bluuebunny/crossref_metadata_2025 huggingface dataset:
Tissue of Origin Dictates GOT1 Dependence and Confers Synthetic Lethality to Radiotherapy
Authors: Nelson Barbara S. , Lin Lin , Kremer Daniel M. , Sousa Cristovão M. , Cotta-Ramusino Cecilia , Myers Amy , Ramos Johanna , Gao Tina , Kovalenko Ilya , Wilder-Romans Kari , Dresser Joseph , Davis Mary , Lee Ho-Joon , Nwosu Zeribe C. , Campit Scott , Mashadova Oksana , Nicolay Brandon N. , Tolstyka Zachary P. , Halbrook Christopher J. , Chandrasekaran Sriram , Asara John M. , Crawford Howard C. , Cantley Lewis C. , Kimmelman Alec C. , Wahl Daniel R. , Lyssiotis Costas A.
Published: July 2019

Metabolic programs in cancer cells are influenced by genotype and the tissue of origin. We have previously shown that central carbon metabolism is rewired in pancreatic ductal adenocarcinoma (PDA) to support proliferation through a glutamate oxaloacetate transaminase 1 (GOT1)-dependent pathway. Here we tested if tissue type impacted GOT1 dependence by comparing PDA and colorectal cancer (CRC) cell lines and tumor models of similar genotype. We found CRC to be insensitive to GOT1 inhibition, contrasting markedly with PDA, which exhibit profound growth inhibition upon GOT1 knockdown. Utilizing a combination of metabolomics strategies and computational modeling, we found that GOT1 inhibition disrupted glycolysis, nucleotide metabolism, and redox homeostasis in PDA but not CRC. These insights were leveraged in PDA, where we demonstrate that radiotherapy potently enhanced the effect of GOT1 inhibition on tumor growth. Taken together, these results illustrate the role of tissue type in dictating metabolic dependencies and provide new insights for targeting metabolism to treat PDA.
Non-spherical coacervate shapes in an enzyme driven active system
Authors: Spoelstra Willem Kasper , van der Sluis Eli O. , Dogterom Marileen , Reese Louis
Published: July 2019

Coacervates are polymer-rich droplets that form through liquid-liquid phase separation in polymer solutions. Liquid-liquid phase separation and coacervation have recently been shown to play an important role in the organization of biological systems. Such systems are highly dynamic and under continuous influence of enzymatic and chemical processes. However, it is still unclear how enzymatic and chemical reactions affect the coacervation process. Here, we present and characterize a system of enzymatically active coacervates containing spermine, RNA, free nucleotides, and the template independent RNA (de)polymerase PNPase. We find that these RNA coacervates display transient non-spherical shapes, and we systematically study how PNPase concentration, UDP concentration and temperature affect coacervate morphology. Furthermore, we show that PNPase localizes predominantly into the coacervate phase and that its depolymerization activity in high-phosphate buffer causes coacervate degradation. Our observations of non-spherical coacervate shapes may have broader implications for the relationship between (bio-)chemical activity and coacervate biology.
Short-term block of CRH receptor in adults mitigates age-related memory impairments provoked by early-life adversity
Authors: Short Annabel K. , Maras Pamela M. , Pham Aidan L. , Ivy Autumn S. , Baram Tallie Z.
Published: July 2019

In humans, early-life adversity (ELA) is associated with impairments in learning and memory that may emerge later in life. In rodent models, ELA directly impacts hippocampal neuron structure and connectivity with progressive deficits in long-term potentiation and spatial memory function. Previous work has demonstrated that augmented release and actions of the stress-activated neuropeptide, CRH, contribute to the deleterious effects of ELA on hippocampal structure and memory-function. Early-life adversity increases CRH production and levels, and blocking CRH receptor type 1 (CRHR1) within the hippocampus immediately following adversity prevented the memory and LTP problems caused by ELA. Here we queried if blocking CRHR1 during adulthood ameliorates the adverse impact of ELA on memory in middle age. Blocking CRHR1 for a week in two month old male rats prevented ELA-induced deficits in object recognition memory that emerge during middle age. The intervention failed to mitigate the reduction of spatial memory at 4 and 8 months, but restored hippocampus-dependent location memory in ELA-experiencing rats during middle age (12 months of age).

Notably, neither ELA nor blocking CRHR1 influenced anxiety- or depression-related behaviors These findings suggest a sensitive period during which interventions can fully prevent long-lasting effects of ELA, yet indicate that interventions later in life offer significant benefits.
Cortical encoding of melodic expectations in human temporal cortex
Authors: Di Liberto Giovanni M. , Pelofi Claire , Bianco Roberta , Patel Prachi , Mehta Ashesh D. , Herrero Jose L. , de Cheveigné Alain , Shamma Shihab , Mesgarani Nima
Published: July 2019

Humans engagement in music rests on underlying elements such as the listeners’ cultural background and general interest in music, all shaping the way music is processed in the brain and perceived. Crucially, these factors modulate how listeners anticipate musical events, a process inducing instantaneous neural responses as the music confronts these expectations. Measuring such neural correlates would represent a direct window into high-level brain processing of music. Here we recorded electroencephalographic and electrocorticographic brain responses as participants listened to Bach melodies. We assessed the relative contributions of the acoustic versus melodic components of the music to the neural signal. Acoustic features included envelope and its derivative. Melodic features included information on melodic progressions (pitch) and their tempo (onsets), which were extracted from a Markov model predicting the next note based on a corpus of Western music and the preceding proximal musical context. We related the music to brain activity with a linear temporal response function, and demonstrated that cortical responses to music encode melodic expectations. Specifically, individual-subject neural signals were better predicted by a combination of acoustic and melodic expectation features than by either alone. This effect was most pronounced at response latencies up to 350ms, and in both planum temporale and Heschl’s gyrus. Finally, expectations of pitch and onset-time of musical notes exerted independent cortical effects, and such influences were modulated by the listeners’ musical expertise. Overall, this study demonstrates how the interplay of experimental and theoretical approaches can yield novel insights into the cortical encoding of melodic expectations.
How to make “number lines” stable in the mind’s eye
Authors: Pinto Mario , Pellegrino Michele , Marson Fabio , Lasaponara Stefano , Cestari Vincenzo , Doricchi Fabrizio
Published: July 2019

Humans are prone to mentally organise the ascending series of integers according to reading habits, so that in western cultures small numbers are positioned to the left of larger ones on a mental number line (MNL, Dehaene et al., 1993). Despite 140 years since seminal observations made by Sir Francis Galton in human observers that experienced vivid MNLs (Galton, 1880a,b), the neural and functional mechanisms that give rise to MNLs remain elusive. Here, in a series of three experiments we show that spatially organised MNLs are not “all or none” phenomena and that MNLs get progressively less noisy and more stable in the mind’s eye, the more an observer fully combines left/right spatial codes with small/large magnitude codes to operate on numbers. These results show that conceptualising the ascending series of integers in spatial terms depends on contextual clues rather than being inherent to the semantic representation of numbers.
Transcription-mediated organization of the replication initiation program across large genes sets up common fragile sites genome-wide
Authors: Brison Olivier , EL-Hilali Sami , Azar Dana , Koundrioukoff Stéphane , Schmidt Mélanie , Naehse-Kumpf Viola , Jaszczyszyn Yan , Lachages Anne-Marie , Dutrillaux Bernard , Thermes Claude , Debatisse Michelle , Chen Chun-Long
Published: July 2019

Common Fragile Sites (CFSs) are chromosome regions prone to breakage under replication stress, known to drive chromosome rearrangements during oncogenesis. Most CFSs nest in large expressed genes, suggesting that transcription elicits their instability but the underlying mechanisms remained elusive. Analyses of genome-wide replication timing of human lymphoblasts here show that stress-induced delayed/under-replication is the hallmark of CFSs. Extensive genome-wide analyses of nascent transcripts, replication origin positioning and fork directionality reveal that 80% of CFSs nest in large transcribed domains poor in initiation events, thus replicated by long-traveling forks. In contrast to formation of sequence-dependent fork barriers or head-on transcription-replication conflicts, traveling-long in late S phase explains CFS replication features. We further show that transcription inhibition during the S phase, which excludes the setting of new replication origins, fails to rescue CFS stability. Altogether, results show that transcription-dependent suppression of initiation events delays replication of large gene body, committing them to instability.
Uncovering Staphylococcus aureus genes with roles in pathogenicity by silkworm infection model
Authors: Paudel Atmika , Hamamoto Hiroshi , Panthee Suresh , Matsumoto Yasuhiko , Sekimizu Kazuhisa
Published: July 2019

The regulatory network of virulence factors production by Staphylococcus aureus, an opportunistic pathogen, is incompletely understood, and the functions of many uncharacterized genes in its genome remain to be uncovered. We screened 380 function unassigned genes disrupted mutants of the community-acquired methicillin-resistant S. aureus USA300 for pathogenicity using silkworms and identified 11 strains with reduced silkworm killing ability. Nine out of the 11 strains displayed reduced virulence in the mouse model as evidenced by reduced colony-forming units in organs of the infected mice. Three of the identified gene-disrupted mutants had reduced hemolytic activity, one among the three also had reduced proteolytic activity and pigment production. These results suggest that silkworm model could identify the genes required for virulence in the mouse model. The newly identified genes involved in virulence in this study facilitates the further understanding of the pathogenicity of S. aureus.

Importance

We performed a large scale screening of mutants of Staphylococcus aureus with disruption in function unassigned genes using silkworm infection model and identified eleven genes required for full virulence in silkworm. Nine of the eleven genes were involved in virulence in mice and were previously not known to aggravate virulence of S. aureus. The results suggest that silkworm model is suitable for quantitative measurement of virulence, which is shared between silkworms and mammals.
NET4 modulates the compactness of vacuoles in Arabidopsis thaliana
Authors: Kaiser Sabrina , Eisa Ahmed , Kleine-Vehn Jürgen , Scheuring David
Published: July 2019

The dimension of the plants largest organelle – the vacuole, plays a major role in defining cellular elongation rates. The morphology of the vacuole is controlled by the actin cytoskeleton but the mechanistic connection between them remains largely elusive. Recently, the NETWORKED (NET) family of membrane-associated, actin-binding proteins has been identified and represent potential candidates to impact on vacuolar morphology. Here, we show that NET4A localizes to highly constricted regions in the vacuolar membrane and contributes to the compactness of the vacuole. Using genetic interference, we found that deregulation of NET4 abundance impacts on vacuole morphogenesis and overexpression leads to more compact vacuoles. We moreover show that the NET4A-induced changes in vacuolar shape correlates with reduced cellular and organ growth in Arabidopsis thaliana. Our results demonstrate that NET4 modulates the compactness of vacuoles and reveal higher complexity in the regulation of actin-reliant vacuolar morphology.
JASS: Command Line and Web interface for the joint analysis of GWAS results
Authors: Julienne Hanna , Lechat Pierre , Guillemot Vincent , Lasry Carla , Yao Chunzi , Laville Vincent , Vilhjalmsson Bjarni , Ménager Hervé , Aschard Hugues
Published: July 2019

Genome Wide Association Study (GWAS) has been the driving force for identifying association between genetic variants and human phenotypes. Thousands of GWAS summary statistics covering a broad range of human traits and diseases are now publicly available, and studies have demonstrated their utility for a range of secondary analyses. This includes in particular the joint analysis of multiple GWAS to identify new genetic variants missed by univariate screenings. However, although several methods have been proposed, there are very few large scale applications published so far because of challenges in implementing these methods on real data. Here, we present JASS (Joint Analysis of Summary Statistics), a polyvalent Python package that addresses this need. Our package solves all practical and computational barriers for large-scale multivariate analysis of GWAS summary statistics. This includes data cleaning and harmonization tools, an efficient algorithm for fast derivation of various joint statistics, an optimized data management process, and a web interface for exploration purposes. Benchmark analyses confirmed the strong performances of JASS. We also performed multiple real data analyses demonstrating the strong potential of JASS for the detection of new associated genetic variants across various scenarios. Our package is freely available at https://gitlab.pasteur.fr/statistical-genetics/jass.
Dopamine-dependent loss aversion during effort-based decision-making
Authors: Chen Xiuli , Voets Sarah , Jenkinson Ned , Galea Joseph M.
Published: July 2019

From psychology to economics there has been substantial interest in how costs (e.g., delay, risk) are represented asymmetrically during decision-making when attempting to gain reward or to avoid punishment. For example, in decision-making under risk, individuals show a tendency to prefer to avoid punishment than to acquire the equivalent reward (loss aversion). Although the cost of physical effort has received significant recent attention due to the evaluation of motor costs being crucial in our daily decisions, it remains unclear whether loss aversion exists during effort-based decision-making. On the one hand, loss aversion may be hardwired due to asymmetric evolutionary pressure on losses and gains and therefore exists across decision-making contexts. On the other hand, distinct brain regions are involved with different decision costs, making it questionable whether similar asymmetries exist. Here, we demonstrate that young healthy participants exhibit loss aversion during effort-based decision-making by exerting more physical effort in order to avoid punishment than to gain a same-size reward. Next, we show that medicated Parkinson’s disease (PD) patients show a reduction in loss aversion compared to age-matched controls. Behavioural and computational analysis revealed that people with PD exerted similar physical effort in return for a reward, but were less willing to produce effort in order to avoid punishment. Therefore, loss aversion is present during effort-based decision-making and can be modulated by altered dopaminergic state. This finding could have important implications for our understanding of clinical disorders that show a reduced willingness to exert effort in the pursuit of reward.

Significance Statement

Loss aversion – preferring to avoid punishment than to acquire equivalent reward – is an important concept in decision-making under risk. However, little is known about whether loss aversion also exists during decisions where the cost is physical effort. This is surprising given that motor cost shapes human behaviour, and a reduced willingness to exert effort is a characteristic of many clinical disorders. Here, we show that healthy individuals exert more effort to minimise punishment than to maximise reward (loss aversion). We also demonstrate that loss aversion is modulated by altered dopaminergic state by showing that medicated Parkinson’s disease patients exert similar effort to gain reward but less effort to avoid punishment. Therefore, dopamine-dependent loss aversion is crucial for explaining effort-based decision-making.
Pre-warming before general anesthesia with isoflurane delays the onset of hypothermia in rats
Authors: Rufiange Maxime , Leung Vivian SY , Simpson Keith , Pang Daniel SJ
Published: July 2019

General anesthesia causes hypothermia by impairing normal thermoregulatory mechanisms. Redistribution of warm blood from the core to the periphery is the primary mechanism in the development of hypothermia and begins following induction of anesthesia. Raising skin temperature before anesthesia reduces the temperature gradient between core and periphery, decreasing the transfer of heat. This prospective, crossover study (n = 17 adult male and female SD rats) compared three treatment groups: PW1% (pre-warming to increase core temperature 1% over baseline), PW40 (pre-warming to increase core temperature to 40°C) and NW (no warming). The PW1% group was completed first to ensure tolerance of pre-warming. Treatment order was then randomized and alternated after a washout period. Once target temperature was achieved, anesthesia was induced and maintained with isoflurane in oxygen without further external temperature support. Pre-warming was effective at delaying the onset of hypothermia, with a significant difference between PW1% (11.2 minutes) and PW40 (14.7 minutes, p = 0.0044 (95%CI −12 to −2.2), PW40 and NW (6.0 minutes, p = 0.003 (95%CI 1.8 to 8.7) and PW1% and PW40 (p = 0.004, 95%CI −12 to −2.2). The rate of heat loss in the pre-warmed groups exceed that of the NW group: PW1% versus NW (p = 0.005, 95%CI 0.004 to 0.027), PW40 versus NW (p < 0.0001, 95%CI 0.014 to 0.036) and PW1% versus PW40 (p = 0.07, 95%CI −0.021 to 0.00066). Pre-warming alone confers a protective effect against hypothermia during volatile anesthesia; however, longer duration procedures would require additional heating support.
Pharmacological evidence for the implication of noradrenaline in effort
Authors: Borderies Nicolas , Mattioni Julia , Bornert Pauline , Gilardeau Sophie , Bouret Sébastien
Published: July 2019

The trade-off between effort and reward is one of the main determinants of behavior and its alteration is at the heart of major disorders such as depression or Parkinson’s disease. Monoaminergic neuromodulators are thought to play a key role in this trade-off, but their relative contribution remains unclear. Rhesus monkeys (Macaca mulatta) performed a choice-task requiring a trade-off between the volume of fluid reward and the amount of force to be exerted on a grip. In line with a causal role of noradrenaline in effort, decreasing noradrenaline levels with systemic clonidine injections (0.01mg/kg) decreased exerted force and enhanced the weight of upcoming force on choices, without any effect on reward sensitivity. Computational modeling demonstrated that NA acted on a single hidden variable, which affected both choices (as a variable of decision) and force production (as a driving force). Thus, our data strongly support noradrenaline’s implication in effort processing.
SMAD3 Determines Conventional versus Plasmacytoid Dendritic Cell Fates
Authors: Yoon Jeong-Hwan , Bae Eunjin , Sudo Katsuko , Han Jin Soo , Park Seok Hee , Nakae Susumu , Yamashita Tadashi , Lee In-Kyu , Ju Ji Hyeon , Matsumoto Isao , Sumida Takayuki , Kuroda Masahiko , Miyazawa Keiji , Kato Mitsuyasu , Mamura Mizuko
Published: July 2019

Transforming growth factor (TGF)-β plays crucial roles in differentiation of dendritic cells (DC). However, molecular mechanisms how TGF-β regulates DC differentiation remain largely unknown. Here, we show that selective repression of one of the TGF-β receptor-regulated SMADs (R-SMADs), SMAD3 directs conventional DC (cDC) differentiation, whereas maintenance of SMAD3 is indispensable for plasmacytoid DC (pDC) differentiation. Expression of SMAD3 was specifically downregulated in CD115+common DC progenitor (CDP), pre-cDCs and cDCs. SMAD3 deficient mice showed a significant reduction in pre-pDCs and pDCs with increased CDP, pre-cDCs and cDCs. SMAD3 upregulated the pDC-related genes: SPI-B, E2-2 and IKAROS, while it repressed FLT3 and the cDC-related genes: IRF4 and ID2. STAT3 and a SMAD transcriptional co-repressor, c-SKI repressed SMAD3 for cDC differentiation, whereas canonical SMAD-mediated TGF-β signalling maintained SMAD3 for pDC differentiation. Thus, SMAD3 is the pivotal determinant to bifurcate cDC and pDC differentiation in the steady-state condition.
Resolvin D3 controls mouse and human nociceptive functions and preclinical progression of psoriasis
Authors: Lee Sang Hoon , Tonello Raquel , Im Sang-Taek , Jeon Hawon , Park Jeongsu , Ford Zachary , Davidson Steve , Kim Yong Ho , Park Chul-Kyu , Berta Temugin
Published: July 2019

Psoriasis is a chronic inflammatory skin disease caused by a complex interplay between the immune and nervous systems. Here, we found that resolvin D3 (RvD3) significantly prevented both skin inflammation and itch in a preclinical animal model of psoriasis induced by repeated applications of imiquimod. We also found that RvD3 anti-psoriatic effects resulted from the inhibition of nociceptive functions, which inhibition was replicated in human nociceptive neurons. We conclude that RvD3 and targeting nociceptive functions are promising strategies to treat psoriasis.
Less is more: Coarse-grained integrative modeling of large biomolecular assemblies with HADDOCK
Authors: Roel-Touris Jorge , Don Charleen G. , Honorato Rodrigo V. , Rodrigues João P.G.L.M , Bonvin Alexandre M.J.J.
Published: July 2019

Predicting the 3D structure of protein interactions remains a challenge in the field of computational structural biology. This is in part due to difficulties in sampling the complex energy landscape of multiple interacting flexible polypeptide chains. Coarse-graining approaches, which reduce the number of degrees of freedom of the system, help address this limitation by smoothing the energy landscape, allowing an easier identification of the global energy minimum. They also accelerate the calculations, allowing to model larger assemblies. Here, we present the implementation of the MARTINI coarse-grained force field for proteins into HADDOCK, our integrative modelling platform. Docking and refinement are performed at the coarse-grained level and the resulting models are then converted back to atomistic resolution through a distance restraints-guided morphing procedure. Our protocol, tested on the largest complexes of the protein docking benchmark 5, shows an overall ~7-fold speed increase compared to standard all-atom calculations, while maintaining a similar accuracy and yielding substantially more near-native solutions. To showcase the potential of our method, we performed simultaneous 7 body docking to model the 1:6 KaiC-KaiB complex, integrating mutagenesis and hydrogen/deuterium exchange data from mass spectrometry with symmetry restraints, and validated the resulting models against a recently published cryo-EM structure.
Hippocampal Subfield Volumes in Abstinent Men and Women with a History of Alcohol Use Disorder
Authors: Sawyer Kayle S. , Adra Noor , Salz Daniel M. , Kemppainen Maaria I. , Ruiz Susan M. , Harris Gordon J. , Oscar-Berman Marlene
Published: July 2019

Alcohol use disorder (AUD) has been associated with abnormalities in hippocampal volumes, but these relationships have not been fully explored with respect to sub-regional volumes, nor in association with individual characteristics such as gender differences, age, and memory. The present study examined the impact of those variables in relation to hippocampal subfield volumes in abstinent men and women with a history of AUD. Using Magnetic Resonance Imaging at 3 Tesla, we obtained brain images from 67 participants (31 women) with AUD and 63 healthy control (NC) participants (30 women) without AUD. We used Freesurfer 6.0 to segment the hippocampus into 12 regions. These were imputed into mixed models to examine the relationships of brain volume with AUD group, gender, age, drinking history, and memory. The AUD group had approximately 5% smaller CA1, hippocampal tail, and molecular layer regions than the NC group. Age was negatively associated with volumes for the AUD group in the hippocampal tail, subiculum, and presubiculum. The relationships for delayed and immediate memory with hippocampal tail volume differed for AUD and NC groups: Higher scores were associated with smaller volumes in the AUD group, but larger volumes in the NC group. Length of sobriety was associated with decreasing CA1 volume in women (0.02% per year) and increasing volume size in men (0.03% per year). These findings confirm and extend evidence that AUD, gender, age, and abstinence differentially impact volumes of component parts of the hippocampus. The course of abstinence on CA1 volume differed for men and women, and the differential relationships of subregional volumes to age and memory could indicate a distinction in the impact of AUD on functions of the hippocampal tail.
High-throughput identification of MHC class I binding peptides using an ultradense peptide array
Authors: Haj Amelia K. , Breitbach Meghan E. , Baker David A. , Mohns Mariel S. , Moreno Gage K. , Wilson Nancy A. , Lyamichev Victor , Patel Jigar , Weisgrau Kim L. , Dudley Dawn M. , O’Connor David H.
Published: July 2019

Rational vaccine development and evaluation requires identifying and measuring the magnitude of epitope-specific CD8 T cell responses. However, conventional CD8 T cell epitope discovery methods are labor-intensive and do not scale well. Here, we accelerate this process by using an ultradense peptide array as a high-throughput tool for screening peptides to identify putative novel epitopes. In a single experiment, we directly assess the binding of four common Indian rhesus macaque MHC class I molecules – Mamu-A1*001, -A1*002, -B*008, and -B*017 – to approximately 61,000 8-mer, 9-mer, and 10-mer peptides derived from the full proteomes of 82 simian immunodeficiency virus (SIV) and simian-human immunodeficiency virus (SHIV) isolates. Many epitope-specific CD8 T cell responses restricted by these four MHC molecules have already been identified in SIVmac239, providing an ideal dataset for validating the array; up to 64% of these known epitopes are found in the top 192 SIVmac239 peptides with the most intense MHC binding signals in our experiment. To assess whether the peptide array identified putative novel CD8 T cell epitopes, we validated the method by IFN-γ ELISPOT assay and found three novel peptides that induced CD8 T cell responses in at least two Mamu-A1*001-positive animals; two of these were validated byex vivotetramer staining. This high-throughput identification of peptides that bind class I MHC will enable more efficient CD8 T cell response profiling for vaccine development, particularly for pathogens with complex proteomes where few epitope-specific responses have been defined.
Functional localization of the frontal eye fields in the common marmoset using microstimulation
Authors: Selvanayagam Janahan , Johnston Kevin D. , Schaeffer David J. , Hayrynen Lauren K. , Everling Stefan
Published: July 2019

The frontal eye field (FEF) is a critical region for the deployment of overt and covert spatial attention. While investigations in the macaque continue to provide insight into the neural underpinnings of the FEF, due to its location within a sulcus the macaque FEF is virtually inaccessible to electrophysiological techniques such as high-density and laminar recordings. With a largely lissencephalic cortex, the common marmoset (Callithrix jacchus) is a promising alternative primate model for studying FEF microcircuitry. Putative homologies have been established with the macaque FEF on the basis of cytoarchitecture and connectivity, however physiological investigation in awake, behaving marmosets is necessary to physiologically locate this area. Here we addressed this gap using intracortical microstimulation in a broad range of frontal cortical areas in marmosets. We implanted marmosets with 96-channel Utah arrays and applied microstimulation trains while they freely viewed video clips. We evoked short-latency fixed vector saccades at low currents (<50 μA) in areas 45, 8aV, 8C and 6DR. We observed a topography of saccade direction and amplitude consistent with findings in macaques and humans; we observed small saccades in ventrolateral FEF and large saccades combined with contralateral neck and shoulder movements encoded in dorsomedial FEF. Our data provide compelling evidence supporting homology between marmoset and macaque FEF and suggest the marmoset is a useful primate model for investigating FEF microcircuitry and its contributions to oculomotor and cognitive functions.

Significance Statement

The frontal eye field (FEF) is a critical cortical region for overt and covert spatial attention. The microcircuitry of this area remains poorly understood, as in the macaque, the most commonly used model, it is embedded within a sulcus and is inaccessible to modern electrophysiological and optical imaging techniques. The common marmoset is a promising alternative primate model due to its lissencephalic cortex and potential for genetic manipulation. However, evidence for homologous cortical areas in this model remains limited and unclear. Here we applied microstimulation in frontal cortical areas in marmosets to physiologically identify the FEF. Our results provide compelling evidence for a frontal eye field in the marmoset, and suggest that the marmoset is a useful model for FEF microcircuitry.
Monotonous behavior with 2-propanol converts into reentrant transition with 1-propanol: Higher-order structure of DNA
Authors: Ma Y. , Yoshikawa Y. , Yoshikawa K.
Published: July 2019

In the present study, we measured the changes in the higher-order structure of genomic DNA molecules in the presence of alcohols through single-DNA observation by use of fluorescence microscopy, with particular focus on the different effects of 1-propanol and 2-propanol. The results showed that, with an increasing concentration of 1-propanol, DNA exhibits reentrant conformational transitions from an elongated coil to a folded globule, and then to an unfolded state. On the other hand, with 2-propanol, DNA exhibits monotonous shrinkage into a compact state. Thus, DNA molecules are more effectively condensed/precipitated with 2-propanol than with 1-propanol. The propanol isomers also had different effects on the changes in the secondary structure of DNA, as revealed by circular dichroism (CD) measurements. With 1-propanol, DNA maintains a B-form secondary structure. An A-like conformation appears with the addition of 2-propanol.

STATEMENT OF SIGNIFICANCE

Currently, 2-propanol has most often been used as the solvent to extract and purify genomic DNA molecules from living cells, according the protocols in molecular biology and biochemistry. Unfortunately, the reason why usage of 2-propanol is recommended instead of ethanol and 1-propanol has never been explained in a clear manner. We believe that the new insight based on chemical physics point of view would play an important role for the development of current chemical procedures/treatments adapted on an empirical basis.
Multiplexed Single Ion Mass Spectrometry Improves Measurement of Proteoforms and Their Complexes
Authors: Kafader Jared O. , Melani Rafael D. , Durbin Kenneth R. , Ikwuagwu Bon , Early Bryan P. , Fellers Ryan T. , Beu Steven C. , Zabrouskov Vlad , Makarov Alexander A. , Maze Joshua T. , Shinholt Deven L. , Yip Ping F. , Tullman-Ercek Danielle , Senko Michael W. , Compton Philip D. , Kelleher Neil L.
Published: July 2019

A new Orbitrap-based single ion analysis procedure is shown to be possible by determining the direct charge on numerous measurements of individual protein ions to generate true mass spectra. The deployment of an Orbitrap system for charge detection enables the characterization of highly complicated mixtures of proteoforms and their complexes in both denatured and native modes of operation, revealing information not obtainable by traditional measurement of an ensemble of ions.
Recognition of histone H3 methylation states by the PHD1 domain of histone demethylase KDM5A
Authors: Longbotham James E , Kelly Mark J S , Galonić Fujimori Danica
Published: July 2019

PHD reader domains are chromatin binding modules often responsible for the recruitment of large protein complexes that contain histone modifying enzymes, chromatin remodelers and DNA repair machinery. A majority of PHD domains recognize N–terminal residues of histone H3 and are sensitive to the methylation state of Lys4 in histone H3 (H3K4). Histone demethylase KDM5A, an epigenetic eraser enzyme that contains three PHD domains, is often overexpressed in various cancers and its demethylation activity is allosterically enhanced when its PHD1 domain is bound to the H3 tail. The allosteric regulatory function of PHD1 expands roles of reader domains, suggesting unique features of this chromatin interacting module. Our previous studies determined the H3 binding site of PHD1, although it remains unclear how the H3 tail interacts with the N–terminal residues of PHD1 and how PHD1 discriminates against H3 tails with varying degrees of H3K4 methylation. Here we have determined the solution structure of apo and H3 bound PHD1. We observe conformational changes occurring in PHD1 in order to accommodate H3, which interestingly binds in a helical conformation. We also observe differential interactions of binding residues with differently methylated H3K4 peptides (me0, me1, me2 or me3), providing a rational for this PHD1 domain’s preference for lower methylation states of H3K4. We further assessed the contributions of various H3 interacting residues in the PHD1 domain to the binding of H3 peptides. The structural information of the H3 binding site could provide useful information to aid development of allosteric small molecule modulators of KDM5A.
Contextual Classifications of Cancer Driver Genes
Authors: Chandrashekar Pramod , Ahmadinejad Navid , Wang Junwen , Sekulic Aleksandar , Egan Jan B. , Asmann Yan W. , Maley Carlo , Liu Li
Published: July 2019

Functions of cancer driver genes depend on cellular contexts that vary substantially across tissues and organs. Distinguishing oncogenes (OGs) and tumor suppressor genes (TSGs) for each cancer type is critical to identifying clinically actionable targets. However, current resources for context-aware classifications of cancer drivers are limited. In this study, we show that the direction and magnitude of somatic selection of missense and truncating mutations of a gene are suggestive of its contextual activities. By integrating these features with ratiometric and conservation measures, we developed a computational method to categorize OGs and TSGs using exome sequencing data. This new method, named genes under selection in tumors (GUST) shows an overall accuracy of 0.94 when tested on manually curated benchmarks. Application of GUST to 10,172 tumor exomes of 33 cancer types identified 98 OGs and 179 TSGs, >70% of which promote tumorigenesis in only one cancer type. In broad-spectrum drivers shared across multiple cancer types, we found heterogeneous mutational hotspots modifying distinct functional domains, implicating the synchrony of convergent and divergent disease mechanisms. We further discovered two novel OGs and 28 novel TSGs with high confidence. The GUST program is available at https://github.com/liliulab/gust. A database with pre-computed classifications is available at https://liliulab.shinyapps.io/gust
Genetic and environmental canalization are not associated among altitudinally varying populations ofDrosophila melanogaster
Authors: Pesevski Maria , Dworkin Ian
Published: July 2019

Organisms are exposed to environmental and mutational effects influencing both mean and variance of phenotypes. Potentially deleterious effects arising from this variation can be reduced by the evolution of buffering (canalizing) mechanisms, ultimately reducing phenotypic variability. As such, there has been interest regarding the plausible conditions that enable canalizing mechanisms to evolve. Under some models, the circumstances under which genetic canalization evolves is limited, despite apparent empirical evidence for it. It has been argued that canalizing mechanisms for mutational effects may evolve as a correlated response to environmental canalization (the congruence model). Yet, empirical evidence has not consistently supported the prediction of a correlation between genetic and environmental canalization. In a recent study, a population ofDrosophila melanogasteradapted to high altitude showed evidence of genetic decanalization relative to those from low-altitudes. Using strains derived from these populations, we tested if they also varied for environmental canalization, rearing them at different temperatures. Using wing morphology, we quantified size, shape, cell (trichome) density and frequencies of mutational defects. We observed the expected differences in wing size and shape, cell density and mutational defects between the high- and low-altitude populations. However, we observed little evidence for a relationship between a number of measures of environmental canalization with population or with visible defect frequency. Our results do not support the predicted association between genetic and environmental canalization.
Deep learning-based cross-classifications reveal conserved spatial behaviors within tumor histological images
Authors: Noorbakhsh Javad , Farahmand Saman , pour Ali Foroughi , Namburi Sandeep , Caruana Dennis , Rimm David , Soltanieh-ha Mohammad , Zarringhalam Kourosh , Chuang Jeffrey H.
Published: July 2019

Histopathological images are a rich but incompletely explored data type for studying cancer. Manual inspection is time consuming, making it challenging to use for image data mining. Here we show that convolutional neural networks (CNNs) can be systematically applied across cancer types, enabling comparisons to reveal shared spatial behaviors. We develop CNN architectures to analyze 27,815 hematoxylin and eosin slides from The Cancer Genome Atlas for tumor/normal, cancer subtype, and mutation classification. Our CNNs are able to classify tumor/normal status of whole slide images (WSIs) in 19 cancer types with consistently high AUCs (0.995±0.008), as well as subtypes with lower but significant accuracy (AUC 0.87±0.1). Remarkably, tumor/normal CNNs trained on one tissue are effective in others (AUC 0.88±0.11), with classifier relationships also recapitulating known adenocarcinoma, carcinoma, and developmental biology. Moreover, classifier comparisons reveal intra-slide spatial similarities, with average tile-level correlation of 0.45±0.16 between classifier pairs. Breast cancers, bladder cancers, and uterine cancers have spatial patterns that are particularly easy to detect, suggesting these cancers can be canonical types for image analysis. Patterns for TP53 mutations can also be detected, with WSI self- and cross-tissue AUCs ranging from 0.65-0.80. Finally, we comparatively evaluate CNNs on 170 breast and colon cancer images with pathologist-annotated nuclei, finding that both cellular and intercellular regions contribute to CNN accuracy. These results demonstrate the power of CNNs not only for histopathological classification, but also for cross-comparisons to reveal conserved spatial biology.
A ciliary BBSome-ARL-6-PDE6D pathway trafficks RAB-28, a negative regulator of extracellular vesicle biogenesis
Authors: Akella Jyothi S. , Carter Stephen P. , Rizvi Fatima , Nguyen Ken C.Q. , Tsiropoulou Sofia , Moran Ailís L. , Silva Malan , Kennedy Breandán N. , Hall David H. , Barr Maureen M. , Blacque Oliver E.
Published: July 2019

Cilia both receive and send information, the latter in the form of extracellular vesicles (EVs). EVs are nano-communication devices that cells shed to influence cell, tissue, and organism behavior. Mechanisms driving ciliary EV biogenesis and environment release are almost entirely unknown. Here, we show that the ciliary G-protein RAB28, associated with human autosomal recessive cone-rod dystrophy, negatively regulates EV levels in the sensory organs of Caenorhabditis elegans. We also find that sequential targeting of lipidated RAB28 to periciliary and ciliary membranes is highly dependent on the BBSome and PDE6D, respectively, and that BBSome loss causes excessive and ectopic EV production. Our data indicate that RAB28 and the BBSome are key in vivo regulators of EV production at the periciliary membrane. Our findings also suggest that EVs control sensory organ homeostasis by mediating communication between ciliated neurons and glia, and that defects in ciliary EV biogenesis may contribute to human ciliopathies.
Rising insecticide potency outweighs falling application rate to make US farmland increasingly hazardous to insects
Authors: Douglas Margaret R. , Sponsler Douglas B. , Lonsdorf Eric V. , Grozinger Christina M.
Published: July 2019

Each year, millions of kilograms of insecticides are applied to crops in the US. While insecticide use supports food, fuel, and fiber production, it can also threaten non-target organisms, a concern underscored by mounting evidence of widespread insect decline. Nevertheless, answers to basic questions about the spatiotemporal patterns of insecticide use remain elusive, due in part to the inherent complexity of insecticide use, and exacerbated by the dispersed nature of the relevant data, divided between several government repositories. Here, we integrate these public datasets to generate county-level annual estimates of total ‘insect toxic load’ (honey bee lethal doses) for insecticides applied in the US between 1997-2012, calculated separately for oral and contact toxicity. To explore the underlying drivers of the observed changes, we divide insect toxic load into the components of extent (area treated) and intensity (application rate x potency). We show that while contact-based insect toxic load remained relatively steady over the period of our analysis, oral-based insect toxic load increased roughly 9-fold, with reductions in application rate outweighed by disproportionate increases in potency (toxicity/kg) and increases in extent. This pattern varied markedly by region, with the greatest increases seen in Heartland and Northern Great Plains regions, likely driven by use of neonicotinoid seed treatments in corn and soybean. In this “potency paradox,” US farmland has become more hazardous to insects despite lower volumes of insecticides applied, raising serious concerns about insect conservation and highlighting the importance of integrative approaches to pesticide use monitoring.

Significance statement

Previous analyses disagree about whether US insecticide use is increasing or decreasing, a question of significant importance given the putative role of insecticides in recent insect declines. We integrated information from multiple national databases to estimate ‘insect toxic load’ (represented as honey bee lethal doses) of the agricultural insecticides applied in each US county from 1997 to 2012, and factors responsible for its change. Across the US, insect toxic load – calculated on the basis of oral toxicity – increased 9-fold. This increase was due to increases in the potency (toxicity/kg) of insecticides applied and in the area treated; the volume of insecticides applied declined. Toxic load increased most dramatically in regions where neonicotinoid seed treatments for field crops are commonly used.
Mitochondrial dysfunction is signaled to the integrated stress response by OMA1, DELE1 and HRI
Authors: Guo Xiaoyan , Aviles Giovanni , Liu Yi , Tian Ruilin , Unger Bret A. , Lin Yu-Hsiu T. , Wiita Arun P. , Xu Ke , Correia M. Almira , Kampmann Martin
Published: July 2019

In mammalian cells, mitochondrial dysfunction triggers the integrated stress response (ISR), in which eIF2α phosphorylation upregulates the transcription factor ATF4. However, how mitochondrial stress is relayed to the ISR is unknown. We found that HRI is the eIF2α kinase necessary and sufficient for this relay. Using an unbiased CRISPRi screen, we identified factors upstream of HRI: OMA1, a mitochondrial stress-activated protease, and DELE1, a little-characterized protein we found to be associated with the inner mitochondrial membrane. Mitochondrial stress stimulates the OMA1-dependent cleavage of DELE1, leading to its accumulation in the cytosol, where it interacts with HRI and activates its eIF2α kinase activity. Blockade of the OMA1-DELE1-HRI pathway is beneficial during some, but not all types of mitochondrial stress, and leads to an alternative response that induces specific molecular chaperones. Therefore, this pathway is a potential therapeutic target enabling fine-tuning of the ISR for beneficial outcomes in diseases involving mitochondrial dysfunction.
Testing the ability of species distribution models to infer variable importance
Authors: Smith Adam B. , Santos Maria J.
Published: July 2019

Models of species’ distributions and niches are frequently used to infer the importance of range- and niche-defining variables. However, the degree to which these models can reliably identify important variables and quantify their influence remains unknown. Here we use a series of simulations to explore how well models can 1) discriminate between variables with different influence and 2) calibrate the magnitude of influence relative to an “omniscient” model. To quantify variable importance, we trained generalized additive models (GAMs), Maxent, and boosted regression trees (BRTs) on simulated data and tested their sensitivity to permutations in each predictor. Importance was inferred by calculating the correlation between permuted and unpermuted predictions, and by comparing predictive accuracy of permuted and unpermuted predictions using AUC and the Continuous Boyce Index. In scenarios with one influential and one uninfluential variable, models were unable to discriminate reliably between variables in conditions that are normally challenging for generating accurate predictions: training occurrences <8-64; prevalence >0.5; small spatial extent; environmental data with coarse resolution when spatial autocorrelation is low; and correlation between environmental variables where |r| >0.7. When two variables influenced the distribution equally, importance was underestimated when species had narrow or intermediate niche breadth. Interactions between variables in how they shaped the niche did not affect inferences about their importance. When variables acted unequally, the effect of the stronger variable was overestimated. GAMs and Maxent discriminated between variables more reliably than BRTs, but no algorithm was consistently well-calibrated vis-à-vis the omniscient model. Algorithm-specific measures of importance like Maxent’s change-in-gain metric were less robust than the permutation test. Overall, high predictive accuracy did not connote robust inferential capacity. As a result, requirements for reliably measuring variable importance are likely more stringent than for creating models with high predictive accuracy.