bluuebunny/crossref_metadata_2025 huggingface dataset:
The Activome: multiplexed probing of activity of proteolytic enzymes using mass cytometry-compatible activity-based probes (TOF-probes)
Authors: Poreba Marcin , Groborz Katarzyna , Rut Wioletta , Pore Milind , Snipas Scott J. , Vizovisek Matej , Turk Boris , Kuhn Peter , Drag Marcin , Salvesen Guy S.
Published: September 2019

The activome can be considered as a subset of the proteome that contains enzymes in their catalytically active form and can be interrogated by using probes targeted towards individual specific enzymes. A subset of such enzymes are proteases that are frequently studied with activity-based probes, small inhibitors equipped with a detectable tag, commonly a fluorophore. Due to the spectral overlap of these commonly used fluorophores, simultaneous analysis becomes limited. To overcome this, we developed a series of protease-selective lanthanide-labeled probes compatible with mass cytometry. Using lanthanide-based tags instead of fluorophores gives us the ability to monitor the activity of multiple proteases in parallel. As proof of concept we developed a panel of cathepsin and legumain specific probes and showed that we were able to identify an activome of these proteases in two cell lines and peripheral blood mononuclear cells, providing a framework for the use of mass cytometry for multiplexed enzyme activity detection.
Coconut inflorescence sap mediated synthesis of silver nanoparticles and its diverse antimicrobial properties
Authors: Rajesh M.K. , Muralikrishna K.S. , Nair Swapna S. , Kumar B. Krishna , Subrahmanya T.M. , Sonu K.P. , Subaharan K. , Sweta H. , Prasad T.S. Keshava , Chandran Neeli , Hebbar K.B. , Karun Anitha
Published: September 2019

Green synthesis of nanoparticles (NPs) involves the use of diverse extracts of biological origin as substrates to synthesize nanoparticles and can overcome the hazards associated with chemical methods. Coconut inflorescence sap, which is unfermented phloem sap obtained by tapping of coconut inflorescence, is a rich source of sugars and secondary metabolites. In this study, coconut inflorescence sap was used to synthesize silver nanoparticles (AgNPs). We have initially undertaken metabolomic profiling of coconut inflorescence sap from West Coast Tall cultivar to delineate its individual components. Secondary metabolites constituted the major portion of the inflorescence sap along with sugars, lipids and, peptides. The concentration of silver nitrate, inflorescence sap and incubation temperature for synthesis of AgNPs were optimized. Incubating the reaction mixture at 40°C was found to enhance AgNP synthesis. The AgNPs synthesized were characterized using UV-Visible spectrophotometry, X-Ray Diffraction (XRD), Fourier Transform Infrared spectroscopy (FTIR), Field Emission Scanning Electron Microscopy (FESEM) and Transmission Electron Microscopy (TEM). Antimicrobial property of AgNP was tested in tissue culture of arecanut (Areca catechu L.) where bacterial contamination (Bacillus pumilus) was a frequent occurrence. Significant reduction in the contamination was observed when plantlets were treated with aqueous solutions of 0.01, 0.02 and 0.03% of AgNPs for one hour. Notably, treatment with AgNPs did not affect growth and development of the arecanut plantlets. Cytotoxicity of AgNPs was quantified in HeLa cells. Viability (%) of HeLa cells declined significantly at 10 ppm concentration of AgNP and complete mortality was observed at 60 ppm. Antimicrobial properties of AgNPs synthesized from inflorescence sap were also evaluated and confirmed in human pathogenic bacteria viz., Salmonella sp., Vibrio parahaemolyticus, and Escherichia coli. The study concludes that unfermented inflorescence sap, with above neutral pH, serves as an excellent reducing agent to synthesize AgNPs from Ag+.

Graphical abstract
Epigenetic rejuvenation of the hippocampus by environmental enrichment
Authors: Zocher Sara , Overall Rupert W. , Lesche Mathias , Dahl Andreas , Kempermann Gerd
Published: September 2019

The decline of brain function during aging is associated with epigenetic changes, including DNA methylation. Lifestyle interventions can improve brain function during aging, but their influence on age-related epigenetic changes is unknown. Using genome-wide DNA methylation sequencing, we here show that environmental enrichment counteracted age-related DNA methylation changes in the hippocampal dentate gyrus of mice. Specifically, environmental enrichment prevented the aging-induced CpG hypomethylation at target sites of the methyl-CpG-binding protein Mecp2, which is known to control neuronal functions. The genes at which environmental enrichment counteracted aging effects have described roles in neuronal plasticity, neuronal cell communication and adult hippocampal neurogenesis and are dysregulated with age-related cognitive decline in the human brain. Our results highlight the rejuvenating effects of environmental enrichment at the level of DNA methylation and give molecular insights into the specific aspects of brain aging that can be counteracted by lifestyle interventions.
Amphipathic helices of cellular proteins can replace the helix in M2 of Influenza A virus with only small effects on virus replication
Authors: Hu Bodan , Siche Stefanie , Möller Lars , Veit Michael
Published: September 2019

M2 of influenza virus functions as proton channel during virus entry. In addition, an amphipathic helix in its cytoplasmic tail plays a role during budding. It targets M2 to the assembly site where it inserts into the inner membrane leaflet to induce curvature that causes virus scission. Since vesicularisation of membranes can be performed by a variety of amphiphilic peptides we used reverse genetics to investigate whether they can substitute for M2’s helix.

Virus could not be generated if M2’s helix was deleted or replaced by a peptide predicted not to form an amphiphilic helix. In contrast, viruses could be rescued if the M2 helix was exchanged by helices known to induce membrane curvature. Infectious virus titers were marginally reduced if M2 contains the helix of the amphipathic lipid packing sensor, from the Epsin N-Terminal Homology domain or the non-natural membrane inducer RW16. Transmission EM of infected cells did not reveal unequivocal evidence that virus budding or membrane scission was disturbed in any of the mutants. Instead, individual virus mutants exhibit other defects in M2, such as reduced surface expression, incorporation into virus particles and ion channel activity. The protein composition and specific infectivity was also altered for mutant virions. We conclude that the presence of an amphiphilic helix in M2 is essential for virus replication, but other helices can replace its basic (curvature-inducing) function.

Importance

Influenza is unique among enveloped viruses since it does not rely on the cellular ESCRT-machinery for budding. Instead viruses encode their own scission machine, the M2 protein. M2 is targeted to the edge of the viral assembly site where it inserts an amphiphilic helix into the membrane to induce curvature. Cellular proteins utilize a similar mechanism for scission of vesicles. We show that the helix of M2 can be replaced by helices from cellular proteins with only small effects on virus replication. No evidence was obtained that budding is disturbed, but individual mutants exhibit other defects in M2 which explain the reduced virus titers. In contrast, no virus could be generated if the helix of M2 is deleted or replaced by irrelevant sequences. These experiments support the concept that M2 requires an amphiphilic helix to induce membrane curvature, but its biophysical properties are more important than the amino acid sequence.
Mating-type specific ribosomal proteins control aspects of sexual reproduction inCryptococcus neoformans
Authors: Ianiri Giuseppe , Fang Yufeng “Francis” , Dahlmann Tim A. , Applen Clancey Shelly , Janbon Guilhem , Kück Ulrich , Heitman Joseph
Published: September 2019

TheMATlocus ofCryptococcus neoformanshas a bipolar organization characterized by an unusually large structure, spanning over 100 kb.MATgenes have been characterized by functional genetics as being involved in sexual reproduction and virulence. However, classical gene replacement failed to achieve mutants for fiveMATgenes (RPL22, RPO41, MYO2, PRT1, RPL39), indicating that they are likely essential. In the present study, targeted gene replacement was performed in a diploid strain for both the α andaalleles of the ribosomal genesRPL22andRPL39. Mendelian analysis of the progeny confirmed that bothRPL22andRPL39are essential for viability. Ectopic integration of theRPL22allele of oppositeMATidentity in the heterozygousRPL22a/rpl22αΔ orRPL22α/rpl22aΔ mutant strains failed to complement their essential phenotype. Evidence suggests that this is due to differential expression of theRPL22genes, and an RNAi-dependent mechanism that contributes to controlRPL22aexpression. Furthermore, via CRISPR/Cas9 technology theRPL22alleles were exchanged in haploidMATα andMATastrains ofC. neoformans. TheseRPL22exchange strains displayed morphological and genetic defects during bilateral mating. These results contribute to elucidate functions ofC. neoformansessential mating type genes that may constitute a type of imprinting system to promote inheritance of nuclei of both mating types.
Influence of plant genotype and soil on the wheat rhizosphere microbiome: Evidences for a core microbiome across eight African and European soils
Authors: Simonin Marie , Dasilva Cindy , Terzi Valeria , Ngonkeu Eddy L. M. , Diouf Diégane , Kane Aboubacry , Béna Gilles , Moulin Lionel
Published: September 2019

Here, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea, bacteria) and eukaryotic (fungi, protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhizosphere core microbiome existed across these different countries. The wheat genotype had a limited effect on the rhizosphere microbiome (2% of variance) as the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in community structure were observed between the eight soils studied (57% variance) and the two agricultural practices (10% variance). Despite these differences between soils, we observed that 179 taxa (2 archaea, 104 bacteria, 41 fungi, 32 protists) were consistently detected in the rhizosphere, constituting a core microbiome. In addition to being prevalent, these core taxa were highly abundant and collectively represented 50% of the reads in our dataset. Based on these results, we identify a list of key taxa as future targets of culturomics, metagenomics and wheat synthetic microbiomes. Additionally, we show that protists are an integral part of the wheat holobiont that is currently overlooked.

Graphical Abstract
LeafByte: A mobile application that measures leaf area and herbivory quickly and accurately
Authors: Getman-Pickering Zoe L. , Campbell Adam T. , Aflitto Nicholas , Ugine Todd A. , Grele Ari , Davis Julie
Published: September 2019

In both basic and applied studies, quantification of herbivory on foliage is a key metric in characterizing plant-herbivore interactions, which underpin many ecological, evolutionary, and agricultural processes. Current methods of quantifying herbivory are slow or inaccurate. We present LeafByte, a free iOS application for measuring leaf area and herbivory. LeafByte can save data automatically, read and record barcodes, handle both light and dark colored plant tissue, and be used non-destructively.

We evaluate its accuracy and efficiency relative to existing herbivory assessment tools.

LeafByte has the same accuracy as ImageJ, the field standard, but is 50% faster. Other tools, such as BioLeaf and grid quantification, are quick and accurate, but limited in the information they can provide. Visual estimation is quickest, but it only provides a coarse measure of leaf damage and tends to overestimate herbivory.

LeafByte is a quick and accurate means of measuring leaf area and herbivory, making it a useful tool for research in fields such as ecology, entomology, agronomy, and plant science.
Chromatin information content landscapes inform transcription factor and DNA interactions
Authors: Albanus Ricardo D’Oliveira , Kyono Yasuhiro , Hensley John , Varshney Arushi , Orchard Peter , Kitzman Jacob O. , Parker Stephen C. J.
Published: September 2019

Interactions between transcription factors (TFs) and chromatin are fundamental to genome organization and regulation and, ultimately, cell state. Here, we use information theory to measure signatures of TF-chromatin interactions encoded in the patterns of the accessible genome, which we call chromatin information enrichment (CIE). We calculate CIE for hundreds of TF motifs across human tissues and identify two classes: low and high CIE. The 10-20% of TF motifs with high CIE associate with higher protein-DNA residence time, including different binding sites subclasses of the same TF, increased nucleosome phasing, specific protein domains, and the genetic control of both gene expression and chromatin accessibility. These results show that variations in the information content of chromatin architecture reflect functional biological variation, with implications for cell state dynamics and memory.
The presence of copy number variants in specific topologically associating domains has prognostic value in many cancer types
Authors: Li Lifei , Barth Nicolai K. H. , Pilarsky Christian , Taher Leila
Published: September 2019

The human genome is organized into topologically associating domains (TADs), which represent contiguous regions with a higher frequency of intra-interactions as opposed to inter-interactions. TADs contribute to gene expression regulation by restricting interactions between regulatory elements, and their disruption by genomic rearrangements can result in altered gene expression and, ultimately, in cancer. Here, we provide a proof-of-principle that mutations within TADs can be used to predict the survival of cancer patients. For this purpose, we first constructed a set of 1,467 TADs representing the three-dimensional organization of genome across 24 normal human tissues. We then used Cox regression analysis to assess the prognostic value of the TADs in different cancer types, and identified a total of 35 TADs that were prognostic for at least one of nine cancer types. Interestingly, only 46% of the prognostic TADs comprised one or more genes with a known causal association with cancer. Moreover, for those TADs encompassing such a gene, the prognostic effect of the TAD was only directed related to the presence/absence of mutations in the gene in 13% of the cases. These observations indicate that the predictive power of a large proportion of the prognostic TADs is independent of whether pan-cancer genes are mutated or not. Furthermore, 34% of the 35 prognostic TADs showed strong structural perturbations in the cancer genome, which might mediate cancer development and progression. This study has important implications for the interpretation of cancer-related non-coding mutations and offer insights to new strategies for personalizing cancer medicine.
FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies
Authors: Garber Arkadiy I. , Nealson Kenneth H. , Okamoto Akihiro , McAllister Sean M. , Chan Clara S. , Barco Roman A. , Merino Nancy
Published: September 2019

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms, and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth’s crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and the associated surge in publicly-available sequence data has now made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition and utilization in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) that is based on genes related to iron acquisition, storage, and reduction/oxidation. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate the provided datasets with respect to iron-related genes and gene clusters. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie’s database will be maintained and continually-updated as new genetic markers are discovered. FeGenie is freely available:https://github.com/Arkadiy-Garber/FeGenie.
Description of Ruminococcus catenae SW178 sp. nov., a new anaerobic species isolated from feral chicken
Authors: Wongkuna Supapit , Ghimire Sudeep , Chankhamhaengdecha Surang , Janvilisri Tavan , Scaria Joy
Published: September 2019

A Gram-positive, obligately anaerobic coccobacillus, with the white raised circular colony was isolated from the cecum of feral chickens in Brookings, South Dakota, USA. The 16S rRNA gene sequence analysis suggested that the closest species to strain SW178 was Ruminococcus torques ATCC 27756T (96.94% similarity) that belongs to the family Lachnospiraceae. The genome of strain SW178 is 3.18 Mbp with G+C content of 46.9 mol%. Based on the phylogenetic and phenotypic comparison, we propose that strain SW178 be assigned to the genus Ruminococcus as a novel species, for which the name Ruminococcus catenae is proposed. The type strain is SW178 (= CCOS 1886 T, =DSM 109242T).
β-adrenergic signaling modulates cancer cell mechanotype through a RhoA-ROCK-myosin II axis
Authors: Kim Tae-Hyung , Vazquez-Hidalgo Esteban , Abdou Alexander , Tan Xing Haw Marvin , Christodoulides Alexei , Farris Carly M. , Chiou Pei-Yu , Sloan Erica K. , Katira Parag , Rowat Amy C.
Published: September 2019

The ability of cells to deform and generate forces are key mechanical properties that are implicated in metastasis. While various soluble and mechanical cues are known to regulate cancer cell mechanical phenotype or mechanotype, our knowledge of how cells translate external signals into changes in mechanotype is still emerging. We previously discovered that activation of β-adrenergic signaling, which results from soluble stress hormone cues, causes cancer cells to be stiffer or less deformable; this stiffer mechanotype was associated with increased cell motility and invasion. Here, we characterize how β-adrenergic activation is translated into changes in cellular mechanotype by identifying molecular mediators that regulate key components of mechanotype including cellular deformability, traction forces, and non-muscle myosin II (NMII) activity. Using a micropillar assay and computational modelling, we determine that βAR activation increases cellular force generation by increasing the number of actin-myosin binding events; this mechanism is distinct from how cells increase force production in response to matrix stiffness, suggesting that cells regulate their mechanotype using a complementary mechanism in response to stress hormone cues. To identify the molecules that modulate cellular mechanotype with βAR activation, we use a high throughput filtration platform to screen the effects of pharmacologic and genetic perturbations on βAR regulation of whole cell deformability. Our results indicate that βAR activation decreases cancer cell deformability and increases invasion by signaling through RhoA, ROCK, and NMII. Our findings establish βAR-RhoA-ROCK-NMII as a primary signaling axis that mediates cancer cell mechanotype, which provides a foundation for future interventions to stop metastasis.
Mechanism of Interaction of BMP and Insulin Signaling inC. elegansDevelopment and Homeostasis
Authors: Clark James F. , Ciccarelli Emma J. , Kayastha Peter , Ranepura Gehan , Hasan Muhammad S. , Meléndez Alicia , Savage-Dunn Cathy
Published: September 2019

A small number of peptide growth factor ligands are used repeatedly in development and homeostasis to drive programs of cell differentiation and function. Cells and tissues must integrate inputs from these diverse signals correctly, while failure to do so leads to pathology, reduced fitness, or death. Previous work using the nematodeC. elegansidentified an interaction between the bone morphogenetic protein (BMP) and insulin/IGF-1-like signaling (IIS) pathways in the regulation of lipid homeostasis. The molecular components required for this interaction, however, were not known. Here we report that INS-4, one of 40 insulin-like peptides (ILPs), is regulated by BMP signaling to modulate fat accumulation. Furthermore, we find that the IIS transcription factor DAF-16/FoxO, but not SKN-1/Nrf, acts downstream of BMP signaling in lipid homeostasis. Interestingly, BMP activity alters sensitivity of these two transcription factors to IIS-promoted cytoplasmic retention in opposite ways. Finally, we probe the extent of BMP and IIS interactions by testing two additional IIS functions, dauer formation and autophagy induction. Coupled with our previous work and that of other groups, we conclude that BMP and IIS pathways have at least three modes of interaction: independent, epistatic, and antagonistic. The molecular interactions we identify provide new insight into mechanisms of signaling crosstalk and potential therapeutic targets for IIS-related pathologies such as diabetes and metabolic syndrome.
Contribution of NPY Y5 Receptors to the Reversible Structural Remodeling Of Basolateral Amygdala Dendrites in Male Rats Associated with NPY-mediated Stress Resilience
Authors: Michaelson Sheldon D. , Tapia Ana Pamela Miranda , McKinty Amanda , Villarroel Heika Silveira , Mackay James P. , Urban Janice H. , Colmers William F.
Published: September 2019

Endogenous neuropeptide Y (NPY) and corticotrophin-releasing factor (CRF) modulate the responses of the Basolateral amygdala (BLA) to stress, and are associated respectively with the development of stress resilience and vulnerability. We characterized the persistent effects of repeated NPY and CRF treatment on the structure and function of BLA principal neurons (PN) in a novel organotypic slice culture (OTC) model of rat BLA, and examined the contributions of specific NPY receptor subtypes to these neural and behavioral effects. In BLA principal neurons within the OTCs, repeated NPY treatment caused persistent attenuation of excitatory input and induced dendritic hypotrophy via Y5 receptors; conversely, CRF increased excitatory input and induced hypertrophy of BLA PNs. Repeated treatment of OTCs with NPY followed by an identical treatment with CRF, or vice versa inhibited or reversed all structural changes in OTCs. These structural responses to NPY or CRF required calcineurin or CaMKII, respectively. Finally, repeated intra-BLA injections of NPY or a Y5 receptor agonist increased social interaction and recapitulated structural changes in BLA neurons seen in OTCs, while a Y5 receptor antagonist prevented NPY’s effects both on behavior and on structure. These results implicate the Y5 receptor in the long-term, anxiolytic-like effects of NPY in the BLA, consistent with an intrinsic role in stress buffering, and highlight a remarkable mechanism by which BLA neurons may adapt to different levels of stress. Moreover, BLA OTCs offer a robust model to study mechanisms associated with resilience and vulnerability to stress in BLA.

Significance Statement

Within the basolateral amygdala (BLA), Neuropeptide Y (NPY) is associated with buffering the neural stress response induced by CRF, and promoting stress resilience. We used a novel organotypic slice culture (OTC) model of BLA, complemented with in vivo studies, to examine the cellular mechanisms associated with the actions of NPY. In OTCs, repeated NPY treatment reduces the complexity of the dendritic extent of anxiogenic BLA principal neurons, making them less excitable. NPY, via activation of Y5 receptors, additionally inhibits and reverses the increases in dendritic extent and excitability induced by the stress hormone, corticotropin releasing factor (CRF). This NPY-mediated neuroplasticity indicates that resilience or vulnerability to stress may thus involve neuropeptide-mediated dendritic remodeling in BLA PNs.
Genetic heterogeneity of the Spy1336/R28 – Spy1337 Virulence Axis inStreptococcus pyogenesand Effect on Gene Transcript Levels and Pathogenesis
Authors: Eraso Jesus M. , Kachroo Priyanka , Olsen Randall J. , Beres Stephen B. , Zhu Luchang , Badu Traci , Shannon Sydney , Cantu Concepcion C. , Saavedra Matthew Ojeda , Kubiak Samantha L. , Porter Adeline R. , DeLeo Frank R. , Musser James M.
Published: September 2019

Streptococcus pyogenesis a strict human pathogen responsible for more than 700 million infections annually worldwide. Strains of serotype M28S. pyogenesare typically among the five more abundant types causing invasive infections and pharyngitis in adults and children. Type M28 strains also have an unusual propensity to cause puerperal sepsis and neonatal disease. We recently discovered that a one-nucleotide indel in an intergenic homopolymeric tract located between genesSpy1336/R28andSpy1337altered virulence in a mouse model of infection. In the present study, we analyzed size variation in this homopolymeric tract and determined the extent of heterogeneity in the number of tandemly-repeated 79-amino acid domains in the coding region ofSpy1336/R28in large samples of strains recovered from humans with invasive infections. Both repeat sequence elements are highly polymorphic in natural populations of M28 strains. Variation in the homopolymeric tract results in (i) changes in transcript levels ofSpy1336/R28andSpy1337 in vitro,(ii) differences in virulence in a mouse model of necrotizing myositis, and (iii) global transcriptome changes as shown by RNAseq analysis of isogenic mutant strains. Variation in the number of tandem repeats in the coding sequence ofSpy1336/R28is responsible for size variation of R28 protein in natural populations. Isogenic mutant strains in which genes encoding R28 or transcriptional regulator Spy1337 are inactivated are significantly less virulent in a nonhuman primate model of necrotizing myositis. Our findings provide impetus for additional studies addressing the role of R28 and Spy1337 variation in pathogen-host interactions.
Transcriptome and translatome profiling and translational network analysis during seed maturation reveals conserved transcriptional and distinct translational regulatory patterns
Authors: Bai Bing , van der Horst Sjors , Delhomme Nicolas , Robles Alexander Vergara , Bentsink Leónie , Hanson Johannes
Published: September 2019

Seed maturation is an important plant developmental process that follows embryo development. It is associated with a series of physiological changes such as the establishment of desiccation tolerance, seed longevity and seed dormancy. However, the translational dynamics associated with seed maturation, especially its connection with seed germination remains largely elusive. Here transcriptome and translatome profiling were performed during seed maturation. During seed maturation we observed a gradual disappearance of polysomes and a relative increase of monosomes, indicating a gradual reduction of global translation. Comparing the levels of polysomal associated mRNAs with total mRNA levels showed that thousands of genes are translationally regulated at early sates of maturation, as judged by dramatic changes in polysomal occupancy. By including previous published data from germination and seedling establishment, a translational regulatory network: SeedTransNet was constructed. Network analysis identified hundreds of gene modules with distinct functions and transcript sequence features indicating the existence of separate translational regulatory circuits possibly acting through specific regulatory elements. The regulatory potential of one such element was confirmed in vivo. The network identified several seed maturation associated genes as central nodes, and we could confirm the importance of many of these hub genes with a maturation associated seed phenotype by mutant analysis. One of the identified regulators an AWPM19 family protein PM19-Like1 (PM19L1) was shown to regulate seed dormancy and longevity. This putative RBP also affects the transitional regulation of one its, by the SeedTransNet identified, target mRNAs. Our data shows the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.
Dopamine Promotes Cognitive Effort by Biasing the Benefits Versus Costs of Cognitive Work
Authors: Westbrook A. , van den Bosch R. , Määttä J. I. , Hofmans L. , Papadopetraki D. , Cools R. , Frank M. J.
Published: September 2019

Stimulants like methylphenidate are increasingly used for cognitive enhancement, but precise mechanisms are unknown. We found that methylphenidate boosts willingness to expend cognitive effort by altering the benefit-to-cost ratio of cognitive work. Willingness to expend effort was greater for participants with higher striatal dopamine synthesis capacity, while methylphenidate and sulpiride – a selective D2 receptor antagonist – increased cognitive motivation more for participants with lower synthesis capacity. A sequential sampling model informed by momentary gaze revealed that decisions to expend effort are related to amplification of benefit-versus-cost information attended early in the decision process, while the effect of benefits is strengthened with higher synthesis capacity and by methylphenidate. These findings demonstrate that methylphenidate boosts the perceived benefits-versus-costs of cognitive effort by modulating striatal dopamine signaling.

One Sentence Summary

Striatal dopamine increases cognitive effort by respectively amplifying and attenuating the subjective benefits and costs of cognitive control.
The Effect of Eucalyptol on Nursing Home Residents
Authors: Goto Seiko , Suzuki Hinako , Nakagawa Toshinori , Shimizu Kuniyoshi
Published: September 2019

Eucalyptol is one of the most popular volatile components used in many essential oils for relieving sinus and lung congestion caused by variety of conditions. This pilot study aims to analyze clinical evidence of the effect of the scent of eucalyptol on dementia patients to answer two questions: 1) whether eucalyptol aroma is an effectiveness at reducing the symptoms of dementia, and 2) if so, how it mitigates those symptoms. 27 nursing-home residents with dementia were recruited to assess the efficacy of the scent of eucalyptol. Two one-week experiments were performed: the scent was diffused only at wake-up time in the first experiment and at wake-up time and bedtime in the second experiment. Results showed MMSE, DBD, CMAI scores slightly improved in the first experiment and significantly improved in the second experiment even though no subject reported perceiving the scent in either experiment. The present results indicate that eucalyptol is effective in mitigating dementia symptoms in an elder population with an impaired sense of smell.
Flossing DNA in a Dual Nanopore Device
Authors: Liu Xu , Zimny Philip , Zhang Yuning , Rana Ankit , Nagel Roland , Reisner Walter , Dunbar William B.
Published: September 2019

Solid-state nanopores are a single-molecule technique that can provide access to biomolecular information that is otherwise masked by ensemble averaging. A promising application uses pores and barcoding chemistries to map molecular motifs along single DNA molecules. Despite recent research breakthroughs, however, it remains challenging to overcome molecular noise to fully exploit single molecule data. Here we present an active control technique termed “flossing” that uses a dual nanopore device to trap a protein-tagged DNA molecule and perform up to 100’s of back-and-forth electrical scans of the molecule in a few seconds. The protein motifs bound to 48 kb λDNA are used as detectable features for active triggering of the bidirectional control. Molecular noise is suppressed by averaging the multi-scan data to produce averaged inter-tag distance estimates that are comparable to their known values. Since nanopore feature-mapping applications require DNA linearization when passing through the pore, a key advantage of flossing is that trans-pore linearization is increased to >98% by the second scan, compared to 35% for single nanopore passage of the same set of molecules. In concert with barcoding methods, the dual-pore flossing technique could enable genome mapping and structural variation applications, or mapping loci of epigenetic relevance.
Analysis of continuous infusion functional PET (fPET) in the human brain
Authors: Li Shenpeng , Jamadar Sharna D. , Ward Phillip G.D. , Premaratne Malin , Egan Gary F. , Chen Zhaolin
Published: September 2019

Functional positron emission tomography (fPET) is a neuroimaging method involving continuous infusion of 18-F-fluorodeoxyglucose (FDG) radiotracer during the course of the PET examination. Compared with the conventional bolus administered static FDG PET which provides only a snapshot of the averaged glucose uptake into the brain in a limited dynamic time window, fPET offers a significantly wider time window to study the dynamics of glucose uptake. Several earlier studies have applied fPET to investigate brain FDG uptake and study its relationship with functional magnetic resonance imaging (fMRI). However, due to the unique characteristics of fPET signals, modelling of the fPET signal is a complex task and poses challenges for accurate interpretation of the results. This study applies independent component analysis (ICA) to analyze resting state fPET data, and to compare the performance of ICA and general linear modelling (GLM) for estimation of brain activation in response to tasks. The fPET signal characteristics were compared using GLM and ICA methods to model the fPET visual activation data. Our aim was to evaluate GLM and ICA methods for analyzing task fPET datasets and present ICA method in the analysis of resting state fPET datasets. Using both simulation and in-vivo experimental datasets, we show that both methods can successfully identify task related brain activation. We report fPET metabolic resting state brain networks analyzed using the fPET ICA method in a cohort of healthy subjects. Functional PET provides a unique method to map dynamic changes of glucose uptake in the resting human brain and in response to extrinsic stimulation.
Role of Chemokine and TNF signaling pathway in oral squamous cell carcinoma: A RNA deep sequencing analysis of oral buccal mucosa squamous carcinoma model of Chinese hamster
Authors: Xu Guoqiang , Wei Jianing , Huangfu Bing , Gao Jiping , Wang Xiaotang , Xiao Lanfei , Xuan Ruijing , Chen Zhaoyang , Song Guohua
Published: September 2019

Oral cancer is one of the most common cancers in the world, meanwhile, differentially expressed genes are thought to regulate the development and progression of oral squamous cell carcinomas (OSCC). In this study we screened RNA transcripts from the oral buccal mucosa of healthy male Chinese hamster, divided into 3 groups: a control group with no disposal, a solvent control group coated with acetone solvent, and an experimental group coated with 0.5% DMBA acetone solution by high-throughput RNA sequencing. Tophat and Bowtie were used to align the high-quality reads into transcripts, DEseq was used to analysis the expression of differential gene. Then, the Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted. The chemokine and TNF signaling pathway were differentially expression and the mRNA expression of CXCL1, CXCL2, CXCL3, CCL7, MMP9, monitored by qRT-PCR, increased remarkably in the cancer group and coincided with the result of RNA-Sequencing. Meanwhile, the CXCL1, CXCL2, CXCL3, and CCL7 are significantly enriched in the chemokine signaling pathway, and CXCL1, CXCL2, CXCL3, and MMP9 are significantly enriched in the tumor necrosis factor (TNF) signaling pathway. The differentially expression of the chemokine and TNF signaling pathway was a response to the invasion of the organism immune system due to oral buccal mucosa squamous carcinoma. All the findings provided novel insights for further molecular researches of oral cancer.
Bub3 and Bub1 maintain the balance of kinetochore-localized Aurora B Kinase and Protein Phosphatase I to Regulate Chromosome Segregation and Anaphase Onset in Meiosis
Authors: Cairo Gisela , MacKenzie Anne M. , Lacefield Soni
Published: September 2019

Accurate chromosome segregation depends on proper attachment of kinetochores to spindle microtubules prior to anaphase onset. The Ipl1/Aurora B kinase corrects improper attachments by phosphorylating kinetochore components and so releasing aberrant kinetochore-microtubule interactions. The localization of Ipl1 to kinetochores in budding yeast depends upon multiple pathways, including the Bub1/Bub3 pathway. We show here that in meiosis, Bub3 is crucial for correction of attachment errors. Depletion of Bub3 results in reduced levels of kinetochore-localized Ipl1, and concomitant massive chromosome mis-segregation caused by incorrect chromosome-spindle attachments. Depletion of Bub3 also results in shorter metaphase I and metaphase II due to premature localization of protein phosphatase 1 (PP1) to kinetochores, which antagonizes Ipl1-mediated phosphorylation. We propose a new role for the Bub1-Bub3 pathway in maintaining the balance between kinetochore-localization of Ipl1 and PP1, a balance that is essential for accurate meiotic chromosome segregation and timely anaphase onset.

Cairoet alshow that inS. cerevisiaemeiosis, spindle checkpoint proteins Bub1 and Bub3 have an essential role in preventing chromosome mis-segregation and setting the normal duration of anaphase I and anaphase II onset by regulating the kinetochore-localization of Ipl1 and PP1.
Transcription profiles of age-at-maturity-associated genes suggest cell fate commitment regulation as a key factor in the Atlantic salmon maturation process
Authors: Kurko Johanna , Debes Paul V. , House Andrew , Aykanat Tutku , Erkinaro Jaakko , Primmer Craig R.
Published: September 2019

Despite recent taxonomic diversification in studies linking genotype with phenotype, follow-up studies aimed at understanding the molecular processes of such genotype-phenotype associations remain rare. The age at which an individual reaches sexual maturity is an important fitness trait in many wild species. However, the molecular mechanisms regulating maturation timing processes remain obscure. A recent genome-wide association study in Atlantic salmon (Salmo salar) identified large-effect age-at-maturity-associated chromosomal regions including genesvgll3,akap11andsix6, which have roles in adipogenesis, spermatogenesis and the hypothalamic-pituitary-gonadal (HPG) axis, respectively. Here, we determine expression patterns of these genes during salmon development and their potential molecular partners and pathways. Using Nanostring transcription profiling technology, we show development- and tissue-specific mRNA expression patterns forvgll3,akap11andsix6. Correlated expression levels ofvgll3andakap11, which have adjacent chromosomal location, suggests they may have shared regulation. Further,vgll3correlating witharhgap6andyap1, andakap11withlats1andyap1suggests that Vgll3 and Akap11 take part in actin cytoskeleton regulation. Tissue-specific expression results indicate thatvgll3andakap11paralogs have sex-dependent expression patterns in gonads. Moreover,six6correlating withslc38a6andrtn1, and Hippo signaling genes suggests that Six6 could have a broader role in the HPG neuroendrocrine and cell fate commitment regulation, respectively. We conclude that Vgll3, Akap11 and Six6 may influence Atlantic salmon maturation timing via affecting on adipogenesis and gametogenesis by regulating cell fate commitment and the HPG axis. These results may help to unravel general molecular mechanisms behind maturation.
Towards the identification of causal genes for age-related macular degeneration
Authors: Cheng Fei-Fei , Zhuang You-Yuan , Wen Xin-Ran , Xue Angli , Yang Jian , Jin Zi-Bing
Published: September 2019

Age-related macular degeneration (AMD) is a leading cause of visual impairment in ageing populations and has no radical treatment or prevention. Although genome-wide association studies (GWAS) have identified many susceptibility loci for AMD, the underlying causal genes remain elusive. Here, we prioritized nine putative causal genes by integrating expression quantitative trait locus (eQTL) data from blood (n = 2,765) with AMD GWAS data (16,144 cases vs. 17,832 controls) and replicated six of them using retina eQTL data (n = 523). Of the six genes, altering expression of cnn2, sarm1 and bloc1s1 led to ocular phenotype, impaired vision and retinal pigment epithelium (RPE) loss in zebrafish. Essential photoreceptor and RPE genes were downregulated in cnn2- and sarm1-knockdown zebrafishes. Through integration of GWAS and eQTL data followed by functional validation, our study reveals potential roles of CNN2, SARM1 and BLOC1S1 in AMD pathogenesis and demonstrates an efficient platform to prioritise causal genes for human complex diseases.
Hap2-Ino80 facilitated transcription promotesde novoestablishment of CENP-A chromatin
Authors: Singh Puneet P. , Shukla Manu , White Sharon A. , Tong Pin , Auchynnikava Tatsiana , Spanos Christos , Rappsilber Juri , Pidoux Alison L. , Allshire Robin C.
Published: September 2019

Centromeres are maintained epigenetically by the presence of CENP-A, an evolutionarily-conserved histone H3 variant, which directs kinetochore assembly and hence, centromere function. To identify factors that promote assembly of CENP-A chromatin, we affinity selected solubilised fission yeast CENP-ACnp1chromatin. All subunits of the Ino80 complex were enriched, including the auxiliary subunit Hap2. In addition to a role in maintenance of CENP-ACnp1chromatin integrity at endogenous centromeres, Hap2 is required forde novoassembly of CENP-ACnp1chromatin on naïve centromere DNA and promotes H3 turnover on centromere regions and other loci prone to CENP-ACnp1deposition. Prior to CENP-ACnp1chromatin assembly, Hap2 facilitates transcription from centromere DNA. These analyses suggest that Hap2-Ino80 destabilises H3 nucleosomes on centromere DNA through transcription-coupled histone H3 turnover, driving the replacement of resident H3 nucleosomes with CENP-ACnp1nucleosomes. These inherent properties define centromere DNA by directing a program that mediates CENP-ACnp1assembly on appropriate sequences.
Resurrecting the ancient glow
Authors: Oba Yuichi , Konishi Kaori , Yano Daichi , Shibata Hideyuki , Kato Dai-ichiro , Shirai Tsuyoshi
Published: September 2019

The colour of firefly bioluminescence is primarily determined by the structure of the enzyme luciferase1. To date, firefly luciferase genes have been isolated from over 30 extant species producing light ranging in colour from deep-green to orange-yellow. We have reconstructed ancestral firefly luciferase genes and characterised the enzymatic properties of the recombinant proteins in order to predict ancestral firefly light emission. Results showed that the synthetic luciferase for the last common firefly ancestor exhibited green light. All known firefly species are bioluminescent in the larval stages2, with a common shared ancestor arising approximately 100 Mya3. Combined, our findings propose within the Cretaceous forest the common ancestor of contemporary fireflies emitted green light, most likely for aposematic display from nocturnal predation.
Circadian regulation of muscle growth independent of locomotor activity
Authors: Kelu Jeffrey J. , Pipalia Tapan G. , Hughes Simon M.
Published: September 2019

Muscle tissue shows circadian variation, but whether and how the intracellular circadian clock per se regulates muscle growth remains unclear. By measuring muscle growth over 12 h periods, here we show that muscle grows more during the day than at night. Inhibition of muscle contraction reduces growth to a similar extent in day and night, but does not ablate the circadian variation in growth. Muscle protein synthesis is higher during the day compared to night, whereas markers of protein degradation are higher at night. Mechanistically, the TORC1 inhibitor rapamycin inhibits the extra daytime growth, but no effect on muscle growth at night was detected. Conversely, the proteasomal inhibitor MG132 increases muscle growth at night, but has no effect during the day, irrespective of activity. Ablation of contractile activity rapidly reduces muscle protein synthesis both during the day and at night and leads to a gradual increase in Murf gene expression without ablating circadian variation in growth. Removal of circadian input by exposure to either permanent light or permanent darkness reduces muscle growth. We conclude that circadian variation in muscle growth is independent of the presence of, or changes in, physical activity and affects both protein synthesis and degradation in distinct circadian phases.
Molecular characterization of carbapenem-resistant Klebsiella pneumoniae isolates with focus on antimicrobial resistance
Authors: Yu Xiaoling , Zhang Wen , Zhao Zhiping , Ye Chengsong , Zhou Shuyan , Wu Shaogui , Han Lifen , Han Zhaofang , Ye Hanhui
Published: September 2019

The enhancing incidence of carbapenem-resistant Klebsiella pneumoniae (CRKP)-mediated infections in Mengchao Hepatobiliary Hospital of Fujian Medical University in 2017 is the motivation behind this investigation to study gene phenotypes and resistance-associated genes of emergence regarding the CRKP strains. In current study, seven inpatients are enrolled in the hospital with complete treatments. The carbapenem-resistant K. pneumoniae whole genome is sequenced using MiSeq short-read and Oxford Nanopore long-read sequencing technology. Prophages are identified to assess genetic diversity within CRKP genomes. The investigation encompassed eight CRKP strains that collected from the patients enrolled as well as the environment, which illustrate that blaKPC-2 is responsible for phenotypic resistance in six CRKP strains that K. pneumoniae sequence type (ST11) is informed. The plasmid with IncR, ColRNAI and pMLST type with IncF[F33:A-:B-] co-exist in all ST11 with KPC-2-producing CRKP strains. Along with carbapenemases, all K. pneumoniae strains harbor two or three extended spectrum β-lactamase (ESBL)-producing genes. fosA gene is detected amongst all the CRKP strains. The single nucleotide polymorphisms (SNP) markers are indicated and validated among all CRKP strains, providing valuable clues for distinguishing carbapenem-resistant strains from conventional K. pneumoniae. In conclusion, ST11 is the main CRKP type, and blaKPC-2 is the dominant carbapenemase gene harbored by clinical CRKP isolates from current investigations.