bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatiotemporal single-cell profiling of gastrointestinal GVHD reveals invasive and resident memory T cell states
Authors: Tkachev Victor , Kaminski James , Potter E. Lake , Furlan Scott N. , Yu Alison , Hunt Daniel J. , McGuckin Connor , Zheng Hengqi , Colonna Lucrezia , Gerdemann Ulrike , Carlson Judith , Hoffman Michelle , Olvera Joe , English Chris , Baldessari Audrey , Panoskaltsis-Mortari Angela , Watkins Benjamin , Qayed Muna , Suessmuth Yvonne , Betz Kayla , Bratrude Brandi , Langston Amelia , Horan John , Ordovas-Montanes Jose , Shalek Alex K. , Blazar Bruce R. , Roederer Mario , Kean Leslie S.
Published: July 2020

One of the central challenges in the field of allo-immunity is deciphering the mechanisms driving T cells to infiltrate and subsequently occupy target organs to cause disease. The act of CD8-dominated T cell infiltration is critical to acute graft-versus-host disease (aGVHD), wherein donor T cells become activated, tissue-infiltrating and highly cytotoxic, causing wide-spread tissue damage after allogeneic hematopoietic stem cell transplant (allo-HCT). However, in human and non-human primate studies, deconvolving the transcriptional programs of newly recruited relative to resident memory T cells in the gastrointestinal (GI) tract has remained a challenge. In this study, we combined the novel technique of Serial Intravascular Staining (SIVS) with single-cell RNA-Seq (scRNA-seq) to enable detailed dissection of the tightly connected processes by which T cells first infiltrate tissues and then establish a pathogenic tissue residency program after allo-HCT in non-human primates. Our results have enabled the creation of a spatiotemporal map of the transcriptional drivers of CD8 T cell infiltration into the primary aGVHD target-organ, the GI tract. We identify the large and small intestines as the only two sites demonstrating allo-specific, rather than lymphdepletion-driven T cell infiltration. The donor CD8 T cells that infiltrate the GI tract demonstrate a highly activated, cytotoxic phenotype while simultaneously rapidly developing canonical tissue-resident memory (TRM) protein expression and transcriptional signatures, driven by IL-15/IL-21 signaling. Moreover, by combining SIVS and transcriptomic analysis, we have been able to work backwards from this pathogenic TRMprograming, and, for the first time, identify a cluster of genes directly associated with tissue invasiveness, prominently including specific chemokines and adhesion molecules and their receptors, as well as a central cytoskeletal transcriptional node. The clinical relevance of this new tissue invasion signature was validated by its ability to discriminate the CD8 T cell transcriptome of patients with GI aGVHD. These results provide new insights into the mechanisms controlling tissue infiltration and pathogenic CD8 TRMtranscriptional programing, uncovering critical transitions in allo-immune tissue invasion and destruction.

One sentence summary

Flow cytometric and transcriptomic analysis reveals coordinated tissue-infiltration and tissue-residency programs driving gastrointestinal aGVHD.
Neural correlates of the shamanic state of consciousness
Authors: Huels Emma R , Kim Hyoungkyu , Lee UnCheol , Bel-Bahar Tarik , Colmenero Angelo , Nelson Amanda , Blain-Moraes Stefanie , Mashour George A , Harris Richard E
Published: July 2020

Despite the use of shamanism as a healing practice for several millennia, few empirical studies of the shamanic state of consciousness exist. We investigated the neural correlates of shamanic trance using high-density electroencephalography (EEG) in 24 shamanic practitioners and 24 healthy controls during rest, shamanic drumming, and classical music listening, followed by a validated assessment of altered states of consciousness. EEG data were used to assess changes in absolute power, connectivity, signal diversity, and criticality, which were correlated with assessment measures. We also compared assessment scores to those of individuals in a previous study under the influence of psychedelics. Shamanic practitioners were significantly different from controls in several domains of altered states of consciousness, with scores comparable to or exceeding that of healthy volunteers under the influence of psychedelics. Practitioners also displayed increased gamma power during drumming that positively correlated with elementary visual alterations. Furthermore, shamanic practitioners had decreased low alpha and increased low beta connectivity during drumming and classical music, and decreased neural signal diversity in the gamma band during drumming that inversely correlated with insightfulness. Finally, criticality in practitioners was increased during drumming in the low and high beta and gamma bands, with increases in the low beta band correlating with complex imagery and elementary visual alterations. These findings suggest that psychedelic drug-induced and non-pharmacologic alterations in consciousness have overlapping phenomenal traits but are distinct states of consciousness, as reflected by the unique brain-related changes during shamanic trance compared to previous literature investigating the psychedelic state.
Impact of cell-type and context-dependent regulatory variants on human immune traits
Authors: Mu Zepeng , Wei Wei , Fair Benjamin , Miao Jinlin , Zhu Ping , Li Yang I
Published: July 2020

The effects of trait-associated variants are often studied in a single relevant cell-type or context. However, for many complex traits, multiple cell-types are involved. This applies particularly to immune-related traits, for which many immune cell-types and contexts play a role. Here, we studied the impact of immune gene regulatory variants on complex traits to better understand genetic risk mediated through immune cell-types. We identified 26,271 expression quantitative trait loci (QTLs) and 23,121 splicing QTLs in 18 immune cell-types, and analyzed their overlap with trait-associated loci from 72 genome-wide association studies (GWAS). We showed that effects on RNA expression and splicing in immune cells colocalize with an average of 40.4% and 27.7% GWAS loci for immune-related and non-immune traits, respectively. Notably, we found that a large number of loci (mean: 14%) colocalize with splicing QTLs but not expression QTLs. The 60% GWAS loci without colocalization harbor genes that have lower expression levels, are less tolerant to loss-of-function mutations, and more enhancerrich than genes at colocalized loci. To further investigate the 60% GWAS loci not explained by our regulatory QTLs, we collected H3K27ac CUT&Tag data from rheumatoid arthritis (RA) and healthy controls. We found several unexplained GWAS hits lying within regions with higher H3K27ac activity in RA patients. We also observed that enrichment of RA GWAS heritability is greater in H3K27ac regions in immune cell-types from RA patients compared to healthy controls. Our study paves the way for future QTL studies to elucidate the mechanisms of as yet unexplained GWAS loci.
Raman imaging analysis of microvesicular and macrovesicular lipid droplets in non-alcoholic fatty liver disease
Authors: Minamikawa Takeo , Ichimura-Shimizu Mayuko , Takanari Hiroki , Morimoto Yuki , Shiomi Ryosuke , Tanioka Hiroki , Hase Eiji , Yasui Takeshi , Tsuneyama Koichi
Published: July 2020

Predominant evidence of non-alcoholic fatty liver disease (NAFLD) is the accumulation of excess lipids in the liver. A small group with NAFLD may have a more serious condition named non-alcoholic steatohepatitis (NASH). However, there is a lack of investigation of the accumulated lipids with spatial and molecular information. Raman microscopy has the potential to characterize molecular species and structures of lipids based on molecular vibration and can achieve high spatial resolution at the organelle level. We aim to demonstrate the feasibility of Raman microscopy for the investigation of NAFLD based on the molecular features of accumulated lipids. By applying the Raman microscopy to the liver of the NASH model mice, we succeeded in visualizing the distribution of lipid droplets (LDs) in hepatocytes. The detailed analysis of Raman spectra revealed the difference of molecular structural features of the LDs, such as the degree of saturation of lipids in the LDs. We also found that the inhomogeneous distribution of cholesterol in the LDs depending on the histology of lipid accumulation. We visualized and characterized the lipids of NASH model mice by Raman microscopy at organelle level. Our findings demonstrated that the Raman imaging analysis was feasible to characterize the NAFLD in terms of the molecular species and structures of lipids.
Magnetic Temporal Interference For Noninvasive, High-resolution, and Localized Deep Brain Stimulation: Concept Validation
Authors: Zaeimbashi Mohsen , Khalifa Adam , Dong Cunzheng , Wei Yuyi , Cash Sydney , Sun Nian
Published: July 2020

Non-invasive deep brain stimulation has been a major challenge in the field of neuroscience and brain stimulation in the past three decades. Current brain stimulation technologies suffer from such hurdles as the inability to do deep brain stimulation, poor spatial resolution, and invasiveness. Transcranial magnetic stimulation (TMS) technique, for instance, cannot target brain regions deeper than ∼2cm and has a poor spatial resolution, impacting a large area of the peripheral region and leading to various side effects. Implantable electrodes, even though effective for deep brain stimulation, are invasive and carry various drawbacks related to the surgery and site infection. In this paper, we propose a new concept that relies on temporal interference of two high- frequency magnetic fields generated by two electromagnetic coils. The neural system does not respond to each of these high-frequency magnetic fields alone because of the intrinsic low-pass filtering properties of the neural membrane. The peripheral areas of the brain are impacted only by the high-frequency magnetic fields that cannot stimulate the nerves, while the deep brain area where the two fields interfere experiences a magnetic field that contains a low-frequency envelope and therefore the nerves can be stimulated. This technique can noninvasively focus a magnetic or electric beam at any depth inside the brain with a high resolution, without impacting the peripheral regions.
Severe perinatal hydrops fetalis in genome edited pigs with a biallelic five base pair deletion of the Marfan syndrome gene, FBN1
Authors: Tsang Hiu-Gwen , Lillico Simon , Proudfoot Christopher , McCulloch Mary E. B. , Markby Greg , Trejo-Reveles Violeta , Corcoran Brendan M. , Whitelaw C. Bruce A. , MacRae Vicky E. , Summers Kim M.
Published: July 2020

This paper describes a genome editing project using CRISPR-Cas9. The objective was to create a large animal model of human Marfan syndrome by targeting the FBN1 gene of the pig, Sus scrofa, using a single guide and non-homologous end joining which was expected to create short insertion or deletion mutations at the 5’ end of the gene. The editing successfully created a five base pair deletion in exon 2 of FBN1, which was homozygous in two animals. However, the phenotype of these piglets was unexpected, since they showed none of the signs consistent with Marfan syndrome but both suffered extreme hydrops fetalis with a large amount of fluid located under the skin and in the abdomen. One of the edited piglets was stillborn and the other was euthanised at birth on welfare grounds. It is likely that this result was due to unanticipated on- or off-target mutations, possibly in the GLDN gene 3 megabases away from FBN1. This result provides more evidence for unexpected outcomes of CRISPR- Cas9 gene editing and supports the proposal that all genome edited individuals should be subjected to strategies to track the CRISPR footprint, such as whole genome sequencing, before being used for further experimentation or in clinical applications.
Fibroblast fusion to the muscle fiber regulates myotendinous junction formation
Authors: Yaseen-Badarneh Wesal , Kraft-Sheleg Ortal , Zaffryar-Eilot Shelly , Melamed Shay , Sun Chengyi , Millay Douglas P. , Hasson Peleg
Published: July 2020

Vertebrate muscles and tendons are derived from distinct embryonic origins yet they must interact in order to facilitate muscle contraction and body movements. How robust muscle tendon junctions (MTJs) form to be able to withstand contraction forces is still not understood. Using techniques at a single cell resolution we reexamined the classical view of distinct identities for the tissues composing the musculoskeletal system. We identified fibroblasts that have switched on a myogenic program and demonstrate these dual identity cells fuse into the developing muscle fibers along the MTJs facilitating the introduction of fibroblast-specific transcripts into the elongating myofibers. We suggest this mechanism resulting in a hybrid muscle fiber, primarily along the fiber tips, enables a smooth transition from muscle fiber characteristics towards tendon features essential for forming robust MTJs. We propose that dual characteristics of junctional cells could be a common mechanism for generating stable interactions between tissues throughout the musculoskeletal system.
Cell biological studies of ethanologenic bacteriumZymomonas mobilis
Authors: Fuchino Katsuya , Chan Helena , Hwang Ling Chin , Bruheim Per
Published: July 2020

AlphaproteobacteriumZymomonas mobilisexhibits extreme ethanologenic physiology, making this species a promising biofuel producer. Numerous studies have investigated its biology relevant to industrial applications and mostly at the population level. However, the organization of single cells in this industrially important, polyploid species has been largely uncharacterized.

In the present study, we characterized basic cellular behaviour ofZ. mobilisstrain Zm6 at a single cell level. We observed that growingZ. mobiliscells often divided at non mid-cell position, which contributed to variant cell size at birth. Yet, the cell size variance was regulated by a modulation of cell cycle span, mediated by a correlation of bacterial tubulin homologue FtsZ-ring accumulation with cell growth. TheZ. mobilisculture also exhibited heterogeneous cellular DNA contents among individual cells, which might have been caused by asynchronous replication of chromosome that was not coordinated to cell growth. Furthermore, slightly angled divisions might have rendered temporary curvatures of attachedZ. mobiliscells. Overall, the presented study uncovered a novel bacterial cell organization inZ. mobilis, the metabolism of which is not favoured for biosynthesis to build biomass.

Importance

With increasing environmental concerns about the exhausting use of fossil fuels, a development of sustainable biofuel production platform has been attracting significant public attention. EthanologenicZ. mobilisspecies are endowed with an efficient ethanol-fermentation capacity that surpass, in several aspects, that of the baker’s yeastSaccharomyces cerevisiae, the most used microorganism for ethanol productions. For a development ofZ. mobilisculture-based biorefinery, an investigation of its uncharacterized cell biology is important, because bacterial cellular organization and metabolism are closely associated with each other in a single cell compartment.

In addition, the current work highlights that polyploid bacteriumZ. mobilisexhibits a distinctive mode of bacterial cell organization, reflecting its unique metabolism that do not prioritize incorporation of nutrients to cell growth. Thus, another significance of presented work is to advance our general understanding in the diversity of bacterial cell architecture.
SLALOM: A Simple and Rapid Method for Enzymatic Synthesis of CRISPR-Cas9 sgRNA Libraries
Authors: Yates Joshua D , Russell Robert C , Yost H Joseph , Hill Jonathon T
Published: July 2020

CRISPR-Cas9 sgRNA libraries have transformed functional genetic screening and have enabled innovative CRISPR-based methods, such as the visualization of chromatin dynamics in living cells. These libraries have the potential to be applied to a vast number of biological systems and aid in the development of new technologies, but their synthesis is hindered by the cost, time requirements, and technical difficulty of current sgRNA library generation methods. Here, we describe SLALOM—a rapid enzymatic method for generating robust, variant-matched sgRNA libraries from any source of DNA in under 3 hours. This method utilizes a custom sgRNA scaffold sequence and a novel method for detaching oligonucleotides from solid supports using a strand displacing polymerase. Using this method, we have constructed libraries targeting theE. coligenome and the transcriptome of developing zebrafish hearts, demonstrating its potential to expand the reach of CRISPR technology and facilitate methods requiring custom sgRNA libraries.
Incident psychopharmacological treatment and psychiatric hospital contact in individuals with newly developed type 2 diabetes
Authors: Rohde Christopher , Schmitz Norbert , Thomsen Reimar W. , Østergaard Søren D.
Published: July 2020

Objective

To investigate the association between newly developed type 2 diabetes (T2D) and incident psychopharmacological treatment and psychiatric hospital contact.

Methods

We identified all individuals from the Central- and Northern Denmark Regions with newly developed T2D (defined by the first HbA1c measurement >6.5%) from 2000-2016 and up to five age and sex matched individuals without T2D (controls). Those having received psychopharmacological treatment or having had a psychiatric hospital contact in the five years prior to the onset of T2D were excluded. For this cohort, we first assessed the incidence of psychopharmacological treatment and psychiatric hospital contact among individuals with T2D and controls, respectively. Secondly, we compared the incidence of psychopharmacological/psychiatric hospital contact among individuals with T2D to propensity score matched controls. Finally, we assessed which baseline (T2D onset) characteristics that were associated with subsequent psychopharmacological treatment and psychiatric hospital contact.

Results

We identified 56,640 individuals with newly developed T2D and 315,694 controls. A total of 8.3% of the individuals with T2D initiated psychopharmacological treatment within the 2 years following onset compared to 4.6% among the age and sex matched controls. Individuals with T2D were at increased risk of initiating psychopharmacological treatment compared to the propensity score matched controls (HR=1.51, 95% CI=1.43-1.59), whereas their risk of psychiatric hospital contact was not increased to the same extent (HR=1.14, 95% CI=0.98-1.32). Older age, somatic comorbidity, and being divorced/widowed was associated with both psychopharmacological treatment and psychiatric hospital contact following T2D.

Conclusion

Individuals with T2D are at elevated risk of requiring psychopharmacological treatment.

Significant outcomes

8.3% of the individuals with T2D initiated psychopharmacological treatment within the 2 years following onset compared to 4.6% among the age and sex matched controls

Individuals with newly developed T2D were at increased risk of initiating psychopharmacological treatment and of having psychiatric hospital contact compared to propensity score matched controls.

Risk factors for psychopharmacological treatment/psychiatric hospital contact following development of T2D include older age, somatic comorbidity and being divorced or widowed.

Limitations

Identification of T2D (a HbA1c level >6.5%) itself might lead to the identification of mental illness and thereby psychopharmacological treatment initiation/psychiatric hospital contact.

A proportion of the individuals with T2D will likely have initiated treatment with an antidepressant due to neuropathic pain developed as a complication to T2D
Mode and dynamics of vanA-type vancomycin-resistance dissemination in Dutch hospitals
Authors: Arredondo-Alonso Sergio , Top Janetta , Corander Jukka , Willems Rob J L , Schürch Anita C
Published: July 2020

Background

Enterococcus faecium is a commensal of the gastrointestinal tract of animals and humans but also a causative agent of hospital-acquired infections. Resistance against glycopeptides and especially to vancomycin, a first-line antibiotic to treat infections with multidrug-resistant Gram-positive pathogens, has motivated the inclusion of E. faecium in the WHO global priority list. Vancomycin resistance can be conferred by the vanA gene cluster on the transposon Tn1546, which is frequently present in plasmids. The vanA gene cluster can be disseminated clonally but also horizontally either by plasmid dissemination or Tn1546 transposition between different genomic locations. Here, we reconstructed all nested genetic elements (clone, plasmid, transposon) to study how the dissemination of vanA-type vancomycin resistance occurred in Dutch hospitals (2012-2015).

Methods

We performed a retrospective study of the genomic epidemiology of 309 vancomycin-resistant E. faecium (VRE) isolates across 32 Dutch hospitals (2012-2015). Genomic information regarding clonality and Tn1546 characterisation was extracted using hierBAPS sequence clusters (SC) and TETyper, respectively. Plasmids were predicted using gplas in combination with a network approach based on shared k-mer content. This allowed determining all nested genomic elements (clone, plasmid and transposon) involved in the dissemination of the vanA gene cluster. Next, we conducted an “all vs. all” pairwise comparison between isolates sharinga potential epidemiological link to elucidate whether clonal, plasmid or Tn1546 spread accounted for the dissemination of vanA resistance.

Results

The 309 VRE isolates belonged to 18 different SCs of which SC13 (n = 102, 33%), SC17 (n = 52, 16.8%) and SC18 (n = 42, 13.6%) were predominant. We identified seven different plasmid types bearing the vanA gene cluster, four of which were highly similar (identity ∼99%, coverage∼84%) to previously described complete plasmid sequences. We estimated that clonal dissemination contributed most (∼45%) to the spread of vancomycin-resistance in Dutch hospitals, followed by Tn1546 mobilisation (∼12%) and plasmid dissemination (∼6%).

Conclusions

The dissemination of the vanA gene cluster in Dutch hospitals between 2012 and 2015 was dominated by clonal spread. However, we also identified outbreak settings with high frequencies of Tn1546 transposition and/or plasmid dissemination in which the spread of resistance was mainly driven by horizontal gene transfer (HGT). This study demonstrates the feasibility of distinguishing between modes of dissemination with short-read data and provides one of the first quantitative assessments to estimate the relative contribution of nested genomic elements in the dissemination of vanA-type vancomycin resistance cluster.
Role of the HIV-sensitive protection services in mitigating the challenges and vulnerability of the children affected by HIV/AIDS in Bangladesh: a qualitative study
Authors: Afroz Tahmina , Camellia Suborna , Oyewale Tajudeen , Uddin M. Ziya , Mahmud Ilias
Published: July 2020

Children are particularly vulnerable to the consequences of HIV/AIDS. HIV-sensitive protection services (HSPS) can reduce vulnerability by increasing access to HIV/AIDS prevention, treatment, and basic social protection services. Few organizations in Bangladesh offer these services to children affected by HIV/AIDS (CABA). This paper reports on the challenges faced by CABA due to their or their parents’ HIV/AIDS status and the role of HSPS on mitigating these challenges. We did fifteen in-depth interviews with purposively chosen CABA, and seventeen in-depth interviews with purposively chosen caregivers of CABA. We found, CABA faced significant challenges such as poverty, emotional stress, stigma in their lives. Gender norms increased these vulnerabilities especially among women. HSPS services helped through motivating parents or guardians to send their children to school and thus reduce child marriage and child labour. Also, helped in improving children’s self-esteem with improving relationships between children and parents. Though the services were available, accessibility was limited due to distance, roundtrip cost, poor health conditions of the parents and gender issues.HSPS are effective in improving children’s well-being. Continued and increased support to access services including financial assistance, psychosocial counselling, and community sensitization activities is recommended.
Overcoming data gaps in life course epidemiology by matching across cohorts
Authors: Kezios Katrina L. , Zimmerman Scott , Rudolph Kara , Calonico Sebastian , Al-Hazzouri Adina Zeki , Glymour M. Maria
Published: July 2020

Lifecourse epidemiology is hampered by the absence of studies with exposures and outcomes measured at different life stages. We describe when the effect of an exposure (A) on an outcome (Y) in a target population is identifiable in a combined (“synthetic”) cohort created by pooling an early-life cohort including exposure measures with a late-life cohort including outcome measures. We enumerate the causal assumptions needed for unbiased effect estimation in the synthetic cohort and illustrate by simulating target populations under four causal models. From each population, we drew hypothetical early- and late-life cohorts and created a synthetic cohort by matching individuals from the two cohorts based on mediators and/or confounders. We compared bias when estimating the effect of A on Y in the synthetic cohort, varying which matching variables were available, the match ratio, and the distance matching criterion. When the set of matching variables includes all variables d-connecting exposure and outcome (i.e., variables blocking all back and front door pathways), the synthetic cohort yields unbiased effect estimates. Methods based on merging cohorts provide opportunities to hasten the evaluation of early- and mid-life determinants of late life health, but rely on available measures of both confounders and mediators.
Irradiance modulates thermal niche in a previously undescribed low-light and cold-adapted nano-diatom
Authors: Kling Joshua D. , Kelly Kyla J. , Pei Sophia , Rynearson Tatiana A. , Hutchins David A.
Published: July 2020

Diatoms have well-recognized roles in fixing and exporting carbon and supplying energy to marine ecosystems, but only recently have we begun to explore the diversity and importance of nano- and pico-diatoms. Here we describe a small (~5 μm) diatom from the genusChaetocerosIsolated from a wintertime temperate estuary (2° C, Narragansett Bay, RI), with a unique obligate specialization for low-light environments (< 120 μmol photons m-2sec-1). This diatom exhibits a striking interaction between irradiance and thermal responses whereby as temperatures increase, so does its susceptibility to light stress. Historical 18S rRNA amplicon data from our study site show this isolate was abundant throughout a six-year period, and its presence strongly correlates with winter and early spring months when light and temperature are low. Two ASVs matching this isolate had a circumpolar distribution in Tara Polar Ocean Circle samples, indicating its unusual light and temperature requirements are adaptations to life in a cold, dark environment. We expect this isolate’s low light, psychrophilic niche to shrink as future warming-induced stratification increases both light and temperature levels experienced by high latitude marine phytoplankton.
Dynamic multi-OMICs of glioblastoma reveal sensitivity to neddylation inhibition dependent on nuclear PTEN and DNA replication pathways: Nuclear PTEN mediates MLN4924 sensitivity in GBM
Authors: Ferdosi S R. , Taylor B , Lee M , Tang N , Peng S , Bybee R , Reid G , Hartman L , Garcia-Mansfield K , Sharma R , Pirrotte P , Ma Jianhui , Parisian Alison D , Furnari F , Dhruv HD , Berens ME
Published: July 2020

Withdrawal Statement

The authors have withdrawn their manuscript because the reported synergy of TOP2A inhibitors plus MLN4924 proved to be untrue (not reproducible). Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author (mberens@tgen.org).
Neural representation of abstract task structure during generalization
Authors: Vaidya Avinash R. , Jones Henry M. , Castillo Johanny , Badre David
Published: July 2020

Cognitive models in psychology and neuroscience widely assume that the human brain maintains an abstract representation of tasks. This assumption is fundamental to theories explaining how we learn quickly, think creatively, and act flexibly. However, neural evidence for a verifiably generative abstract task representation has been lacking. Here, we report an experimental paradigm that requires forming such a representation to act adaptively in novel conditions without feedback. Using functional magnetic resonance imaging, we observed that abstract task structure was represented within left mid-lateral prefrontal cortex, bilateral precuneus and inferior parietal cortex. These results provide support for the neural instantiation of the long-supposed abstract task representation in a setting where we can verify its influence. Such a representation can afford massive expansions of behavioral flexibility without additional experience, a vital characteristic of human cognition.
Mycorrhizal symbiosis alleviates plant water deficit within and across plant generations via plasticity
Authors: Puy Javier , Carmona Carlos P. , Hiiesalu Inga , Öpik Maarja , de Bello Francesco , Moora Mari
Published: July 2020

Phenotypic plasticity is essential for organisms to adapt to local ecological conditions. It is expected that mutualistic interactions, such as arbuscular mycorrhizal (AM) symbiosis, mediate plant phenotypic plasticity, although it is not clear to what extent this plasticity may be heritable (i.e., transgenerational plasticity).

We tested for plant plasticity within- and across-generations in response to AM symbiosis and varying water availability in a full factorial experiment over two generations, using a genetically uniform line of a perennial apomictic herb,Taraxacum brevicorniculatum. We examined changes in phenotype, performance, and AM fungal colonization of the offspring throughout plant development.

AM symbiosis and water availability triggered phenotypic changes during the life cycle of plants. Additionally, both triggered adaptive transgenerational effects, especially detectable during the juvenile stage of the offspring. Water deficit and absence of AM fungi caused concordant plant phenotypic modifications towards a “stress-coping phenotype”, both within- and across-generations. AM fungal colonization of offspring was also affected by the parental environment.

AM symbiosis can trigger within-generation and transgenerational plasticity in terms of functional traits related to resource-use acquisition and AM fungal colonization. Thus, transgenerational effects of mycorrhizal symbiosis are not limited to plant fitness, but also improve plants’ ability to cope with environmental stress.
A spatially resolved single cell atlas of human gastrulation
Authors: Tyser Richard C.V. , Mahammadov Elmir , Nakanoh Shota , Vallier Ludovic , Scialdone Antonio , Srinivas Shankar
Published: July 2020

Gastrulation is the fundamental process during the embryogenesis of all multicellular animals through which the basic body plan is first laid down. It is pivotal in generating cellular diversity coordinated with spatial patterning. Gastrulation in humans occurs in the third week following fertilization. Our understanding of this process in humans is extremely limited, and based almost entirely on experimental models. Here, we characterize in a spatially resolved manner the single cell transcriptional profile of an entire gastrulating human embryo approximately 16 to 19 days after fertilization. We used these data to provide the first unequivocal demonstration that human embryonic stem cells represent the early post implantation epiblast. We identified both primordial germ cells and red blood cells, which had never been characterized so early during human development. Comparison with mouse gastrula transcriptomes revealed many commonalities between the human and mouse but also several key differences, particularly in FGF signaling, that we validated experimentally. This unique dataset offers a unique glimpse into a central but generally inaccessible stage of our development, provides new context for interpreting experiments in other model systems and represents a valuable resource for guiding directed differentiation of human cellsin vitro.
Overlapping and non-overlapping roles of the class-I histone deacetylase-1 corepressors, LET-418, SIN-3, and SPR-1 inCaenorhabditis elegansembryonic development
Authors: Kubota Yukihiro , Ohnishi Yuto , Hamasaki Tasuku , Yasui Gen , Ota Natsumi , Kitagawa Hiromu , Esaki Arashi , Fahmi Muhamad , Ito Masahiro
Published: July 2020

Histone deacetylases (HDACs) are divided into four classes. Class-I HDAC, HDAC-1 forms three types of complexes, namely the Nucleosome Remodeling Deacetylase complex, the Sin3 complex, and the CoREST complex, with specific corepressor component Mi2/CHD-3, Sin3, and RCOR1 in human, respectively. The functions of these HDAC-1 complexes are regulated by their corepressors, however, their exact mechanistic roles in several biological processes remain unexplored, such as in embryonic development. Here, we report that each of the corepressors, LET-418, SIN-3, and SPR-1, the homologous of Mi2, Sin3, and RCOR1, respectively, were expressed throughoutCaenorhabditis elegansembryonic development and served essential roles in the process. Moreover, genetic analysis suggested that three pathways (i.e., LET-418– SIN-3–SPR-1, SIN-3–SPR-1, and LET-418) participated in embryonic development. Our terminal-phenotype observations of single mutants of each corepressor implied that LET-418, SIN-3, and SPR-1 played similar roles in promoting advancement to the middle and late embryonic stages. Genome-wide comparative-transcriptome analysis indicated that 47.5% and 42.3% of genes were commonly increased and decreased insin-3andspr-1mutants, respectively. These results suggest that among the three pathways studied, the SIN-3–SPR-1 pathway mainly serves to regulate embryonic development. Comparative-Gene Ontology analysis indicated that these three pathways played overlapping and distinct roles in regulatingC. elegansembryonic development.
Genome-wide binding analysis of 195 DNA Binding Proteins reveals “reservoir” promoters and human specific SVA-repeat family regulation
Authors: Shehata Soraya , Spradlin Savannah , Swearingen Alison , Wheeler Graycen , Das Arpan , Corbet Giulia , Nebenfuehr Benjamin , Ahrens Daniel , Tauber Devin , Lennon Shelby , Choi Kevin , Huynh Thao , Weiser Tom , Schneider Kristen , Bradshaw Michael , Lai Maria , Basken Joel , Read Tim , Demasi Jon , Hynes-Grace Matt , Timmons Dan , Smallegan Michael , Rinn John L.
Published: July 2020

A key aspect in defining cell state is the complex choreography of DNA binding events in a given cell type, which in turn establishes a cell-specific gene-expression program. In the past two decades since the sequencing of the human genome there has been a deluge of genome-wide experiments which have measured gene-expression and DNA binding events across numerous cell-types and tissues. Here we re-analyze ENCODE data in a highly reproducible manner by utilizing standardized analysis pipelines, containerization, and literate programming with Rmarkdown. Our approach validated many findings from previous independent studies, underscoring the importance of ENCODE’s goals in providing these reproducible data resources. This approach also revealed several new findings: (i) 1,362 promoters, termed ‘reservoirs,’ have up to 111 different DNA binding-proteins localized on one promoter yet do not have any expression of steady-state RNA (ii) The human specific SVA repeat element may have been co-opted for enhancer regulation. Collectively, this study performed by the students of a CU Boulder computational biology class (BCHM 5631 – Spring 2020) demonstrates the value of reproducible findings and how resources like ENCODE that prioritize data standards can foster new findings with existing data in a didactic environment.
Delta/Theta band EEG activity shapes the rhythmic perceptual sampling of auditory scenes
Authors: Kubetschek Cora , Kayser Christoph
Published: July 2020

Many studies speak in favor of a rhythmic mode of listening, by which the encoding of acoustic information is structured by rhythmic neural processes at the time scale of about 1 to 4 Hz. Indeed, psychophysical data suggest that humans sample acoustic information in extended soundscapes not uniformly, but weigh the evidence at different moments for their perceptual decision at the time scale of about 2 Hz. We here test the critical prediction that such rhythmic perceptual sampling is directly related to the state of ongoing brain activity prior to the stimulus. Human participants judged the direction of frequency sweeps in 1.2 s long soundscapes while their EEG was recorded. Computing the perceptual weights attributed to different epochs within these soundscapes contingent on the phase or power of pre-stimulus oscillatory EEG activity revealed a direct link between the 4Hz EEG phase and power prior to the stimulus and the phase of the rhythmic component of these perceptual weights. Hence, the temporal pattern by which the acoustic information is sampled over time for behavior is directly related to pre-stimulus brain activity in the delta/theta band. These results close a gap in the mechanistic picture linking ongoing delta band activity with their role in shaping the segmentation and perceptual influence of subsequent acoustic information.
Lactate promotes cardiomyocyte dedifferentiation through metabolic reprogramming
Authors: Ordoño Jesús , Pérez-Amodio Soledad , Ball Kristen , Aguirre Aitor , Engel Elisabeth
Published: July 2020

Cardiomyocytes undergo different metabolic changes during development and differentiation crucial for their maturation and adult function, such as contraction, growth and survival. Alterations of cardiac metabolism have been associated with multiple disease states and pathological hypertrophy. The shift in substrate preference can impair the stress response, but it may also have a role in cell growth and survival. Here, we evaluated the response of cardiomyocytes to the presence of exogenous lactate, an important metabolite for the fetal heart and cardiogenesis. Lactate-exposed mouse primary cardiomyocytes and human iPSC-derived cardiomyocytes quickly acquired a characteristic dedifferentiated phenotype, with enhanced proliferative capacity as determined by an increased expression of cell cycle (Ki67) and cytokinesis (Aurora-B) effectors. This effect was specific to cardiomyocytes and did not affect other heart cell populations (e.g. cardiac fibroblasts). Nevertheless, cardiac fibroblasts exposed to lactate promoted a pro-regenerative environment through the modulation of the release of cytokines (such as Fas, IL-13 or SDF1a). We characterized lactate-induced cardiomyocyte dedifferentiation through RNA-sequencing and gene expression analysis and identified increased expression of BMP10 (a TGFβ family protein involved in embryonic cardiomyocyte proliferation and stemness) and proteins associated to cell fate regulation (LIN28, TCIM) together with downregulation of cardiac maturation genes (GRIK1, DGKK). Bottom-up analysis suggested the phenotype promoted by lactate could be related to the activation of hypoxia signaling pathways. This finding indicated that, indeed, lactate may be a key player of hypoxic regenerative responses in the heart, as it usually accumulates as a result of glycolysis. In addition,ex vivoneonatal heart culture showed prolonged beating function and cardiac tissue integrity when culture media was supplemented with lactate. Thus, we conclude that lactate enhances cardiac proliferation by reprogramming cardiomyocytes towards a dedifferentiated stem cell-like state, supporting the notion that modulation of the metabolic microenvironment might be a powerful novel approach for promoting cardiac regeneration and tissue engineering applications.
Numerical simulation of the two-locus Wright-Fisher stochastic differential equation with application to approximating transition probability densities
Authors: He Zhangyi , Beaumont Mark , Yu Feng
Published: July 2020

Over the past decade there has been an increasing focus on the application of the Wright-Fisher diffusion to the inference of natural selection from genetic time series. A key ingredient for modelling the trajectory of gene frequencies through the Wright-Fisher diffusion is its transition probability density function. Recent advances in DNA sequencing techniques have made it possible to monitor genomes in great detail over time, which presents opportunities for investigating natural selection while accounting for genetic recombination and local linkage. However, most existing methods for computing the transition probability density function of the Wright-Fisher diffusion are only applicable to one-locus problems. To address two-locus problems, in this work we propose a novel numerical scheme for the Wright-Fisher stochastic differential equation of population dynamics under natural selection at two linked loci. Our key innovation is that we reformulate the stochastic differential equation in a closed form that is amenable to simulation, which enables us to avoid boundary issues and reduce computational costs. We also propose an adaptive importance sampling approach based on the proposal introduced by Fearnhead (2008) for computing the transition probability density of the Wright-Fisher diffusion between any two observed states. We show through extensive simulation studies that our approach can achieve comparable performance to the method of Fearnhead (2008) but can avoid manually tuning the parameterρto deliver superior performance for different observed states.
Intranasal Vaccination with a Lentiviral Vector Strongly Protects against SARS-CoV-2 in Mouse and Golden Hamster Preclinical Models
Authors: Ku Min-Wen , Bourgine Maryline , Authié Pierre , Lopez Jodie , Nemirov Kirill , Moncoq Fanny , Noirat Amandine , Vesin Benjamin , Nevo Fabien , Blanc Catherine , Souque Philippe , Tabbal Houda , Simon Emeline , Le Dudal Marine , Guinet Françoise , Fiette Laurence , Mouquet Hugo , Anna François , Martin Annette , Escriou Nicolas , Majlessi Laleh , Charneau Pierre
Published: July 2020

To develop a vaccine candidate against COVID-19, we generated a Lentiviral Vector (LV), eliciting neutralizing antibodies against the Spike glycoprotein of SARS-CoV-2. Systemic vaccination by this vector in mice, in which the expression of the SARS-CoV-2 receptor hACE2 has been induced by transduction of respiratory tract cells by an adenoviral vector, conferred only partial protection, despite an intense serum neutralizing activity. However, targeting the immune response to the respiratory tract through an intranasal boost with this LV resulted in > 3 log10 decrease in the lung viral loads and avoided local inflammation. Moreover, both integrative and non-integrative LV platforms displayed a strong vaccine efficacy and inhibited lung deleterious injury in golden hamsters, which are naturally permissive to SARS-CoV-2 replication and restitute the human COVID-19 physiopathology. Our results provide evidence of marked prophylactic effects of the LV-based vaccination against SARS-CoV-2 and designate the intranasal immunization as a powerful approach against COVID-19.

Highlights

A lentiviral vector encoding for Spike predicts a promising COVID-19 vaccine

Targeting the immune response to the upper respiratory tract is key to protection

Intranasal vaccination induces protective mucosal immunity against SARS-CoV-2

Lung anti-Spike IgA responses correlate with protection and reduced inflammation
Effects of early life stress on bone homeostasis in mice and humans
Authors: Wuertz-Kozak Karin , Roszkowski Martin , Cambria Elena , Block Andrea , Kuhn Gisela A. , Abele Thea , Hitzl Wolfgang , Drießlein David , Müller Ralph , Rapp Michael A. , Mansuy Isabelle M. , Peters Eva M. J. , Wippert Pia M.
Published: July 2020

Bone pathology is frequent in stressed individuals. A comprehensive examination of mechanisms linking life stress, depression and disturbed bone homeostasis is missing. In this translational study, mice exposed to early life stress (MSUS) were examined on bone microarchitecture (μCT), metabolism (qPCR), and neuronal stress mediator expression (qPCR) and contrasted with a sample of depressive patients with or without early life stress by analyzing bone mineral density [BMD] (DXA) and metabolic changes in serum (osteocalcin, PINP, CTX-I). MSUS mice showed a significant decrease in NGF, NPYR1, VIPR1 and TACR1 expression, higher innervation density in bone and increased serum levels of CTX-I, suggesting a milieu in favor of catabolic bone turnover. MSUS mice had a significantly lower body weight compared to control mice, and this caused minor effects on bone micro-CT. Depressive patients with experiences of childhood neglect also showed a catabolic pattern. A significant reduction in BMD was observed in depressive patients with childhood abuse and stressful life events during childhood. Therefore, future studies on prevention and treatment strategies for both mental and bone disease should consider early life stress as a risk factor for bone pathologies.
TRPC5-CaV3 complex mediates Leptin-induced excitability in hypothalamic neurons
Authors: Perissinotti Paula P. , Martínez-Hernández Elizabeth , Piedras-Rentería Erika S.
Published: July 2020

Leptin regulates hypothalamic POMC+(pro-opiomelanocortin) neurons by inducing TRPC (Transient Receptor Potential Cation) channel-mediate membrane depolarization. Here we assessed the role of T-type channels on POMC neuron excitability and leptin-induced depolarizationin vitro. We demonstrate T-type currents are indispensable for both processes, as treatment with NNC-55-0396 prevented the membrane depolarization and rheobase changes induced by leptin in cultured mouse POMC neurons. Furthermore, we demonstrate TRPC1/C5 channels and CaV3.1 and CaV3.2 channels co-exist in complex. The functional relevance of this complex was corroborated using intracellular Ca2+chelators; intracellular BAPTA (but not EGTA) application was sufficient to preclude POMC neuron excitability by preventing leptin-induced calcium influx through TRPC channels and T-type channel function.

We conclude T-type channels are integral in POMC neuron excitability. Leptin activation of TRPC channels existing in a macromolecular complex with T-type channels recruits the latter by locally-induced membrane depolarization, further depolarizing POMC neurons, triggering action potentials and excitability.
The TAZ2 domain of CBP/p300 directs acetylation towards H3K27 within chromatin
Authors: Sheahan Thomas W. , Major Viktoria , Webb Kimberly M. , Bryan Elana , Voigt Philipp
Published: July 2020

The closely related acetyltransferases CBP and p300 are key regulators of gene expression in metazoans. CBP/p300 acetylate several specific lysine residues within nucleosomes, including histone H3 lysine 27 (H3K27), a hallmark of active enhancers and promoters. However, it has remained largely unclear how specificity of CBP/p300 towards H3K27 is achieved. Here we show that the TAZ2 domain of CBP is required for efficient acetylation of H3K27, while curbing activity towards other lysine residues within nucleosomes. We find that TAZ2 is a sequence-independent DNA binding module, promoting interaction between CBP and nucleosomes, thereby enhancing enzymatic activity and regulating substrate specificity of CBP. TAZ2 is further required to stabilize CBP binding to chromatin in mouse embryonic stem cells, facilitating specificity towards H3K27 and modulating gene expression. These findings reveal a crucial role of TAZ2 in regulating H3K27ac, while highlighting the importance of correct site-specific acetylation for proper regulation of gene expression.