bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulation of cGAS activity through RNA-mediated phase separation
Authors: Chen Silian , Rong Miao , Lv Yun , Zhu Deyu , Xiang Ye
Published: September 2020

Cyclic GMP-AMP synthase (cGAS) is a double-stranded DNA (dsDNA) sensor that functions in the innate immune system. Upon binding dsDNA in the cytoplasm, cGAS and dsDNA form phase-separated aggregates in which cGAS catalyzes synthesis of 2’3’-cyclic GMP-AMP that subsequently triggers a STING-dependent, type I IFN response. Here, we showed that cytoplasmic RNAs, especially tRNAs, regulate cGAS activity. We discovered that RNAs did not activate cGAS but rather promoted phase separationin vitro. In cells, cGAS colocalized with RNAs and formed phase-separated granules even in the absence of cytoplasmic dsDNA. An Opti-prep gradient analysis of cell lysates showed that the endogenous cGAS was associated with cytoplasmic RNAs in an aggregative form. Furtherin vitroassays showed that RNAs compete for binding of cGAS with dsDNA and inhibit cGAS activity when the dsDNA concentration is high and promote the formation of phase separations and enhance cGAS activity when the dsDNA concentration is low. Thus, cytoplasmic RNAs regulate cGAS activity by interfering with formation of cGAS-containing aggregates.
Assessment of Risk Factors Correlated with Age-Adjusted Mortality by Region for Prostate Cancer in Japan: an epidemiological study
Authors: Nagano Takuya , Hoshi Akihiko
Published: September 2020

Introduction

Previous studies have suggested that smoking and drinking alcohol are prostate cancer risks. However, how regional unevenness of radiation oncologists/urologists in Japan or other risk factors including social background correlate with age-adjusted mortality of prostate cancer remain unknown.

Methods

In addition to known factors like smoking, we examined whether various other factors, such as the regional unevenness of radiotherapists/urologists, correlated with age-adjusted mortality rate (AAMR) for prostate cancer by prefecture. Statistical data were obtained from Annual Report of Hospital-Based Cancer Registries, Comprehensive Survey of Living Conditions and etc. We used the 10-year averages of AAMR from 2009 to 2018 in each prefecture to determine mortality rates.

Results

There was no correlation between the number of radiation oncologists/urologists per 100,000 and the 10-year averages of AAMR by prefecture in Japan. On the other hand, smoking rates and drinking per capita were correlated, respectively (P = 0.0002 and 0.0008).

Conclusion

The current study of statistics by prefecture in Japan also suggests that factors such as smoking and drinking alcohol are correlated with the risk of prostate cancer mortality. On the other hand, regional unevenness of radiation oncologists did not correlate. These results suggest that there is validity in this study design of analyzing factors of risk of prostate cancer mortality. And the study design was suggested to be useful for comparing various patient background factors.
Performance characteristics of the VIDAS® SARS-COV-2 IgM and IgG serological assays
Authors: Renard Nathalie , Daniel Soizic , Cayet Nadège , Pecquet Matthieu , Raymond Frédérique , Pons Sylvie , Lupo Julien , Tourneur Carole , Pretis Catherine , Gerez Guillaume , Blasco Patrick , Combe Maxime , Canova Imen , Lesénéchal Mylène , Berthier Franck
Published: September 2020

The COVID-19 pandemic, caused by the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to spread worldwide. Serological testing for SARS-CoV-2-specific antibodies plays an important role in understanding and controlling the pandemics, notably through epidemiological surveillance. Well validated and highly specific SARS-CoV-2 serological assays are urgently needed. We describe here the analytical and clinical performance of VIDAS® SARS-CoV-2 IgM and VIDAS® SARS-CoV-2 IgG, two CE-marked, EUA-authorized, automated, qualitative assays for the detection of SARS-CoV-2-specific IgM and IgG, respectively. Both assays showed high within-run and within-laboratory precision (coefficients of variation < 11.0%) and very low cross-reactivity towards sera of patients with a past common coronavirus or respiratory virus infection. Clinical specificity determined on up to 989 pre-pandemic healthy donors was ≥ 99% with a narrow 95% confidence interval for both IgM and IgG assays. Clinical sensitivity was determined on up to 232 samples from 130 RT-PCR-confirmed SARS-CoV-2 patients. The positive percent agreement (PPA) with SARS-CoV-2 PCR reached 100% at ≥ 16 days (VIDAS® SARS-CoV-2 IgM) and ≥ 32 days (VIDAS® SARS-CoV-2 IgG) of symptom onset. Combined IgM/IgG test results improved the PPA compared to each test alone. SARS-CoV-2 IgG seroconversion followed closely that of SARS-CoV-2 IgM and remained stable over time, while SARS-CoV-2 IgM levels rapidly declined. Interestingly, SARS-CoV-2-specific IgM and IgG responses were significantly higher in COVID-19 hospitalized vs. non-hospitalized patients. Altogether, the VIDAS® SARS-CoV-2 IgM and IgG assays are highly specific and sensitive serological tests suitable for the reliable monitoring of past SARS-CoV-2 infections and for seroepidemiology investigations.
A decoupled, modular and scriptable architecture for tools to curate data platforms
Authors: Langenstein Moritz , Hermjakob Henning , Llinares Manuel Bernal
Published: September 2020

Motivation

Curation is essential for any data platform to maintain the quality of the data it provides. Existing databases, which require maintenance, and the amount of newly published information that needs to be surveyed, are growing rapidly. More efficient curation is often vital to keep up with this growth, requiring modern curation tools. However, curation interfaces are often complex and difficult to further develop. Furthermore, opportunities for experimentation with curation workflows may be lost due to a lack of development resources, or a reluctance to change sensitive production systems.

Results

We propose a decoupled, modular and scriptable architecture to build curation tools on top of existing platforms. Instead of modifying the existing infrastructure, our architecture treats the existing platform as a black box and relies only on its public APIs and web application. As a decoupled program, the tool’s architecture gives more freedom to developers and curators. This added flexibility allows for quickly prototyping new curation workflows as well as adding all kinds of analysis around the data platform. The tool can also streamline and enhance the curator’s interaction with the web interface of the platform. We have implemented this design in cmd-iaso, a command-line curation tool for the identifiers.org registry.

Availability

The cmd-iaso curation tool is implemented in Python 3.7+ and supports Linux, macOS and Windows. Its source code and documentation are freely available fromhttps://github.com/identifiers-org/cmd-iaso. It is also published as a Docker container athttps://hub.docker.com/r/identifiersorg/cmd-iaso.

Contact

hhe@ebi.ac.uk
GHB confers neuroprotection by stabilizing the CaMKIIα hub domain
Authors: Leurs Ulrike , Klein Anders B. , McSpadden Ethan D. , Griem-Krey Nane , Solbak Sara M. Ø. , Houlton Josh , Villumsen Inge S. , Vogensen Stine B. , Hamborg Louise , Gauger Stine J. , Palmelund Line B. , Larsen Anne Sofie G. , Shehata Mohamed A. , Kelstrup Christian D. , Olsen Jesper V. , Bach Anders , Burnie Robert O. , Kerr D. Steven , Gowing Emma K. , Teurlings Selina M. W. , Chi Chris C. , Gee Christine L. , Frølund Bente , Kornum Birgitte R. , van Woerden Geeske M. , Clausen Rasmus P. , Kuriyan John , Clarkson Andrew N. , Wellendorph Petrine
Published: September 2020

Ca2+/calmodulin-dependent protein kinase II alpha (CaMKIIα) is an abundant neuronal signaling protein involved in synaptic plasticity and memory formation1,2. The central hub domain regulates the activity of CaMKIIα by organizing the holoenzyme complex into functional oligomers3-6. Recent findings have suggested that the hub is also an allosteric determinant of kinase activity7, and is thus an emerging target for therapies to correct CaMKIIα dysregulation8,9. However, pharmacological modulation of the hub domain has never been demonstrated. Here we show that stabilization of the CaMKIIα hub domain confers neuroprotection. By combining photoaffinity labeling and chemical proteomics using small molecule analogs of the natural metabolite γ-hydroxybutyrate (GHB)10we reveal that CaMKIIα is the selective target for GHB. We further find that these GHB analogs bind to the hub interior by solving a 2.2 Å crystal structure of CaMKIIα with bound ligand. Using differential scanning fluorimetry, we show that binding of ligands to the hub interior increases the thermal stability of hub oligomers in a concentration-dependent manner. Moreover, we demonstrate the functional significance of this hub stabilization by showing substantial neuroprotective effects in cellular excitotoxicity assays and in a mouse model of cerebral ischemia. Together, our results reveal that CaMKIIα hub stabilization is the mechanism by which GHB provides endogenous neuroprotection and that small-molecule CaMKIIα-selective ligands have therapeutic potential.
Bipartite influence of abscisic acid on xylem differentiation trajectories is dependent on distinct VND transcription factors in Arabidopsis
Authors: Ramachandran Prashanth , Augstein Frauke , Mazumdar Shamik , Van Nguyen Thanh , Minina Elena A. , Melnyk Charles W. , Carlsbecker Annelie
Published: September 2020

Plants display a remarkable ability to adjust their growth and development to changes in environmental conditions, such as reduction in water availability. This high degree of plasticity is apparent not only as altered root and shoot growth rates, but also as changes to tissue patterning and cell morphology [1,2]. We have previously shown thatArabidopsis thalianaroot xylem displays plastic developmental responses to limited water availability, mediated by non-cell autonomous action of abscisic acid, ABA [2]. Here, we show through analyses of ABA response reporters and tissue specific suppression of ABA signalling that xylem cells act as primary signalling centres for mediation of changes to both xylem cell fate and differentiation rate revealing a cell autonomous control of xylem development by ABA. Transcriptomic changes in response to ABA showed that members of the VASCULAR RELATED NAC DOMAIN (VND) transcription factor family are rapidly activated. Molecular and genetic analyses revealed that the two aspects of xylem developmental changes, cell fate and differentiation rate, are dependent on distinct members of this transcription factor family. Thus, this study provides insights into how different aspects of developmental plasticity can be interlinked, yet genetically independent of each other. Moreover, similarities in phenotypic and molecular responses to ABA in diverse species indicate an evolutionary conservation of the ABA-xylem development regulatory network among eudicots. Hence, this study gives molecular insights on how environmental stress promotes anatomical plasticity to key plant traits with potential relevance for water use optimization and adaptation to drought conditions.
Macrophages respond rapidly to ototoxic injury of lateral line hair cells but are not required for hair cell regeneration
Authors: Warchol Mark E. , Schrader Angela , Sheets Lavinia
Published: September 2020

The sensory organs of the inner ear contain resident populations of macrophages, which are recruited to sites of cellular injury. Such macrophages are known to phagocytose the debris of dying cells but the full role of macrophages in otic pathology is not understood. Lateral line neuromasts of zebrafish contain hair cells similar to those in the inner ear, and the optical clarity of larval zebrafish permits direct imaging of cellular interactions. In this study, we used larval zebrafish to characterize the response of macrophages to ototoxic injury of lateral line hair cells. Macrophages migrated into neuromasts within 20 min of exposure to the ototoxic antibiotic neomycin. The number of macrophages in close proximity of injured neuromasts was similar to that observed near uninjured neuromasts, suggesting that this early inflammatory response was mediated by ‘local’ macrophages. Upon entering injured neuromasts, macrophages actively phagocytosed hair cell debris. Such phagocytosis was significantly reduced by inhibiting Src-family kinases. Using chemical-genetic ablation of macrophages prior to ototoxic injury, we also examined whether macrophages were essential for the initiation of hair cell regeneration after neomycin exposure. Results revealed only minor differences in hair cell recovery in macrophage-depleted vs. control fish, suggesting that macrophages are not essential for the regeneration of lateral line hair cells.
Development of EphA2 siRNA-loaded lipid nanoparticles and combination with a small-molecule histone demethylase inhibitor in prostate cancer cells and tumor spheroids
Authors: Oner Ezgi , Kotmakci Mustafa , Baird Anne-Marie , Gray Steven G. , Butuner Bilge Debelec , Bozkurt Emir , Kantarci Ayse Gulten , Finn Stephen P.
Published: September 2020

siRNAs hold a great potential for cancer therapy, however, poor stability in body fluids and low cellular uptake limit their use in the clinic. To enhance the bioavailability of siRNAs in tumors, novel, safe, and effective carriers are needed. Here, we developed cationic solid lipid nanoparticles (cSLNs) to carry siRNAs targeting EphA2 receptor tyrosine kinase (siEphA2), which is overexpressed in many solid tumors including prostate cancer (PCa). Using DDAB cationic lipid instead of DOTMA reduced nanoparticle size and enhanced both cellular uptake and gene silencing in PCa cells. After verifying the efficacy of siEphA2-loaded nanoparticles, we further evaluated a potential combination with a histone lysine demethylase inhibitor, JIB-04. Silencing EphA2 by siEphA2-loaded DDAB-cSLN did not affect the viability (2D and 3D), migration, and clonogenicity of PC-3 cells alone. However, upon co-administration, there was a decrease in the aforementioned cellular responses due to JIB-04. Furthermore, JIB-04 decreased EphA2 expression, and thus, silencing efficiency of siEphA2-loaded nanoparticles was further increased with co-treatment. In conclusion, we have successfully developed a novel siRNA-loaded lipid nanoparticle for targeting EphA2. Moreover, detailed preliminary results of the effects of JIB-04, alone and in combination with siEphA2, on PCa cells and tumor spheroids were presented for the first time. Our delivery system provides high transfection efficiency and shows a great promise for targeting other genes and cancer types in furtherin vitroandin vivostudies.
DIA-based systems biology approach unveils novel E3-dependent responses to a metabolic shift
Authors: Karayel Ozge , Michaelis André C. , Mann Matthias , Schulman Brenda A. , Langlois Christine R.
Published: September 2020

YeastSaccharomyces cerevisiaeis a powerful model system for systems-wide biology screens and large-scale proteomics methods. Nearly complete proteomics coverage has been achieved owing to advances in mass spectrometry. However, it remains challenging to scale this technology for rapid and high-throughput analysis of the yeast proteome to investigate biological pathways on a global scale. Here we describe a systems biology workflow employing plate-based sample preparation and rapid, single-run data independent mass spectrometry analysis (DIA). Our approach is straightforward, easy to implement and enables quantitative profiling and comparisons of hundreds of nearly complete yeast proteomes in only a few days. We evaluate its capability by characterizing changes in the yeast proteome in response to environmental perturbations, identifying distinct responses to each of them, and providing a comprehensive resource of these responses. Apart from rapidly recapitulating previously observed responses, we characterized carbon source dependent regulation of the GID E3 ligase, an important regulator of cellular metabolism during the switch between gluconeogenic and glycolytic growth conditions. This unveiled new regulatory targets of the GID ligase during a metabolic switch. Our comprehensive yeast system read-out pinpointed effects of a single deletion or point mutation in the GID complex on the global proteome, allowing the identification and validation novel targets of the GID E3 ligase. Moreover, our approach allowed the identification of targets from multiple cellular pathways that display distinct patterns of regulation. Although developed in yeast, rapid whole proteome-based readouts can serve as comprehensive systems-level assay in all cellular systems.
Fluorescence-detection size-exclusion chromatography utilizing nanobody technology for expression screening of membrane proteins
Authors: Jin Fei , Wang Yao , Wang Mengqi , Sun Minxuan , Hattori Motoyuki
Published: September 2020

Membrane proteins play numerous physiological roles and are thus of tremendous interest in pharmacology. Nevertheless, stable and homogeneous sample preparation is one of the bottlenecks in biophysical and pharmacological studies of membrane proteins because membrane proteins are typically unstable and poorly expressed. To overcome such obstacles, GFP fusion-based Fluorescence-detection Size-Exclusion Chromatography (FSEC) has been widely employed for membrane protein expression screening for over a decade. However, fused GFP itself may occasionally affect the expression and/or stability of the targeted membrane protein, leading to both false-positive and false-negative results in expression screening. Furthermore, GFP fusion technology is not well suited for some membrane proteins depending on their membrane topology. Here, we developed an FSEC assay utilizing nanobody (Nb) technology, named FSEC-Nb, in which targeted membrane proteins are fused to a small peptide tag and recombinantly expressed. The whole-cell extracts are solubilized, mixed with anti-peptide Nb fused to GFP and applied to a size-exclusion chromatography column attached to a fluorescence detector for FSEC analysis. FSEC-Nb enables one to evaluate the expression, monodispersity and thermostability of membrane proteins without the need of purification by utilizing the benefits of the GFP fusion-based FSEC method, but does not require direct GFP fusion to targeted proteins. We applied FSEC-Nb to screen zinc-activated ion channel (ZAC) family proteins in the Cys-loop superfamily and membrane proteins from SARS-CoV-2 as examples of the practical application of FSEC-Nb. We successfully identified a ZAC ortholog with high monodispersity but moderate expression levels that could not be identified with the previously developed GFP fusion-free FSEC method. Consistent with the results of FSEC-Nb screening, the purified ZAC ortholog showed monodispersed particles by both negative staining EM and cryo-EM. Furthermore, we identified two membrane proteins from SARS-CoV-2 with high monodispersity and expression level by FSEC-Nb, which may facilitate structural and functional studies of SARS-CoV-2. Overall, our results show FSEC-Nb as a powerful tool for membrane protein expression screening that can provide further opportunity to prepare well-behaved membrane proteins for structural and functional studies.
Measuring effects of trainee professional development on research productivity: A cross-institutional meta-analysis
Authors: Brandt Patrick D. , Varvayanis Susi Sturzenegger , Baas Tracey , Bolgioni Amanda F. , Alder Janet , Petrie Kimberly A. , Dominguez Isabel , Brown Abigail M. , Abigail Stayart C. , Singh Harinder , Wart Audra Van , Chow Christine S. , Mathur Ambika , Schreiber Barbara M. , Fruman David A. , Bowden Brent , Holmquist Chris E. , Arneman Daniel , Hall Joshua D. , Hyman Linda E. , Gould Kathleen L. , Chalkley Roger , Brennwald Patrick J. , Layton Rebekah L.
Published: September 2020

PhD-trained scientists are essential contributors to the workforce in diverse employment sectors that include academia, industry, government, and non-profit organizations. Hence, best practices for training the future biomedical workforce are of national concern. Complementing coursework and laboratory research training, many institutions now offer professional training that enables career exploration and develops a broad set of skills critical to various career paths. The National Institutes of Health funded academic institutions to design innovative programming to enable this professional development through a mechanism known as Broadening Experiences in Scientific Training (BEST). Programming at the BEST awardee institutions included career panels, skill-building workshops, job-searching workshops, site visits, and internships. An initial concern was since doctoral training is lengthy and requires focused attention on dissertation research, having students participate in additional complementary training activities might lengthen time to degree and hamper student research productivity. To address this concern, using time to degree and publication records as measures of efficiency and productivity, metrics were analyzed from ten BEST awardee institutions. Comparing doctoral students who participated to those who did not, results revealed that across these diverse academic institutions, there were no differences in time to degree or manuscript output. Furthermore, a few institutions even demonstrated a positive correlation between participation in career and professional development activities and productivity. Our findings suggest that doctoral students should be encouraged to participate in career and professional development opportunities to ensure their preparedness for a variety of diverse and important careers in the workforce.

Significance Statement

Our study is unique in that it compiled doctoral degree durations at ten different universities, recorded individual participation in career and professional development activities in terms of dosage, and tracked individual engagement in real-time rather than relying on surveys sent to trainees after graduation. Participation in career and professional development activities, including internships, did not decrease efficiency or productivity. Our findings suggest that doctoral students should be encouraged to participate in career and professional development opportunities to ensure their preparedness for a variety of diverse and important careers in the workforce.
pyTFM: A tool for Traction Force and Monolayer Stress Microscopy
Authors: Bauer Andreas , Prechová Magdalena , Gregor Martin , Fabry Ben
Published: September 2020

Cellular force generation and force transduction are of fundamental importance for numerous biological processes and can be studied with the methods of Traction Force Microscopy (TFM) and Monolayer Stress Microscopy. Traction Force Microscopy and Monolayer Stress Microscopy solve the inverse problem of reconstructing cell-matrix tractions and inter- and intra-cellular stresses from the measured cell force-induced deformations of an adhesive substrate with known elasticity. Although several laboratories have developed software for Traction Force Microscopy and Monolayer Stress Microscopy computations, there is currently no software package available that allows non-expert users to perform a full evaluation of such experiments. Here we present pyTFM, a tool to perform Traction Force Microscopy and Monolayer Stress Microscopy on single cells, cell patches and cell layers grown in a 2-dimensional environment. pyTFM was optimized for ease-of-use; it is open-source and well documented (hosted athttps://pytfm.readthedocs.io/) including usage examples and explanations of the theoretical background. pyTFM can be used as a standalone Python package or as an add-on to the image annotation toolClickPoints. In combination with theClickPointsenvironment, pyTFM allows the user to set all necessary analysis parameters, select regions of interest, examine the input data and intermediary results, and calculate a wide range of parameters describing forces, stresses, and their distribution. The Monolayer Stress Microscopy implementation in pyTFM allows for the analysis of small cell patches and single cells; we analyze the accuracy and performance of Traction Force Microscopy and Monolayer Stress Microscopy algorithms using synthetic and experimental data from epithelial cell patches.
Identification of novel regulators of dendrite arborization using cell type-specific RNA metabolic labeling
Authors: Aboukilila Mohamed Y. , Sami Josephine D. , Wang Jingtian , England Whitney , Spitale Robert C. , Cleary Michael D.
Published: September 2020

Obtaining neuron transcriptomes is challenging; their complex morphology and interconnected microenvironments make it difficult to isolate neurons without potentially altering gene expression. Multidendritic sensory neurons (md neurons) ofDrosophilalarvae are commonly used to study peripheral nervous system biology, particularly dendrite arborization. We sought to test if EC-tagging, a biosynthetic RNA tagging and purification method that avoids the caveats of physical isolation, would enable discovery of novel regulators of md neuron dendrite arborization. RNAs were biosynthetically tagged by expressing CD:UPRT (a nucleobase-converting fusion enzyme) in md neurons and feeding 5-ethynylcytosine (EC) to larvae. Tagged RNAs were subsequently purified and used for RNA-sequencing. Reference RNA was prepared in a similar manner using 5-ethynyluridine (EUd) to tag RNA in all cells and negative control RNA-seq was performed on “mock tagged” samples to identify non-specifically purified transcripts. Differential expression analysis identified md neuron enriched and depleted transcripts. Three candidate genes encoding RNA-binding proteins (RBPs) were tested for a role in md neuron dendrite arborization. Loss-of-function for the m6A-binding factor Ythdc1 did not cause any dendrite arborization defects while RNAi of the other two candidates, the poly(A) polymerase Hiiragi and the translation regulator Hephaestus, caused significant defects in dendrite arborization. This work provides an expanded view of transcription in md neurons and a technical framework for combining EC-tagging with RNA-seq to profile transcription in cells that may not be amenable to physical isolation.
FRUITFULL-like genes regulate flowering time and inflorescence architecture in tomato
Authors: Jiang Xiaobing , Lubini Greice , Hernandes-Lopes José , Rijnsburger Kim , Veltkamp Vera , de Maagd Ruud A. , Angenent Gerco C. , Bemer Marian
Published: September 2020

The timing of flowering and inflorescence architecture are critical for the reproductive success of tomato, but the gene regulatory networks underlying these traits have not been fully explored. Here we show that the tomatoFRUITFULL-like (FUL-like) genesFUL2andMADS-BOX PROTEIN 20 (MBP20)induce flowering and repress inflorescence branching by promoting floral meristem determinacy.FUL1fulfils a less prominent role and appears to depend on FUL2 and MBP20 for its upregulation in the inflorescence- and floral meristems.MBP10, the fourth tomatoFUL-like gene, has probably lost its function. The tomato FUL-like proteins cannot homodimerize inin vitroassays, but heterodimerize with various other MADS-domain proteins, potentially forming distinct complexes in the transition meristem and floral meristem. Transcriptome analysis of the primary shoot meristems revealed various interesting downstream targets, including four repressors of cytokinin signalling that are upregulated during the vegetative-to-reproductive transition inful1 ful2 mbp10 mbp20mutants. FUL2 and MBP20 can also bindin vitroto the upstream regions of these genes, thereby probably directly stimulating cell division in the meristem upon the transition to flowering. The control of inflorescence branching does not occur via the CKXs, but appears regulated by repression of transcription factors such asTM3, APETALA 2b(AP2b) andAP2a.
Multiple pathways of LRRK2-G2019S / Rab10 interaction in dopaminergic neurons
Authors: Fellgett Alison , Middleton C. Adam , Munns Jack , Ugbode Chris , Jaciuch David , Wilson Laurence , Chawla Sangeeta , Elliott Christopher J. H.
Published: September 2020

Background

Inherited mutations in the LRRK2 protein are the most common known cause of Parkinson’s, but the mechanisms by which increased kinase activity of mutant LRRK2 leads to pathological events remain to be determined.In vitroassays (heterologous cell culture, phospho-protein mass spectrometry) suggest that several Rab proteins might be directly phosphorylated byLRRK2-G2019S. Which Rabs interact with LRRK2 in dopaminergic neurons to facilitate normal and pathological physiological responses remains to be determined. Anin vivoscreen of Rab expression in dopaminergic neurons in young adult Drosophila demonstrated a strong genetic interaction between LRRK2-G2019Sand Rab10. We now ask if Rab10 is required for LRRK2-induced physiological responses in DA neurons.

Methods

LRRK2-G2019Swas expressed in Drosophila dopaminergic neurons and the effects of Rab10 depletion on Proboscis Extension, vision, circadian activity pattern and courtship memory determined in aged flies.

Results

Rab10 loss-of-function rescued bradykinesia of the Proboscis Extension Response (PER) and visual defects of aged flies expressing LRRK2-G2019S in DA neurons. Rab10 knock-down however, did not rescue the marked sleep phenotype which results from dopaminergic expression ofLRRK2-G2019S. Courtship memory is not affected by LRRK2 expression, but is markedly improved by Rab10 depletion. Anatomically, both LRRK2-G2019S and Rab10 are seen in the cytoplasm and at the synaptic endings of dopaminergic neurons.

Conclusions

We conclude that, in Drosophila dopaminergic neurons, Rab10 is involved differentially in LRRK2-induced behavioral deficits. Therefore, variations in Rab expression may contribute to susceptibility of different dopaminergic nuclei to neurodegeneration seen in people with Parkinson’s.

Graphical Abstract

Rab10 depletion ameliorates the proboscis extension bradykinesia and loss of synaptic signalling in the retina induced byLRRK2-G2019Sexpression (magenta arrows / orange crosses). Rab10 manipulation does not affect the ‘sleep’ phenotype fromLRRK2-G2019S(magenta arrow). Reduction of Rab10 facilitates conditioned courtship memory, but LRRK2 has no effect (yellow arrow). All manipulations of Rab10 andG2019Sin dopaminergic neurons, shown in the outline of the brain (filled cells have high levels of Rab10). We conclude that Rab10 and LRRK2 interact in some, but not all dopaminergic neurons. This may underlie differences in the susceptibility of different human striatal dopaminergic cells to Parkinson’s and explain why different symptoms initiate particular ages.
Metabolomic Profiling and Mechanotransduction of Single Chondrocytes Encapsulated in Alginate Microgels
Authors: Fredrikson Jacob P. , Brahmachary Priyanka , Erdoğan Ebru , Archambault Zach , June Ronald K. , Chang Connie B.
Published: September 2020

Human articular cartilage is comprised of two main components, the extracellular matrix (ECM) and the pericellular matrix (PCM). The PCM helps to protect chondrocytes in the cartilage from mechanical loads, but in patients with osteoarthritis, the PCM is weakened resulting in increased chondrocyte stress. As chondrocytes are responsible for cartilage synthesis and maintenance, it is important to understand how mechanical loads affect cellular responses of chondrocytes. Many studies have examined the chondrocyte response toin vitromechanical loading by embedding in stiff agarose. However, these experiments are mostly performed in the absence of PCM which may obscure important responses to mechanotransduction. Here, we demonstrate that drop-based microfluidics allows culture of single chondrocytes in alginate microgels for cell-directed PCM synthesis that closely mimics thein vivomicroenvironment. Chondrocytes form PCM over 10 days in these single cell microenvironments. Single cell microgels and monolayer controls were encapsulated in high stiffness agarose to mimic the cartilage PCM. After physiological dynamic compression in a custom-built bioreactor, microgels exhibited distinct metabolomic profiles from both uncompressed and monolayer controls. These results demonstrate the potential of single cell encapsulation in alginate microgels to advance cartilage tissue engineering and basic chondrocyte mechanobiology.
Phenolic acid-degradingParaburkholderiaprime decomposition in forest soil
Authors: Wilhelm Roland C. , DeRito Christopher M. , Shapleigh James P. , Madsen Eugene L. , Buckley Daniel H.
Published: September 2020

Plant-derived phenolic acids are metabolized by soil microorganisms whose activity may enhance the decomposition of soil organic carbon (SOC). We characterized whether phenolic acid-degrading bacteria would enhance SOC mineralization in forest soils when primed with13C-labeledp-hydroxybenzoic acid (PHB). We further investigated whether PHB-induced priming could explain differences in SOC content among mono-specific tree plantations in a 70-year-old common garden experiment. The activity ofParaburkholderiaandCaballeroniadominated PHB degradation in all soils regardless of tree species or soil type. We isolated the principal PHB-degrading phylotype (Paraburkholderia madsenianaRP11T), which encoded numerous oxidative enzymes, including secretion signal-bearing laccase, aryl-alcohol oxidase and DyP-type peroxidase, and confirmed its ability to degrade phenolics. The addition of PHB to soil led to significant enrichment (23-fold) of the RP11Tphylotype (RP11ASV), as well as enrichment of other phylotypes ofParaburkholderiaandCaballeronia. Metabolism of PHB primed significant loss of SOC (3 to 13 µmols C g-1dry wt soil over 7 days). In contrast, glucose addition reduced SOC mineralization (−3 to -8 µmols C g-1dry wt soil over 7 days). RP11ASVabundance and the expression of PHB monooxygenase (pobA) correlated with PHB respiration and were inversely proportional to SOC content in the field. We propose that plant-derived phenolics stimulate the activity of phenolic acid-degrading bacteria thereby causing soil priming and SOC loss. We show thatBurkholderiaceaedominate soil priming in diverse forest soils and this observation counters the prevailing view that priming phenomena are a generalized non-specific response of community metabolism.
Genetic structure of Photosystem II functionality in rice unraveled by GWAS analysis
Authors: Vilas Juan Manuel , Burgos Estanislao , Puig Maria Lucrecia , Colazo Jose , Livore Alberto , Ruiz Oscar Adolfo , Carrari Fernando , Rodriguez Andrés Alberto , Maiale Santiago Javier
Published: September 2020

Rice production is a particularly important crop for the half-world population. Therefore, knowledge about which genes are implicated in the functionality of the Photosystem II, that are still poorly explored could collaborate in the assisted selection of rice improving. In the present study, we applied Genome wide Association Studies of PSII chlorophyll fluorescence under two contrasting environmental conditions in 283 rice accessions highly diverse. A total of 110 significant association SNP-phenotype were observed, and 69 quantitative trait loci identified with a total of 157 genes, of which 38 were highly significant, mapped spread out through rice genome. These underlying regions are enriched in genes related to biotic and abiotic stresses, transcription factors, Calvin cycle, senescence, and grain characters. The correlations analyses PSII chlorophyll fluorescence parameters and some panicle characteristics found here suggest the possibility of developing molecular markers to assist the breeding programs that improve photosynthesis and yield in rice.

Highlight

The genetic structure of the Photosystem II functionality in rice was studied by using genome-wide association through chlorophyll fluorescence.
A rapidly evolving actin mediates fertility and developmental tradeoffs inDrosophila
Authors: Schroeder Courtney M. , Tomlin Sarah A. , Valenzuela John R. , Malik Harmit S.
Published: September 2020

Most actin-related proteins (Arps) are highly conserved in eukaryotes, where they carry out well-defined cellular functions.Drosophilaand mammals also encode divergent non-canonical Arps in their male-germline whose roles remain unknown. Here, we show that Arp53D, a rapidly-evolvingDrosophilaArp, localizes to fusomes and actin cones, two male germline-specific actin structures critical for sperm maturation, via its non-canonical N-terminal tail. Although we expected thatArp53Dloss would reduce male fertility, we instead find thatArp53D-KO males are more fertile, both in isolation and in competition with wildtype males. Upon investigating why evolution would retain a gene that negatively impacts male fertility, we unexpectedly found thatArp53D-KOfemales are less fertile. Moreover, KO embryos exhibit reduced viability, which worsens under heat stress. We conclude that ‘testis-specific’Arp53Dis detrimental to male fertility, but is required for female fertility and early development, leading to its long-term retention and recurrent adaptation inDrosophila.
Allele frequency differentiation at height-associated SNPs among continental human populations
Authors: Chen Minhui , Chiang Charleston W. K.
Published: September 2020

Polygenic adaptation is thought to be an important mechanism of phenotypic evolution in humans, although recent evidence of confounding due to residual stratification in consortium GWAS made studies of polygenic adaptation more difficult to interpret. Using FSTas a measure of allele frequency differentiation, a previous study has shown that the mean FSTamong African, East Asian, and European populations is significantly higher at height-associated SNPs than that found at matched non-associated SNPs, suggesting that polygenic adaptation is one of the reasons for differences in human height among these continental populations. However, we showed here even though the height-associated SNPs were identified using only European ancestry individuals, the estimated effect sizes are significantly associated with structures across continental populations, potentially explaining the elevated level of differentiation previously reported. To alleviate concerns of biased ascertainment of SNPs, we re-examined the distribution of FSTat height-associated alleles ascertained from two biobank level GWAS (UK Biobank, UKB, and Biobank Japan, BBJ). We showed that when compared to non-associated SNPs, height-associated SNPs remain significantly differentiated among African, East Asian, and European populations from both 1000 Genomes (p= 0.0012 andp= 0.0265 when height SNPs were ascertained from UKB and BBJ, respectively), and Human Genome Diversity Panels (p= 0.0225 for UKB andp= 0.0032 for BBJ analyses). In contrast to FST-based analyses, we found no significant difference or consistent ranked order among continental populations in polygenic height scores constructed from SNPs ascertained from UKB and BBJ. In summary, our results suggest that, consistent with previous reports, height-associated SNPs are significantly differentiated in frequencies among continental populations after removing concerns of confounding by uncorrected stratification. Polygenic score-based analysis in this context appears to be susceptible to the choice of SNPs and, as we compared to FST-based statistics in simulations, would lose power in detecting polygenic adaptation if there are independent converging selections in more than one population.
Trim39 regulates neuronal apoptosis by acting as a SUMO-targeted E3 ubiquitin-ligase for the transcription factor NFATc3
Authors: Shrivastava Meenakshi Basu , Mojsa Barbara , Mora Stéphan , Robbins Ian , Bossis Guillaume , Lassot Iréna , Desagher Solange
Published: September 2020

NFATc3 is the predominant member of the NFAT family of transcription factor in neurons, where it plays a pro-apoptotic role. Mechanisms controlling NFAT protein stability are poorly understood. Here we identify Trim39 as an E3 ubiquitin-ligase of NFATc3. Indeed, Trim39 ubiquitinates NFATc3in vitroand in cells, whereas silencing of endogenous Trim39 decreases NFATc3 ubiquitination. We also show that Trim17 inhibits Trim39-mediated ubiquitination of NFATc3 by reducing both the E3 ubiquitin-ligase activity of Trim39 and the NFATc3/Trim39 interaction. Moreover, mutation of SUMOylation sites in NFATc3 or SUMO-interacting motif in Trim39 reduces the NFATc3/Trim39 interaction and Trim39-induced ubiquitination of NFATc3. As a consequence, silencing of Trim39 increases the protein level and transcriptional activity of NFATc3, resulting in enhanced neuronal apoptosis. Likewise, a SUMOylation-deficient mutant of NFATc3 exhibits increased stability and pro-apoptotic activity. Taken together, these data indicate that Trim39 modulates neuronal apoptosis by acting as a SUMO-targeted E3 ubiquitin-ligase for NFATc3.
A two-step model of autophagy: autophagosome formation, degradation and net turnover
Authors: Plaza-Zabala Ainhoa , Sierra-Torre Virginia , Sierra Amanda
Published: September 2020

Autophagy is a complex process that encompasses the enclosure of cytoplasmic debris or dysfunctional organelles in membranous vesicles, the autophagosomes, for their elimination in the lysosomes. A gold-standard method to assess its induction is the analysis of the autophagic flux using as a surrogate the expression of the microtubule-associated light chain protein 3 conjugated to phosphatidylethanolamine (LC3-II) by Western blot, in the presence of lysosomal inhibitors. Therefore, the current definition of autophagy flux actually puts the focus on the degradation stage of autophagy. In contrast, the most important autophagy controlling genes that have been identified in the last few years in fact target early stages of autophagosome formation. From a biological standpoint is therefore conceivable that autophagosome formation and degradation are independently regulated and we argue that both stages need to be systematically analyzed. Here, we propose a simple two-step model to understand changes in autophagosome formation and degradation using data from conventional LC3-II Western blot, and test it using two models of autophagy modulation in cultured microglia, the brain macrophages: rapamycin and the ULK1/2 inhibitor, MRT68921. Our model provides a comprehensive understanding of the autophagy process and will help to unravel the effect of genetic, pharmacological, and environmental manipulations on both the formation and degradation of autophagosomes.
Structural variant evolution after telomere crisis
Authors: Dewhurst S.M , Yao X , Rosiene Joel , Tian Huasong , Behr Julie , Bosco Nazario , Takai Kaori K. , de Lange T , Imielinski M
Published: September 2020

Telomere crisis contributes to cancer genome evolution, yet only a subset of cancers display breakage-fusion-bridge (BFB) cycles and chromothripsis, hallmarks of previous experimental telomere crisis studies. We examine the spectrum of SVs instigated by natural telomere crisis. Spontaneous post-crisis clones from prior studies had both complex and simple SVs without BFB cycles or chromothripsis. In contrast, BFB cycles and chromothripsis occurred in clones that escaped from telomere crisis after CRISPR-controlled telomerase activation in MRC5 fibroblasts. This system revealed convergent evolutionary lineages altering one allele of 12p, where a short telomere likely predisposed to fusion. Remarkably, the 12p chromothripsis and BFB events were stabilized by independent fusions to 21. Telomere crisis can therefore generate a wide spectrum of SVs, and lack of BFB patterns and chromothripsis does not indicate absence of past crisis.
Bragg coherent imaging of nanoprecipitates: role of superstructure reflections
Authors: Dupraz Maxime , Leake Steven J. , Richard Marie-Ingrid
Published: September 2020

Coherent precipitation of ordered phases is responsible for providing exceptional high-temperature mechanical properties in a wide range of compositionally complex alloys. Ordered phases are also essential to enhance the magnetic or catalytic properties of alloyed nanoparticles. The present work aims to demonstrate the relevance of Bragg coherent diffraction imaging (BCDI) for studying bulk and thin-film samples or isolated nanoparticles containing coherent nanoprecipitates/ordered phases. The structures of crystals of a few tens of nanometres in size are modelled with realistic interatomic potentials and are relaxed after introduction of coherent ordered nanoprecipitates. Diffraction patterns from fundamental and superstructure reflections are calculated in the kinematic approximation and used as input to retrieve the strain fields using algorithmic inversion. First, the case of single nanoprecipitates is tackled and it is shown that the strain field distribution from the ordered phase is retrieved very accurately. Then, the influence of the order parameter S on the strain field retrieved from the superstructure reflections is investigated. A very accurate strain distribution can be retrieved for partially ordered phases with large and inhomogeneous strains. Subsequently, the relevance of BCDI is evaluated for the study of systems containing many precipitates, and it is demonstrated that the technique is relevant for such systems. Finally, the experimental feasibility of using BCDI to image ordered phases is discussed in the light of the new possibilities offered by fourth-generation synchrotron sources.
A new P,S-coordinating ferrocenyl ligand: synthesis of a precursor and its coordination compounds with PdII and PtII. Corrigendum
Authors: Mouas Toma Nardjes , Daran Jean-Claude , Merazig Hocine , Manoury Eric
Published: September 2020

In the paper by Mouas Toma et al. [Acta Cryst. (2014), C70, 460–464], there was an error in the name of the first author.
Globalisation and regional income growth disparity in India and the People’s Republic of China (PRC)
Authors: Mallick Jagannath , Fukumi Atsushi
Published: September 2020

Purpose

This study aims to explain the role of globalisation on the regional income growth disparities in the states of India and provinces in the People’s Republic of China (PRC).

Design/methodology/approach

The authors use two approaches to analyse regional growth disparities: growth accounting and the panel spatial Durbin model.

Findings

The growth accounting shows that contributions of growth of capital intensity (GKI) and total factor productivity growth (TFPG) distinguish the high-income (HI) regions from medium-income (MI) and lower-income (LI) regions in India. In the PRC, the contributions of GKI and TFPG in MI regions are slightly higher than HI regions, but significantly higher than the LI regions. The empirical results find that foreign direct investment (FDI), domestic investment, human capital, and interaction of FDI and human capital explain income growth states/provinces in India and the PRC. A region’s income growth and FDI inflows spread the benefit to neighbourhoods in both countries.

Originality/value

The paper contributes by performing a comparative analysis of Indian states and the PRC’s provinces by capturing the neighbourhood effects of economic growth, FDI, investment and human capital and also the interaction effects of FDI with human capital and domestic investment. A comparison of the decomposition of income growth to the growth of factor inputs and efficiency in Indian states and the PRC’s provinces also adds to the existing literature.