bluuebunny/crossref_metadata_2025 huggingface dataset:
Relative adrenal insufficiency is a risk factor and an endotype of sepsis - A proof of concept study to support a precision medicine approach for glucocorticoid sepsis therapy
Authors: Wu Chia-Hua , Guo Ling , Wang Qian , Ye Xiang , Mineo Chieko , Shaul Philip W. , Li Xiang-An
Published: April 2020

Rational

25-60% of septic patients experience relative adrenal insufficiency (RAI) and glucocorticoid (GC) is frequently used in septic patients. However, the efficacy of GC therapy and whether the GC therapy should be based on the status of RAI are highly controversial. Critical barriers include technical limitations in properly identifying RAI in septic patients and a lack of RAI animal model.

Objectives

We established a new RAI animal model to test our hypothesis that precision medicine approach should be used for GC sepsis therapy - only applying GC to a subgroup of septic mice with RAI.

Methods

We generated SF1CreSR-BIfl/flconditional knockout mice. The mice exhibited specific depletion of SR-BI expression in adrenal gland, resulting in a lack of production of inducible GC in response to ACTH stimulation or sepsis, but the mice had normal basal GC levels. Mice were treated with cecal ligation and puncture to develop sepsis. Mice were also supplemented with or without GC to study the effect of GC in sepsis therapy. Plasma and organs were collected for biochemical assays. BODIPY™FL-conjugatedEscherichia coliwas used for phagocytosis assay. Macrophages were used to study effects of GC on inflammatory responses.

Measurements and Main Results

Using SF1CreSR-BIfl/flmice as a RAI model, we found that mice with RAI were susceptible to CLP-induced sepsis compared to controls (6.7% survival in SF1CreSR-BIfl/flmice versus 86.4% in SR-BIfl/flmice; p=0.0001). Supplementation of hydrocortisone significantly improved survival in CLP-treated SF1CreSR-BIfl/flmice. Surprisingly, wild type mice receiving GC treatment exhibited significantly less survival compared to wild type mice without GC treatment. We further found that, in contrast to wild type mice which displayed a well-controlled systemic inflammatory response, the mice with RAI featured a persisted systemic response as shown by high levels of plasma inflammatory cytokines/chemokines 20 hours post CLP, and supplementation of GC kept the inflammatory response under control. In vitro analysis revealed that stress level of GC is required to suppress inflammatory response through modulating MAPK signaling in macrophages.

Conclusions

We demonstrate that RAI is a risk factor and an endotype for sepsis, and GC treatment benefits mice with RAI but harms mice without RAI. We further demonstrate that inducible GC functions to keep the systemic inflammatory response under control through modulating MAPK signaling, but mice with RAI lose such protection and supplementation of GC regains the protection. Our study provides a proof of concept to support the use of a precision medicine approach for sepsis therapy – selectively applying GC therapy for a subgroup of patients with RAI.
Two dynamically distinct circuits driving inhibition in sensory thalamus
Authors: Martinez-Garcia Rosa I. , Voelcker Bettina , Zaltsman Julia B. , Patrick Saundra L. , Stevens Tanya R. , Connors Barry W. , Cruikshank Scott J.
Published: April 2020

Most sensory information destined for the neocortex is relayed through the thalamus, where considerable transformation occurs1,2. One powerful means of transformation involves interactions between excitatory thalamocortical neurons that carry data to cortex and inhibitory neurons of the thalamic reticular nucleus (TRN) that regulate flow of those data3-6. Despite enduring recognition of its importance7-9, understanding of TRN cell types, their organization, and their functional properties has lagged that of the thalamocortical systems they control.

Here we address this, investigating somatosensory and visual circuits of the TRN. In the somatosensory TRN we observed two groups of genetically defined neurons that are topographically segregated, physiologically distinct, and connect reciprocally with independent thalamocortical nuclei via dynamically divergent synapses. Calbindin-expressing cells, located in the central core, connect with the ventral posterior nucleus (VP), the primary somatosensory thalamocortical relay. In contrast, somatostatin-expressing cells, residing along the surrounding edges of TRN, synapse with the posterior medial thalamic nucleus (POM), a higher-order structure that carries both top-down and bottom-up information10-12. The two TRN cell groups process their inputs in pathway-specific ways. Synapses from VP to central TRN cells transmit rapid excitatory currents that depress deeply during repetitive activity, driving phasic spike output. Synapses from POM to edge TRN cells evoke slower, less depressing excitatory currents that drive more persistent spiking. Differences in intrinsic physiology of TRN cell types, including state-dependent bursting, contribute to these output dynamics. Thus, processing specializations of two somatosensory TRN subcircuits appear to be tuned to the signals they carry—a primary central subcircuit to discrete sensory events, and a higher-order edge subcircuit to temporally distributed signals integrated from multiple sources. The structure and function of visual TRN subcircuits closely resemble those of the somatosensory TRN. These results provide fundamental insights about how subnetworks of TRN neurons may differentially process distinct classes of thalamic information.
Self-organized patterning of cell morphology via mechanosensitive feedback
Authors: Dye Natalie A. , Popovic Marko , Iyer K. Venkatesan , Eaton Suzanne , Julicher Frank
Published: April 2020

Tissue organization is often characterized by specific patterns of cell morphology. How such patterns emerge in developing tissues is a fundamental open question. Here, we investigate the emergence of tissue-scale patterns of cell shape and mechanical tissue stress in theDrosophilawing imaginal disc during larval development. Using quantitative analysis of the cellular dynamics, we reveal a pattern of radially oriented cell rearrangements that is coupled to the buildup of tangential cell elongation. Developing a laser ablation method, we map tissue stresses and extract key parameters of tissue mechanics. We present a continuum theory showing that this pattern of cell morphology and tissue stress can arise via self-organization of a mechanical feedback that couples cell polarity to active cell rearrangements. The predictions of this model are supported by knockdown of MyoVI, a component of mechanosensitive feedback. Our work reveals a mechanism for the emergence of cellular patterns in morphogenesis.
ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis
Authors: Griss Johannes , Viteri Guilherme , Sidiropoulos Konstantinos , Nguyen Vy , Fabregat Antonio , Hermjakob Henning
Published: April 2020

Pathway analyses are key methods to analyse ‘omics experiments. Nevertheless, integrating data from different ‘omics technologies and different species still requires considerable bioinformatics knowledge.

Here we present the novel ReactomeGSA resource for comparative pathway analyses of multi-omics datasets. ReactomeGSA can be used through Reactome’s existing web interface and the novel ReactomeGSA R Bioconductor package with explicit support for scRNA-seq data. Data from different species is automatically mapped to a common pathway space. Public data from ExpressionAtlas and Single Cell ExpressionAtlas can be directly integrated in the analysis. ReactomeGSA thereby greatly reduces the technical barrier for multi-omics, cross-species, comparative pathway analyses.

We used ReactomeGSA to characterise the role of B cells in anti-tumour immunity. We compared B cell rich and poor human cancer samples from five TCGA transcriptomics and two CPTAC proteomics studies. There, B cell-rich lung adenocarcinoma samples lack the otherwise present activation through NFkappaB. This may be linked to the presence of a specific subset of tumour associated IgG+ plasma cells that lack NFkappaB activation in scRNA-seq data from human melanoma. This showcases how ReactomeGSA can derive novel biomedical insights by integrating large multi-omics datasets.
The determinants of aggression in male Siamese fighting fish,Betta splendens
Authors: McGoran R. E. , Papworth S. K. , Portugal S. J.
Published: April 2020

Siamese fighting fish,Betta splendens, have been extensively studied due to their aggression and stereotypical displays. Many studies have focused on their characteristic opercular flaring, while the less aggressive and less energetically costly lateral display have been comparatively understudied. Many factors have been shown to influence aggression inBettas, notably body length and the personality trait of boldness, however, the role that colour plays in determining an individual’s aggressiveness is much less clear. The role of colour has only been briefly studied, and based on human interpretations of colour, i.e. limited to what the receivers’ eyes and sensory systems actually can process and discriminate, with results suggesting blue males are more aggressive than red males. Using male-male interactions, measuring opercular flaring and lateral display we found that colour and personality do play a role in determining the degree of aggressiveness inBetta splendens. Blue-finned males were more aggressive, performing longer lateral displays more frequently. Blue fins are a phenotype observed in wild type males and is likely selected for to allow visual cues to travel through the murky water they inhabit. Body mass was positively correlated with lateral display frequency, and opercular flare frequency and duration. Finally, neophobic individuals – individuals that were less willing to approach a novel object – were more aggressive, performing significantly more lateral displays. This indicates that personality may impact fighting strategy, with males either choosing to end conflicts quickly with more aggressive displays or to outlast their opponent with less energetically costly displays.
Transcranial Focused Ultrasound Generates Skull-Conducted Shear Waves: Computational Model and Implications for Neuromodulation
Authors: Salahshoor Hossein , Shapiro Mikhail G. , Ortiz Michael
Published: April 2020

Focused ultrasound (FUS) is an established technique for non-invasive surgery and has recently attracted considerable attention as a potential method for non-invasive neuromodulation. While the pressure waves generated by FUS in this context have been extensively studied, the accompanying shear waves are often neglected due to the relatively high shear compliance of soft tissues. However, in bony structures such as the skull, acoustic pressure can also induce significant shear waves that could propagate outside the ultrasound focus. Here, we investigate wave propagation in the human cranium by means of a finite-element model that accounts for the anatomy, elasticity and viscoelasticity of the skull and brain. We show that, when a region on the frontal lobe is subjected to FUS, the skull acts as a wave guide for shear waves, resulting in their propagation to off-target structures such as the cochlea. This effect helps explain the off-target auditory responses observed during neuromodulation experiments and informs the development of mitigation and sham control strategies.
Holistic Characterization of Single Hepatocyte Transcriptome Responses to High Fat Diet
Authors: Park Sung Rye , Cho Chun-Seok , Xi Jingyue , Kang Hyun Min , Lee Jun Hee
Published: April 2020

During nutritional overload and obesity, hepatocyte function is grossly altered, and a subset of hepatocytes begins to accumulate fat droplets, leading to non-alcoholic fatty liver disease (NAFLD). Recent single cell studies revealed how non-parenchymal cells, such as macrophages, hepatic stellate cells, and endothelial cells, heterogeneously respond to NAFLD. However, it remains to be characterized how hepatocytes, the major constituents of the liver, respond to nutritional overload in NAFLD. Here, using droplet-based single cell RNA-sequencing (Drop-seq), we characterized how the transcriptomic landscape of individual hepatocytes is altered in response to high-fat diet (HFD) and NAFLD. We showed that the entire hepatocytes population undergoes substantial transcriptome changes upon HFD, although the patterns of alteration were highly heterogeneous with zonation-dependent and –independent effects. Periportal (zone 1) hepatocytes downregulated many zone 1-specific marker genes, while a small number of genes mediating gluconeogenesis were upregulated. Pericentral (zone 3) hepatocytes also downregulated many zone 3-specific genes; however, they upregulated several genes that promote HFD-induced fat droplet formation, consistent with findings that zone 3 hepatocytes accumulate more lipid droplets. Zone 3 hepatocytes also upregulated ketogenic pathways as an adaptive mechanism to HFD. Interestingly, many of the top HFD-induced genes, which encode proteins regulating lipid metabolism, were strongly co-expressed with each other in a subset of hepatocytes, producing a variegated pattern of spatial co-localization that is independent of metabolic zonation. In conclusion, our dataset provides a useful resource for understanding hepatocellular alteration during NAFLD at single cell level.
Comprehension of computer code relies primarily on domain-general executive brain regions
Authors: Ivanova Anna A. , Srikant Shashank , Sueoka Yotaro , Kean Hope H. , Dhamala Riva , O’Reilly Una-May , Bers Marina U. , Fedorenko Evelina
Published: April 2020

Computer programming is a novel cognitive tool that has transformed modern society. What cognitive and neural mechanisms support this skill? Here, we used fMRI to investigate two candidate brain systems: the multiple demand (MD) system, typically recruited during math, logic, problem solving, and executive tasks, and the language system, typically recruited during linguistic processing. We examined MD and language system responses to code written in Python, a text-based programming language (Experiment 1) and in ScratchJr, a graphical programming language (Experiment 2); for both, we contrasted responses to code problems with responses to content-matched sentence problems. We found that the MD system exhibited strong bilateral responses to code in both experiments, whereas the language system responded strongly to sentence problems, but weakly or not at all to code problems. Thus, the MD system supports the use of novel cognitive tools even when the input is structurally similar to natural language.
Horseshoe crab genomes reveal the evolutionary fates of genes and microRNAs after three rounds (3R) of whole genome duplication
Authors: Nong Wenyan , Qu Zhe , Li Yiqian , Barton-Owen Tom , Wong Annette Y.P. , Yip Ho Yin , Lee Hoi Ting , Narayana Satya , Baril Tobias , Swale Thomas , Cao Jianquan , Chan Ting Fung , Kwan Hoi Shan , Ming Ngai Sai , Panagiotou Gianni , Qian Pei-Yuan , Qiu Jian-Wen , Yip Kevin Y. , Ismail Noraznawati , Pati Siddhartha , John Akbar , Tobe Stephen S. , Bendena William G. , Cheung Siu Gin , Hayward Alexander , Hui Jerome H. L.
Published: April 2020

Whole genome duplication (WGD) has occurred in relatively few sexually reproducing invertebrates. Consequently, the WGD that occurred in the common ancestor of horseshoe crabs ~135 million years ago provides a rare opportunity to decipher the evolutionary consequences of a duplicated invertebrate genome. Here, we present a high-quality genome assembly for the mangrove horseshoe crabCarcinoscorpius rotundicauda(1.7Gb, N50 = 90.2Mb, with 89.8% sequences anchored to 16 pseudomolecules, 2n = 32), and a resequenced genome of the tri-spine horseshoe crabTachypleus tridentatus(1.7Gb, N50 = 109.7Mb). Analyses of gene families, microRNAs, and synteny show that horseshoe crabs have undergone three rounds (3R) of WGD, and that these WGD events are shared with spiders. Comparison of the genomes ofC. rotundicaudaandT. tridentatuspopulations from several geographic locations further elucidates the diverse fates of both coding and noncoding genes. Together, the present study represents a cornerstone for a better understanding of the consequences of invertebrate WGD events on evolutionary fates of genes and microRNAs at individual and population levels, and highlights the genetic diversity with practical values for breeding programs and conservation of horseshoe crabs.
Colistin susceptibility pattern in gram negative bacilli isolated from patients of dhaka medical college hospital with distribution of antibiotic resistance genes among them
Authors: Mostofa Hasbi Ara , Shamsuzzaman S.M. , Hasan MD. Maniul
Published: April 2020

Colistin is one of the last resort of antibiotics used specifically in the treatment of multidrug resistant gram negative bacilli. Though an older class of antibiotic with no use in last four decades, resurgence of colistin use is also causing emergence of colistin resistant gram negative bacilli.The aim of this cross sectional study was to investigate the colistin susceptibility and resistant pattern along with colistin resistant genes in gram negative bacilli among different samples in Dhaka medical college hospital. Total 300 samples (wound swab, urine, endotracheal aspirate, blood and sputum) were collected from 2015 to 2016. 204 gram negative bacilli were isolated and tested for resistance to colistin by disc diffusion method. Then, the prevalence of colistin resistant genes (pmrA, pmrB, pmrC, mgrB, phoP, phoQ, lpxA, lpxC, lpxD, mcr-1) was detected by polymerase chain reaction method (PCR). Among 204 gram negative bacilli, 22 (10.78%) colistin resistance was identified. PCR analysis revealed that 50% of these isolates contained pmrA gene, followed by phoP gene (27.27%). The prevalence of pmrB, phoQ, mgrB, lpxC and lpxD were 22.72%, 13.63%, 13.63%, 13.63%, 13.63%, and 13.63% respectively among the isolates. Colistin resistance is widespread among gram negative bacilli isolated from human infections. Colistin resistance (10.78%) found in the study is quite alarming. A restricted and rational use of the colistin is the need of hour.
RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
Authors: Yuan Yuxuan , Bayer Philipp E. , Anderson Robyn , Lee HueyTyng , Chan Chon-Kit Kenneth , Zhao Ruolan , Batley Jacqueline , Edwards David
Published: April 2020

Recent advances in long-read sequencing have the potential to produce more complete genome assemblies using sequence reads which can span repetitive regions. However, overlap based assembly methods routinely used for this data require significant computing time and resources. Here, we have developed RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligningk-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step. During benchmarking, we assembled the wheat Chinese Spring (CS) genome using publicly available PacBio reads in parallel in 168 wall hours on a 250 CPU system. The maximum RAM used was 300 Gb and the computing time was 42,000 CPU hours. The approach opens applications for the assembly of other large and complex genomes with much-reduced computing requirements. The RefKA pipeline is available athttps://github.com/AppliedBioinformatics/RefKA
Learning a tactile sequence induces selectivity to action decisions and outcomes in the mouse somatosensory cortex
Authors: Bale Michael R. , Bitzidou Malamati , Giusto Elena , Kinghorn Paul , Maravall Miguel
Published: April 2020

Sequential temporal ordering and patterning are key features of natural signals used by the brain to decode stimuli and perceive them as sensory objects. To explore how cortical neuronal activity underpins sequence recognition, we developed a task in which mice distinguished between tactile ‘words’ constructed from distinct vibrations delivered to the whiskers, assembled in different orders. Animals licked to report the presence of the target sequence. Mice could respond to the earliest possible cues allowing discrimination, effectively solving the task as a ‘detection of change’ problem, but enhanced their performance when deliberating for longer. Optogenetic inactivation showed that both primary somatosensory ‘barrel’ cortex (S1bf) and secondary somatosensory cortex were necessary for sequence recognition. Two-photon imaging of calcium activity in S1bf layer 2/3 revealed that, in well-trained animals, neurons had heterogeneous selectivity to multiple task variables including not just sensory input but also the animal’s action decision and the trial outcome (presence or absence of a predicted reward). A large proportion of neurons were activated preceding goal-directed licking, thus reflecting the animal’s learnt response to the target sequence rather than the sequence itself; these neurons were found in S1bf as soon as mice learned to associate the rewarded sequence with licking. In contrast, learning evoked smaller changes in sensory responses: neurons responding to stimulus features were already found in naïve mice, and training did not generate neurons with enhanced temporal integration or categorical responses. Therefore, in S1bf sequence learning results in neurons whose activity reflects the learnt association between the target sequence and licking, rather than a refined representation of sensory features.
Insights into the evolution of symbiosis gene copy number and distribution from a chromosome-scale Lotus japonicus Gifu genome sequence
Authors: Kamal Nadia , Mun Terry , Reid Dugald , Lin Jie-shun , Akyol Turgut Yigit , Sandal Niels , Asp Torben , Hirakawa Hideki , Stougaard Jens , Mayer Klaus F. X. , Sato Shusei , Andersen Stig Uggerhøj
Published: April 2020

Aim

Lotus japonicus is a herbaceous perennial legume that has been used extensively as a genetically tractable model system for deciphering the molecular genetics of symbiotic nitrogen fixation. Our aim is to improve the L. japonicus reference genome sequence, which has so far been based on Sanger and Illumina sequencing reads from the L. japonicus accession MG-20 and contained a large fraction of unanchored contigs.

Methods and Results

Here, we use long PacBio reads from L. japonicus Gifu combined with Hi-C data and new high-density genetic maps to generate a high-quality chromosome-scale reference genome assembly for L. japonicus. The assembly comprises 554 megabases of which 549 were assigned to six pseudomolecules that appear complete with telomeric repeats at their extremes and large centromeric regions with low gene density.

Conclusion and Perspectives

The new L. japonicus Gifu reference genome and associated expression data represent valuable resources for legume functional and comparative genomics. Here, we provide a first example by showing that the symbiotic islands recently described in Medicago truncatula do not appear to be conserved in L. japonicus.
Perturbation ofin vivoneural activity following α-Synuclein seeding in the olfactory bulb
Authors: Kulkarni Aishwarya S. , del Mar Cortijo Maria , Roberts Elizabeth R. , Suggs Tamara L. , Stover Heather B. , Pena-Bravo José I. , Steiner Jennifer A. , Luk Kelvin C. , Brundin Patrik , Wesson Daniel W.
Published: April 2020

BACKGROUND

Parkinson’s disease (PD) neuropathology is characterized by intraneuronal protein aggregates composed of misfolded α-Synuclein (α-Syn), as well as degeneration of substantia nigra dopamine neurons. Deficits in olfactory perception and aggregation of α-Syn in the olfactory bulb (OB) are observed during early stages of PD, and have been associated with the PD prodrome, before onset of the classic motor deficits. α-Syn fibrils injected into the OB of mice cause progressive propagation of α-Syn pathology throughout the olfactory system and are coupled to olfactory perceptual deficits.

OBJECTIVE

We hypothesized that accumulation of pathogenic α-Syn in the OB impairs neural activity in the olfactory system.

METHODS

To address this, we monitored spontaneous and odor-evoked local field potential dynamics in awake wild type mice simultaneously in the OB and piriform cortex (PCX) one, two, and three months following injection of pathogenic preformed α-Syn fibrils in the OB.

RESULTS

We detected α-Syn pathology in both the OB and PCX. We also observed that α-Syn fibril injections influenced odor-evoked activity in the OB. In particular, α-Syn fibril-injected mice displayed aberrantly high odor-evoked power in the beta spectral range. A similar change in activity was not detected in the PCX, despite high levels of α-Syn pathology.

CONCLUSIONS

Together, this work provides evidence that synucleinopathy impactsin vivoneural activity in the olfactory system at the network-level.
Emergence of complex dynamics of choice due to repeated exposures to extinction learning
Authors: Donoso José R. , Packheiser Julian , Pusch Roland , Lederer Zhiyin , Walther Thomas , Uengoer Metin , Lachnit Harald , Güntürkün Onur , Cheng Sen
Published: April 2020

Extinction learning, the process of ceasing an acquired behavior in response to altered reinforcement contingencies, is not only essential for survival in a changing environment, but also plays a fundamental role in the treatment of pathological behaviors. During therapy and other forms of training involving extinction, subjects are typically exposed to several sessions with a similar structure. The effects of this repeated exposure are not well understood. Here, we studied the behavior of pigeons across several sessions of a discrimination learning task in context A, extinction in context B, and a return to context A to test the context-dependent return of the learned responses (ABA renewal). By focusing on individual learning curves across animals, we uncovered a session-dependent variability of behavior: (1) During extinction, pigeons preferred the unrewarded alternative choice in one-third of the sessions, predominantly during the first one. (2) In later sessions, abrupt transitions of behavior at the onset of context B emerged, and (3) the renewal effect decayed as sessions progressed. We show that the observed results can be parsimoniously accounted for by a computational model based only on associative learning between stimuli and actions. Our work thus demonstrates the critical importance of studying the trial-by-trial dynamics of learning in individual sessions, and the power of “simple” associative learning processes.
Powered flight potential approached by wide range of close avian relatives but achieved selectively
Authors: Pei R. , Pittman M. , Goloboff P.A. , Dececchi T.A. , Habib M.B. , Kaye T.G. , Larsson H.C.E. , Norell M.A. , Brusatte S.L. , Xu X.
Published: April 2020

Evolution of birds from non-flying theropod dinosaurs is a classic evolutionary transition, but a deeper understanding of early flight has been frustrated by disagreement on the relationships between birds (Avialae) and their closest theropod relatives. We address this through a larger, more resolved evolutionary hypothesis produced by a novel automated analysis pipeline tailored for large morphological datasets. We corroborate the grouping of dromaeosaurids + troodontids (Deinonychosauria) as the sister taxon to birds (Paraves), as well as the recovery of Anchiornithidae as basalmost avialans. Using these phylogenetic results and available data for vaned feathered paravians, maximum and minimum estimates of wing loading and specific lift calculated using ancestral state reconstruction analysis are used as proxies for the potential for powered flight through this transition. We found a broad range of paravian ancestors with estimates approaching values that are indicative of powered flight potential. This suggests that prior to the evolution of flight there was a wider extent of experimentation with wing-assisted locomotion among paravians than previously appreciated. We recovered wing loading and specific lift estimates indicating the potential for powered flight among fossil birds as well as unenlagiine and microraptorine dromaeosaurids. In the context of our phylogeny and of Mesozoic palaeogeography, our results suggest that the potential for powered flight originated three or more times from a broad range of ancestors already nearing this potential, providing a well-supported scenario for the origin of theropod flight to further explore.
Shotgun proteomics of SARS-CoV-2 infected cells and its application to the optimisation of whole viral particle antigen production for vaccines
Authors: Grenga Lucia , Gallais Fabrice , Pible Olivier , Gaillard Jean-Charles , Gouveia Duarte , Batina Hélène , Bazaline Niza , Ruat Sylvie , Culotta Karen , Miotello Guylaine , Debroas Stéphanie , Roncato Marie-Anne , Steinmetz Gérard , Foissard Charlotte , Desplan Anne , Alpha-Bazin Béatrice , Almunia Christine , Gas Fabienne , Bellanger Laurent , Armengaud Jean
Published: April 2020

Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has resulted in a pandemic and continues to spread quickly around the globe. Currently, no effective vaccine is available to prevent COVID-19 and an intense global development activity is in progress. In this context, the different technology platforms face several challenges resulting from the involvement of a new virus still not fully characterised. Finding of the right conditions for virus amplification for the development of vaccines based on inactivated or attenuated whole viral particles is among them. Here, we describe the establishment of a workflow based on shotgun tandem mass spectrometry data to guide the optimisation of the conditions for viral amplification. In parallel, we analysed the dynamic of the host cell proteome following SARS-CoV-2 infection providing a global overview of biological processes modulated by the virus and that could be further explored to identify drug targets to address the pandemic.
Obstructed tear duct causes epiphora and precocious eyelid opening due to disruption of Prickle 1-mediated Wnt/PCP signaling
Authors: Guo Dianlei , Ru Jiali , Fan Jiaying , Ju Rong , Jin Kangxin , Ouyang Hong , Wei Lai , Liu Yizhi , Liu Chunqiao
Published: April 2020

The tear drainage apparatus evolved in terrestrial animals serving as conduits for tear flow. Obstruction of tear drainage causes a range of ocular surface disorders. Hitherto, genetics of tear duct development and obstruction has been scarcely explored. Here we report that a severePrickle 1hypomorph mouse line exhibited epiphora. This phenotype was due to blockage of the tear drainage by the incompletely formed nasolacrimal duct (NLD) and lacrimal canaliculi (CL). Further analysis revealed that the precocious eyelid opening, previously observed in the same type ofPrickle 1mutants, is also caused by tear duct dysplasia. A comparison of wild type, thePrickle 1hypomorph and null mutants revealed a dose-dependent requirement ofPrickle 1for tear duct outgrowth. As a key component of a set of six Wnt/PCP core proteins, Prickle 1 usually works together with other PCP components. An investigation of expression of Wnt/PCP core genes demonstrated three of the six PCP components in tear duct, supporting the notion of context-dependent organization of PCP protein complexes. Furthermore, expression ofFgfr2/Fgf10andp63genes, mutations of which are associated with NLD and CL hypoplasia in human, were not altered inPrickle 1mutant mice. Lastly, we showed thatPrickle 1expression in developing tear drainage system is conserved between mouse and human despite anatomical differences. Altogether, the study uncovered how obstruction of the tear drainage could lead to a complex ocular surface disorder, which may have genetic implications in human ocular health.
Correlation between cancer stem cells, inflammation and malignant transformation in a DEN-induced model of hepatic carcinogenesis
Authors: Wu Chun-Chieh , Lin Chien-Ju , Kuo Kong-Kai , Chen Wan-Tzu , Ker Chen-Guo , Chai Chee-Yin , Tsai Hung-Pei , Yang Sheau-Fang
Published: April 2020

Aims

Chronic inflammation and cancer stem cells are known risk factors for tumorigenesis. The aetiology of hepatocellular carcinoma (HCC) involves a multistep pathological process characterised by chronic inflammation and hepatocyte damage but the correlation between HCC, inflammation and cancer stem cell remains unclear. In this study, we examined the role of hepatic progenitor cells in a mouse model of chemical-induced hepatocarcinogenesis to elucidate the relationship between inflammation, malignant transformation and cancer stem cells.

Methods and results

We used diethylnitrosamine (DEN) to induce liver tumour and scored for H&E and reticulin staining, and also immunohistochemistry staining for OV-6 expression and analysed the statistical correlation between each other. DEN progressively induced inflammation at 7 week 7 (40%, 2/5), week 27 (75%, 6/8), week 33 (62.5%, 5/8) and week 50 (100%, 12/12). DEN progressively induced malignant transformation at week 7 (0%, 0/5), week 27 (87.5%, 7/8), week 33 (100%, 8/8) and week 50 (100%, 12/12). Data obtained showed that DEN progressively induced high-levels of OV-6 expression at week 7 (20%, 1/5), week 27 (37.5%, 3/8), week 33 (50%, 4/8) and week 50 (100%, 12/12). DEN-induced inflammation, malignant transformation and high-level OV-6 expression in hamster liver as shown above and applying Spearman’s correlation to the data showed that expression of OV-6 was significantly correlated to inflammation (p= 0.001) and malignant transformation (p< 0.001)

Conclusions

There was a significant correlation between number of cancer stem cells, inflammation and malignant transformation in a DEN-induced model of hepatic carcinogenesis in the hamster.
First-generation EGFR-TKI plus chemotherapy versus EGFR-TKI alone as first-line treatment in advanced NSCLC with EGFR activating mutation: a systematic review and meta-analysis of randomized controlled trials
Authors: Wu Qiang , Luo Wuxia , Li Wen , Wang Ting , Huang Lin , Xu Feng
Published: April 2020

The aim of this meta-analysis was to evaluate efficacy and toxicity of epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) in combination with chemotherapy (CT) compared to EGFR-TKI monotherapy as first-line treatment in advanced non-small cell lung cancer (NSCLC) harboring activating EGFR mutation. A systematic literature search of randomized controlled trials using Cochrane Library, PubMed, Embase, and Web of Science, was performed up to Jan. 7th, 2020. A total of eight randomized trials involving 1,349 advanced NSCLC patients with sensitive EGFR mutation were included in the meta-analysis. All patients in both groups received first-generation TKI as first-line treatment. The pooled HR of PFS and OS was 0.56 (95% CI=0.50-0.64; P < 0.00001) and 0.70 (95% CI=0.54-0.90; P=0.005), respectively. Subgroup analysis showed significantly higher OS advantages in patients receiving doublet CT (P=0.02) and concurrent therapy (P=0.002). The ORR in the EGFR-TKI plus CT group was significantly higher than in the EGFR-TKI monotherapy group (RR = 1.18, 95% CI = 1.10–1.26). The combination regimen showed a higher incidence of chemotherapy-induced toxicities. Subgroup analysis indicated that doublet chemotherapy rather than single-agent chemotherapy significantly increased incidence of grade 3 or higher leukopenia, neutropenia and anemia. In conclusion, compared with EGFR-TKI monotherapy, the combination of first-generation EGFR-TKI and CT, especially when applying concurrent delivery of platinum-based doublet chemotherapeutic drugs, significantly improve ORR and prolong PFS and OS in first-line treatment for advanced EGFR-mutated NSCLC, yet at the price of increasing incidence of chemotherapy-induced toxicities that is well tolerated and clinically manageable.
Systematic review of the validity of the hepatitis B virus detection tests in blood banks from 2000 to 2018
Authors: Orrego-Marín Claudia Patricia , Cardona-Arias Jaiberth Antonio , Medina-Moreno Sandra , Zapata Juan Carlos
Published: April 2020

Background

Hepatitis B Virus (HBV) is a public health problem that causes chronic hepatitis, eventually evolving to cirrhosis and hepatocellular carcinoma. Given the low frequency of screening in the general population, blood banks represent a key element for monitoring and controlling HBV transmission. The objective of this work was to evaluate the validity of the diagnosis of HBV in blood banks, based on studies published in the world scientific literature from 2000 to 2018.

Methods

We used a Meta-analysis of random effects with application of a search and selection protocol according to Cochrane and PRISMA guidelines. Reproducibility, completeness and quality assessment were affirmed with QUADAS, a tool for assessing diagnostics. The parameters of sensitivity, specificity, likelihood ratios, odds ratio and ROC curve were analyzed in MetaDisc with 95% confidence.

Results

From 4,061 studies screened, only 12 complied with the protocol, and the compliant studies included a population of 17,391 healthy people and 1,229 infected. The compliant studies evaluated mainly immunodiagnostics (ELISA) using HB surface antigen (HBsAg) and less frequently anti-HBc (HB core antigen) and PCR. The tests for HBsAg presented sensitivity of 94.1% (95% CI = 92.9% - 95.1%), specificity 98.2% (95% CI = 97.8% - 98.6%), diagnostic OR of 1721 (95% CI = 607.18 - 4418.8) and Area Under the Curve of 99.7%.

Conclusion

With a large sample size and with the high quality of the studies evaluated in this review, we confirm that HBsAg for HBV immunodiagnostics has excellent validity, which supports its use in clinical screening, blood banks and population surveillance programs.
Evolution of immune escape mechanisms in the progression from preinvasive to invasive human lung adenocarcinoma
Authors: Altorki Nasser K. , Borczuk Alain C. , Mittal Vivek , Elemento Olivier , McGraw Timothy E.
Published: April 2020

The tumor microenvironment (TME) of lung adenocarcinoma (LUAD) precursor lesions has not been described. We interrogated by multiplex immunofluorescence the TME of preinvasive and invasive Stage 1A LUADs selected by computer tomography (CT) scan-density. Pure non-solid (p-NS) CT density nodules are preinvasive/minimally invasive, whereas solid CT density nodules are frankly invasive cancers. Our data reveal an intensely immune-suppressive immune TME in p-NS tumors characterized by an increase in Treg cells and a decrease in cytotoxic T cells relative to normal lung. The TME of the solid tumor group, more advanced lesions than the p-NS yet still early in disease development, were increasingly more immune-suppressive. Provocatively, there was a further increase in both Treg cells and cytotoxic T cells, establishing a nascent albeit ineffective anti-tumor immune response in transition from preinvasive p-NS to invasive solid tumors. Regulatory T cells play a dominant role throughout progression, while additional immune evasive mechanisms are employed at different stages of disease progression, including T cell exclusion from cancer cell nests early and activation of immune checkpoints later. Our study establishes that different immune-targeted strategies are required to intercept disease progression at these two distinct early points of lung cancer development.

Statement of Significance

Using multiplexed IF, we compared the cellular composition and activation state of the tumor immune microenvironment between pre/minimally invasive and frankly invasive adenocarcinoma. We found a progressive increase in immunosuppressive mechanisms in association with disease progression suggesting that Interception strategies should be specifically tailored based on underlying immune escape mechanisms
Regulation of olfactory associative memory by the circadian clock output signal Pigment-dispersing factor (PDF)
Authors: Flyer-Adams Johanna G. , Rivera-Rodriguez Emmanuel J. , Mardovin Jacob D. , Yu Junwei , Griffith Leslie C.
Published: April 2020

Dissociation between the output of the circadian clock and external environmental cues is a major cause of human cognitive dysfunction. While the effects of ablation of the molecular clock on memory have been studied in many systems, little has been done to test the role of specific clock circuit output signals. To address this gap, we examined the effects of mutation ofPigment-dispersing factor (Pdf)and its receptor,Pdfron associative memory in male and femaleDrosophila. Loss of PDF signaling significantly decreases the ability to form associative memory. Appetitive short-term memory (STM), which in wildtype is time-of-day (TOD)-independent, is decreased across the day by mutation ofPdforPdfr, but more substantially in the morning than in the evening. This defect is due to PDFR expression in adult neurons outside the core clock circuit and the mushroom body Kenyon cells. The acquisition of a TOD difference in mutants implies the existence of multiple oscillators that act to normalize memory formation across the day for appetitive processes. Interestingly, aversive STM requires PDF but not PDFR, suggesting that there are valence-specific pathways downstream of PDF that regulate memory formation. These data argue that the circadian clock uses circuit-specific and molecularly diverse output pathways to enhance the ability of animals to optimize responses to changing conditions.

SIGNIFICANCE STATEMENT

From humans to invertebrates, cognitive processes are influenced by organisms’ internal circadian clocks, the pace of which is linked to the solar cycle. Disruption of this link is increasingly common (e.g. jetlag, social jetlag disorders) and causes cognitive impairments that are costly and long-lasting. A detailed understanding of how the internal clock regulates cognition is critical for the development of therapeutic methods. Here, we show for the first time that olfactory associative memory inDrosophilarequires signaling by Pigment-dispersing factor (PDF), a neuromodulatory signaling peptide produced only by circadian clock circuit neurons. We also find a novel role for the clock circuit in stabilizing appetitive sucrose/odor memory across the day.
ConditionalPtenknockout in parvalbumin- or somatostatin-positive neurons sufficiently leads to autism-related behavioral phenotypes
Authors: Shin Sangyep , Santi Andrea , Huang Shiyong
Published: April 2020

Disrupted GABAergic neurons have been extensively described in brain tissues from individuals with autism spectrum disorder (ASD) and animal models for ASD. However, the contribution of these aberrant inhibitory neurons to autism-related behavioral phenotypes is not well understood. We examined ASD-related behaviors in mice with conditionalPtenknockout in parvalbumin (PV)-expressing or somatostatin (Sst)-expressing neurons, two common subtypes of GABAergic neurons. We found that mice with deletion ofPtenin either PV-neurons or Sst-neurons displayed social deficits, repetitive behaviors and impaired motor coordination/learning. In addition, mice with one copy ofPtendeletion in PV-neurons exhibited hyperlocomotion in novel open fields and home cages. We also examined anxiety behaviors and found that mice withPtendeletion in Sst-neurons displayed anxiety-like behaviors, while mice withPtendeletion in PV-neurons exhibited anxiolytic-like behaviors. These behavioral assessments demonstrate thatPtenknockout in the subtype of inhibitory neurons sufficiently gives rise to ASD-core behaviors, providing evidence that both PV- and Sst-neurons may play a critical role in ASD symptoms.
Rare variants association testing for a binary outcome when pooling individual level data from heterogeneous studies
Authors: Sofer Tamar , Guo Na
Published: April 2020

Whole genome and exome sequencing studies are used to test the association of rare genetic variants with health traits. Many existing WGS efforts now aggregate data from heterogeneous groups, e.g. combining sets of individuals of European and African ancestries. We here investigate the statistical implications on rare variant association testing with a binary trait when combining together heterogeneous studies, defined as studies with potentially different disease proportion and different frequency of variant carriers. We study and compare in simulations the type 1 error control and power of the naïve Score test, the saddlepoint approximation to the score test (SPA test), and the BinomiRare test in a range of settings, focusing on low numbers of variant carriers. We show that type 1 error control and power patterns depend on both the number of carriers of the rare allele and on disease prevalence in each of the studies. We develop recommendations for association analysis of rare genetic variants. (1) The Score test is preferred when the case proportion in the sample is 50%. (2) Do not down-sample controls to balance case-control ratio, because it reduces power. Rather, use a test that controls the type 1 error. (3) Conduct stratified analysis in parallel with combined analysis. Aggregated testing may have lower power when the variant effect size differs between strata.
Suppression of COVID-19 outbreak in the municipality of Vo’, Italy
Authors: Lavezzo Enrico , Franchin Elisa , Ciavarella Constanze , Cuomo-Dannenburg Gina , Barzon Luisa , Vecchio Claudia Del , Rossi Lucia , Manganelli Riccardo , Loregian Arianna , Navarin Nicolò , Abate Davide , Sciro Manuela , Merigliano Stefano , Decanale Ettore , Vanuzzo Maria Cristina , Saluzzo Francesca , Onelia Francesco , Pacenti Monia , Parisi Saverio , Carretta Giovanni , Donato Daniele , Flor Luciano , Cocchio Silvia , Masi Giulia , Sperduti Alessandro , Cattarino Lorenzo , Salvador Renato , Gaythorpe Katy A. M. ,   Imperial College London COVID-19 Response Team, Brazzale Alessandra R. , Toppo Stefano , Trevisan Marta , Baldo Vincenzo , Donnelly Christl A. , Ferguson Neil M. , Dorigatti Ilaria , Crisanti Andrea
Published: April 2020

On the 21st of February 2020 a resident of the municipality of Vo’, a small town near Padua, died of pneumonia due to SARS-CoV-2 infection1. This was the first COVID-19 death detected in Italy since the emergence of SARS-CoV-2 in the Chinese city of Wuhan, Hubei province2. In response, the regional authorities imposed the lockdown of the whole municipality for 14 days3. We collected information on the demography, clinical presentation, hospitalization, contact network and presence of SARS-CoV-2 infection in nasopharyngeal swabs for 85.9% and 71.5% of the population of Vo’ at two consecutive time points. On the first survey, which was conducted around the time the town lockdown started, we found a prevalence of infection of 2.6% (95% confidence interval (CI) 2.1-3.3%). On the second survey, which was conducted at the end of the lockdown, we found a prevalence of 1.2% (95% CI 0.8-1.8%). Notably, 43.2% (95% CI 32.2-54.7%) of the confirmed SARS-CoV-2 infections detected across the two surveys were asymptomatic. The mean serial interval was 6.9 days (95% CI 2.6-13.4). We found no statistically significant difference in the viral load (as measured by genome equivalents inferred from cycle threshold data) of symptomatic versus asymptomatic infections (p-values 0.6 and 0.2 for E and RdRp genes, respectively, Exact Wilcoxon-Mann-Whitney test). Contact tracing of the newly infected cases and transmission chain reconstruction revealed that most new infections in the second survey were infected in the community before the lockdown or from asymptomatic infections living in the same household. This study sheds new light on the frequency of asymptomatic SARS-CoV-2 infection and their infectivity (as measured by the viral load) and provides new insights into its transmission dynamics, the duration of viral load detectability and the efficacy of the implemented control measures.