bluuebunny/crossref_metadata_2025 huggingface dataset:
BNT162b2 vaccination induces SARS-CoV-2 specific antibody secretion into human milk with minimal transfer of vaccine mRNA
Authors: Low Jia Ming , Gu Yue , Ng Melissa Shu Feng , Amin Zubair , Lee Le Ye , Ng Yvonne Peng Mei , D/O Shunmuganathan Bhuvaneshwari , Niu Yuxi , Gupta Rashi , Tambyah Paul Anantharajah , MacAry Paul A , Wang Liang Wei , Zhong Youjia
Published: April 2021

Importance

To examine the impact of SARS-CoV-2 vaccination of lactating mothers on human milk

Objective

(1) To quantify SARS-CoV-2-specific immunoglobulin A (IgA) and immunoglobulin G (IgG) in human milk of lactating mothers who received the BNT162b2 vaccine, with reference to a cohort convalescent from antenatal COVID-19, and healthy lactating mothers. (2) To detect and quantify vaccine mRNA in human milk after BNT162b2 vaccination.

Design

Gestational Immunity For Transfer 2 (GIFT-2) is a prospective cohort study of lactating mothers who were due to receive two doses of BNT162b2 vaccine, recruited between 5th February 2021 and 9th February 2021.

Setting

Lactating healthcare workers living in Singapore

Participants

Convenience sample of ten lactating healthcare workers. Human milk samples were collected at four time points: pre-vaccination, 1-3 days after dose one, 7-10 days after dose one, and 3-7 days after dose two of the BNT162b2 vaccine.

Exposure

Two doses of the BNT162b2 vaccine 21 days apart.

Main Outcome and Measure

(i) SARS-CoV-2-specific IgA and IgG in human milk of lactating mothers who received BNT162b2 vaccine, (ii) Detection and quantification of vaccine mRNA in human milk after BNT162b2 vaccination.

Results

Ten lactating healthcare workers aged 32.5 years (range 29 – 42) were recruited, with 40 human milk samples collected and analysed. SARS-CoV-2-specific IgA was predominant in human milk of lactating mothers who received BNT162b2 vaccine. The sharpest rise in antibody production was 3 −7 days after dose two of the BNT162b2 vaccine, with medians of 1110 picomolar of anti-SARS-CoV-2 spike and 374 picomolar of anti-Receptor Binding Domain IgA. Vaccine mRNA was detected only on rare occasions, at a maximum concentration of 2 ng/mL.

Conclusions and Relevance

In this cohort of ten lactating mothers following BNT162b2 vaccination, nine (90%) produced SARS-CoV-2 IgA, and ten (100%) produced IgG in human milk with minimal amounts of vaccine mRNA. Lactating individuals should continue breastfeeding in an uninterrupted manner after receiving mRNA vaccination for SARS-CoV-2.

Trial Registration

Registered atclinicaltrials.gov(NCT04802278).

Key Points

Question

Does BNT162b2 (i) induce the production and secretion of SARS-CoV-2 specific antibodies into human milk, and/or (ii) get secreted into human milk?

Findings

In this cohort that included ten lactating healthcare workers following BNT162b2 vaccination, 90% produced SARS-CoV-2 immunoglobulin A, and 100% produced immunoglobulin G in human milk, with minimal amounts of vaccine mRNA transfer.

Meaning

Lactating individuals should continue breastfeeding in an uninterrupted manner after receiving SARS-CoV-2 mRNA vaccination.
DeepFake electrocardiograms: the key for open science for artificial intelligence in medicine
Authors: Thambawita Vajira , Isaksen Jonas L. , Hicks Steven A. , Ghouse Jonas , Ahlberg Gustav , Linneberg Allan , Grarup Niels , Ellervik Christina , Olesen Morten Salling , Hansen Torben , Graff Claus , Holstein-Rathlou Niels-Henrik , Strümke Inga , Hammer Hugo L. , Maleckar Molly , Halvorsen Pål , Riegler Michael A. , Kanters Jørgen K.
Published: April 2021

Recent global developments underscore the prominent role big data have in modern medical science. Privacy issues are a prevalent problem for collecting and sharing data between researchers. Synthetic data generated to represent real data carrying similar information and distribution may alleviate the privacy issue.

In this study, we present generative adversarial networks (GANs) capable of generating realistic synthetic DeepFake 12-lead 10-sec electrocardiograms (ECGs). We have developed and compare two methods, WaveGAN* and Pulse2Pulse GAN. We trained the GANs with 7,233 real normal ECG to produce 121,977 DeepFake normal ECGs. By verifying the ECGs using a commercial ECG interpretation program (MUSE 12SL, GE Healthcare), we demonstrate that the Pulse2Pulse GAN was superior to the WaveGAN to produce realistic ECGs. ECG intervals and amplitudes were similar between the DeepFake and real ECGs. These synthetic ECGs are fully anonymous and cannot be referred to any individual, hence they may be used freely. The synthetic dataset will be available as open access for researchers at OSF.io and the DeepFake generator available at the Python Package Index (PyPI) for generating synthetic ECGs.

In conclusion, we were able to generate realistic synthetic ECGs using adversarial neural networks on normal ECGs from two population studies, i.e., there by addressing the relevant privacy issues in medical datasets.
Psychosocial family-level mediators in the intergenerational transmission of trauma: Protocol for a systematic review and meta-analysis
Authors: Mew Emma J. , Nyhan Kate , Bonumwezi Jessica L. , Blas Vanessa , Gorman Hannah , Hennein Rachel , Quach Kevin , Hawley Nicola L. , Lowe Sarah R.
Published: April 2021

Introduction

Family-level psychosocial factors appear to play a critical role in mediating the intergenerational transmission of trauma; however, no review article has quantitatively synthesized causal mechanisms across a diversity of trauma types. This study aims to systematically consolidate the epidemiological research on family-level psychosocial mediators and moderators to ultimately produce causal diagram(s) of the intergenerational transmission of trauma.

Methods

We will identify epidemiological peer-reviewed publications, dissertations, and conference abstracts that measure the impact of at least one psychosocial family-level factor mediating or moderating the relationship between parental trauma exposure and a child mental health outcome. English, French, Kinyarwanda, and Spanish articles will be eligible. We searched MEDLINE, PsycINFO, PTSDpubs, Scopus and ProQuest Dissertations and Theses and will conduct forward citation chaining of included documents. Two reviewers will perform screening independently. We will extract reported mediators, moderators, and relevant study characteristics for included studies. Findings will be presented using narrative syntheses, descriptive analyses, mediation meta-analyses, moderating meta-analyses, and causal diagram(s), where possible. We will perform a risk of bias assessment and will assess for publication bias.

Discussion

The development of evidence-based causal diagram(s) would provide more detailed understanding of the paths by which unresolved trauma can be transmitted intergenerationally at the family-level. This review could provide evidence to better support interventions that interrupt the cycle of intergenerational trauma.

Systematic review registration

PROSPERO registration ID #CRD42021251053.
Population level risk stratification of hypertensive patients by predictive modeling
Authors: Bandhakavi Sricharan , Liu Zhipeng , Karigowda Sunil , McCammon Jasmine M. , Rahmanian Farbod , Lavoie Heather M.
Published: April 2021

Objective

We recently reported that hypertension (HTN) patients having at least three rounds of distinct treatment options (atl_three_roto) in a 12-month window have elevated risk of next-year complications. However, early identification of these “challenge to treat” patients is non-trivial and “drivers” of complications in these vs remaining HTN patients are not fully defined. To address these challenges/gaps, we present predictive models for preceding outcomes, delineate their “drivers”, and highlight value of their integration for population level risk stratification/management of HTN patients.

Materials and Methods

2.47 million HTN patients enrolled through 2015-2016 were selected from a nation-wide commercial claims database. Features associated with their treatment patterns, comedications, and comorbidities were extracted for 2015 and used to model/predict 2016 outcomes of atl_three_roto status and/or HTN complications. Logistic regression-derived odds-ratios were used to delineate drivers of each outcome.

Results

Prior year treatment patterns, specific hypertension drugs (anti-hypertensives, calcium channel blockers, beta blockers), and congestive heart failure most increased future odds of atl_three_roto status. Regardless of prior year atl_three_roto status, specific comorbidities (renal disease, congestive heart failure, myocardial infarction, vascular disease, diabetes with chronic complications) and comedications (beta blockers, cardiac agents, anti-lipidemics) most increased future odds of HTN complications. Proof-of-concept analysis with an independent dataset demonstrated that integrating these model predictions/drivers thereof can be leveraged for risk stratification/management of HTN patients.

Discussion

Integrating predictions and their “drivers” from above models supports early identification and targeted management of “at-risk” HTN patients.

Conclusion

We have developed a predictive modeling based approach for risk stratification and management of HTN patients.
Biliary Duct Hamartomas: A Systematic Review
Authors: Sheikh Abu Baker , Shekhar Rahul , Javed Nismat , Leyba Katarina , Sheikh Abdul Ahad Ehsan , Upadhyay Shubhra , Kapuria Devika , Cormier Christopher , Rustagi Tarun
Published: April 2021

Biliary duct hamartomas are benign lesions of intrahepatic bile ducts. Oftentimes an incidental finding on imaging, these lesions can pose a diagnostic dilemma because of their overlapping features with malignant masses. We performed a structured systematic review of literature and identified 139 cases of biliary duct hamartomas. Patient demographics, clinical presentation with key laboratory and imaging findings, diagnostic modalities, management strategies, and outcomes were analyzed and systematically summarized. The systematic review is aimed to help with better understanding of biliary duct hamartomas and its principal features.
SARS-CoV-2 serological findings and exposure risk among employees in school and retail after first and second wave COVID-19 pandemic in Oslo, Norway: a cohort study
Authors: Gjestvang Moe Anne-Mari , Eriksen Mina , Schjølberg Tiril , Haugen Fred
Published: April 2021

Background

During initial phases of the coronavirus disease 2019 (COVID-19) pandemic, many workplaces were affected by closures and various preventive measures intended to limit infections. Here, we characterize and compare in an ambidirectional cohort study SARS-CoV-2 serology among Norwegian school employees and retail employees at baseline following the first epidemiological wave, and at follow-up after a second wave.

Methods

We enrolled a cohort of 238 school and retail employees after the first COVID-19 pandemic wave. Self-reported exposure history and serum samples were collected at 10 schools and 15 retail stores in Oslo, Norway, sampled at two time-points, baseline (May 18. to July 2. 2020) and follow-up (Jan 7. to Mar 17. 2021). SARS-CoV-2 antibodies targeting both spike and nucleocapsid were characterized by multiplex microsphere-based serological methods.

Results

At baseline, 6 enrolled workers presented with positive SARS-CoV-2 serology (3%; CI [1, 6]; P=0.019), which was significantly higher than the expected 1% prevalence in the general Oslo-population at this time-point. Five of the positive cases were retail employees. However, school and retail groups distributions at baseline were not significantly different as the number of seropositive observations were limited. Due to a school closure effectuated during the first wave, half of the school employees reported ≤2 days of physical workplace presence per week, while 65% of the retail employees reported ≥5 days per week. Eight months later, after passing a second epidemiological wave, school and retail groups presented 11 new seropositive cases altogether, but there was still no significant differences between the groups. Physical attendance at the workplace was similar between the groups during the second wave, but some preventive measures against viral transmission at workplaces were different. Self-reported virus diagnostics (RNA) for the same period were compared to the serological data obtained in this study, showing that all but one positive SARS-CoV-2 serological findings arising between baseline and follow-up had been diagnosed with virus testing.

Conclusions

After the first wave, distribution of SARS-CoV-2 positive serology was slightly higher than expected in a cohort of school and retail employees. Distribution of infection was not significantly different between the groups at baseline nor at follow-up, even though physical workplace attendance had been different. Nearly all new seropositive cases discovered in this study between baseline and follow-up, had already been diagnosed due to widespread virus testing during the second wave. This highlights the importance of extensive viral testing among workers.
Animal lifestyle changes acceptable mass limits for attached tags
Authors: Wilson Rory P , Rose Kayleigh A , Gunner Richard , Holton Mark D. , Marks Nikki J , Bennett Nigel C , Bell Stephen H. , Twining Joshua P , Hesketh Jamie , Duarte Carlos M. , Bezodis Neil , Jezek Milos , Painter Michael , Silovsky Vaclav , Crofoot Margaret C. , Harel Roi , Arnould John P. Y. , Allan Blake M. , Whisson Desley A. , Alagaili Abdulaziz , Scantlebury D. Michael
Published: April 2021

Animal-attached devices have transformed our understanding of vertebrate ecology. To minimize tag-related harm for these studies, researchers have long advocated that tag masses should not exceed 3% of the animal’s body mass. However, this proposition ignores tag forces generated as a result of animal movement.

Using data from collar-attached accelerometers on diverse free-ranging terrestrial animals, we detail a tag-based acceleration method (TbAM) in which we quantify animal athleticism in terms of fractions of animal movement time devoted to different collar-recorded accelerations. The varying accelerations are converted to forces imposed on the animals based on the acceleration and tag mass and allow derivation of defined force limits, including those amounting to 3% of the animal’s mass, for specified fractions of any animal’s active time.

We demonstrate how species athleticism is the principal determinant of tag forces, whereas body mass is of little importance. Forces exerted by ‘3%’ tags were mostly equivalent to 4-19% of the animals’ masses during moving, with a maximum of 54% in a hunting cheetah. Cumulative frequency curves of tag acceleration for periods when animals were active, all showed a characteristic sigmoid pattern, which was displaced further to the right as higher acceleration activities accounted for an increasing proportion of any animal’s time. Specifying that tags should exert forces that are less than 3% of the animal’s body mass for 95% of the time led to corrected tag masses constituting between 1.6% and 2.98% of our study animals’ masses, with values depending on animal athleticism.

Recognition that animal athleticism affects tag forces of their carriers fundamentally changes how acceptable tag mass limits should be determined by ethics bodies. In order to have a scientifically robust acceptable threshold to limit the forces experienced by an animal carrier, we suggest practitioners derive a similar cumulative acceleration profile for their study species and use a minimum of the 95% limits on the plot (although higher limits may be more appropriate).
Using Stakeholder Insights to Enhance Engagement in PhD Professional Development
Authors: Ramadoss Deepti , Bolgioni Amanda F. , Layton Rebekah L. , Alder Janet , Lundsteen Natalie , Stayart C. Abigail , Yellin Jodi B. , Smart Conrad L. , Varvayanis Susi S.
Published: April 2021

There is increasing awareness of the need for predoctoral and postdoctoral professional development and career guidance, however many academic institutions are only beginning to build out these functional roles. As a graduate career educator, accessing the vast silos and resources at a university and with industrial partners can be daunting, yet collaborative endeavors and network development both on and off campus are crucial to the success of any career and professional development office. To better inform and direct the efforts of graduate career offices, forty-five stakeholders external and internal to academic institutions were identified and interviewed to gather and categorize perspectives on topics critical to career and professional development offices. Using a stakeholder network visualization tool developed by the authors, stakeholder engagement can be rapidly assessed to ascertain areas where offices have strong connections and other areas where additional efforts could be directed to enhance engagement. General themes from interviews with internal and external stakeholders are discussed to provide graduate career educators with various stakeholder subgroup perspectives to help prepare for successful interactions. Benefits include increased engagement and opportunities to collaborate, as well as the opportunity to build or expand graduate career development offices.
Genome assemblies of three closely related leaf beetle species (Galerucellaspp)
Authors: Yang Xuyue , Slotte Tanja , Hambäck Peter A.
Published: April 2021

Galerucella(Coleoptera: Chrysomelidae) is a leaf beetle genus that has been extensively used for ecological and evolutionary studies. It has also been used as biological control agent against invading purple loosestrife in North America, with large effects on biodiversity. Here we report genome assembly and annotation of three closely relatedGalerucellaspecies:G. calmariensis,G. pusillaandG. tenella. The three assemblies have a genome size ranging from 460Mb to 588Mb, with N50 from 31,588kb to 79.674kb, containing 29,202 to 40,929 scaffolds. Using anab initioevidence-driven approach, 30,302 to 33,794 protein-coding genes were identified and functionally annotated. These draft genomes will contribute to the understanding of host-parasitoid interactions, evolutionary comparisons of leaf beetle species and future population genomics studies.
Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace
Authors: Heimhalt Maren , Berndt Alex , Wagstaff Jane , Anandapadamanaban Madhanagopal , Perisic Olga , Maslen Sarah , McLaughlin Stephen , Yu Conny Wing-Heng , Masson Glenn R. , Boland Andreas , Ni Xiaodan , Yamashita Keitaro , Murshudov Garib N. , Skehel Mark , Freund Stefan M. , Williams Roger L.
Published: April 2021

mTORC1 is a kinase complex regulating cell growth, proliferation and survival. Because mis-regulation of DEPTOR, an endogenous mTORC1 inhibitor, is associated with some cancers, we reconstituted mTORC1 with DEPTOR to understand its function. We find that DEPTOR is a uniquepartialmTORC1 inhibitor that may have evolved to preserve feedback inhibition of PI3K. Counterintuitively, mTORC1 activated by RHEB or oncogenic mutation is much more potently inhibited by DEPTOR. Although DEPTOR partially inhibits mTORC1, mTORC1 prevents this inhibition by phosphorylating DEPTOR, a mutual antagonism that requires no exogenous factors. Structural analyses of the mTORC1/DEPTOR complex showed DEPTOR’s PDZ domain interacting with the mTOR FAT region, and the unstructured linker preceding the PDZ binding to the mTOR FRB domain. Here we show, in contrast to previous cellular studies, that both the PDZ and linker regions are essential for inhibition, and it is likely that interaction with the FRB is crucial to the unique partial inhibition.
A Single Cell Atlas of Spared Tissue Below a Spinal Cord Injury Reveals Cellular Mechanisms of Repair
Authors: Matson Kaya J.E. , Russ Daniel E. , Kathe Claudia , Maric Dragan , Hua Isabelle , Krynitsky Jonathan , Pursley Randall , Sathyamurthy Anupama , Squair Jordan W. , Courtine Gregoire , Levine Ariel J.
Published: April 2021

After spinal cord injury (SCI), the “spared” tissue below the lesion contains undamaged cells that could support or augment recovery, but targeting these cells requires a clearer understanding of their injury responses and capacity for repair. Here, we used single nucleus sequencing to profile how each cell type in the lumbar spinal cord changes over time after a thoracic injury. We present an atlas of these dynamic responses and explore two unexpected findings. Amongst neurons, rare cell types expressed a molecular signature of regeneration and amongst microglia, we identified a population of “trauma associated microglia” (TAM). These TAM cells were present in the white matter near degenerating axons and expressed the trophic factorsIgf1andSpp1(OPN). Viral over-expression ofIgf1andSpp1(OPN) expanded the TAM population and promoted the clearance of myelin debris. These findings expose endogenous mechanisms of repair in spared neural tissue, uncovering potential candidates for targeted therapy.
Protracted yet coordinated differentiation of long-lived SARS-CoV-2-specific CD8+ T cells during COVID-19 convalescence
Authors: Ma Tongcui , Ryu Heeju , McGregor Matthew , Babcock Benjamin , Neidleman Jason , Xie Guorui , George Ashley F. , Frouard Julie , Murray Victoria , Gill Gurjot , Ghosn Eliver , Newell Evan , Lee Sulggi , Roan Nadia R.
Published: April 2021

CD8+ T cells are important antiviral effectors that can potentiate long-lived immunity against COVID-19, but a detailed characterization of these cells has been hampered by technical challenges. We screened 21 well-characterized, longitudinally-sampled convalescent donors that recovered from mild COVID-19 against a collection of SARS-CoV-2 tetramers, and identified one participant with an immunodominant response against Nuc322-331, a peptide that is conserved in all the SARS-CoV-2 variants-of-concern reported to date. We conducted 38- parameter CyTOF phenotyping on tetramer-identified Nuc322-331-specific CD8+ T cells, and on CD4+ and CD8+ T cells recognizing the entire nucleocapsid and spike proteins from SARS- CoV-2, and took 32 serological measurements on longitudinal specimens from this participant. We discovered a coordination of the Nuc322-331-specific CD8+ T response with both the CD4+ T cell and antibody pillars of adaptive immunity. Nuc322-331-specific CD8+ T cells were predominantly central memory T cells, but continually evolved over a ∼6-month period of convalescence. We observed a slow and progressive decrease in the activation state and polyfunctionality of the Nuc322-331-specific CD8+ T cells, accompanied by an increase in their lymph-node homing and homeostatic proliferation potential. These results suggest that following a typical case of mild COVID-19, SARS-CoV-2-specific CD8+ T cells not only persist but continuously differentiate in a coordinated fashion well into convalescence, into a state characteristic of long-lived, self-renewing memory.
Ground tissue circuitry regulates organ complexity in cereal roots
Authors: Ortiz-Ramírez Carlos , Dias Araujo Poliana Coqueiro , Zhang Sanqiang , Demesa-Arevalo Edgar , Yan Zhe , Xu Xiosa , Rahni Ramin , Gingeras Thomas R. , Jackson David , Gallagher Kimberly L. , Birnbaum Kenneth D.
Published: April 2021

Most plant roots have multiple cortex layers that make up the bulk of the organ and play key roles in physiology, such as flood tolerance and symbiosis. However, little is known about the formation of cortical layers outside of the highly reduced anatomy of the modelArabidopsis. Here we use single-cell RNAseq to rapidly generate a cell resolution map of the maize root, revealing an alternative configuration of the tissue formative SHORT-ROOT (SHR) signaling pathway adjacent to an expanded cortex. We show that maize SHR protein is hypermobile, moving at least eight cell layers into the cortex. Higher-order SHR mutants in both maize andSetariahave reduced numbers of cortical layers, showing that the SHR pathway controls expansion of cortical tissue in grasses that sets up anatomical complexity and a host of key traits.

One sentence summary

Single-cell RNA-seq maps the maize root transcriptome uncovering a mechanism that regulates cortex layer number.
Virus-Targeted Transcriptomic Analyses Implicate Ranaviral Interaction with Host Interferon Response in Frog Virus 3-infected Frog Tissues
Authors: Tian Yun , De Jesús Andino Francisco , Robert Jacques , Sang Yongming
Published: April 2021

Frog Virus 3 (FV3) is a large dsDNA virus that cause global infections in amphibians, fish and reptiles, and contribute to amphibian declines. FV3’s genome contains near 100 putative open reading frames (ORFs). Previous studies have classified these coding genes into temporal classes as immediate early, delayed early and late viral transcripts based on their sequential expression during FV3 infection. To genome-wide characterize ranaviral gene expression, we performed a whole transcriptomic analysis (RNA-Seq) using total RNA samples containing both viral and cellular transcripts from FV3-infectedXenopus laevisadult tissues using two FV3 strains, a wild type (FV3-WT) and an ORF64R-deleted recombinant (FV3-Δ64R). In samples from the infected intestine, liver, spleen, lung and especially kidney, a FV3-targeted transcriptomic analysis mapped reads spanning the full-genome coverage at ∼10× depth on both positive and negative strands. By contrast, reads were only mapped to partial genomic regions in samples from the infected thymus, skin and muscle. Extensive analyses validated the expression of almost all annotated 98 ORFs and profiled their differential expression in a tissue-, virus-, and temporal class-dependent manners. Further studies identified several putative ORFs that encode hypothetical proteins containing viral mimicking conserved domains found in host interferon (IFN) regulatory factors (IRFs) and IFN receptors. This study provides the first comprehensive genome-wide viral transcriptome profiling during infection and across multiple amphibian host tissues that will serve as instrumental reference. It also presents evidence implying that ranaviruses like FV3 have acquired previously unknown molecular mimics interfering with host IFN signaling during evolution.

Importance

Frog Virus 3 (FV3), are large dsDNA viruses that cause devastating infections globally in amphibians, fish and reptiles, and contribute to catastrophic amphibian declines. FV3’s large genome encodes near 100 coding genes, of which most have been functionally uncharacterized in the viral pathogenesis. Using a whole transcriptomic analysis (RNA-Seq) in FV3-infected amphibian samples, we determined a genome-wide virus transcriptome and profiled their differential expression in a tissue-, virus-, and temporal class-dependent manners. Further studies identified several putative ORFs that encode hypothetical proteins containing viral mimicking conserved domains found in host interferon (IFN) regulatory factors (IRFs) and IFN receptors. This study provides the first comprehensive genome-wide viral transcriptome profiling during infection and across multiple amphibian host tissues that will serve as instrumental reference. It also presents evidence implying that ranaviruses like FV3 have acquired previously unknown molecular mimics interfering with host IFN signaling during evolution.
Phosphorylation of the M1 muscarinic acetylcholine receptor mediates protection in neurodegenerative disease
Authors: Scarpa Miriam , Molloy Colin , Jenkins Laura , Tejeda Gonzalo , Rossi Mario , Dwomoh Louis , Marsango Sara , Ahmed Zeshan , Milligan Graeme , Hudson Brian D. , Tobin Andrew B. , Bradley Sophie J.
Published: April 2021

There are currently no treatments that can slow the progression of neurodegenerative diseases such as Alzheimer’s disease (AD). There is, however, a growing body of evidence that activation of the M1 muscarinic acetylcholine receptor (M1-receptor) can not only restore memory loss in AD patients, but in preclinical animal models can also slow neurodegenerative disease progression. The generation of an effective medicine targeting the M1-receptor has however been severely hampered by associated cholinergic adverse responses. By using genetically engineered mouse models that express a G protein-biased M1-receptor, we recently established that M1-receptor mediated adverse responses can be minimised by ensuring activating ligands maintain receptor phosphorylation/arrestin-dependent signalling. Here, we use these same genetic models in concert with murine prion disease, a terminal neurodegenerative disease showing key hallmarks of AD, to establish that phosphorylation/arrestin-dependent signalling delivers neuroprotection that both extends normal animal behaviour and prolongs the life span of prion diseased mice. Our data point to an important neuroprotective property inherent to the M1-receptor and indicate that next generation M1-receptor ligands designed to drive receptor phosphorylation/arrestin-dependent signalling would potentially show low adverse responses whilst delivering neuroprotection that will slow disease progression.
Cost-effective mapping of genetic interactions in mammalian cells
Authors: Khan Arshad H. , Smith Desmond J.
Published: April 2021

Comprehensive maps of genetic interactions in mammalian cells are daunting to construct because of the large number of potential interactions, ~ 2 × 108for protein coding genes. We previously used co-inheritance of distant genes from published radiation hybrid (RH) datasets to identify genetic interactions. However, it was necessary to combine six legacy datasets from four species to obtain adequate statistical power. Mapping resolution was also limited by the low density PCR genotyping. Here, we employ shallow sequencing of nascent human RH clones as an economical approach to constructing interaction maps. In this initial study, 15 clones were analyzed, enabling construction of a network with 225 genes and 2359 interactions (FDR < 0.05). Despite its small size, the network showed significant overlap with the previous RH network and with a protein-protein interaction network. Consumables were ≲ $50 per clone, showing that affordable, high quality genetic interaction maps are feasible in mammalian cells.
Effect of the shrimp farming wastes as co-feed on growth performance and digestibility of juvenile grey mullet,Mugil cephalus
Authors: Madrid Jorge , Ibarra-Zatarain Zohar , Viera-Pérez Jorge E. , Campos-Ezpinoza Abelardo , Peña-Messina Emilio
Published: April 2021

A feeding trial was carried out to evaluate the utilization of residual nutrients from a shrimp farming wastes as co-feed in different proportions in juvenile grey mullets. Four treatments were designed offering shrimp farming wastes at 0, 33, 66, and 100%. The 4 % of feed respecting the total biomass of each experimental tank was offered daily. The total feed ratio was completed with commercial feed for marine fish in the treatments where it was needed. At the end of the feeding trial, final weight, weight gain, relative weight gain, and thermal growth coefficient were reduced in the fish when increasing the amount of SFW as feed. However, the fish showed a digestive capacity to use residual nutrients up to 66 %, increasing their initial weight by up to 25 %. The increase of shrimp farming waste as feed negatively affected the whole-body proximal composition. The digestibility results showed that the fish could digest up to 41 % of the shrimp farming waste protein. Results suggest that juvenile grey mullets are capable of utilizing residual nutrients from shrimp farming waste. However, it is necessary to use an alternative feed source to induce an optimal growth performance for the juvenile grey mullets. It is also recommended that mullets be fed with formulated feed to meet their nutritional requirements to maintain the protein and lipid content of the whole-body under culture conditions.
Crystal structures of the σ2receptor template large-library docking for selective chemotypes activein vivo
Authors: Alon Assaf , Lyu Jiankun , Braz Joao M. , Tummino Tia A. , Craik Veronica , O’Meara Matthew J. , Webb Chase M. , Radchenko Dmytro S. , Moroz Yurii S. , Huang Xi-Ping , Liu Yongfeng , Roth Bryan L. , Irwin John J. , Basbaum Allan I. , Shoichet Brian K. , Kruse Andrew C.
Published: April 2021

The σ2receptor is a poorly understood transmembrane receptor that has attracted intense interest in many areas of biology including cancer imaging, Alzheimer’s disease, schizophrenia, and neuropathic pain. However, little is known regarding the molecular details of the receptor, and few highly selective ligands are available. Here, we report the crystal structure of the σ2receptor in complex with the clinical drug candidate roluperidone and the probe compound PB28. These structures, in turn, templated a large-scale docking screen of 490 million make-on-demand molecules. Of these, 484 compounds were synthesized and tested, prioritizing not only high-ranking docked molecules, but also those with mediocre and poor scores. Overall, 127 compounds with binding affinities superior to 1 μM were identified, all in new chemotypes, 31 of which had affinities superior to 50 nM. Intriguingly, hit rate fell smoothly and monotonically with docking score. Seeking to develop selective and biologically active probe molecules, we optimized three of the original docking hits for potency and for selectivity, achieving affinities in the 3 to 48 nM range and to up to 250-fold selectivity vs. the σ1receptor. Crystal structures of the newly discovered ligands bound to the σ2receptor were subsequently determined, confirming the docked poses. To investigate the contribution of the σ2receptor in pain processing, and to distinguish it from the contribution of the σ1receptor, two potent σ2-selective and one potent σ1/σ2non-selective ligand were tested for efficacy in a mouse model of neuropathic pain. All three ligands demonstrated timedependent decreases in mechanical hypersensitivity in the spared nerve injury model, supporting a role for the σ2receptor in nociception, and a possible role for σ1/σ2polypharmacology. This study illustrates the opportunities for rapid discovery ofin vivoactive and selective probes to study under-explored areas of biology using structurebased screens of diverse, ultra-large libraries following the elucidation of protein structures.
Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti)
Authors: O’Connor Timothy K. , Sandoval Marissa C. , Wang Jiarui , Hans Jacob C. , Takenaka Risa , Child Myron , Whiteman Noah K.
Published: April 2021

Color polymorphic species can offer exceptional insight into the ecology and genetics of adaptation. Although the genetic architecture of animal coloration is diverse, many color polymorphisms are associated with large structural variants and maintained by biotic interactions. Grasshoppers are exceptionally polymorphic in both color and karyotype, making them excellent models for understanding the ecological drivers and genetic underpinnings of color variation. Banded and uniform morphs of the desert clicker grasshopper (Ligurotettix coquilletti) are found across the western deserts of North America. To address the hypothesis that predation maintains local color polymorphism and shapes regional crypsis variation, we surveyed morph frequencies and tested for covariation with two predation environments. Morphs coexisted at intermediate frequencies at most sites, consistent with local balancing selection. Morph frequencies covaried with the appearance of desert substrate – an environment used only by females – indicating that ground-foraging predators are major agents of selection on crypsis. We next addressed the hypothesized link between morph variation and genome structure. To do so, we designed an approach for detecting inversions and indels using only RADseq data. The banded morph was perfectly correlated with a large putative indel. Remarkably, indel dominance differed among populations, a rare example of dominance evolution in nature.
Thein vivoRNA structurome of the malaria parasitePlasmodium falciparum, a protozoan with an A/T-rich transcriptome
Authors: Dumetz F , Enright AJ , Zhao J , Kwok CK , Merrick CJ
Published: April 2021

Plasmodium falciparum, a protozoan parasite and causative agent of human malaria, has one of the most A/T-biased genomes sequenced to date. This may give the genome and the transcriptome unusual structural features. Recent progress in sequencing techniques has made it possible to study the secondary structures of RNA molecules at the transcriptomic level. Thus, in this study we produced thein vivoRNA structurome of a protozoan parasite with a highly A/U-biased transcriptome. We showed that it is possible to probe the secondary structures ofP. falciparumRNA moleculesin vivousing two different chemical probes, and obtained structures for more than half of all transcripts in the transcriptome. These showed greater stability (lower free energy) than the same structures modelledin silico, and structural features appeared to influence translation efficiency and RNA decay. Finally, we compared theP. falciparumRNA structurome with the predicted RNA structurome of an A/T-balanced species,P. knowlesi, finding a bias towards lower overall transcript stability and more hairpins and multi-stem loops inP. falciparum. This unusual protozoan RNA structurome will provide a basis for similar studies in other protozoans and also in other unusual genomes.
Morphine exposure bidirectionally alters c-Fos expression in a sex-, age-, and brain region-specific manner during adolescence
Authors: Figueroa C , Yang H , DiSpirito J , Bourgeois JR , Kalyanasundaram G , Doshi I , Bilbo SD , Kopec AM
Published: April 2021

Drug and alcohol use during adolescence is common, and data in both humans and preclinical animal models clearly indicate drug exposure during adolescence increases the risk of substance use and other mental health disorders later in life. Adolescence is a period of social, emotional, and cognitive development, and is characterized by increased exploratory behavior, risk-taking, and peer-centered social interactions. These are thought to be behavioral manifestations of developmental plasticity in ‘reward’ regions of the brain. Human data indicate that adolescence is not a unitary developmental period, but rather different neural and behavioral sequelae can be observed in early vs. late adolescence. However, most studies with rodent models examine a single adolescent age compared to a mature adult age, and often only in males. Herein, we sought to determine whether the acute response to the opioid morphine would also differ across adolescence, and by sex. By quantifying c-Fos positive cells, a proxy for neural activity, at different stages during adolescence (pre-, early, mid-, and late adolescence) and in multiple reward regions (prefrontal cortex, nucleus accumbens, caudate/putamen), we determined that acute morphine can either reduce or increase c-Fos expression dependent on adolescent age, sex, and brain region. These data suggest that heterogeneity in the consequences of adolescent opioid exposure may be due to the interaction between age- and sex-specific developmental profiles of reward processing in individual brain regions. In future studies, it will be important to add age within adolescence as an independent variable to fully capture the consequences of healthy or abnormal reward-related neural development.
Virtual partition digital PCR for high precision chromosomal counting applications
Authors: Jacky Lucien , Yurk Dominic , Alvarado John , Leatham Bryan , Schwartz Jerrod , MacDonald Chris , Rajagopal Aditya
Published: April 2021

Digital PCR (dPCR) is the gold standard analytical platform for rapid high precision quantification of genomic fragments. However, current dPCR assays are generally limited to monitoring 1-2 analytes per sample, thereby limiting the platform’s ability to address some clinical applications that require the simultaneous monitoring of 20 – 50 analytes per sample. Here we present Virtual Partition dPCR (VPdPCR), a novel analysis methodology enabling the detection of 10 or more target regions per color channel using conventional dPCR hardware and workflow. Furthermore, VPdPCR enables dPCR instruments to overcome upper quantitation limits caused by partitioning error. While traditional dPCR analysis establishes a single threshold to separate negative and positive partitions, VPdPCR establishes multiple thresholds to identify the number of unique targets present in each positive droplet based on fluorescent intensity. Each physical partition is then divided into a series of virtual partitions, and the resulting increase in partition count substantially decreases partitioning error. We present both a theoretical analysis of the advantages of VPdPCR and an experimental demonstration in the form of a 20-plex assay for non-invasive fetal aneuploidy testing. This demonstration assay – tested on 432 samples contrived from sheared cell-line DNA at multiple input concentrations and simulated fractions of euploid or trisomy-21 “fetal” DNA – is analyzed using both traditional dPCR thresholding and VPdPCR. VPdPCR analysis significantly lowers variance of chromosome ratio across replicates and increases the accuracy of trisomy identification when compared to traditional dPCR, yielding >98% single-well sensitivity and specificity. VPdPCR has substantial promise for increasing the utility of dPCR in applications requiring ultra-high-precision quantitation.
Biofilm hydrophobicity in environmental isolates ofBacillus subtilis
Authors: Kalamara Margarita , Abbott James C. , MacPhee Cait E. , Stanley-Wall Nicola. R.
Published: April 2021

Biofilms are communities of bacteria that are attached to a surface and surrounded by an extracellular matrix. The extracellular matrix protects the community from stressors in the environment, making biofilms robust. The Gram-positive soil bacteriumBacillus subtilis, particularly the isolate NCIB 3610, is widely used as a model for studying biofilm formation.B. subtilisNCIB 3610 forms colony biofilms that are architecturally complex and highly hydrophobic. The hydrophobicity is linked, in part, to the localisation of the protein BslA at the surface of the biofilm, which provides the community with increased resistance to biocides. As most of our knowledge aboutB. subtilisbiofilm formation comes from one isolate, it is unclear if biofilm hydrophobicity is a widely distributed feature of the species. To address this knowledge gap, we collated a library ofB. subtilissoil isolates and acquired their whole genome sequences. We used our new isolates to examine biofilm hydrophobicity and found that, although BslA is encoded and produced by all isolates in our collection, hydrophobicity is not a universal feature ofB. subtiliscolony biofilms. To test whether the matrix exopolymer poly γ-glutamic acid could be masking hydrophobicity in our hydrophilic isolates, we constructed deletion mutants and found, contrary to our hypothesis, that the presence of poly γ-glutamic acid was not the reason behind the observed hydrophilicity. This study highlights the natural variation in the properties of biofilms formed by different isolates and the importance of using a more diverse range of isolates as representatives of a species.

Repositories

Raw sequence reads and annotated assemblies have been submitted to the European Nucleotide Archive under accession PRJEB43128.
Defects in autophagy lead to selectivein vivochanges in turnover of cytosolic and organelle proteins in Arabidopsis
Authors: Li Lei , Lee Chun Pong , Wijerathna-Yapa Akila , Broda Martyna , Otegui Marisa S. , Millar A. Harvey
Published: April 2021

Identification of autophagic protein cargo in plants by their abundance inautophagy related genes(ATG) mutants is complicated by changes in both protein synthesis and protein degradation. To detect autophagic cargo, we measured protein degradation rate in shoots and roots of Arabidopsisatg5andatg11mutant plants. These data show that less than a quarter of proteins changing in abundance are probable cargo and revealed roles of ATG11 and ATG5 in degradation of specific cytosol, chloroplast and ER-resident proteins, and a specialized role for ATG11 in degradation of proteins from mitochondria and chloroplasts. Our data support a role for autophagy in degrading glycolytic enzymes and the chaperonin containing T-complex polypeptide-1 complex. Autophagy induction by Pi limitation changed metabolic profiles and the protein synthesis and degradation rates ofatg5andatg11plants. A general decrease in the abundance of amino acids and increase in several secondary metabolites in autophagy mutants was consistent with altered catabolism and changes in energy conversion caused by reduced degradation rate of specific proteins. Combining measures of changes in protein abundance and degradation rates, we also identify ATG11 and ATG5 associated protein cargo of low Pi induced autophagy in chloroplasts and ER-resident proteins involved in secondary metabolism.

Single Sentence Summary

Protein cargo of autophagy in plants can be discovered by identifying proteins that increase in abundance and decrease in degradation rate in mutants deficient in autophagy machinery
Water Stress and Disruption of Mycorrhizae Induce Parallel Shifts in Phyllosphere Microbiome Composition
Authors: Debray Reena , Socolar Yvonne , Kaulbach Griffin , Guzman Aidee , Hernandez Catherine A. , Curley Rose , Dhond Alexander , Bowles Timothy , Koskella Britt
Published: April 2021

Water and nutrient limitation are key stressors that affect plant health and ecosystem function. These environmental factors impact both soil- and root-associated microbial communities, and systemically alter plant physiology, but it is less clear how they affect aboveground plant-microbe interactions. Through experimental manipulations in the field and growth chamber, we examined the interacting effects of irrigation, soil fertility, and root mycorrhizal associations on bacterial and fungal communities of the tomato phyllosphere (Solanum lycopersicum). Both water stress and mycorrhizal disruption reduced bacterial richness within plants, homogenized bacterial community diversity among plants, and reduced the relative abundance of dominant fungal taxa. We observed striking parallelism in the individual microbial taxa affected by irrigation and mycorrhizal associations. Given the increasingly understood role of the phyllosphere in shaping plant health and pathogen susceptibility, these results offer an additional mechanism by which belowground conditions shape plant fitness.