bluuebunny/crossref_metadata_2025 huggingface dataset:
Elucidating the molecular interactions between uremic toxins and the Sudlow II binding site of human serum albumin
Authors: Smith Josh , Pfaendtner Jim
Published: February 2020

Protein bound uremic toxins (PBUTs) are known to bind strongly with the primary drug carrying sites of human serum albumin (HSA), Sudlow site I and Sudlow site II. A detailed energetic and structural description of PBUT interactions with these binding sites would provide useful insight into the design of materials that specifically displace and capture PBUTs. In this work, we used molecular dynamics (MD) simulations to study in atomistic detail 4 PBUTs bound in Sudlow site II. Specifically, we used the experimentally resolved X-ray structure of simulated indoxyl sulfate (IS) bound to Sudlow site II (PBD ID: 2BXH) to generate initial binding poses for p-cresyl sulfate (pCS), indole-3-acetic acid (IAA), and hippuric acid (HA). We calculated the interaction energy between toxin and protein in MD simulations and performed mean shift clustering on the collection of molecular structures from MD to identify the primary binding modes of each toxin. We find that all 4 toxins are primarily stabilized by electrostatic interactions between their anionic moiety and the hydrophilic residues in Sudlow site II. We observed transience in the strongest toxin-protein interaction, a charge-pairing with the positively charged R410 residue. We confirm the finding that the primary binding pose of IS in Sudlow site II is stabilized by a hydrogen bond with the carbonyl oxygen of L430, and find that this is also true for IAA. We provide insight into the chemical functional groups that might be incorporated to improve the specificity of synthetic materials for PBUT capture. This work represents a next step toward the de novo design of solutions to the problem of PBUT management in CKD patients.

Significance Statement

In spite of their implication in poor clinical outcomes, surprisingly little information is available about the structure and mechanisms that govern the binding of protein bound uremic toxins to their primary carrier human serum albumin. To date, only the structure of indoxyl sulfate has been determined by experiment. This paper describes a comprehensive characterization of four toxins that are known to bind Sudlow site II using molecular dynamics simulations. Based on the experimental structure of indoxyl sulfate bound to HSA, the binding mode within Sudlow site II of three additional PBUTs was determined. The structures, energetic and mechanistic analysis provide substantial new information for the nephrology community about these toxins as well as new protocols to aid future studies of PBUTs.
Differential gene expression inDrosophila melanogasterandD. nigrosparsainfected with the sameWolbachiastrain
Authors: Detcharoen Matsapume , Schilling Martin P. , Arthofer Wolfgang , Schlick-Steiner Birgit C. , Steiner Florian M.
Published: February 2020

Wolbachia, maternally inherited endosymbionts, infect nearly half of all arthropod species.Wolbachiamanipulate their hosts to maximize their transmission, but they can also provide benefits such as nutrients and resistance to viruses for their hosts. TheWolbachiastrainwMel was recently found to increase locomotor activities and possibly trigger cytoplasmic incompatibility in the flyDrosophila nigrosparsa. Here, we compared differential gene expression inDrosophila melanogaster(original host) andD. nigrosparsa(novel host), both uninfected and infected withwMel, using RNA sequencing to see if the two Drosophila species respond to the infection in the same or different ways. A total of 2164 orthologous genes were used. We found species-specific gene expression patterns. Significant changes shared by the fly species were confined to the expression of genes involved in heme binding and oxidation-reduction; the two host species differently changed the expression of genes when infected. Some of the genes were down-regulated in the infectedD. nigrosparsa, which might indicate small positive effects ofWolbachia. We discuss our findings also in the light of howWolbachiasurvive within both the native and the novel host.
Rare Genetic Variants Underlie Outlying levels of DNA Methylation and Gene-Expression
Authors: Chundru V. Kartik , Marioni Riccardo E. , Pendergast James G. D. , Lin Tian , Beveridge Allan J. , Martin Nicholas G. , Montgomery Grant W. , Hume David A. , Deary Ian J. , Visscher Peter M. , Wray Naomi R. , McRae Allan F.
Published: February 2020

Testing the effect of rare variants on phenotypic variation is difficult due to the need for extremely large cohorts to identify associated variants given expected effect sizes. An alternative approach is to investigate the effect of rare genetic variants on low-level genomic traits, such as gene expression or DNA methylation (DNAm), as effect sizes are expected to be larger for low-level compared to higher-order complex traits. Here, we investigate DNAm in healthy ageing populations - the Lothian Birth cohorts of 1921 and 1936 and identify both transient and stable outlying DNAm levels across the genome. We find an enrichment of rare genetic variants within 1kb of DNAm sites in individuals with stable outlying DNAm, implying genetic control of this extreme variation. Using a family-based cohort, the Brisbane Systems Genetics Study, we observed increased sharing of DNAm outliers among more closely related individuals, consistent with these outliers being driven by rare genetic variation. We demonstrated that outlying DNAm levels have a functional consequence on gene expression levels, with extreme levels of DNAm being associated with gene expression levels towards the tails of the population distribution. Overall, this study demonstrates the role of rare variants in the phenotypic variation of low-level genomic traits, and the effect of extreme levels of DNAm on gene expression.
Activation and self-inactivation mechanisms of the cyclic oligoadenylate-dependent CRISPR ribonuclease Csm6
Authors: Garcia-Doval Carmela , Schwede Frank , Berk Christian , Rostøl Jakob T. , Niewoehner Ole , Tejero Oliver , Hall Jonathan , Marraffini Luciano A. , Jinek Martin
Published: February 2020

Upon target RNA recognition, type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers to activate downstream effectors including Csm6-family ribonucleases via their CARF domains. Here we show thatEnteroccocus italicusCsm6 (EiCsm6) degrades its cognate cyclic hexa-AMP (cA6) activator and report the crystal structure of EiCsm6 bound to a cA6 mimic. The structure, combined with biochemical and in vivo functional assays, reveal how cA6 recognition by the CARF domain activates the Csm6 HEPN domains for collateral RNA degradation, and how CARF domain-mediated cA6 cleavage provides an intrinsic off-switch to limit Csm6 activity in the absence of ring nucleases. These mechanisms facilitate rapid invader clearance and ensure termination of CRISPR interference to limit self-toxicity.
CoolMPS™: Advanced massively parallel sequencing using antibodies specific to each natural nucleobase
Authors: Drmanac Snezana , Callow Matthew , Chen Linsu , Zhou Ping , Eckhardt Leon , Xu Chongjun , Gong Meihua , Gablenz Scott , Rajagopal Jyothi , Yang Qing , Villarosa Christian , Au Anthony , Davis Kyle , Jorjorian Alexander , Wang Jingjing , Chen Ao , Zhang Xian , Borcherding Adam , Wei Xiaofang , Zhang Mingxuan , Xie Yonghui , Barua Nina , Shafto Jay , Dong Yuliang , Zheng Yue , Wang Lin , Zhai Lili , Li Jiguang , Liao Sha , Zhang Wenwei , Liu Jian , Jiang Hui , Wang Jian , Li Handong , Xu Xun , Drmanac Radoje
Published: February 2020

Massively parallel sequencing (MPS) on DNA nanoarrays provides billions of reads at relatively low cost and enables a multitude of genomic applications. Further improvement in read length, sequence quality and cost reduction will enable more affordable and accurate comprehensive health monitoring tests. Currently the most efficient MPS uses dye-labeled reversibly terminated nucleotides (RTs) that are expensive to make and challenging to incorporate. Furthermore, a part of the dye-linker (scar) remains on the nucleobase after cleavage and interferes with subsequent sequencing cycles. We describe here the development of a novel MPS chemistry (CoolMPS™) utilizing unlabeled RTs and four natural nucleobase-specific fluorescently labeled antibodies with fast (30 sec) binding. We implemented CoolMPS™ on MGI’s PCR-free DNBSEQ MPS platform using arrays of 200nm DNA nanoballs (DNBs) generated by rolling circle replication and demonstrate 3-fold improvement in signal intensity and elimination of scar interference. Single-end 100-400 base and pair-end 2×150 base reads with high quality were readily generated with low out-of-phase incorporation. Furthermore, DNBs with less than 50 template copies were successfully sequenced by strong-signal CoolMPS™ with 3-times higher accuracy than in standard MPS. CoolMPS™ chemistry based on natural nucleobases has potential to provide longer, more accurate and less expensive MPS reads, including highly accurate “4-color sequencing” on the most efficient dye-crosstalk-free 2-color imagers with an estimated sequencing error rate of 0.00058% (one error in 170,000 base calls) in a proof-of-concept demonstration.
The brain ofCataglyphisants: neuronal organization and visual projections
Authors: Habenstein Jens , Amini Emad , Grübel Kornelia , el Jundi Basil , Rössler Wolfgang
Published: February 2020

Cataglyphisants are known for their outstanding navigational abilities. They return to their inconspicuous nest after far-reaching foraging trips using path integration, and whenever available, learn and memorize visual features of panoramic sceneries. To achieve this, the ants combine directional visual information from celestial cues and panoramic scenes with distance information from an intrinsic odometer. The largely vision-based navigation inCataglyphisrequires sophisticated neuronal networks to process the broad repertoire of visual stimuli. AlthoughCataglyphisants have been subject to many neuroethological studies, little is known about the general neuronal organization of their central brain and the visual pathways beyond major circuits. Here, we provide a comprehensive, three-dimensional neuronal map of synapse-rich neuropils in the brain ofCataglyphis nodusincluding major connecting fiber systems. In addition, we examined neuronal tracts underlying the processing of visual information in more detail. This study revealed a total of 33 brain neuropils and 30 neuronal fiber tracts including six distinct tracts between the optic lobes and the cerebrum. We also discuss the importance of comparative studies on insect brain architecture for a profound understanding of neuronal networks and their function.
A quantitative biophysical principle to explain the 3D cellular connectivity in curved epithelia
Authors: Gómez-Gálvez Pedro , Vicente-Munuera Pablo , Anbari Samira , Tagua Antonio , Gordillo-Vázquez Carmen , Andrés-San Román Jesús A. , Franco-Barranco Daniel , Palacios Ana M. , Velasco Antonio , Capitán-Agudo Carlos , Grima Clara , Annese Valentina , Arganda-Carreras Ignacio , Robles Rafael , Márquez Alberto , Buceta Javier , Escudero Luis M.
Published: February 2020

Epithelial cell organization and the mechanical stability of tissues are closely related. In this context, it has been recently shown that packing optimization in bended/folded epithelia is achieved by a surface tension energy minimization mechanism that leads to a novel cellular shape: thescutoid. However, further cellular and tissue level implications of this new developmental paradigm remain unknown. Here we focus on the relationship between this complex cellular shape and the connectivity between cells. We address this problem using a combination of computational, experimental, and biophysical approaches in tubular epithelia. In particular, we examine how energy drivers affect the three-dimensional packing of these tissues. We challenge our biophysical model by reducing the cell adhesion in epithelial cells. As a result, we observed an increment on the cell apico-basal intercalation propensity that correlated with a decrease of the energy barrier necessary to connect with new cells. We conclude that tubular epithelia satisfy a quantitative biophysical principle, that links tissue geometry and energetics with the average cellular connectivity.
Pupil dilation is sensitive to semantic ambiguity and acoustic degradation
Authors: Kadem Mason , Herrmann Björn , Rodd Jennifer M. , Johnsrude Ingrid S.
Published: February 2020

Speech comprehension is often challenged by background noise or other acoustic interference. It can also be challenged by linguistic factors, such as complex syntax, or the presence of words with more than one meaning. Pupillometry is increasingly recognized as a technique that provides a window onto acoustic challenges, but this work has not been well integrated with an older literature linking pupil dilation to “mental effort”, which would include linguistic challenges. Here, we measured pupil dilation while listeners heard spoken sentences with clear sentence-level meaning that contained words with more than one meaning (“The shell was fired towards the tank”) or matched sentences without ambiguous words (“Her secrets were written in her diary”). This semantic-ambiguity manipulation was crossed with an acoustic manipulation: two levels of a 30-talker babble masker in Experiment 1; and presence or absence of a pink noise masker in Experiment 2. Speech comprehension, indexed by a semantic relatedness task, was high (above 82% correct) in all conditions. Pupils dilated when sentences included semantically ambiguous words compared to matched sentences and when maskers were present compared to absent (Experiment 2) or were more compared to less intense (Experiment 1). The current results reinforce the idea that many different challenges to speech comprehension, that afford different cognitive processes and are met by the brain in different ways, manifest as an increase in pupil dilation.
BiteOscope: an open platform to study mosquito blood-feeding behavior
Authors: Hol Felix JH , Lambrechts Louis , Prakash Manu
Published: February 2020

Female mosquitoes need a blood meal to reproduce, and in obtaining this essential nutrient they transmit deadly pathogens. Although crucial for the spread of mosquito-borne diseases, our understanding of skin exploration, probing, and engorgement, is limited due to a lack of quantitative tools. Indeed, studies often expose human subjects to assess biting behavior. Here, we present the biteOscope, a device that attracts mosquitoes to a host mimic which they bite to obtain an artificial blood meal. The host mimic is transparent, allowing high-resolution imaging of the feeding mosquito. Using machine learning we extract detailed behavioral statistics describing the locomotion, pose, biting, and feeding dynamics ofAedes aegypti, Aedes albopictus, Anopheles stephensi, andAnopheles coluzzii. In addition to characterizing behavioral patterns, we discover that the common insect repellent DEET repelsAnopheles coluzziiupon contact with their legs. The biteOscope provides a new perspective on mosquito blood feeding, enabling high-throughput quantitative characterization of the effects physiological and environmental factors have on this lethal behavior.
Increasing muscle speed drives changes in the neuromuscular transform of motor commands during postnatal development in songbirds
Authors: Adam Iris , Elemans Coen P.H.
Published: February 2020

Progressive changes in vocal behavior over the course of vocal imitation leaning are often attributed exclusively to developing neural circuits, but the effects of postnatal body changes remain unknown. In songbirds, the syrinx transforms song system motor commands into sound, and exhibits changes during song learning. Here we test the hypothesis that the transformation from motor commands to force trajectories by syringeal muscles functionally changes over vocal development in zebra finches. Our data collected in both sexes show that only in males, muscle speed significantly increases and that supralinear summation occurs and increases with muscle contraction speed. Furthermore, we show that previously reported sub-millisecond spike timing in the avian cortex can be resolved by superfast syringeal muscles and that the sensitivity to spike timing increases with speed. Because motor neuron and muscle properties are tightly linked, we make predictions on the boundaries of the yet unknown motor code that correspond well with cortical activity. Taken together, we show that syringeal muscles undergo essential transformations during song learning that drastically change how neural commands are translated into force profiles and thereby acoustic features. We propose that the song system motor code must compensate for these changes to achieve its acoustic targets. Our data thus supports the hypothesis that the neuromuscular transformation changes over vocal development and emphasizes the need for an embodied view of song motor learning.

Significance statement

Fine motor skill learning typically occurs in a postnatal period when the brain is learning to control a body that is changing dramatically due to growth and development. How the developing body influences motor code formation and vice versa remains largely unknown. Here we show that vocal muscles in songbirds undergo critical transformations during song learning that drastically change how neural commands are translated into force profiles and thereby acoustic features. We propose that the motor code must compensate for these changes to achieve its acoustic targets. Our data thus support the hypothesis that the neuromuscular transformation changes over vocal development and emphasizes the need for an embodied view of song motor learning.
Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs
Authors: Mauri Marco , Gouzé Jean-Luc , de Jong Hidde , Cinquemani Eugenio
Published: February 2020

Synthetic microbial consortia have been increasingly utilized in biotechnology and experimental evidence shows that suitably engineered consortia can outperform individual species in the synthesis of valuable products. Despite significant achievements, though, a quantitative understanding of the conditions that make this possible, and of the trade-offs due to the concurrent growth of multiple species, is still limited. In this work, we contribute to filling this gap by the investigation of a known prototypical synthetic consortium. A firstE. colistrain, producing a heterologous protein, is sided by a secondE. colistrain engineered to scavenge toxic byproducts, thus favoring the growth of the producer at the expense of diverting part of the resources to the growth of the cleaner. The simplicity of the consortium is ideal to perform an in depth-analysis and draw conclusions of more general interest. We develop a coarse-grained mathematical model that quantitatively accounts for literature data from different key growth phenotypes. Based on this, assuming growth in chemostat, we first investigate the conditions enabling stable coexistence of both strains and the effect of the metabolic load due to heterologous protein production. In these conditions, we establish when and to what extent the consortium outperforms the producer alone in terms of productivity. Finally, we show in chemostat as well as in a fed-batch scenario that gain in productivity comes at the price of a reduced yield, reflecting at the level of the consortium resource allocation trade-offs that are well-known for individual species.
Endosomes facilitate mitochondrial clearance by enhancing Parkin recruitment to mitochondria
Authors: Ravindran Rishith , Velikkakath Anoop Kumar G. , Narendradev Nikhil Dev , Chandrasekharan Aneesh , Santhoshkumar T. R. , Srinivasula Srinivasa M.
Published: February 2020

Mutations in ubiquitin ligase Parkin are associated with Parkinson’s disease and defective mitophagy. Conceptually, Parkin-dependent mitophagy is classified into two phases; 1. Parkin recruits to and ubiquitinates mitochondrial proteins, 2. Formation of autophagosome membrane, sequestering mitochondria for degradation. Recently, endosomal machineries were reported to contribute to the later stage for membrane assembly. We report a role for endosomes in the events upstream of phase 1. We demonstrate that an endosomal ubiquitin ligase CARP2 associates with damaged mitochondria, and this association precedes that of Parkin. CARP2 interacts with Parkin, and stable recruitment of Parkin to damaged mitochondria was substantially reduced in CARP2 KO cells. Our study unravels a novel role of endosomes in modulating upstream pathways of Parkin-dependent mitophagy initiation.
Analysis of structure of the population, kinship coefficients and inbreeding trend depending on sex, type of breeding of Tatra Sheepherd dogs
Authors: Edyta Sweklej , Elżbieta Horoszewicz , Roman Niedziółka
Published: February 2020

The aim of the study was to analyse the structure of the population, kinship coefficients and inbreeding trend taking into account the sex, breeding system: champions (CH) and non-champions (nCH), breeding country: Poland (PL) and foreign country (Z) and the inbreeding degree of Tatra Shepherd dogs. Out of the currently registered 587 Tatra Shepherd dogs, 41.9% have been qualified for breeding. In the past decade, 1961 puppies were born, which corresponds to an average litter of 5.8 puppies. The breed’s inbreeding rate amounted to 6.34%, and for a 4-generation population was 6.68%. The highest inbreeding rate was found in nCH and PL groups consisting of both male and female dogs. The inbreeding rate was significantly higher in 2005-2014 compared to the years 1994-2004. The limit value FXwas exceeded for 25.65% of Shepherd dogs, and the critical value was exceeded for 11.52%. An increasing ancestor loss coefficient (AVK) was found, which may result in an increased number of inbred animals. In particular, it referred to female dogs in the nCH, PL, and F group, whereas a significant increase of AVK was observed in the group of male dogs from foreign kennels. The resulting COR values, respectively 55.58% for males and 55.44% for females, testify to insignificant inbreeding and suggest that breeders look for male inbreds. Studies have shown that there is no risk of inbred depression yet; however, the gene pool of the Tatra Shepherd dog breed has become noticeably restricted. In addition, leaving the stud book for the breed open must be considered due to an increase in the popularity of the breed, and thus an increase in mating.
Temporal and spatial dynamics in the apple flower microbiome in the presence of the phytopathogenErwinia amylovora
Authors: Cui Zhouqi , Huntley Regan B. , Zeng Quan , Steven Blaire
Published: February 2020

Plant microbiomes have important roles in plant health and productivity. However, despite flowers being directly linked to reproductive outcomes, little is known about the microbiomes of flowers and their potential interaction with pathogen infection. Here, we investigated the temporal dynamics and spatial traits of the apple stigma microbiome when challenged with a phytopathogenErwinia amylovora, the causal agent of fire blight disease. We profiled the microbiome from the stigmas of a single flower, greatly increasing the resolution at which we can characterize shifts in the composition of the microbiome. Individual flowers harbored unique microbiomes at the OTU level. However, taxonomic analysis of community succession showed a population gradually dominated by bacteria within the familiesEnterobacteriaceaeandPseudomonadaceae. Flowers inoculatedE. amylovoraestablished large populations of the phytopathogen, with pathogen specific gene counts of >3.0 × 107in 90% of the flowers. Yet, only 42% of inoculated flowers later developed fire blight symptoms. This reveals pathogen amount on the stigma is not sufficient to predict disease outcome. Our data demonstrate that apple flowers represent an excellent model in which to characterize how plant microbiomes establish, develop, and interact with biological processes such as disease progression in an experimentally tractable plant organ.
The Sigma-2 Receptor/TMEM97, PGRMC1, and LDL Receptor complex are responsible for the cellular uptake of Aβ42 and its protein aggregates
Authors: Riad Aladdin , Lengyel-Zhand Zsofia , Zeng Chenbo , Weng Chi-Chang , Lee Virginia M.-Y. , Trojanowski John Q. , Mach Robert H.
Published: February 2020

Background

Our lab has recently shown that the Sigma-2 Receptor/Transmembrane Protein 97 (TMEM97) and Progesterone Receptor Membrane Component 1 (PGRMC1) form a complex with the Low Density Lipoprotein Receptor (LDLR), and this intact complex is required for efficient uptake of lipoproteins such as LDL and apolipoprotein E (apoE). These receptors are expressed in the nervous system where they have implications in neurodegenerative diseases such as Alzheimer’s Disease (AD), where apoE is involved in neuronal uptake and accumulation of Aβ42, eventually cascading into neurodegeneration, synaptic dysfunction, and ultimately, dementia.

Hypothesis

We hypothesize that the intact Sigma-2 receptor complex –TMEM97, PGRMC1, and LDLR— is necessary for internalization of apoE and Aβ42 monomers (mAβ42) and oligomers (oAβ42), and the disruption of the receptor complex inhibits uptake.

Results

The results of this study suggest that the intact Sigma-2 receptor complex is a binding site for mAβ42 and oAβ42, in the presence or absence of apoE2, apoE3, and apoE4. The loss or pharmacological inhibition of one or both of these proteins results in the disruption of the complex leading to decreased uptake of mAβ42 and oAβ42 and apoE in primary neurons.

Conclusion

The TMEM97, PGRMC1, and LDLR complex is a pathway for the cellular uptake of Aβ42 via apoE dependent and independent mechanisms. This study suggests that the complex may potentially be a novel pharmacological target to decrease neuronal Aβ42 internalization and accumulation, which may represent a new strategy for inhibiting the rate of neurotoxicity, neurodegeneration, and progression of AD.
Redundant function of Ets1 and Ets2 in regulating M-phase progression in post-natal angiogenesis
Authors: Ghosh Sankha , MarElia-Bennett Catherine B. , Hildreth Blake E. , Lefler Julia E. , Sharma Sudarshana M. , Ostrowski Michael C.
Published: February 2020

Angiogenesis is a highly orchestrated process involving complex crosstalk between several endothelial cell processes including cell cycle, cell survival and migration. Transcription factors ETS1 and ETS2 are required for EC functions necessary for embryonic angiogenesis. Here, by utilizing endothelial cell-specific deletion ofEts1andEts2on post-natal angiogenesis we demonstrate that ETS1 and ETS2 have a redundant regulatory role in controlling the expression of key G2/M regulators and anti-apoptotic gene modules by recruiting the transcriptional activator CBP/p300 to the enhancers of these genes. Further, cultured aortic ECs lacking both ETS1 and ETS2 demonstrated G2/M phase arrest and increased apoptosis.In vivo, EC infiltration and invasion was attenuated when matrigel admixed with mouse mammary tumor cells was injected into adult mice with EC-specific ablation ofEts1andEts2. These results demonstrate that deletion ofEts1andEts2in endothelial cells inhibits angiogenesis by altering cell cycle progression and decreasing cell survival.
The MSP-RON axis stimulates cancer cell growth in models of triple negative breast cancer
Authors: Millar Rhona , Kilbey Anna , Remak Sarah-Jane , Severson Tesa M. , Dhayade Sandeep , Sandilands Emma , Foster Kyla , Bryant David M. , Blyth Karen , Coffelt Seth B.
Published: February 2020

Triple negative breast cancer is the most aggressive subtype of breast cancer with poor prognosis and high rates of relapse. The lack of actionable targets for TNBC has contributed to the high mortality rates of this disease, and new candidate molecules for potential manipulation are urgently required. Here, we show that macrophage-stimulating protein (MSP) and its tyrosine kinase receptor, RON, are potent drivers of cancer cell growth and tumor progression in a mouse model of TNBC driven by the loss ofTrp53andBrca1. After comparison of two genetically engineered mouse models of TNBC, we found that mammary tumors fromK14-Cre;Brca1F/F;Trp53F/F(KB1P) mice exhibit high endogenous levels of MSP and RON expression. We show that MSP stimulates AKT and ERK1/2 activation as well as cancer cell growth in KB1P cell lines, while genetic and pharmacological inhibition of RON prevents these effects. Similarly, KB1P tumor progression in mice was robustly attenuated by treatment with a RON inhibitor with accompanied reduction in the proliferation marker, Ki-67. Our findings in a mouse model where MSP and RON expression are naturally increased provide evidence that this receptor and its ligand are viable candidate molecules for targeted treatment of TNBC.
Cold priming memory reduces plant pathogen susceptibility based on a functional plastid peroxidase system
Authors: Griebel Thomas , Ebert Alina , Nguyen Hoang Hung , Baier Margarete
Published: February 2020

Chloroplasts, as recently shown, serve as cold priming hubs in modulating the transcriptional response ofArabidopsis thalianato a second cold stimulus after a stress-free interphase of several days. Here, we studied if such a single 24 h cold stress at 4 °C also alters the susceptibility of Arabidopsis to virulentPseudomonas syringaepv.tomatoDC3000. Our data show that cold priming did not only increase resistance of Arabidopsis to a subsequent infection immediately, but also after a memory phase of 5 days, during which thylakoid ascorbate peroxidases accumulate. Contrasting to susceptibility, the prior cold exposure did not alter resistance against avirulent and effector-triggered immunity-inducingPseudomonas syringaestrains. The effect of cold priming on the plant pathogen susceptibility was independent of the central nucleo-cytoplasmic immune regulator EDS1 (Enhanced Disease Susceptibility 1) and uncoupled from classical immune gene activation. The priming benefits against pathogens required thylakoid and stromal ascorbate peroxidase activity. Combinatorial priming of Arabidopsis pathogen susceptibility by metastable regulation of stromal ascorbate peroxidase activity and post-cold expression of thylakoid ascorbate peroxidase guarantees immediate protection without latency time and prolonged protection by the memory element that regulates future cold responses.

One-sentence summary

24 hour cold exposure reduces plant susceptibility against virulent pathogens dependent on chloroplast ascorbate peroxidases.
Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein
Authors: Walls Alexandra C. , Park Young-Jun , Tortorici M. Alexandra , Wall Abigail , McGuire Andrew T. , Veesler David
Published: February 2020

The recent emergence of a novel coronavirus associated with an ongoing outbreak of pneumonia (Covid-2019) resulted in infections of more than 72,000 people and claimed over 1,800 lives. Coronavirus spike (S) glycoprotein trimers promote entry into cells and are the main target of the humoral immune response. We show here that SARS-CoV-2 S mediates entry in VeroE6 cells and in BHK cells transiently transfected with human ACE2, establishing ACE2 as a functional receptor for this novel coronavirus. We further demonstrate that the receptor-binding domains of SARS-CoV-2 S and SARS-CoV S bind with similar affinities to human ACE2, which correlates with the efficient spread of SARS-CoV-2 among humans. We found that the SARS-CoV-2 S glycoprotein harbors a furin cleavage site at the boundary between the S1/S2 subunits, which is processed during biogenesis and sets this virus apart from SARS-CoV and other SARS-related CoVs. We determined a cryo-electron microscopy structure of the SARS-CoV-2 S ectodomain trimer, demonstrating spontaneous opening of the receptor-binding domain, and providing a blueprint for the design of vaccines and inhibitors of viral entry. Finally, we demonstrate that SARS-CoV S murine polyclonal sera potently inhibited SARS-CoV-2 S-mediated entry into target cells, thereby indicating that cross-neutralizing antibodies targeting conserved S epitopes can be elicited upon vaccination.
Chronic stress exacerbates acute stress-induced neuronal activation in the anterior cingulate cortex and ventral hippocampus that correlates with behavioral deficits in mice
Authors: Fee Corey , Prevot Thomas , Misquitta Keith , Banasr Mounira , Sibille Etienne
Published: February 2020

Altered activity of corticolimbic brain regions is a hallmark of stress-related illnesses, including mood disorders, neurodegenerative diseases, and substance abuse disorders. Acute stress adaptively recruits brain region-specific functions for coping, while sustained activation under chronic stress may overwhelm feedback mechanisms and lead to pathological cellular and behavioral responses. The neural mechanisms underlying dysregulated stress response and how they contribute to behavioral deficits are poorly characterized. Here, we tested whether prior exposure to chronic restraint stress (CRS) or unpredictable chronic mild stress (UCMS) in mice could alter neuronal response to acute stress and whether these changes are associated with chronic stress-induced behavioral deficits. More specifically, we assessed neuronal activation indexed by c-Fos+ cell counts in 24 stress- and mood-related brain regions, and determined if changes in acute stress-induced neuronal activation were linked to chronic stress-induced behavioral impairments. Results indicated that CRS and UCMS led to convergent physiological and anxiety-like deficits, whereas cognition was impaired only in UCMS mice. CRS and UCMS exposure exacerbated neuronal activation in response to an acute stressor in anterior cingulate cortex (ACC) area 24b and ventral hippocampal (vHPC) CA1, CA3, and subiculum. In dysregulated brain regions, levels of neuronal activation were positively correlated with principal components capturing variance across widespread behavioral alterations relevant to stress-related disorders. Our data supports an association between a dysregulated stress response, altered corticolimbic excitation/inhibition balance, and the expression of maladaptive behaviors.

Highlights

Chronic stress models produce variable profiles of physiological deficits, anxiety-like behavior, and impaired cognition

Acute stress-induced activation of ACC A24b & vHPC is exacerbated by prior chronic stress exposure

In regions dysregulated by chronic stress, altered neuronal activation is positively correlated with behavioral deficits
A method for predicting evolved fold switchers exclusively from their sequences
Authors: Kim Allen K. , Looger Loren L. , Porter Lauren L.
Published: February 2020

Although most proteins with known structures conform to the longstanding rule-of-thumb that high levels of aligned sequence identity tend to indicate similar folds and functions, an increasing number of exceptions is emerging. In spite of having highly similar sequences, these “evolved fold switchers” (1) can adopt radically different folds with disparate biological functions. Predictive methods for identifying evolved fold switchers are desirable because some of them are associated with disease and/or can perform different functions in cells. Previously, we showed that inconsistencies between predicted and experimentally determined secondary structures can be used to predict fold switching proteins (2). The usefulness of this approach is limited, however, because it requires experimentally determined protein structures, whose magnitude is dwarfed by the number of genomic proteins. Here, we use secondary structure predictions to identify evolved fold switchers from their amino acid sequences alone. To do this, we looked for inconsistencies between the secondary structure predictions of the alternative conformations of evolved fold switchers. We used three different predictors in this study: JPred4, PSIPRED, and SPIDER3. We find that overall inconsistencies are not a significant predictor of evolved fold switchers for any of the three predictors. Inconsistencies between α-helix and β-strand predictions made by JPred4, however, can discriminate between the different conformations of evolved fold switchers with statistical significance (p < 1.7*10−13). In light of this observation, we used these inconsistencies as a classifier and found that it could robustly discriminate between evolved fold switchers and evolved non-fold-switchers, as evidenced by a Matthews correlation coefficient of 0.90. These results indicate that inconsistencies between secondary structure predictions can indeed be used to identify evolved fold switchers from their genomic sequences alone. Our findings have implications for genomics, structural biology, and human health.
Social isolation modulates appetite and defensive behavior via a common oxytocinergic circuit in larval zebrafish
Authors: Wee Caroline L. , Song Erin , Nikitchenko Maxim , Herrera Kristian J. , Wong Sandy , Engert Florian , Kunes Sam
Published: February 2020

Animal brains have evolved to encode social stimuli and transform these representations into advantageous behavioral responses. The commonalities and differences of these representations across species are not well-understood. Here, we show that social isolation activates an oxytocinergic (OXT), nociceptive circuit in the larval zebrafish hypothalamus and that chemical cues released from conspecific animals are potent modulators of this circuit’s activity. We delineate an olfactory to subpallial pathway that transmits chemical social cues to OXT circuitry, where they are transformed into diverse outputs simultaneously regulating defensive and feeding behaviors. Our data allow us to propose a model through which social stimuli are integrated within a fundamental neural circuit to mediate diverse adaptive behaviours.
Respiratory and Gut Microbiota in Commercial Turkey Flocks with Disparate Weight Gain Trajectories Display Differential Compositional Dynamics
Authors: Taylor Kara J.M. , Ngunjiri John M. , Abundo Michael C. , Jang Hyesun , Elaish Mohamed , Ghorbani Amir , KC Mahesh , Weber Bonnie P. , Johnson Timothy J. , Lee Chang-Won
Published: February 2020

Host-associated communities of bacteria (microbiota) substantially contribute to the overall poultry health and performance. Gut microbiota are known to play roles in resistance to pathogen infection and optimal weight gain in turkey flocks. However, knowledge of turkey respiratory microbiota and its link to gut microbiota is lacking. This study presents a 16S rRNA gene-based census of the turkey respiratory microbiota (nasal cavity and trachea) alongside gut microbiota (cecum and ileum) in two identical commercial Hybrid Converter turkey flocks raised in parallel under typical field commercial conditions. The flocks were housed in adjacent barns during the brood stage and in geographically separated farms during the grow-out stage. Several bacterial taxa that were acquired in the respiratory tract (RT) at the beginning of the brood stage persisted throughout the flock cycle, primarilyStaphylococcus. Late-emerging predominant taxa in RT includedDeinococcusandCorynebacterium. Tracheal and nasal microbiota of turkeys were identifiably distinct from one another and from gut microbiota. Nevertheless, gut and RT microbiota changed in parallel over time and appeared to share many taxa. During the brood stage, the two flocks generally acquired similar gut and RT microbiota, and their average body weights were comparable. Separating the flocks during the grow-out stage resulted in divergent microbial profiles and body weight gain trajectories. Lower weight gain corresponded with emergence ofDeinococcusandOrnithobacteriumin RT, andFusobacteriumandParasutterellain gut. This study provides an overview of turkey microbiota under field conditions and suggests several hypotheses concerning the respiratory microbiome.

IMPORTANCE

Turkey meat is an important source of animal protein, and the industry around its production contributes significantly to the agricultural economy. The nonpathogenic symbionts present in the gut of turkeys are known to impact bird health and flock performance. However, the respiratory microbiota in turkeys are entirely unexplored. This study has elucidated the microbiota of respiratory tracts of turkeys from two commercial flocks raised in parallel throughout a normal flock cycle. Further, the study suggests that bacteria originating in the gut or in poultry house environments may influence respiratory communities and consequently induce poor performance, either directly or indirectly. Future attempts to develop microbiome-based interventions for turkey health should delimit the contributions of respiratory microbiota and aim to limit disturbances to those communities.
Heimdallarchaeota harness light energy through photosynthesis
Authors: Liu Rui , Cai Ruining , Zhang Jing , Sun Chaomin
Published: February 2020

Photosynthesis is an ancient process that originated after the origin of life, and has only been found in the Bacterial and Eukaryotic kingdoms, but has never been reported in any member of the domain Archaea. Heimdallarchaeota, a member of Asgard archaea, are supposed as the most probable candidates (to date) for the archaeal protoeukaryote ancestor and might exist in light-exposed habitats during their evolutionary history. Here we describe the discovery that Heimdallarchaeota genomes are enriched for proteins formerly considered specific to photosynthetic apparatus and are suggestive performing oxygenic photosynthesis. Our results provide strong support for hypotheses in which Heimdallarchaeota harvest light by bacteriochlorophyll and/or carotenoid, then transport electron from photosystems to Calvin-Benson-Bassham cycle along with CO2fixation and ATP biosynthesis, and release oxygen as a waste product. Given the possessing of phototrophic lifestyle together with other anaerobic and aerobic metabolic pathways, Heimdallarchaeota are firmly believed to be photomixotrophic and have a facultative aerobic metabolism. Our results expand our knowledge that archaea have played an important role in the molecular evolution of eukaryotic photosynthesis and raise the significant possibility that Heimdallarchaeota might be ancestor of eukaryotic photosynthetic organisms.
Estrogen-related receptors are targetable ROS sensors
Authors: Vernier Mathieu , Dufour Catherine R. , McGuirk Shawn , Scholtes Charlotte , Li Xiaojing , Bourmeau Guillaume , Kuasne Hellen , Park Morag , St-Pierre Julie , Audet-Walsh Etienne , Giguère Vincent
Published: February 2020

Excessive reactive oxygen species (ROS) can cause oxidative stress and consequently cell injury contributing to a wide range of diseases. Addressing the critical gaps in our understanding of the adaptive molecular events downstream ROS provocation holds promise for the identification of druggable metabolic vulnerabilities. Here, we unveil a direct molecular link between the activity of two estrogen-related receptor (ERR) isoforms and the control of glutamine utilization and glutathione antioxidant production. ERRα down-regulation restricts glutamine entry into the TCA cycle, while ERRγ up-regulation promotes glutamine-driven glutathione production. Notably, we identify increased ERRγ expression/activation as a hallmark of oxidative stress triggered by mitochondrial disruption or chemotherapy. Enhanced tumor antioxidant capacity is an underlying feature of human breast cancer (BCa) patients that respond poorly to treatment. We demonstrate that pharmacological inhibition of ERRγ with the selective inverse agonist GSK5182 increases antitumor efficacy of the chemotherapeutic paclitaxel on poor outcome BCa tumor organoids. Our findings thus underscore the ERRs as novel redox sensors and effectors of a ROS defense program and highlight the potential therapeutic advantage of exploiting ERRγ inhibitors for the treatment of BCa and other diseases where oxidative stress plays a central role.
MDM2 and MDMX promote ferroptosis by PPARα-mediated lipid remodeling
Authors: Venkatesh Divya , O'Brien Nicholas A. , Zandkarimi Fereshteh , Tong David R. , Stokes Michael E. , Dunn Denise E. , Kengmana Everett S. , Aron Allegra T. , Klein Alyssa M. , Csuka Joleen M. , Moon Sung-Hwan , Conrad Marcus , Chang Christopher J. , Lo Donald C. , D'Alessandro Angelo , Prives Carol , Stockwell Brent R.
Published: February 2020

MDM2 and MDMX, negative regulators of the tumor suppressor p53, can work separately and as a heteromeric complex to restrain p53's functions. MDM2 also has pro-oncogenic roles in cells, tissues, and animals that are independent of p53. There is less information available about p53-independent roles of MDMX or the MDM2–MDMX complex. We found that MDM2 and MDMX facilitate ferroptosis in cells with or without p53. Using small molecules, RNA interference reagents, and mutant forms of MDMX, we found that MDM2 and MDMX, likely working in part as a complex, normally facilitate ferroptotic death. We observed that MDM2 and MDMX alter the lipid profile of cells to favor ferroptosis. Inhibition of MDM2 or MDMX leads to increased levels of FSP1 protein and a consequent increase in the levels of coenzyme Q10, an endogenous lipophilic antioxidant. This suggests that MDM2 and MDMX normally prevent cells from mounting an adequate defense against lipid peroxidation and thereby promote ferroptosis. Moreover, we found that PPARα activity is essential for MDM2 and MDMX to promote ferroptosis, suggesting that the MDM2–MDMX complex regulates lipids through altering PPARα activity. These findings reveal the complexity of cellular responses to MDM2 and MDMX and suggest that MDM2–MDMX inhibition might be useful for preventing degenerative diseases involving ferroptosis. Furthermore, they suggest that MDM2/MDMX amplification may predict sensitivity of some cancers to ferroptosis inducers.
Recounting the FANTOM CAGE-Associated Transcriptome
Authors: Imada Eddie Luidy , Sanchez Diego Fernando , Collado-Torres Leonardo , Wilks Christopher , Matam Tejasvi , Dinalankara Wikum , Stupnikov Aleksey , Lobo-Pereira Francisco , Yip Chi-Wai , Yasuzawa Kayoko , Kondo Naoto , Itoh Masayoshi , Suzuki Harukazu , Kasukawa Takeya , Hon Chung-Chau , de Hoon Michiel J.L. , Shin Jay W. , Carninci Piero , Jaffe Andrew E. , Leek Jeffrey T. , Favorov Alexander , Franco Gloria R. , Langmead Ben , Marchionni Luigi
Published: February 2020

Long noncoding RNAs (lncRNAs) have emerged as key coordinators of biological and cellular processes. Characterizing lncRNA expression across cells and tissues is key to understanding their role in determining phenotypes, including human diseases. We present here FC-R2, a comprehensive expression atlas across a broadly defined human transcriptome, inclusive of over 109,000 coding and noncoding genes, as described in the FANTOM CAGE-Associated Transcriptome (FANTOM-CAT) study. This atlas greatly extends the gene annotation used in the originalrecount2resource. We demonstrate the utility of the FC-R2 atlas by reproducing key findings from published large studies and by generating new results across normal and diseased human samples. In particular, we (a) identify tissue-specific transcription profiles for distinct classes of coding and noncoding genes, (b) perform differential expression analysis across thirteen cancer types, identifying novel noncoding genes potentially involved in tumor pathogenesis and progression, and (c) confirm the prognostic value for several enhancer lncRNAs expression in cancer. Our resource is instrumental for the systematic molecular characterization of lncRNA by the FANTOM6 Consortium. In conclusion, comprised of over 70,000 samples, the FC-R2 atlas will empower other researchers to investigate functions and biological roles of both known coding genes and novel lncRNAs.