bluuebunny/crossref_metadata_2025 huggingface dataset:
High-throughput imaging of Caenorhabditis elegans aging using collective activity monitoring
Authors: Fouad Anthony D , Churgin Matthew A , Hayden Julia , Xu Joyce , Park Jeong-Inn , Liu Alice , Teng Christopher , Sun Hongjing , Parrado Mateo , Bowlin Peter , De La Torre Miguel , Crombie Timothy A. , Sedore Christine A. , Coleman-Hulbert Anna L. , Johnson Erik , Philips Patrick , Andersen Erik C. , Fang-Yen Christopher
Published: October 2021

The genetic manipulability and short lifespan of C. elegans make it an important model for aging research. Widely applied methods for measurements of worm aging based on manual observation are labor intensive and low-throughput. Here, we describe the Worm Collective Activity Monitoring Platform (WormCamp), a system for assaying aging in C. elegans by monitoring activity of populations of worms in standard 24-well plates. We show that metrics based on the rate of decline in collective activity can be used to estimate the average lifespan and locomotor healthspan in the population. Using the WormCamp, we assay a panel of highly divergent natural isolates of C. elegans and show that both lifespan and locomotor healthspan display substantial heritability. To facilitate analysis of large numbers of worms, we developed a robotic imaging system capable of simultaneous automated monitoring of activity, lifespan, and locomotor healthspan in up to 2,304 populations containing a total of ~90,000 animals. We applied the automated system to conduct a large-scale RNA interference screen for genes that affect lifespan and locomotor healthspan. The WormCamp system is complementary to other current automated methods for assessing C. elegans aging and is well suited for efficiently screening large numbers of conditions.
Wastewater-Based Epidemiological Modeling for Continuous Surveillance of COVID-19 Outbreak
Authors: Fazli Mehrdad , Sklar Samuel , Porter Michael D. , French Brent A. , Shakeri Heman
Published: October 2021

Using wastewater surveillance as a continuous pooled sampling technique has been in place in many countries since the early stages of the outbreak of COVID-19. Since the beginning of the outbreak, many research works have emerged, studying different aspects of viral SARS-CoV-2 DNA concentrations (viral load) in wastewater and its potential as an early warning method. However, one of the questions that has remained unanswered is the quantitative relation between viral load and clinical indicators such as daily cases, deaths, and hospitalizations. Few studies have tried to couple viral load data with an epidemiological model to relate the number of infections in the community to the viral burden. This paper proposes a stochastic wastewater-based SEIR model to showcase the importance of viral load in the early detection and prediction of an outbreak in a community. We built three models based on whether or not they use the case count and viral load data and compared their simulations and forecasting quality. Our results demonstrate that a simple SEIR model based on viral load data can reliably predict the number of infections in the future. Therefore, wastewater-based surveillance is a promising way of monitoring the spread of COVID-19 and can provide city officials with timely information about the circulation of COVID-19 in the community.
Single cell transcriptomics reveals distinct effector profiles of infiltrating T cells in lupus skin and kidney
Authors: Dunlap Garrett S. , Billi Allison C. , Ma Feiyang , Maz Mitra P. , Tsoi Lam C. , Wasikowski Rachael , Gudjonsson Johann E. , Kahlenberg J. Michelle , Rao Deepak A.
Published: October 2021

Cutaneous lupus is commonly present in patients with systemic lupus erythematosus (SLE) but can also exist as an isolated manifestation without further systemic involvement. T cells have been strongly suspected to contribute to the pathology of cutaneous lupus, yet our understanding of the T cell phenotypes and functions in the skin in lupus remains incomplete, and the extent to which lupus T cell infiltrates in skin resemble those in other tissue beds is unknown. Here, we present a detailed single-cell RNA sequencing profile of T and NK cell populations present within lesional and non-lesional skin biopsies of patients with cutaneous lupus. We identified multiple lymphocyte clusters, including both CD4 and CD8 T cells, NK cells, regulatory T cells, and a population of strongly interferon-responding cells that was present in patients with cutaneous lupus but absent in healthy donors. T cells across clusters from both lesional and non-lesional skin biopsies expressed elevated levels of interferon simulated genes (ISGs); however, compared to T cells from control skin, T cells from cutaneous lupus lesions did not show elevated expression profiles of activation, cytotoxicity, or exhaustion. Integrated analyses comparing skin T/NK cells to lupus nephritis kidney T/NK cells indicated that skin lymphocytes appeared less activated and lacked the expanded cytotoxic populations prominent in lupus nephritis. An integrated comparison of skin T cells from lupus and systemic sclerosis revealed similar activation profiles but an elevated ISG signature specific to cells from lupus skin biopsies. Overall, these data represent the first detailed transcriptomic analysis of the of T and NK cells in cutaneous lupus at the single cell level and have enabled a cross-tissue comparison that highlighted the stark differences in composition and activation of T/NK cells in distinct tissues in lupus.
Machine Learning Prediction of Non-Coding Variant Impact in Human Retinal Cis-Regulatory Elements
Authors: VandenBosch Leah S. , Luu Kelsey , Timms Andrew E. , Challam Shriya , Wu Yue , Lee Aaron Y. , Cherry Timothy J.
Published: October 2021

Purpose

Prior studies demonstrate the significance of specific cis-regulatory variants in retinal disease, however determining the functional impact of regulatory variants remains a major challenge. In this study, we utilize a machine learning approach, trained on epigenomic data from the adult human retina, to systematically quantify the predicted impact of cis-regulatory variants.

Methods

We used human retinal DNA accessibility data (ATAC-seq) to determine a set of 18.9k high-confidence putative cis-regulatory elements. 80% of these elements were used to train a machine learning model utilizing a gapped k-mer support vector machine-based approach. In silico saturation mutagenesis and variant scoring was applied to predict the functional impact of all potential single nucleotide variants within cis-regulatory elements. Impact scores were tested in a 20% hold-out dataset and compared to allele population frequency, phylogenetic conservation, transcription factor (TF) binding motifs, and existing massively parallel reporter assay (MPRA) data.

Results

We generated a model that distinguishes between human retinal regulatory elements and negative test sequences with 95% accuracy. Among a hold-out test set of 3.7k human retinal CREs, all possible single nucleotide variants (SNVs) were scored. Variants with negative impact scores correlated with reduced population allele frequency, higher phylogenetic conservation of the reference allele, disruption of predicted TF binding motifs, and massively-parallel reporter expression.

Conclusions

We demonstrated the utility of human retinal epigenomic data to train a machine learning model for the purpose of predicting the impact of non-coding regulatory sequence variants. Our model accurately scored sequences and predicted putative transcription factor binding motifs. This approach has the potential to expedite the characterization of pathogenic non-coding sequence variants in the context of unexplained retinal disease.
Chikungunya virus vaccine candidate incorporating synergistic mutations is attenuated and protects against virulent virus challenge
Authors: Lentscher Anthony J. , McAllister Nicole , Griswold Kira A. , Martin James L. , Welsh Olivia L. , Sutherland Danica M. , Silva Laurie A. , Dermody Terence S.
Published: October 2021

Background

Chikungunya virus (CHIKV) is an arbovirus that periodically reemerges to cause large epidemics of arthritic disease. While the robust immunity elicited by live-attenuated virus (LAV) vaccine candidates makes them attractive, CHIKV vaccine development has been hampered by a high threshold for acceptable adverse events.

Methods

We evaluated the vaccine potential of a recently described LAV, SKE, that exhibits diminished replication in skeletal muscle cells due to insertion of target sequences for skeletal muscle-specific miR-206. We also evaluated whether these target sequences could augment safety of a LAV encoding a previously described attenuating mutation, E2 G82R, which on its own was too reactogenic in clinical trials. Attenuation of viruses containing these mutations was compared with a double mutant, SKE G82R.

Results

SKE was attenuated in both immunodeficient and immunocompetent mice and induced a robust neutralizing antibody response, indicating its vaccine potential. However, only SKE G82R elicited diminished swelling in immunocompetent mice at early time points post-inoculation, indicating that these mutations synergistically enhance safety of the vaccine candidate.

Conclusions

These data suggest that restriction of LAV replication in skeletal muscle enhances tolerability of reactogenic vaccine candidates and may improve the rational design of CHIKV vaccines.
Structural identification of individual helical amyloid filaments by integration of cryo-electron microscopy-derived maps in comparative morphometric atomic force microscopy image analysis
Authors: Lutter Liisa , Al-Hilaly Youssra K. , Serpell Christopher J. , Tuite Mick F. , Wischik Claude M. , Serpell Louise C. , Xue Wei-Feng
Published: October 2021

The presence of amyloid fibrils is a hallmark of more than 50 human disorders, including neurodegenerative diseases and systemic amyloidoses. A key unresolved challenge in understanding the involvement of amyloid in disease is to explain the relationship between individual structural polymorphs of amyloid fibrils, in potentially mixed populations, and the specific pathologies with which they are associated. Although cryo-electron microscopy (cryo-EM) and solid-state nuclear magnetic resonance (ssNMR) spectroscopy methods have been successfully employed in recent years to determine the structures of amyloid fibrils with high resolution detail, they rely on ensemble averaging of fibril structures in the entire sample or significant subpopulations. Here, we report a method for structural identification of individual fibril structures imaged by atomic force microscopy (AFM) by integration of high-resolution maps of amyloid fibrils determined by cryo-EM in comparative AFM image analysis. This approach was demonstrated using the hitherto structurally unresolved amyloid fibrils formed in vitro from a fragment of tau (297-391), termed ‘dGAE’. Our approach established unequivocally that dGAE amyloid fibrils bear no structural relationship to heparin-induced tau fibrils formed in vitro. Furthermore, our comparative analysis resulted in the prediction that dGAE fibrils are closely related structurally to the paired helical filaments (PHFs) isolated from Alzheimer’s disease (AD) brain tissue characterised by cryo-EM. These results show the utility of individual particle structural analysis using AFM, provide a workflow of how cryo-EM data can be incorporated into AFM image analysis and facilitate an integrated structural analysis of amyloid polymorphism.
In an arms race between host and parasite, a lungworm’s ability to infect a toad is determined by host susceptibility, not parasite preference
Authors: Eyck Harrison JF. , Brown Gregory P. , Rollins Lee A. , Shine Richard
Published: October 2021

Evolutionary arms races can alter both parasite infectivity and host resistance, and it is difficult to separate the effects of these twin determinants of infection outcomes. Using a co-introduced, invasive host-parasite system (the lungworm Rhabdias pseudosphaerocephala and the cane toad Rhinella marina), we quantified behavioural responses of parasite larvae to skin-chemical cues of toads from different invasive populations, and rates at which hosts became infected following standardised exposure to lungworms. Chemical cues from toad skin altered host-seeking behaviour by parasites, similarly among populations. The number of infection attempts (parasite larvae entering the host’s body) also did not differ between populations, but rates of successful infection (establishment of adult worm in host lungs) was higher for range-edge toads than for range-core conspecifics. Thus, lower resistance to parasite infection in range-edge toads appears to be due to less effective immune defences of the host rather than differential behavioural responses of the parasite. In this ongoing host-parasite arms-race, changing outcomes appear to be driven by shifts in host immunocompetence.
CandyCollect: At-home saliva sampling for capture of respiratory pathogens
Authors: Lee Ulri N. , Su Xiaojing , Hieber Damielle L. , Tu Wan-chen , McManamen Anika M. , Takezawa Meg G. , Hassan Grant W. , Chan Tung Ching , Adams Karen N. , Wald Ellen R. , DeMuri Gregory P. , Berthier Erwin , Theberge Ashleigh B. , Thongpang Sanitta
Published: October 2021

Streptococcus pyogenes is a major human-specific bacterial pathogen and a common cause of a wide range of symptoms from mild infection such as pharyngitis (commonly called strep throat) to life-threatening invasive infection and post-infectious sequelae. Traditional methods for diagnosis include collecting a sample using a pharyngeal swab, which can cause discomfort and even discourage adults and children from seeking proper testing and treatment in the clinic. Saliva samples are an alternative to pharyngeal swabs. To improve the testing experience for strep throat, we developed a novel lollipop-inspired sampling platform (called CandyCollect) to capture bacteria in saliva. The device can be used in clinics or in the home and shipped back to a lab for analysis, integrating with telemedicine. CandyCollect is designed to capture bacteria on an oxygen plasma treated polystyrene surface embedded with flavoring substances to enhance the experience for children and inform the required time to complete the sampling process. In addition, the open channel structure prevents the tongue from scraping and removing the captured bacteria. Flavoring substances did not affect bacterial capture and the device has a shelf life of at least 2 months (with experiments ongoing to extend the shelf life). We performed a usability study with 17 participants who provided feedback on the device design and the dissolving time of the candy. This technology and advanced processing techniques, including polymerase chain reaction (PCR), will enable user-friendly and effective diagnosis of streptococcal pharyngitis.
Tuning the Pennes Perfusion Rate to Model Large Vessel Cooling Effects in Hepatic Radiofrequency Ablation
Authors: Vaidya Nikhil , Baragona Marco , Lavezzo Valentina , Maessen Ralph , Veroy Karen
Published: October 2021

Radio-frequency ablation (RFA) has become a popular method for the minimally invasive treatment of liver cancer. However, the success rate of these treatments depends heavily on the amount of experience the clinician possesses. Mathematical modelling can help mitigate this problem by providing an indication of the treatment outcome. Thermal lesions in RFA are affected by the cooling effect of both fine-scale and large-scale blood vessels. The exact model for large-scale blood vessels is advection-diffusion, i.e. a model capable of producing directional effects, which are known to occur in certain cases. In previous research, in situations where directional effects do not occur, the advection term in the blood vessel model has been typically replaced with the Pennes perfusion term, albeit with a higher-than usual perfusion rate. Whether these values of the perfusion rate appearing in literature are optimal for the particular vessel radii in question, has not been investigated so far. The present work aims to address this issue. An attempt has been made to determine, for values of vessel radius between 0.55 mm and 5 mm, best estimates for the perfusion rate which minimize the error in thermal lesion volumes between the perfusion-based model and the advection-based model. The results for the best estimate of the perfusion rate presented may be used in existing methods for fast estimation of RFA outcomes. Furthermore, the possible improvements to the presented methodology have been highlighted.
Cryo-EM Structures of Amyloid-β 42 Filaments from Human Brain
Authors: Yang Yang , Arseni Diana , Zhang Wenjuan , Huang Melissa , Lövestam Sofia , Schweighauser Manuel , Kotecha Abhay , Murzin Alexey G. , Peak-Chew Sew Y. , Macdonald Jennifer , Lavenir Isabelle , Garringer Holly J. , Gelpi Ellen , Newell Kathy L. , Kovacs Gabor G. , Vidal Ruben , Ghetti Bernardino , Falcon Benjamin , Scheres Sjors H.W. , Goedert Michel
Published: October 2021

Filament assembly of amyloid-β peptides ending at residue 42 (Aβ42) is a central event in Alzheimer’s disease. We report the cryo-EM structures of Aβ42 filaments from brain. Two structurally related S-shaped protofilament folds give rise to two types of filaments. Type I filaments were found mostly in the brains of individuals with sporadic Alzheimer’s disease and Type II filaments in individuals with familial Alzheimer’s disease and other conditions. The structures of Aβ42 filaments from brain differ from those of filaments assembled in vitro. By contrast, in AppNL-F knock-in mice, Aβ42 deposits were made of Type II filaments. Knowledge of Aβ42 filament structures from human brain may lead to the development of inhibitors of assembly and improved imaging agents.
Fetal neural progenitors process TLR signals from bacterial components to enhance proliferation and rework brain development
Authors: Mann Beth , Crawford Jeremy Chase , Reddy Kavya , Lott Josi , Youn Yong Ha , Gao Geli , Guy Cliff , Chou Ching-Heng , Darnell Daniel , Trivedi Sanchit , Bomme Perrine , Loughran Allister J. , Thomas Paul G. , Han Young-Goo , Tuomanen Elaine I.
Published: October 2021

Bacterial cell wall, a universal pathogen-associated molecular pattern (PAMP), crosses the placenta into the fetal brain. We determined that PAMPs interact with TLR2/6 on murine fetal neural progenitor cells (NPCs) to induce overexpansion of all neocortical layers leading to a larger, folded cortex and abnormal postnatal behavior. The NPC overexpansion originated at E10 and targeted ventricular radial glia (vRG), the primary NPC, by shortening cell cycle and increasing self-renewal. The mechanism involved two novel signaling pathways in NPCs mediated by recognition of bacterial PAMPs by TLR2/6 including: a) loss of primary cilia, activation of hedgehog signaling, and increased FOXG1 and b) increased PI3K/AKT activity. These findings reveal PAMP/TLR2/6 acts as a morphogen in fetal neurodevelopment. In addition, the loss ofTlr2orTlr6without pathogenic challenge, increased the number of neurons, establishing the requirement for an endogenous TLR2 signal for normal neurodevelopment in the embryo.
Valuation of carbon services produced by wild animals finances conservation
Authors: Berzaghi Fabio , Chami Ralph , Cosimano Thomas , Fullenkamp Connel
Published: October 2021

Filling the global biodiversity financing gap will require significant investments from financial markets, which demand credible valuations of ecosystem services and natural capital. However, current valuation approaches discourage investment in conservation because their results cannot be verified using market-determined prices. Here, we bridge the gap between finance and conservation by valuing only wild animals’ carbon services for which market prices exist. By projecting the future path of carbon service production using a spatially-explicit demographic model, we place a credible value on the carbon-capture services produced by African forest elephants. If elephants were protected, their services would be worth $35.9 billion (24.3-41.2) and store 377 MtC (318-388) across tropical Africa. Our methodology can also place lower bounds on the social cost of nature degradation. Poaching would result in $10-14 billion of lost carbon services. Our methodology enables the integration of animal services into global financial markets with major implications for conservation, local socio-economies, and conservation.
Specificities and commonalities of carbapenemase producing Escherichia coli isolated in France from 2012 to 2015
Authors: Patiño-Navarrete Rafael , Rosinski-Chupin Isabelle , Cabanel Nicolas , Dieudonné Zongo Pengdbamba , Héry Mélanie , Oueslati Saoussen , Girlich Delphine , Dortet Laurent , Bonnin Rémy A , Naas Thierry , Glaser Philippe
Published: October 2021

Carbapenemase-producing Escherichia coli (CP-Ec) represent a major public health threat with a risk of dissemination in the community as it has occurred for lineages producing extended spectrum ß-lactamases. To characterize the extend of CP-Ec spread in France, isolates from screening and infection samples received at the French National Reference Centre laboratory (F-NRC) for carbapenemase-producing Enterobacterales were investigated. Six hundred and ninety one CP-Ec isolates collected between 2012 and 2015 and 22 before were fully sequenced. Analysis of their genome sequences revealed some disseminating multidrug resistant (MDR) lineages frequently acquiring diverse carbapenemase genes mainly belonging to clonal complex (CC) 23 (ST 410) and CC10 (ST10, ST167) and sporadic isolates including rare ST131 isolates (n=17). However, the most represented ST was ST38 (n=92) with four disseminated lineages carrying blaOXA-48-like genes inserted in the chromosome. Globally, the most frequent carbapenemase gene (n=457) was blaOXA-48. It was also less frequently associated with MDR isolates being the only resistance gene in 119 isolates. Thus, outside the ST38 clades, its acquisition was frequently sporadic with no sign of dissemination, reflecting the circulation of the IncL plasmid pOXA-48 in France and its high frequency of conjugation. In contrast blaOXA-181 or blaNDM genes were often associated with the evolution of MDR E. coli lineages characterized by mutations in ftsI and ompC.

IMPORTANCE

Carbapenemase-producing Escherichia coli (CP-Ec) might be difficult to detect, as minimal inhibitory concentrations can be very low. However, their absolute number and their proportion among carbapenem-resistant Enterobacterales have been increasing, as reported by WHO and national surveillance programs. This suggests a still largely uncharacterized community spread of these isolates. Here we have characterized the diversity and evolution of CP-Ec isolated in France before 2016. We show that carbapenemase genes are associated with a wide variety of E. coli genomic backgrounds and a small number of dominant phylogenetic lineages. In a significant proportion of CP-Ec, the most frequent carbapenemase gene blaOXA-48, was detected in isolates lacking any other resistance gene, reflecting the dissemination of pOXA-48 plasmids, likely in the absence of any antibiotic pressure. In contrast carbapenemase gene transfer may also occur in multi-drug resistant E. coli, ultimately giving rise to at-risk lineages encoding carbapenemases with a high potential of dissemination.
Genetic Mouse Models of Autism Spectrum Disorder Present Subtle Heterogenous Cardiac Abnormalities
Authors: Assimopoulos Stephania , Hammill Christopher , Fernandes Darren J. , Spencer Noakes Tara Leigh , Zhou Yu-Qing , Nutter Lauryl M. J. , Ellegood Jacob , Anagnostou Evdokia , Sled John G. , Lerch Jason P.
Published: October 2021

Background

Autism Spectrum Disorder (ASD) and Congenital Heart Disease (CHD) are strongly linked on a functional and genetic level. Most work has been focused on neurodevelopmental abnormalities in CHD. Conversely, cardiac abnormalities in ASD have been less studied. In this work we investigate the prevalence of cardiac comorbidities relative to genetic contributors of ASD.

Methods

Using high frequency ultrasound imaging, we screened 9 mouse models with ASD-related genetic alterations (Arid1b(+/-),Chd8(+/-), 16p11.2 (deletion),Sgsh(+/-),Sgsh(-/-),Shank3 Δexon 4-9(+/-),Shank3 Δexon 4-9(-/-),Fmr1(-/-),Vps13b(+/-)), and pooled wild-type littermates (WT). Using a standardised imaging protocol, we measured heart rate (HR), aorta diameter (AoD), thickness and thickening of the left-ventricular (LV) anterior and posterior walls, LV chamber diameter, fractional shortening, stroke volume and cardiac output, Peak E and A velocity ratio of mitral inflow, Velocity Time Integral (VTI) through the ascending aorta.

Results

Mutant groups presented small-scale alterations in cardiac structure and function compared to WTs. A greater number of significant differences was observed among mutant groups than between mutant groups and WTs. Mutant groups differed primarily in measures of structure (LV chamber diameter and anterior wall thickness, HR, AoD). When compared to WTs, they differed in both structure and function (LV anterior wall thickness and thickening, chamber diameter and fractional shortening, HR). The mutant groups with most differences to WTs were 16p11.2 (deletion),Fmrl(-/-),Arid1b(+/-). Among mutant groups, the groups differing most from others were 16p11.2 (deletion),Sgsh(+/-),Fmrl(-/-). Our results broadly recapitulate the associated clinical findings.

Limitations

Various genetically driven cardiac abnormalities occur early in life, so repeating this work in non-adult mice may be valuable. To identify possible sex differences, we must extend this work to female mice. The downsampling procedure used (total correlation calculation) must be verified. Only indirect comparison between our results and clinical literature is possible due to differing study designs.

Conclusions

The characteristic heterogeneity of ASD was recapitulated in the observed cardiac phenotype. The type of measures (morphological, functional) mutant groups differ in can highlight common underlying mechanisms. Clinically, knowledge of cardiac abnormalities in ASD can be essential as even non-lethal cardiac abnormalities can impact normal development.
Controlling Selectivity of Modular Microbial Biosynthesis of Butyryl-CoA-Derived Designer Esters
Authors: Lee Jong-Won , Trinh Cong T.
Published: October 2021

Short-chain esters have broad utility as flavors, fragrances, solvents, and biofuels. Controlling selectivity of ester microbial biosynthesis has been an outstanding metabolic engineering problem. Here, we present a generalizable framework to enable thede novofermentative microbial biosynthesis of butyryl-CoA-derived designer esters (e.g., butyl acetate, ethyl butyrate, butyl butyrate) with controllable selectivity. Using the modular design principles, we generated the butyryl-CoA-derived ester pathways as exchangeable production modules compatible with an engineered chassis cell for anaerobic production of designer esters. We designed these modules derived from an acyl-CoA submodule (e.g., acetyl-CoA, butyryl-CoA), an alcohol submodule (e.g., ethanol, butanol), a cofactor regeneration submodule (e.g., NADH), and an alcohol acetyltransferase (AAT) submodule (e.g., ATF1, SAAT) for rapid module construction and optimization by manipulating replication (e.g., plasmid copy number), transcription (e.g., promoters), translation (e.g., codon optimization), pathway enzymes, and pathway induction conditions. To further enhance production of designer esters with high selectivity, we systematically screened various strategies of protein solubilization using protein fusion tags and chaperones to improve the soluble expression of multiple pathway enzymes. Finally, our engineered ester-producing strains could achieve 19-fold increase in butyl acetate production (0.64 g/L, 96% selectivity), 6-fold increase in ethyl butyrate production (0.41 g/L, 86% selectivity), and 13-fold increase in butyl butyrate production (0.45 g/L, 54% selectivity) as compared to the initial strains. Overall, this study presented a generalizable framework to engineer modular microbial platforms for anaerobic production of butyryl-CoA-derived designer esters from renewable feedstocks.
Resolving the 3D rotational and translational dynamics of single molecules using radially and azimuthally polarized fluorescence
Authors: Zhang Oumeng , Zhou Weiyan , Lu Jin , Wu Tingting , Lew Matthew D.
Published: October 2021

We report a radially and azimuthally polarized (raPol) microscope for high detection and estimation performance in single-molecule orientation-localization microscopy (SMOLM). With 5000 photons detected from Nile red (NR) transiently bound within supported lipid bilayers (SLBs), raPol SMOLM achieves 2.9 nm localization precision, 1.5° orientation precision, and 0.17 sr precision in estimating rotational wobble. Within DPPC SLBs, SMOLM imaging reveals the existence of randomly oriented binding pockets that prevent NR from freely exploring all orientations. Treating the SLBs with cholesterol-loaded methyl-β-cyclodextrin (MβCD-chol) causes NR’s orientational diffusion to be dramatically reduced, but curiously, NR’s median lateral displacements drastically increase from 20.8 nm to 75.5 nm (200 ms time lag). These jump diffusion events overwhelmingly originate from cholesterol-rich nanodomains within the SLB. These detailed measurements of single-molecule rotational and translational dynamics are made possible by raPol’s high measurement precision and are not detectable in standard SMLM.
The miR-124-AMPAR pathway connects polygenic risks with behavioral changes shared between schizophrenia and bipolar disorder
Authors: Namkung Ho , Yukitake Hiroshi , Fukudome Daisuke , Lee Brian J. , Ursini Gianluca , Lam Shravika , Kannan Suvarnambiga , Saito Atsushi , Niwa Minae , Sharma Kamal , Zandi Peter , Jaaro-Peled Hanna , Ishizuka Koko , Chatterjee Nilanjan , Huganir Richard , Sawa Akira
Published: October 2021

Schizophrenia (SZ) and bipolar disorder (BP) are highly heritable major psychiatric disorders that share a substantial portion of genetic risk as well as their clinical manifestations. This raises a fundamental question of whether, and how, common neurobiological pathways translate their shared polygenic risks into shared clinical manifestations. The present study shows the miR-124-AMPAR pathway as a key common neurobiological mediator that connects polygenic risks with behavioral changes shared between these two psychotic disorders. We discovered upregulation of miR-124 in biopsied neuronal cells and postmortem prefrontal cortex from both SZ and BP patients, implying its role not only as a biomarker, but also as a pathophysiological mediator. Intriguingly, the upregulation is associated with the polygenic risks shared between these two disorders. Seeking mechanistic dissection, we generated a mouse model that upregulates miR-124 in the medial prefrontal cortex, which includes brain regions homologous to sub-regions of the human prefrontal cortex. We demonstrated that upregulation of miR-124 increases GRIA2-lacking calcium permeable-AMPARs and perturbs AMPAR-mediated excitatory synaptic transmission, leading to deficits in the behavioral dimensions shared between SZ and BP.
Proteomic and functional comparison between human induced and embryonic stem cells
Authors: Brenes Alejandro J. , Griesser Eva , Sinclair Linda V. , Davidson Lindsay , Prescott Alan R. , Singh Francois , Hogg Elizabeth K.J. , Espejo-Serrano Carmen , Jiang Hao , Yoshikawa Harunori , Platani Melpomeni , Swedlow Jason , Findlay Greg M. , Cantrell Doreen A. , Lamond Angus I.
Published: October 2021

Human induced pluripotent stem cells (hiPSCs) have great potential to be used as alternatives to embryonic stem cells (hESCs) in regenerative medicine and disease modelling, thereby avoiding many of the ethical issues arising from the use of embryo-derived cells. However, despite clear similarities between the two cell types, it is likely they are not identical. In this study, we characterise the proteomes of multiple hiPSC and hESC lines derived from independent donors. We find that while hESCs and hiPSCs express a near identical set of proteins, they show consistent quantitative differences in the expression levels of a wide subset of proteins.

hiPSCs have increased total protein content, while maintaining a comparable cell cycle profile to hESCs. The proteomic data show hiPSCs have significantly increased abundance of vital cytoplasmic and mitochondrial proteins required to sustain high growth rates, including nutrient transporters and metabolic proteins, which correlated with phenotypic differences between hiPSCs and hESCs. Thus, higher levels of glutamine transporters correlated with increased glutamine uptake, while higher levels of proteins involved in lipid synthesis correlated with increased lipid droplet formation. Some of the biggest metabolic changes were seen in proteins involved in mitochondrial metabolism, with corresponding enhanced mitochondrial potential, shown experimentally using high-resolution respirometry. hiPSCs also produced higher levels of secreted proteins, including ECM components and growth factors, some with known tumorigenic properties, as well as proteins involved in the inhibition of the immune system. Our data indicate that reprogramming of human fibroblasts to iPSCs effectively restores protein expression in cell nuclei to a state comparable to hESCs, but does not similarly restore the profile of cytoplasmic and mitochondrial proteins, with consequences for cell phenotypes affecting growth and metabolism. The data improve understanding of the molecular differences between induced and embryonic stem cells, with implications for potential risks and benefits for their use in future disease modelling and therapeutic applications.
Identifying the oncogenic potential of gene fusions exploiting miRNAs
Authors: Barrese Venere S , Montemurro Marilisa , Lovino Marta , Ficarra Elisa
Published: October 2021

Background

It is estimated that oncogenic gene fusions cause about 20% of human cancer morbidity. Identifying potentially oncogenic gene fusions may improve affected patients’ diagnosis and treatment. Previous approaches to this issue included exploiting specific gene-related information, such as gene function and regulation. Here we propose a model that profits from the previous findings and includes the microRNAs in the oncogenic assessment. We present a classifier called ChimerDriver for the classification of gene fusions as oncogenic or not oncogenic. ChimerDriver is based on a specifically designed neural network and trained on genetic and post-transcriptional information to obtain a reliable classification.

Results and discussion

The designed neural network integrates information related to transcription factors, gene ontologies, microRNAs and other detailed information related to the functions of the genes involved in the fusion and the gene fusion structure. As a result, the performances on the test set reached 0.83 f1-score and 96% recall. The comparison with state-of-the-art tools returned comparable or higher results. Moreover, ChimerDriver performed well in a real-world case where 21 out of 24 validated gene fusion samples were detected by the gene fusion detection tool Starfusion.

Conclusions

ChimerDriver integrated transcriptional and post-transcriptional information in an ad-hoc designed neural network to effectively discriminate oncogenic gene fusions from passenger ones.
PIK3CAmutation in a case ofCTNNB1-mutant sinonasal glomangiopericytoma
Authors: Hong Christopher S. , Khan Mohammad , Sukys Jordan M. , Prasad Manju , Erson-Omay E. Zeynep , Vining Eugenia M. , Omay Sacit Bulent
Published: October 2021

Glomangiopericytomas are rare, primary sinonasal tumors. The existing literature is mostly limited to reports describing the clinicopathologic characteristics of these tumors. Comprehensive genetic characterization of glomangiopericytomas remains lacking. Whole-exome sequencing of a case of glomangiopericytoma was performed under an institutional review board–approved protocol. A 69-yr-old female underwent surgical resection of a glomangiopericytoma. Whole-exome sequencing revealed somatic mutations inCTNNB1andPIK3CA, the former previously associated with this pathology but the latter not described. Concurrent dysregulation of Wnt/β-catenin and PI3K/AKT/mTOR signaling, secondary to mutations in these two oncogenes, may be amenable to targeted treatment with existing clinically approved drugs. Genomic characterization of glomangiopericytomas remains lacking. This study reports novel coexistence ofPIK3CAandCTNNB1mutations in a case of glomangiopericytoma that may offer insight into the pathogenesis and potential for targeted medical therapies of this rare tumor.
New solvates and a salt of the anti-HIV compound etravirine
Authors: Muresan-Pop Marieta , Macavei Sergiu , Turza Alexandru , Borodi Gheorghe
Published: October 2021

Four new solvates of the anti-HIV compound etravirine [systematic name: 4-({6-amino-5-bromo-2-[(4-cyanophenyl)amino]pyrimidin-4-yl}oxy)-3,5-dimethylbenzonitrile, C20H15BrN6O] with dimethyl sulfoxide (C2H6OS, two distinct monosolvates), 1,4-dioxane (C4H8O2, the 0.75-solvate) and N,N-dimethylacetamide (C4H9NO, the monosolvate), which exhibit conversion to the same anhydrous etravirine phase upon desolvation, and a stable etravirinium oxalate salt {6-amino-5-bromo-4-(4-cyano-2,6-dimethylphenoxy)-2-[(4-cyanophenyl)amino]pyrimidin-1-ium hemioxalate, C20H16BrN6O+·0.5C2O4
2−} were obtained. The crystal structures were solved by single-crystal X-ray diffraction and analyzed by powder X-ray diffraction, and the intermolecular interactions were explored by Hirshfeld surface analysis. Lattice energies were evaluated using the atom–atom force field Coulomb–London–Pauli (AA CLP) approximation, which distributes the total energy as four separate contributions: Coulombic, polarization, dispersion and repulsion. The formation of the solvates and the oxalate salt was further characterized by thermal analysis and IR spectroscopy.
A new three-dimensional twofold interpenetrated cadmium(II) metal–organic framework: synthesis, structure and photoluminescence properties
Authors: Zhang Hong-Tao , Wang Xiao-Long
Published: October 2021

The design and synthesis of metal–organic frameworks (MOFs) have attracted much interest due to the aesthetics of their crystalline architectures and their potential applications as new functional materials. A new twofold interpenetrated three-dimensional (3D) MOF, namely, poly[[triaqua(μ4-(2R,2′R)-2,2′-{[1,4-phenylenebis(carbonyl)]bis(azanediyl)}dipropionato-κ7
O
1:O
1,O
1′:O
4:O
4,O
4′,O
4′′)(μ3-(2R,2′R)-2,2′-{[1,4-phenylenebis(carbonyl)]bis(azanediyl)}dipropionato-κ3
O
1:O
4:O
4)dicadmium(II)] dihydrate], {[Cd2(C14H14N2O6)2(H2O)3]·2H2O}
n
, (I), has been synthesized by the reaction of Cd(CH3COO)2·2H2O with the synthesized ligand (2R,2′R)-2,2′-{[1,4-phenylenebis(carbonyl)]bis(azanediyl)}dipropionic acid (H2
L). Single-crystal X-ray diffraction analysis reveals that the carboxylate groups from two crystallographically independent L
2− dianions link the cadmium cations into a one-dimensional helical secondary building unit (SBU). The resulting SBUs are extended into a 3D metal–organic framework via the terephthalamide moiety of the ligand as a spacer. In the crystal, two independent MOFs interpenetrate each other, thus producing a twofold interpenetrated 3D architecture, which shows an unprecedented 2-nodal (7,9)-connected net with the point (Schläfli) symbol (37·46·58)(38·411·516·6). MOF (I) was further characterized by elemental analysis, IR spectroscopy, powder X-ray diffraction and thermogravimetric analysis. The photoluminescence properties and UV–Vis absorption spectrum of (I) have also been investigated. The MOF exhibits enhanced fluorescence emission with a high photoluminescence quantum yield of 31.55% and a longer lifetime compared with free H2
L.
Identifying the latent shortcomings of force account projects in Tanzania: the case of construction projects in the education sector
Authors: Matto Mordecai Chrysostom
Published: October 2021

Purpose

The study investigates the latent shortcomings of projects implemented under the force account approach. The study offers implications to the policymakers, practitioners and society at large for the effective and efficient application of the force account method in construction projects.

Design/methodology/approach

The study adopted an explanatory sequential mixed method of which the quantitative data were collected first and then analysis was performed. Then, the results of quantitative data were used to plan for the collection of qualitative data. The quantitative data were collected from performance audit report while the qualitative data were collected using semi-structured interviews.

Findings

The study identified six (6) general latent shortcomings and twenty-one (21) detailed latent shortcomings. The general latent shortcomings were inadequate planning and designing of the project; inappropriate adhering to the procurement procedures for materials; inadequate contract supervision; lack of qualified personnel to execute and supervise the works; lack of appropriate equipment and tools; and improper recording of cost of materials, labour and overheads in the books of accounts.

Research limitations/implications

The research focused on the force account construction approach as applied in the Tanzania context.

Practical implications

The research stresses that policymakers and practitioners are required to evaluate critically the scope and application of the force account mechanism. The force account procedures should be made based on the nature, scope, magnitude and thresholds of the project. The procuring organisations should ensure that the cost–benefit analysis is undertaken before implementing the force account projects. The findings of this study can be used as inputs to the present laws, regulations and guidelines related to the force account projects.

Social implications

The present study has the potentials to the communities of which force account projects are undertaken. It stresses that the force account method offers employments opportunity to the social communities.

Originality/value

The study has identified the latent shortcomings of the projects implemented under the force account method. This topic has received attention in Tanzania and developing countries. The study can be credited for its implications to policymakers, practitioners and communities including its emphasis on conducting a cost–benefit analysis.
The development of posture supporting soft exosuit design for adolescent idiopathic scoliosis
Authors: Cakmak Sukran , Cegindir Nese Yasar , Yilmaz Hurriyet Gursel
Published: October 2021

Purpose

Adolescent idiopathic scoliosis (AIS) is a three-dimensional deformity of the spine. Orthoses are the most commonly used treatment material in AIS. However, the physiological and psychological problems that arise due to these orthoses' rigid structures prevent their use by patients. Due to these problems, the authors have developed a posture supporting garment (soft exosuit) design for individuals aged 10–18, with Cobb angles of 25°–40°, which is the most rapidly progressing stage of the disease.

Design/methodology/approach

Soft exosuit prepared with experimental research method and user-centered design approach. The posture supporting effect is achieved by pattern engineering using fabric, belts, baleens and a gradual zipper system for to increase functionality, ease of use and fit.

Findings

The first six-month clinical trial in prototype use was carried out with a female patient with a 29° scoliosis Cobb angle and suitable wearing a rigid corset due to AIS. The patient was satisfied with the prototype and its functionality, ease of use, fit and comfort. Cosmetic body deformity due to scoliosis was not observed, and the Cobb angle was decreased by 10.7% at the end of the sixth month. Soft exosuit has been found effective in supporting the posture of individuals who had ongoing spinal growth.

Research limitations/implications

The most important limitation of this study is that, despite a large number of prototype and prototype studies, trials could not be conducted on a large number of patients with different characteristics due to the COVID-19 pandemic. More experimental studies are needed to generalize the product to large audiences. The first goal is to investigate more patients with different spinal deformities in the future. The second goal is to measure the materials used and the quantitative measurement of body responses with the biomechanics field. It is planned to increase the soft exosuit functionality with smart textiles by adding wearable devices with future research.

Practical implications

This study is important because it constitutes the basis for future studies on pattern cutting soft materials' positioning.

Social implications

It is thought that the study will contribute to functional solutions for different spinal deformities.

Originality/value

It is an entire functional soft garment without an actuator. It is customizable and modular for patients with spinal deformities. It is thought that the study will contribute to functional solutions for spinal deformities.
Web analytics: more than website performance evaluation?
Authors: Önder Irem , Berbekova Adiyukh
Published: October 2021

Purpose

The purpose of this study is to understand the status quo of the use of Web analytics tools by European destination management organizations (DMOs) and to provide guidelines in using these metrics for business intelligence and tourism design. In addition, the goal is to improve destination management at the city level using Web analytics data.

Design/methodology/approach

In this exploratory study, the authors analyze how European DMOs view Web analytics data through the lens of the “data to knowledge to results” framework. The authors analyze the use of Web analytics tools by DMOs through the theory of affordances and “data-to-knowledge framework” developed by Davenport et al., which incorporates several factors that contribute to a successful transformation of data available to an organization to knowledge, desirable results and ultimately to building an analytical capability.

Findings

The results show that European DMOs mainly use Web analytics data for website quality assurance, but that some are also using them to drive marketing programs. The study concludes by providing several suggestions for ways in which DMOs might optimize the use of Web analytics data, which will also improve the management of destinations.

Originality/value

Web analytics tools are used by many organizations such as DMOs to collect traffic data, to evaluate and optimize websites. However, these metrics can also be combined with other data such as bednights numbers and used for forecasting or other managerial decisions for destination management at the city level. There is a research gap in this area that focuses on using Web analytics data for business intelligence in the tourism industry and this research aims to fill this gap.