bluuebunny/crossref_metadata_2025 huggingface dataset:
The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis inCaulobacter
Authors: Woldemeskel Selamawit Abi , Alvarez Laura , Daitch Allison K. , Zeinert Rilee , Bhargava Anant , Gonzalez Diego , Collier Justine , Chien Peter , Cava Felipe , Goley Erin D.
Published: February 2019

Bacterial growth and division require regulated synthesis of the macromolecules used to expand and replicate components of the cell. Transcription of housekeeping genes required for metabolic homeostasis and cell proliferation is guided by the sigma factor σ70. The conserved CarD-like transcriptional regulator, CdnL, associates with promoter regions where σ70localizes and stabilizes the open promoter complex. However, the contributions of CdnL to metabolic homeostasis and bacterial physiology are not well understood. Here, we show thatCaulobacter crescentuscells lacking CdnL have severe morphological and growth defects. Specifically,ΔcdnLcells grow slowly in both rich and defined media, and are wider, more curved, and have shorter stalks than WT cells. These defects arise from transcriptional downregulation of most major classes of biosynthetic genes. Notably, we find thatΔcdnLcells are severely limited in glutamate synthesis, rendering them auxotrophic for that amino acid. Moreover,ΔcdnLcells produce low amounts of the cell wall precursor lipid II, andΔcdnLis synthetic lethal with other genetic perturbations that limit lipid II production.ΔcdnLcells also have aberrant localization of MreB and CtpS, cytoskeletal proteins required for maintaining proper cell width and curvature. Interestingly, the localization of CtpS is dependent on availability of CTP, which is predicted to be low inΔcdnLcells. Our findings implicate CdnL as a global regulator of genes required for metabolic homeostasis that impacts morphogenesis through availability of lipid II and through metabolite-mediated changes in localization of cytoskeletal regulators of cell shape.
Latent Space Phenotyping: Automatic Image-Based Phenotyping for Treatment Studies
Authors: Ubbens Jordan , Cieslak Mikolaj , Prusinkiewicz Przemyslaw , Stavness Ian
Published: February 2019

Association mapping studies have enabled researchers to identify candidate loci for many important environmental resistance factors, including agronomically relevant resistance traits in plants. However, traditional genome-by-environment studies such as these require a phenotyping pipeline which is capable of accurately and consistently measuring stress responses, typically in an automated high-throughput context using image processing. In this work, we present Latent Space Phenotyping (LSP), a novel phenotyping method which is able to automatically detect and quantify response to treatment directly from images. Using two synthetically generated image datasets, we first show that LSP is able to successfully recover the simulated QTL in both simple and complex synthetic imagery. We then demonstrate an example application of an interspecific cross of the model C4grassSetaria. We propose LSP as an alternative to traditional image analysis methods for phenotyping, enabling association mapping studies without the need for engineering complex image processing pipelines.
Glutarate metabolism in Pseudomonas putida is regulated by two distinct glutarate sensing transcription factors
Authors: Thompson Mitchell G. , Cruz-Morales Pablo , Krishna Rohith N. , Blake-Hedges Jacquelyn M. , Incha Matthew R. , Keasling Jay D.
Published: February 2019

Transcription factor based biosensors can be leveraged to screen thousands of genetics designs for optimal production in engineered microbes. In this study we characterize two glutarate sensing transcription factors (CsiR and GcdR) from Pseudomonas putida. The genomic contexts of CsiR homologs were analyzed and DNA binding sites were bioinformatically predicted. Both CsiR and GcdR were purified and shown to bind upstream of their coding sequencing in vitro. CsiR was shown to dissociate from DNA in vitro when exogenous glutarate was added confirming it acts as a genetic repressor. Both transcription factors were then engineered into plasmid based biosensors and their respective sensing performance features calculated. Both sensor plasmids were then reintroduced into P. putida and were evaluated for their ability to sense flux through glutarate when grown on various lysine metabolites as sole carbon sources. These findings provide information describing glutarate flux in P. putida, and potentially useful tools for future metabolic engineering and synthetic biology efforts.
Pathogen-encoded evasion of CXCL10 and T cell responses
Authors: Antonia Alejandro L. , Alvarez Monica I. , Trahair Esme , Gibbs Kyle D. , Pittman Kelly J. , Barnes Alyson B. , Smith Jeffrey S. , Rajagopal Sudarshan , Thompson J. Will , Reinhardt R. Lee , Ko Dennis C.
Published: February 2019

Clearance of intracellular pathogens, such asLeishmania (L.) major, depends on a well-regulated adaptive T cell response. Here we describe a pathogen-encoded mechanism to alter T cell recruitment by suppressing CXCL10, a chemokine that recruits CD4+ and CD8+ T cells by signaling through the CXCR3 receptor.L. majorsuppresses CXCL10 through the virulence factor and protease, glycoprotein-63(gp63).GP63 cleaves CXCL10 after amino acid A81, impairing T-cell chemotaxisin vitro.GP63 from either extracellular promastigotes or intracellular amastigotes is capable of cleaving CXCL10. Consistent with CXCL10 cleavage during infection, we observed GP63-mediated impairment of activated CD8+ T-cells in the draining lymph nodes of C57BL/6JWTmice. Correspondingly, in C57BL/6JWTmice,gp63deletion resulted in slower lesion development and a smaller maximum lesion size. However, infection in C57BL/6Jcxcr3−/−mice revealed the delay to lesion development required CXCR3 signaling. Finally,Salmonella entericaandChlamydia trachomatisinfection also suppress CXCL10, demonstrating convergent evolution of this immune evasion strategy in diverse intracellular pathogens. Understanding mechanisms of CXCL10 evasion may facilitate the development of novel therapeutic strategies to treat intracellular pathogens.

Author Summary

Leishmaniasis is an infectious disease that affects over one million people annually. It is caused by intracellular parasites that have evolved to evade the host’s attempts to eliminate the parasite. The most common form of disease, cutaneous leishmaniasis, causes disfiguring skin lesions if the host immune system does not appropriately respond to the infection. A family of molecules called chemokines are critical for the recruitment of specific subsets of immune cells required to eliminate infection. Here, we demonstrate a novel mechanism that the parasiteLeishmania (L.) majoremploys to disrupt the immune response by interfering with chemokine signaling. By this strategy,L. majoruses a protease to cleave chemokines known to recruit T-cells required for fighting off infection. We show thatL. majorcleavage of these immune signals changes the recruitment of CD8+ T-cells and alters disease progression in mice. Finally, we observe that multiple common human intracellular pathogens, includingChlamydia trachomatisandSalmonella enterica, interfere with the same chemokines, suggesting a strong selective pressure to avoid this component of the immune response. Our study provides new insights into how intracellular pathogens interact with the host immune response to enhance pathogen survival and exacerbate disease outcomes.
ANME-2d anaerobic methanotrophic archaea differ from other ANME archaea in lipid composition and carbon source
Authors: Kurth Julia M. , Smit Nadine T. , Berger Stefanie , Schouten Stefan , Jetten Mike S.M. , Welte Cornelia U.
Published: February 2019

The anaerobic oxidation of methane (AOM) is a microbial process present in marine and freshwater environments. AOM is important for reducing the emission of the second most important greenhouse gas methane. In marine environments anaerobic methanotrophic archaea (ANME) are involved in sulfate-reducing AOM. In contrast,Ca. Methanoperedens of the ANME-2d cluster carries out nitrate AOM in freshwater ecosystems. Despite the importance of those organisms for AOM in non-marine environments not much is known about their lipid composition or carbon sources. To close this gap, we analyzed the lipid composition of ANME-2d archaea and found that they mainly synthesize archaeol and hydroxyarchaeol as well as different (hydroxy-) glycerol dialkyl glycerol tetraethers, albeit in much lower amounts. Abundant lipid headgroups were dihexose, monomethyl-phosphatidyl ethanolamine and phosphatidyl hexose. Moreover, a monopentose was detected as a lipid headgroup which is rare among microorganisms. Batch incubations with13C labelled bicarbonate and methane showed that methane is the main carbon source of ANME-2d archaea varying from ANME-1 archaea which primarily assimilate dissolved inorganic carbon (DIC). ANME-2d archaea also assimilate DIC, but to a lower extent than methane. The lipid characterization and analysis of the carbon source ofCa.Methanoperedens facilitates distinction between ANME-2d and other ANMEs.
Facets of diazotrophy in the OMZ off Peru revisited- what we couldn’t see from a single marker gene approach
Authors: Christiansen Christian Furbo , Löscher Carolin Regina
Published: February 2019

Biological dinitrogen (N2) fixation is the pathway making the large pool of atmospheric N2available to marine life. Besides direct rate measurements, a common approach to explore the potential for N2fixation in the ocean is a mining based on molecular genetic methods targeting the key functional genenifH, coding for a subunit of the nitrogenase reductase. As novel sequencing and single cell techniques improved, our knowledge on the diversity of marine N2fixers grew exponentially. However, to date one aspect of N2fixation in the ocean is commonly left aside. This is the existence of two alternative types of nitrogenases, which are besides the Mo-Fe nitrogenaseNif, the Fe-Fe nitrogenaseAnf, and the V-Fe nitrogenaseVnf, which differ with regard to their metal co-enzymes, as well as regarding their operon structure and composition.nifH-based studies may thus be biased, and alternative nitrogenases could not be recovered. Here, we screened a set of 6 metagenomes and -transcriptomes from a sulfidic water patch from the oxygen minimum zone off Peru for genes involved in N2fixation. We identified genes related to all three nitrogenases, and generally increased diversity as compared to our previousnifH-based study from the same waters. While we could not confirm gene expression of the alternative nitrogenases from our transcriptomes, we detected additional diazotrophs involved in N2fixation. We suggest that alternative nitrogenases may not be used under conditions present in those waters, however, depending on trace metal limitation in the future they may become active.

Significance statement

This study addresses the important process of N2fixation, based on a whole-metagenome and –transcriptome screening, reports an increased diversity of N2fixing microbes in the sulfidic shelf water off Peru, as compared to previous target-gene based studies from the same waters. In addition to a generally higher diversity, genes encoding for alternative nitrogenases, which were previously not subject of any study on N2fixation in oxygen minimum zones, were detected. The ecological meaning and evolutionary history of those alternative nitrogenases is subject of ongoing debates, however, their presence in OMZ waters would allow for N2fixation at extreme anoxia, which may become important in a future ocean challenged by progressive deoxygenation.
Cancer-Associated Fibroblasts Promote Prostate Cancer Malignancy via Metabolic Rewiring and Mitochondrial Transfer
Authors: Ippolito Luigi , Morandi Andrea , Taddei Maria Letizia , Parri Matteo , Comito Giuseppina , Iscaro Alessandra , Raspollini Maria Rosaria , Magherini Francesca , Rapizzi Elena , Masquelier Julien , Muccioli Giulio G. , Sonveaux Pierre , Chiarugi Paola , Giannoni Elisa
Published: February 2019

Cancer-associated fibroblasts (CAFs) are the major cellular stromal component of many solid tumors. In prostate cancer (PCa), CAFs establish a metabolic symbiosis with PCa cells, contributing to cancer aggressiveness through lactate shuttle. In this study, we report that lactate uptake alters the NAD+/NADH ratio in the cancer cells, which culminates with SIRT1-dependent PGC-1α activation and subsequent enhancement of mitochondrial mass and activity. The high exploitation of mitochondria results in tricarboxylic acid cycle deregulation, accumulation of oncometabolites and in the altered expression of mitochondrial complexes, responsible for superoxide generation. Additionally, cancer cells hijack CAF-derived functional mitochondria through the formation of cellular bridges, a phenomenon that we observed in both in vitro and in vivo PCa models. Our work reveals a crucial function of tumor mitochondria as the energy sensors and transducers of CAF-dependent metabolic reprogramming and underscores the reliance of PCa cells on CAF catabolic activity and mitochondria trading.
Spatiotemporal functional organization of excitatory synaptic inputs onto macaque V1 neurons
Authors: Ju Niansheng , Li Yang , Liu Fang , Jiang Hongfei , Macknik Stephen L. , Martinez-Conde Susana , Tang Shiming
Published: February 2019

The integration of synaptic inputs onto dendrites provides the basis for computation within individual neurons. Whereas recent studies have begun to outline the spatial organization of synaptic inputs on individual neurons, the underlying principles related to the specific neural functions is not well known. Here we performed two-photon dendritic imaging with genetically-encoded glutamate sensor in awake monkeys, and successfully mapped the excitatory synaptic inputs on dendrites of individual V1 neurons with high spatial and temporal resolution. We found that although synaptic inputs on dendrites were functionally clustered by feature, they were highly scattered in multidimensional feature space, providing a potential substrate of local feature integration on dendritic branches. We also found that nearly all individual neurons received both abundant orientation-selective and color-selective inputs. Furthermore, we found apical dendrites received more diverse inputs than basal dendrites, with larger receptive fields, and relatively longer response latencies, suggesting a specific apical role in integrating feedback in visual information processing.
High extracellular lactate increases reductive carboxylation in breast tissue cell lines grown under normoxic conditions
Authors: Brodsky Arthur Nathan , Odenwelder Daniel C. , Harcum Sarah W.
Published: February 2019

In cancer tumors, lactate accumulation was initially attributed to high glucose consumption associated with the Warburg Effect. Now it is evident that lactate can also serve as an energy source in cancer cell metabolism. Additionally, lactate has been shown to promote metastasis, generate gene expression patterns in cancer cells consistent with “cancer stem cell” phenotypes, and result in treatment resistant tumors. Therefore, the goal of this work was to quantify the impact of lactate on metabolism in three breast cell lines (one normal and two breast cancer cell lines – MCF 10A, MCF7, and MDA-MB-231), in order to better understand the role lactate may have in different disease cell types. Parallel labeling metabolic flux analysis (13C-MFA) was used to quantify the intracellular fluxes under normal and high extracellular lactate culture conditions. Additionally, high extracellular lactate cultures were labelled in parallel with [U-13C] lactate, which provided qualitative information regarding the lactate uptake and metabolism. The 13C-MFA model, which incorporated the measured extracellular fluxes and the parallel labeling mass isotopomer distributions (MIDs) for five glycolysis, four tricarboxylic acid cycle (TCA), and three intracellular amino acid metabolites, predicted lower glycolysis fluxes in the high lactate cultures. All three cell lines experienced increased reductive carboxylation of glutamine to citrate in the TCA cycle as a result of high extracellular lactate. Increased reductive carboxylation previously has been observed under hypoxia and other mitochondrial stresses, whereas these cultures were grown aerobically. In addition, this is the first study to investigate the intracellular metabolic responses of different stages of breast cancer progression to high lactate exposure. These results provide insight into the role lactate accumulation has on metabolic reaction distributions in the different disease cell types while the cells are still proliferating in lactate concentrations that do not significantly decrease exponential growth rates.
Tissue-specific mouse mRNA isoform networks
Authors: Kandoi Gaurav , Dickerson Julie A.
Published: February 2019

Alternative Splicing produces multiple mRNA isoforms of genes which have important diverse roles such as regulation of gene expression, human heritable diseases, and response to environmental stresses. However, little has been done to assign functions at the mRNA isoform level. Functional networks, where the interactions are quantified by their probability of being involved in the same biological process are typically generated at the gene level. We use a diverse array of tissue-specific RNA-seq datasets and sequence information to train random forest models that predict the functional networks. Since there is no mRNA isoform-level gold standard, we use single isoform genes co-annotated to Gene Ontology biological process annotations, Kyoto Encyclopedia of Genes and Genomes pathways, BioCyc pathways and protein-protein interactions as functionally related (positive pair). To generate the non-functional pairs (negative pair), we use the Gene Ontology annotations tagged with “NOT” qualifier. We describe 17 Tissue-spEcific mrNa iSoform functIOnal Networks (TENSION) following a leave-one-tissue-out strategy in addition to an organism level reference functional network for mouse. We validate our predictions by comparing its performance with previous methods, randomized positive and negative class labels, updated Gene Ontology annotations, and by literature evidence. We demonstrate the ability of our networks to reveal tissue-specific functional differences of the isoforms of the same genes.
PAK4 regulates stemness and progression in endocrine resistant ER-positive metastatic breast cancer
Authors: Santiago-Gómez Angélica , Dragoni Ilaria , NicAmhlaoibh Roisin , Trivier Elisabeth , Sabin Verity , Simões Bruno M. , Gee Julia M. , Sims Andrew H. , Howell Sacha J. , Clarke Robert B.
Published: February 2019

Despite the effectiveness of endocrine therapies to treat estrogen receptor-positive (ER+) breast tumours, two thirds of patients will eventually relapse due tode novoor acquired resistance to these agents. Cancer Stem-like Cells (CSCs), a rare cell population within the tumour, accumulate after anti-estrogen treatments and are likely to contribute to their failure. Here we studied the role of p21-activated kinase 4 (PAK4) as a promising target to overcome endocrine resistance and disease progression in ER+ breast cancers. PAK4 predicts for resistance to tamoxifen and poor prognosis in 2 independent cohorts of ER+ tumours. We observed that PAK4 strongly correlates with CSC activity in metastatic patient-derived samples irrespective of breast cancer subtype. However, PAK4-driven mammosphere-forming CSC activity increases alongside progression only in ER+ metastatic samples. PAK4 activity increases in ER+ models during acquired resistance to endocrine therapies. Targeting PAK4 with either CRT PAKi, a small molecule inhibitor of PAK4, or with specific siRNAs abrogates CSC activity/self-renewal in clinical samples and endocrine-resistant cells. Together, our findings establish that PAK4 regulates stemness during disease progression and that its inhibition reverses endocrine resistance in ER+ breast cancers.

Highlights

PAK4 predicts for failure of endocrine therapies and poor prognosis

PAK4 drives stemness and progression in ER+ metastatic breast cancer

Targeting PAK4 abrogates breast CSC activity and restores sensitivity to endocrine treatments

Targeting PAK4 will improve outcome of ER+ breast cancer patients

List of Abbreviations that appeared in abstract

Cancer Stem-like Cells (CSCs)

p21-activated kinase 4 (PAK4)

Estrogen Receptor (ER)
Cell-type specific mechanical response and myosin dynamics during retinal lens development in Drosophila
Authors: Blackie Laura , Walther Rhian F. , Staddon Michael F. , Banerjee Shiladitya , Pichaud Franck
Published: February 2019

During organogenesis, different cell types need to work together to induce functional multicellular structures. To study this process, we made use of the genetically tractable fly retina, with a focus on the mechanisms that coordinate morphogenesis between the different epithelial cell types that make up the optical lens. Our work shows that these epithelial cells present contractile apical-medial MyosinII meshworks, which control the apical area and junctional geometry of these cells during lens development. Our study also suggests that MyosinII meshworks drive cell shape changes in response to external forces, and thus they mediate part of the biomechanical coupling that takes place between these cells. Importantly, our work, including mathematical modelling of forces and material stiffness during lens development, raises the possibility that increased cell stiffness acts as a mechanism for limiting this mechanical coupling. We propose this might be required in complex tissues, where different cell types undergo concurrent morphogenesis and where averaging out of forces across cells could compromise individual cell apical geometry and thereby organ function.
Intrinsic checkpoint deficiency during cell cycle re-entry from quiescence
Authors: Matson Jacob Peter , House Amy M. , Grant Gavin D. , Wu Huaitong , Perez Joanna , Cook Jeanette Gowen
Published: February 2019

The authors find that human cells re-entering the cell cycle from quiescence have both an impaired p53-dependent DNA replication origin licensing checkpoint and slow origin licensing. This combination makes every first S phase underlicensed and hypersensitive to replication stress.

To maintain tissue homeostasis, cells transition between cell cycle quiescence and proliferation. An essential G1 process is Minichromosome Maintenance complex (MCM) loading at DNA replication origins to prepare for S phase, known as origin licensing. A p53-dependent origin licensing checkpoint normally ensures sufficient MCM loading prior to S phase entry. We used quantitative flow cytometry and live cell imaging to compare MCM loading during the long first G1 upon cell cycle entry and the shorter G1 phases in the second and subsequent cycles. We discovered that despite the longer G1 phase, the first G1 after cell cycle re-entry is significantly underlicensed. As a result, the first S phase cells are hypersensitive to replication stress. This underlicensing is from a combination of slow MCM loading with a severely compromised origin licensing checkpoint. The hypersensitivity to replication stress increases over repeated rounds of quiescence. Thus, underlicensing after cell cycle re-entry from quiescence distinguishes a higher risk cell cycle that promotes genome instability.
Phosphoinositides regulate the TRPV1 channel via two functionally distinct binding sites
Authors: Yazici Aysenur Torun , Gianti Eleonora , Kasimova Marina A. , Carnevale Vincenzo , Rohacs Tibor
Published: February 2019

Regulation of the heat- and capsaicin-activated Transient Receptor Potential Vanilloid 1 (TRPV1) channel by phosphoinositides is controversial. In a recent cryoEM structure, an endogenous phosphoinositide was detected in the vanilloid binding site, and phosphoinositides were proposed to act as competitive vanilloid antagonists. This model is difficult to reconcile with phosphatidylinositol 4,5- bisphosphate [PtdIns(4,5)P2] being a well established positive regulator of TRPV1. To resolve this controversy, we propose that phosphoinositides regulate TRPV1 via two functionally distinct binding sites. Our molecular dynamics simulations show that phosphatidylinositol (PtdIns) is more stable in the vanilloid binding site, whereas a distinct site responsible for activation is preferentially occupied by PtdIns(4,5)P2. Consistently, we show that in the presence of PtdIns(4,5)P2 in excised patches PtdIns partially inhibited TRPV1 activity induced by low, but not high capsaicin concentrations. In the absence of PtdIns(4,5)P2 on the other hand, PtdIns partially stimulated TRPV1 activity presumably by binding to the activating site. Overall, our data resolve a major controversy in the regulation of TRPV1.
Endocytosis against high turgor pressure is made easier by partial protein coating and a freely rotating base
Authors: Ma Rui , Berro Julien
Published: February 2019

During clathrin-mediated endocytosis, a patch of flat plasma membrane is deformed into a vesicle. In walled cells, such as plants and fungi, the turgor pressure is high and pushes the membrane against the cell wall, thus hindering membrane internalization. In this paper, we study how a patch of membrane is deformed against turgor pressure by force and by curvature-generating proteins. We show that a large amount of force is needed to merely start deforming the membrane and an even larger force is needed to pull a membrane tube. The magnitude of these forces strongly depends on how the base of the membrane is constrained and how the membrane is coated with curvature-generating proteins. In particular, these forces can be reduced by partially but not fully coating the membrane patch with curvature-generating proteins. Our theoretical results show excellent agreement with experimental data.

SIGNIFICANCE

Yeast cells have been widely used as a model system to study clathrin-mediated endocytosis. The mechanics of membrane during endocytosis has been extensively studied mostly in low turgor pressure condition, which is relevant for mammalian cells but not for yeast cells. It has been suggested that as a result of high turgor pressure in yeast cells, a large amount of force is needed to drive the progress of the membrane invagination. In this paper, we investigated biologically relevant mechanisms to reduce the force requirement. We highlight the role of boundary conditions at the membrane base, which is a factor that has been largely ignored in previous studies. We also investigate the role of curvature-generating proteins and show that a large protein coat does not necessarily reduce the force barrier for endocytosis.
Gene-drive-mediated extinction is thwarted by evolution of sib mating
Authors: Bull James J , Remien Christopher H , Krone Stephen M
Published: February 2019

Genetic engineering combined with CRISPR technology has developed to the point that gene drives can, in theory, be engineered to cause extinction in countless species. Success of extinction programs now rests on the possibility of resistance evolution, which is largely unknown. For CRISPR technology, resistance may take many forms, from mutations in the nuclease target sequence to specific types of non-random population structures that limit the drive. We develop mathematical models of various deviations from random mating to consider escapes from extinction-causing gene drives. We use a version of Maynard Smith’s haystack model to show that population structure can enable drive-free subpopulations to be maintained against gene drives. Our main emphasis, however, is sib mating in the face of recessive-lethal and Y-chromosome drives. Sib mating easily evolves in response to both kinds of gene drives and maintains mean fitness above 0, with equilibrium fitness depending on the level of inbreeding depression. Environmental determination of sib mating (as might stem from population density crashes) can also maintain mean fitness above 0. Translation of mean fitness into population size depends on ecological details, so understanding mean fitness evolution and dynamics is merely the first step in predicting extinction. Nonetheless, these results point to possible escapes from gene drive-mediated extinctions that lie beyond the control of genome engineering.
Phosphorylation of Nephrin induces phase separated domains that move through actomyosin contraction
Authors: Kim Soyeon , Kalappurakkal Joseph M. , Mayor Satyajit , Rosen Michael K.
Published: February 2019

The plasma membrane of eukaryotic cells is organized into lipid and protein microdomains, whose assembly mechanisms and functions are incompletely understood. We demonstrate that proteins in the Nephrin/Nck/N-WASP actin-regulatory pathway cluster into micron-scale domains at the basal plasma membrane upon triggered phosphorylation of transmembrane Nephrin. The domains are persistent but readily exchange components with their surroundings, and their formation is dependent on the number of Nck SH3 domains, suggesting they are phase separated polymers assembled through multivalent interactions among the three proteins. The domains form independent of the actin cytoskeleton, but acto-myosin contractility induces their rapid lateral movement. Nephrin phosphorylation induces larger clusters at the cell periphery, which are associated with extensive actin assembly and dense filopodia. Our studies illustrate how multivalent interactions between proteins at the plasma membrane can produce micron-scale organization of signaling molecules, and how the resulting clusters can both respond to and control the actin cytoskeleton.
High multiplex, digital spatial profiling of proteins and RNA in fixed tissue using genomic detection methods
Authors: Merritt Christopher R. , Ong Giang T. , Church Sarah , Barker Kristi , Geiss Gary , Hoang Margaret , Jung Jaemyeong , Liang Yan , McKay-Fleisch Jill , Nguyen Karen , Sorg Kristina , Sprague Isaac , Warren Charles , Warren Sarah , Zhou Zoey , Zollinger Daniel R. , Dunaway Dwayne L. , Mills Gordon B. , Beechem Joseph M.
Published: February 2019

We have developed Digital Spatial Profiling (DSP), a non-destructive method for high-plex spatial profiling of proteins and RNA, using oligonucleotide detection technologies with unlimited multiplexing capability. The key breakthroughs underlying DSP are threefold: (1) multiplexed readout of proteins/RNA using oligo-tags; (2) oligo-tags attached to affinity reagents (antibodies/RNA probes) through a photocleavable (PC) linker; (3) photocleaving light projected onto the tissue sample to release PC-oligos in any spatial pattern. Here we show precise analyte reproducibility, validation, and cellular resolution using DSP. We also demonstrate biological proof-of-concept using lymphoid, colorectal tumor, and autoimmune tissue as models to profile immune cell populations, stroma, and cancer cells to identify factors specific for the diseased microenvironment. DSP utilizes the unlimited multiplexing capability of modern genomic approaches, while simultaneously providing spatial context of protein and RNA to examine biological questions based on analyte location and distribution.
12h-clock control of central dogma information flow by XBP1s
Authors: Pan Yinghong , Ballance Heather , Meng Huan , Gonzalez Naomi , Dacso Clifford C. , Chen Xi , Levy Oren , Coarfa Cristian , O’Malley Bert W , Zhu Bokai
Published: February 2019

Our group recently discovered a cell-autonomous mammalian 12h-clock regulating physiological unfolded protein response. Xbp1s ablation impairs 12h-transcript oscillations in vitro, and we now show liver-specific deletion of XBP1s globally impaired murine 12h-transcriptome, but not the circadian rhythms in vivo. XBP1s-dependent 12h-transcriptome is enriched for transcription, mRNA processing, ribosome biogenesis, translation, and protein ER-Golgi processing/sorting in a temporal order consistent with the progressive molecular processing sequence described by the central dogma information flow (CEDIF). The 12h-rhythms of CEDIF are cell-autonomous and evolutionarily conserved in circatidal marine animals. Mechanistically, we found the motif stringency of promoter XBP1s binding sites, but not necessarily XBP1s expression, dictates its ability to drive 12h-rhythms of transcription and further identified GABP as putative novel transcriptional regulator of 12h-clock. We hypothesize the 12h-rhythms of CEDIF allows rush hours’ gene expression and processing, with the particular genes processed at each rush hour regulated by circadian and/or tissue specific pathways.
Uncertainty Quantification of Complement Sensitivity Indices in Dynamic Computer Models
Authors: Drignei Dorin , Mourelatos Zissimos , Hu Zhen
Published: February 2019

This paper addresses the sensitivity analysis of time-dependent computer models. Often, in practice, we partition the inputs into a subset of inputs relevant to the application studied, and a complement subset of nuisance inputs that are not of interest. We propose sensitivity measures for the relevant inputs of such dynamic computer models. The subset of nuisance inputs is used to create replication-type information to help quantify the uncertainty of sensitivity measures (or indices) for the relevant inputs. The method is first demonstrated on an analytical example. Then we use the proposed method in an application about the safety of restraint systems in light tactical vehicles. The method indicates that chest deflection curves are more sensitive to the addition of pretensioners and load limiters than to the type of seatbelt.
Determination of the Structural Elasticity of Human Fingernails by Bending Test and Comparison With the Structural Elasticity of Human Hair
Authors: Tohmyoh Hironori , Taniguchi Daiki
Published: February 2019

A bending test scheme for accurately determining the structural elasticity of human nails is reported. The structural elasticity expresses the deformability of a multilayered material for bending, and it is the flexural rigidity without depending on the external dimensions. The human nail samples used in this study were prepared from the free ends of the nails and are, therefore, curved, so the equation to determine the structural elasticity was derived from elastic, curved beam theory. The structural elasticity of the nail samples determined by the bending tests was found to be 2.19 GPa, and this value decreased by about 50% when nail polish was put on the nails. Lower value of the Young's modulus of the nail polish was found to cause decrease in the structural elasticity of the sample. Moreover, we also measured the structural elasticity of samples of hair prepared from the same person by the bending tests. Surprisingly, the structural elasticity of the hair (4.37 GPa) was found to be twice that of the nails.
Suppressing Random Response of a Regular Structure by an Inerter-Based Dynamic Vibration Absorber
Authors: Jin Xiaoling , Chen M. Z. Q. , Huang Zhilong
Published: February 2019

This paper concentrates on the random vibration suppression of a regular straight beam by using an inerter-based dynamic vibration absorber. For a wideband random point-driven straight beam with an inerter-based dynamic vibration absorber, the distribution of mean-square velocity response along the axis of the straight beam as well as the mean kinetic energy of the whole beam are first analytically derived through the classical linear random vibration theory. Two optimization objectives are established to determine the optimal design parameters: (1) minimizing the maximal mean-square velocity along the axis of the straight beam, which corresponds to the maximal mean kinetic energy density along the axis and (2) minimizing the mean kinetic energy of the whole beam. Numerical search gives the optimal location and the associated optimal parameters of the inerter-based dynamic vibration absorber. Numerical results for a simply supported straight beam illustrate the better performance of an inerter-based dynamic vibration absorber than a traditional dynamic vibration absorber. Parametric sensitivity studies for the robustness analysis of the beam response to deviations from the optimal parameters are conducted. The optimal location locates on the force-excited point, while the suboptimal location locates on its symmetry position. Furthermore, the optimal and suboptimal locations remain invariable regardless of the upper cutoff frequency of band-limited noise, which is fairly important to the location optimization of the inerter-based dynamic vibration absorber.
Relative Vibration of Suspended Particles With Respect to Microchannel Resonators and Its Effect on the Mass Measurement
Authors: Yan Han , Zhang Wen-Ming , Jiang Hui-Ming , Hu Kai-Ming , Peng Zhi-Ke , Meng Guang
Published: February 2019

In this work, the three-dimensional fluid–solid interaction vibration of particle in the oscillating resonator and its effect on the dynamic characteristics are analyzed and discussed. It demonstrates that the displacement of a particle is composed of two components, one is in phase with the acceleration of resonator and the other is out of phase. The former is responsible for the added mass effect and the latter results in a small damping. A modified measurement principle for detecting the buoyant mass is then presented by considering the in-phase component. The three-dimensional (3D) fluid–solid interaction problem involving the particle, fluid, and resonator is numerically solved, and the effects of density ratio, inverse Stokes number, and the ratio of channel height to particle diameter are studied. Based on the numerical results, a function characterizing the in-phase component is identified through a fitting procedure. According to the modified measurement principle and the analytical expression for the in-phase component, a calibration method is developed for measuring buoyant mass. Using this calibration method, the systematic measurement error induced by the vibration of particles can be effectively reduced.
Fatigue Analysis of a Jacket Structure to Linear and Weakly Nonlinear Random Waves
Authors: Shabakhty Naser , Khansari Arash
Published: February 2019

Jacket structures have been widely used in oil and gas industry and are increasingly becoming competitive as a support structure of wind turbines at different water depths. These types of structures usually fix in transition or shallow waters where numerous field observations and experiments have shown that water particles tend to exhibit non-Gaussian characteristics. However, current engineering practice ignores the wave nonlinearity for the analysis and design of these structures. The application of linear irregular models might result in considerable uncertainties in the obtained wave loads and consequently the dynamic response and thus it is highly questionable. Therefore, it is crucial to calculate the dynamic response of jacket structures under both linear and nonlinear wave models to investigate the validity of linear wave models in different sea states. In this paper, the finite element (FE) model of a jacket structure located in Persian Gulf (SP17 jacket) is setup and applied to perform a comparative study of the dynamic response to both linear and weakly nonlinear random waves. The fatigue life of the jacket structure is then calculated under both wave models. This paper will substantially improve the understanding of the dynamic response of jacket structures under fatigue damage.
Stabilization and Optimization of Design Parameters for Control of Inverted Pendulum
Authors: Maity Sayani , Luecke Greg R.
Published: February 2019

In this work, we study the dynamic response of the most popular unstable control problem, the inverted pendulum in terms of classical control theory. The theoretical and experimental results presented here explore the relationship between changes in the indirect tuning parameters from the linear quadratic regulator (LQR) design, and the final system performance effected using the feedback gains specified as the LQR weight constraints are changed. First, we review the development of the modern control approach using full state-feedback for stabilization and regulation, and present simulation and experimental comparisons as we change the optimization targets for the overall system and as we change one important system parameter, the length of the pendulum. Second, we explore the trends in the response by developing the generalized root locus for the system using incremental changes in the LQR weights. Next, we present a family of curves showing the local root locus and develop relationships between the weight changes and the system performance. We describe how these locus trends provide insight that is useful to the control designer during the effort to optimize the system performance. Finally, we use our general results to design an effective feedback controller for a new system with a longer pendulum and present experiment results that demonstrate the effectiveness of our analysis.
Girls on the Run: Impact of a Physical Activity Youth Development Program on Psychosocial and Behavioral Outcomes
Authors: Weiss Maureen R. , Kipp Lindsay E. , Phillips Reichter Alison , Espinoza Sarah M. , Bolter Nicole D.
Published: February 2019

Purpose: Girls on the Run is an after-school physical activity-based positive youth development program designed to enhance girls’ social, psychological, and physical development. We evaluated the effectiveness of the program by employing a longitudinal design and mixed methods. Methods: Girls (N = 203; aged 8–11 y) completed survey measures of positive youth development constructs (competence, confidence, connection, character, and caring), physical activity, and sedentary behavior prior to, at the end of, and 3 months after the season. Subsamples of girls, coaches, caregivers, and school personnel participated in focus groups. Coaches completed information about their team’s community impact project and number of girls who completed the season-ending 5k. Results: The full sample improved in confidence and connection, whereas girls who started below the preseason average showed the greatest gains from preseason to postseason on all measures, and scores were maintained or continued to improve at follow-up. All stakeholders in focus groups corroborated evidence of season-long improvement in social and emotional behaviors and health outcomes. Involvement in the community impact project contributed to girls’ growth in character and empathy skills. Conclusion: Findings provide empirical evidence that Girls on the Run is effective in promoting positive youth development, including season-long and lasting change in competence, confidence, connection, character, caring, and physical activity, especially among girls who exhibited lower preseason scores than their peers.
Telecom-band lasing in single InP/InAs heterostructure nanowires at room temperature
Authors: Zhang Guoqiang , Takiguchi Masato , Tateno Kouta , Tawara Takehiko , Notomi Masaya , Gotoh Hideki
Published: February 2019

We demonstrate optically pumped telecom-band lasing in single InAs/InP nanowires at room temperature.
A nanofluidic ion regulation membrane with aligned cellulose nanofibers
Authors: Li Tian , Li Sylvia Xin , Kong Weiqing , Chen Chaoji , Hitz Emily , Jia Chao , Dai Jiaqi , Zhang Xin , Briber Robert , Siwy Zuzanna , Reed Mark , Hu Liangbing
Published: February 2019

A nanofluidic membrane for ion regulation with aligned cellulose nanofibers was directly obtained from wood.
Probing vacancy behavior across complex oxide heterointerfaces
Authors: Zhu Jiaxin , Lee Jung-Woo , Lee Hyungwoo , Xie Lin , Pan Xiaoqing , De Souza Roger A. , Eom Chang-Beom , Nonnenmann Stephen S.
Published: February 2019

Real-time probes profile changes in vacancy distributions within substrate-supported oxide films induced by deposition processes.
Ultrafast photoactivation of C─H bonds inside water-soluble nanocages
Authors: Das Ankita , Mandal Imon , Venkatramani Ravindra , Dasgupta Jyotishman
Published: February 2019

Catalytic oxidation of nanoconfined benzylic C─H bonds by light, water, and O
2
.
Theophylline and aminophylline for prevention of acute kidney injury in neonates and children: a systematic review
Authors: Bhatt Girish Chandra , Gogia Priya , Bitzan Martin , Das Rashmi Ranjan
Published: February 2019

Objective

To compare the efficacy and safety of theophylline or aminophylline for prevention of acute kidney injury (AKI) in neonates and children.

Design

Systematic review and meta-analysis with application of Grading of Recommendations, Assessment, Development and Evaluation system.

Data sources

PubMed/MEDLINE, Embase, Google Scholar and Cochrane renal group were searched from 1970 to May 2018.

Eligibility criteria

Randomised clinical trials and quasi-randomised trials comparing the efficacy and safety of prophylactic theophylline or aminophylline for prevention of AKI in neonates and children were included. The primary outcomes were: incidence of AKI, serum creatinine levels and all-cause mortality.

Results

A total of nine trials were included in the qualitative synthesis. Six trials including 436 term neonates with birth asphyxia who received a single dose of theophylline were finally included in the meta-analysis. The pooled estimate showed 60% reduction in the incidence of AKI in neonates with severe birth asphyxia (RR: 0.40; 95% CI 0.3 to 0.54; heterogeneity: I2=0%) (moderate quality evidence), decrease in serum creatinine over days 2–5 (very low to low quality evidence) without significant difference in all-cause mortality (RR: 0.88; 95% CI 0.52 to 1.50; heterogeneity: I2=0%) (very low-quality evidence). A significant difference in the negative fluid balance, increase in GFR and decrease in urinary β2 microglobulin was seen in favour of theophylline.

Conclusion and relevance

A single dose of prophylactic theophylline helps in prevention of AKI/severe renal dysfunction in term neonates with severe birth asphyxia (moderate quality evidence) without increasing the risk of complications and without affecting all-cause mortality (very low-quality evidence).

Trial registration number

CRD 42017073600.
Epidemiology of paediatric chronic fatigue syndrome in Australia
Authors: Knight Sarah , Elders Shane , Rodda Jill , Harvey Adrienne , Lubitz Lionel , Rowe Kathy , Reveley Colette , Hennel Sabine , Towns Susan , Kozlowska Kasia , Payne Donald N , Marshall-Gradisnik Sonya , Scheinberg Adam
Published: February 2019

Objective

To estimate the paediatrician-diagnosed incidence of chronic fatigue syndrome (CFS) in Australia, and describe demographic and clinical features, as well as approaches to diagnosis and management.

Methods

The Australian Paediatric Surveillance Unit facilitates monthly national surveillance of uncommon conditions seen by paediatricians. Data from young people aged <18 years diagnosed with CFS were collected. Incidence was estimated based on new cases reported from April 2015 to April 2016.

Results

A total of 164 cases of newly diagnosed CFS in young people aged 4–17 years were identified for inclusion. The estimated national incidence for children aged 4–9 years was 0.25 per 100 000 per annum. In children aged 10–17 years, the estimated incidence of paediatrician-diagnosed cases for Victoria (17.48 per 100 000) was substantially greater than other Australian states (range 1.31–5.51 per 100 000). Most cases were female and Caucasian, most commonly presenting after an infectious illness with symptoms gradual in onset. The majority were diagnosed at least 13 months after symptom onset. Symptoms, associations, investigations and management strategies were highly variable.

Conclusions

Current findings suggest that, consistent with other countries, the Australian incidence of CFS in children aged <10 years is very low. In contrast, the national incidence of CFS in older children and adolescents (aged 10–17 years) is more unclear, with marked variability between geographical regions apparent. This may be due to variation in service accessibility and clinician understanding of CFS. Accordingly, national initiatives to improve equity of care for children with CFS may be required.