compounds with negligible affinity for 5-HT2AR, EPS is robustly predicted by a D2R specific rebinding model that integrates D2R association and dissociation rates to calculate the net rate of reversal of receptor blockade (kr). However, we show that for compounds with significant affinity for the 5-HT2AR, such as sertindole, higher relative 5-HT2A occupancy over time is an indicator for a reduced propensity to cause EPS.

This study suggests that there is room for the development of novel kinetically optimised antipsychotic agents that modulate both serotonergic and dopamine function in a manner beneficial in the treatment of this chronic and debilitating disease.
Regulation of tumor angiogenesis by p53-induced degradation of hypoxia-inducible factor 1α
Authors: Ravi Rajani , Mookerjee Bijoyesh , Bhujwalla Zaver M. , Sutter Carrie Hayes , Artemov Dmitri , Zeng Qinwen , Dillehay Larry E. , Madan Ashima , Semenza Gregg L. , Bedi Atul
Published: November 2021

The switch to an angiogenic phenotype is a fundamental determinant of neoplastic growth and tumor progression. We demonstrate that homozygous deletion of the p53 tumor suppressor gene via homologous recombination in a human cancer cell line promotes the neovascularization and growth of tumor xenografts in nude mice. We find that p53 promotes Mdm2-mediated ubiquitination and proteasomal degradation of the HIF-1α subunit of hypoxia-inducible factor 1 (HIF-1), a heterodimeric transcription factor that regulates cellular energy metabolism and angiogenesis in response to oxygen deprivation. Loss of p53 in tumor cells enhances HIF-1α levels and augments HIF-1-dependent transcriptional activation of the vascular endothelial growth factor (VEGF) gene in response to hypoxia. Forced expression of HIF-1α in p53-expressing tumor cells increases hypoxia-induced VEGF expression and augments neovascularization and growth of tumor xenografts. These results indicate that amplification of normal HIF-1-dependent responses to hypoxia via loss of p53 function contributes to the angiogenic switch during tumorigenesis.
Isolation of a novel histone deacetylase reveals that class I and class II deacetylases promote SMRT-mediated repression
Authors: Kao Hung-Ying , Downes Michael , Ordentlich Peter , Evans Ronald M.
Published: November 2021

The transcriptional corepressor SMRT functions by mediating the repressive effect of transcription factors involved in diverse signaling pathways. The mechanism by which SMRT represses basal transcription has been proposed to involve the indirect recruitment of histone deacetylase HDAC1 via the adaptor mSin3A. In contrast to this model, a two-hybrid screen on SMRT-interacting proteins resulted in the isolation of the recently described HDAC5 and a new family member termed HDAC7. Molecular and biochemical results indicate that this interaction is direct and in vivo evidence colocalizes SMRT, mHDAC5, and mHDAC7 to a distinct nuclear compartment. Surprisingly, HDAC7 can interact with mSin3A in yeast and in mammalian cells, suggesting association of multiple repression complexes. Taken together, our results provide the first evidence that SMRT-mediated repression is promoted by class I and class II histone deacetylases and that SMRT can recruit class II histone deacetylases in a mSin3A-independent fashion.
An evolutionarily conserved RNA stem–loop functions as a sensor that directs feedback regulation of RNase E gene expression
Authors: Diwa Alexis , Bricker Angela L. , Jain Chaitanya , Belasco Joel G.
Published: November 2021

RNase E is a key regulatory enzyme that controls the principal pathway for mRNA degradation in Escherichia coli. The cellular concentration of this endonuclease is governed by a feedback mechanism in which RNase E tightly regulates its own synthesis. Autoregulation is mediated in cis by the 361-nucleotide 5′ untranslated region (UTR) of rne (RNase E) mRNA. Here we report the determination of the secondary structure of the rne 5′ UTR by phylogenetic comparison and chemical alkylation, together with dissection studies to identify the 5′ UTR element that mediates autoregulation. Our findings reveal that the structure and function of the rne 5′ UTRs are evolutionarily well conserved despite extensive sequence divergence. Within the rne 5′ UTRs are multiple RNA secondary structure elements, two of which function incis to mediate feedback regulation of rne gene expression. The more potent of these two elements is a stem–loop structure containing an internal loop whose sequence is the most highly conserved of any region of the rne 5′ UTR. Our data show that this stem–loop functions as a sensor of cellular RNase E activity that directs autoregulation by modulating the degradation rate ofrne mRNA in response to changes in RNase E activity.
The protein encoded by the proto-oncogene DEK changes the topology of chromatin and reduces the efficiency of DNA replication in a chromatin-specific manner
Authors: Alexiadis Vassilios , Waldmann Tanja , Andersen Jens , Mann Matthias , Knippers Rolf , Gruss Claudia
Published: November 2021

The structure of chromatin regulates the genetic activity of the underlying DNA sequence. We report here that the protein encoded by the proto-oncogene DEK, which is involved in acute myelogenous leukemia, induces alterations of the superhelical density of DNA in chromatin. The change in topology is observed with chromatin but not with naked DNA and does not involve dissociation of core histones from chromatin. Moreover, these effects require histone H2A/H2B dimers in addition to histone H3/H4. We additionally tested whether the DEK protein affects DNA-utilizing processes and found that the DEK protein substantially reduces the replication efficiency of chromatin but not of naked DNA templates.
Gross chromosomal rearrangements and genetic exchange between nonhomologous chromosomes following BRCA2 inactivation
Authors: Yu Veronica P.C.C. , Koehler Michael , Steinlein Claus , Schmid Michael , Hanakahi Leslyn A. , van Gool Alain J. , West Stephen C. , Venkitaraman Ashok R.
Published: November 2021

Cancer-causing mutations often arise from gross chromosomal rearrangements (GCRs) such as translocations, which involve genetic exchange between nonhomologous chromosomes. Here we show that murineBrca2 has an essential function in suppressing GCR formation after chromosome breakage. Cells that harbor truncated Brca2spontaneously incur GCRs and genomic DNA breaks during division. They exhibit hypersensitivity to DNA damage by interstrand cross-linkers, which even at low doses trigger aberrant genetic exchange between nonhomologous chromosomes. Therefore, genetic instability in Brca2-deficient cells results from the mutagenic processing of spontaneous or induced DNA damage into gross chromosomal rearrangements, providing a mechanistic basis for cancer predisposition.
Dictyostelium RasD is required for normal phototaxis, but not differentiation
Authors: Wilkins Andrew , Khosla Meenal , Fraser Derek J. , Spiegelman George B. , Fisher Paul R. , Weeks Gerald , Insall Robert H.
Published: November 2021

RasD, a Dictyostelium homolog of mammalian Ras, is maximally expressed during the multicellular stage of development. Normal Dictyostelium aggregates are phototactic and thermotactic, moving towards sources of light and heat with great sensitivity. We show that disruption of the gene for rasDcauses a near-total loss of phototaxis and thermotaxis in mutant aggregates, without obvious effects on undirected movement. Previous experiments had suggested important roles for RasD in development and cell-type determination. Surprisingly, rasD− cells show no obvious changes in these processes. These cells represent a novel class of phototaxis mutant, and indicate a role for a Ras pathway in the connections between stimuli and coordinated cell movement.
Chaperone Hsp27 inhibits translation during heat shock by binding eIF4G and facilitating dissociation of cap-initiation complexes
Authors: Cuesta Rafael , Laroia Gaurav , Schneider Robert J.
Published: November 2021

Inhibition of protein synthesis during heat shock limits accumulation of unfolded proteins that might damage eukaryotic cells. We demonstrate that chaperone Hsp27 is a heat shock-induced inhibitor of cellular protein synthesis. Translation of most mRNAs requires formation of a cap-binding initiation complex known as eIF4F, consisting of factors eIF4E, eIF4A, eIF4E kinase Mnk1, poly(A)-binding protein, and adaptor protein eIF4G. Hsp27 specifically bound eIF4G during heat shock, preventing assembly of the cap-initiation/eIF4F complex and trapping eIF4G in insoluble heat shock granules. eIF4G is a specific target of Hsp27, as eIF4E, eIF4A, Mnk1, poly(A)-binding protein, eIF4B, and eIF3 were not bound by Hsp27 and were not recruited into insoluble complexes. Dissociation of eIF4F was enhanced during heat shock by ectopic overexpression of Hsp25, the murine homolog of human Hsp27. Overexpression of Hsc70, a constitutive homolog of Hsp70, prevented loss of cap-initiation complexes and maintained eIF4G solubility. Purified Hsp27 specifically bound purified eIF4G in vitro, prevented in vitro translation, eliminated eIF4G interaction with protein binding factors, and promoted eIF4G insolubilization. These results therefore demonstrate that Hsp27 is a heat-induced inhibitor of eIF4F-dependent mRNA translation.
A novel Smad nuclear interacting protein, SNIP1, suppresses p300-dependent TGF-β signal transduction
Authors: Kim Richard H. , Wang David , Tsang Michael , Martin Jennifer , Huff Carla , de Caestecker Mark P. , Parks W. Tony , Meng Xianwang , Lechleider Robert J. , Wang Tongwen , Roberts Anita B.
Published: November 2021

Members of the transforming growth factor-β superfamily play critical roles in controlling cell growth and differentiation. Effects of TGF-β family ligands are mediated by Smad proteins. To understand the mechanism of Smad function, we sought to identify novel interactors of Smads by use of a yeast two-hybrid system. A 396-amino acid nuclear protein termed SNIP1 was cloned and shown to harbor a nuclear localization signal (NLS) and a Forkhead-associated (FHA) domain. The carboxyl terminus of SNIP1 interacts with Smad1 and Smad2 in yeast two-hybrid as well as in mammalian overexpression systems. However, the amino terminus of SNIP1 harbors binding sites for both Smad4 and the coactivator CBP/p300. Interaction between endogenous levels of SNIP1 and Smad4 or CBP/p300 is detected in NMuMg cells as well as in vitro. Overexpression of full-length SNIP1 or its amino terminus is sufficient to inhibit multiple gene responses to TGF-β and CBP/p300, as well as the formation of a Smad4/p300 complex. Studies in Xenopus laevisfurther suggest that SNIP1 plays a role in regulating dorsomedial mesoderm formation by the TGF-β family member nodal. Thus, SNIP1 is a nuclear inhibitor of CBP/p300 and its level of expression in specific cell types has important physiological consequences by setting a threshold for TGF-β-induced transcriptional activation involving CBP/p300.
Bcl-2 antiapoptotic protein mediates verotoxin II–induced cell death: possible association between Bcl-2 and tissue failure by E. coli O157:H7
Authors: Suzuki Atsushi , Doi Hirofumi , Matsuzawa Fumiko , Aikawa Sei-ichi , Takiguchi Kyoko , Kawano Hirokazu , Hayashida Midori , Ohno Susumu
Published: November 2021

Verotoxin II (VTII: or Shiga-like toxin 2) is a key factor forEscherichia coli O157:H7–induced multiple tissue failure and contains a pentameric sequence (NWGRI) similar to the Bcl-2 homolog domain, BH1. In the current study, we demonstrate that VTII, but not VTI, interacts with Bcl-2 through each BH1 domain pentameric sequence (NWGRI) and that the VTII/Bcl-2 complex is necessary for cell-death induction in target cells. VTII translocates to mitochondria and induces cell death only when target cells are expressing Bcl-2. In addition, interruption of VTII-Bcl-2 complex formation by a pentameric BH1 synthetic peptide suppresses VTII-induced cell death. In the present article, we propose that Bcl-2 mediates VTII-induced target cell death by the interaction with each pentameric sequence of BH1 domain.
The Saccharomyces telomere-binding protein Cdc13p interacts with both the catalytic subunit of DNA polymerase α and the telomerase-associated Est1 protein
Authors: Qi Haiyan , Zakian Virginia A.
Published: November 2021

Saccharomyces telomeres consist of ∼350 bp of C1-3A/TG1-3 DNA. Most of this ∼350 bp is replicated by standard, semiconservative DNA replication. After conventional replication, the C1-3A strand is degraded to generate a long single strand TG1-3 tail that can serve as a substrate for telomerase. Cdc13p is a single strand TG1-3DNA-binding protein that localizes to telomeres in vivo. Genetic data suggest that the Cdc13p has multiple roles in telomere replication. We used two hybrid analysis to demonstrate that Cdc13p interacted with both the catalytic subunit of DNA polymerase α, Pol1p, and the telomerase RNA-associated protein, Est1p. The association of these proteins was confirmed by biochemical analysis using full-length or nearly full-length proteins. Point mutations in either CDC13 orPOL1 that reduced the Cdc13p–Pol1p interaction resulted in telomerase mediated telomere lengthening. Over–expression of the carboxyl terminus of Est1p partially suppressed the temperature sensitive lethality of a cdc13-1 strain. We propose that Cdc13p's interaction with Est1p promotes TG1-3 strand lengthening by telomerase and its interaction with Pol1p promotes C1-3A strand resynthesis by DNA polymerase α.
p300-Mediated acetylation facilitates the transfer of histone H2A–H2B dimers from nucleosomes to a histone chaperone
Authors: Ito Takashi , Ikehara Tsuyoshi , Nakagawa Takeya , Kraus W. Lee , Muramatsu Masami
Published: November 2021

We have used a purified recombinant chromatin assembly system, including ACF (Acf-1 + ISWI) and NAP-1, to examine the role of histone acetylation in ATP-dependent chromatin remodeling. The binding of a transcriptional activator (Gal4–VP16) to chromatin assembled using this recombinant assembly system dramatically enhances the acetylation of nucleosomal core histones by the histone acetyltransferase p300. This effect requires both the presence of Gal4-binding sites in the template and the VP16-activation domain. Order-of-addition experiments indicate that prior activator-meditated, ATP-dependent chromatin remodeling by ACF is required for the acetylation of nucleosomal histones by p300. Thus, chromatin remodeling, which requires a transcriptional activator, ACF and ATP, is an early step in the transcriptional process that regulates subsequent core histone acetylation. Glycerol gradient sedimentation and immunoprecipitation assays demonstrate that the acetylation of histones by p300 facilitates the transfer of H2A–H2B from nucleosomes to NAP-1. The results from these biochemical experiments suggest that (1) transcriptional activators (e.g., Gal4–VP16) and chromatin remodeling complexes (e.g., ACF) induce chromatin remodeling in the absence of histone acetylation; (2) transcriptional activators recruit histone acetyltransferases (e.g., p300) to promoters after chromatin remodeling has occurred; and (3) histone acetylation is important for a step subsequent to chromatin remodeling and results in the transfer of histone H2A–H2B dimers from nucleosomes to a histone chaperone such as NAP-1. Our results indicate a precise role for histone acetylation, namely to alter the structure of nucleosomes (e.g., facilitate the loss of H2A–H2B dimers) that have been remodeled previously by the action of ATP-dependent chromatin remodeling complexes. Thus, transcription from chromatin templates is ordered and sequential, with precise timing and roles for ATP-dependent chromatin remodeling, subsequent histone acetylation, and alterations in nucleosome structure.
The Dlk1 and Gtl2 genes are linked and reciprocally imprinted
Authors: Schmidt Jennifer V. , Matteson Paul G. , Jones Beverly K. , Guan Xiao-Juan , Tilghman Shirley M.
Published: November 2021

Genes subject to genomic imprinting exist in large chromosomal domains, probably reflecting coordinate regulation of the genes within a cluster. Such regulation has been demonstrated for the H19,Igf2, and Ins2 genes that share a bifunctional imprinting control region. We have identified the Dlk1 gene as a new imprinted gene that is paternally expressed. Furthermore, we show that Dlk1 is tightly linked to the maternally expressedGtl2 gene. Dlk1 and Gtl2 are coexpressed and respond in a reciprocal manner to loss of DNA methylation. These genes are likely to represent a new example of coordinated imprinting of linked genes.
The checkpoint protein Ddc2, functionally related to S. pombe Rad26, interacts with Mec1 and is regulated by Mec1-dependent phosphorylation in budding yeast
Authors: Paciotti Vera , Clerici Michela , Lucchini Giovanna , Longhese Maria Pia
Published: November 2021

DDC2 is a novel component of the DNA integrity checkpoint pathway, which is required for proper checkpoint response to DNA damage and to incomplete DNA replication. Moreover, Ddc2 overproduction causes sensitivity to DNA-damaging agents and checkpoint defects. Ddc2 physically interacts with Mec1 and undergoes Mec1-dependent phosphorylation both in vitro and in vivo. The phosphorylation of Ddc2 takes place in late S phase and in G2 phase during an unperturbed cell cycle and is further increased in response to DNA damage. Because Ddc2 phosphorylation does not require any other known tested checkpoint factors but Mec1, the Ddc2–Mec1 complex might respond to the presence of some DNA structures independently of the other known checkpoint proteins. Our findings suggest that Ddc2 may be the functional homolog of Schizosaccharomyces pombe Rad26, strengthening the hypothesis that the mechanisms leading to checkpoint activation are conserved throughout evolution.
A mechanism of suppression of TGF–β/SMAD signaling by NF-κB/RelA
Authors: Bitzer Markus , von Gersdorff Gero , Liang Dan , Dominguez-Rosales Alfredo , Beg Amer A. , Rojkind Marcos , Böttinger Erwin P.
Published: November 2021

A number of pathogenic and proinflammatory stimuli, and the transforming growth factor-β (TGF-β) exert opposing activities in cellular and immune responses. Here we show that the RelA subunit of nuclear factor κB (NF-κB/RelA) is necessary for the inhibition of TGF-β-induced phosphorylation, nuclear translocation, and DNA binding of SMAD signaling complexes by tumor necrosis factor-α (TNF-α). The antagonism is mediated through up-regulation of Smad7 synthesis and induction of stable associations between ligand-activated TGF-β receptors and inhibitory Smad7. Down-regulation of endogenous Smad7 by expression of antisense mRNA releases TGF-β/SMAD-induced transcriptional responses from suppression by cytokine-activated NF-κB/RelA. Following stimulation with bacterial lipopolysaccharide (LPS), or the proinflammatory cytokines TNF-α and interleukin-1β (IL-1β, NF-κB/RelA induces Smad7 synthesis through activation of Smad7 gene transcription. These results suggest a mechanism of suppression of TGF-β/SMAD signaling by opposing stimuli mediated through the activation of inhibitory Smad7 by NF-κB/RelA.
Transient depletion of xDnmt1 leads to premature gene activation in Xenopus embryos
Authors: Stancheva Irina , Meehan Richard R.
Published: November 2021

In Xenopus laevis zygotic transcription begins at the midblastula transition (MBT). Prior to this the genome is organized into chromatin that facilitates rapid cycles of DNA replication but not transcription. Here we demonstrate that DNA methylation contributes to the overall transcriptional silencing before MBT. Transient depletion of the maternal DNA methyltransferase (xDnmt1) by anti sense RNA during cleavage stages is associated with a decrease in the genomic 5-methyl-cytosine content and leads to the activation of zygotic transcription approximately two cell cycles earlier than normal. Hypomethylation allows the early expression of mesodermal marker genes such as Xbra, Cerberus, and Otx2, which are subsequently down-regulated during gastrulation of thexDnmt1-depleted embryos. The temporal switch in gene expression may account for the appearance of body plan defects that we observe. Loss of xDnmt1 can be rescued by the coinjection of mouse or human Dnmt1 protein. These results demonstrate that DNA methylation has a role in the regulation of immediately early genes in Xenopusat MBT.
Nucleotide excision repair of DNA with recombinant human proteins: definition of the minimal set of factors, active forms of TFIIH, and modulation by CAK
Authors: Araújo Sofia J. , Tirode Franck , Coin Frederic , Pospiech Helmut , Syväoja Juhani E. , Stucki Manuel , Hübscher Ulrich , Egly Jean-Marc , Wood Richard D.
Published: November 2021

During human nucleotide excision repair, damage is recognized, two incisions are made flanking a DNA lesion, and residues are replaced by repair synthesis. A set of proteins required for repair of most lesions is RPA, XPA, TFIIH, XPC–hHR23B, XPG, and ERCC1–XPF, but additional components have not been excluded. The most complex and difficult to analyze factor is TFIIH, which has a 6-subunit core (XPB, XPD, p44, p34, p52, p62) and a 3-subunit kinase (CAK). TFIIH has roles both in basal transcription initiation and in DNA repair, and several inherited human disorders are associated with mutations in TFIIH subunits. To identify the forms of TFIIH that can function in repair, recombinant XPA, RPA, XPC–hHR23B, XPG, and ERCC1–XPF were combined with TFIIH fractions purified from HeLa cells. Repair activity coeluted with the peak of TFIIH and with transcription activity. TFIIH from cells with XPB or XPD mutations was defective in supporting repair, whereas TFIIH from spinal muscular atrophy cells with a deletion of one p44 gene was active. Recombinant TFIIH also functioned in repair, both a 6- and a 9-subunit form containing CAK. The CAK kinase inhibitor H-8 improved repair efficiency, indicating that CAK can negatively regulate NER by phosphorylation. The 15 recombinant polypeptides define the minimal set of proteins required for dual incision of DNA containing a cisplatin adduct. Complete repair was achieved by including highly purified human DNA polymerase δ or ε, PCNA, RFC, and DNA ligase I in reaction mixtures, reconstituting adduct repair for the first time with recombinant incision factors and human replication proteins.
Mammalian hepatocyte differentiation requires the transcription factor HNF-4α
Authors: Li Jixuan , Ning Gang , Duncan Stephen A.
Published: November 2021

HNF-4α is a transcription factor of the nuclear hormone receptor family that is expressed in the hepatic diverticulum at the onset of liver development. Mouse embryos lacking HNF-4α fail to complete gastrulation due to dysfunction of the visceral endoderm. This early embryonic lethality has so far prevented any analyses of the contribution of HNF-4α toward liver development and hepatocyte differentiation. However, we have shown that complementation ofHNF-4 α−/−embryos with a tetraploid embryo-derived wild-type visceral endoderm rescues this early developmental arrest and allowsHNF-4 α−/−embryos to proceed normally through midgestation stages of development. Examination of these rescued embryos revealed that HNF-4α was dispensable for specification and early development of the liver. However,HNF-4α−/− fetal livers failed to express a large array of genes whose expression in differentiated hepatocytes is essential for a functional hepatic parenchyma, including genes encoding several apolipoproteins, metabolic proteins, and serum factors. In addition, we have demonstrated that HNF-4α is essential for expression of the transcription factors HNF-1α and PXR within the fetal liver. We therefore conclude that HNF-4α is both essential for hepatocyte differentiation during mammalian liver development and also crucial for metabolic regulation and liver function.
A Krüppel-like zinc finger protein is involved in nitrogen-fixing root nodule organogenesis
Authors: Frugier Florian , Poirier Simone , Satiat-Jeunemaître Béatrice , Kondorosi Adam , Crespi Martin
Published: November 2021

Mechanisms regulating plant host differentiation of the nitrogen-fixing root nodules remain mostly unknown. Sinorhizobium meliloti induces this process in Medicago sativa in which the Mszpt2-1 gene is expressed in vascular bundles of roots and nodules. This gene codes for a Krüppel-like zinc finger protein, a class of transcription factors involved in many animal developmental processes. Expression of Mszpt2-1 in yeast cells conferred osmotic tolerance. Antisense plants grew normally but developed nonfunctional nodules, in which differentiation of the nitrogen-fixing zone and bacterial invasion were arrested. Hence, a vascular bundle-associated Krüppel-like gene is required for the formation of the central nitrogen-fixing zone of the root nodule.
Progression of meiotic DNA replication is modulated by interchromosomal interaction proteins, negatively by Spo11p and positively by Rec8p
Authors: Cha Rita S. , Weiner Beth M. , Keeney Scott , Dekker Job , Kleckner N.
Published: November 2021

Spo11p is a key mediator of interhomolog interactions during meiosis. Deletion of the SPO11 gene decreases the length of S phase by ∼25%. Rec8p is a key coordinator of meiotic interhomolog and intersister interactions. Deletion of the REC8 gene increases S-phase length, by ∼10% in wild-type and ∼30% in aspo11Δ background. Thus, the progression of DNA replication is modulated by interchromosomal interaction proteins. Thespo11–Y135F DSB (double strand break) catalysis-defective mutant is normal for S-phase modulation and DSB-independent homolog pairing but is defective for later events, formation of DSBs, and synaptonemal complexes. Thus, earlier and later functions of Spo11 are defined. We propose that meiotic S-phase progression is linked directly to development of specific chromosomal features required for meiotic interhomolog interactions and that this feedback process is built upon a more fundamental mechanism, common to all cell types, by which S-phase progression is coupled to development of nascent intersister connections and/or related aspects of chromosome morphogenesis. Roles for Rec8 and/or Spo11 in progression through other stages of meiosis are also revealed.
NUC-1, aCaenorhabditis elegansDNase II homolog, functions in an intermediate step of DNA degradation during apoptosis
Authors: Wu Yi-Chun , Stanfield Gillian M. , Horvitz H. Robert
Published: November 2021

One hallmark of apoptosis is the degradation of chromosomal DNA. We cloned theCaenorhabditis elegansgenenuc-1, which is involved in the degradation of the DNA of apoptotic cells, and found thatnuc-1encodes a homolog of mammalian DNase II. We used the TUNEL technique to assay DNA degradation innuc-1and other mutants defective in programmed cell death and discovered that TUNEL labels apoptotic cells only during a transient intermediate stage. Mutations innuc-1allowed the generation of TUNEL-reactive DNA but blocked the conversion of TUNEL-reactive DNA to a subsequent TUNEL-unreactive state. Completion of DNA degradation did not occur in the absence of cell-corpse engulfment. Our data suggest that the process of degradation of the DNA of a cell corpse occurs in at least three distinct steps and requires activities provided by both the dying and the engulfing cell.
An auxiliary mode of apoptotic DNA fragmentation provided by phagocytes
Authors: McIlroy Dorian , Tanaka Masato , Sakahira Hideki , Fukuyama Hidehiro , Suzuki Misao , Yamamura Ken-ichi , Ohsawa Yoshiyuki , Uchiyama Yasuo , Nagata Shigekazu
Published: November 2021

CAD (caspase-activated DNase) can cause DNA fragmentation in apoptotic cells. Transgenic mice that ubiquitously express a caspase-resistant form of the CAD inhibitor (ICAD) were generated. Thymocytes prepared from the mice were resistant to DNA fragmentation induced by a variety of stimuli. However, similar numbers of TUNEL-positive cells were present in adult tissues of transgenic and wild-type mice. Exposure to γ-irradiation caused a striking increase in the number of TUNEL-positive cells in the thymus of wild-type, but not transgenic, mice. TUNEL-positive nuclei in transgenic mice were confined to thymic macrophages. When apoptotic thymocytes from the transgenic mice were cocultured with macrophages, the thymocytes underwent phagocytosis and their chromosomal DNA underwent fragmentation. This DNA fragmentation was sensitive to inhibitors that block the acidification of lysosomes. Hence, we conclude that the DNA fragmentation that occurs during apoptosis not only can result cell-autonomously from CAD activity but can also be attributed to a lysosomal acid DNase(s), most likely DNase II, after the apoptotic cells are engulfed.
Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences
Authors: Mohr Georg , Smith Dorie , Belfort Marlene , Lambowitz Alan M.
Published: November 2021

Group II intron homing occurs primarily by a mechanism in which the intron RNA reverse splices into a DNA target site and is then reverse transcribed by the intron-encoded protein. The DNA target site is recognized by an RNP complex containing the intron-encoded protein and the excised intron RNA. Here, we analyzed DNA target-site requirements for the Lactococcus lactis Ll.LtrB group II intron in vitro and in vivo. Our results suggest a model similar to yeast mtDNA introns, in which the intron-encoded protein first recognizes a small number of nucleotide residues in double-stranded DNA and causes DNA unwinding, enabling the intron RNA to base-pair with the DNA for reverse splicing. Antisense-strand cleavage requires additional interactions between the protein and 3′ exon. Key nucleotide residues are recognized directly by the intron-encoded protein independent of sequence context, and there is a stringent requirement for fixed spacing between target site elements recognized by the protein and RNA components of the endonuclease. Experiments with DNA substrates containing GC-clamps or “bubbles” indicate a requirement for DNA unwinding in the 3′ exon but not the distal 5′ exon region. Finally, by applying the target-site recognition rules, we show that the L1.LtrB intron can be modified to insert at new sites in a plasmid-borne thyA gene inEscherichia coli. This strategy should be generally applicable to retargeting group II introns and to delivering foreign sequences to specific sites in heterologous genomes.
The carboxyl terminus of phage HK022 Nun includes a novel zinc-binding motif and a tryptophan required for transcription termination
Authors: Watnick Randolph S. , Herring Stephanie Chiyoko , Palmer Arthur G. , Gottesman Max E.
Published: November 2021

The amino-terminal arginine-rich motif of the phage HK022 Nun protein binds phage λ nascent mRNA transcripts while the carboxy-terminal domain binds RNA polymerase and arrests transcription. The role of specific residues in the carboxy-terminal domain in transcription termination were investigated by mutagenesis, in vitro and in vivo functional assays, and NMR spectroscopy. Coordination of zinc to three histidine residues in the carboxy-terminus inhibited RNA binding by the amino-terminal domain; however, only two of these histidines were required for transcription arrest. These results suggest that additional zinc-coordinating residues are supplied by RNA polymerase in the context of the Nun–RNA polymerase complex. Substitution of the penultimate carboxy-terminal tryptophan residue with alanine or leucine blocks transcription arrest, whereas a tyrosine substitution is innocuous. Wild-type Nun fails to arrest transcription on single-stranded templates. These results suggest that Nun inhibition of transcription elongation is due in part to interactions between the carboxy-terminal tryptophan of Nun and double-stranded DNA, possibly by intercalation. A model for the termination activity of Nun is developed on the basis of these data.
A core SMRT corepressor complex containing HDAC3 and TBL1, a WD40-repeat protein linked to deafness
Authors: Guenther Matthew G. , Lane William S. , Fischle Wolfgang , Verdin Eric , Lazar Mitchell A. , Shiekhattar Ramin
Published: November 2021

The corepressor SMRT mediates repression by thyroid hormone receptor (TR) as well as other nuclear hormone receptors and transcription factors. Here we report the isolation of a novel SMRT-containing complex from HeLa cells. This complex contains transducin β-like protein 1 (TBL1), whose gene is mutated in human sensorineural deafness. It also contains HDAC3, a histone deacetylase not previously thought to interact with SMRT. TBL1 displays structural and functional similarities to Tup1 and Groucho corepressors, sharing their ability to interact with histone H3. In vivo, TBL1 is bridged to HDAC3 through SMRT and can potentiate repression by TR. Intriguingly, loss-of-function TRβ mutations cause deafness in mice and humans. These results define a new TR corepressor complex with a physical link to histone structure and a potential biological link to deafness.
The ShcA phosphotyrosine docking protein sensitizes cardiovascular signaling in the mouse embryo
Authors: Lai Ka-Man Venus , Pawson Tony
Published: November 2021

The ShcA gene products have served as a model for the analysis of phosphotyrosine-recognition domains, and for the functions of docking proteins during tyrosine kinase signaling. Here we show that ShcA is primarily expressed in the cardiovascular system during early mouse embryogenesis and regulates both heart development and establishment of mature blood vessels. Targeted mutation suggests that the ShcA adaptor is a pivotal target of tyrosine kinases that selectively potentiates activation of the MAP kinase pathway in the remodeling vasculature. Biochemical analysis of mutant cells shows that ShcA sensitizes cells to growth factor-induced MAP kinase activation, and also organizes cytoskeletal rearrangement in response to the extracellular matrix. ShcA may therefore orchestrate complex interactions within the vascular compartment by rendering cells permissive to respond to soluble and adhesive external cues.
SPC4/PACE4 regulates a TGFβ signaling network during axis formation
Authors: Constam Daniel B. , Robertson Elizabeth J.
Published: November 2021

In vertebrates, specification of anteroposterior (A/P) and left–right (L/R) axes depends on TGFβ-related signals, including Nodal, Lefty, and BMPs. Endoproteolytic maturation of these proteins is probably mediated by the proprotein convertase SPC1/Furin. In addition, precursor processing may be regulated by related activities such as SPC4 (also known as PACE4). Here, we show that a proportion of embryos lacking SPC4 develop situs ambiguus combined with left pulmonary isomerism or complex craniofacial malformations including cyclopia, or both. Gene expression analysis during early somite stages indicates that spc4 is genetically upstream of nodal, pitx2, lefty1, and lefty2 and perhaps maintains the balance between Nodal and BMP signaling in the lateral plate that is critical for L/R axis formation. Furthermore, genetic interactions betweennodal and spc4, together with our analysis of chimeric embryos, strongly suggest that during A/P axis formation, SPC4 acts primarily in the foregut. These findings establish an important role for SPC4 in patterning the early mouse embryo.
The RNA-binding protein Tsunagi interacts with Mago Nashi to establish polarity and localize oskar mRNA during Drosophila oogenesis
Authors: Mohr Stephanie E. , Dillon Simon T. , Boswell Robert E.
Published: November 2021

In Drosophila melanogaster, formation of the axes and the primordial germ cells is regulated by interactions between the germ line-derived oocyte and the surrounding somatic follicle cells. This reciprocal signaling results in the asymmetric localization of mRNAs and proteins critical for these oogenic processes. Mago Nashi protein interprets the posterior follicle cell-to-oocyte signal to establish the major axes and to determine the fate of the primordial germ cells. Using the yeast two-hybrid system we have identified an RNA-binding protein, Tsunagi, that interacts with Mago Nashi protein. The proteins coimmunoprecipitate and colocalize, indicating that they form a complex in vivo. Immunolocalization reveals that Tsunagi protein is localized within the posterior oocyte cytoplasm during stages 1–5 and 8–9, and that this localization is dependent on wild-type mago nashifunction. When tsunagi function is removed from the germ line, egg chambers develop in which the oocyte nucleus fails to migrate,oskar mRNA is not localized within the posterior pole, and dorsal–ventral pattern abnormalities are observed. These results show that a Mago Nashi–Tsunagi protein complex is required for interpreting the posterior follicle cell-to-oocyte signal to define the major body axes and to localize components necessary for determination of the primordial germ cells.
Reconstitution of recombinant chromatin establishes a requirement for histone-tail modifications during chromatin assembly and transcription
Authors: Loyola Alejandra , LeRoy Gary , Wang Yuh-Hwa , Reinberg Danny
Published: November 2021

The human ISWI-containing factor RSF (remodeling andspacing factor) was found to mediate nucleosome deposition and, in the presence of ATP, generate regularly spaced nucleosome arrays. Using this system, recombinant chromatin was reconstituted with bacterially produced histones. Acetylation of the histone tails was found to play an important role in establishing regularly spaced nucleosome arrays. Recombinant chromatin lacking histone acetylation was impaired in directing transcription. Histone-tail modifications were found to regulate transcription from the recombinant chromatin. Acetylation of the histone tails by p300 was found to increase transcription. Methylation of the histone H3 tail by Suv39H1 was found to repress transcription in an HP1-dependent manner. The effects of histone-tail modifications were observed in nuclear extracts. A highly reconstituted RNA polymerase II transcription system was refractory to the effect imposed by acetylation and methylation.
A multi-enhancer RET regulatory code is disrupted in Hirschsprung disease
Authors: Chatterjee Sumantra , Karasaki Kameko M. , Fries Lauren E. , Kapoor Ashish , Chakravarti Aravinda
Published: November 2021

The major genetic risk factors for Hirschsprung disease (HSCR) are three common polymorphisms within cis-regulatory elements (CREs) of the receptor tyrosine kinase gene RET, which reduce its expression during enteric nervous system (ENS) development. These risk variants attenuate binding of the transcription factors RARB, GATA2, and SOX10 to their cognate CREs, reduce RET gene expression, and dysregulate other ENS and HSCR genes in the RET–EDNRB gene regulatory network (GRN). Here, we use siRNA, ChIP, and CRISPR-Cas9 deletion analyses in the SK-N-SH cell line to ask how many additional HSCR-associated risk variants reside in RET CREs that affect its gene expression. We identify 22 HSCR-associated variants in candidate RET CREs, of which seven have differential allele-specific in vitro enhancer activity, and four of these seven affect RET gene expression; of these, two enhancers are bound by the transcription factor PAX3. We also show that deleting multiple variant-containing enhancers leads to synergistic effects on RET gene expression. These, coupled with our prior results, show that common sequence variants in at least 10 RET enhancers affect HSCR risk, seven with experimental evidence of affecting RET gene expression, extending the known RET–EDNRB GRN to reveal an extensive regulatory code modulating disease risk at a single gene.
Maintained goal-directed control with overtraining on ratio schedules
Authors: Garr Eric , Padovan-Hernandez Yasmin , Janak Patricia H. , Delamater Andrew R.
Published: November 2021

It is thought that goal-directed control of actions weakens or becomes masked by habits over time. We tested the opposing hypothesis that goal-directed control becomes stronger over time, and that this growth is modulated by the overall action–outcome contiguity. Despite group differences in action–outcome contiguity early in training, rats trained under random and fixed ratio schedules showed equivalent goal-directed control of lever pressing that appeared to grow over time. We confirmed that goal-directed control was maintained after extended training under another type of ratio schedule—continuous reinforcement—using specific satiety and taste aversion devaluation methods. These results add to the growing literature showing that extensive training does not reliably weaken goal-directed control and that it may strengthen it, or at least maintain it.
The inhibition activity of lemongrass extract (LGE) for mild steel acid corrosion: Electrochemical, surface and theoretical investigations
Authors: El-Katori Emad ElDin , Hashem Nady
Published: November 2021

Purpose

The purpose of this paper is to minimize corrosion-related pollution in the environment. From the lemongrass extract (LGE), the authors selected one of the best green inhibitors.

Design/methodology/approach

The corrosion and inhibition of mild steel in traditional acidification solutions were estimated by electrochemical measurements. The corrosion appearance was observed with scanning electron microscopy, atomic force microscopy micrographs and attenuated total reflectance infrared spectroscopy spectrum. The correlation was formed between the gained inhibition efficiency (IE)% from electrochemical measurements and certain quantum chemical parameters.

Findings

The results displayed that the IE was up to 90% when the LGE concentration was 300 ppm. The results confirmed that the theoretical experiments are very similar to the experimental observations.

Originality/value

For the first time, LGE was used as a cheap and safe corrosion inhibitor for mild steel corrosion in the acidification process. The mechanism of mild steel corrosion and anti-corrosion in acid solution has been suggested.