bluuebunny/crossref_metadata_2025 huggingface dataset:
Sparse Epistatic Regularization of Deep Neural Networks for Inferring Fitness Functions
Authors: Aghazadeh Amirali , Nisonoff Hunter , Ocal Orhan , Brookes David H. , Huang Yijie , Koyluoglu O. Ozan , Listgarten Jennifer , Ramchandran Kannan
Published: November 2020

Despite recent advances in high-throughput combinatorial mutagenesis assays, the number of labeled sequences available to predict molecular functions has remained small for the vastness of the sequence space combined with the ruggedness of many fitness functions. Expressive models in machine learning (ML), such as deep neural networks (DNNs), can model the nonlinearities in rugged fitness functions, which manifest as high-order epistatic interactions among the mutational sites. However, in the absence of an inductive bias, DNNs overfit to the small number of labeled sequences available for training. Herein, we exploit the recent biological evidence that epistatic interactions in many fitness functions are sparse; this knowledge can be used as an inductive bias to regularize DNNs. We have developed a method for sparse epistatic regularization of DNNs, called theepistatic net(EN), which constrains the number of non-zero coefficients in the spectral representation of DNNs. For larger sequences, where finding the spectral transform becomes computationally intractable, we have developed a scalable extension of EN, which subsamples the combinatorial sequence space uniformly inducing a sparse-graph-code structure, and regularizes DNNs using the resulting greedy optimization method. Results on several biological landscapes, from bacterial to protein fitness functions, show that EN consistently improves the prediction accuracy of DNNs and enables them to outperform competing models which assume other forms of inductive biases. EN estimates all the higher-order epistatic interactions of DNNs trained on massive sequence spaces—a computational problem that takes years to solve without leveraging the epistatic sparsity in the fitness functions.
Overall patient’s survival of glioblastoma associated to molecular markers: a pan-proteomic prospective study
Authors: Drelich Lauranne , Duhamel Marie , Wisztorski Maxence , Aboulouard Soulaimane , Gimeno Jean-Pascal , Caux Pierre-Damien , Ogrinc Nina , Devos Patrick , Cardon Tristan , Weller Michael , Escande Fabienne , Zairi Fahed , Maurage Claude-Alain , Fournier Isabelle , Le Rhun Emilie , Salzet Michel
Published: November 2020

Molecular heterogeneities are a key feature of glioblastoma (GBM) pathology impeding patient’s stratification and leading to high discrepancies between patients mean survivals. Here, we established a molecular classification of GBM tumors using a pan-proteomic analysis. Then, we identified, from our proteomic data, 2 clusters of biomarkers associated with good or bad patient survival from 46 IDH wild-type GBMs. Three molecular groups have been identified and associated with systemic biology analyses. Group A tumors exhibit neurogenesis characteristics and tumorigenesis. Group B shows a strong immune cell signature and express poor prognosis markers while group C tumors are characterized by an anti-viral signature and tumor growth proteins. 124 proteins were found statistically different based on patient’s survival times, of which 10 are issued from alternative AltORF or non-coding RNA. After statistical analysis, a panel of markers associated to higher survival (PPP1R12A, RPS14, HSPD1 and LASP1) and another panel associated to lower survival (ALCAM, ANXA11, MAOB, IP_652563 and IGHM) has been validated by immunofluorescence. Taken together, our data will guide GBM prognosis and help to improve the current GBM classification by stratifying the patients and may open new opportunities for therapeutic development.

Significance

Glioblastoma are very heterogeneous tumors with median survivals usually inferior to 20 months. We conducted a pan-proteomics analysis of glioblastoma (GBM) in order to stratify GBM based on the molecular contained. Forty-six GBM cases were classified into three groups where proteins are involved in specific pathwaysi.e.the first group has a neurogenesis signature and is associated with a better prognosis while the second group of patients has an immune profile with a bad prognosis. The third group is more associated to tumorigenesis. We correlated these results with the TCGA data. Finally, we have identified 28 new prognostic markers of GBM and from these 28, a panel of 4 higher and 5 lower survival markers were validated. With these 9 markers in hand, now pathologist can stratify GBM patients and can guide the therapeutic decision.

Highlights

A novel stratification of glioblastoma based on mass spectrometry was established.

Three groups with different molecular features and survival were identified.

This new classification could improve prognostication and may help therapeutic options.

8 prognosis markers for oncologist therapeutic decision have been validated.
RpoS Contributes to Successful Opportunistic Colonization by Human Enteric Pathogens during Plant Disease
Authors: Lovelace Amelia H. , Lee Sangwook , Downs Diana M. , Soufi Ziad , Bota Pedro , Preston Gail M. , Kvitko Brian H.
Published: November 2020

With an increase in foodborne illnesses associated with the consumption of fresh produce, it is important to understand the interactions between human bacterial enteric pathogens and plants. It was previously established that diseased plants can create a permissive environment for opportunistic endophytic colonization of enteric pathogens. However, the factors that contribute to the colonization of enteric pathogens during plant disease are largely unknown. Here, we show that both strain and plant host factors contribute to significantly increased populations of enteric pathogens when co-inoculated with the plant pathogen,P. syringaepv.tomato. The twoSalmonella entericastrains DM10000 and 14028S, differ in their ability to metabolize host-derived apoplastic carbohydrates dependent on the sigma factor RpoS. TherpoSgene is an important strain factor for endophytic colonization byS. entericaduring plant disease. Our results suggest thatrpoSplays a crucial role duringin plantacolonization, balancing nutrient metabolism and stress responses.

Importance

Foodborne illnesses caused by the bacterial human enteric pathogens,E. coliO157:H7 andS. enterica, often results in vomiting and diarrhea. If left untreated, this illness can cause dehydration and sometimes death of a patient. BothE. coliO157:H7 andS. entericahave caused repeated fresh produce-associated epidemics. Crop disease could promote the ability of plants to act as reservoirs for produce-borne outbreaks. Plant pathogens dampen plant immunity, which allows for a more permissive environment for human enteric pathogens to grow. These internalized enteric pathogen populations are especially dangerous since they cannot be removed by washing alone. Therefore, the need to understand the factors that contribute to the opportunistic colonization of human enteric pathogens during plant disease is apparent. Our research has identified host and strain factors that contribute to opportunistic colonization of diseased plants, which will inform the development of future management strategies to mitigate future outbreaks.
Bacterial community associated with the dry-rot fungusSerpula lacrymansis dominated by Firmicutes and Proteobacteria
Authors: Embacher Julia , Neuhauser Sigrid , Zeilinger Susanne , Kirchmair Martin
Published: November 2020

The dry-rot fungusSerpula lacrymanscauses enormous structural damage by decaying construction timber thereby resulting in tremendous financial loss. Dry-rot fungi decompose cellulose and hemicellulose and, if the wood remains wet, are often accompanied by a succession of bacteria and other fungi. Bacterial-fungal interactions have considerable impact on all interaction partners ranging from antagonistic to beneficial relationships. However, little is known about possible interaction partners ofS. lacrymans. Here we show thatS. lacrymanshas many co-existing, mainly Gram-positive bacteria. By investigating differences in the bacterial community associated with fruiting bodies, mycelia and rhizomorphs, we provide evidence of preferential colonization ofS. lacrymanstissues by certain bacterial phyla. Bacteria isolated from fruiting bodies and mycelia were dominated by Firmicutes, while bacteria isolated from rhizomorphs were dominated by Proteobacteria. Actinobacteria and Bacteroidetes were found in lower abundances.In situfluorescence hybridization (FISH) analysis revealed that bacteria were not present biofilm-like, but occurred as independent cells, sometimes also attached to fungal spores. In co-culture, single bacterial isolates caused growth inhibition ofS. lacrymansand vice versa. Additionally, certain bacteria induced pigment production in the fungus. Our results provide first insights for a better understanding of the holobiontS. lacrymansand give hints that bacteria are able to influence the behavior, e.g. growth and secondary metabolite production, ofS. lacrymansin culture.

Importance

Serpula lacrymansis a very effective dry-rot causing fungus, specialized in degradation of coniferous timber in houses. The initial colonization is favored by water damage, and after establishment, the fungus starts to destruct cellulose and hemicellulose. It is among the most feared wood-rotting fungi in the built environment as the remediation ofS. lacrymansdamaged buildings is expensive and tedious. After improper renovation, the possibility of a recolonization byS. lacrymansis likely. As bacteria influence fungal establishment on wood, the need to investigate the bacterial community associated withS. lacrymansis apparent. The significance of our research is in identifying and characterizing bacteria associated withS. lacrymans.This will allow the assessment of their influence on fungal life style, leading to a broader understanding of the properties that makeS. lacrymansso extraordinarily aggressive at decaying wood compared to other indoor wood destroyers.
Saccharomyces cerevisiaeRequiresCFF1to Produce 4-hydroxy-5-methylfuran-3(2H)-one, a Mimic of the Bacterial Quorum-Sensing Autoinducer AI-2
Authors: Valastyan Julie S. , Kraml Christina M. , Pelczer Istvan , Ferrante Thomas , Bassler Bonnie L.
Published: November 2020

Quorum sensing is a process of cell-to-cell communication that bacteria use to orchestrate collective behaviors. Quorum sensing depends on the production, release, and detection of extracellular signal molecules called autoinducers (AIs) that accumulate with increasing cell density. While most AIs are species-specific, the AI called AI-2 is produced and detected by diverse bacterial species and it mediates inter-species communication. We recently reported that mammalian cells produce an AI-2 mimic that can be detected by bacteria through the AI-2 receptor, LuxP, potentially expanding the role of the AI-2 system to inter-domain communication. Here, we describe a second molecule capable of inter-domain signaling through LuxP, 4-hydroxy-5-methylfuran-3(2H)-one (MHF) that is produced by the yeastSaccharomyces cerevisiae. Screening theS. cerevisiaedeletion collection revealed Cff1p, a protein with no known role, to be required for MHF production. Cff1p is proposed to be an enzyme, possibly an epimerase or isomerase, and substitution at the putative catalytic residue eliminated MHF production inS. cerevisiae. Sequence analysis uncovered Cff1p homologs in many species, primarily bacterial and fungal, but also viral, archaeal, and higher eukaryotic. Cff1p homologs from organisms from all domains can complement aS. cerevisiae cff1Δmutant and restore MHF production. In all test cases, the identified catalytic residue is conserved and required for MHF to be produced. These findings increase the scope of possibilities for inter-domain interactions via AI-2 and AI-2 mimics, highlighting the breadth of molecules and organisms that could participate in quorum sensing.

Importance

Quorum sensing is a cell-to-cell communication process that bacteria use to monitor local population density. Quorum sensing relies on extracellular signal molecules called autoinducers (AIs). One AI, called AI-2, is broadly made by bacteria and used for inter-species communication. Here, we describe a eukaryotic AI-2 mimic, 5-methylfuran-3(2H)-one, (MHF), that is made by the yeastSaccharomyces cerevisiae, and we identify the Cff1p protein as essential for MHF production. Hundreds of viral, archaeal, bacterial, and eukaryotic organisms possess Cff1p homologs. This finding, combined with our results showing that homologs from all domains can replaceS. cerevisiaeCff1p, suggests that like AI-2, MHF is widely produced. Our results expand the breadth of organisms that may participate in quorum-sensing-mediated interactions.
Network mapping of root-microbe interactions inArabidopsis thaliana
Authors: He Xiaoqing , Zhang Qi , Jin Yi , Jiang Libo , Wu Rongling
Published: November 2020

Understanding how plants interact with their colonizing microbiota to determine plant phenotypes is a fundamental question in modern plant science. Existing approaches for genome-wide association studies (GWAS) are based on the association analysis between host genes and the abundance of individual microbes, failing to characterize the genetic architecture of microbial interactions that are thought to a determinant of microbiota structure, organization, and function. Here, we implement a behavioral model to quantify various patterns of microbe-microbe interactions, i.e., mutualism, antagonism, aggression, and altruism, and map host genes that modulate microbial networks constituted by these interaction types. We reanalyze a root-microbiome data involving 179 accessions ofArabidopsis thalianaand find that the four networks differ structurally in the pattern of bacterial-fungal interactions and microbiome complexity. We identify several fungus and bacterial hubs that play a central role in mediating microbial community assembly surroundingA. thalianaroot systems. We detect 1142 significant host genetic variants throughout the plant genome and then implement Bayesian networks (BN) to reconstruct epistatic networks involving all significant SNPs and find 91 hub QTLs. Gene annotation shows that a number of the hub genes detected are biologically relevant, playing roles in plant growth and development, resilience against pathogens, root development, and improving resistance against abiotic stress conditions. The new model allows us to better understand the underlying mechanisms that govern the relationships between plants and their entire microbiota and harness soil microbes for plant production.
Genomic investigation of a dengue virus outbreak in Thiès, Senegal, in 2018
Authors: Gaye Amy , Ndiaye Tolla , Sy Mouhamad , Deme Awa B. , Thiaw Alphonse B. , Sene Aita , Ndiaye Cheikh , Diedhiou Younouss , Mbaye Amadou M. , Ndiaye Ibrahima , Tomkins-Tinch Christopher , Gomis Jules F. , Badiane Aida S. , MacInnis Bronwyn , Park Daniel J. , Ndiaye Mouhamadou , Sy Ngayo , Sabeti Pardis C. , Siddle Katherine J. , Ndiaye Daouda
Published: November 2020

Dengue virus is a major and rapidly growing public health concern in tropic and subtropic regions across the globe. In late 2018, Senegal experienced its largest dengue virus outbreak to date, covering several regions. However, little is known about the genetic diversity of dengue virus (DENV) in Senegal. Here we used molecular tools including metagenomic sequencing to identify 19 previously undetected dengue virus cases from the city of Thiès and assemble 17 complete virus genomes. DENV3 was the most frequent serotype; 11 sequences (65%) were DENV3, 4 sequences were DENV2 and 2 were DENV1. Sequences were closest to recent sequences from West Africa, suggesting ongoing local circulation of viral populations; however, detailed inference is limited by the scarcity of available genomic data. We did not find clear associations with reported clinical signs or symptoms, highlighting the importance of testing for diagnosing febrile diseases. Overall, these findings expand the known range of DENV in Senegal, and underscore the need for better genomic characterization of DENV in West Africa.
Systematic evaluation of transcriptomic disease risk and diagnostic biomarker overlap between COVID-19 and tuberculosis: a patient-level meta-analysis
Authors: Sheerin Dylan , Abhimanyu  , Wang Xutao , Johnson W Evan , Coussens Anna
Published: November 2020

Background

The novel coronavirus, SARS-CoV-2, has increased the burden on healthcare systems already strained by a high incidence of tuberculosis (TB) as co-infection and dual presentation are occurring in syndemic settings. We aimed to understand the interaction between these diseases by profiling COVID-19 gene expression signatures on RNA-sequencing data from TB-infected individuals.

Methods

We performed a systematic review and patient-level meta-analysis by querying PubMed and pre-print servers to derive eligible COVID-19 gene expression signatures from human whole blood (WB), PBMCs or BALF studies. A WB influenza dataset served as a control respiratory disease signature. Three large TB RNA-seq datasets, comprising multiple cohorts from the UK and Africa and consisting of TB patients across the disease spectrum, were chosen to profile these signatures. Putative “COVID-19 risk scores” were generated for each sample in the TB datasets using the TBSignatureProfiler package. Risk was stratified by time to TB diagnosis in progressors and contacts of pulmonary and extra-pulmonary TB. An integrative analysis between TB and COVID-19 single-cell RNA-seq data was performed and a population-level meta-analysis was conducted to identify shared gene ontologies between the diseases and their relative enrichment in COVID-19 disease severity states.

Results

35 COVID-19 gene signatures from nine eligible studies comprising 98 samples were profiled on TB RNA-seq data from 1181 samples from 853 individuals. 25 signatures had significantly higher COVID-19 risk in active TB (ATB) compared with latent TB infection (p <0·005), 13 of which were validated in two independent datasets.FCN1- andSPP1-expressing macrophages enriched in BALF during severe COVID-19 were identified in circulation during ATB. Shared perturbed ontologies included antigen presentation, epigenetic regulation, platelet activation, and ROS/RNS production were enriched with increasing COVID-19 severity. Finally, we demonstrate that the overlapping transcriptional responses may complicate development of blood-based diagnostic signatures of co-infection.

Interpretation

Our results identify shared dysregulation of immune responses in COVID-19 and TB as a dual risk posed by co-infection to COVID-19 severity and TB disease progression. These individuals should be followed up for TB in the months subsequent to SARS-CoV-2 diagnosis.
Diabetes and Mortality Among 1.6 Million Adult Patients Screened for SARS-CoV-2 in Mexico
Authors: Woolcott Orison O. , Castilla-Bancayán Juan P.
Published: November 2020

Background

Whether diabetes is associated with COVID-19-related mortality remains unclear.

Methods

In this retrospective case-series study we examined the risk of death associated with self-reported diabetes in symptomatic adult patients with laboratory-confirmed COVID-19 who were identified through the System of Epidemiological Surveillance of Viral Respiratory Disease in Mexico from January 1 through November 4, 2020. Survival time was right-censored at 28 days of follow-up.

Results

Among 757,210 patients with COVID-19 included in the study, 120,476 (16%) had diabetes and 80,616 died. Patients with diabetes had a 49% higher relative risk of death than those without diabetes (Cox proportional-hazard ratio; 1.49 (95% confidence interval [CI], 1.47-1.52), adjusting for age, sex, smoking habit, obesity, hypertension, immunodeficiency, and cardiovascular, pulmonary, and chronic renal disease. The relative risk of death associated with diabetes decreased with age (P=0.004). The hazard ratios were 1.66 (1.58-1.74) in outpatients and 1.14 (1.12-1.16) in hospitalized patients. The 28-day survival for inpatients with and without diabetes was, respectively, 73.5% and 85.2% for patients 20-39 years of age; 66.6% and 75.9% for patients 40-49 years of age; 59.4% and 66.5% for patients 50-59 years of age; 50.1% and 54.6% for patients 60-69 years of age; 42.7% and 44.6% for patients 70-79 years of age; and 38.4% and 39.0% for patients 80 years of age or older. In patients without COVID-19 (878,840), the adjusted hazard ratio for mortality was 1.78 (1.73-1.84).

Conclusion

In symptomatic adult patients with COVID-19 in Mexico, diabetes was associated with higher mortality. This association decreased with age.
Structural basis for the association of PLEKHA7 with membrane-embedded phosphatidylinositol lipids
Authors: Aleshin Alexander E. , Yao Yong , Iftikhar Amer , Bobkov Andrey A. , Yu Jinghua , Cadwell Gregory , Klein Michael G. , Dong Chuqiao , Bankston Laurie A. , Liddington Robert C. , Im Wonpil , Powis Garth , Marassi Francesca M.
Published: November 2020

PLEKHA7 (pleckstrin homology domain containing family A member 7) plays key roles in intracellular signaling, cytoskeletal organization and cell adhesion, and is associated with multiple human cancers. The interactions of its pleckstrin homology (PH) domain with membrane phosphatidyl-inositol-phosphate (PIP) lipids, are critical for proper cellular localization and function, and their inhibition is an attractive target for anti-cancer therapy. While structural data can provide insights in this area, little is known about the way in which PLEKHA7 and other PH domains interact with membrane-embedded PIPs. Here we report atomic-resolution structures of the PLEHA7 PH domain and describe the molecular mechanism for its recognition of membrane-bound PIPs. Using X-ray crystallography, nuclear magnetic resonance (NMR), molecular dynamics (MD) simulations, and isothermal titration calorimetry (ITC), we show – in atomic-level detail – that the interaction of PLEKHA7 with PIPs is multivalent and induces PIP clustering. The PIP binding mechanism is distinct from a discrete one-to-one interaction. Our findings reveal a central role of the membrane assembly in mediating protein-PIP association and provide a roadmap for the design of PLEKHA7-PIP inhibitors.
Inactivation of SARS-CoV-2 on surfaces and in solution with Virusend (TX-10), a novel disinfectant
Authors: Anderson Enyia R. , Hughes Grant L. , Patterson Edward I.
Published: November 2020

Until an effective vaccine against SARS-CoV-2 is available on a widespread scale, the control of the COVID-19 pandemic is reliant upon effective pandemic control measures. The ability of SARS-CoV-2 to remain viable on surfaces and in aerosols, means indirect contact transmission can occur and so there is an opportunity to reduce transmission using effective disinfectants in public and communal spaces. Virusend (TX-10), a novel disinfectant, has been developed as a highly effective disinfectant against a range of microbial agents. Here we investigate the ability of Virusend (TX-10) to inactivation SARS-CoV-2. Using surface and solution inactivation assays, we show that Virusend (TX-10) is able to reduce SARS-CoV-2 viral titre by 4log10PFU/mL within 1 minute of contact. Ensuring disinfectants are highly effective against SARS-CoV-2 is important in eliminating environmental sources of the virus to control the COVID-19 pandemic.
How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a microendemic Malagasy tree
Authors: Salmona Jordi , Dresen Axel , Ranaivoson Anicet E. , Manzi Sophie , Le Pors Barbara , Hong-Wa Cynthia , Razanatsoa Jacqueline , Andriaholinirina Nicole V. , Rasoloharijaona Solofonirina , Vavitsara Marie-Elodie , Besnard Guillaume
Published: November 2020

Understanding landscape changes is central to predicting evolutionary trajectories and defining conservation practices. While human-driven deforestation is intense throughout Madagascar, exceptions in areas like the Loky-Manambato region (North) raise questions. Such regions also harbor a rich and endemic flora, whose evolutionary origin remains poorly understood. We assessed the genetic diversity of an endangered microendemic Malagasy olive species (Noronhia spinifolia Hong-Wa) to better understand the vegetation dynamic in the Loky-Manambato region and its influence on past evolutionary processes. We characterized 72 individuals sampled across eight forests through nuclear and mitochondrial restriction associated sequencing data (RADseq) and chloroplast microsatellites (cpSSR). Combined population and landscape genetics analyses indicate that N. spinifolia diversity is largely explained by the current forest cover, highlighting a long-standing habitat mosaic in the region. This sustains a major and long-term role of riparian corridors in maintaining connectivity across those antique mosaic-habitats, calling for the study of organismal interactions that promote gene flow.
N-terminal VP1 truncations favorT=1 norovirus-like particles
Authors: Pogan Ronja , Weiss Victor U. , Bond Kevin , Dülfer Jasmin , Krisp Christoph , Lyktey Nicholas , Müller-Guhl Jürgen , Zoratto Samuele , Allmaier Günter , Jarrold Martin F. , Muñoz-Fontela Cesar , Schlüter Hartmut , Uetrecht Charlotte
Published: November 2020

Noroviruses cause immense sporadic gastroenteritis outbreaks worldwide. Emerging genotypes, which are divided based on VP1 sequence, further enhance this public threat. Self-assembling properties of the human norovirus major capsid protein VP1 are crucial for using virus-like particles (VLPs) for vaccine development. However, there is no vaccine available yet. Here, VLPs from different variants produced in insect cells are characterized in detail using a set of biophysical and structural tools. We are using native mass spectrometry, gas-phase electrophoretic mobility molecular analysis and proteomics to get clear insights into particle size, structure, composition as well as stability. Generally, noroviruses have been known to form mainlyT=3 particles. Importantly, we identify a major truncation in the capsid proteins as a likely cause for the formation of merelyT=1 particles. For vaccine development, particle production needs to be a reproducible, reliable process. Understanding the underlying processes in capsid size variation will help to produce particles of a defined capsid size presenting antigens consistent with intact virions. Next to vaccine production itself, this would be immensely beneficial for bio-/nano-technological approaches using viral particles as carriers or triggers for immunological reactions.
AKAP79/150 coordinates leptin-induced PKA activation to regulate KATPchannel trafficking in pancreatic β-cells
Authors: Cochrane Veronica A. , Yang Zhongying , Dell’Acqua Mark , Shyng Show-Ling
Published: November 2020

The adipocyte hormone leptin regulates glucose homeostasis both centrally and peripherally. A key peripheral target is the pancreatic β-cell, which secretes insulin upon glucose stimulation. Leptin suppresses glucose-stimulated insulin secretion by promoting trafficking of KATPchannels to the β-cell surface, which increases K+conductance and causes β-cell hyperpolarization. Here we investigate the signaling mechanism underlying leptin-induced KATPchannel translocation with a focus on protein kinase A (PKA). Using FRET-based PKA activity reporters, we show that leptin increases PKA activity at the cell membrane via a signaling pathway involving NMDA receptors, CaMKKβ and AMPK. Genetic knockdown and rescue experiments reveal that leptin activation of PKA requires tethering of PKA to the membrane-targeted PKA-anchoring protein AKAP79/150. Interestingly, disrupting protein phosphatase 2B (PP2B) anchoring to AKAP79/150, known to elevate basal PKA signaling, increases surface KATPchannels. Our findings uncover a novel role of AKAP79/150 in coordinating leptin and PKA signaling to regulate β-cell function.
SpheroidPicker: An Automated 3D cell culture manipulator robot using deep learning
Authors: Grexa Istvan , Diosdi Akos , Kriston Andras , Moshkov Nikita , Harmati Maria , Buzas Krisztina , Pietiainen Vilja , Koos Krisztian , Horvath Peter
Published: November 2020

Recent statistics report that more than 3.7 million new cases of cancer occur in Europe yearly, and the disease accounts for approximately 20 % of all deaths. High-throughput screening of cancer cell cultures has dominated the search for novel, effective anticancer therapies in the past decades. Recently, ex vivo 3D cell cultures from the patient’s own cancer cells have gained importance. We recently evaluated the major advancements and needs of the 3D cell cultures screening field, and we concluded that strictly standardized sample preparation is the most desired development. Here we propose an artificial intelligence-guided low-cost 3D cell culture delivery system. It consists of a light microscope, a micromanipulator, a syringe pump, and a controller computer. The system performs morphology-based feature analysis on spheroids and transfers the most appropriate ones between various sample holders. It can select the samples from standard sample holders, including Petri dishes and microwell plates, and then transfer them to a variety of holders up to 384 well plates. The device performs reliable semi- and fully automated spheroid transfer. This results in highly controlled experimental conditions and eliminates non-trivial side effects of sample variability that is a key aspect towards next-generation precision medicine.
Control of stem cell niche and fruit development inArabidopsis thalianabyAGO10/ZWLrequires the bHLH transcription factorINDEHISCENT
Authors: Valluru Manoj , Sorefan Karim
Published: November 2020

Background

The shoot apical meristem (SAM) in plants is composed of a small mound of pluripotent stem cells that generate new organs. ARGONAUTE10 (AGO10) is known to be critical for maintenance of the embryonic SAM by regulating the expression ofClass III HOMEODOMAIN-LEUCINE ZIPPER(HD-ZIP III) transcription factors, which then modulate downstream responses to the key phytohormone auxin. However, we do not understand how AGO10 modulates auxin responses after embryogenesis in the mature plant.

Results

Here we show thatAGO10regulates auxin responses in the post-embryonic SAM via the bHLH transcription factorINDEHISCENT(IND). IND directly regulates auxin responses in the SAM regulating the auxin transporter PIN1 via direct transcriptional regulation ofPINOIDkinase. We show that a loss of functionindmutation significantly restoresago10zwl-3mutant SAM and fruit phenotypes.ago10zwl-3mutants overexpressINDand overexpression of IND phenocopies theago10zwl-3SAM phenotypes, and regulates auxin transport and responses in the SAM. AGO10 also regulates post-embryonic development in the fruit via a similar genetic pathway.

Conclusions

We characterise a molecular mechanism that is conserved during post embryonic development linkingAGO10directly to auxin responses.
Prognostic Biomarkers for Predicting Papillary Thyroid Carcinoma Patients at High Risk Using Nine Genes of Apoptotic Pathway
Authors: Arora Chakit , Kaur Dilraj , Raghava G.P.S
Published: November 2020

Objectives

Aberrant expression of apoptotic genes has been associated with papillary thyroid carcinoma (PTC) in the past, however, their prognostic role and utility as biomarkers remains poorly understood.

Materials and methods

In this study, we analysed 505 PTC patients by employing Cox-PH regression techniques, prognostic index models and machine learning methods to elucidate the relationship between overall survival (OS) of PTC patients and 165 apoptosis related genes.

Results

It was observed that nine genes (ANXA1, TGFBR3, CLU, PSEN1, TNFRSF12A, GPX4, TIMP3, LEF1, BNIP3L) showed significant association with OS of PTC patients. Five out of nine genes were found to be positively correlated with OS of the patients, while the remaining four genes were negatively correlated. These genes were used for developing risk prediction models. Our voting-based model achieved highest performance (HR=41.59, p=3.36×10−4, C=0.84, logrank-p=3.8×10−8). The performance of voting-based model improved significantly when we used the age of patients with prognostic biomarker genes and achieved HR=57.04 with p=10−4(C=0.88, logrank-p=1.44×10−9). We also developed classification models that can classify high risk patients (survival ≤ 6 years) and low risk patients (survival > 6 years). Our best model achieved AUROC of 0.92. Since these genes can also be used as potential therapeutic targets in PTC, we identified potential drug molecules which could modulate their expression profile.

Conclusion

This study briefly revealed the key prognostic biomarker genes in the apoptotic pathway whose altered expression is associated with PTC progression and aggressiveness. In addition to this, risk assessment models proposed here can help in efficient management of PTC patients.
Integration in or Near Oncogenes Plays Only a Minor Role in Determining the in Vivo Distribution of HIV Integration Sites Before or During Suppressive Antiretroviral Therapy
Authors: Coffin John M. , Bale Michael J. , Wells Daria , Guo Shuang , Luke Brian , Zerbato Jennifer M. , Sobolewskii Michele D. , Sia Twan , Shao Wei , Wu Xiaolin , Maldarelli Frank , Kearney Mary F. , Mellors John W. , Hughes Stephen H.
Published: November 2020

HIV persists during antiretroviral therapy (ART) as integrated proviruses in cells descended from a small fraction of the CD4+ T cells infected prior to the initiation of ART. To better understand what controls HIV persistence and the distribution of integration sites (IS), we compared about 16,000 and 54,000 IS from individuals pre-ART and on ART, respectively, with approximately 385,000 IS from PBMC infected in vitro. The distribution of IS in vivo is quite similar to the distribution in PBMC, modified by selection against proviruses in expressed genes, by selection for proviruses integrated into one of 6 specific genes, and by clonal expansion. The clones in which a provirus integrated in an oncogene contributed to the survival of the clone comprise only a small fraction of the clones that persist in HIV-infected individuals on ART. Mechanisms that do not involve the provirus, or its location in the host genome, are more important in determining which clones expand and persist.

Author Summary

In HIV-infected individuals, a small fraction of the infected cells persist and divide. This reservoir persists on ART and can rekindle the infection if ART is discontinued. Because the number of possible sites of HIV DNA integration is very large, each infected cell, and all of its descendants, can be identified by the site where the provirus is integrated (IS). To understand the selective forces that determine the fates of infected cells in vivo, we compared the distribution of HIV IS in freshly-infected cells to cells from HIV-infected donors sampled both before and during ART. We found that, as has been previously reported, integration favors highly-expressed genes. However, over time the fraction of cells with proviruses integrated in highly-expressed genes decreases, implying that they grow less well. There are exceptions to this broad negative selection. When a provirus is integrated in a specific region in one of six genes, the proviruses affect the expression of the target gene, promoting growth and/or survival of the cell. Although this effect is striking, it is only a minor component of the forces that promote the growth and survival of the population of infected cells during ART.
Arabidopsis thalianagenes contributing to differences in the outcome of infection with generalist and specialist strains ofTurnip mosaic virusidentified by genome-wide association studies
Authors: Butković Anamarija , González Rubén , Rivarez Mark Paul Selda , Elena Santiago F.
Published: November 2020

Pathogens can be classified as generalists or specialists depending on their host breadth. While generalists are able to successfully infect a wide variety of host species, the host range of specialists is limited to a few related species. Even though generalists seem to gain an advantage due to their wide host range, they usually pay a cost in terms of fitness within each host species (i.e., the jack-of-all trades, master of none). On the contrary, specialists have high fitness within their own host. A highly relevant yet poorly explored question is whether generalist and specialist viruses differ in the way they interact with their host’s gene expression networks. To identify host genetic factors relevant for the infection of specialist or generalist viruses, we undertook a genome-wide association study (GWAS) approach. Four hundred fifty natural accessions ofArabidopsis thalianawere inoculated with turnip mosaic potyvirus strains that were either generalist (TuMV-G) or specialist (TuMV-S). Several disease-related traits have been associated with different sets of host genes for each TuMV strain. While most of the mapped loci were traitor strain-specific, one shared locus was mapped for both strains, a disease resistance TIR-NBS-LRR class protein. Likewise, only one locus was found involved in more than one of the disease-related traits evaluated, a putative cysteine-rich receptor-like protein kinase 20. To validate these results, the corresponding null mutant plants were inoculated with TuMV-G or -S and the outcome of infection was characterized.

Author summary

Generalist and specialist viruses are commonly found in nature, where they have potential for epidemics, and are classified depending on their host breath. In this study we used a genome-wide association study to characterize differences in the genetic basis of both infection strategies from a host perspective. Our experimental setup consisted of 450 accessions ofA. thalianaand two strains of TuMV. We found differences in the number of associated genes and their functions in disease-related traits. Results were validated by characterization of viral infections in null mutant plants deficient for a set of the identified genes.
Extensive phylogenies of human development reveal variable embryonic patterns
Authors: Coorens Tim H. H. , Moore Luiza , Robinson Philip S. , Sanghvi Rashesh , Christopher Joseph , Hewinson James , Cagan Alex , Oliver Thomas R. W. , Neville Matthew D. C. , Hooks Yvette , Noorani Ayesha , Mitchell Thomas J. , Fitzgerald Rebecca C. , Campbell Peter J. , Martincorena Iñigo , Rahbari Raheleh , Stratton Michael R.
Published: November 2020

Starting from the zygote, all cells in the developing and adult human body continuously acquire mutations. A mutation shared between two different cells implies a shared progenitor cell and can thus be used as a naturally occurring marker for lineage tracing. Here, we reconstruct extensive phylogenies of normal tissues from three adult individuals using whole-genome sequencing of 511 laser capture microdissected samples from multiple organs. Early embryonic progenitor cells inferred from the phylogenies often contribute in different proportions to the adult body and the extent of this asymmetry is variable between individuals, with ratios between the first two reconstructed cells ranging from 56:44 to 92:8. Asymmetries also pervade subsequent cell generations and can differ between tissues in the same individual. The phylogenies also resolve the spatial embryonic origins and patterning of tissues, revealing a spatial effect in the development of the human brain. Supplemented by data on eleven men, we timed the split between soma and germline, with the earliest observed segregation occurring at the first cell divisions. This research demonstrates that, despite reaching the same ultimate tissue patterns, early bottlenecks and lineage commitments lead to substantial variation in embryonic patterns both within and between individuals.
Single-nucleus full-length RNA profiling in plants incorporates isoform information to facilitate cell type identification
Authors: Long Yanping , Liu Zhijian , Jia Jinbu , Mo Weipeng , Fang Liang , Lu Dongdong , Liu Bo , Zhang Hong , Chen Wei , Zhai Jixian
Published: November 2020

The broad application of large-scale single-cell RNA profiling in plants has been restricted by the prerequisite of protoplasting. We recently found that the Arabidopsis nucleus contains abundant polyadenylated mRNAs, many of which are incompletely spliced. To capture the isoform information, we combined 10x Genomics and Nanopore long-read sequencing to develop a protoplasting-free full-length single-nucleus RNA profiling method in plants. Our results demonstrated using Arabidopsis root that nuclear mRNAs faithfully retain cell identity information, and single-molecule full-length RNA sequencing could further improve cell type identification by revealing splicing status and alternative polyadenylation at single-cell level.
A Synergistic Workspace for Human Consciousness Revealed by Integrated Information Decomposition
Authors: Luppi Andrea I. , Mediano Pedro A.M. , Rosas Fernando E. , Allanson Judith , Pickard John D. , Carhart-Harris Robin L. , Williams Guy B. , Craig Michael M , Finoia Paola , Owen Adrian M. , Naci Lorina , Menon David K. , Bor Daniel , Stamatakis Emmanuel A.
Published: November 2020

A central goal of neuroscience is to understand how the brain orchestrates information from multiple input streams into a unified conscious experience. Here, we address two fundamental questions: how is the human information-processing architecture functionally organised, and how does its organisation support consciousness? We combine network science and a rigorous information-theoretic notion of synergy to delineate a “synergistic global workspace”, comprising gateway regions that gather synergistic information from specialised modules across the brain. This information is then integrated within the workspace and widely distributed via broadcaster regions. Through functional MRI analysis, we show that gateway regions of the synergistic workspace correspond to the brain’s default mode network, whereas broadcasters coincide with the executive control network. Demonstrating the empirical relevance of our proposed architecture for neural information processing, we show that loss of consciousness due to general anaesthesia or disorders of consciousness corresponds to a diminished ability of the synergistic workspace to integrate information, which is restored upon recovery. Thus, loss of consciousness coincides with a breakdown of information integration within the synergistic workspace of the human brain. This work contributes to conceptual and empirical reconciliation between two prominent scientific theories of consciousness, the Global Neuronal Workspace and Integrated Information Theory. Taken together, this work provides a new perspective on the role of prominent resting-state networks within the human information-processing architecture, while also advancing our understanding of how the human brain supports consciousness through the synergistic integration of information.
Transient active osmotic swelling of epithelium upon curvature induction
Authors: Tomba Caterina , Luchnikov Valeriy , Barberi Luca , Blanch-Mercader Carles , Roux Aurélien
Published: November 2020

Generation of tissue curvature is essential to morphogenesis. However, how cells adapt to changing curvature is still unknown because tools to dynamically control curvature in vitro are lacking. Here we developed self-rolling substrates to study how flat epithelial cell monolayers adapt to a rapid, anisotropic change of curvature. We show that the primary response is an active and transient osmotic swelling of cells. This cell volume increase is not observed on inducible wrinkled substrates, where concave and convex regions alternate each other over short distances, identifying swelling as a collective response to changes of curvature with persistent sign over large distances. It is triggered by a drop in membrane tension and actin depolymerization, perceived by cells as a hypertonic shock. Osmotic swelling restores tension while actin reorganizes, probably to comply with curvature. Epithelia are thus unique materials that transiently, actively swell while adapting to large curvature induction.
Early-life mitochondrial DNA damage results in lifelong deficits in energy production mediated by redox signaling inCaenorhabditis elegans
Authors: Rooney John P. , Hershberger Kathleen A. , Turner Elena A. , Donoghue Lauren J. , Maurer Laura L. , Ryde Ian T. , Kim Jina J , Joglekar Rashmi , Hibshman Jonathan D. , Smith Latasha L. , Bhatt Dhaval P. , Ilkayeva Olga R. , Hirschey Matthew D. , Meyer Joel N.
Published: November 2020

The consequences of damage to the mitochondrial genome (mtDNA) are poorly understood, although mtDNA is more susceptible to damage than nuclear DNA (nucDNA), and many environmental toxicants target the mitochondria. Reports from the toxicological literature suggest that exposure to early-life mitochondrial damage could lead to deleterious consequences later in life (the “Developmental Origins of Health and Disease” paradigm) but reports from other fields often report beneficial (“mitohormetic”) responses to such damage. Here, we test the effects of low (causing no change in lifespan) levels of ultraviolet C (UVC)-induced, irreparable mtDNA damage during early development inCaenorhabditis elegans. This exposure led to life-long reductions in mtDNA copy number and steady-state ATP levels, accompanied by increased oxygen consumption and altered metabolite profiles, suggesting inefficient mitochondrial function. Exposed nematodes were also developmentally delayed, reached smaller adult size, and were rendered more susceptible to subsequent exposure to chemical mitotoxicants. Metabolomic and genetic analysis of key signaling and metabolic pathways supported redox signaling during early development as a mechanism for establishing these persistent alterations. Our results highlight the importance of early-life exposures to environmental pollutants, especially in the context of exposure to chemicals that target mitochondria.