bluuebunny/crossref_metadata_2025 huggingface dataset:
The evolution of the 9aaTAD domain in Sp2 proteins: inactivation with valines and intron reservoirs
Authors: Piskacek Martin , Havelka Marek , Jendruchova Kristina , Knight Andrea , Keegan Liam P.
Published: March 2019

The Sp1 transcription factor has been defined as glutamine-rich activator. The Nine amino acid TransActivation Domains (9aaTAD) have been identified in numerous transcription activators. Here, we identified the conserved 9aaTAD motif in the Sp1 and in all nine members of SP family with broad natural 9aaTAD variations. We showed by the amino acid substitutions that the glutamine residues are completely dispensable for 9aaTADs function. We described the 9aaTAD domains’ origin and evolutionary history. The ancestral Sp2 gene with inactive 9aaTAD has duplicated in early chordates and created new paralogs Sp1, Sp3 and Sp4. We discovered that the accumulation of valines in the 9aaTADs correlated with the domain inactivation. The Sp2 activation domain, whose dormancy have lasted over 100 million years during chordate evolution, enabled later diversification in the Sp1-4 clade, including both repressors and activators. The new paralogs Sp1 and Sp3 activation domains have regained their original activator function by loss of valines in their 9aaTADs.
Simulations of the effect of diffusion on asymmetric spin echo based quantitative BOLD: An investigation of the origin of deoxygenated blood volume overestimation
Authors: Stone Alan J , Holland Naomi C , Berman Avery J L , Blockley Nicholas P
Published: March 2019

Quantitative BOLD (qBOLD) is a technique for mapping oxygen extraction fraction (OEF) and deoxygenated blood volume (DBV) in the human brain. Recent measurements using an asymmetric spin echo (ASE) based qBOLD approach produced estimates of DBV which were systematically higher than measurements from other techniques. In this study, we investigate two hypotheses for the origin of this DBV overestimation using simulations and consider the implications for experimental measurements. Investigations were performed by combining Monte Carlo simulations of extravascular signal with an analytical model of the intravascular signal.

Hypothesis 1

DBV overestimation is due to the presence of intravascular signal which is not accounted for in the analysis model. Intravascular signal was found to have a weak effect on qBOLD parameter estimates.

Hypothesis 2

DBV overestimation is due to the effects of diffusion which are not accounted for in the analysis model. The effect of diffusion on the extravascular signal was found to result in a vessel radius dependent variation in qBOLD parameter estimates. In particular, DBV overestimation peaks for vessels with radii from 20 to 30 μm and is OEF dependent. This results in the systematic underestimation of OEF.

Implications

The impact on experimental qBOLD measurements was investigated by simulating a more physiologically realistic distribution of vessel sizes with a small number of discrete radii. Overestimation of DBV consistent with previous experiments was observed, which was also found to be OEF dependent. This results in the progressive underestimation of the measured OEF. Furthermore, the relationship between the measured OEF and the true OEF was found to be dependent on echo time and spin echo displacement time.

The results of this study demonstrate the limitations of current ASE based qBOLD measurements and provide a foundation for the optimisation of future acquisition approaches.
Pervasive head-to-tail insertions of DNA templates mask desired CRISPR/Cas9-mediated genome editing events
Authors: Skryabin Boris V. , Gubar Leonid , Seeger Birte , Kaiser Helena , Stegemann Anja , Roth Johannes , Meuth Sven G. , Pavenstädt Hermann , Sherwood Joanna , Pap Thomas , Wedlich-Söldner Roland , Sunderkötter Cord , Schwartz Yuri B. , Brosius Juergen , Rozhdestvensky Timofey S.
Published: March 2019

CRISPR/Cas9 mediated homology-directed DNA repair is the method of choice for precise gene editing in a wide range of model organisms, including mouse and human. Broad use by the biomedical community refined the method, making it more efficient and sequence specific. Nevertheless, the rapidly evolving technique still contains pitfalls. During the generation of six different conditional knock-out mouse models, we discovered that frequently (sometimes solely) homology-directed repair and/or non-homologous end-joining mechanisms caused multiple unwanted head-to-tail insertions of donor DNA templates. Disturbingly, conventionally applied PCR analysis—in most cases—failed to identify such multiple integration events, which led to a high rate of falsely claimed precisely edited alleles. We caution that comprehensive analysis of modified alleles is essential, and offer practical solutions to correctly identify precisely edited chromosomes.
The Neural Basis of Shared Preference Learning
Authors: Farmer Harry , Hertz Uri , Hamilton Antonia
Published: March 2019

During our daily lives, we often learn about the similarity of the traits and preferences of others to our own and use that information during our social interactions. However, it is unclear how the brain represents similarity between the self and others. One possible mechanism is to track similarity to oneself regardless of the identity of the other (Similarity account); an alternative is to track each confederate in terms of consistency of the similarity to the self, with respect to the choices they have made before (consistency account). Our study combined fMRI and computational modelling of reinforcement learning (RL) to investigate the neural processes that underlie learning about preference similarity. Participants chose which of two pieces of artwork they preferred and saw the choices of one confederate who usually shared their preference and another who usually did not. We modelled neural activation with RL models based on the similarity and consistency accounts. Data showed more brain regions whose activity pattern fits with the consistency account, specifically, areas linked to reward and social cognition. Our findings suggest that impressions of other people can be calculated in a person-specific manner which assumes that each individual behaves consistently with their past choices.
The order of trait emergence in the evolution of cyanobacterial multicellularity
Authors: Hammerschmidt Katrin , Landan Giddy , Tria Fernando Domingues Kümmel , Alcorta Jaime , Dagan Tal
Published: March 2019

The transition from unicellular to multicellular organisms is one of the most significant events in the history of life. Key to this process is the emergence of Darwinian individuality at the higher level: groups must become single entities capable of reproduction for selection to shape their evolution. Evolutionary transitions in individuality are characterized by cooperation between the lower level entities and by division of labor. Theory suggests that division of labor may drive the transition to multicellularity by eliminating the trade-off between two incompatible processes that cannot be performed simultaneously in one cell. Here we examine the evolution of the most ancient multicellular transition known today, that of cyanobacteria, where we reconstruct the sequence of ecological and phenotypic trait evolution. Our results show that the prime driver of multicellularity in cyanobacteria was the expansion in metabolic capacity offered by nitrogen fixation, which was accompanied by the emergence of the filamentous morphology and succeeded by a reproductive life cycle. This was followed by the progression of multicellularity into higher complexity in the form of differentiated cells and patterned multicellularity.

Significance Statement

The emergence of multicellularity is a major evolutionary transition. The oldest transition, that of cyanobacteria, happened more than 3 to 3.5 billion years ago. We find N2 fixation to be the prime driver of multicellularity in cyanobacteria. This innovation faced the challenge of incompatible metabolic processes since the N2 fixing enzyme (nitrogenase) is sensitive to oxygen, which is abundantly found in cyanobacteria cells performing photosynthesis. At the same time, N2-fixation conferred an adaptive benefit to the filamentous morphology as cells could divide their labour into performing either N2-fixation or photosynthesis. This was followed by the culmination of complex multicellularity in the form of differentiated cells and patterned multicellularity.
Genomic analysis reveals shared genes and pathways in human and canine angiosarcoma
Authors: Megquier Kate , Turner-Maier Jason , Swofford Ross , Kim Jong-Hyuk , Sarver Aaron L. , Wang Chao , Sakthikumar Sharadha , Johnson Jeremy , Koltookian Michele , Lewellen Mitzi , Scott Milcah C. , Graef Ashley J. , Borst Luke , Tonomura Noriko , Alfoldi Jessica , Painter Corrie , Thomas Rachael , Karlsson Elinor K. , Breen Matthew , Modiano Jaime F. , Elvers Ingegerd , Lindblad-Toh Kerstin
Published: March 2019

Angiosarcoma is a highly aggressive cancer of blood vessel-forming cells with high fatality and few effective treatment options. It is both rare and heterogenous, making large, well powered genomic studies nearly impossible. In dogs, angiosarcoma is common, with breeds like the golden retriever carrying heritable genetic factors that put them at very high risk. If the clinical similarity of canine and human angiosarcoma reflects shared genomic etiology, dogs could be a critically needed model for advancing angiosarcoma research. We assessed the genomic landscape of canine angiosarcoma via whole exome sequencing (47 golden retriever angiosarcomas) and RNA sequencing (74 angiosarcomas from multiple breeds). The predominant mutational signature was the age-associated deamination of cytosine to thymine, and somatic coding mutations occurred most frequently in the tumor suppressorTP53(59.6% of cases) as well as two genes in the PI3K pathway: the oncogenePIK3CA(29.8%) and its regulatory subunitPIK3R1(8.5%). We compared the canine data to human data recently released by The Angiosarcoma Project, and found the same genes and many of the same pathways significantly enriched for somatic mutations, most notably protein kinases, glycoproteins, fibronectin Type III domains, EGF-like domains, and cell adhesion proteins such as cadherins. As in human angiosarcoma,CDKN2A/Bwas recurrently deleted andVEGFA, KDR, and KITrecurrently gained. Canine angiosarcoma closely models human angiosarcoma on a genomic level, and is a powerful tool for investigating the pathogenesis of this devastating disease.
Designing a novel multi-epitope T vaccine for “targeting protein for Xklp-2” (TPX2) in hepatocellular carcinoma based on immunoinformatics approach
Authors: Ghahremanifard Parisa , Afzali Farzaneh , Rostami Amin , Nayeri Zahra , Bambai Bijan , Minuchehr Zarrin
Published: March 2019

Hepatocellular carcinoma (HCC) is one of the leading cancer-related deaths worldwide. Recently, studies for HCC treatment are focused on cancer immunotherapy, particularly cancer vaccines, to complete and assist other therapies. TPX2 is a microtubule-associated protein necessary for cell division; therefore, alteration in its expression, especially up regulation, is associated with several human carcinomas such as HCC.

In this study, immunoinformatics tools were used to design a rational multi-epitope T vaccine against TPX2 in HCC. Cytotoxic T lymphocytes (CTL) and Helper T lymphocytes (HTL) epitopes were predicted and Maltose-binding protein (MBP) was added to the construct as an adjuvant. Evaluation of vaccine properties was indicated that our construct is stable and immunogenic enough to induce relevant responses besides not being allergic. After predicting the tertiary structure and energy minimization, protein-protein docking was performed to calculate the free energy of possible interactions between the vaccine and toll-like receptor 4 (TLR4) to assure that simultaneous complementary responses would be activated by our construct. Finally, Codon optimization and in-silico cloning were performed to ensure the vaccine expression efficiency in the desired host.
Genetic determinants inSalmonella entericaserotype Typhimurium required for overcoming stressors in the host environment
Authors: Mandal Rabindra K. , Jiang Tieshan , Min Kwon Young
Published: March 2019

Salmonella entericaserovar Typhimurium (S. Typhimurium), a non-typhoidalSalmonella(NTS), result in a range of diseases, including self-limiting gastroenteritis, bacteremia, enteric fever, and focal infections representing a major disease burden worldwide. There is still a significant portion ofSalmonellagenes whose functional basis to overcome host innate defense mechanisms, consequently causing disease in host, largely remains unknown. Here, we have applied a high-throughput transposon sequencing (Tn-seq) method to unveil the genetic factors required for the growth or survival of S. Typhimurium under various host stressors simulatedin vitro. A highly saturating Tn5 library ofS. Typhimurium 14028s was subjected to selection during growth in the presence of short chain fatty acid (100 mM propionate), osmotic stress (3% NaCl) or oxidative stress (1 mM H2O2) or survival in extreme acidic pH (30 min in pH3) or starvation (12 days in 1X PBS). We have identified an overlapping set of 339 conditionally essential genes (CEGs) required byS. Typhimurium to overcome these host insults. Interestingly, entire eight genes encoding F0F1-ATP synthase subunit proteins were required for fitness in all five stresses. Intriguingly, total 88 genes inSalmonellapathogenicity island (SPI), including SPI-1, SPI-2, SPI-3, SPI-5, SPI-6 and SPI-11 are also required for fitness under thein vitroconditions evaluated in this study. Additionally, by comparative analysis of the genes identified in this study and the genes previously shown to be required forin vivofitness, we identified novel genes (marBCT,envF,barA,hscA,rfaQ,rfbIand putative proteins STM14_1138, STM14_3334, STM14_4825, and STM_5184) that has compelling potential to be exploited as vaccine development and/or drug target to curb theSalmonellainfection.
Fear Learning Induces Long-Lasting Changes in Gene Expression and Pathway Specific Presynaptic Growth
Authors: Dillingham Blythe C. , Cameron Peter , Pieraut Simon , Cardozo Leonardo M. , Yoo Eun J. , Maximov Anton , Stowers Lisa , Mayford Mark
Published: March 2019

The stabilization or consolidation of long-term memories lasting more than a few hours requires new gene expression. While neural activity has been shown to induce expression of a variety of genes within several hours of learning, whether this leads to persistent changes in gene expression that lasts for days or weeks remains unclear. We developed a novel mouse line which expresses Cre recombinase in an inducible manner and used it to examine gene expression in learning-activated neurons of the medial prefrontal cortex (mPFC) one month following contextual fear conditioning. The mPFC is not required for the initial retrieval of contextual memory but becomes necessary after one month, suggesting a slowly developing plasticity. We found a variety of changes in gene expression in learning-activated neural ensembles that were specific to the mPFC. One group of transcriptional changes observed was the coordinated upregulation of presynaptic proteins suggesting a potential learning-induced elaboration of presynaptic terminals. We tested this idea by labeling the projections of mPFC neurons active during initial learning and found an increase in the number of terminals in neurons projecting to the basolateral amygdala at 1 month following training. These results suggest a presynaptic growth mechanism that could account for the enhanced role of the mPFC in fear memory retrieval at long time points after learning.
Mechanical stress compromises multicomponent efflux complexes in bacteria
Authors: Genova Lauren A. , Roberts Melanie F. , Wong Yu-Chern , Harper Christine E. , Santiago Ace George , Fu Bing , Srivastava Abhishek , Jung Won , Wang Lucy M. , Krzemiński Łukasz , Mao Xianwen , Sun Xuanhao , Hui Chung-Yuen , Chen Peng , Hernandez Christopher J.
Published: March 2019

Physical forces have long been recognized for their effects on the growth, morphology, locomotion, and survival of eukaryotic organisms1. Recently, mechanical forces have been shown to regulate processes in bacteria, including cell division2, motility3, virulence4, biofilm initiation5,6, and cell shape7,8, although it remains unclear how mechanical forces in the cell envelope lead to changes in molecular processes. In Gram-negative bacteria, multicomponent protein complexes that form rigid links across the cell envelope directly experience physical forces and mechanical stresses applied to the cell. Here we manipulate tensile and shear mechanical stress in the bacterial cell envelope and use single-molecule tracking to show that shear (but not tensile) stress within the cell envelope promotes disassembly of the tripartite efflux complex CusCBA, a system used by E. coli to resist copper and silver toxicity, thereby making bacteria more susceptible to metal toxicity. These findings provide the first demonstration that mechanical forces, such as those generated during colony overcrowding or bacterial motility through submicron pores, can inhibit the contact and function of multicomponent complexes in bacteria. As multicomponent, trans-envelope efflux complexes in bacteria are involved in many processes including antibiotic resistance9, cell division10, and translocation of outer membrane components11, our findings suggest that the mechanical environment may regulate multiple processes required for bacterial growth and survival.
Protein kinase B controls Mycobacterium tuberculosis growth via phosphorylation of the global transcriptional regulator Lsr2
Authors: Alqaseer Kawther , Turapov Obolbek , Barthe Philippe , Jagatia Heena , De Visch Angélique , Roumestand Christian , Wegrzyn Malgorzata , Bartek Iona L. , Voskuil Martin I. , O’Hare Helen , Witney Adam A. , Cohen-Gonsaud Martin , Waddell Simon J. , Mukamolova Galina V.
Published: March 2019

Mycobacterium tuberculosis is able to persist in the body through months of multi-drug therapy. Mycobacteria possess a wide range of regulatory proteins, including the essential protein kinase B (PknB), that control transitions between growth states. Here, we establish that depletion of PknB in replicating M. tuberculosis results in transcriptional adaptations that implicate the DNA-binding protein Lsr2 in coordinating these changes. We show that Lsr2 is phosphorylated by PknB, and that phosphorylation of Lsr2 at threonine 112 is important for M. tuberculosis growth and survival under hypoxic conditions. Fluorescence anisotropy and electrophoretic mobility shift assays demonstrate that phosphorylation reduces Lsr2 binding to DNA, and ChIP-sequencing confirms increased DNA binding of a phosphoablative (T112A) Lsr2 mutant in M. tuberculosis. Altered expression of target genes in T112A Lsr2 compared to wild type Lsr2 M. tuberculosis offers further evidence that phosphorylation mediates expression of the Lsr2 regulon. Structural studies reveal increased dynamics of the Lsr2 DNA binding domain from a T112D phosphomimetic Lsr2 mutant, providing a molecular basis for decreased DNA binding by phosphorylated Lsr2. Our findings suggest that, the essential protein kinase, PknB controls M. tuberculosis growth and adaptations to the changing host environment by phosphorylating the global transcriptional regulator Lsr2.
An atlas of anteriorhoxgene expression in the embryonic sea lamprey head:hox-code evolution in vertebrates
Authors: Parker Hugo J. , Bronner Marianne E. , Krumlauf Robb
Published: March 2019

In the hindbrain and the adjacent cranial neural crest (NC) cells of jawed vertebrates (gnathostomes), nested and segmentally-restricted domains ofHoxgene expression provide a combinatorialHox-code for specifying regional properties during head development. Extant jawless vertebrates, such as the sea lamprey(Petromyzon marinus),can provide insights into the evolution and diversification of thisHox-code in vertebrates. There is evidence for gnathostome-like spatial patterns ofHoxexpression in lamprey; however, the expression domains of the majority of lampreyhoxgenes from paralogy groups (PG) 1-4 are yet to be characterized, so it is unknown whether they are coupled to hindbrain segments (rhombomeres) and NC. In this study, we systematically describe the spatiotemporal expression of all 14 sea lampreyhoxgenes from PG1-PG4 in the developing hindbrain and pharynx to investigate the extent to which their expression conforms to the archetypal gnathostome hindbrain and pharyngealhox-codes. We find many similarities inHoxexpression between lamprey and gnathostome species, particularly in rhombomeric domains during hindbrain segmentation and in the cranial neural crest, enabling inference of aspects ofHoxexpression in the ancestral vertebrate embryonic head. These data are consistent with the idea that aHoxregulatory network underlying hindbrain segmentation is a pan vertebrate trait. We also reveal differences in hindbrain domains at later stages, as well as expression in the endostyle and in pharyngeal arch (PA) 1 mesoderm. Our analysis suggests that manyHoxexpression domains that are observed in extant gnathostomes were present in ancestral vertebrates but have been partitioned differently acrossHoxclusters in gnathostome and cyclostome lineages after duplication.
Functional and signaling characterization of the neutrophil FPR2 selective agonist Act-389949
Authors: Lind Simon , Sundqvist Martina , Holmdahl Rikard , Dahlgren Claes , Forsman Huamei , Olofsson Peter
Published: March 2019

Despite the steadily increased numbers of formyl peptide receptor (FPR) ligands identified over the years, few have been characterized in studies using animal disease models and even less have entered clinical trials in human subjects. A small-molecule compound, Act-389949, was however recently tested in a phase I clinical trial and found to be safe and well tolerated in healthy human subjects. The desired anti-inflammatory property of Act-389949 was proposed to be mediated through FPR2, one of the FPRs expressed in neutrophils, but no basic characterization was included in the study. To gain more insights into FPR2 recognition of this first-in-class compound for future utility of the agonist, we have in this study determined the receptor preference and down-stream signaling characteristics induced by Act-389949 in human blood neutrophils isolated from healthy donors. Our data demonstrate that Act-389949 is an agonist for FPR2 that triggers functional/signaling repertoires comparable to what has been earlier described for other FPR2 agonists, including neutrophil chemotaxis, granule mobilization and activation of the NADPH-oxidase. In fact, Act-389949 was found to be as potent as the prototype FPR2 peptide agonist WKYMVM and had the advantage of being resistant to oxidation by the MPO-H2O2-halide derived oxidants, as compared to the sensitive WKYMVM. The down-stream signals generated by Act-389949 include an FPR2-dependent and Gαq-independent transient rise in intracellular Ca2+and recruitment of β-arrestin. In summary, our data show that Act-389949 serves as an excellent tool-compound for further dissection of FPR2-regulated activitiesin vitroandin vivo. Potent and stable FPR ligands such as Act-389949 may therefore be used to develop the next generation of FPR signaling regulating anti-inflammatory therapeutics.
Fast dose fractionation using ultra-short laser accelerated proton pulses can increase cancer cell mortality, which relies on functional PARP1 protein
Authors: Bayart E. , Flacco A. , Delmas O. , Pommarel L. , Levy D. , Cavallone M. , Megnin-Chanet F. , Deutsch E. , Malka V.
Published: March 2019

Radiotherapy is a cornerstone of cancer management. The improvement of spatial dose distribution in the tumor volume by minimizing the dose deposited in the healthy tissues have been a major concern during the last decades. Temporal aspects of dose deposition are yet to be investigated. Laser-plasma-based particle accelerators are able to emit pulsed-proton beams at extremely high peak dose rates (~109Gy/s) during several nanoseconds. The impact of such dose rates on resistant glioblastoma cell lines, SF763 and U87-MG, was compared to conventionally accelerated protons and X-rays. No difference was observed in DNA double-strand breaks generation and cells killing. The variation of the repetition rate of the proton bunches produced an oscillation of the radio-induced cell susceptibility in HCT116 cells, which appeared to be related to the presence of the PARP1 protein and an efficient parylation process. Interestingly, when laser-driven proton bunches were applied at 0.5 Hz, survival of the radioresistant HCT116 p53−/−cells equaled that of its radiosensitive counterpart, HCT116 WT, which was also similar to cells treated with the PARP1 inhibitor Olaparib. Altogether, these results suggest that the application modality of ultrashort bunches of particles could provide a great therapeutic potential in radiotherapy.
β-Catenin tumour-suppressor activity depends on its ability to promote Pro-N-Cadherin maturation
Authors: Herrera Antonio , Menendez Anghara , Torroba Blanca , Pons Sebastian
Published: March 2019

Neural stem cells (NSCs) form a pseudostratified, single-cell layered epithelium with a marked apico-basal polarity. In these cells, β-Catenin associates with classic cadherins in order to form the apical adherens junctions (AJs). We previously reported that oncogenic forms of β-Catenin (sβ-Catenin) maintain neural precursors as progenitors, while also enhancing their polarization and adhesiveness, thereby limiting their malignant potential. Here we show that β-Catenin can bind to phosphorylated Pro-N-Cadherin, promoting the excision of the propeptide and its maturation into N-Cadherin in the trans-Golgi network (TGN). Moreover, β-Catenin-assisted maturation of Pro-N-Cadherin is required for the formation of the AJs and for them to recruit other apical complex (AC) components like aPKC, and accordingly, to establish apico-basal polarity. Notably, we show that NSCs expressing unprocessed Pro-N-Cadherin invade the ventricle and they breach the basement membrane to invade the surrounding mesenchyme. Hence, we propose that the tumour-suppressor activity of sβ-Catenin depends on it promoting Pro-N-Cadherin processing.
An evolutionary-conserved redox regulatory mechanism in human Ser/Thr protein kinases
Authors: Byrne Dominic P. , Shrestha Safal , Kannan Natarajan , Eyers Patrick A.
Published: March 2019

Reactive oxygen species (ROS) are products of oxygen metabolism, but are also recognized as endogenous physiological mediators of cellular signaling. Eukaryotic protein kinase (ePK) regulation occurs through reversible phosphorylation events in the flexible activation segment. In this study, we demonstrate that the catalytic phosphotransferase output from the mitotic Ser/Thr kinase Aurora A is also controlled by cysteine (Cys) oxidation. Reversible regulation occurs by direct modification of a conserved residue (Cys 290), which lies adjacent to Thr 288, the activating site of phosphorylation. Strikingly, redox modulation of the Cys 290-equivalent in other ePKs is predicted to be an underappreciated regulatory mechanism, since ~100 human Ser/Thr kinases possess a Cys at this position in the conserved activation loop. Using real-time enzyme assays, we confirm that the presence of the equivalent Cys residue is prognostic for redox-sensitivity amongst a cohort of human CAMK, AGC and AGC-like kinases, including AKT, AMPK, CAMK1, MAPKAP-K2/3 and SIK1-3. Our findings demonstrate that dominant Cys-based redox-switching in the activation segment represents an evolutionary-conserved mode of regulation for a significant subset of the human kinome. This finding has important implications for understanding physiological and pathological signaling responses to ROS, and emphasises the importance of multivalent activation segment regulation in ePKs.

ONE-SENTENCE SUMMARY

The catalytic activity of Ser/Thr kinases is regulated through a conserved Cys-based redox mechanism.
Chromosomes function as a barrier to mitotic spindle bipolarity in polyploid cells
Authors: Goupil Alix , Nano Maddalena , Letort Gaëlle , Gogendeau Delphine , Pennetier Carole , Basto Renata
Published: March 2019

Whole genome duplications (WGDs) are found in a variety of tumors and are associated with chromosomal instability (CIN) and poor prognosis [1,2]. When induced experimentally, through cytokinesis failure, polyploid cells generate tumors [3]. Cytokinesis failure results in the accumulation of double DNA content, but also of cytoplasmic organelles, such as centrosomes, which are the major microtubule (MT) organizing centers of animal cells. Importantly, even if there is a correlation between polyploidy and CIN [4], the underlying mechanisms generating error-prone mitosis in cells with extra DNA and extra centrosomes are not known. When considering polyploid mitosis, it is essential to take into account the increase in MT nucleation due to the presence of extra centrosomes and extra DNA. The presence of supernumerary centrosomes in a cell, centrosome amplification [5], is associated with mitotic spindle multipolarity and CIN [6–9]. Importantly, additional MTs can be nucleated from the chromatin (chromatin mediated pathway-CMP) or from pre-existing MTs-through the Augmin pathway. We hypothesized that the increase in DNA and centrosome content in a cell could lead to an increased MT mass, which might account for abnormal mitosis described in polyploid cells [4, 10, 11, 12]. Using genetics, live imaging and modeling approaches, we investigated the mechanisms establishing multipolarity in vivo in polyploid cells. We found that MT nucleation from the centrosomes is the major contributor to multipolarity, while other pathways seem to play minor roles. Unexpectedly, we found that even if Ncd/HSET, plays an essential role in promoting centrosome clustering in early mitosis, the increase in chromosome mass associated with cytokinesis failure functions as a barrier to centrosome clustering into two main poles. Our work provides a mechanistic link between polyploidy and the generation of CIN.
The rise and fall of the new variant ofChlamydia trachomatisin Sweden: mathematical modelling study
Authors: Smid Joost , Althaus Christian L. , Low Nicola , Unemo Magnus , Herrmann Björn
Published: March 2019

Objectives

A new variant ofChlamydia trachomatis(nvCT) was discovered in Sweden in 2006. The nvCT has a plasmid deletion, which escaped detection by two nucleic acid amplification tests (Abbott/Roche, AR), which were used in 14 of 21 Swedish counties. The objectives of this study were to assess when and where nvCT emerged in Sweden, the proportion of nvCT in each county, and the role of a potential fitness difference between nvCT and co-circulating wild-type strains (wtCT).

Methods

We used a compartmental mathematical model describing the spatial and temporal spread of nvCT and wtCT. We parameterised the model using sexual behaviour data and Swedish spatial and demographic data. We used Bayesian inference to fit the model to surveillance data about reported diagnoses of chlamydia infection in each county and data from four counties that assessed the proportion of nvCT in multiple years.

Results

Model results indicated that nvCT emerged in central Sweden (Dalarna, Gävleborg, Västernorrland), reaching a proportion of 1% of prevalent CT infections in late 2002 or early 2003. The diagnostic selective advantage enabled rapid spread of nvCT in the presence of high treatment rates. After detection, the proportion of nvCT decreased from 30-70% in AR counties and 5-20% in counties that Becton Dickinson tests, to around 5% in 2015 in all counties. The decrease in nvCT was consistent with an estimated fitness cost of around 5% in transmissibility or 17% reduction in infectious duration.

Conclusions

We reconstructed the course of a natural experiment in which a mutant strain ofC. trachomatisspread across Sweden. Our modelling study provides support, for the first time, of a reduced transmissibility or infectious duration of nvCT. This mathematical model improved our understanding of the first nvCT epidemic in Sweden and can be adapted to investigate the impact of future diagnostic escape mutants.

Key messages

The dynamics of a new variant ofChlamydia trachomatis(nvCT) that escaped testing and treatment in Sweden can be reconstructed using a mathematical transmission model.

Our study for the first time provides support of a reduced transmissibility or infectious duration of the nvCT in Sweden.

This mathematical model improved our understanding of the nvCT epidemic in Sweden and can be adapted to investigate the impact of future diagnostic escape mutants.
The solution structure of Dead End bound to AU-rich RNA reveals an unprecedented mode of tandem RRM-RNA recognition required for mRNA regulation
Authors: Duszczyk Malgorzata M. , Wischnewski Harry , Kazeeva Tamara , Loughlin Fionna E. , von Schroetter Christine , Pradère Ugo , Hall Jonathan , Ciaudo Constance , Frédéric H.-T. Allain
Published: March 2019

Dead End (DND1) is an RNA-binding protein essential for germline development through its role in post-transcriptional gene regulation. The molecular mechanisms behind selection and regulation of its targets are unknown. Here, we present the solution structure of DND1’s tandem RNA Recognition Motifs (RRMs) bound to AU-rich RNA. The structure reveals how an NYAYUNN element is specifically recognized, reconciling seemingly contradictory sequence motifs discovered in recent genome-wide studies. RRM1 acts as a main binding platform, including atypical extensions to the canonical RRM fold. RRM2 acts cooperatively with RRM1, capping the RNA using an unusual binding pocket, leading to an unprecedented mode of tandem RRM-RNA recognition. We show that the consensus motif is sufficient to mediate upregulation of a reporter gene in human cells and that this process depends not only on RNA binding by the RRMs, but also on DND1’s double-stranded RNA binding domain (dsRBD), which is dispensable for target binding in cellulo. Our results point to a model where DND1 target selection is mediated by a non-canonical mode of AU-rich RNA recognition by the tandem RRMs and a role for the dsRBD in the recruitment of effector complexes responsible for target regulation.
The type VII secretion system protectsStaphylococcus aureusagainst antimicrobial host fatty acids
Authors: Tchoupa Arnaud Kengmo , Watkins Kate E. , Jones Rebekah A. , Kuroki Agnès , Alam Mohammad Tauqeer , Perrier Sebastien , Chen Yin , Unnikrishnan Meera
Published: March 2019

TheStaphylococcus aureustype VII secretion system (T7SS) exports several proteins that are pivotal for bacterial virulence. The mechanisms underlying T7SS-mediated staphylococcal survival during infection nevertheless remain unclear. Here we show that the absence of EsxC, a small secreted effector implicated in bacterial persistence, results in cell membrane defects inS. aureus. Interestingly, isogenic mutants lacking EsxC, other T7SS effectors EsxA and EsxB, or the membrane-bound ATPase EssC, are more sensitive to killing by the host-derived antimicrobial fatty acid, linoleic acid (LA), compared to the wild-type (WT). LA induces more cell membrane damage in the T7SS mutants compared to the WT. Although WT and mutant strains did not differ in their ability to bind labelled LA, membrane lipid profiles show that T7SS mutants are less able to incorporate LA into their membrane phospholipids. Furthermore, proteomic analyses of WT and mutant cell fractions reveal that, in addition to compromising membranes, T7SS defects induce oxidative stress and hamper their response to LA challenge. Thus, our findings indicate that T7SS is crucial forS. aureusmembrane integrity and homeostasis, which is critical when bacteria encounter antimicrobial fatty acids.
The evolution and phylodynamics of serotype A and SAT2 foot-and-mouth disease viruses in endemic regions of Africa
Authors: Lycett S. , Tanya V.N. , Hall M. , King D. , Mazeri S. , Mioulet V. , Knowles N. , Wadsworth J. , Bachanek-Bankowska K. , Ngwa Victor N. , Morgan K.L. , Bronsvoort B.M.deC.
Published: March 2019

Foot-and-mouth disease (FMD) is a major livestock disease with direct clinical impacts as well as indirect trade implications. Control through vaccination and stamping-out has successfully reduced or eradicated the disease from Europe and large parts of South America. However, sub-Saharan Africa remains endemically affected with 5/7 serotypes currently known to be circulating across the continent. This has significant implications both locally for livestock production and poverty reduction but also globally as it represents a major reservoir of viruses, which could spark new epidemics in disease free countries or vaccination zones. This paper describes the phylodynamics of serotypes A and SAT2 in Africa including recent isolates from Cameroon in Central Africa. We estimated the most recent common ancestor for serotype A was an East African virus from the 1930s compared to SAT2 which has a much older common ancestor from the early 1700s. Detailed analysis of the different clades shows clearly that different clades are evolving and diffusing across the landscape at different rates with both serotypes having a particularly recent clade that is evolving and spreading more rapidly than other clades within their serotype. However, the lack of detailed sequence data available for Africa seriously limits our understanding of FMD epidemiology across the continent. A comprehensive view of the evolutionary history and dynamics of FMD viruses is essential to understand many basic epidemiological aspects of FMD in Africa such as the scale of persistence and the role of wildlife and thus the opportunities and scale at which vaccination and other controls could be applied. Finally we ask endemic countries to join the OIE/FAO supported regional networks and take advantage of new cheap technologies being rolled out to collect isolates and submit them to the World Reference Laboratory.
Somatic structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma
Authors: Lopez Gonzalo , Conkrite Karina L. , Doepner Miriam , Rathi Komal S. , Modi Apexa , Vaksman Zalman , Farra Lance M. , Hyson Eric , Noureddine Moataz , Wei Jun S. , Smith Malcolm A. , Asgharzadeh Shahab , Seeger Robert C. , Khan Javed , Auvil Jaime Guidry , Gerhard Daniela S. , Maris John M. , Diskin Sharon J.
Published: March 2019

Neuroblastoma is a malignancy of the developing sympathetic nervous system that accounts for 12% of childhood cancer deaths. Like many childhood cancers, neuroblastoma exhibits a relative paucity of somatic single nucleotide variants (SNVs) and small insertions and deletions (indels) compared to adult cancers. Here, we assessed the contribution of somatic structural variation (SV) in neuroblastoma using a combination of whole genome sequencing (WGS; n=135) and single nucleotide polymorphism (SNP) genotyping (n=914) of matched tumor-normal pairs. Our study design allowed for orthogonal validation and replication across platforms. SV frequency, type, and localization varied significantly among high-risk tumors. MYCN non-amplified high-risk tumors harbored an increased SV burden overall, including a substantial excess of tandem-duplication events across the genome. Genes disrupted by SV breakpoints were enriched in neuronal lineages and autism spectrum disorder (ASD). The postsynaptic adapter protein-coding gene SHANK2, located on chromosome 11q13, was disrupted by SVs in 14% of MYCN non-amplified high-risk tumors based on WGS and 10% in the SNP array cohort. Expression of SHANK2 was low across human-derived neuroblastoma cell lines and high-risk neuroblastoma tumors. Forced expression of SHANK2 in neuroblastoma cell models resulted in significant growth inhibition (P=2.62×10-2 to 3.4×10-5) and accelerated neuronal differentiation following treatment with all-trans retinoic acid (P=3.08×10-13 to 2.38×10-30). These data further define the complex landscape of structural variation in neuroblastoma and suggest that events leading to deregulation of neurodevelopmental processes, such as inactivation of SHANK2, are key mediators of tumorigenesis in this childhood cancer.
Distinct Narrow and Broadband Gamma Responses in Human Visual Cortex
Authors: Bartoli Eleonora , Bosking William , Li Ye , Beauchamp Michael S. , Yoshor Daniel , Foster Brett L.
Published: March 2019

High frequency activity (> 30 Hz) in the neocortical local field potential, typically referred to as the ‘gamma’ range, is thought to have a critical role in visual perception and cognition more broadly. Historically, animal studies recording from visual cortex documented clear narrowband gamma oscillations (NBG; ∼20-60 Hz) in response to visual stimuli. However, invasive measurements from human neocortex have highlighted a different broadband or ‘high’ gamma response (BBG; ∼70-150+ Hz). Growing evidence suggests these two forms of gamma response are distinct, but often conceptually or analytically conflated as the same ‘gamma’ response. Furthermore, recent debate has highlighted that both the occurrence and spectral properties of gamma band activity in visual cortex appears to be dependent on the attributes and class of presented visual stimuli. Using high-density intracranial recordings from human visual cortex, we integrate and extend these findings, dissociating the spectral, temporal and functional properties of NBG and BBG activity. We report results from two experiments, manipulating visual stimulus attributes (contrast-varying gratings) and class (object categories) dissecting the differential properties of NBG and BBG responses. NBG oscillations were only reliably recorded for grating stimuli, while their peak frequency varied with contrast level. Whereas BBG activity was observed in response to all stimulus classes tested, with no systematic change in its spectral features. Temporally, induced NBG was sustained throughout stimulus presentation, in opposition to a more transient response for the BBG. These findings challenge the ubiquity of ‘gamma’ activity in visual cortex, by clearly dissociating oscillatory and broadband effects.

Significance Statement

Neocortical narrowband gamma oscillations (∼20-60 Hz) have been implicated in vision and cognition as a mechanism for synchronizing brain regions. Efforts to study this phenomenon have revealed an additional ‘high-gamma’ range response (∼70-150+ Hz), which is broadband and non-oscillatory. These different gamma range activities are often conflated in support of the same functional role. Using invasive recordings from human visual cortex, we show that narrow and broadband gamma can be dissociated by spectral, temporal and functional response properties. While broadband gamma responses were more transient to the presentation of all stimuli, narrowband gamma responses were sustained and only occurred reliably to grating stimuli. These differences have important implications for the study, analysis and interpretation of neocortical gamma range activity.
Whole exome sequencing and characterization of coding variation in 49,960 individuals in the UK Biobank
Authors: Van Hout Cristopher V. , Tachmazidou Ioanna , Backman Joshua D. , Hoffman Joshua X. , Ye Bin , Pandey Ashutosh K. , Gonzaga-Jauregui Claudia , Khalid Shareef , Liu Daren , Banerjee Nilanjana , Li Alexander H. , Colm O’Dushlaine , Marcketta Anthony , Staples Jeffrey , Schurmann Claudia , Hawes Alicia , Maxwell Evan , Barnard Leland , Lopez Alexander , Penn John , Habegger Lukas , Blumenfeld Andrew L. , Yadav Ashish , Praveen Kavita , Jones Marcus , Salerno William J. , Chung Wendy K. , Surakka Ida , Willer Cristen J. , Hveem Kristian , Leader Joseph B. , Carey David J. , Ledbetter David H. ,   Geisinger-Regeneron DiscovEHR Collaboration, Cardon Lon , Yancopoulos George D. , Economides Aris , Coppola Giovanni , Shuldiner Alan R. , Balasubramanian Suganthi , Cantor Michael , Nelson Matthew R. , Whittaker John , Reid Jeffrey G. , Marchini Jonathan , Overton John D. , Scott Robert A. , Abecasis Gonçalo , Yerges-Armstrong Laura , Baras Aris ,   on behalf of the Regeneron Genetics Center
Published: March 2019

The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world. Here we describe the first tranche of large-scale exome sequence data for 49,960 study participants, revealing approximately 4 million coding variants (of which ~98.4% have frequency < 1%). The data includes 231,631 predicted loss of function variants, a >10-fold increase compared to imputed sequence for the same participants. Nearly all genes (>97%) had ≥1 predicted loss of function carrier, and most genes (>69%) had ≥10 loss of function carriers. We illustrate the power of characterizing loss of function variation in this large population through association analyses across 1,741 phenotypes. In addition to replicating a range of established associations, we discover novel loss of function variants with large effects on disease traits, including PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on blood cell traits. We further demonstrate the value of exome sequencing by surveying the prevalence of pathogenic variants of clinical significance in this population, finding that 2% of the population has a medically actionable variant. Additionally, we leverage the phenotypic data to characterize the relationship between rare BRCA1 and BRCA2 pathogenic variants and cancer risk. Exomes from the first 49,960 participants are now made accessible to the scientific community and highlight the promise offered by genomic sequencing in large-scale population-based studies.
Blue light induces neuronal-activity-regulated gene expression in the absence of optogenetic proteins
Authors: Tyssowski Kelsey M. , Gray Jesse M.
Published: March 2019

Optogenetics is widely used to control diverse cellular functions with light, requiring experimenters to expose cells to bright light. Because extended exposure to visible light can be toxic to cells, it is important to characterize the effects of light stimulation on cellular function in the absence of exogenous optogenetic proteins. Here we exposed cultured mouse cortical neurons that did not express optogenetic proteins to several hours of flashing blue, red, or green light. We found that exposing neurons to as short as one hour of blue, but not red or green, light results in the induction of neuronal-activity-regulated genes without inducing neuronal activity. Our findings suggest blue light stimulation is ill-suited to long-term optogenetic experiments, especially those that measure transcription.

Significance Statement

Optogenetics is widely used to control cellular functions using light. In neuroscience, channelrhodopsins, exogenous light-sensitive channels, are used to achieve light-dependent control of neuronal firing. This optogenetic control of neuronal firing requires exposing neurons to high-powered light. We ask how this light exposure, in the absence of channelrhodopsin, affects the expression of neuronal-activity-regulated genes, i.e., the genes that are transcribed in response to neuronal stimuli. Surprisingly, we find that neurons without channelrhodopsin express neuronal-activity-regulated genes in response to as short as an hour of blue, but not red or green, light exposure. These findings suggest that experimenters wishing to achieve longer-term (an hour or more) optogenetic control over neuronal firing should avoid using systems that require blue light.