bluuebunny/crossref_metadata_2025 huggingface dataset:
Hyperoxia or Therapeutic Hypothermia During Resuscitation from Non-Lethal Hemorrhagic Shock in Swine
Authors: Nussbaum Benedikt L. , Stenzel Tatjana , Merz Tamara , Scheuerle Angelika , McCook Oscar , Wachter Ulrich , Vogt Josef A. , Matallo José , Gässler Holger , Gröger Michael , Matejovic Martin , Calzia Enrico , Lampl Lorenz , Georgieff Michael , Möller Peter , Asfar Pierre , Radermacher Peter , Hafner Sebastian
Published: May 2017

We previously demonstrated beneficial effects of 22 h of hyperoxia following near-lethal porcine hemorrhagic shock, whereas therapeutic hypothermia was detrimental. Therefore, we investigated whether shorter exposure to hyperoxia (12 h) would still improve organ function, and whether 12 h of hypothermia with subsequent rewarming could avoid deleterious effects after less severe hemorrhagic shock.

Twenty-seven anesthetized and surgically instrumented pigs underwent 3 h of hemorrhagic shock by removal of 30% of the blood volume and titration of the mean arterial blood pressure (MAP) to 40 mm Hg. Post-shock, pigs were randomly assigned to control, hyperoxia (FIO2 100% for 12 h) or hypothermia group (34°C core temperature for 12 h with subsequent rewarming). Before, at the end of shock, after 12 and 23 h of resuscitation, data sets comprising hemodynamics, blood gases, and parameters of inflammation and organ function were acquired. Postmortem, kidney samples were collected for immunohistochemistry and western blotting.

Hyperoxia exerted neither beneficial nor detrimental effects. In contrast, mortality in the hypothermia group was significantly higher compared with controls (67% vs. 11%). Hypothermia impaired circulation (MAP 64 (57;89) mm Hg vs. 104 (98; 114) mm Hg) resulting in metabolic acidosis (lactate 11.0 (6.6;13.6) mmol L−1 vs. 1.0 (0.8;1.5) mmol L−1) and reduced creatinine clearance (26 (9;61) mL min−1 vs. 77 (52;80) mL min−1) compared to the control group after 12 h of resuscitation. Impaired kidney function coincided with increased renal 3-nitrotyrosine formation and extravascular albumin accumulation.

In conclusion, hyperoxia proved to be safe during resuscitation from hemorrhagic shock. The lacking organ-protective effects of hyperoxia compared to resuscitation from near-lethal hemorrhage suggest a dependence of the effectiveness of hyperoxia from shock severity. In line with our previous report, therapeutic hypothermia (and rewarming) was confirmed to be detrimental most likely due to vascular barrier dysfunction.
Shaping development by stochasticity and dynamics in gene regulation
Authors: Dong Peng , Liu Zhe
Published: May 2017

Animal development is orchestrated by spatio-temporal gene expression programmes that drive precise lineage commitment, proliferation and migration events at the single-cell level, collectively leading to large-scale morphological change and functional specification in the whole organism. Efforts over decades have uncovered two ‘seemingly contradictory’ mechanisms in gene regulation governing these intricate processes: (i) stochasticity at individual gene regulatory steps in single cells and (ii) highly coordinated gene expression dynamics in the embryo. Here we discuss how these two layers of regulation arise from the molecular and the systems level, and how they might interplay to determine cell fate and to control the complex body plan. We also review recent technological advancements that enable quantitative analysis of gene regulation dynamics at single-cell, single-molecule resolution. These approaches outline next-generation experiments to decipher general principles bridging gaps between molecular dynamics in single cells and robust gene regulations in the embryo.
Chimpanzee intellect: personality, performance and motivation with touchscreen tasks
Authors: Altschul Drew M. , Wallace Emma K. , Sonnweber Ruth , Tomonaga Masaki , Weiss Alexander
Published: May 2017

Human intellect is characterized by intercorrelated psychological domains, including intelligence, academic performance and personality. Higher openness is associated with higher intelligence and better academic performance, yet high performance among individuals is itself attributable to intelligence, not openness. High conscientiousness individuals, although not necessarily more intelligent, are better performers. Work with other species is not as extensive, yet animals display similar relationships between exploration- and persistence-related personality traits and performance on cognitive tasks. However, previous studies linking cognition and personality have not tracked learning, performance and dropout over time—three crucial elements of cognitive performance. We conducted three participatory experiments with touchscreen cognitive tasks among 19 zoo-housed chimpanzees, whose personalities were assessed 3 years prior to the study. Performance and participation were recorded across experiments. High conscientiousness chimpanzees participated more, dropped out less and performed better, but their performance could be explained by their experience with the task. High openness chimpanzees tended to be more interested, perform better and continue to participate when not rewarded with food. Our results demonstrate that chimpanzees, like humans, possess broad intellectual capacities that are affected by their personalities.
The effect of surface tension on steadily translating bubbles in an unbounded Hele-Shaw cell
Authors: Green Christopher C. , Lustri Christopher J. , McCue Scott W.
Published: May 2017

New numerical solutions to the so-called selection problem for one and two steadily translating bubbles in an unbounded Hele-Shaw cell are presented. Our approach relies on conformal mapping which, for the two-bubble problem, involves the Schottky-Klein prime function associated with an annulus. We show that a countably infinite number of solutions exist for each fixed value of dimensionless surface tension, with the bubble shapes becoming more exotic as the solution branch number increases. Our numerical results suggest that a single solution is selected in the limit that surface tension vanishes, with the scaling between the bubble velocity and surface tension being different to the well-studied problems for a bubble or a finger propagating in a channel geometry.
Untangling the roles of microclimate, behaviour and physiological polymorphism in governing vulnerability of intertidal snails to heat stress
Authors: Dong Yun-wei , Li Xiao-xu , Choi Francis M. P. , Williams Gray A. , Somero George N. , Helmuth Brian
Published: May 2017

Biogeographic distributions are driven by cumulative effects of smaller scale processes. Thus, vulnerability of animals to thermal stress is the result of physiological sensitivities to body temperature (Tb), microclimatic conditions, and behavioural thermoregulation. To understand interactions among these variables, we analysed the thermal tolerances of three species of intertidal snails from different latitudes along the Chinese coast, and estimated potentialTbin different microhabitats at each site. We then empirically determined the temperatures at which heart rate decreased sharply with rising temperature (Arrhenius breakpoint temperature, ABT) and at which it fell to zero (flat line temperature, FLT) to calculate thermal safety margins (TSM). Regular exceedance of FLT in sun-exposed microhabitats, a lethal effect, was predicted for only one mid-latitude site. However, ABTs of some individuals were exceeded at sun-exposed microhabitats in most sites, suggesting physiological impairment for snails with poor behavioural thermoregulation and revealing inter-individual variations (physiological polymorphism) of thermal limits. An autocorrelation analysis ofTbshowed that predictability of extreme temperatures was lowest at the hottest sites, indicating that the effectiveness of behavioural thermoregulation is potentially lowest at these sites. These results illustrate the critical roles of mechanistic studies at small spatial scales when predicting effects of climate change.
China's fight to halt tree cover loss
Authors: Ahrends Antje , Hollingsworth Peter M. , Beckschäfer Philip , Chen Huafang , Zomer Robert J. , Zhang Lubiao , Wang Mingcheng , Xu Jianchu
Published: May 2017

China is investing immense resources for planting trees, totalling more than US$ 100 billion in the past decade alone. Every year, China reports more afforestation than the rest of the world combined. Here, we show that China's forest cover gains are highly definition-dependent. If the definition of ‘forest’ follows FAO criteria (including immature and temporarily unstocked areas), China has gained 434 000 km
2
between 2000 and 2010. However, remotely detectable gains of vegetation that non-specialists would view as forest (tree cover higher than 5 m and minimum 50% crown cover) are an order of magnitude less (33 000 km
2
). Using high-resolution maps and environmental modelling, we estimate that approximately 50% of the world's forest with minimum 50% crown cover has been lost in the past approximately 10 000 years. China historically lost 1.9–2.7 million km
2
(59–67%), and substantial losses continue. At the same time, most of China's afforestation investment targets environments that our model classes as unsuitable for trees. Here, gains detectable via satellite imagery are limited. Conversely, the regions where modest gains are detected are environmentally suitable but have received little afforestation investment due to conflicting land-use demands for agriculture and urbanization. This highlights the need for refined forest monitoring, and greater consideration of environmental suitability in afforestation programmes.
Developmental roles of tyrosine metabolism enzymes in the blood-sucking insect
Rhodnius prolixus
Authors: Sterkel Marcos , Oliveira Pedro L.
Published: May 2017

The phenylalanine/tyrosine degradation pathway is frequently described as a catabolic pathway that funnels aromatic amino acids into citric acid cycle intermediates. Previously, we demonstrated that the accumulation of tyrosine generated during the hydrolysis of blood meal proteins in
Rhodnius prolixus
is potentially toxic, a harmful outcome that is prevented by the action of the first two enzymes in the tyrosine degradation pathway. In this work, we further evaluated the relevance of all other enzymes involved in phenylalanine/tyrosine metabolism in the physiology of this insect. The knockdown of most of these enzymes produced a wide spectrum of distinct phenotypes associated with reproduction, development and nymph survival, demonstrating a highly pleiotropic role of tyrosine metabolism. The phenotypes obtained for two of these enzymes, homogentisate dioxygenase and fumarylacetoacetase, have never before been described in any arthropod. To our knowledge, this report is the first comprehensive gene-silencing analysis of an amino acid metabolism pathway in insects. Amino acid metabolism is exceptionally important in haematophagous arthropods due to their particular feeding behaviour.
Eggshell structure in
Caiman latirostris
eggs improves embryo survival during nest inundation
Authors: Cedillo-Leal César , Simoncini Melina S. , Leiva Pamela M. L. , Larriera Alejandro , Lang Jeffrey W. , Piña Carlos I.
Published: May 2017

Egg inundation often results in poor hatching success in crocodylians. However, how tolerant eggs are to submergence, and/or how eggshell ultrastructure may affect embryo survival when inundated, are not well understood. In this study, our objective was to determine if embryo survival in
Caiman latirostris
is affected by eggshell surface roughness, when eggs are submerged under water. Tolerance to inundation was tested early (day 30) versus late (day 60) in development, using eight clutches (four per time treatments), subdivided into four groups: (
N
= 9 per clutch per treatment; 9 × 4 = 36 eggs per group). ‘Rough’ eggshell represented the natural, unmodified eggshell surface structure. ‘Smooth’ eggshell surface structure was created by mechanically sanding the natural rough surface to remove surface columnar elements and secondary layer features, e.g. irregularities that result in ‘roughness’. When inundated by submerging eggs under water for 10 h at day 30, ‘smooth’ eggshell structure resulted in more than twice as many dead embryos (16 versus 6, smooth versus rough;
N
= 36), and fewer than half as many healthy embryos (6 versus 13, smooth versus rough, respectively;
N
= 36). By contrast, at day 60, inundation resulted in very low hatching success, regardless of eggshell surface structure. Only two hatchlings survived the inundation, notably in the untreated group with intact, rough eggshells. Inundation produced a high rate of malformations (58% at day 30), but did not affect hatchling size. Our results indicate that eggshell roughness enhances embryo survival when eggs are inundated early in development, but not late in development. Apparently, the natural surface ‘roughness’ entraps air bubbles at the eggshell surface during inundation, thereby facilitating gas exchange through the eggshell even when the egg is submerged under water.
Trophic level, successional age and trait matching determine specialization of deadwood-based interaction networks of saproxylic beetles
Authors: Wende Beate , Gossner Martin M. , Grass Ingo , Arnstadt Tobias , Hofrichter Martin , Floren Andreas , Linsenmair Karl Eduard , Weisser Wolfgang W. , Steffan-Dewenter Ingolf
Published: May 2017

The specialization of ecological networks provides important insights into possible consequences of biodiversity loss for ecosystem functioning. However, mostly mutualistic and antagonistic interactions of living organisms have been studied, whereas detritivore networks and their successional changes are largely unexplored. We studied the interactions of saproxylic (deadwood-dependent) beetles with their dead host trees. In a large-scale experiment, 764 logs of 13 tree species were exposed to analyse network structure of three trophic groups of saproxylic beetles over 3 successional years. We found remarkably high specialization of deadwood-feeding xylophages and lower specialization of fungivorous and predatory species. During deadwood succession, community composition, network specialization and network robustness changed differently for the functional groups. To reveal potential drivers of network specialization, we linked species' functional traits to their network roles, and tested for trait matching between plant (i.e. chemical compounds) and beetle (i.e. body size) traits. We found that both plant and animal traits are major drivers of species specialization, and that trait matching can be more important in explaining interactions than neutral processes reflecting species abundance distributions. High network specialization in the early successional stage and decreasing network robustness during succession indicate vulnerability of detritivore networks to reduced tree species diversity and beetle extinctions, with unknown consequences for wood decomposition and nutrient cycling.
Statistical mechanics of phase space partitioning in large-scale spiking neuron circuits
Authors: Touzel Maximilian Puelma , Wolf Fred
Published: May 2017

Synaptic interactions structure the phase space of the dynamics of neural circuits and constrain neural computation. Understanding how requires methods that handle those discrete interactions, yet few exist. Recently, it was discovered that even random networks exhibit dynamics that partitions the phase space into numerous attractor basins. Here we utilize this phenomenon to develop theory for the geometry of phase space partitioning in spiking neural circuits. We find basin boundaries structuring the phase space are pre-images of spike-time collision events. Formulating a statistical theory of spike-time collision events, we derive expressions for the rate of divergence of neighboring basins and for their size distribution. This theory reveals that the typical basin diameter grows with inhibitory coupling strength and shrinks with the rate of spike events. Our study provides an analytical and generalizable approach for dissecting how connectivity, coupling strength, single neuron dynamics and population activity shape the phase space geometry of spiking circuits.
Hebbian Learning in a Random Network Captures Selectivity Properties of Prefrontal Cortex
Authors: Lindsay Grace W. , Rigotti Mattia , Warden Melissa R. , Miller Earl K. , Fusi Stefano
Published: May 2017

Complex cognitive behaviors, such as context-switching and rule-following, are thought to be supported by prefrontal cortex (PFC). Neural activity in PFC must thus be specialized to specific tasks while retaining flexibility. Nonlinear ‘mixed’ selectivity is an important neurophysiological trait for enabling complex and context-dependent behaviors. Here we investigate (1) the extent to which PFC exhibits computationally relevant properties such as mixed selectivity and (2) how such properties could arise via circuit mechanisms. We show that PFC cells recorded from male and female rhesus macaques during a complex task show a moderate level of specialization and structure that is not replicated by a model wherein cells receive random feedforward inputs. While random connectivity can be effective at generating mixed selectivity, the data shows significantly more mixed selectivity than predicted by a model with otherwise matched parameters. A simple Hebbian learning rule applied to the random connectivity, however, increases mixed selectivity and allows the model to match the data more accurately. To explain how learning achieves this, we provide analysis along with a clear geometric interpretation of the impact of learning on selectivity. After learning, the model also matches the data on measures of noise, response density, clustering, and the distribution of selectivities. Of two styles of Hebbian learning tested, the simpler and more biologically plausible option better matches the data. These modeling results give intuition about how neural properties important for cognition can arise in a circuit and make clear experimental predictions regarding how various measures of selectivity would evolve during animal training.

Significance Statement

Prefrontal cortex (PFC) is a brain region believed to support the ability of animals to engage in complex behavior. How neurons in this area respond to stimuli—and in particular, to combinations of stimuli (”mixed selectivity”)—is a topic of interest. Despite the fact that models with random feedforward connectivity are capable of creating computationally-relevant mixed selectivity, such a model does not match the levels of mixed selectivity seen in the data analyzed in this study. Adding simple Hebbian learning to the model increases mixed selectivity to the correct level and makes the model match the data on several other relevant measures. This study thus offers predictions on how mixed selectivity and other properties evolve with training.
Network reconstruction and systems analysis of plant cell wall deconstruction byneurospora crassa
Authors: Samal Areejit , Craig James P. , Coradetti Samuel T. , Philipp Benz J. , Eddy James A. , Price Nathan D. , Louise Glass N.
Published: May 2017

Plant biomass degradation by fungal derived enzymes is rapidly expanding in economic importance as a clean and efficient source for biofuels. The ability to rationally engineer filamentous fungi would facilitate biotechnological applications for degradation of plant cell wall polysaccharides. However, incomplete knowledge of biomolecular networks responsible for plant cell wall deconstruction impedes experimental efforts in this direction. To expand this knowledge base, a detailed network of reactions important for deconstruction of plant cell wall polysaccharides into simple sugars was constructed for the filamentous fungusNeurospora crassa. To reconstruct this network, information was integrated from five heterogeneous data types: functional genomics, transcriptomics, proteomics, genetics, and biochemical characterizations. The combined information was encapsulated into a feature matrix and the evidence weighed to assign annotation confidence scores for each gene within the network. Comparative analyses of RNA-seq and ChIP-seq data shed light on the regulation of the plant cell wall degradation network (PCWDN), leading to a novel hypothesis for degradation of the hemicellulose mannan. The transcription factor CLR-2 was subsequently experimentally shown to play a key role in the mannan degradation pathway ofNeurospora crassa. Our network serves as a scaffold for integration of diverse experimental data, leading to elucidation of regulatory design principles for plant cell wall deconstruction by filamentous fungi, and guiding efforts to rationally engineer industrially relevant hyper-production strains.
Splatter: simulation of single-cell RNA sequencing data
Authors: Zappia Luke , Phipson Belinda , Oshlack Alicia
Published: May 2017

As single-cell RNA sequencing technologies have rapidly developed, so have analysis methods. Many methods have been tested, developed and validated using simulated datasets. Unfortunately, current simulations are often poorly documented, their similarity to real data is not demonstrated, or reproducible code is not available.

Here we present the Splatter Bioconductor package for simple, reproducible and well-documented simulation of single-cell RNA-seq data. Splatter provides an interface to multiple simulation methods including Splat, our own simulation, based on a gamma-Poisson distribution. Splat can simulate single populations of cells, populations with multiple cell types or differentiation paths.
Redox-Dependent Condensation Of the Mycobacterial Nucleoid By WhiB4
Authors: Chawla Manbeena , Mishra Saurabh , Parikh Pankti , Mehta Mansi , Shukla Prashant , Vij Manika , Singh Parul , Jakkala Kishore , Verma H N , AjitKumar Parthasarathi , Ganguli Munia , Seshasayee Aswin Sai Narain , Singh Amit
Published: May 2017

Oxidative stress response in bacteria is generally mediated through coordination between the regulators of oxidant-remediation systems (e.g.OxyR, SoxR) and nucleoid condensation (e.g.Dps, Fis). However, these genetic factors are either absent or rendered nonfunctional in the human pathogenMycobacterium tuberculosis(Mtb). Therefore, howMtborganizes genome architecture and regulates gene expression to counterbalance oxidative imbalance during infection is not known. Here, we report that an intracellular redox-sensor, WhiB4, dynamically links genome condensation and oxidative stress response inMtb. Disruption of WhiB4 affects the expression of genes involved in maintaining redox homeostasis, central carbon metabolism (CCM), respiration, cell wall biogenesis, DNA repair and protein quality control under oxidative stress. Notably, disulfide-linked oligomerization of WhiB4 in response to oxidative stress activates the protein’s ability to condense DNAin vitroandin vivo. Further, overexpression of WhiB4 led to hypercondensation of nucleoids, redox imbalance and increased susceptibility to oxidative stress, whereas WhiB4 disruption reversed this effect. In accordance with the findingsin vitro, ChIP-Seq data demonstrated non-specific binding of WhiB4 to GC-rich regions of theMtbgenome. Lastly, data indicate that WhiB4 deletion affected the expression of only a fraction of genes preferentially bound by the protein, suggesting its indirect effect on gene expression. We propose that WhiB4 is a novel redox-dependent nucleoid condensing protein that structurally couplesMtb’sresponse to oxidative stress with genome organization and transcription.

Significance Statement

Mycobacterium tuberculosis (Mtb)needs to adapt in response to oxidative stress encountered inside human phagocytes. In other bacteria, condensation state of nucleoids modulates gene expression to coordinate oxidative stress response. However, this relation remains elusive inMtb. We performed molecular dissection of a mechanism controlled by an intracellular redox sensor, WhiB4, in organizing both chromosomal structure and selective expression of adaptive traits to counter oxidative stress inMtb. Using high-resolution sequencing, transcriptomics, imaging, and redox biosensor, we describe how WhiB4 modulates nucleoid condensation, global gene expression, and redox-homeostasis. WhiB4 over-expression hypercondensed nucleoids and perturbed redox homeostasis whereas WhiB4 disruption had an opposite effect. Our study discovered an empirical role for WhiB4 in integrating redox signals with nucleoid condensation inMtb.
Mitochondria are physiologically maintained at close to 50 °C
Authors: Chrétien Dominique , Bénit Paule , Ha Hyung-Ho , Keipert Susanne , El-Khoury Riyad , Chang Young-Tae , Jastroch Martin , Jacobs Howard T , Rustin Pierre , Rak Malgorzata
Published: May 2017

In endothermic species, heat released as a product of metabolism ensures stable internal temperature throughout the organism, despite varying environmental conditions. Mitochondria are major actors in this thermogenic process. Part of the energy released by the oxidation of respiratory substrates drives ATP synthesis and metabolite transport, while a noticeable proportion is released as heat. Using a temperature-sensitive fluorescent probe targeted to mitochondria, we measured mitochondrial temperaturein situunder different physiological conditions. At a constant external temperature of 38 °C, mitochondria were more than 10 °C warmer when the respiratory chain was fully functional, both in HEK293cells and primary skin fibroblasts. This differential was abolished in cells lacking mitochondrial DNA or by respiratory inhibitors, but preserved or enhanced by expressing thermogenic enzymes such as the alternative oxidase or the uncoupling protein 1. The activity of various RC enzymes was maximal at, or slightly above, 50 °C. Our study prompts a re-examination of the literature on mitochondria, taking account of the inferred high temperature.
Recurrent convolutional neural networks: a better model of biological object recognition
Authors: Spoerer Courtney J. , McClure Patrick , Kriegeskorte Nikolaus
Published: May 2017

Feedforward neural networks provide the dominant model of how the brain performs visual object recognition. However, these networks lack the lateral and feedback connections, and the resulting recurrent neuronal dynamics, of the ventral visual pathway in the human and nonhuman primate brain. Here we investigate recurrent convolutional neural networks with bottom-up (B), lateral (L), and top-down (T) connections. Combining these types of connections yields four architectures (B, BT, BL, and BLT), which we systematically test and compare. We hypothesized that recurrent dynamics might improve recognition performance in the challenging scenario of partial occlusion. We introduce two novel occluded object recognition tasks to test the efficacy of the models,digit clutter(where multiple target digits occlude one another) anddigit debris(where target digits are occluded by digit fragments). We find that recurrent neural networks outperform feedforward control models (approximately matched in parametric complexity) at recognising objects, both in the absence of occlusion and in all occlusion conditions. Recurrent networks were also found to be more robust to the inclusion of additive Gaussian noise. Recurrent neural networks are better in two respects: (1) they are more neurobiologically realistic than their feedforward counterparts; (2) they are better in terms of their ability to recognise objects, especially under challenging conditions. This work shows that computer vision can benefit from using recurrent convolutional architectures and suggests that the ubiquitous recurrent connections in biological brains are essential for task performance.
Concentration Dependent Chromatin States Induced by the Bicoid Morphogen Gradient
Authors: Hannon Colleen E. , Blythe Shelby A. , Wieschaus Eric F.
Published: May 2017

InDrosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. We have measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into four classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classesin vitroand genome-wide chromatin accessibility by ATAC-seq, we found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by chromatin context. Bcd drives an open chromatin state at a subset its targets. Our data support a model where Bcd influences chromatin structure to gain access to concentration-sensitive targets at high concentrations, while concentration-insensitive targets are found in more accessible chromatin and are bound at low concentrations.
Deconvolution of Transcriptional Networks Identifies TCF4 as a Master Regulator in Schizophrenia
Authors: Torshizi Abolfazl Doostparast , Armoskus Chris , Zhang Hanwen , Forrest Marc P. , Zhang Siwei , Souaiaia Tade , Evgrafov Oleg V. , Knowles James A. , Duan Jubao , Wang Kai
Published: May 2017

Tissue-specific reverse engineering of transcriptional networks has uncovered master regulators (MRs) of cellular networks in various cancers, yet the application of this method to neuropsychiatric disorders is largely unexplored. Here, using RNA-Seq data on postmortem dorsolateral prefrontal cortex (DLPFC) from schizophrenia (SCZ) patients and control subjects, we deconvolved the transcriptional network to identify MRs that mediate expression of a large body of target genes. Together with an independent RNA-Seq data on cultured cells derived from olfactory neuroepithelium, we identifiedTCF4, a leading SCZ risk locus implicated by genome-wide association studies, as one of the top candidate MRs that may be potentially dysregulated in SCZ. We validated the dysregulated TCF4-related transcriptional network through examining the transcription factor binding footprints inferred from human induced pluripotent stem cell (hiPSC)-derived neuronal ATAC-Seq data, as well as direct binding sites obtained from ChIP-seq data in SH-SY5Y cells. The predictedTCF4transcriptional targets were enriched for genes showing transcriptomic changes upon knockdown ofTCF4in hiPSC-derived neural progenitor cells (NPC) and glutamatergic neurons (Glut_N), based on observations from three separate cell lines. The alteredTCF4gene network perturbations in NPC, as compared to that in Glut_N, was more similar to the expression differences in theTCF4gene network observed in the DLPFC of individuals with SCZ. Moreover,TCF4-associated gene expression changes in NPC were more enriched than Glut_N for pathways involved in neuronal activity, genome-wide significant SCZ risk genes, and SCZ-associatedde novomutations. Our results suggest thatTCF4may potentially serve as a MR of a gene network that confers susceptibility to SCZ at early stage of neurodevelopment, highlighting the importance of network dysregulation involving core genes and many hundreds of peripheral genes in conferring susceptibility to neuropsychiatric diseases.
Elevated FOXG1 and SOX2 in glioblastoma enforces neural stem cell identity through transcriptional control of cell cycle and epigenetic regulators
Authors: Bulstrode Harry , Johnstone Ewan , Marques-Torrejon Maria Angeles , Ferguson Kirsty M. , Bressan Raul Bardini , Blin Carla , Grant Vivien , Gogolok Sabine , Gangoso Ester , Gagrica Sladjana , Ender Christine , Fotaki Vassiliki , Sproul Duncan , Bertone Paul , Pollard Steven M.
Published: May 2017

Glioblastoma multiforme (GBM) is an aggressive brain tumor driven by cells with hallmarks of neural stem (NS) cells. GBM stem cells frequently express high levels of the transcription factors FOXG1 and SOX2. Here we show that increased expression of these factors restricts astrocyte differentiation and can trigger dedifferentiation to a proliferative NS cell state. Transcriptional targets include cell cycle and epigenetic regulators (e.g., Foxo3, Plk1, Mycn, Dnmt1, Dnmt3b, and Tet3). Foxo3 is a critical repressed downstream effector that is controlled via a conserved FOXG1/SOX2-bound cis-regulatory element. Foxo3 loss, combined with exposure to the DNA methylation inhibitor 5-azacytidine, enforces astrocyte dedifferentiation. DNA methylation profiling in differentiating astrocytes identifies changes at multiple polycomb targets, including the promoter of Foxo3. In patient-derived GBM stem cells, CRISPR/Cas9 deletion of FOXG1 does not impact proliferation in vitro; however, upon transplantation in vivo, FOXG1-null cells display increased astrocyte differentiation and up-regulate FOXO3. In contrast, SOX2 ablation attenuates proliferation, and mutant cells cannot be expanded in vitro. Thus, FOXG1 and SOX2 operate in complementary but distinct roles to fuel unconstrained self-renewal in GBM stem cells via transcriptional control of core cell cycle and epigenetic regulators.
Mutant IDH1 regulates the tumor-associated immune system in gliomas
Authors: Amankulor Nduka M. , Kim Youngmi , Arora Sonali , Kargl Julia , Szulzewsky Frank , Hanke Mark , Margineantu Daciana H. , Rao Aparna , Bolouri Hamid , Delrow Jeff , Hockenbery David , Houghton A. McGarry , Holland Eric C.
Published: May 2017

Gliomas harboring mutations in isocitrate dehydrogenase 1/2 (IDH1/2) have the CpG island methylator phenotype (CIMP) and significantly longer patient survival time than wild-type IDH1/2 (wtIDH1/2) tumors. Although there are many factors underlying the differences in survival between these two tumor types, immune-related differences in cell content are potentially important contributors. In order to investigate the role of IDH mutations in immune response, we created a syngeneic pair mouse model for mutant IDH1 (muIDH1) and wtIDH1 gliomas and demonstrated that muIDH1 mice showed many molecular and clinical similarities to muIDH1 human gliomas, including a 100-fold higher concentration of 2-hydroxygluratate (2-HG), longer survival time, and higher CpG methylation compared with wtIDH1. Also, we showed that IDH1 mutations caused down-regulation of leukocyte chemotaxis, resulting in repression of the tumor-associated immune system. Given that significant infiltration of immune cells such as macrophages, microglia, monocytes, and neutrophils is linked to poor prognosis in many cancer types, these reduced immune infiltrates in muIDH1 glioma tumors may contribute in part to the differences in aggressiveness of the two glioma types.
The Significance of Digital Gene Expression Profiles
Authors: Audic Stéphane , Claverie Jean-Michel
Published: May 2017

Genes differentially expressed in different tissues, during development, or during specific pathologies are of foremost interest to both basic and pharmaceutical research. “Transcript profiles” or “digital Northerns” are generated routinely by partially sequencing thousands of randomly selected clones from relevant cDNA libraries. Differentially expressed genes can then be detected from variations in the counts of their cognate sequence tags. Here we present the first systematic study on the influence of random fluctuations and sampling size on the reliability of this kind of data. We establish a rigorous significance test and demonstrate its use on publicly available transcript profiles. The theory links the threshold of selection of putatively regulated genes (e.g., the number of pharmaceutical leads) to the fraction of false positive clones one is willing to risk. Our results delineate more precisely and extend the limits within which digital Northern data can be used.
High Throughput Fingerprint Analysis of Large-Insert Clones
Authors: Marra Marco A. , Kucaba Tamara A. , Dietrich Nicole L. , Green Eric D. , Brownstein Buddy , Wilson Richard K. , McDonald Ken M. , Hillier LaDeana W. , McPherson John D. , Waterston Robert H.
Published: May 2017

As part of the Human Genome Project, the Washington University Genome Sequencing Center has commenced systematic sequencing of human chromsome 7. To organize and supply the effort, we have undertaken the construction of sequence-ready physical maps for defined chromosomal intervals. Map construction is a serial process composed of three main activities. First, candidate STS-positive large-insert PAC and BAC clones are identified. Next, these candidate clones are subjected to fingerprint analysis. Finally, the fingerprint data are used to assemble sequence-ready maps. The fingerprinting method we have devised is key to the success of the overall approach. We present here the details of the method and show that the fingerprints are of sufficient quality to permit the construction of megabase-size contigs in defined regions of the human genome. We anticipate that the high throughput and precision characteristic of our fingerprinting method will make it of general utility.
Genetic Mapping of 262 Loci Derived from Expressed Sequences in a Murine Interspecific Cross Using Single-Strand Conformational Polymorphism Analysis
Authors: Brady Kevin P. , Rowe Lucy B. , Her Helen , Stevens Tamara J. , Eppig Janan , Sussman Daniel J. , Sikela James , Beier David R.
Published: May 2017

We have demonstrated previously that noncoding sequences of genes are a robust source of polymorphisms between mouse species when tested using single-strand conformation polymorphism (SSCP) analysis, and that these polymorphisms are useful for genetic mapping. In this report we demonstrate that presumptive 3′-untranslated region sequence obtained from expressed sequence tags (ESTs) can be analyzed in a similar fashion, and we have used this approach to map 262 loci using an interspecific backcross. These results demonstrate SSCP analysis of genes or ESTs is a simple and efficient means for the genetic localization of transcribed sequences, and is furthermore an approach that is applicable to any system for which there is sufficient sequence polymorphism.
The Complete Set of Predicted Genes from Saccharomyces cerevisiae in a Readily Usable Form
Authors: Hudson James R. , Dawson Elliott P. , Rushing Kimberly L. , Jackson Cynthia H. , Lockshon Daniel , Conover Diana , Lanciault Christian , Harris James R. , Simmons Steven J. , Rothstein Rodney , Fields Stanley
Published: May 2017

Nearly all of the open reading frames (ORFs) of the yeastSaccharomyces cerevisiae have been synthesized by PCR using a set of ∼6000 primer pairs. Each of the forward primers has a common 22-base sequence at its 5′ end, and each of the back primers has a common 20-base sequence at its 5′ end. These common termini allow reamplification of the entire set of original PCR products using a single pair of longer primers—in our case, 70 bases. The resulting 70-base elements that flank each ORF can be used for rapid and efficient cloning into a linearized yeast vector that contains these same elements at its termini. This cloning by genetic recombination obviates the need for ligations or bacterial manipulations and should permit convenient global approaches to gene function that require the assay of each putative yeast gene.
Large-Scale Concatenation cDNA Sequencing
Authors: Yu Wei , Andersson Björn , Worley Kim C. , Muzny Donna M. , Ding Yan , Liu Wen , Ricafrente Jennifer Y. , Wentland Meredith A. , Lennon Greg , Gibbs Richard A.
Published: May 2017

A total of 100 kb of DNA derived from 69 individual human brain cDNA clones of 0.7–2.0 kb were sequenced by concatenated cDNA sequencing (CCS), whereby multiple individual DNA fragments are sequenced simultaneously in a single shotgun library. The method yielded accurate sequences and a similar efficiency compared with other shotgun libraries constructed from single DNA fragments (>20 kb). Computer analyses were carried out on 65 cDNA clone sequences and their corresponding end sequences to examine both nucleic acid and amino acid sequence similarities in the databases. Thirty-seven clones revealed no DNA database matches, 12 clones generated exact matches (≥98% identity), and 16 clones generated nonexact matches (57%–97% identity) to either known human or other species genes. Of those 28 matched clones, 8 had corresponding end sequences that failed to identify similarities. In a protein similarity search, 27 clone sequences displayed significant matches, whereas only 20 of the end sequences had matches to known protein sequences. Our data indicate that full-length cDNA insert sequences provide significantly more nucleic acid and protein sequence similarity matches than expressed sequence tags (ESTs) for database searching.

[All 65 cDNA clone sequences described in this paper have been submitted to the GenBank data library under accession nos. U79240–U79304.]
An STS-Based Radiation Hybrid Map of the Human Genome
Authors: Stewart Elizabeth A. , McKusick Kathleen B. , Aggarwal Amita , Bajorek Ewa , Brady Shannon , Chu Angela , Fang Nicole , Hadley David , Harris Mark , Hussain Sami , Lee Richard , Maratukulam Annu , O’Connor Kyle , Perkins Shanti , Piercy Mark , Qin Fawn , Reif Tim , Sanders Carla , She Xiaohong , Sun Wei-Lin , Tabar Poroshat , Voyticky Susan , Cowles Sid , Fan Jian-Bing , Mader Chris , Quackenbush John , Myers Richard M. , Cox David R.
Published: May 2017

We have constructed a physical map of the human genome by using a panel of 83 whole genome radiation hybrids (the Stanford G3 panel) in conjunction with 10,478 sequence-tagged sites (STSs) derived from random genomic DNA sequences, previously mapped genetic markers, and expressed sequences. Of these STSs, 5049 are framework markers that fall into 1766 high-confidence bins. An additional 945 STSs are indistinguishable in their map location from one or more of the framework markers. These 5994 mapped STSs have an average spacing of 500 kb. An additional 4484 STSs are positioned with respect to the framework markers. Comparison of the orders of markers on this map with orders derived from independent meiotic and YAC STS-content maps indicates that the error rate in defining high-confidence bins is <5%. Analysis of 322 random cDNAs indicates that the map covers the vast majority of the human genome. This STS-based radiation hybrid map of the human genome brings us one step closer to the goal of a physical map containing 30,000 unique ordered landmarks with an average marker spacing of 100 kb.
A Differential Hybridization Scheme to Identify Photoreceptor-Specific Genes
Authors: Swanson Deborah A. , Freund Carol L. , Steel Jason M. , Xu Shunbin , Ploder Lynda , McInnes Roderick R. , Valle David
Published: May 2017

Identification of genes expressed preferentially or exclusively in photoreceptors will facilitate the understanding of photoreceptor biology as well as provide candidate genes for inherited retinal degenerations. To achieve this goal we performed a differential hybridization screen of 3717 well-isolated phage clones from a human retinal cDNA library. Clones were selected for further study if they hybridized exclusively or strongly preferentially to a probe derived from RNA isolated from the cone-predominant retina of 13-line ground squirrels as compared to a probe derived from human fibroblast RNA. Twenty percent of clones (9/45) identified by this screen were derived from photoreceptor-specific genes and an additional 24.4% (11/45) were from neural-specific genes, demonstrating the utility of this strategy in identifying genes important for retinal biology.

[The sequence tags of cDNAs identified in this screen have been deposited in GenBank under accession nos. U89715, U89878–U89888, andU89951–U89955.]
Identification and Chromosomal Localization of Human Genes Containing CAG/CTG Repeats Expressed in Testis and Brain
Authors: Bulle Frédérique , Chiannilkulchai Nuchanard , Pawlak André , Weissenbach Jean , Gyapay Gabor , Guellaën Georges
Published: May 2017

Human genes containing triplet repeats have been demonstrated to be involved in several neurodegenerative diseases by expansion of the repeat in succeeding generations. To identify novel genes involved in such pathologies, we have isolated transcripts containing (CAG/CTG)n repeats using two approaches. First, we screened 4 × 106 clones representing 10 copies of a human testis cDNA library using a (CAG)14 oligonucleotide probe. Among the 910 clones identified, the 243 clones with the strongest hybridization signal were sequenced partially from 3′ or 5′ ends. This provided us with 251 partial sequences that grouped into clusters corresponding to 39 genes, of which 19 represent unknown species. Second, we selected 203 additional ESTs containing (CAG/CTG)n repeats representing 121 clusters from the IMAGE consortium infant brain cDNA library. From these two series of sequences, we have localized 95 genes on human chromosomes using a panel of whole genome radiation hybrid (Genebridge 4). These genes are located on all of the chromosomes except for chromosome X, the highest density being observed on chromosome 19.

[The sequence data described in this paper have been submitted to GenBank under accession nos. AA065241–AA065346.]
A Transcript Map for the 2.8-Mb Region Containing the Multiple Endocrine Neoplasia Type 1 Locus
Authors: Guru Siradanahalli C. , Agarwal Sunita K. , Manickam Pachiappan , Olufemi Shodimu-Emmanuel , Crabtree Judy S. , Weisemann Jane M. , Kester Mary Beth , Kim Young S. , Wang Yingping , Emmert-Buck Michael R. , Liotta Lance A. , Spiegel Allen M. , Boguski Mark S. , Roe Bruce A. , Collins Francis S. , Marx Stephen J. , Burns Lee , Chandrasekharappa Settara C.
Published: May 2017

Multiple endocrine neoplasia type 1 (MEN 1) is an inherited cancer syndrome in which affected individuals develop multiple parathyroid, enteropancreatic, and pituitary tumors. The locus for MEN1 is tightly linked to the marker PYGM on chromosome 11q13, and linkage analysis places the MEN1 gene within a 2-Mb interval flanked by the markers D11S1883 and D11S449. Loss of heterozygosity studies in MEN 1 and sporadic tumors suggest that theMEN1 gene encodes a tumor suppressor and have helped to narrow the location of the gene to a 600-kb interval between PYGM andD11S449. Focusing on this smaller MEN1 interval, we have identified and mapped 12 transcripts to this 600-kb region. A precise ordered map of 33 transcripts, including 12 genes known to map to this region, was generated for the 2.8-Mb D11S480–D11S913interval. Fifteen candidate genes (of which 10 were examined exhaustively) were evaluated by Southern blot and/or dideoxy fingerprinting analysis to identify the gene harboring disease-causing mutations.

[The sequence data described in this paper have been submitted to GenBank under accession nos. EST06996, U93236,AF001540–AF001547, AF001433–AF001436, AF001891–AF001893,N55476, R19205, and W37647 (see Table 1 for listing of transcripts). The BAC clone sequences have been submitted to GenBank under accession nos. AC000134, AC000159, and AC000353.]
Detection of RAPD Markers Correlated with Chloroquine Resistance in Plasmodium falciparum
Authors: Lescuyer Pierre , Picot Stéphane , Bracchi Valérie , Burnod Josette , Austin Juliet , Pérard Alain , Ambroise-Thomas Pierre
Published: May 2017

We described the use of the random amplified polymorphic DNA (RAPD) technique on Plasmodium falciparum DNA to detect genetic markers for chloroquine-resistant strains. Fourteen RAPD primers were tested, three of which generated banding patterns correlated with chloroquine resistance. To measure this correlation, the RAPD profiles were analyzed using the Nei and Li similarity coefficient. Detection of distinctive RAPD bands allowed us to synthesize specific PCR primers to be used on whole-blood samples. Two primer sets were synthesized and tested on sensitive and resistant strains for their ability to amplify the DNA fragment corresponding to the RAPD marker. These results suggest that RAPD and PCR techniques can be used as powerful tools for the detection of genetic markers associated with drug resistance.

[The nucleotide sequence data described in this paper have been submitted to the EMBL, GenBank, and DDBJ Nucleotide Sequence databases under accession nos. A863W25C and U854T571.]