bluuebunny/crossref_metadata_2025 huggingface dataset:
Associations of adiposity, kidney stone disease, and serum calcium concentrations; observational and genetic epidemiological studies
Authors: Lovegrove Catherine E , Bešević Jelena , Wiberg Akira , Lacey Ben , Littlejohns Thomas J , Allen Naomi E , Goldsworthy Michelle , Kim Jihye , Hannan Fadil , Curhan Gary C , Turney Ben , McCarthy Mark , Mahajan Anubha , Thakker Rajesh V , Holmes Michael V , Furniss Dominic , Howles Sarah A
Published: June 2022

Background

Kidney stone disease (KSD) is linked to obesity, metabolic syndrome and biochemical alterations including higher serum calcium concentration. The mechanisms by which these phenotypes associate with KSD are uncertain. We aimed to establish the effects of adiposity on KSD using conventional and genetic epidemiological techniques.

Methods

We assessed observational associations between measures of adiposity and incident KSD in 479,405 people from the UK Biobank. To facilitate Mendelian randomization (MR) analyses, we undertook genome-wide association studies (GWAS) of KSD in the UK Biobank in combined and sex-specific subsets. Univariable, multivariable and mediation MR analyses were used to calculate odds ratio (OR) or beta coefficient (ß) for risk of KSD per genetically instrumented higher marker of adiposity, metabolic syndrome parameter, biochemical phenotype, and inflammation and identify violations of MR assumptions.

Findings

Observational analyses demonstrated that measures of central adiposity (waist-to-hip ratio (WHR) and waist circumference (WC)) are more strongly associated with incident KSD than measures of general adiposity (body mass index (BMI)). Three novel KSD-GWAS loci were identified (SLC2A12, TRPV5, and SLC28A1); no sex-specific loci were detected. MR analyses established that higher central adiposity is causally linked to both KSD and higher adjusted serum calcium concentrations independent of BMI (one standard deviation higher WHR: OR for KSD=1·43, p=4·1×10−6; ß for serum calcium concentration=0·11mmol/L, p=2·7×10−7). Mediation analyses indicated that 12% of the effect of WHR on KSD is due its role in elevating serum calcium concentration. Our MR studies indicated that other components of the metabolic syndrome, serum uric acid levels, and biomarkers of inflammation are unlikely to be implicated in the causation of KSD.

Interpretation

Our study indicates that visceral adipose depots elevate serum calcium concentration and cause an increased risk of KSD. Therapies targeting central adipose deposition may affect calcium homeostasis and have utility for the prevention of KSD.
Metabolomics and transcriptomics reveal the response mechanisms of Mikania micrantha to Puccinia spegazzinii infection
Authors: Ren Xinghai , Zhang Guangzhong , Gu Yujuan , Jin Mengjiao , Day Michael D. , Liu Huai , Qian Wanqiang , Liu Bo
Published: June 2022

Mikania micrantha is one of the 100 worst invasive species globally and can cause significant negative impacts to agricultural and forestry economics, particularly in Asia and the Pacific region. The rust Puccinia spegazzinii has been used successfully as a biological control agent in several countries to help manage M. micrantha. However, the response mechanisms of M. micrantha to P. spegazzinii infection have never been studied. To investigate the response of M. micrantha to infection by P. spegazzinii, an integrated analysis of metabolomics and transcriptomics was performed. The levels of 101 metabolites, including organic acids, amino acids and secondary metabolites in M. micrantha infected with P. spegazzinii, were significantly different compared to those in plants that were not infected. The relative amounts of L-leucine, L-ioleucine, L-tryptophan, histidine, L-phenylalanine and L-citrulline were increased under P. spegazzinii infection. These may convert to intermediates within the TCA cycle, participating in energy biosynthesis. In addition, phytoalexins, such as maackiain, nobiletin, vasicin, arachidonic acid and JA-Ile, were synthesized and accumulated in M. micrantha in response to P. spegazzinii infection. A total of 4,978 differentially expressed genes were identified in M. micrantha infected by P. spegazzinii. Many key genes of the Mitogen-activated protein kinase (MAPK) signalling pathway, showed significantly higher expression under P. spegazzinii infection. These results not only help us to understand the response of metabolites and gene expression in M. micrantha following infection by P. spegazzinii, but also help us understand the potential for the continuous biological control of M. micrantha using P. spegazzinii.
Nervous system reduction in branched-chain amino acid metabolism disrupts hippocampal neurogenesis and memory
Authors: Abdi Khadar , Rodriguiz Ramona M. , Wetsel William C. , Arlotto Michelle E. , McGarrah Robert W. , White Phillip J.
Published: June 2022

A role for macronutrient metabolism in learning and memory is supported by numerous epidemiological studies. The Ppm1k gene encodes the branched-chain keto acid dehydrogenase (BCKDH) phosphatase that promotes the metabolism of branched-chain amino acids (BCAA). Here we show that nervous system deletion of Ppm1k in mice increases BCAA levels in brain tissue but not in plasma. These mice have significant impairments in working memory accompanied by a robust accumulation of DCX+/NeuroD1+ immature neurons within the dentate gyrus granule cell layer. Through single cell RNA sequencing and pathway analysis we identified substantial increases in transit-amplifying cells and immature neurons along with activated hedgehog signaling in Ppm1k deficient primary neural stem cells (NSCs). Inhibition of mTOR signaling reversed the effects of Ppm1k deletion on neuronal progenitor gene activation in primary NSCs. Together our findings uncover a new molecular link between BCAA metabolism, hippocampal neurogenesis, and cognitive performance.
Beyond the circuit architecture : attractor dynamics reveals the mechanism of improved performance in decision-making and working memory
Authors: Yan Han , Wang Jin
Published: June 2022

Understanding the underlying mechanisms of cognitive functions such as decision-making(DM) and working memory(WM) is always one of the most essential concerns in modern neuroscience.Recent experimental and modelling works suggest that decision-making is supported by the selective subnetwork of inhibitory neurons, rejecting the previously proposed circuit mechanisms assuming a single non-selective pool of inhibitory neurons. The mechanism underlying decision-making and working memory functions based on such circuit architecture is still unclear. Here we applied a general non-equilibrium landscape and flux approach to a biophysically based model that can perform the decision-making and working memory functions. The quantified attractor landscapes reveal that the accuracy in decision-making can be improved due to the stronger resting state in the circuit architecture with selective inhibition, while robustness of working memory against distractors is weakened, which implies a trade-off between DM and WM. We found that the presence of a ramping non-selective input during the delay period of the decision-making tasks can serve as a cost-effective mechanism of temporal gating of distractors. This temporal gating mechanism, combined with the selective-inhibition circuit architecture, can support a dynamical modulation for emphasizing the robustness or the flexibility to incoming stimuli in working memory tasks according to the cognitive task demands. These mechanisms can also achieve an optimal balance in the trade-off between DM and WM. Our approach can provide a global and physical quantification which helps to uncover the underlying mechanisms of various biological functions beyond the circuit architectures.
Kidney patients remain at increased risk for succumbing to COVID-19
Authors: Hendrickx Rodinde , Jellingsø Mads , Sommer Morten OA
Published: June 2022

Immunocompromised patients have been at an increased risk of succumbing to COVID-19 already since the beginning of the pandemic. Here we analyzed data from patients with end stage renal disease, including those on dialysis and patients with a kidney transplant, and compared them to the general population. We found that kidney patients remain at increased risk of succumbing to COVID-19 despite all available countermeasures. The analyses underline the need for additional protection for this vulnerable population.
Occupation, Worker Vulnerability, and COVID-19 Vaccination Uptake: Analysis of the Virus Watch prospective cohort study
Authors: Beale Sarah , Burns Rachel , Braithwaite Isobel , Byrne Thomas , Erica Fong Wing Lam , Fragaszy Ellen , Geismar Cyril , Hoskins Susan , Kovar Jana , Navaratnam Annalan M D , Nguyen Vincent , Patel Parth , Yavlinsky Alexei , Van Tongeren Martie , Aldridge Robert W , Hayward Andrew
Published: June 2022

Background

Occupational disparities in COVID-19 vaccine uptake can impact the effectiveness of vaccination programmes and introduce particular risk for vulnerable workers and those with high workplace exposure. This study aimed to investigate COVID-19 vaccine uptake by occupation, including for vulnerable groups and by occupational exposure status.

Methods

We used data from employed or self-employed adults who provided occupational information as part of the Virus Watch prospective cohort study (n=19,595) and linked this to study-obtained information about vulnerability-relevant characteristics (age, medical conditions, obesity status) and work-related COVID-19 exposure based on the Job Exposure Matrix. Participant vaccination status for the first, second, and third dose of any COVID-19 vaccine was obtained based on linkage to national records and study records. We calculated proportions and Sison-Glaz multinomial 95% confidence intervals for vaccine uptake by occupation overall, by vulnerability-relevant characteristics, and by job exposure.

Findings

Vaccination uptake across occupations ranged from 89-96% for the first dose, 87-94% for the second dose, and 75-86% for the third dose, with transport, trade, service and sales workers persistently demonstrating the lowest uptake. Vulnerable workers tended to demonstrate fewer between-occupational differences in uptake than non-vulnerable workers, although clinically vulnerable transport workers (76%-89% across doses) had lower uptake than several other occupational groups (maximum across doses 86-96%). Workers with low SARS-CoV-2 exposure risk had higher vaccine uptake (86%-96% across doses) than those with elevated or high risk (81-94% across doses).

Interpretation

Differential vaccination uptake by occupation, particularly amongst vulnerable and highly-exposed workers, is likely to worsen occupational and related socioeconomic inequalities in infection outcomes. Further investigation into occupational and non-occupational factors influencing differential uptake is required to inform relevant interventions for future COVID-19 booster rollouts and similar vaccination programmes.
An attenuated vaccinia vaccine encoding the SARS-CoV-2 spike protein elicits broad and durable immune responses, and protects cynomolgus macaques and human ACE2 transgenic mice from SARS-CoV-2 and its variants
Authors: Ishigaki Hirohito , Yasui Fumihiko , Nakayama Misako , Endo Akinori , Yamamoto Naoki , Yamaji Kenzaburo , Nguyen Cong Thanh , Kitagawa Yoshinori , Sanada Takahiro , Honda Tomoko , Munakata Tsubasa , Higa Masahiko , Toyama Sakiko , Kono Risa , Takagi Asako , Matsumoto Yusuke , Hayashi Kaori , Shiohara Masanori , Ishii Koji , Saeki Yasushi , Itoh Yasushi , Kohara Michinori
Published: June 2022

As long as the coronavirus disease 2019 (COVID-19) pandemic continues, new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with altered antigenicity will emerge. The development of vaccines that elicit robust, broad, and durable protection against SARS-CoV-2 variants is urgently needed. We have developed a vaccine (rDIs-S) consisting of the attenuated vaccinia virus DIs strain platform carrying the SARS-CoV-2 S gene. rDIs-S induced neutralizing antibody and T-lymphocyte responses in cynomolgus macaques and human angiotensin converting enzyme 2 (hACE2) transgenic mice, and showed broad protection against SARS-CoV-2 isolates ranging from the early-pandemic strain (WK-521) to the recent Omicron BA. 1 variant (TY38-839). Using a tandem mass tag (TMT) -based quantitative proteomic analysis of lung homogenates from hACE2 transgenic mice, we found that, among mice subjected to challenge infection with WK-521, vaccination with rDIs-S prevented protein expression related to the severe pathogenic effects of SARS-CoV-2 infection (tissue destruction, inflammation, coagulation, fibrosis, and angiogenesis) and restored protein expression related to immune responses (antigen presentation and cellular response to stress). Furthermore, long-term studies in mice showed that rDIs-S maintains S protein-specific antibody titers for at least 6 months after a 1st vaccination. Thus, rDIs-S appears to provide broad and durable protective immunity against SARS-CoV-2, including current and possibly future variants.
Male-killing-associated bacteriophage WO identified from comparisons of Wolbachia endosymbionts of Homona magnanima
Authors: Arai Hiroshi , Anbutsu Hisashi , Nishikawa Yohei , Kogawa Masato , Ishii Kazuo , Hosokawa Masahito , Lin Shiou-Ruei , Ueda Masatoshi , Nakai Madoka , Kunimi Yasuhisa , Harumoto Toshiyuki , Kageyama Daisuke , Takeyama Haruko , Inoue Maki N.
Published: June 2022

The origin and mechanism of male-killing, an advantageous strategy employed by maternally transmitted symbionts such as Wolbachia, remain unclear. We compared genomes of four Wolbachia strains derived from Homona magnanima, a male-killing strain wHm-t (1.5 Mb), and three non-male-killing strains, wHm-a (1.1 Mb), wHm-b (1.3 Mb), and wHm-c (1.4 Mb). A wHm-t-specific 76-kbp prophage region harboured two tandemly arrayed WO-mediated killing (wmk) gene homologs (wmk-1/wmk-2 and wmk-3/wmk-4). Of these, wmk-1 or wmk-3 killed almost all Drosophila melanogaster individuals when transgenically overexpressed. Dual expression of wmk-3 and wmk-4 killed all males and rescued females. We propose a novel hypothesis wherein horizontally transmitted proto-Wolbachia with a single wmk killed both sexes, and tandem duplication of wmk allowed an evolutionary transition to a vertically transmitted symbiont, causing male-killing. Our study highlights the bacteriophage as a critical driver of the evolution of male-killing and argues for a conserved male-killing mechanism in diverse insects.
Epidemiological Correlates of Overweight and Obesity in the Northern Cape Province, South Africa
Authors: Smith Mackenzie H , Myrick Justin W , Oyageshio Oshiomah , Uren Caitlin , Saayman Jamie , Boolay Sihaam , van der Westhuizen Lena , Werely Cedric , Möller Marlo , Henn Brenna M , Reynolds Austin W
Published: June 2022

Background

In the past several decades, obesity has become a major public health issue worldwide, associated with increased rates of chronic disease and death. Like many developing nations, South Africa is experiencing rapid increases in BMI, and as a result, evidence-based preventive strategies are needed to reduce the increasing burden of overweight and obesity. This study aimed to determine the prevalence and predictors of overweight and obesity among a multi-ethnic cohort from the rural Northern Cape of South Africa.

Methods

These data were collected as part of a tuberculosis (TB) case-control study, with 395 healthy control participants included in the final analysis. Overweight and obesity were defined according to WHO classification. Multivariate linear models of BMI were generated using sex, age, education level, smoking, alcohol consumption, and diabetes as predictor variables. We also used multivariable logistic regression analysis to assess the relationship of these factors with overweight and obesity.

Results

The average BMI in our study cohort was 25.1. The prevalence overweight was 18.6% and the prevalence of obesity was 23.5%. We find that female gender, being older, and having more years of formal education are all positively associated with BMI in our dataset. Women (OR = 5.4, CI = 3.2-9.4), older individuals (OR = 1.02, CI = 1-1.04), and those with more years of education (OR = 1.18, CI = 1.07-1.29) were all more likely to be overweight or obese. Alternatively, being a smoker is negatively associated with BMI and decreases one’s odds of being overweight or obese (OR = 0.25, CI = 0.15-0.42).

Conclusions

We observed a high prevalence of overweight and obesity in this study. The odds of being overweight and obesity was higher in women and those with more education and increases with age. Community-based interventions to control obesity in these communities should pay special attention to these groups.
Repeated mass testing of staff and residents in prison outbreaks of Covid-19: an enhanced outbreak investigation in two adult prisons in England, 2021
Authors: Czachorowski Maciej , Bashton Matthew , O’Moore Eamonn , McGrath Nuala , Smith Darren , Gutridge Kerry , Parkes Julie , Plugge Emma
Published: June 2022

Background

The management of Covid-19 outbreaks presented particular challenges in the prison setting. In this study we describe the results from the implementation of a serial mass testing approach in two adult prisons in northern England. The overall aim was to examine the epidemiology of Covid-19 outbreaks in prisons and help inform public health policy and practice during the pandemic.

Methods

Repeat mass testing was offered to all eligible staff and residents in a women’s (nresidents=239; nstaff=246) and a men’s (nresidents=703; nstaff=340) prison in February and March 2021 at days 0, 7 and 28 after Covid-19 outbreaks were declared. Positive swab samples were sent for viral whole genome sequencing by COG-UK.

Findings

Participation in at least one testing round ranged from a low of 67% of staff in the men’s prison to a high of 98% of residents in the women’s prison. The largest outbreak, in the men’s prison (261 cases in residents and 37 cases in staff), continued to see new cases identified at the last testing round on day 28. Test positivity in residents of both prisons was significantly lower (p<0.05) at day 28 than on preceding test days, but no significant difference was observed for staff (p>0.05). Epidemiological data in conjunction with sequencing information provided evidence for multiple introductions of the SARS-CoV-2 virus from the local community into the prisons, with transmission identified both within wings and between wings among residents and staff. Two distinct SARS-CoV-2 lineages were identified in the women’s and men’s prisons, B.1.177 and B.1.17, respectively.

Conclusions

During a Covid-19 outbreak, timely implementation of a whole prison testing regime can serve to inform a targeted approach to infection prevention and control by identifying the true extent of disease transmission in all (including asymptomatic) individuals. Staff, in particular, should be tested regularly and testing uptake should be as high as possible to minimise the risk of infection incursion. Ensuring high testing uptake across all testing rounds remains a challenge.
Telemedicine Ready or Not? a cross-sectional assessment of telemedicine maturity of federally funded tertiary health institutions in Nigeria
Authors: Olufunlayo Tolulope F. , Ojo Oluwadamilola O. , Ozoh Obianuju B. , Agabi Osigwe P. , Opara Chuks R. , Taiwo Funlola T. , Fasanmade Olufemi A. , Okubadejo Njideka U.
Published: June 2022

Background and Objective

Telemedicine (TM) has solidified its place as a means for continuity of healthcare services and a cost-effective approach for improving health equity as demonstrated during the COVID-19 pandemic. Preparedness of health systems for telemedicine is an indicator of the scalability of their services, especially during disasters. We aimed to assess the maturity and preparedness of federally funded tertiary health institutions (FFTHIs) in Nigeria, to deploy and integrate telemedicine

Methods

We conducted a cross-sectional study of randomly selected FFTHIs in Nigeria using PAHO’s tool for assessing the maturity level of health institutions to implement telemedicine services. Descriptive statistics were used for overall maturity levels and non-parametric tests to compare scores for overall maturity and specific PAHO domains per region. The level of significance was set at p value <0.05.

Results

Twenty-four of thirty randomly polled FFTHIs responded (response rate of 77.4%). Overall, the median TM maturity level was 2.0 (1.75) indicating beginner level. No significant inter-zonal difference in median overall maturity level (p=0.87). The median maturity levels for telemedicine readiness in specific domains were organizational readiness - 2.0 (2.0), processes 1.0 (1.0), digital environment 2.0 (3.0), human resources 2.0 (1.0), regulatory issues- 1.5 (1.0) and expertise 2.0 (2.0); mostly at beginner level, with no inter-zonal differences. Most participating institutions had no initiatives in place for domains of processes and regulatory issues.

Conclusions

The current status of telemedicine maturity of FFTHIs in Nigeria behoves policy makers to advance the implementation of telemedicine across the country as part of national digital quality healthcare.
High-throughput engineering of cytoplasmic- and nuclear-replicating large dsDNA viruses by CRISPR/Cas9
Authors: López-Muñoz Alberto Domingo , Rastrojo Alberto , Martín Rocío , Alcamí Antonio
Published: June 2022

The application of CRISPR/Cas9 to improve genome engineering efficiency of large dsDNA viruses has been extensively described, but a robust and versatile method for high-throughput generation of marker-free recombinants for a desire locus has not been reported yet. Cytoplasmic-replicating viruses use their own repair enzymes for homologous recombination, while nuclear-replicating viruses use the host repair machinery. This is translated into a wide range of Cas9-induced homologous recombination efficiency depending on the virus replication compartment and viral/host repair machinery characteristics and accessibility. However, the use of Cas9 as a selection agent to target parental virus genomes robustly improves the selection of desired recombinants across large dsDNA viruses. We used ectromelia virus (ECTV) and herpes simplex viruses (HSV) type 1 and 2, to optimize a CRISPR/Cas9 method that can be versatilely used for efficient genome editing and selection of both cytoplasmic- and nuclear-replicating viruses. We performed a genome-wide genetic variant analysis of mutations located at predicted off-target sequences for 20 different recombinants, showing off-target-free accuracy by deep-sequencing. Our results support this optimized method as an efficient, accurate and versatile approach to enhance the two critical factors of high-throughput viral genome engineering: generation and color-based selection of recombinants. This application of CRISPR/Cas9 reduces time and labor of screening of desired recombinants, allowing for high-throughput generation of large collections of mutant dsDNA viruses for a desire locus in less than two weeks.

DATA SUMMARY

Raw sequence reads are available at the European Bioinformatics Institute (EMBL-EBI) European Nucleotide Archive (ENA) as Bioproject ID PRJEB32151 and PRJEB32152.

Six supplementary figures, eleven supplementary tables and supplementary methods are available with the online version of this article. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
Elucidating dynamic anaerobe metabolism with Live Cell HRMAS 13C NMR and genome-scale metabolic modeling
Authors: Pavao Aidan , Girinathan Brintha , Peltier Johann , Silva Pamela Altamirano , Dupuy Bruno , Muti Isabella H. , Malloy Craig , Cheng Leo L. , Bry Lynn
Published: June 2022

Anaerobic microbial metabolism drives critical functions within global ecosystems, host-microbiota interactions, and industrial applications, yet remains ill-defined. Here we advance versatile approaches to elaborate dynamic metabolism in living cells of obligate anaerobes, using the pathogen Clostridioides difficile, an amino acid and carbohydrate-fermenting Clostridia. High-Resolution Magic Angle Spinning (HRMAS) Nuclear Magnetic Resonance (NMR) spectroscopy of C. difficile grown with uniformly labeled 13C substrates informed dynamic flux balance analysis (dFBA) of the pathogen’s genome-scale metabolism. Predictions identified metabolic integration of glycolytic and amino acid fermentation pathways at alanine’s biosynthesis, to support efficient energy generation, maintenance of redox balance, nitrogen handling, and biomass generation. Model predictions advanced an approach using the sensitivity of 13C NMR spectroscopy to simultaneously track cellular carbon and nitrogen flow, from [U-13C]glucose and [15N] leucine, confirming the formation of [13C,15N]alanine. We illustrate experimental and computational approaches to elaborate complex anaerobic metabolism for diverse applications.
Methylated guanosine and uridine modifications inS. cerevisiaemRNAs modulate translation elongation
Authors: Jones Joshua D. , Franco Monika K. , Smith Tyler J. , Snyder Laura R. , Anders Anna G. , Ruotolo Brandon T. , Kennedy Robert T. , Koutmou Kristin S.
Published: June 2022

Chemical modifications to protein encoding messenger RNA (mRNA) can modulate their localization, translation and stability within cells. Over 15 different types of mRNA modifications have been identified by sequencing and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) technologies. While LC-MS/MS is arguably the most essential tool available for studying analogous protein post-translational modifications, the high-throughput discovery and quantitative characterization of mRNA modifications by LC-MS/MS has been hampered by the difficulty of obtaining sufficient quantities of pure mRNA and limited sensitivities for modified nucleosides. To overcome these challenges, we improved the mRNA purification and LC-MS/MS pipelines to identify newS. cerevisiaemRNA modifications and quantify 50 ribonucleosides in a single analysis. The methodologies we developed result in no detectable non-coding RNA modifications signals in our purified mRNA samples and provide the lowest limit of detection reported for ribonucleoside modification LC-MS/MS analyses. These advancements enabled the detection and quantification of 13S. cerevisiaemRNA ribonucleoside modifications and revealed four newS. cerevisiaemRNA modifications at low to moderate levels (1-methyguanosine, N2-methylguanosine, N2, N2-dimethylguanosine, and 5-methyluridine). We identified four enzymes that incorporate these modifications intoS. cerevisiaemRNAs (Trm10, Trm11, Trm1, and Trm2), though our results suggest that guanosine and uridine nucleobases are also non-enzymatically methylated at low levels. Regardless of whether they are incorporated in a programmed manner or as the result of RNA damage, we reasoned that the ribosome will encounter the modifications that we detect in cells and used a reconstituted translation system to discern the consequences of modifications on translation elongation. Our findings demonstrate that the introduction of 1-methyguanosine, N2-methylguanosine and 5-methyluridine into mRNA codons impedes amino acid addition in a position dependent manner. This work expands the repertoire of nucleoside modifications that the ribosome must decode inS. cerevisiae. Additionally, it highlights the challenge of predicting the effect of discrete modified mRNA sites on translationde novobecause individual modifications influence translation differently depending on mRNA sequence context.
Inhibition of vaccinia virus L1 N-myristoylation by the host N-myristoyltransferase inhibitor IMP-1088 generates non-infectious virions defective in cell entry
Authors: Priyamvada Lalita , Kallemeijn Wouter W. , Faronato Monica , Wilkins Kimberly , Goldsmith Cynthia S. , Cotter Catherine A. , Ojeda Suany , Solari Roberto , Moss Bernard , Tate Edward W. , Satheshkumar Panayampalli Subbian
Published: June 2022

We have recently shown that the replication of rhinovirus, poliovirus and foot-and-mouth disease virus requires the co-translational N-myristoylation of viral proteins by human host cell N-myristoyltransferases (NMTs), and is inhibited by treatment with IMP-1088, an ultrapotent small molecule NMT inhibitor. Here, we reveal the role of N-myristoylation during vaccinia virus (VACV) infection in human host cells and demonstrate the anti-poxviral effects of IMP-1088. N-myristoylated proteins from VACV and the host were metabolically labelled with myristic acid alkyne during infection using quantitative chemical proteomics. We identified VACV proteins A16, G9 and L1 to be N-myristoylated. Treatment with NMT inhibitor IMP-1088 potently abrogated VACV infection, while VACV gene expression, DNA replication, morphogenesis and EV formation remained unaffected. Importantly, we observed that loss of N-myristoylation resulted in greatly reduced infectivity of assembled mature virus particles, characterized by significantly reduced host cell entry and a decline in membrane fusion activity of progeny virus. While the N-myristoylation of VACV entry proteins L1, A16 and G9 was inhibited by IMP-1088, mutational and genetic studies demonstrated that the N-myristoylation of L1 was the most critical for VACV entry. Given the significant genetic identity between VACV, monkeypox virus and variola virus L1 homologs, our data provides a basis for further investigating the role of N-myristoylation in poxviral infections as well as the potential of selective NMT inhibitors like IMP-1088 as broad-spectrum poxvirus inhibitors.
Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback
Authors: Gutiérrez Joaquín , Kumar Sant , Khammash Mustafa
Published: June 2022

Communities of microbes play important roles in natural environments and hold great potential for deploying division-of-labor strategies in synthetic biology and bioproduction. However, the difficulty of controlling the composition of microbial consortia over time hinders their optimal use in many applications. Here, we present a fully automated, high-throughput platform that combines real-time measurements and computer-controlled optogenetic modulation of bacterial growth to implement precise and robust compositional control of a two-strainE. colicommunity. Additionally, we develop a general framework for dynamic modeling of synthetic genetic circuits in the physiological context ofE. coliand use a host-aware model to determine the optimal control parameters of our closed-loop compositional control system. Our platform succeeds in stabilizing the strain ratio of multiple parallel co-cultures at arbitrary levels and in changing these targets over time, opening the door for the implementation of dynamic compositional programs in synthetic bacterial communities.
Extracellular appendages govern spatial dynamics and growth of Caulobacter crescentus on a prevalent biopolymer
Authors: Povolo Vanessa R , D’Souza Glen G , Kaczmarczyk Andreas , Stubbusch Astrid KM , Jenal Urs , Ackermann Martin
Published: June 2022

Microbial breakdown of carbon polymers is an essential process in all ecosystems. Carbon polymers generally require extracellular breakdown by secreted exoenzymes. Exoenzymes and breakdown products can be lost through diffusion or flow. This diffusional loss is reduced when bacteria grow in surface-associated populations where they benefit from each other’s metabolic activities. The aquatic organism Caulobacter crescentus was recently shown to form clonal microcolonies on the carbon polymer xylan, but to grow solitary on the monosaccharide xylose. The underlying mechanisms of this substrate-mediated microcolony formation are unknown. In particular, the importance of extracellular appendages such as pili, adhesive holdfast, and flagellum in governing the spatial arrangement of surface-grown cells is unclear. Using microfluidics coupled to automated time-lapse microscopy and quantitative image analysis, we compared the temporal and spatial dynamics of C. crescentus wildtype and mutant strains grown on xylan, xylose, or glucose. We found that mutants lacking type IV pili or holdfast showed altered spatial patterns in microcolonies and were unable to maintain cell densities above a threshold required for maximal growth rates on the xylan polymer, whereas mutants lacking flagella showed increased cell densities that potentially lead to increased local competition. Our results demonstrate that extracellular appendages allow bacteria to reach local cell densities that maximize single-cell growth rates in response to their nutrient environment.
The human brain reactivates context-specific past information at event boundaries of naturalistic experiences
Authors: Hahamy Avital , Dubossarsky Haim , Behrens Timothy E. J.
Published: June 2022

Although we perceive the world in a continuous manner, our experience is partitioned into discrete events. However, to make sense of these events, they must be stitched together into an overarching narrative – a model of unfolding events. It has been proposed that such a stitching process happens in offline neural reactivations when rodents build models of spatial environments. Here we show that, whilst understanding a natural narrative, humans reactivate neural representations of past events. Similar to offline replay, these reactivations occur in hippocampus and default mode network, where reactivations are selective to relevant past events. However, these reactivations occur, not during prolonged offline periods, but at the boundaries between ongoing narrative events. These results, replicated across two datasets, suggest reactivations as a candidate mechanism for binding temporally distant information into a coherent understanding of ongoing experience.
Brain and Organoid Manifold Alignment (BOMA), a machine learning framework for comparative gene expression analysis across brains and organoids
Authors: He Chenfeng , Kalafut Noah Cohen , Sandoval Soraya O. , Risgaard Ryan , Yang Chen , Khullar Saniya , Suzuki Marin , Chang Qiang , Zhao Xinyu , Sousa Andre M.M. , Wang Daifeng
Published: June 2022

Organoids have become valuable models for understanding cellular and molecular mechanisms in human development including brains. However, whether developmental gene expression programs are preserved between human organoids and brains, especially in specific cell types, remains unclear. Importantly, there is a lack of effective computational approaches for comparative data analyses between organoids and developing humans. To address this, by considering the public data availability and research significance, we developed a machine learning framework, Brain and Organoid Manifold Alignment (BOMA) for comparative gene expression analysis of brains and organoids, to identify conserved and specific developmental trajectories as well as developmentally expressed genes and functions, especially at cellular resolution. BOMA first performs a global alignment and then uses manifold learning to locally refine the alignment, revealing conserved developmental trajectories between brains and organoids. Using BOMA, we found that human cortical organoids better align with certain brain cortical regions than other non-cortical regions, implying organoid-preserved developmental gene expression programs specific to brain regions. Additionally, our alignment of non-human primate and human brains reveals highly conserved gene expression around birth. Also, we integrated and analyzed developmental scRNA-seq data of human brains and organoids, showing conserved and specific cell trajectories and clusters. Further identification of expressed genes of such clusters and enrichment analyses reveal brain- or organoid-specific developmental functions and pathways. Finally, we experimentally validated important specific expressed genes using immunofluorescence. BOMA is open-source available as a web tool for general community use.
A lysosomal surveillance response (LySR) that reduces proteotoxicity and extends healthspan
Authors: Li Terytty Yang , Gao Arwen W. , Li Xiaoxu , Liu Yasmine J. , Arey Rachel N. , Morales Kimberly , Lalou Amélia , Wang Qi , Lima Tanes , Auwerx Johan
Published: June 2022

Lysosomes are cytoplasmic organelles central for the degradation of macromolecules to maintain cellular homeostasis and health. Here, we discovered an adaptive lysosomal transcriptional response that we termed the Lysosomal Surveillance Response (LySR). Typified by the induction of a large group of transcripts involved in lysosomal function and proteolysis, the LySR can be triggered by silencing of specific vacuolar H+-ATPase subunits in Caenorhabditis elegans. Notably, LySR activation enhances the clearance of protein aggregates in worm models of Alzheimer’s and Huntington’s disease and amyotrophic lateral sclerosis, thereby boosting fitness and extending lifespan. The GATA transcription factor, ELT-2, regulates the LySR program as well as its associated beneficial effects. In mammalian cells, overexpression of GATA4/GATA6, the mammalian orthologs of ELT-2, is sufficient to induce the expression of multiple lysosome-specific proteases and alleviate proteotoxicity. Activating the LySR pathway may therefore represent an attractive mechanism to reduce proteotoxicity and, as such, potentially extend healthspan.

Highlights

RNAi of specific v-ATPase subunits extends C. elegans lifespan and activates LySR

GATA transcription factor ELT-2 regulates LySR and LySR-associated lifespan extension

LySR activation reduces protein aggregates and extends worm healthspan

Overexpression of GATA4/GATA6 alleviates amyloid-β proteotoxicity in mammalian cells
Cas12a2 elicits abortive infection via RNA-triggered destruction of double-stranded DNA
Authors: Dmytrenko Oleg , Neumann Gina C. , Hallmark Thomson , Keiser Dylan J. , Crowley Valerie M. , Vialetto Elena , Mougiakos Ioannis , Wandera Katharina G. , Domgaard Hannah , Weber Johannes , Metcalf Josie , Begemann Matthew B. , Gray Benjamin N. , Jackson Ryan N. , Beisel Chase L.
Published: June 2022

Bacterial abortive infection systems limit the spread of foreign invaders by shutting down or killing infected cells before the invaders can replicate1, 2. Several RNA-targeting CRISPR-Cas systems (e.g., types III and VI) cause Abi phenotypes by activating indiscriminate RNases3–5. However, a CRISPR-mediated abortive mechanism that relies on indiscriminate DNase activity has yet to be observed. Here we report that RNA targeting by the type V Cas12a2 nuclease drives abortive infection through non-specific cleavage of double-stranded (ds)DNA. Upon recognition of an RNA target with an activating protospacer-flanking sequence, Cas12a2 efficiently degrades single-stranded (ss)RNA, ssDNA, and dsDNA. Within cells, the dsDNase activity induces an SOS response and impairs growth, stemming the infection. Finally, we harnessed the collateral activity of Cas12a2 for direct RNA detection, demonstrating that Cas12a2 can be repurposed as an RNA-guided, RNA-targeting tool. These findings expand the known defensive capabilities of CRISPR-Cas systems and create additional opportunities for CRISPR technologies.
Dissociating the contributions of sensorimotor striatum to automatic and visually-guided motor sequences
Authors: Mizes Kevin G. C. , Lindsey Jack , Escola G. Sean , Ölveczky Bence P.
Published: June 2022

The ability to sequence movements in response to new task demands enables rich and adaptive behavior. Such flexibility, however, is computationally costly and can result in halting performances. Practicing the same motor sequence repeatedly can render its execution precise, fast, and effortless, i.e., ‘automatic’. The basal ganglia are thought to underlie both modes of sequence execution, yet whether and how their contributions differ is unclear. We parse this in rats trained to perform the same motor sequence in response to cues and in an overtrained, or ‘automatic’, condition. Neural recordings in the sensorimotor striatum revealed a kinematic code independent of execution mode. While lesions affected the detailed kinematics similarly across modes, they disrupted high-level sequence structure for automatic, but not visually-guided, behaviors. These results suggest that the basal ganglia contribute to learned movement kinematics and are essential for ‘automatic’ motor skills but can be dispensable for sensory-guided motor sequences.
Disruption of CFAP418 interaction with lipids causes abnormal membrane-associated cellular processes in retinal degenerations
Authors: Clark Anna M. , Yu Dongmei , Neiswanger Grace , Zhu Daniel , Maschek J. Alan , Burgoyne Thomas , Yang Jun
Published: June 2022

Syndromic ciliopathies and retinal degenerations are large heterogeneous groups of genetic diseases. CFAP418 is a causative gene of both disorders, and its protein sequence is evolutionarily conserved. However, the pathogenic mechanism caused by CFAP418 mutations is largely unknown. Here, we employed affinity purification coupled with mass spectrometry and quantitative lipidomic, proteomic, and phosphoproteomic approaches to address the molecular function of CFAP418 in mouse retinas. We showed that CFAP418 bound to lipid metabolism precursor phosphatidic acid (PA) and mitochondrion-specific lipid cardiolipin but did not form a tight and static complex with proteins. Loss of Cfap418 led to membrane lipid imbalance and protein-membrane association alteration, which subsequently caused mitochondrial defects and membrane remodeling abnormalities in multiple vesicular trafficking pathways. Loss of Cfap418 also increased the activity of PA-binding protein kinase Cα. Our results indicate that membrane lipid imbalance is a new pathological mechanism underlying syndromic ciliopathies and retinal degenerations, which is associated with other known causative genes for these diseases, such as RAB28 and BBS genes.
Connexin43 Overexpression Promotes Bone Regeneration by Osteogenesis and Angiogenesis in Rat Glucocorticoid-Induced Osteonecrosis of the Femoral Head
Authors: Zhao Xin , Chen Changjun , Luo Yue , Li Donghai , Wang Qiuru , Fang Yuying , Kang Pengde
Published: June 2022

Glucocorticoids induced osteonecrosis of the femoral head (GIONFH) is a devastating orthopedic disease. Previous studies suggested that connexin43 (Cx43) is involved in the process of osteogenesis and angiogenesis. However, the role of Cx43 potentiates in the osteogenesis and angiogenesis of bone marrow-derived stromal stem cells (BMSCs) in GIONFH is still not investigated. In this study, BMSCs were isolated and transfected with green fluorescent protein (GFP) or the fusion gene encoding GFP and Cx43. The osteogenic differentiation of BMSCs were detected after transfected with Cx43. In addition, the migration abilities and angiogenesis of human umbilical vein endothelial cells (HUVECs) were been detected after induced by transfected BMSCs supernatants in vitro. Our results showed that Cx43 overexpression in BMSCs promoted osteogenic differentiation and angiogenesis in vitro. Finally, we established GC-ONFH rat model, then, a certain amount of transfected or controlled BMSCs were injected into the tibia of the rats. Immunohistological staining and micro-CT scanning results showed that the transplanted experiment group had significantly promoted more bone regeneration, vessel volume and the expressions of Runx2, ALP, COL I, VEGF and CD31 when compared with the effects of the negative or control groups. This study demonstrated for the first time that the Cx43 overexpression in BMSCs could promote bone regeneration as seen in the osteogenesis and angiogenesis process, suggesting that Cx43 may serve as a therapeutic gene target for GIONFH treatment.
Chimpanzee play sequences are structured hierarchically as games
Authors: Mielke Alexander , Carvalho Susana
Published: June 2022

Social play is ubiquitous in the development of many animal species and involves players adapting actions flexibly to their own previous actions and partner responses. Play differs from other behavioural contexts for which fine-scale analyses of action sequences are available, such as tool use and communication, in that its form is not defined by its functions, making it potentially more unpredictable. In humans, play is often organised in games, where players know context-appropriate actions but string them together unpredictably. Here, we use the sequential nature of play elements to explore whether play elements in chimpanzees are structured hierarchically and follow predictable game-like patterns. Based on 5711 play elements from 143 bouts, we extracted individual-level play sequences of 11 Western chimpanzees (Pan troglodytes verus) of different ages from the Bossou community. We detected transition probabilities between play elements that exceeded expected levels and show that play elements form hierarchically clustered and interchangeable groups, indicative of at least six ‘games’ that can be identified from transition networks, some with different roles for different players. We also show that increased information about preceding play elements improved predictability of subsequent elements, further indicating that play elements are not strung together randomly but that flexible action rules underlie their usage. Thus, chimpanzee play is hierarchically structured in short ‘games’ which limit acceptable play elements and allow players to predict and adapt to partners’ actions. This ‘grammar of action’ approach to social interactions can be valuable in understanding cognitive and communicative abilities within and across species.
Structural basis of ligand recognition and transport by Sfh2, a yeast phosphatidylinositol transfer protein of the Sec14 superfamily
Authors: Chen Lin , Tan Lingchen , Im Young Jun
Published: June 2022

Sec14-like phosphatidylinositol transfer proteins (PITPs) are involved in lipid metabolism and phosphatidylinositol 4-phosphate signaling by transporting phosphatidylinositol (PI) and a secondary ligand between the organellar membranes in eukaryotes. Yeast Sfh2 is a PITP that transfers PI and squalene without phosphatidylcholine transfer activity. To investigate the structural determinants for ligand specificity and transport in Sfh2, crystal structures of Sfh2 in complex with PI and squalene were determined at 1.5 and 2.4 Å resolution, respectively. The inositol head group of PI is recognized by highly conserved residues around the pocket entrance. The acyl chains of PI bind into a large hydrophobic cavity. Squalene is accommodated in the bottom of the cavity entirely by hydrophobic interactions. The binding of PI and squalene are mutually exclusive due to their overlapping binding sites, correlating with the role in lipid exchange. The binding mode of PI is well conserved in Sfh family proteins. However, squalene binding is unique to the Sfh2 homolog due to the specific hydrophobic residues forming a shape-complementary binding pocket. Recombinant apo Sfh2 forms a homodimer in vitro by the hydrophobic interaction of the gating α10–α11 helices in an open conformation. Ligand binding closes the lid and dissociates the dimer into monomers. This study reveals the structural determinants for the recognition of the conserved PI and a secondary ligand, squalene, and provides implications for the lipid-transfer function of Sfh2.