bluuebunny/crossref_metadata_2025 huggingface dataset:
Marking RNA: m6A writers, readers, and functions in Arabidopsis
Authors: Reichel Marlene , Köster Tino , Staiger Dorothee
Published: July 2019

N6-methyladenosine (m6A) emerges as an important modification in eukaryotic mRNAs. m6A has first been reported in 1974, and its functional significance in mammalian gene regulation and importance for proper development have been well established. An arsenal of writer, eraser, and reader proteins accomplish deposition, removal, and interpretation of the m6A mark, resulting in dynamic function. This led to the concept of an epitranscriptome, the compendium of RNA species with chemical modification of the nucleobases in the cell, in analogy to the epigenome. While m6A has long been known to also exist in plant mRNAs, proteins involved in m6A metabolism have only recently been detected by mutant analysis, homology search, and mRNA interactome capture in the reference plant Arabidopsis thaliana. Dysregulation of the m6A modification causes severe developmental abnormalities of leaves and roots and altered timing of reproductive development. Furthermore, m6A modification affects viral infection. Here, we discuss recent progress in identifying m6A sites transcriptome-wide, in identifying the molecular players involved in writing, removing, and reading the mark, and in assigning functions to this RNA modification in A. thaliana. We highlight similarities and differences to m6A modification in mammals and provide an outlook on important questions that remain to be addressed.
Preliminary Evidence for a Hormetic Effect on DNA Nucleotide Excision Repair in Veterans with Gulf War Illness
Authors: Latimer Jean J , Alhamed Abdullah , Sveiven Stefanie , Almutairy Ali , Klimas Nancy G , Abreu Maria , Sullivan Kimberly , Grant Stephen G
Published: July 2019

Introduction

Veterans of the 1991 Gulf War were potentially exposed to a mixture of stress, chemicals and radiation that may have contributed to the persistent symptoms of Gulf War Illness (GWI). The genotoxic effects of some of these exposures are mediated by the DNA nucleotide excision repair (NER) pathway. We hypothesized that individuals with relatively low DNA repair capacity would suffer greater damage from cumulative genotoxic exposures, some of which would persist, causing ongoing problems.

Materials and Methods

Blood samples were obtained from symptomatic Gulf War veterans and age-matched controls. The unscheduled DNA synthesis assay, a functional measurement of NER capacity, was performed on cultured lymphocytes, and lymphocyte mRNA was extracted and analyzed by sequencing.

Results

Despite our hypothesis that GWI would be associated with DNA repair deficiency, NER capacity in lymphocytes from affected GWI veterans actually exhibited a significantly elevated level of DNA repair (p = 0.016). Both total gene expression and NER gene expression successfully differentiated individuals with GWI from unaffected controls. The observed functional increase in DNA repair capacity was accompanied by an overexpression of genes in the NER pathway, as determined by RNA sequencing analysis.

Conclusion

We suggest that the observed elevations in DNA repair capacity and NER gene expression are indicative of a “hormetic,” i.e., induced or adaptive protective response to battlefield exposures. Normally such effects are short-term, but in these individuals this response has resulted in a long-term metabolic shift that may also be responsible for the persistent symptoms of GWI.
Influence of Time to Transport to a Higher Level Facility on the Clinical Outcomes of US Combat Casualties with TBI: A Multicenter 7-Year Study
Authors: Maddry Joseph K , Arana Allyson A , Perez Crystal A , Medellin Kimberly L , Paciocco Joni A , Mora Alejandra G , Holder William G , Davis William T , Herson Paco , Bebarta Vikhyat S
Published: July 2019

Introduction

Traumatic brain injury (TBI) is a leading cause of death and disability worldwide and is associated with mortality rates as high as 30%. Patients with TBI are at high risk for secondary injury and need to be transported to definitive care expeditiously. However, the physiologic effects of aeromedical evacuation are not well understood and may compound these risks. Combat TBI patients may benefit from delayed aeromedical evacuation. The goal of this study was to evaluate the impact of transport timing out of theater via Critical Care Air Transport Teams (CCATT) to a higher level facility on the clinical outcomes of combat casualties with TBI.

Materials and Methods

We performed a retrospective review of patients with TBI who were evacuated out of theater by CCATT from January 2007 to May 2014. Data abstractors collected flight information, vital signs, procedures, in-flight assessments, and outcomes. Time to transport was defined as the time from injury to CCATT evacuation out of combat theater. We calculated descriptive statistics and constructed regression models to determine the association between time to transport and clinical outcomes. This study was approved by the U.S. Air Force 59th Medical Wing Institutional Review Board.

Results

We analyzed the records of 438 patients evacuated out of theater via CCATT and categorized them into three groups: patients who were transported in one day or less (n = 165), two days (n = 163), and three or more days (n = 110). We used logistic regression models to compare outcomes among patients who were evacuated in two days or three or more days to those who were transported within one day while adjusting for demographics, injury severity, and injury type. Patients who were evacuated in two days or three or more days had 50% lower odds of being discharged on a ventilator and were twice as likely to return to duty or be discharged home than those who were evacuated within one day. Additionally, patients transported in three or more days were 70% less likely to be ventilated at discharge with a GCS of 8 or lower and had 30% lower odds of mortality than those transported within one day.

Conclusions

In patients with moderate to severe TBI, a delay in aeromedical evacuation out of the combat theater was associated with improved mortality rates and a higher likelihood of discharge to home and return to duty dispositions. This study is correlational in nature and focused on CCATT transports from Role III to Role IV facilities; as such, care must be taken in interpreting our findings and future studies are needed to establish a causal link between delayed evacuation and improved discharge disposition. Our study suggests that delaying aeromedical evacuation of TBI patients when feasible may confer benefit.
A humanized yeast phenomic model of deoxycytidine kinase to predict genetic buffering of nucleoside analog cytotoxicity
Authors: Santos Sean M. , Icyuz Mert , Pound Ilya , William Doreen , Guo Jingyu , McKinney Brett A. , Niederweis Michael , Rodgers John , Hartman John L.
Published: July 2019

Knowledge about synthetic lethality can be applied to enhance the efficacy of anti-cancer therapies in individual patients harboring genetic alterations in their cancer that specifically render it vulnerable. We investigated the potential for high-resolution phenomic analysis in yeast to predict such genetic vulnerabilities by systematic, comprehensive, and quantitative assessment of drug-gene interaction for gemcitabine and cytarabine, substrates of deoxycytidine kinase that have similar molecular structures yet distinct anti-tumor efficacy. Human deoxycytidine kinase (dCK) was conditionally expressed in theS. cerevisiaegenomic library of knockout and knockdown (YKO/KD) strains, to globally and quantitatively characterize differential drug-gene interaction for gemcitabine and cytarabine. Pathway enrichment analysis revealed that autophagy, histone modification, chromatin remodeling, and apoptosis-related processes influence gemcitabine specifically, while drug-gene interaction specific to cytarabine was less enriched in Gene Ontology. Processes having influence over both drugs were DNA repair and integrity checkpoints and vesicle transport and fusion. Non-GO-enriched genes were also informative. Yeast phenomic and cancer cell line pharmacogenomics data were integrated to identify yeast-human homologs with correlated differential gene expression and drug-efficacy, thus providing a unique resource to predict whether differential gene expression observed in cancer genetic profiles are causal in tumor-specific responses to cytotoxic agents.
Altering microtubule dynamics is synergistically toxic with inhibition of the spindle checkpoint
Authors: Schukken Klaske M. , Lin Yi-Chih , Schubert Michael , Preuss Stephanie F. , Simon Judith E. , van den Bos Hilda , Storchova Zuzana , Colome-Tatche Maria , Bastians Holger , Spierings Diana C.J. , Foijer Floris
Published: July 2019

Chromosome instability (CIN) and aneuploidy are hallmarks of cancer. As the majority of cancers are aneuploid, targeting aneuploidy or CIN may be an effective way to target a broad spectrum of cancers. Here, we perform two small molecule compound screens to identify drugs that selectively target cells that are aneuploid or exhibit a CIN phenotype. We find that aneuploid cells are much more sensitive to the energy metabolism regulating drug ZLN005 than their euploid counterparts. Furthermore, cells with an ongoing CIN phenotype, induced by spindle assembly checkpoint (SAC) alleviation, are significantly more sensitive to the Src kinase inhibitor SKI606. We show that inhibiting Src kinase increases microtubule polymerization rates and, more generally, that deregulating microtubule polymerization rates is particularly toxic to cells with a defective SAC. Our findings therefore suggest that tumors with a dysfunctional SAC are particularly sensitive to microtubule poisons and, vice versa, that compounds alleviating the SAC provide a powerful means to treat tumors with deregulated microtubule dynamics.
Heterologous caffeic acid biosynthesis in Escherichia coli is affected by choice of tyrosine ammonia lyase and redox partners for bacterial Cytochrome P450
Authors: Haslinger Kristina , Prather Kristala L.J.
Published: July 2019

Background

Caffeic acid is industrially recognized for its antioxidant activity and therefore its potential to be used as an anti-inflammatory, anticancer, antiviral, antidiabetic and antidepressive agent. It is traditionally isolated from lignified plant material under energy-intensive and harsh chemical extraction conditions. However, over the last decade bottom-up biosynthesis approaches in microbial cell factories have been established, that have the potential to allow for a more tailored and sustainable production. One of these approaches has been implemented in Escherichia coli and only requires a two-step conversion of supplemented L-tyrosine by the actions of a tyrosine ammonia lyase and a bacterial Cytochrome P450 monooxygenase. Although the feeding of intermediates demonstrated the great potential of this combination of heterologous enzymes compared to others, no de novo synthesis of caffeic acid from glucose has been achieved utilizing the bacterial Cytochrome P450 thus far.

Results

The herein described work aimed at improving the efficiency of this two-step conversion in order to establish de novo caffeic acid formation from glucose. We implemented alternative tyrosine ammonia lyases that were reported to display superior substrate binding affinity and selectivity, and increased the efficiency of the Cytochrome P450 by altering the electron-donating redox system. With this strategy we were able to achieve final titers of more than 300 μM or 47 mg/L caffeic acid over 96 h in an otherwise wild type E. coli MG1655(DE3) strain with glucose as the only carbon source. We observed that the choice and gene dose of the redox system strongly influenced the Cytochrome P450 catalysis. In addition, we were successful in applying a tethering strategy that rendered even an initially unproductive Cytochrome P450/ redox system combination productive.

Conclusions

The caffeic acid titer achieved in this study is about 25% higher than titers reported for other heterologous caffeic acid pathways in wildtype E. coli without L-tyrosine supplementation. The tethering strategy applied to the Cytochrome P450 appears to be particularly useful for non-natural Cytochrome P450/redox partner combinations and could be useful for other recombinant pathways utilizing bacterial Cytochromes P450.
Mutations in CalDAG-GEFI Lead to Striatal Signaling Deficits and Psychomotor Symptoms in Multiple Species Including Human
Authors: Crittenden Jill R. , Sauvage Magdalena , Kitsukawa Takashi , Burguière Eric , Cepeda Carlos , André Véronique M. , Canault Matthias , Thomsen Morgane , Zhang Hui , Costa Cinzia , Martella Giuseppina , Ghiglieri Veronica , Pescatore Karen A. , Unterwald Ellen M. , Jackson Walker , Housman David E. , Caine S. Barak , Sulzer David , Calabresi Paolo , Levine Michael S. , Brefel-Courbon Christine , Smith Anne C. , Alessi Marie-Christine , Azulay Jean-Phillipe , Graybiel Ann M.
Published: July 2019

Syndromes caused by mutations in Ras-MAP kinase signaling molecules are known as RASopathies and share features such as developmental delay, autistic traits, and cancer. Syndromic features of Rap-MAP kinase signaling defects remain undefined. CalDAG-GEFI is a calcium-responsive Rap-GTPase activator that is enriched in the matrix of the sensorimotor striatum and down-regulated in Huntington’s disease. We show here that CalDAG-GEFI mutations, including striatum-specific deletions and spontaneous mutations in the enzymatic domain, are associated with psychomotor phenotypes in humans, dogs and mice. The identification of these neural mutants was guided by the overt bleeding phenotype in CalDAG-GEFI knockout mice, and then in humans and other species with conserved platelet signaling deficits. Knockout mice exhibit loss of striatal long-term potentiation and deficits in dopamine, acetylcholine and glutamate signaling, along with delayed motor learning and drug-induced perseverative behaviors. Thus, loss of CalDAG-GEFI signaling produces an evolutionarily conserved syndrome characterized by bleeding and psychomotor dysfunction.
Phylogenetic diversity efficiently and accurately prioritizes the conservation of aquatic macroinvertebrate communities
Authors: Weglarz Kathryn M. , Saunders W. Carl , Van Wagenen Andrew , Pearse William D.
Published: July 2019

Land degradation is a leading cause of biodiversity loss yet its consequences on freshwater ecosystems are poorly understood, exacerbating difficulties with assessing ecosystem quality and the effectiveness of restoration practices.

Many monitoring programs rely on macroinvertebrates to assess the biotic effects of degradation and/or restoration and management actions on freshwater ecosystems. The ratio of Observed (O) to Expected (E) macroinvertebrate taxa at a given site—O/E—is often used for this purpose, despite the amount of modeling and data required to generate expectations and difficulties quantitatively assessing the degree of degradation at a site.

Despite widespread use in academic biology, phylogenetic diversity is rarely applied in management, regardless of empirical correlations between phylogenetic diversity and management targets such as ecosystem structure and function.

We use macroinvertebrate data from 1,400 watersheds to evaluate the potential for phylogenetic metrics to inform evaluations of management practices. These data have been collected since 1998, and have been used to determine the effectiveness of conservation management for the maintenance and restoration of riparian and aquatic systems.

Phylogenetic diversity detected degradation as effectively as O/E, despite not having baseline ‘expectation’ data. Site disturbance, road density, and broader environmental drivers such as mean annual temperature strongly predicted site phylogenetic diversity, providing concrete management objectives to increase site health.

Synthesis and applications.Management efforts targeted solely at taxonomic metrics, such as O/E, have been successfully used to manage sites. We show here that phylogenetic diversity metrics can support such efforts by providing additional information about the kind of species at sites. Given the ease with which such approaches can be applied, we call on others to use them to supplement existing prioritization schemes.
When to be Temperate: On the Fitness Benefits of Lysis vs. Lysogeny
Authors: Li Guanlin , Cortez Michael H. , Dushoff Jonathan , Weitz Joshua S.
Published: July 2019

Bacterial viruses, i.e., ‘bacteriophage’ or ‘phage’, can infect and lyse their bacterial hosts, releasing new viral progeny. In addition to the lytic pathway, certain bacteriophage (i.e., ‘temperate’ bacteriophage) can also initiate lysogeny, a latent mode of infection in which the viral genome is integrated into and replicated with the bacterial chromosome. Subsequently, the integrated viral genome, i.e., the ‘prophage’, can induce and restart the lytic pathway. Here, we explore the relationship between infection mode, ecological context, and viral fitness, in essence asking: when should viruses be temperate? To do so, we use network loop analysis to quantify fitness in terms of network paths through the life history of an infectious pathogen that start and end with infected cells. This analysis reveals that temperate strategies, particularly those with direct benefits to cellular fitness, should be favored at low host abundances. This finding applies to a spectrum of mechanistic models of phage-bacteria dynamics spanning both explicit and implicit representations of intracellular infection dynamics. However, the same analysis reveals that temperate strategies, in and of themselves, do not provide an advantage when infection imposes a cost to cellular fitness. Hence, we use evolutionary invasion analysis to explore when temperate phage can invade microbial communities with circulating lytic phage. We find that lytic phage can drive down niche competition amongst microbial cells, facilitating the subsequent invasion of latent strategies that increase cellular resistance and/or immunity to infection by lytic viruses – notably this finding holds even when the prophage comes at a direct fitness cost to cellular reproduction. Altogether, our analysis identifies broad ecological conditions that favor latency and provide a principled framework for exploring the impacts of ecological context on both the short- and long-term benefits of being temperate.
Machine learning aided analyses of thousands of draft genomes reveal plant- and environment-specific features of activated sludge process
Authors: Ye Lin , Mei Ran , Liu Wen-Tso , Ren Hongqiang , Zhang Xuxiang
Published: July 2019

Microorganisms in activated sludge (AS) play key roles in the wastewater treatment process. However, the ecological behavior of microorganisms in AS and their differences with microorganisms in other environments have mainly been studied using 16S rRNA gene that may not truly represent their in-situ functions. Here, we present 2045 bacterial and archaeal metagenome-assembled genomes (MAGs) recovered from 1.35 Tb of metagenomic sequencing data generated from 114 AS samples of 23 full-scale wastewater treatment plants (WWTPs). The average completeness and contamination of the MAGs are 82.0% and 2.0%, respectively. We find that the AS MAGs have obviously plant-specific features and few proteins are shared by different WWTPs, especially for WWTPs located in geographically distant areas. Despite the differences, specific functional traits (e.g. functions related to aerobic metabolism, nutrient sensing/acquisition, biofilm formation, etc.) of AS MAGs could be identified by a machine learning approach, and based on these traits, AS MAGs could be differentiated from MAGs of other environments with an accuracy of 96.6%. Our work provides valuable genome resources for future investigation of the AS microbiome and also introduces a novel approach to understand the microbial ecology in different ecosystems.
Cooption and Specialization of Endothelin Signaling Pathways Drove Elaboration of the Neural Crest in Early Vertebrates
Authors: Square Tyler A. , Jandzik David , Massey James L. , Romášek Marek , Stein Haley P. , Hansen Andrew W. , Purkayastha Amrita , Cattell Maria V. , Medeiros Daniel M.
Published: July 2019

The neural crest (NC) is a vertebrate-specific embryonic tissue that forms an array of clade-defining adult features. A key step in the formation of these diverse derivatives is the partitioning of NC cells into subpopulations with distinct migration routes and potencies1. The evolution of these developmental modules is poorly understood. Endothelin (Edn) signaling is unique to vertebrates, and performs various functions in different NC subpopulations2–5. To better understand the evolution of NC patterning, we used CRISPR/Cas9-driven mutagenesis to disrupt Edn receptors, ligands, and Dlx transcription factors in the sea lamprey,Petromyzon marinus. Lampreys and modern gnathostomes last shared a common ancestor 500 million years ago6. Thus, comparisons between the two groups can identify deeply conserved and divergent features of vertebrate development. UsingXenopus laevisto facilitate side-by-side analyses, we show here that lamprey and gnathostomes display fundamental differences in Edn signaling function. Unlike gnathostomes, both lamprey Ednrs cooperate during oropharyngeal skeleton development. Furthermore, neither paralog regulateshandtranscription factors, which are required for mandible development in gnathostomes. We also identify conserved roles for Edn signaling indlxgene regulation, pigment cell, and heart development. Together our results illustrate the stepwise neofunctionalization and specialization of this vertebrate-specific signaling pathway, and suggest key intermediate stages in the early evolution of the NC.
Genome-wide survey of ribosome collision
Authors: Han Peixun , Mito Mari , Shichino Yuichi , Hashimoto Satoshi , Udagawa Tsuyoshi , Kohno Kenji , Mishima Yuichiro , Inada Toshifumi , Iwasaki Shintaro
Published: July 2019

In protein synthesis, ribosome movement is not always smooth and is rather often impeded for numerous reasons. Although the deceleration of the ribosome defines the fates of the mRNAs and synthesizing proteins, fundamental issues remain to be addressed, including where ribosomes pause in mRNAs, what kind of RNA/amino acid sequence causes this pause, and the physiological significance of this slowdown of protein synthesis. Here, we surveyed the positions of ribosome collisions caused by ribosome pausing in humans and zebrafish on a genome-wide level using modified ribosome profiling. The collided ribosomes, i.e., disomes, emerged at various sites: the proline-proline-lysine motif, stop codons, and the 3′ untranslated region (UTR). The number of ribosomes involved in a collision is not limited to two, but rather four to five ribosomes can form a queue of ribosomes. In particular, XBP1, a key modulator of the unfolded protein response, shows striking queues of collided ribosomes and thus acts as a substrate for ribosome-associated quality control (RQC) to avoid the accumulation of undesired proteins in the absence of stress. Our results provide an insight into the causes and consequences of ribosome slowdown by dissecting the specific architecture of ribosomes.
25 years of propagation in suspension cell culture results in substantial alterations of theArabidopsis thalianagenome
Authors: Pucker Boas , Rückert Christian , Stracke Ralf , Viehöver Prisca , Kalinowski Jörn , Weisshaar Bernd
Published: July 2019

Arabidopsis thalianais one of the best studied plant model organisms. Besides cultivation in greenhouses, cells of this plant can also be propagated in suspension cell culture. At7 is one such cell line that has been established about 25 years ago. Here we report the sequencing and the analysis of the At7 genome. Large scale duplications and deletions compared to the Col-0 reference sequence were detected. The number of deletions exceeds the number of insertions thus indicating that a haploid genome size reduction is ongoing. Patterns of small sequence variants differ from the ones observed betweenA. thalianaaccessions e.g. the number of single nucleotide variants matches the number of insertions/deletions. RNA-Seq analysis reveals that disrupted alleles are less frequent in the transcriptome than the native ones.
Mathematical modeling with single-cell sequencing data
Authors: Cho Heyrim , Rockne Russell C.
Published: July 2019

Single-cell sequencing technologies have revolutionized molecular and cellular biology and stimulated the development of computational tools to analyze the data generated from these technology platforms. However, despite the recent explosion of computational analysis tools, relatively few mathematical models have been developed to utilize these data. Here we compare and contrast two approaches for building mathematical models of cell state-transitions with single-cell RNA-sequencing data with hematopoeisis as a model system; by solving partial differential equations on a graph representing discrete cell state relationships, and by solving the equations on a continuous cell state-space. We demonstrate how to calibrate model parameters from single or multiple time-point single-cell sequencing data, and examine the effects of data processing algorithms on the model calibration and predictions. As an application of our approach, we demonstrate how the calibrated models may be used to mathematically perturb normal hematopoeisis to simulate, predict, and study the emergence of novel cell types during the pathogenesis of acute myeloid leukemia. The mathematical modeling framework we present is general and can be applied to study cell state-transitions in any single-cell genome sequencing dataset.

Author summary

Here we compare and contrast graph- and continuum-based approaches for constructing mathematical models of cell state-transitions using single-cell RNA-sequencing data. Using two publicly available datasets, we demonstrate how to calibrate mathematical models of hematopoeisis and how to use the models to predict dynamics of acute myeloid leukemia pathogenesis by mathematically perturbing the process of cellular proliferation and differentiation. We apply these modeling approaches to study the effects of perturbing individual or sets of genes in subsets of cells, or by modeling the dynamics of cell state-transitions directly in a reduced dimensional space. We examine the effects of different graph abstraction and trajectory inference algorithms on calibrating the models and the subsequent model predictions. We conclude that both the graph- and continuum-based modeling approaches can be equally well calibrated to data and discuss situations in which one method may be preferable over the other. This work presents a general mathematical modeling framework, applicable to any single-cell sequencing dataset where cell state-transitions are of interest.
Early fate of Exogenous promoters in E. coli
Authors: Yousuf Malikmohamed , Iuliani Ilaria , Veetil Reshma T. , Seshasayee Aswin Sai Narain , Sclavi Bianca , Lagomarsino Marco Cosentino
Published: July 2019

Gene gain by horizontal gene transfer is a major pathway of genome innovation in bacteria. The current view posits that acquired genes initially need to be silenced and that a bacterial chromatin protein, H-NS, plays a role in this silencing. However, we lack direct observation of the early fate of a horizontally transferred gene to prove this theory. We combine sequencing, flow cytometry and sorting, and microscopy to monitor gene expression and its variability after large-scale random insertions of a reporter gene in a population. We find that inserted promoters have a wide range of gene-expression variability related to their location. We find that high-expression clones carry insertions that are not correlated with H-NS binding. Conversely, binding of H-NS correlates with silencing. Finally, while most promoters show a common level of extrinsic noise, some insertions show higher noise levels. Analysis of these high-noise clones supports a scenario of switching due to transcriptional interference from divergent ribosomal promoters. Altogether, our findings point to evolutionary pathways where newly-acquired genes are not necessarily silenced, but may immediately explore a wide range of expression levels to probe the optimal ones.
Impaired lysosomal acidification triggers iron deficiency, necrotic cell death and inflammationin vivo
Authors: Yambire King Faisal , Rostosky Christine , Watanabe Takashi , Pacheu-Grau David , Torres-Odio Sylvia , Sanchez-Guerrero Angela , Senderovich Ola , Meyron-Holtz Esther G. , Milosevic Ira , Frahm Jens , West Phillip , Raimundo Nuno
Published: July 2019

Lysosomal acidification is a key feature of healthy cells. Inability to maintain lysosomal acidic pH is associated with aging and neurodegenerative diseases. However, the mechanisms elicited by impaired lysosomal acidification remain unknown. We show here that inhibition of lysosomal acidification triggers cellular iron deficiency, which results in impaired mitochondrial function and necrotic cell death. These effects are recovered by supplying iron via a lysosome-independent pathway. Notably, iron deficiency is sufficient to trigger inflammatory signaling in cultured primary neurons. Using a mouse model of impaired lysosomal acidification, we observed a robust iron deficiency response in the brain, verified byin vivomagnetic resonance imaging. Furthermore, the brains of these mice present a pervasive inflammatory signature associated with instability of mitochondrial DNA (mtDNA), both corrected by supplementation of the mice diet with iron. Our results highlight a novel mechanism linking lysosomal dysfunction, mitochondrial malfunction and inflammationin vivo.
A Membrane-Targeted Photoswitch Potently Modulates Neuronal Firing
Authors: DiFrancesco Mattia L. , Lodola Francesco , Colombo Elisabetta , Maragliano Luca , Paternò Giuseppe M. , Bramini Mattia , Cimò Simone , Colella Letizia , Fazzi Daniele , Eleftheriou Cyril G. , Maya-Vetencourt José Fernando , Bertarelli Chiara , Lanzani Guglielmo , Benfenati Fabio
Published: July 2019

Optical technologies allowing modulation of neuronal activity at high spatio-temporal resolution are becoming paramount in neuroscience. We engineered novel light-sensitive molecules by adding polar groups to a hydrophobic backbone containing azobenzene and azepane moieties. We demonstrate that the probes stably partition into the plasma membrane, with affinity for lipid rafts, and cause thinning of the bilayer through their trans-dimerization in the dark. In neurons pulse-labeled with the compound, light induces a transient hyperpolarization followed by a delayed depolarization that triggers action potential firing. The fast hyperpolarization is attributable to a light-dependent decrease in capacitance due to membrane relaxation that follows disruption of the azobenzene dimers. The physiological effects are persistent and can be evoked in vivo after labeling the mouse somatosensory cortex. These data demonstrate the possibility to trigger neural activity in vitro and in vivo by modulating membrane capacitance, without directly affecting ion channels or local temperature.
Intracellular enhancement of BMP signaling by LIM-domain protein FHL3 controls spatiotemporal emergence of the neural crest driven by WNT signaling
Authors: Alkobtawi Mansour , Pla Patrick , Monsoro-Burq Anne H.
Published: July 2019

How multiple morphogen signals are coordinated in space and time to position key embryonic tissues remains elusive. During neural crest formation, bone morphogenetic protein (BMP), fibroblast growth factor (FGF) and WNT signaling cooperate by acting either on the paraxial mesoderm or directly on the neural border ectoderm, but how each tissue interprets this complex information remains poorly understood. Here we show that Fhl3, a scaffold LIM domain protein of previously unknown developmental function, is essential for neural crest formation by linking BMP and WNT signaling thereby positioning the neural crest-inducing signaling center in the paraxial mesoderm. During gastrulation, Fhl3 promotes Smad phosphorylation and Smad-dependentwnt8activation specifically in the paraxial mesoderm, thus modifying the respective mesoderm or ectoderm cell response to the extracellular BMP gradient. This ensures neural border ectoderm specification by the underlying mesoderm via non-cell autonomous WNT signaling. During neurulation, neural crest inducers activatefhl3,promoting BMP/Smad-dependent WNT activity required for neural crest specification. Our findings highlight how Fhl3, acting cell-autonomously, ensures a fine spatial, temporal and germ layer-specific coordination of BMP and WNT signaling at several steps of neural crest development.

Highlights:

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FHL3 is a novel intracellular enhancer of BMP signaling during early development.

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FHL3 ensures cross-talk between BMP and WNT signaling by Smad1-dependent wnt8 activation in the paraxial mesoderm.

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FHL3 reiterated function in paraxial mesoderm and in neural border ectoderm is essential for neural crest development at the border of the neural plate.
Tunable genetic devices through simultaneous control of transcription and translation
Authors: Bartoli Vittorio , Meaker Grace A. , Bernardo Mario di , Gorochowski Thomas E.
Published: July 2019

Synthetic genetic circuits allow us to modify the behavior of living cells. However, changes in environmental conditions and unforeseen interactions with the host cell can cause deviations from a desired function, resulting in the need for time-consuming reassembly to fix these issues. Here, we use a regulatory motif that controls transcription and translation to create genetic devices whose response functions can be dynamically tuned. This allows us, after construction, to shift the on and off states of a sensor by 4.5- and 28-fold, respectively, and modify genetic NOT and NOR logic gates to allow their transitions between states to be varied over a >6-fold range. In all cases, tuning leads to trade-offs in the fold-change and the ability to distinguish cellular states. This work lays the foundation for adaptive genetic circuits that can be tuned after their physical assembly to maintain functionality across diverse environments and design contexts.
An artificial neural network identifies glyphosate-impacted brackish communities based on 16S rRNA amplicon MiSeq read counts
Authors: Janßen René , Zabel Jakob , von Lukas Uwe , Labrenz Matthias
Published: July 2019

Artificial neural networks can be trained on complex data sets to detect, predict, or model specific aspects. Aim of this study was to train an artificial neural network to support environmental monitoring efforts in case of a contamination event by detecting induced changes towards the microbial communities. The neural net was trained on taxonomic cluster count tables obtained via next-generation amplicon sequencing of water column samples originating from a lab microcosm incubation experiment conducted over 140 days to determine the effects of the herbicide glyphosate on succession within brackish-water microbial communities. Glyphosate-treated assemblages were classified correctly; a subsetting approach identified the clusters primarily responsible for this, permitting the reduction of input features. This study demonstrates the potential of artificial neural networks to predict indicator species in cases of glyphosate contamination. The results could empower the development of environmental monitoring strategies with applications limited to neither glyphosate nor amplicon sequence data.

Highlight bullet points

An artificial neural net was able to identify glyphosate-affected microbial community assemblages based on next generation sequencing data

Decision-relevant taxonomic clusters can be identified by a stochastically subsetting approach

Just a fraction of present clusters is needed for classification

Filtering of input data improves classification
Dirichlet-multinomial modelling outperforms alternatives for analysis of microbiome and other ecological count data
Authors: Harrison Joshua G. , Calder W. John , Shastry Vivaswat , Buerkle C. Alex
Published: July 2019

Molecular ecology regularly requires the analysis of count data that reflect the relative abundance of features of a composition (e.g., taxa in a community, gene transcripts in a tissue). The sampling process that generates these data can be modeled using the multinomial distribution. Replicate multinomial samples inform the relative abundances of features in an underlying Dirichlet distribution. These distributions together form a hierarchical model for relative abundances among replicates and sampling groups. This type of Dirichlet-multinomial modelling (DMM) has been described previously, but its benefits and limitations are largely untested. With simulated data, we quantified the ability of DMM to detect differences in proportions between treatment and control groups, and compared the efficacy of three computational methods to implement DMM—Hamiltonian Monte Carlo (HMC), variational inference (VI), and Gibbs Markov chain Monte Carlo. We report that DMM was better able to detect shifts in relative abundances than analogous analytical tools, while identifying an acceptably low number of false positives. Among methods for implementing DMM, HMC provided the most accurate estimates of relative abundances, and VI was the most computationally efficient. The sensitivity of DMM was exemplified through analysis of previously published data describing lung microbiomes. We report that DMM identified several potentially pathogenic, bacterial taxa as more abundant in the lungs of children who aspirated foreign material during swallowing; these differences went undetected with different statistical approaches. Our results suggest that DMM has strong potential as a statistical method to guide inference in molecular ecology.
Coronary arterial development is regulated by a Dll4-Jag1-EphrinB2 signaling cascade
Authors: Travisano Stanislao Igor , Oliveira Vera Lucia , Prados Belén , Grego-Bessa Joaquim , Bou Vanesa , Gómez Manuel José , Sánchez-Cabo Fátima , MacGrogan Donal , de la Pompa José Luis
Published: July 2019

Coronaries are essential for myocardial growth and heart function. Notch is crucial for mouse embryonic angiogenesis, but its role in coronary development remains uncertain. We show Jag1, Dll4 and activated Notch1 receptor expression in sinus venosus (SV) endocardium. EndocardialJag1removal blocks SV capillary sprouting, whileDll4inactivation stimulates excessive capillary growth, suggesting that ligand antagonism regulates coronary primary plexus formation. Later endothelial ligand removal, or forced expression of Dll4 or the glycosyltransferase MFng, blocks coronary plexus remodeling, arterial differentiation, and perivascular cell maturation. Endocardial deletion ofEfnb2phenocopies the coronary arterial defects of Notch mutants. Angiogenic rescue experiments in ventricular explants, or in primary human endothelial cells, indicate that EphrinB2 is a critical effector of antagonistic Dll4 and Jag1 functions in arterial morphogenesis. Thus, coronary arterial precursors are specified in the SV prior to primary coronary plexus formation and subsequent arterial differentiation depends on a Dll4-Jag1-EphrinB2 signaling cascade.
Detection of novel allelic variations in soybean mutant population using Tilling by Sequencing
Authors: Millas Reneth , Espina Mary , Ahmed CM Sabbir , Bernardini Angelina , Adeleke Ekundayo , Yadegari Zeinab , Dumenyo Korsi , Taheri Ali
Published: July 2019

One of the most important tools in genetic improvement is mutagenesis, which is a useful tool to induce genetic and phenotypic variation for trait improvement and discovery of novel genes. JTN-5203 (MG V) mutant population was generated using an induced ethyl methane sulfonate (EMS) mutagenesis and was used for detection of induced mutations in FAD2-1A and FAD2-1B genes using reverse genetics approach. Optimum concentration of EMS was used to treat 15,000 bulk JTN-5203 seeds producing 1,820 M2 population. DNA was extracted, normalized, and pooled from these individuals. Specific primers were designed from FAD2-1A and FAD2-1B genes that are involved in the fatty acid biosynthesis pathway for further analysis using next-generation sequencing. High throughput mutation discovery through TILLING-by-Sequencing approach was used to detect novel allelic variations in this population. Several mutations and allelic variations with high impacts were detected for FAD2-1A and FAD2-1B. This includes GC to AT transition mutations in FAD2-1A (20%) and FAD2-1B (69%). Mutation density for this population is estimated to be about 1/136kb. Through mutagenesis and high-throughput sequencing technologies, novel alleles underlying the mutations observed in mutants with reduced polyunsaturated fatty acids will be identified, and these mutants can be further used in breeding soybean lines with improved fatty acid profile, thereby developing heart-healthy-soybeans.
Neuromagnetic activation dynamics of stimulus-locked processing during a naturalistic viewing
Authors: Nunes Adonay S. , Kozhemiako Nataliia , Moiseev Alexander , Seymour Robert A. , Cheung Teresa P. L. , Ribary Urs , Doesburg Sam M.
Published: July 2019

Naturalistic stimuli such as watching a movie while in the scanner provide an ecologically valid paradigm that has the potential of extracting valuable information on how the brain processes complex stimuli in a short period of time. Naturalistic viewing is also easier to conduct with challenging participant groups including patients and children. Given the high temporal resolution of MEG, in the present study, we demonstrate how a short movie clip can be used to map distinguishable activation dynamics underlying the processing of specific classes of visual stimuli such as face and hand manipulations, as well as auditory stimuli with words and non-words.

MEG data were collected from 22 healthy volunteers (6 females, 3 left handed, mean age – 27.7 ± 5.28 years) during the presentation of naturalistic audiovisual stimuli. The MEG data were split into trials with the onset of the stimuli belonging to classes of interest (words, non-words, faces, hand manipulations). Based on the components of the averaged sensor ERFs time-locked to the visual and auditory stimulus onset, four and three time-windows, respectively, were defined to explore brain activation dynamics. Pseudo-Z, defined as the ratio of the source-projected time-locked power to the projected noise power for each vertex, was computed and used as a proxy of time-locked brain activation. Statistical testing using the mean-centered Partial Least Squares analysis indicated periods where a given visual or auditory stimuli had higher activation. Based on peak pseudo-Z differences between the visual conditions, time-frequency resolved analyses were carried to assess beta band desynchronization in motor-related areas, and inter-trial phase synchronization between face processing areas. Our results provide the first evidence that activation dynamics in canonical brain regions associated with the processing of particular classes of visual and auditory stimuli (words, faces, etc.) can be reliably mapped using MEG during presentation of naturalistic stimuli. Given the strength of MEG for brain mapping in temporal and frequency domains, the use of naturalistic stimuli may open new techniques in analyzing brain dynamics during ecologically valid sensation and perception.

Highlights

A time-locking analysis was employed in naturalistic stimuli paradigm.

Specific visual and auditory stimuli from the movie were mapped in brain space.

Motor β-suppression was evident in periods of watching hand manipulation.

Increased synchronization between core face-processing areas was found around 200 and 300ms in the face condition.

Naturalistic viewing paradigms provide a reliable approach for investigating brain dynamics.
Evidence that the TRPV1 S1-S4 Membrane Domain Contributes to Thermosensing
Authors: Kim Minjoo , Sisco Nicholas J. , Hilton Jacob K. , Montano Camila M. , Castro Manuel A. , Cherry Brian R. , Levitus Marcia , Van Horn Wade D.
Published: July 2019

Sensing and responding to temperature is crucial in biology. The TRPV1 ion channel is a well-studied heat-sensing receptor that is also activated by vanilloid compounds including capsaicin. Despite significant interest, the molecular underpinnings of thermosensing have remained elusive. The TRPV1 S1-S4 membrane domain couples chemical ligand binding to the pore domain during channel gating. However, the role of the S1-S4 domain in thermosensing is unclear. Evaluation of the isolated human TRPV1 S1-S4 domain by solution NMR, Far-UV CD, and intrinsic fluorescence shows that this domain undergoes a non-denaturing temperature-dependent transition with a high thermosensitivity. Further NMR characterization of the temperature-dependent conformational changes suggests the contribution of the S1-S4 domain to thermosensing shares features with known coupling mechanisms between this domain with ligand and pH activation. Taken together, this study shows that the TRPV1 S1-S4 domain contributes to TRPV1 temperature-dependent activation.
Dicer1 is reduced in APPswe/PSEN1dE9 mice and is regulated by Nrf2
Authors: Wang Yan , Lian Meiling , Zhou Jing , Wu Shengzhou
Published: July 2019

The pathogenesis of Alzheimer’s disease (AD) involves the central roles of oxidative stress. Oxidative stress due to Dicer1 depletion may underline the neurodegeneration in the central nervous system and degeneration of retinal pigment epithelial cells in geographic atrophy form of age-related macular degeneration. We hypothesized that Dicer1 may play roles in AD pathogenesis. Indeed, Dicer1 was reduced in the hippocampus and cortex of APPswe/PSEN1dE9 mice, an AD model. Dicer1 knockdown induced oxidative stress, mitochondrial dysfunction, apoptosis in cultured neurons, and increased secretions of interleukin-1β/-18, indicators of inflammasome activation. Accordingly, Dicer1 was decreased by amyloid peptide and the effect was connected with down-regulation of nuclear factor erythroid 2-related factor 2 (Nrf2). Anti-oxidant response elements (AREs) were identified in the promoter ofDicer1and Keap1-Nrf2-AREs signaling was demonstrated to regulate Dicer1 expression. Furthermore, overexpression of Dicer1 carried by adenovirus in the cultured neurons rescued neurite deficit induced by amyloid peptide. In consistent with thein vitroresults, injection of Dicer1-overexperssion adenovirus in the hippocampus of the AD mice significantly improved spatial learning. Altogether, we unveiled an unexploited roles of Dicer1 in AD and a novel way of Dicer1 regulation. These findings suggest that Dicer1 may be a target in AD therapy.

Significance Statement

Dicer1 is a microRNA-processing enzyme, which is central to microRNA maturation. For the first time, we herein reported that Dicer1 was reduced in the hippocampus or the cortex of AD mice before overt amyloid plque deposition and overexpression of Dicer1 in the hippocampus significantly improved spatial learning in AD mice. We also demonstrated that Dicer1 was regulated by Keap1-Nrf2-ARE signaling which is unreported before. These findings advance understandings of AD pathogenesis and suggest that Dicer1 may be a molecular target in AD therapy.