bluuebunny/crossref_metadata_2025 huggingface dataset:
Solid-Phase Peptide Capture and Release for Bulk and Single-Molecule Proteomics
Authors: Howard Cecil J , Floyd Brendan M. , Bardo Angela M. , Swaminathan Jagannath , Marcotte Edward M. , Anslyn Eric V.
Published: January 2020

The field of proteomics has expanded recently with more sensitive techniques for the bulk measurement of peptides as well as single-molecule techniques. One limiting factor for some of these methods is the need for multiple chemical derivatizations and highly pure proteins free of contaminants. We demonstrate a solid-phase capture strategy suitable for the proteolysis, purification, and subsequent chemical modification of peptides. We use this resin on an HEK293T cell lysate and perform one-pot proteolysis, capture, and derivatization to generate a cellular proteome that identified over 40,000 bead-bound peptides. We also show that this capture can be reversed in a traceless manner, such that it is amenable for single-molecule proteomics techniques. With this technique, we perform a fluorescent labeling and C-terminal derivatization on a peptide and subject it to fluorosequencing, demonstrating that washing the resin is sufficient to remove excess dyes and other reagents prior to single-molecule protein sequencing.
Functionalized Mesoporous Silicas Direct Structural Polymorphism of Amyloid-β Fibrils
Authors: Lucas Michael J. , Pan Henry S. , Verbeke Eric J. , Webb Lauren J. , Taylor David W. , Keitz Benjamin K.
Published: January 2020

The aggregation of Amyloid-β (Aβ) is associated with the onset of Alzheimer’s Disease (AD) and involves a complex kinetic pathway as monomers self-assemble into fibrils. A central feature of amyloid fibrils is the existence of multiple structural polymorphs, which complicates the development of disease-relevant structure-function relationships. Developing these relationships requires new methods to control fibril structure. In this work, we demonstrate that mesoporous silicas (SBA-15) functionalized with hydrophobic (SBA-PFDTS) and hydrophilic groups (SBA-PEG) direct the aggregation kinetics and resulting structure of Aβ1-40fibrils. The hydrophilic SBA-PEG had little effect on amyloid kinetics while as-synthesized and hydrophobic SBA-PFDTS accelerated aggregation kinetics. Subsequently, we quantified the relative population of fibril structures formed in the presence of each material using electron microscopy. Fibrils formed from Aβ1-40exposed to SBA-PEG were structurally similar to control fibrils. In contrast, Aβ1-40incubated with SBA-15 or SBA-PFDTS formed fibrils with shorter cross-over distances that were more structurally representative of fibrils found in AD patient-derived samples. Overall, these results suggest that mesoporous silicas and other exogenous materials are promising scaffolds for thede novoproduction of specific fibril polymorphs of Aβ1-40and other amyloidogenic proteins.

Significance Statement

A major challenge in understanding the progression of Alzheimer’s Disease lies in the various fibril structures, or polymorphs, adopted by Amyloid-β (Aβ). Heterogenous fibril populations may be responsible for different disease phenotypes and growing evidence suggests that Aβ fibrils formedin vitroare structurally distinct from patient-derived fibrils. To help bridge this gap, we used surface-functionalized mesoporous silicas to influence the formation of Aβ1-40fibrils and evaluated the distribution of resulting fibril polymorphs using electron microscopy (EM). We found that silicas modified with hydrophobic surfaces resulted in fibril populations with shorter cross-over distances that are more representative of Aβ fibrils observedex vivo. Overall, our results indicate that mesoporous silicas may be leveraged for the production of specific Aβ polymorphs.
A novel redox-active switch in Fructosamine-3-kinases expands the regulatory repertoire of the protein kinase superfamily
Authors: Shrestha Safal , Katiyar Samiksha , Sanz-Rodriguez Carlos E. , Kemppinen Nolan R. , Kim Hyun W. , Kadirvelraj Renuka , Panagos Charalampos , Keyhaninejad Neda , Colonna Maxwell , Chopra Pradeep , Byrne Dominic P. , Boons Geert J. , van der Knaap Esther , Eyers Patrick A. , Edison Arthur S. , Wood Zachary A. , Kannan Natarajan
Published: January 2020

Aberrant regulation of metabolic kinases by altered redox homeostasis is a major contributing factor in aging and disease such as diabetes. However, the biochemical mechanisms by which metabolic kinases are regulated under oxidative stress is poorly understood. In this study, we demonstrate that the catalytic activity of a conserved family of Fructosamine-3-kinases (FN3Ks), which are evolutionarily related to eukaryotic protein kinases (ePKs), are regulated by redox-active cysteines in the kinase domain. By solving the crystal structure of FN3K homolog fromArabidopsis thaliana(AtFN3K), we demonstrate that it forms an unexpected strand-exchange dimer in which the ATP binding P-loop and adjoining beta strands are swapped between two chains in the dimer. This dimeric configuration is characterized by strained inter-chain disulfide bonds that stabilize the P-loop in an extended conformation. Mutational analysis and solution studies confirm that the strained disulfides function as redox “switches” to reversibly regulate FN3K activity and dimerization. Consistently, we find that human FN3K (HsFN3K), which contains an equivalent P-loop Cys, is also redox-sensitive, whereas ancestral bacterial FN3K homologs, which lack a P-loop Cys, are not. Furthermore, CRISPR knockout of FN3K in human HepG2 cells results in significant upregulation of redox metabolites including glutathione. We propose that redox regulation evolved progressively in FN3Ks in response to changing cellular redox conditions. Our studies provide important new insights into the origin and evolution of redox regulation in the protein kinase superfamily and open new avenues for targeting HsFN3K in diabetic complications.
A healthy childhood environment helps to combat inherited susceptibility to obesity
Authors: Hüls Anke , Wright Marvin N , Bogl Leonie H , Kaprio Jaakko , Lissner Lauren , Molnár Denes , Moreno Luis , De Henauw Stefaan , Siani Alfonso , Veidebaum Toomas , Ahrens Wolfgang , Pigeot Iris , Foraita Ronja ,   on behalf of the IDEFICS/I.Family consortia
Published: January 2020

Objectives

To investigate the degree by which the inherited susceptibility to obesity is modified by environmental factors during childhood and adolescence.

Design

Cohort study with repeated measurements of diet, lifestyle factors and anthropometry.

Setting

The pan-European IDEFICS/I.Family cohort

Participants

8,609 repeated observations from 3,098 children aged 2 to 16 years, examined between 2007 and 2014.

Main outcome measures

Body mass index (BMI) and waist circumference. Genome-wide polygenic risk scores (PRS) to capture the inherited susceptibility of obesity were calculated using summary statistics from independent genome-wide association studies of BMI. Gene-environment interactions of the PRS with sociodemographic (European region, socioeconomic status) and lifestyle factors (diet, screen time, physical activity) were estimated.

Results

The PRS was strongly associated with BMI (r2= 0.11, p-value = 7.9 × 10−81) and waist circumference (r2= 0.09, p-value = 1.8 × 10−71) in our cohort. The associations with BMI increased from r2=0.03 in 3-year olds to r2=0.18 in 14-year olds and associations with waist circumference from r2=0.03 to r2=0.14. Being in the top decile of the PRS distribution was associated with 3.63 times higher odds for obesity (95% confidence interval (CI): [2.57, 5.14]). We observed significant interactions with demographic and lifestyle factors for BMI as well as waist circumference. The risk of becoming obese among those with higher genetic susceptibility was ~38% higher in children from Southern Europe (BMI: p-interaction = 0.0066, Central vs. Southern Europe) and ~61% higher in children with a low parental education (BMI: p-interaction = 0.0012, low vs. high). Furthermore, the risk was attenuated by a higher intake of dietary fiber (BMI: p-interaction=0.0082) and shorter screen times (BMI: p-interaction=0.018).

Conclusions

Our results highlight that a healthy childhood environment might partly offset a genetic predisposition to obesity during childhood and adolescence.
Recessive deleterious variation has a limited impact on signals of adaptive introgression in human populations
Authors: Zhang Xinjun , Kim Bernard , Lohmueller Kirk E. , Huerta-Sánchez Emilia
Published: January 2020

Admixture with archaic hominins has altered the landscape of genomic variation in modern human populations. Several gene regions have been previously identified as candidates of adaptive introgression (AI) that facilitated human adaptation to specific environments. However, simulation-based studies have suggested that population genetics processes other than adaptive mutations, such as heterosis from recessive deleterious variants private to populations before admixture, can also lead to patterns in genomic data that resemble adaptive introgression. The extent to which the presence of deleterious variants affect the false-positive rate and the power of current methods to detect AI has not been fully assessed. Here, we used extensive simulations to show that recessive deleterious mutations can increase the false positive rates of tests for AI compared to models without deleterious variants. We further examined candidates of AI in modern humans identified from previous studies and show that, although deleterious variants may hinder the performance of AI detection in modern humans, most signals remained robust when deleterious variants are included in the null model. While deleterious variants may have a limited impact on detecting signals of adaptive introgression in humans, we found that at least two AI candidate genes,HYAL2andHLA, are particularly susceptible to high false positive rates due to the recessive deleterious mutations. By quantifying parameters that affect heterosis, we show that the high false positives are largely attributed to the high exon densities together with low recombination rates in the genomic regions, which can further be exaggerated by the population growth in recent human evolution. Although the combination of such parameters is rare in the human genome, caution is still warranted in other species with different genomic composition and demographic histories.
Combined Treatment with Dopamine Receptor Antagonists and Radiation Creates a Metabolic Vulnerability in Mouse Models of Glioblastoma
Authors: Saki Mohammad , Bhat Kruttika , Cheng Fei , He Ling , Zhang Le , Ioannidis Angeliki , Nathanson David , Tsang Jonathan , Nghiemphu Phioanh Leia , Cloughesy Timothy F. , Liau Linda M. , Kornblum Harley I. , Pajonk Frank
Published: January 2020

Background

Glioblastoma is the deadliest brain tumor in adults and the standard-of-care consists of surgery followed by radiation and treatment with temozolomide. Overall survival times for patients suffering from glioblastoma are unacceptably low indicating an unmet need for novel treatment options.

Methods

Using patient-derived glioblastoma lines and mouse models of glioblastoma we test the effect of radiation and the dopamine receptor antagonist on glioblastoma self-renewalin vitroand survivalin vivo.A possible resistance mechanism is investigated using RNA-Sequencing.

Results

Treatment of glioma cells with the dopamine receptor antagonist quetiapine reduced glioma cell self-renewalin vitroand combined treatment of mice with quetiapine and radiation prolonged the survival of glioma-bearing animals. The combined treatment induced the expression of genes involved in cholesterol biosynthesis. This rendered the tumors vulnerable to simultaneous treatment with atorvastatin and further significantly prolonged the survival of the animals.

Conclusions

Our results indicate high efficacy of a triple combination of quetiapine, atorvastatin and radiation against glioblastoma without increasing the toxicity of radiation. With both drugs readily available for clinical use our study could be rapidly translated into a clinical trial.
Defoliation-induced compensatory transpiration is compromised inSUT4-RNAiPopulus
Authors: Harding Scott A. , Frost Christopher J. , Tsai Chung-Jui
Published: January 2020

Leaf sucrose contents are high in species of the genusPopulusand other temperate tree taxa. Sucrose is subcellularly compartmentalized, but assumptions about the physiological relevance of such partitioning remain largely unexplored. In this study, the effects of partial defoliation treatments on water uptake, leaf gas exchange properties, non-structural carbohydrate abundance in source and sink organs, and growth were compared in poplars with normal or impaired intracellular sucrose trafficking. The tonoplast sucrose transporter PtaSUT4 is well expressed in leaves ofP. tremula×P. alba(INRA 717-IB4), and its inhibition by RNA-interference (RNAi) is known to affect leaf sucrose abundance. After partial defoliation, maximum photosynthesis rates increased while intercellular CO2decreased with trajectories that were similar in wild type andSUT4-RNAi lines. Leaf transpiration increased more robustly in wild-type than RNAi plants, while leaf water content increased more in RNAi lines. Stomatal conductance did not differ between genotypes, nor did it increase with defoliation. Post-defoliation reductions in steady-state levels of sucrose, the major hexoses (glucose and fructose) and starch were similar in wild-type andSUT4-RNAi shoot sinks. Water uptake and stem growth after partial defoliation were not as well sustained in RNAi as in wild-type plants. The data suggest that vacuolar efflux of sucrose by PtaSUT4 more clearly facilitated adjustments in water uptake than sucrose export following leaf removal.
Rotten-skin disease significantly changed giant spiny frog(Paa spinosa) gut microbiota
Authors: He Tuoyu , Jiang Yun , Wang Pengpeng , Xiang Jianguo , Pan Wangcheng
Published: January 2020

The composition and abundance of gut microbiota is essential for host health and immunity. Gut microbiota is symbiotic with the host, so changes in the host diet, development, and health will lead to changes in the gut microbiota. Conversely, changes in the gut microbiota also affect the host conditions. In this experiment, 16S rRNA high-throughput sequencing was used to compare the gut microbiota composition of 5 healthyPaa Spinosaand 6P. spinosawith rotten-skin disease. Results: the gut microbiota composition was significant difference between diseasedP. spinosaand the healthyP. spinosa; LEfSe analysis showed that the relative abundance ofMethanocorpusculum, Parabacteroides, AF12, PW3, Epulopiscium, andOscillospirawere significantly higher in the diseasedP. spinosa, while the relative abundance ofSerratia, Eubacteium, Citrobacter, andMorganellawere significantly lower. Conclusion: Rotten-skin disease changedP. spinosagut microbiota significantly; The relative abundance ofEpulopisciumandOscillospiramight be related to the health conditions of the host skin and gallbladder; The relative abundance ofSerratiaandEubacteiummight be important for maintaining the gut microbiota ecosystem.
SpikeForest: reproducible web-facing ground-truth validation of automated neural spike sorters
Authors: Magland Jeremy F. , Jun James J. , Lovero Elizabeth , Morley Alexander J. , Hurwitz Cole L. , Buccino Alessio P. , Garcia Samuel , Barnett Alex H.
Published: January 2020

Spike sorting is a crucial but time-intensive step in electrophysiological studies of neuronal activity. While there are many popular software packages for spike sorting, there is little consensus about which are the most accurate under different experimental conditions. SpikeForest is an open-source and reproducible software suite that benchmarks the performance of automated spike sorting algorithms across an extensive, curated database of electrophysiological recordings with ground truth, displaying results interactively on a continuously-updating website. With contributions from over a dozen participating laboratories, our database currently comprises 650 recordings (1.3 TB total size) with around 35,000 ground-truth units. These data include extracellular recordings paired with intracellular voltages, state-of-the-art simulated recordings, and hybrid synthetic datasets. Ten of the most frequently used modern spike sorting codes are wrapped under a common Python framework and evaluated on a compute cluster using an automated pipeline. SpikeForest validates and documents community progress in automated spike sorting, and guides neuroscientists to an optimal choice of sorter and parameters for a wide range of probes and brain regions.
Impact of phosphorylation on thermal stability of proteins
Authors: Potel Clément M. , Kurzawa Nils , Becher Isabelle , Typas Athanasios , Mateus André , Savitski Mikhail M.
Published: January 2020

Reversible protein phosphorylation regulates virtually every cellular process and is arguably the most well-studied post-translational modification. Still, less than 3% of the phosphorylation sites identified in humans have annotated functions. Functionally-relevant phosphorylation sites are known to trigger conformational changes to proteins and/or to regulate their interactions with other proteins, nucleic acids and small molecules - all of which can be reflected in the thermal stability of a protein. Thus, combining thermal proteome profiling (TPP) with phosphoproteomics (phospho-TPP) provides a way to assess the functional relevance of identified phosphorylation sites on a proteome-wide scale by comparing the melting behavior of a protein and its phosphorylated form(s). We performed phospho-TPP experiments in HeLa cells with an optimized protocol, and conclude that phosphorylation does affect protein thermal stability, but to a much lesser extent than previously reported.
Identification of phosphosites that alter protein thermal stability
Authors: Smith Ian R. , Hess Kyle N. , Bakhtina Anna A. , Valente Anthony S. , Rodríguez-Mias Ricard A. , Villén Judit
Published: January 2020

Proteomics has enabled the cataloguing of 100,000s of protein phosphorylation sites1, however we lack methods to systematically annotate their function. Phosphorylation has numerous biological functions, yet biochemically all involve changes in protein structure and interactions. These biochemical changes can be recapitulated by measuring the difference in stability between the protein and the phosphoprotein. Building on recent work, we present a method to infer phosphosite functionality by reliably measuring such differences at the proteomic scale.
SMRT sequencing of theOryza rufipogongenome reveals the genomic basis of rice adaptation
Authors: Li Wei , Li Kui , Huang Ying , Shi Cong , Hu Wu-Shu , Zhang Yun , Zhang Qun-Jie , Xia En-Hua , Hutang Ge-Ran , Zhu Xun-Ge , Liu Yun-Long , Liu Yuan , Tong Yan , Zhu Ting , Huang Hui , Zhang Dan , Zhao Yuan , Jiang Wen-Kai , Yuan Jie , Niu Yong-Chao , Gao Cheng-Wen , Gao Li-Zhi
Published: January 2020

Asian cultivated rice is believed to have been domesticated from an immediate ancestral progenitor,Oryza rufipogon, which provides promising sources of novel alleles for world rice improvement. Here we first present a high-qualityde novoassembly of the typicalO. rufipogongenome through the integration of single-molecule sequencing (SMRT), 10× and Hi-C technologies. This chromosome-based reference genome allows a multi-species comparative analysis of the annual selfingO. sativaand its two wild progenitors, the annual selfingO. nivaraand perennial outcrossingO. rufipogon, identifying massive numbers of dispensable genes that are functionally enriched in reproductive process. Comparative genomic analyses identified millions of genomic variants, of which large-effect mutations (e.g., SVs, CNV and PAVs) may affect the variation of agronomically significant traits. We demonstrate how lineage-specific expansion of rice gene families may have contributed to the formation of reproduction isolation (e.g., the recognition of pollen and male sterility), thus brightening the role in driving mating system evolution during the evolutionary process of recent speciation. We document thousands of positively selected genes that are mainly involved in flower development, ripening, pollination, reproduction and response to biotic- and abiotic stresses. We show that selection pressures may serve as crucial forces to govern substantial genomic alterations among the three rice species that form the genetic basis of rapid evolution of mating and reproductive systems under diverse habitats. This first chromosome-based wild rice genome in the genusOryzawill become powerful to accelerate the exploration of untapped genomic diversity from wild rice for the enhancement of elite rice cultivars.
LRP::FLAG reduces phosphorylated tau levels in Alzheimer’s Disease
Authors: Cuttler Katelyn , Bignoux Monique J. , Otgaar Tyrone C. , Chigumba Stephanie , Ferreira Eloise , Weiss Stefan F.T.
Published: January 2020

Alzheimer’s disease (AD) is characterized by amyloid beta (Aβ) plaque and neurofibrillary tangle formation, respectively. Neurofibrillary tangles form as a result of the intracellular accumulation of hyperphosphorylated tau. Telomerase activity and levels of the human reverse transcriptase (hTERT) subunit of telomerase are significantly decreased in AD. Recently it has been demonstrated that the 37kDa/67kDa laminin receptor (LRP/LR) interacts with telomerase and is implicated in Aβ pathology. Here we show that LRP/LR co-localizes with tau in the perinuclear cell compartment and FRET confirmed a direct interaction between LRP/LR and tau in HEK-293 cells. Overexpression of LRP::FLAG in HEK-293 and SH-SY5Y cells decreased total and phosphorylated tau levels with a concomitant decrease in PrPclevels, a tauopathy-related protein. Additionally, LRP::FLAG overexpression resulted in increased hTERT levels. These data indicate for the first time a role of LRP/LR in tauopathy of Alzheimer’s Disease and recommend LRP::FLAG as a potential alternative therapeutic tool for Alzheimer’s Disease treatment through rescuing cells from Aβ induced cytotoxicity and, as shown in this report, decreased phosphorylated tau levels.
Genetic ablation of the mitochondrial ribosome inPlasmodium falciparumsensitizes the human malaria parasite to antimalarial drugs targeting mitochondrial functions
Authors: Ling Liqin , Mulaka Maruthi , Munro Justin , Dass Swati , Mather Michael W. , Riscoe Michael K. , Llinás Manuel , Zhou Jing , Ke Hangjun
Published: January 2020

The mitochondrion of malaria parasites contains clinically validated drug targets. WithinPlasmodium spp., the mitochondrial DNA (mtDNA) is only 6 kb long, being the smallest mitochondrial genome among all eukaryotes. The mtDNA encodes only three proteins of the mitochondrial electron transport chain and ∼ 27 small, fragmented rRNA genes in length of 22-195 nucleotides. The rRNA fragments are thought to form a mitochondrial ribosome (mitoribosome), together with ribosomal proteins imported from the cytosol. The mitoribosome ofPlasmodium falciparumhas been shown to be essential for maintenance of the mitochondrial membrane potential and parasite viability. However, the role of mitoribosomes in sustaining the metabolic status of the parasite mitochondrion remains unknown. Here, among the 14 annotated mitoribosomal proteins of the small subunit ofP. falciparum, we verified the localization and tested the essentiality of three candidates (PfmtRPS12, PfmtRPS17, PfmtRPS18), employing a CRISPR/Cas9 mediated conditional knockdown tool. Using immuno-electron microscopy, we provided evidence that the mitoribosome is closely associated with the mitochondrial inner membrane in the parasite. Upon knockdown of the mitoribosome, the parasites became hypersensitive to inhibitors targeting thebc1complex, dihydroorotate dehydrogenase andF1FoATP synthase complex. Furthermore, knockdown of the mitoribosome blocked the pyrimidine biosynthesis pathway and reduced the pool of pyrimidine nucleotides. Together, our data suggest that disruption of theP. falciparummitoribosome compromises the metabolic capability of the mitochondrion, rendering the parasite hypersensitive to a panel of inhibitors targeting mitochondrial functions.
Negative regulation of the Rcs phosphorelay via IgaA contact with the RcsD phosphotransfer protein
Authors: Wall Erin A. , Majdalani Nadim , Gottesman Susan
Published: January 2020

Two-component systems and phosphorelays play central roles in the ability of bacteria to rapidly respond to changing environments. InE. coliand related enterobacteria, the complex Rcs phosphorelay is a critical player in changing bacterial behavior in response to antimicrobial peptides, beta-lactam antibiotics, and other challenges to the cell surface. The Rcs system is unusual in that IgaA, an inner membrane protein, is essential due to its negative regulation of the RcsC/RcsD/RcsB phosphorelay. While it has previously been shown that IgaA transduces signals from the outer membrane lipoprotein RcsF, how it interacts with the phosphorelay was unknown. Here we use in vivo interaction assays and genetic dissection of the critical proteins to demonstrate that IgaA interacts with the phosphorelay protein RcsD, and that this interaction is necessary for regulation. Interactions in periplasmic domains of these two proteins anchor repression of signaling. However, the signaling response depends on a weaker interaction between cytoplasmic loop 1 of IgaA and a truncated PAS domain in RcsD. A point mutation in the PAS domain increases interactions between the two proteins and is sufficient to abolish induction of this phosphorelay. RcsC, the histidine kinase that initiates phosphotransfer through the phosphorelay, appears to be indirectly regulated by IgaA via the contacts with RcsD. Unlike RcsD, and unlike many other histidine kinases, the periplasmic domain of RcsC is not necessary for the response to inducing signals. The multiple contacts between IgaA and RcsD form a poised sensing system, preventing over-activation of this apparently toxic phosphorelay but allowing it to be rapidly and quantitatively responsive to signals.

Author Summary

The Rcs phosphorelay plays a central role in allowing enterobacteria to sense and respond to antibiotics, host-produced antimicrobials, and interactions with surfaces. A unique negative regulator, IgaA, keeps signaling from this pathway under control when it is not needed, but how it controls the phosphorelay has been unclear. We define a set of critical interactions between IgaA and the phosphotransfer protein RcsD. A periplasmic contact between IgaA and RcsD provides a necessary inhibition of Rcs signaling, modulated further by regulated interactions in the cytoplasmic domains of each protein. This multipartite interaction provides a sensitive regulatory switch.
PD-L1 upregulation by IFN-α/γ-mediated Stat1 suppresses anti-HBV T cell response
Authors: Liu LanLan , Hou Junwei , Qin Lijuan , Liu Weiwei , Zhang Han , Li Yang , Chen Mi , Deng Mengmeng , Zhao Bao , Hu Jun , Zheng Huaguo , Meng Songdong
Published: January 2020

Programmed death ligand 1 (PD-L1) has been recently shown to be a major obstacle to antiviral immunity by binding to its receptor programmed death 1 (PD-1) on specific IFN-γ producing T cells in chronic hepatitis B. Currently, IFN-α is widely used to treat hepatitis B virus(HBV) infection, but its antiviral effect vary greatly and the mechanism is not totally clear. We found that IFN-α/γ induced a marked increase of PD-L1 expression in hepatocytes. Signal and activators of transcription (Stat1) was then identified as a major transcription factor involved in IFN-α/γ-mediated PD-L1 elevation bothin vitroand in mice. Blockage of the PD-L1/PD-1 interaction by a specific mAb greatly enhanced HBV-specific T cell activity by the gp96 adjuvanted therapeutic vaccine, and promoted HBV clearance in HBV transgenic mice. Our results demonstrate the IFN-α/γ-Stat1-PD-L1 axis plays an important role in mediating T cell hyporesponsiveness and inactivating liver-infiltrating T cells in the hepatic microenvironment. These data raise further potential interest in enhancing the anti-HBV efficacy of IFN-α and therapeutic vaccines.
Dynamin-like proteins are essential for vesicle biogenesis inMycobacterium tuberculosis
Authors: Gupta Shamba , Palacios Ainhoa , Khataokar Atul , Weinrick Brian , Lavín Jose L. , Sampedro Leticia , Gil David , Anguita Juan , Menendez M. Carmen , García M. Jesus , Dogra Navneet , Neiditch Matthew B. , Prados-Rosales Rafael , Rodríguez G. Marcela
Published: January 2020

Mycobacterium tuberculosis (Mtb)secretes pathogenicity factors and immunologically active molecules via membrane vesicles. However, nothing is known about the mechanisms involved in mycobacterial vesicle biogenesis. This study investigates molecular determinants of membrane vesicle production inMtbby analyzingMtbcells under conditions of high vesicle production: iron limitation and VirR restriction. Ultrastructural analysis showed extensive cell envelope restructuring in association with vesicle release that correlated with downregulation of cell surface lipid biosynthesis and peptidoglycan alterations. Comparative transcriptomics showed common upregulation of theiniBACoperon in association with high vesicle production inMtbcells. Vesicle production analysis demonstrated that the dynamin-like proteins (DLPs) encoded by this operon, IniA and IniC, are necessary for release of EV byMtbin culture and in infected macrophages. Isoniazid, a first-line antibiotic, used in tuberculosis treatment, was found to stimulate vesicle release in a DLP-dependent manner. Our results provide a new understanding of the function of mycobacterial DLPs and mechanistic insights into vesicle biogenesis. The findings will enable further understanding of the relevance ofMtb-derived extracellular vesicles in the pathogenesis of tuberculosis and may open new avenues for therapeutic research.

IMPORTANCE

Iron is an essential nutrient that promotes survival and growth ofM. tuberculosis, the bacterium that causes human tuberculosis (TB). Limited availability of iron, often encountered in the host environment, stimulatesM. tuberculosisto secrete membrane-bound extracellular vesicles containing molecules that may help it evade the immune system. Characterizing the bacterial factors and mechanisms involved in the production of mycobacterial vesicles is important for envisioning ways to interfere with this process. Here, we report the discovery of proteins required byM. tuberculosisfor vesicle biogenesis in culture and during host cell infection. We also demonstrate a connection between antibiotic response and extracellular vesicle production. The work provides insights into the mechanisms underlying vesicle biogenesis inM. tuberculosisand permits better understanding of the significance of vesicle production toM. tuberculosis-host interactions and antibiotic stress response.
A Temporal Quantitative Profiling of Newly Synthesized Proteins during Aβ Accumulation
Authors: Ma Yuanhui , McClatchy Daniel B. , Martínez-Bartolomé Salvador , Bamberger Casimir , Yates John R.
Published: January 2020

Accumulation of aggregated amyloid beta (Aβ) in the brain is believed to impair multiple cellular pathways and play a central role in Alzheimer’s disease pathology. But how this process is regulated remains unclear. In theory, measuring protein synthesis is the most direct way to evaluate a cell’s response to stimuli, but to date there have been few reliable methods to do this. To identify the protein regulatory network during the development of Aβ deposition in AD, we applied a new proteomic technique to quantitate newly synthesized protein (NSP) changes in the cerebral cortex and hippocampus of 2, 5 and 9-month-old APP/PS1 AD transgenic mice. This bioorthogonal non-canonical amino acid tagging (BONCAT) analysis combined PALM (Pulse Azidohomoalanine Labeling in Mammals) and HILAQ (Heavy Isotope Labeled AHA Quantitation) to reveal a comprehensive dataset of NSPs prior to and post Aβ deposition, including the identification of proteins not previously associated with AD, and demonstrated that the pattern of differentially expressed NSPs is age-dependent. We also found dysregulated vesicle transportation networks including endosomal subunits, coat protein complex I (COPI) and mitochondrial respiratory chain throughout all timepoints and two brain regions. These results point to a pathological dysregulation of vesicle transportation that occurs prior to Aβ accumulation and the onset of AD symptoms, which may progressively impact the entire protein network and thereby drive neurodegeneration. This study illustrates key pathway regulation responses to the development of AD pathogenesis by directly measuring the changes of protein synthesis and provides unique insights into the mechanisms that underlie AD.
Clustered γ-Protocadherins Regulate Cortical Interneuron Programmed Cell Death
Authors: Mancia Walter , Spatazza Julien , Rakela Benjamin , Chatterjee Ankita , Pande Viraj , Maniatis Tom , Hasenstaub Andrea R. , Stryker Michael P. , Alvarez-Buylla Arturo
Published: January 2020

Cortical function critically depends on inhibitory/excitatory balance. GABAergic cortical inhibitory interneurons (cINs) are born in the ventral forebrain. After completing their migration into cortex, their final numbers are adjusted-during a period of postnatal development - by programmed cell death (PCD). The mechanisms that regulate cIN elimination remain controversial. Here we show that genes in the protocadherin (Pcdh)-γ gene cluster, but not in the Pcdh-α or Pcdh-β clusters, are required for survival of cINs through a BAX-dependent mechanism. Surprisingly, the physiological and morphological properties of Pcdh-γ deficient and wild type cINs during PCD were indistinguishable. Co-transplantation of wild type and Pcdh-γ deficient interneuron precursor cells demonstrate that: 1) the number of mutant cINs eliminated was much higher than that of wild type cells, but the proportion of mutant or WT cells undergoing cell death was not affected by their density; 2) the presence of mutant cINs increases cell death among wild-type counterparts, and 3) cIN survival is dependent on the expression of Pcdh-γ C3, C4, and C5. We conclude that Pcdh-γ, and specifically γC3, γC4, and γC5, play a critical role in regulating cIN survival during the endogenous period of PCD.

Significance

GABAergic cortical inhibitory interneurons (cINs) in the cerebral cortex originate from the ventral embryonic forebrain. After a long migration, they come together with local excitatory neurons to form cortical circuits. These circuits are responsible for higher brain functions, and the improper balance of excitation/inhibition in the cortex can result in mental diseases. Therefore, an understanding of how the final number of cINs is determined is both biologically and, likely, therapeutically significant. Here we show that cell surface homophilic binding proteins belonging to the clustered protocadherin gene family, specifically three isoforms in the Pcdh-γ cluster, play a key role in the regulation cIN programmed cell death. Co-transplantation of mutant and wild-type cINs shows that Pcdh-γ genes have cell-autonomous and non-cell autonomous roles in the regulation of cIN cell death. This work will help identify the molecular mechanisms and cell-cell interactions that determine how the proper ratio of excitatory to inhibitory neurons is determined in the cerebral cortex.
Sponge Physioecology On Moorea, French Polynesia: Local Distribution And Filtration Efficiency OfLamellodysideaUnder Varying Temperatures
Authors: Leveque-Eichhorn Lily
Published: January 2020

This physio-ecological study investigated the physiology and distribution ofLamellodysidea sp.in Moorea, French Polynesia. Specifically, its distribution was described across three reef types—fringing, mid-barrier, and barrier reefs—as well as across sites between Cook’s Bay and Opunohu Bay. Additionally, filtration experiments were conducted to test how temperature impacts filtration efficiency. This is informative when predicting how future ocean temperatures are going to affect sponge’s success and distribution. Sponge abundance was found to decrease from the fringing reef out to the barrier reef, with the highest number of sponges in the fringing reef, less in the mid-barrier reef, and none found in the barrier reef. Sponges were also unevenly distributed across sites, with sponge abundance clearly increasing as you move away from Cook’s Bay. Together, these data show that sponges demonstrate habitat preference that is related to their physiological tolerances. Filtration data showed that over a 3-hour period sponges increase their physiological output when introduced to environments 3-6 degrees Celsius above normal. This suggests that as ocean temperatures warm, sponges are likely to increase their filtration efficiency, thus increasing their ecological role as filter feeders, or struggle to survive at this new level of physiological function.
Sampling artifacts in single-cell genomics cohort studies
Authors: Massoni-Badosa Ramon , Iacono Giovanni , Moutinho Catia , Kulis Marta , Palau Núria , Marchese Domenica , Rodríguez-Ubreva Javier , Ballestar Esteban , Rodriguez-Esteban Gustavo , Marsal Sara , Aymerich Marta , Colomer Dolors , Campo Elias , Julià Antonio , Martín-Subero José Ignacio , Heyn Holger
Published: January 2020

Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample acquisition can hinder solid, reproducible results and a systematic benchmarking is required before entering large-scale data production. Here, we report the existence and extent of gene expression and chromatin accessibility artifacts introduced during sampling and identify experimental and computational solutions for their prevention.
Reduced PABPN1 levels causes cytoskeleton disorganization and aberrant differentiation
Authors: Olie Cyriel Sebastiaan , van der Wal Erik , Domagoj Cikes , Maton Loes , de Greef Jessica C. , Lin I-Hsuan , Chen Yi-Fan , Kareem Elsayad , Penninger Josef M. , Kessler Benedikt M. , Raz Vered
Published: January 2020

The polyadenylation binding protein nucleus 1 (PABPN1), a multifactorial regulator of mRNA processing, regulates muscle wasting and atrophy. Previously, we elucidated the PABPN1-dependent proteome and found that levels of structural proteins, sarcomeric and cytoskeletal, were highly altered. We identified MURC, a plasma membrane-associated protein, to be affected by the cytoskeletal stability and suggest that MURC is a novel marker for impaired regeneration in muscles. We also studied the spatial organization of muscle structural proteins in 2D and 3D cell models with reduced PABPN1 levels (named here as shPAB). We show that dysregulation of cytoskeletal proteins in the shPab proteome is associated with a cytoskeleton lacking a polarized organization in muscle cells. We show that consequently, the cell mechanical features as well as myogenic differentiation are significantly reduced. We then show that restoring cytoskeletal stability, by actin overexpression in shPAB was beneficial for cell fusion and for the expression of sarcomeric proteins in shPAB models. We suggest that poor cytoskeleton mechanical features are caused by altered expression levels and contribute to aging-associated muscle wasting and atrophy.
Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for twelve immune-mediated diseases
Authors: Kundu Kousik , Mann Alice L. , Tardaguila Manuel , Watt Stephen , Ponstingl Hannes , Vasquez Louella , Morrell Nicholas W. , Stegle Oliver , Pastinen Tomi , Sawcer Stephen J. , Anderson Carl A. , Walter Klaudia , Soranzo Nicole
Published: January 2020

The identification of causal genetic variants for common diseases improves understanding of disease biology. Here we use data from the BLUEPRINT project to identify regulatory quantitative trait loci (QTL) for three primary human immune cell types and use these to fine-map putative causal variants for twelve immune-mediated diseases. We identify 340 unique, non major histocompatibility complex (MHC) disease loci that colocalise with high (>98%) posterior probability with regulatory QTLs, and apply Bayesian frameworks to fine-map associations at each locus. We show that fine-mapping applied to regulatory QTLs yields smaller credible set sizes and higher posterior probabilities for candidate causal variants compared to disease summary statistics. We also describe a systematic under-representation of insertion/deletion (INDEL) polymorphisms in credible sets derived from publicly available disease meta-analysis when compared to QTLs based on genome-sequencing data. Overall, our findings suggest that fine-mapping applied to disease-colocalising regulatory QTLs can enhance the discovery of putative causal disease variants and provide insights into the underlying causal genes and molecular mechanisms.
Age-Stage, Two-Sex Life Table of the Menochilus sexmaculatus (Coccinellidae: Coleoptera) Feeding on Different Aphid Species
Authors: Abbas Khalid , Zaib Muhammad Shah , Zakria Muhammad , Hani Umm-e , Zaka Syed Muhammad , Ain Noor-ul
Published: January 2020

Ladybird beetle, Menochilus sexmaculatus (Fabricius) (Coleoptera: Coccinellidae), is biological control agent that predate the different aphid species. Both adults and larval stage of M. sexmaculatus feed on aphid species. In this experiment Life table and predation data were collected for M. sexmaculatus feed on four different aphid species Lipaphis erysimi, Myzus persicae, Aphis nerii and Diuraphis noxia. This experiment was conducted under laboratory conditions at 25±2°C, 60±5% RH and L14: D10 h. Different numbers of aphid were provided as a pray in petri dish. The pre-adult development duration of M. sexmaculatus was maximum when fed on M. persicae (12.18 d) and minimum on D. noxia (10.64 d). Similarly, male and female duration was maximum on M. persicae (26.7 d), minimum on L. erysimi (23.67 d) in male and in female maximum on D. noxia (28.00 d), minimum on A. nerii (24.33 d). Net reproductive rate (Ro) range from 117.9 on L. erysimi to 99.55 on M. persicae and intrinsic rate of increase (r) range was 0.21197 d-1on A. nerii to 0.021559 d-1on D. noxia. The finite rate of increase (λ) range was 1.240592 d-1on D. noxia to 1.204918 d-1on M. persicae, the mean of generation (T) range was 24.68 d-1on M. persicae to 22.476 d-1on A. nerii, similarly, the gross reproductive rate (GRR) range was 172.2 d-1on D. noxia to 115.02 d-1on M. persicae and Fecundity (F) eggs per female range was 316.8 on D. noxia to 199.1 on M. persicae. In present Study, age-stage two-sex life table gives complete understanding of predator biological aspects against different aphid species. This study will help us to improve mass rearing and use of M. sexmaculatus in biological control of aphids.
Factors affecting purchase intention of foreign food products
Authors: Zarif Sagheb Maryam , Ghasemi Behzad , Nourbakhsh Seyed Kamran
Published: January 2020

Purpose

The purpose of this paper is to present the factors affecting purchase intention of foreign food products in the Iranian context.

Design/methodology/approach

The present study is a survey research and has a quantitative approach. According to Morgan’s table, 384 people were selected as sample size. Based on an in-depth review of previous literature, a comprehensive set of sub-factors related to customer’s purchase intention was extracted to design questionnaire. Then, exploratory factor analysis and confirmatory factor analysis were applied to identify and confirm the factors affecting purchase intention of foreign food products in Iran.

Findings

The obtained results illustrate 13 factors as follows: “corporate social responsibility,” “customer knowledge and awareness,” “perceived risk,” “retailer’s commercial image,” “customer’s personality characteristics,” “social identity,” “product features,” “attitude,” “country-of-origin,” “perceived value,” “subjective norm,” “loyalty” and “perceived behavioral control.”

Research limitations/implications

As the present research was carried out in the Iranian context, the generalization of the findings is limited and caution should be taken in this regard.

Practical implications

The identified factors could contribute to international food companies and retailers to understand customers’ expectations and to gain more market share in Iran.

Originality/value

The originality of this paper lies in identifying a comprehensive set of the factors affecting purchase intention of foreign food products and developing the theoretical literature in the field of the present research.
The tragedy of Mariana in management’s tragedy
Authors: Saraiva Carolina Machado , Ferreira Pamella Thaís Magalhães
Published: January 2020

Purpose

This paper aims to unveil the spheres that were silenced by the media and academia with regard to the collapse of the Fundão Dam that occurred in 2015, in Mariana (Minas Gerais - Brazil).

Design/methodology/approach

In an attempt to contribute to studies into the evil side of organizations, the authors use the theoretical contributions of corporate crime and the one-dimensional society. The authors used the “Samarco Mud” corporate crime case as an object of analysis, while a press conference with the company’s CEO and representatives from its parent companies was used as the analytical corpus. For the analysis, the authors used the content analysis technique.

Findings

The conclusions of this study point to the existence of subjects who were silenced about the phenomenon of the Fundão Dam collapse, a situation that reveals the power exercised by corporations and the totalitarian domination of the one-dimensional society as a social factor that favors the occurrence of corporate crimes.

Originality/value

The case in question is recent and not fully understood by academia. Neither is its organization around political and social movements understood with regard to the management implications for society and the environment. With a discussion that mixes the concepts of corporate crime and the one-dimensional society, this paper contributes to the base of critical studies in management, especially as far as concerns the mining policies used in the Southern Hemisphere.
Fuzzy-based MTD
Authors: Jaya Eppili , Krishna B.T.
Published: January 2020

Purpose

Synthetic aperture radar exploits the receiving signals in the antenna for detecting the moving targets and estimates the motion parameters of the moving objects. The limitation of the existing methods is regarding the poor power density such that those received signals are essentially to be transformed to the background ratio. To overcome this issue, fractional Fourier transform (FrFT) is employed in the moving target detection (MTD) process. The paper aims to discuss this issue.

Design/methodology/approach

The proposed MTD method uses the fuzzy decisive approach for detecting the moving target in the search space. The received signal and the FrFT of the received signal are subjected to the calculation of correlation using the ambiguity function. Based on the correlation, the location of the target is identified in the search space and is fed to the fuzzy decisive module, which detects the target location using the fuzzy linguistic rules.

Findings

The simulation is performed, and the analysis is carried out based on the metrics, like detection time, missed target rate, and MSE. From the analysis, it can be shown that the proposed Fuzzy-based MTD process detected the object in 5.0237 secs with a minimum missed target rate of 0.1210 and MSE of 23377.48.

Originality/value

The proposed Fuzzy-MTD is the application of the fuzzy rules for locating the moving target in search space based on the peak energy of the original received signal and FrFT of the original received signal.