bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical and demographic factors associated with early relapse in patients with schizophrenia: a naturalistic observation study
Authors: Gündoğmuş İbrahim , Aydin Mikail Burak , Öz Sefa , Taşçi Azize Beril , Uzun Özcan
Published: August 2021

Schizophrenia is a chronic psychiatric disorder progressing in relapses. Identification of many factors that may potentially increase the risk of relapse will be an important step in preventing relapses. The aim of this study was to determine the rate of early relapse in patients with schizophrenia and possible risk factors related to early relapse. The sample of this prospective study with the naturalistic observation design consisted of 308 patients with schizophrenia. The cutoff value for early relapse was determined as 1 year. The mean age of participants was 37.38 ± 12.28 years and 66.6% of them were male (n = 205). The early relapse rate was 38.3%. The age younger than 35 [hazard ratio (HR) = 2.313; 95% confidence interval (CI), 1.518–3.526; P < 0.001], use of psychoactive substance (HR = 2.200; 95% CI, 1.407–3.440; P = 0.001), previous attempt of suicide (HR = 1.565; 95% CI, 1.028–2.384; P = 0.037), bad adherence to treatment (HR = 3.102; 95% CI, 1.358–7.086; P = 0.007), long-acting injectables (LAIs) antipsychotics in the treatment (HR = 0.534; 95% CI, 0.351–0.812; P = 0.003), combination typical–atypical antipsychotics (HR = 0.326; 95% CI, 0.131–0.807; P = 0.015), number of episodes (HR = 1.088; 95% CI, 1.043–1.134), and the score on the Side Effect factor of the Clinical Global Impressions Scale (HR = 1.826; 95% CI, 1.357–2.458; P < 0.001) were identified as the independent predictors of early relapse. It is remarkable that treatment bad adherence, use of psychoactive substance, no LAIs antipsychotics included in the treatment, and the no presence of the combination of typical and atypical antipsychotics are alterable predictors of early relapse.
Self-testing and vaccination against COVID-19 to minimize school closure
Authors: Colosi Elisabetta , Bassignana Giulia , Contreras Diego Andrés , Poirier Canelle , Cauchemez Simon , Yazdanpanah Yazdan , Lina Bruno , Fontanet Arnaud , Barrat Alain , Colizza Vittoria
Published: August 2021

Schools were largely closed in 2020-2021 to counter COVID-19 spread, impacting students’ education and well-being. With highly contagious variants expanding in Europe while vaccine hesitancy persists, safe options to maintain schools open are urgently needed. We developed an agent-based model of SARS-CoV-2 transmission in school. We used empirical contact data measured in a primary and a secondary school in France, and field estimates for adherence to screening from 683 schools during the spring 2021 wave. Examining different screening protocols, we performed a cost-benefit analysis for varying epidemic conditions and vaccination scenarios. In a partially immunized school population, weekly screening would reduce the number of cases on average by 24% in the primary and 53% in the secondary school compared to symptom-based testing alone, if R=1.3 and 50% adhered to screening. This adherence was met in primary schools (53% (95% confidence interval 21-85%)), but insufficient participation was recorded in secondary schools (10% (1-38%) in middle schools, 6% (2-12%) in high schools). Regular screening would also reduce by 90% the number of student-days lost compared to reactive class closure. No difference was predicted when fully vaccinating teachers, due to their limited number and mixing. Partially vaccinating adolescents would still require regular screening for additional control (20% case reduction with 50% vaccinated students). In the upcoming fall, COVID-19 epidemic will likely continue to pose a risk to the safe opening of schools. Increasing vaccination coverage in adolescents and implementing regular testing while largely incentivizing adherence are essential steps to keep schools open.
Regional comparisons of COVID reporting rates, burden, and mortality age-structure using auxiliary data sources
Authors: Van Gordon Mollie M. , Mwananyanda Lawrence , Gill Christopher J. , McCarthy Kevin A.
Published: August 2021

We correct common assumptions about COVID burden and disease characteristics in high-income (HIC) versus low- and middle-income (LMIC) countries by augmenting widely-used surveillance data with auxiliary data sources. We constructed an empirically-based model of serological detection rates to quantify COVID reporting rates in national and sub-national locations. From those reporting rates, we estimated relative COVID burden, finding results that contrast with estimates based on case counts and modeling. To investigate COVID mortality by age in an LMIC context, we utilized a unique morgue study of COVID in Lusaka alongside the population attributable fraction method to account for HIV comorbidity. We calculated the comorbidity-corrected age-adjusted mortality curve in Lusaka and found it significantly skewed toward younger age groups as compared to HICs. This unexpected result recommends against the unexamined use of HIC-derived parameterizations of COVID characteristics in LMIC settings, and challenges the hypothesis of an age-structure protective factor for COVID burden in Africa. Indeed, we found overall COVID burden to be higher in Lusaka than in HICs. Concurrent with high COVID burden, many LMICs have high prevalence of other public health issues such as HIV, which compete for limited health investment resources. Given differences in age-structure, comorbidities, and healthcare delivery costs, we provide a case study comparing the cost efficacy of investment in COVID versus HIV and found that even in a high HIV prevalence setting, investment in COVID remains cost-effective. As a whole, these analyses have broad implications for interpretations of COVID burden, modeling applications, and policy decision-making.

Significance Statement

The analyses presented here demonstrate the power of auxiliary COVID data sources to fill information gaps, particularly for LMICs. Our results reveal differences in COVID surveillance and disease dynamics between HICs and LMICs that challenge common perceptions and assumptions about COVID in these respective contexts. We show the divergence of COVID reporting rates between HICs and LMICs and the effects on relative estimated burden. Contradicting common modeling practices, our analysis demonstrates that the age-structure of COVID mortality cannot be accurately generalized from HICs to LMICs. We find higher COVID burden in LMIC contexts than HICs particularly in younger age groups and show that investment in COVID is cost-effective even in light of other public health concerns.
Platelet proteome analysis reveals an early hyperactive phenotype in SARS-CoV-2-infected humanized ACE2 mice
Authors: Subramaniam Saravanan , Hekman Ryan Matthew , Jayaraman Archana , O’Connell Aoife Kateri , Montanaro Paige , Blum Benjamin , Kenney Devin , Ericsson Maria , Ravid Katya , Crossland Nicholas A , Emili Andrew , Douam Florian , Bosmann Markus
Published: August 2021

Coronavirus disease-2019 (COVID-19) provokes a hypercoagulable state with increased incidence of thromboembolism and mortality. Platelets are major effectors of thrombosis and hemostasis. Suitable animal models are needed to better understand COVID-19-associated coagulopathy (CAC) and underlying platelet phenotypes. Here, we assessed K18-hACE2 mice undergoing a standardized SARS-CoV-2 infection protocol to study dynamic platelet responses via mass spectrometry-based proteomics. In total, we found significant changes in >1,200 proteins. Strikingly, protein alterations occurred rapidly by 2 days post-infection (dpi) and preceded outward clinical signs of severe disease. Pathway enrichment analysis of 2dpi platelet proteomes revealed that SARS-CoV-2 infection upregulated complement-coagulation networks (F2, F12, CFH, CD55/CD59), platelet activation-adhesion-degranulation proteins (PF4, SELP, PECAM1, HRG, PLG, vWF), and chemokines (CCL8, CXCL5, CXCL12). When mice started to lose weight at 4dpi, pattern recognition receptor signaling (RIG-I/MDA5, CASP8, MAPK3), and interferon pathways (IFIT1/IFIT3, STAT1) were predominant. Interestingly, SARS-CoV-2 spike protein in the lungs was observed by immunohistochemistry, but in platelets was undetected by proteomics. Similar to patients, K18-hACE2 mice during SARS-CoV-2 infection developed progressive lymphohistiocytic interstitial pneumonia with platelet aggregates in the lungs and kidneys. In conclusion, this model recapitulates activation of coagulation, complement, and interferon responses in circulating platelets, providing valuable insight into platelet pathology during COVID-19.

Key Points

SARS-CoV-2-infected humanized ACE2 mice recapitulate platelet reprogramming towards activation-degranulation-aggregation.

Complement/coagulation pathways are dominant in platelets at 2 days post-infection (dpi), while interferon signaling is dominant at 4dpi.
Discovery of 42 Genome-Wide Significant Loci Associated with Dyslexia
Authors: Doust Catherine , Fontanillas Pierre , Eising Else , Gordon Scott D , Wang Zhengjun , Alagöz Gökberk , Molz Barbara ,   23andMe Research Team,   Quantitative Trait Working Group of the GenLang Consortium, Pourcain Beate St , Francks Clyde , Marioni Riccardo E , Zhao Jingjing , Paracchini Silvia , Talcott Joel B , Monaco Anthony P , Stein John F , Gruen Jeffrey R , Olson Richard K , Willcutt Erik G , DeFries John C , Pennington Bruce F , Smith Shelley D , Wright Margaret J , Martin Nicholas G , Auton Adam , Bates Timothy C , Fisher Simon E , Luciano Michelle
Published: August 2021

Reading and writing are crucial for many aspects of modern life but up to 1 in 10 children are affected by dyslexia [1, 2], which can persist into adulthood. Family studies of dyslexia suggest heritability up to 70% [3, 4], yet no convincing genetic markers have been found due to limited study power [5]. Here, we present a genome-wide association study representing a 20-fold increase in sample size from prior work, with 51,800 adults self-reporting a dyslexia diagnosis and 1,087,070 controls. We identified 42 independent genome-wide significant loci: 17 are in genes linked to or pleiotropic with cognitive ability/educational attainment; 25 are novel and may be more specifically associated with dyslexia. Twenty-three loci (12 novel) were validated in independent cohorts of Chinese and European ancestry. We confirmed a similar genetic aetiology of dyslexia between sexes, and found genetic covariance with many traits, including ambidexterity, but not neuroanatomical measures of language-related circuitry. Causal analyses revealed a directional effect of dyslexia on attention deficit hyperactivity disorder and bidirectional effects on socio-educational traits but these relationships require further investigation. Dyslexia polygenic scores explained up to 6% of variance in reading traits in independent cohorts, and might in future enable earlier identification and remediation of dyslexia.
Virtual Delivery of Simulation Education to Undergraduate Medical Students During the COVID-19 Pandemic
Authors: Wu Kay , Chan Alex , Pandey Avinash , Panchal Puru , Khalid Maroof , Bala Sudarshan , Shah Samveg , Miller Matthew C.
Published: August 2021

Background

The COVID-19 pandemic has restricted in-person clinical training for medical students. Simulation-based teaching is a promising tool to introduce learners to the clinical environment. MacSim is a student-led simulation workshop for learners to develop clinical competencies. The objective of this study was to assess the impacts of MacSim and participants’ perspectives regarding simulation-based teaching.

Methods

A comprehensive simulation, representative of a virtual care scenario, was delivered to 42 pre-clerkship medical students via video conferencing. In pairs, participants obtained histories and carried out management plans for simulated patients. Participants were surveyed and interviewed. Survey data were analyzed using the Wilcoxon signed-ranks test. Interview transcript data were thematically analyzed.

Results

Post-simulation, participants (n=24) felt more prepared to make clinical decisions, collaborate, and communicate in a virtual setting. 92% of respondents agreed MacSim was a valuable learning experience and 96% agreed more simulation-based learning should be integrated into curricula. Emergent themes from interviews (n=12) included: 1) value of simulation fidelity, 2) value of physician feedback, and 3) effectiveness of MacSim in improving virtual clinical skills.

Conclusion

Simulation-based teaching is of importance and educational value to medical students. It may play an increasingly prevalent role in education as virtual care is likely to become more prevalent.
SafeSwab, a sample collection and dispensing device for near-patient testing
Authors: Grys Thomas E. , McAulay Kathrine , Ingram Darrell , Duffy Craig , Williams Ashley , Arumugam Siddarth , Ma Jiawei , Macar Uzay , Han Guangxing , Reynolds Andy , Chang Shih-Fu , Sia Samuel K. , Mayer Ken
Published: August 2021

Background

The COVID-19 pandemic has accelerated the pace of innovation around virtual care visits and testing technology. Here we present the SafeSwab (Safe Health Systems, Los Angeles, CA), an integrated, universal sample collection and dispensing device that is designed to minimize user error and enable rapid testing in a point of care or self-testing format.

Methods

The SafeSwab was used with the Safe Health Systems HealthCheck digital health application to enable self-testing by patients using lateral flow tests for SARS-CoV-2 antigen or for antibodies against SARS-CoV-2.

Results

Patients (n=74) using the SafeSwab produced a valid rapid test result in 96% of attempts, and 96% of patients felt confident that they had collected a good sample. The Safe HealthCheck app has an integrated image analysis algorithm, AutoAdapt LFA, that interprets a picture of a rapid test result, and the algorithm interpreted the result correctly 100% of the time.

Conclusion

The SafeSwab was found to be versatile and easy to use for both self-collected nasal sampling as well as fingerstick blood sampling. The use of Safe Health Systems HealthCheck app allows an integrated solution for patient instruction and test interpretation
Homologous recombination induced by a replication fork barrier requires cooperation between strand invasion and strand annealing activities
Authors: Marie Léa , Symington Lorraine S.
Published: August 2021

Replication stress and abundant repetitive sequences have emerged as primary conditions underlying genomic instability in eukaryotes. Elucidating the mechanism of recombination between repeated sequences in the context of replication stress is essential to understanding how genome rearrangements occur. To gain insight into this process, we used a prokaryotic Tus/Ter barrier designed to induce transient replication fork stalling near inverted repeats in the budding yeast genome. Remarkably, we show that the replication fork block stimulates a unique recombination pathway dependent on Rad51 strand invasion and Rad52-Rad59 strand annealing activities, as well as Mph1/Rad5 fork remodelers, Mre11/Exo1 short and long-range resection machineries, Rad1-Rad10 nuclease and DNA polymerase δ. Furthermore, we show recombination at stalled replication forks is limited by the Srs2 helicase and Mus81-Mms4/Yen1 structure-selective nucleases. Physical analysis of replication-associated recombinants revealed that half are associated with an inversion of sequence between the repeats. Based on our extensive genetic characterization, we propose a model for recombination of closely linked repeats at stalled replication forks that can actively contribute to genomic rearrangements.
Novel roles of small extracellular vesicles in regulating the quiescence and proliferation of neural stem cells
Authors: Zhang Jingtian , Uchiyama Junki , Imami Koshi , Ishihama Yasushi , Kageyama Ryoichiro , Kobayashi Taeko
Published: August 2021

Neural stem cells (NSCs) quiescence plays pivotal roles in securing sustainable neurogenesis and avoiding stemness exhaustion in the adult brain. The maintenance of quiescence and transition between proliferation and quiescence are complex processes associated with multiple niche signals, and environmental stimuli. Though the mechanisms of the transitions between NSC states have been extensively investigated, they remain to be fully elucidated. Exosomes are small extracellular vesicles (sEVs) containing functional units such as proteins, microRNAs, and mRNAs. It has already been demonstrated that sEVs actively participate in cancer cell proliferation and metastasis. However, the role of sEVs in NSC quiescence has not been investigated. Here, we applied proteomics to analyze the protein cargos of sEVs derived from proliferating, quiescent, and reactivating NSCs. Our findings revealed expression level fluctuations of NSCs sEV protein cargo at different proliferative conditions. We also identified functional clusters of gene ontology annotations from differentially expressed proteins in three sources of exosomes. Moreover, the use of exosome inhibitors revealed the contribution of exosomes to NSC quiescence at the entrance into quiescence, as well as in quiescence maintenance. Exosome inhibition delayed the entrance into quiescence by proliferating NSCs and allowed quiescent NSCs to exit from the G0 phase of the cell cycle. Protein translation was significantly upregulated in both quiescent NSCs and quiescent-induced NSCs via the exosome inhibition. Our results demonstrated that NSC exosomes are involved in regulating the quiescence of NSCs and provide a functional prediction of NSCs exosome protein cargos in terms of cell-cycle regulation and protein synthesis.
Computational metabolomics illuminates the lineage-specific diversification of resin glycoside acylsugars in the morning glory (Convolvulaceae) family
Authors: Kruse Lars H. , Bennett Alexandra A. , Mahood Elizabeth H. , Lazarus Elena , Park Se Jin , Schroeder Frank , Moghe Gaurav D.
Published: August 2021

Acylsugars are a class of plant defense compounds produced across many distantly related families. Members of the horticulturally important morning glory (Convolvulaceae) family produce a diverse sub-class of acylsugars called resin glycosides (RGs), which comprise oligosaccharide cores, hydroxyacyl chain(s), and decorating aliphatic and aromatic acyl chains. While many RG structures are characterized, the extent of structural diversity of this class in different genera and species is not known. In this study, we asked whether there has been lineage-specific diversification of RG structures in different Convolvulaceae species that may suggest diversification of the underlying biosynthetic pathways. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was performed from root and leaf extracts of 26 species sampled in a phylogeny-guided manner. LC-MS/MS revealed thousands of peaks with signature RG fragmentation patterns with one species producing over 300 signals, mirroring the diversity in Solanaceae-type acylsugars. A novel RG from Dichondra argentea was characterized using Nuclear Magnetic Resonance spectroscopy, supporting previous observations of RGs with open hydroxyacyl chains instead of closed macrolactone ring structures. Substantial lineage-specific differentiation in utilization of sugars, hydroxyacyl chains, and decorating acyl chains was discovered, especially among Ipomoea and Convolvulus – the two largest genera in Convolvulaceae. Adopting a computational, knowledge-based strategy, we further developed a high-recall workflow that successfully explained ~72% of the MS/MS fragments, predicted the structural components of 11/13 previously characterized RGs, and partially annotated ~45% of the RGs. Overall, this study improves our understanding of phytochemical diversity and lays a foundation for characterizing the evolutionary mechanisms underlying RG diversification.
Cross-scale Analysis of Temperature Compensation in the Cyanobacterial Circadian Clock System
Authors: Furuike Yoshihiko , Ouyang Dongyan , Tominaga Taiki , Matsuo Tatsuhito , Mukaiyama Atsushi , Kawakita Yukinobu , Fujiwara Satoru , Akiyama Shuji
Published: August 2021

Clock proteins maintain constant enzymatic activity regardless of temperature, even though thermal fluctuation is accelerated as temperature increases. We investigated temperature influences on the dynamics of KaiC, a temperature-compensated ATPase in the cyanobacterial circadian clock system, using quasielastic neutron scattering. The frequency of picosecond to sub-nanosecond incoherent local motions in KaiC was accelerated very slightly in a temperature-dependent manner. Our mutation studies revealed that internal motions of KaiC include several contributions of opposing temperature sensitivities. To take advantage of this balancing effect, the motional frequency of local dynamics in KaiC needs to exceed ∼0.3 ps-1. Some of the mutation sites may be in a pathway through which the motional frequency in the C-terminal domain of KaiC is fed back to the active site of ATPase in its N-terminal domain. The temperature-compensating ability at the dynamics level is likely crucial for circadian clock systems, into which the clock proteins are incorporated, to achieve reaction- or even system-level temperature compensation of the oscillation frequency.
Free for all, or free-for-all? A content analysis of Australian university open access policies
Authors: Wakeling Simon , Kingsley Danny , Jamali Hamid R. , Kennan Mary Anne , Jamali Hamid , Sarrafzadeh Maryam
Published: August 2021

Recent research demonstrates that Australia lags in providing open access to research outputs. In Australia, while the two major research funding bodies require open access of outputs from projects they fund, these bodies only fund a small proportion of research conducted. The major source of research and experimental development funding in Australian higher education is general university, or institutional, funding, and such funds are not subject to national funder open access policies. Thus, institutional policies and other institutional supports for open access are important in understanding Australia’s OA position. The purpose of this paper is, therefore, to understand the characteristics of Australian institutional open access policies and to explore the extent they represent a coherent and unified approach to delivering and promoting open access in Australia. Open access policies were located using a systematic web search approach and then their contents were analysed. Only half of Australian universities were found to have an open access policy. There was a wide variation in language used, expressed intent of the policy and expectations of researchers. Few policies mention monitoring or compliance and only three mention consequences for non-compliance. While it is understandable that institutions develop their own policies, when language is used which does not reflect national and international understandings, when requirements are not clear and with consequences, policies are unlikely to contribute to understanding of open access, to uptake of the policy, or to ease of transferring understanding and practices between institutions. A more unified approach to open access is recommended.
Mg2+-dependent conformational equilibria in CorA: an integrated view on transport regulation
Authors: Johansen Nicolai Tidemand , Bonaccorsi Marta , Bengtsen Tone , Larsen Andreas Haahr , Tidemand Frederik Grønbæk , Pedersen Martin Cramer , Huda Pie , Berndtsson Jens , Darwish Tamim , Yepuri Nageshwar Rao , Martel Anne , Pomorski Thomas Günther , Bertarello Andrea , Sansom Mark , Rapp Mikaela , Crehuet Ramon , Schubeis Tobias , Lindorff-Larsen Kresten , Pintacuda Guido , Arleth Lise
Published: August 2021

The CorA family of proteins regulates the homeostasis of divalent metal ions in many bacteria, archaea, and eukaryotic mitochondria, making it an important target in the investigation of the mechanisms of transport and its functional regulation. Although numerous structures of open and closed channels are now available for the CorA family, the mechanism of the transport regulation remains elusive. Here, we investigated the conformational distribution and associated dynamic behaviour of the pentameric Mg2+ channel CorA at room temperature using small-angle neutron scattering (SANS) in combination with molecular dynamics (MD) simulations and solid-state nuclear magnetic resonance spectroscopy (NMR). We find that neither the Mg2+-bound closed structure nor the Mg2+-free open forms are sufficient to explain the average conformation of CorA. Our data support the presence of conformational equilibria between multiple states, and we further find a variation in the behaviour of the backbone dynamics with and without Mg2+. We propose that CorA must be in a dynamic equilibrium between different non-conducting states, both symmetric and asymmetric, regardless of bound Mg2+ but that conducting states become more populated in Mg2+-free conditions. These properties are regulated by backbone dynamics and are key to understanding the functional regulation of CorA.
Voltage imaging identifies spinal circuits that modulate locomotor adaptation in zebrafish
Authors: Böhm Urs L. , Kimura Yukiko , Kawashima Takashi , Ahrens Misha B. , Higashijima Shin-ichi , Engert Florian , Cohen Adam E.
Published: August 2021

Motor systems must continuously adapt their output to maintain a desired trajectory. While the spinal circuits underlying rhythmic locomotion are well described, little is known about how the network modulates its output strength. A major challenge has been the difficulty of recording from spinal neurons during behavior. Here, we use voltage imaging to map the membrane potential of glutamatergic neurons throughout the spinal cord of the larval zebrafish during fictive swimming in a virtual environment. We mapped the spiking, subthreshold dynamics, relative timing, and sub-cellular electrical propagation across large populations of simultaneously recorded cells. We validated the approach by confirming properties of known sub-types, and we characterized a yet undescribed sub-population of tonic-spiking ventral V3 neurons whose spike rate correlated with swimming strength and bout length. Optogenetic activation of V3 neurons led to stronger swimming and longer bouts but did not affect tail-beat frequency. Genetic ablation of V3 neurons led to reduced locomotor adaptation. The power of voltage imaging allowed us to identify V3 neurons as a critical driver of locomotor adaptation in zebrafish.
Time evolution of PEG-shedding and serum protein coronation determines the cell uptake kinetics and delivery of lipid nanoparticle formulated mRNA
Authors: Gallud A. , Munson M. J. , Liu K. , Idström A. , Barriga H. M. G. , Tabaei S. R. , Aliakbarinodehi N. , Ojansivu M. , Lubart Q. , Doutch J. J. , Holme M. N. , Evenäs L. , Lindfors L. , Stevens M. M. , Collén A. , Sabirsh A. , Höök F. , Esbjörner E. K.
Published: August 2021

Development of efficient lipid nanoparticle (LNP) vectors remains a major challenge towards broad clinical translation of RNA therapeutics. New lipids will be required, but also better understanding LNP interactions with the biological environment. Herein, we model protein corona formation on PEG-ylated DLin-MC3-DMA LNPs and identify time-dependent maturation steps that critically unlock their cellular uptake and mRNA delivery. Uptake requires active serum proteins and precedes after a significant (∼2 hours) lag-time, which we show can be eliminated by pre-incubating LNPs for 3-4 hours in serum-containing media. This indicates an important role of protein corona maturation for the pharmacokinetic effects of these LNPs. We show, using single-nanoparticle imaging, NMR diffusometry, SANS, and proteomics, that the LNPs, upon serum exposure, undergo rapid PEG-shedding (∼30 minutes), followed by a slower rearrangement of the adsorbed protein layer. The PEG-shedding coincides in time with high surface abundance of Apolipoprotein A-II, whereas the LNPs preferentially bind Apolipoprotein E when their maximum uptake-competent state is reached. Finally, we show that pre-incubation of the LNPs enables rapid uptake and allows pulse-chase video-microscopy colocalization experiments with sufficiently short pulse durations to gain improved mechanistic understanding of how intracellular trafficking events determine delivery efficacy, emphasizing early endosomes as important delivery-mediating compartments.
Avifauna recovers faster in areas less accessible to trapping in regenerating tropical forests
Authors: Sagar H S Sathya Chandra , Gilroy James J. , Swinfield Tom , Yong Ding Li , Gemita Elva , Burivalova Zuzana , Novriyanti Novriyanti , Lee David C. , Janra Muhammad Nazri , Balmford Andrew , Hua Fangyuan
Published: August 2021

Tropical forest restoration stands to deliver important conservation gains, particularly in lowland Southeast Asia, which has suffered some of the world’s highest rates of forest loss and degradation. This promise, however, depends on the extent to which biodiversity at forest restoration sites continues to be exposed to threats. A key knowledge gap concerns the extent to which biodiversity recovery in naturally regenerating tropical forests is impacted by trapping for the multi-million-dollar wildlife trade. Here, we use a repeated survey dataset to quantify rates of avian community recovery under forest regeneration, at a flagship restoration site in the lowland rainforests of Sumatra, Indonesia. We show that over a decade, forest regeneration was associated with significant abundance increases for 43.8% of bird species.

However, the apparent negative impacts of trade-driven trapping on avian populations also intensified: the proportion of species that show increased abundance only in very remote forests increased from 5.4% to 16.2%, while the overall accessibility of the forest increased. We found that 14% of species did not recover as fast as predicted based on the observed improvement in forest conditions over the study period. Our results highlight the potential for rapid avifaunal recovery in regenerating tropical forests, but also emphasize the urgency of tackling the serious threat of wildlife trade to Southeast Asia’s biodiversity.
The properties of human disease mutations at protein interfaces
Authors: Livesey Benjamin J. , Marsh Joseph A.
Published: August 2021

The assembly of proteins into complexes and interactions with other biomolecules are often vital for their biological function. While it is known that mutations at protein interfaces have a high potential to be damaging and cause human genetic disease, there has been relatively little consideration for how this varies between different types of interfaces. Here we investigate the properties of human pathogenic and putatively benign missense variants at homomeric (isologous and heterologous), heteromeric, DNA, RNA and other ligand interfaces, and at different regions with respect to those interfaces. We find that different types of interfaces vary greatly in their propensity to be associated with pathogenic mutations, with homomeric heterologous and DNA interfaces being particularly enriched in disease. We also find that residues that do not directly participate in an interface, but are close in 3D space, also show a significant disease enrichment. Finally, we show that mutations at different types of interfaces tend to have distinct property changes when undergoing amino acid substitutions associated with disease, and that this is linked to substantial variability in their identification by computational variant effect predictors.
Epigenetic MRI: Noninvasive Imaging of DNA Methylation in the Brain
Authors: Lam Fan , Chu James , Choi Ji Sun , Cao Chang , Hitchens T. Kevin , Silverman Scott K. , Liang Zhi-Pei , Dilger Ryan N. , Robinson Gene E. , Li King C.
Published: August 2021

Both neuronal and genetic mechanisms regulate brain function. While there are excellent methods to study neuronal activity in vivo, there are no nondestructive methods to measure global gene expression in living brains. Here we present a method, epigenetic magnetic resonance imaging (eMRI), that overcomes this limitation via direct imaging of DNA methylation, a major gene expression regulator. eMRI exploits the methionine metabolic pathways for DNA methylation to label genomic DNA through 13C-enriched diets. A novel 13C magnetic resonance spectroscopic imaging method then maps the spatial distribution of labeled DNA. We validated eMRI using pigs, whose brains have stronger similarity to humans in volume and anatomy than rodents, and confirmed efficient 13C labeling of brain DNA. We also discovered strong regional differences in global DNA methylation. Just as MRI measurements of regional neuronal activity have had a transformational effect on neuroscience, we expect that the eMRI signal as a surrogate for regional gene expression will enable many new investigations into the roles of gene expression in human brain function, behavior, and disease.
A Network Approach to Identify Biomarkers of Differential Chemotherapy Response Using Patient-Derived Xenografts of Triple-Negative Breast Cancer
Authors: Petrosyan Varduhi , Dobrolecki Lacey E. , Thistlethwaite Lillian , Lewis Alaina N. , Sallas Christina , Rajaram Ramakrishnan , Lei Jonathan T. , Ellis Matthew J. , Osborne C. Kent , Rimawi Mothaffar F. , Pavlick Anne , Shafaee Maryam Nemati , Dowst Heidi , Saltzman Alexander B. , Malovannaya Anna , Marangoni Elisabetta , L.Welm Alana , Welm Bryan E. , Li Shunqiang , Wulf Gerburg , Sonzogni Olmo , Hilsenbeck Susan G. , Milosavljevic Aleksandar , Lewis Michael T.
Published: August 2021

Triple negative breast cancer (TNBC) is a highly heterogeneous set of diseases that has, until recently, lacked any FDA-approved, molecularly targeted therapeutics. Thus, systemic chemotherapy regimens remain the standard of care for many. Unfortunately, even combination chemotherapy is ineffective for many TNBC patients, and side-effects can be severe or lethal. Identification of predictive biomarkers for chemotherapy response would allow for the prospective selection of responsive patients, thereby maximizing efficacy and minimizing unwanted toxicities. Here, we leverage a cohort of TNBC PDX models with responses to single-agent docetaxel or carboplatin to identify biomarkers predictive for differential response to these two drugs. To demonstrate their ability to function as a preclinical cohort, PDX were molecularly characterized using whole-exome DNA sequencing, RNAseq transcriptomics, and mass spectrometry-based total proteomics to show proteogenomic consistency with TCGA and CPTAC clinical samples. Focusing first on the transcriptome, we describe a network-based computational approach to identify candidate epithelial and stromal biomarkers of response to carboplatin (MSI1, TMSB15A, ARHGDIB, GGT1, SV2A, SEC14L2, SERPINI1, ADAMTS20, DGKQ) and docetaxel (ITGA7, MAGED4, CERS1, ST8SIA2, KIF24, PARPBP). Biomarker panels are predictive in PDX expression datasets (RNAseq and Affymetrix) for both taxane (docetaxel or paclitaxel) and platinum-based (carboplatin or cisplatin) response, thereby demonstrating both cross expression platform and cross drug class robustness. Biomarker panels were also predictive in clinical datasets with response to cisplatin or paclitaxel, thus demonstrating translational potential of PDX-based preclinical trials. This network-based approach is highly adaptable and can be used to evaluate biomarkers of response to other agents.
Spacer2PAM: A computational framework for identification of functional PAM sequences for endogenous CRISPR systems
Authors: Rybnicky Grant A. , Fackler Nicholas A. , Karim Ashty S. , Köpke Michael , Jewett Michael C.
Published: August 2021

RNA-guided nucleases from clustered regularly interspaced short palindromic repeats (CRISPR) systems expand opportunities for precise, targeted genome modification. Endogenous CRISPR systems in many bacteria and archaea are particularly attractive to circumvent expression, functionality, and unintended activity hurdles posed by heterologous CRISPR effectors. However, each CRISPR system recognizes a unique set of PAM sequences, which requires extensive screening of randomized DNA libraries. This challenge makes it difficult to develop endogenous CRISPR systems, especially in organisms that are slow-growing or have transformation idiosyncrasies. To address this limitation, we present Spacer2PAM, an easy-to-use, easy-to-interpret R package built to identify potential PAM sequences for any CRISPR system given its corresponding CRISPR array as input. Spacer2PAM can be used in “Quick” mode to generate a single PAM prediction that is likely to be functional or in “Comprehensive” mode to inform targeted, unpooled PAM libraries small enough to screen in difficult to transform organisms. We demonstrate Spacer2PAM by predicting PAM sequences for industrially relevant organisms and experimentally identifying seven PAM sequences that mediate interference from the Spacer2PAM-predicted PAM library for the type I-B CRISPR system from Clostridium autoethanogenum. We anticipate that Spacer2PAM will facilitate the use of endogenous CRISPR systems for industrial biotechnology and synthetic biology.
Genome of a novel Sediminibacterium discovered in association with two species of freshwater stream Cyanobacteria in Southern California
Authors: Castro David , Sanders Ciara , Lastor Sandy , Moron-Solano Andrea , Vega Briana , Hausknecht-Buss Hannah , Henry Simone , Zhang Andrew , Johansen Haven , Caceres Lakme , Kasler Antolette , Massaro Isabelle , Mekuria Immanuel , Vengerova Gretchen , Hristova Rosalina Stancheva , Zhang Xiaoyu , Read Betsy , Sethuraman Arun
Published: August 2021

Here we report the discovery of a novel Sediminibacterium sequenced from laboratory cultures of freshwater stream cyanobacteria from sites in Southern California, grown in BG11 media.
Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors
Authors: Shi Guangda , Robles Jaylissa Torres , Song Claire , Salichos Leonidas , Lou Hua Jane , Gerstein Mark , Turk Benjamin E.
Published: August 2021

Essential functions of mitogen-activated protein kinases (MAPKs) depend on their capacity to selectively phosphorylate a limited repertoire of substrates. MAPKs harbor a conserved groove located outside of the catalytic cleft that binds to short linear sequence motifs found in substrates and regulators. However, the weak and transient nature of these “docking” interactions poses a challenge to defining MAPK interactomes and associated sequence motifs. Here, we describe a yeast-based genetic screening pipeline to evaluate large collections of MAPK docking sequences in parallel. Using this platform we analyzed a combinatorial library based on the docking sequences from the MAPK kinases MKK6 and MKK7, defining features critical for binding to the stress-activated MAPKs JNK1 and p38α. We subsequently screened a library consisting of ~12,000 sequences from the human proteome, revealing a large number of MAPK-selective interactors, including many not conforming to previously defined docking motifs. Analysis of p38α/JNK1 exchange mutants identified specific docking groove residues mediating selective binding. Finally, we verified that docking sequences identified in the screen could function in substrate recruitmentin vitroand in cultured cells. Collectively, these studies establish an approach for characterization of MAPK docking sequences and provide a resource for future investigation of signaling downstream of p38 and JNK MAP kinases.
Role of miR-181c in Diet-Induced Obesity Through Regulation of Lipid Synthesis in Liver
Authors: Akiyoshi Kei , Boersma Gretha J. , Johnson Miranda D. , Velasquez Fernanda Carrizo , Dunkerly-Eyring Brittany , O’Brien Shannon , Yamaguchi Atsushi , Steenbergen Charles , Tamashiro Kellie L. K. , Das Samarjit
Published: August 2021

We recently identified a nuclear-encoded miRNA (miR-181c) in cardiomyocytes that can translocate into mitochondria to regulate mitochondrial gene (mt-COX1), and influence obesity-induced cardiac dysfunction through mitochondrial pathway. Liver plays a pivotal role during obesity. Therefore, we hypothesized that miR-181c plays an important role in pathophysiological complications associated with obesity. We used miR-181c/d-/- mice to study the miR-181c role in lipogenesis in hepatocytes during diet-induced obesity (DIO). Indirect calorimetric measurements were made during the 26 weeks high fat diet (HFD) exposure. qPCR was performed to examine the gene expression involved in lipid synthesis. Here, we show that miR-181c/d-/- mice are not protected against all metabolic consequences of HFD exposure. After 26 weeks of the HFD, miR-181c/d-/- mice had a significantly higher body fat (%) compared to WT. Glucose tolerance tests showed hyperinsulinemia and hyperglycemia, indicative of insulin insensitivity in the miR-181c/d-/- mice. HFD-fed miR-181c/d-/- mice had higher serum and liver triglyceride levels compared to HFD-fed WT mice. qPCR data demonstrated that several genes which are regulated by isocitrate dehydrogenase 1 (IDH1) were upregulated in miR-181c/d-/- liver compared to WT liver. Furthermore, an AAV-8 was used to deliver miR-181c, in vivo, to validate the potential role of miR-181c in the liver. miR-181c delivery attenuate the lipogenesis by downregulating the same lipid synthesis genes in the liver. In hepatocytes, miR-181c regulates lipid biosynthesis by targeting IDH1. Taken together, the data indicate that overexpression of miR-181c can be beneficial for various lipid metabolism disorders.
Neuron-specific coding and regulatory sequences are the most highly conserved in amniote brains despite neuron-specific cell size diversity
Authors: Xu Linhe , Herculano-Houzel Suzana
Published: August 2021

Neurons are unique in that they are the only cell type in the body to display massive diversity in cell size, morphology, phenotype, and function both within individuals and across species. Here we use datasets encompassing up to 92 mammalian and 31 sauropsidian species to examine whether neuron-specific diversity occurs with higher evolutionary variation of neuron-specific coding and regulatory sequences compared to non-neuronal cell-specific sequences. We find that the opposite is true: Neuronal diversity in mammalian and sauropsidian evolution arose despite extreme levels of negative selection on neuron-specific protein-coding sequences on par with ATPase coding sequences, the benchmark of evolutionary conservation. We propose that such strong evolutionary conservation is imposed by excitability, which continually exposes cells to the risk of excitotoxic death, and speculate that neuronal cell size diversity is a self-organized consequence of variability in levels of activity, possibly constrained by energy supply to the developing brain.
Melanomagenesis driven by a kinase-dead mutant BRAF lacking codons 600-618
Authors: Girtman Megan A. , Richmond Craig S. , Campbell Meagan E. , Rehrauer William M. , Kenny Paraic A.
Published: August 2021

While considerable success has been achieved with treating BRAF-V600E mutant tumors in several organ systems, tumors expressing non-V600E BRAF mutations remain a significant clinical challenge. Such atypical BRAF mutations are classified based on their kinase activity, RAS-dependence and their requirement for dimerization to function. We identified an unusually large in-frame deletion in a melanoma patient, encompassing codons 600-618 in the kinase domain. This patient experienced rapid disease progression when treated with dual BRAF/MEK inhibition. To determine whether and how such a large in-frame BRAF deletion might be activating, we ectopically expressed it in HEK293 cells and monitored BRAF pathway activation and response to BRAF and MEK inhibitors. We demonstrate that this mutation results in a kinase-deficient BRAF mutant which, nevertheless, activates MEK/ERK signaling in a dimerization-dependent manner, placing this mutation among the class III BRAF mutants.
Riceberry rice bran protein hydrolyzed fractions induced apoptosis, senescence and G1/S cell cycle arrest in human colon cancer cell lines
Authors: Wattayagorn Vichugorn , Kongsema Mesayamas , Tadakittisarn Sukuntaros , Chumnanpuen Pramote
Published: August 2021

Riceberry rice bran is the part of rice that has been scrubbed out during coloring process. There are various health benefits with high protein content and antioxidant ability. The hydrolyzed rice bran consists of diverse peptides that provide various bioactive properties. This work aimed to study the effect of hydrolyzed riceberry rice bran extracted on colon cancer cell lines (HT-29 and SW-620) compared to normal cell (PCS-291-010). The MTT assay result showed that our extract has less cytotoxicity on normal cell (PCS-291-010, IC50 = 6,680.00 μg/ml) compared to the colon cancer cell lines and has more effect on metastatic cancer cell line (SW-620, IC50 = 5,492.31 μg /ml) than non-metastatic cancer cell line (HT-29, IC50 =6,040.76 μg/ml). According to the DNA fragmentation pattern analysis, the ladder pattern indicated that the rice bran extract can induce the apoptosis process in SW-620 cell line. Confirmed the pattern of apoptotic cell by AO/PI double stain test and quantified apoptotic cells by Annexin V. For the cell senescence analysis, SA-β-gal staining technique was performed at 24 h after treatments, HT-29 reached maximum senescence rate at 85.74% while SW-620 had only 17.23% of senescence. And a result of cell cycle analysis, HT-29 were decreased the number of cells in S, M/G2 phase, and increased the number of cells in G0/G1 phase. Furthermore > 50 kDa peptide fraction separated from HRBE has a potent anti-cancer cells (SW-620, IC50 = 4,908 μg/ml). In conclusion, the hydrolyzed riceberry rice bran extract can inhibit colon cancer cell lines with less effect on normal cell. The extracts could induce apoptosis process in metastatic cancer cell and induce senescence process in non-metastatic cancer cell. This observed information will be useful and applicable for medical research and colon cancer treatment in the future.
Integrative molecular roadmap for direct conversion of fibroblasts into myocytes and myogenic progenitor cells
Authors: Kim Inseon , Ghosh Adhideb , Bundschuh Nicola , Hinte Laura , von Meyenn Ferdinand , Bar-Nur Ori
Published: August 2021

Transient MyoD overexpression in concert with small molecules treatment reprograms mouse fibroblasts into induced myogenic progenitor cells (iMPCs). However, the molecular landscape and mechanisms orchestrating this cellular conversion remain unknown. Here, we undertook an integrative multi-omics approach to delineate the process of iMPC reprogramming in comparison to myogenic transdifferentiation mediated solely by MyoD. Utilizing transcriptomics, proteomics and genome-wide chromatin accessibility assays, we unravel distinct molecular trajectories which govern the two processes. Notably, iMPC reprogramming is characterized by gradual upregulation of stem and progenitor cell markers, unique signaling pathways, chromatin remodelers and cell cycle regulators which manifest via rewiring of the chromatin in core myogenic promoters. Furthermore, we determine that only iMPC reprogramming is mediated by Notch pathway activation, which is indispensable for iMPC formation and self-renewal. Collectively, this study charts divergent molecular blueprints for myogenic transdifferentiation or reprogramming and underpins the heightened capacity of iMPCs in capturing myogenesis ex vivo.