bluuebunny/crossref_metadata_2025 huggingface dataset:
The intergenerational transmission of educational attainment: A closer look at the (interrelated) roles of paternal involvement and genetic inheritance
Authors: Verweij Renske , Keizer Renske
Published: April 2022

Numerous studies have documented a strong intergenerational transmission of educational attainment. In explaining this transmission, separate fields of research have studied separate mechanisms. To obtain a more complete understanding, the current study integrates insights from the fields of behavioural sciences and genetics and examines the extent to which factors from each field are unique underlying mechanisms, correlate with each other, and/or act as important confounders in the intergenerational transmission of educational attainment. Specifically, we focus on paternal involvement as our behavioural indicator and children’s polygenic score (PGS) for education as our genetic indicator and assess the role that fathers play in the intergenerational transmission of educational attainment. To answer our research questions, we use rich data from The National Longitudinal Study of Adolescent to Adult Health (n=4,579). Firstly, results from our mediation analyses showed that about 4 per cent of the effect of fathers’ educational attainment on children’s educational attainment is explained by paternal involvement, whereas a much larger share, 21 per cent, is explained by children’s education PGS. Secondly, our results showed that these genetic and behavioural influences are significantly correlated to each other. Thirdly, we found support for genetic confounding, as adding children’s education PGS to the model reduced the effect of paternal involvement by 11 per cent. Fourthly, evidence for social confounding was almost negligible (a reduction of half a per cent of the genetic effect). Our findings highlight the importance of integrating insights and data from multiple disciplines in understanding the mechanisms underlying the intergenerational transmission of inequality, as our study reveals that behavioural and genetic influences overlap, correlate, and confound each other as mechanisms underlying this transmission.
Deposit-feeding worms control subsurface ecosystem functioning in intertidal sediment with strong physical forcing
Authors: Deng Longhui , Meile Christof , Fiskal Annika , Bölsterli Damian , Han Xingguo , Gajendra Niroshan , Dubois Nathalie , Bernasconi Stefano M. , Lever Mark A.
Published: April 2022

Intertidal sands are global hotspots of terrestrial and marine carbon cycling with strong hydrodynamic forcing by waves and tides and high macrofaunal activity. Yet, the relative importance of hydrodynamics and macrofauna in controlling these ecosystems remains unclear. Here we compare bacterial, archaeal, and eukaryotic communities in upper intertidal sands dominated by subsurface deposit-feeding worms (Abarenicola pacifica) to adjacent worm-free areas. We show that hydrodynamic forcing controls organismal assemblages in surface sediments, while in deeper layers selective feeding by worms on fine, algae-rich particles strongly decreases the abundance and richness of all three domains. In these deeper layers, bacterial and eukaryotic network connectivity decreases, while percentages of taxa involved in degradation of refractory organic macrostructures, oxidative nitrogen and sulfur cycling, and macrofaunal symbioses, increase. Our findings reveal macrofaunal activity as the key driver of ecosystem functioning and carbon cycling in intertidal sands below the mainly physically controlled surface layer.

Significance Statement

Hydrodynamics and bioturbation are the main forces controlling chemical exchanges between sediment and seawater in coastal environments. However, little is known about the relative impact of both processes on sediment biological communities. We show that intertidal sand ecosystems dominated by lugworms can be divided into vertically distinct hydrodynamically and biologically controlled layers. Hydrodynamic forcing controls biological communities in surface layers by regulating organic carbon and electron acceptor inputs. By contrast, lugworms structure subsurface ecosystems through the selective consumption of fine particles, which diminishes microbial and eukaryotic populations and weakens ecological networks, while promoting the burial of, mostly terrestrial, macrodetritus. Our study demonstrates that globally distributed marine invertebrates control intertidal sand ecosystems below the physically controlled surface layer.
Stabilizing brain-computer interfaces through alignment of latent dynamics
Authors: Karpowicz Brianna M. , Ali Yahia H. , Wimalasena Lahiru N. , Sedler Andrew R. , Keshtkaran Mohammad Reza , Bodkin Kevin , Ma Xuan , Miller Lee E. , Pandarinath Chethan
Published: April 2022

Intracortical brain-computer interfaces (iBCIs) restore motor function to people with paralysis by translating brain activity into control signals for external devices. In current iBCIs, instabilities at the neural interface result in a degradation of decoding performance, which necessitates frequent supervised recalibration using new labeled data. One potential solution is to use the latent manifold structure that underlies neural population activity to facilitate a stable mapping between brain activity and behavior. Recent efforts using unsupervised approaches have improved iBCI stability using this principle; however, existing methods treat each time step as an independent sample and do not account for latent dynamics. Dynamics have been used to enable high performance prediction of movement intention, and may also help improve stabilization. Here, we present a platform for Nonlinear Manifold Alignment with Dynamics (NoMAD), which stabilizes iBCI decoding using recurrent neural network models of dynamics. NoMAD uses unsupervised distribution alignment to update the mapping of nonstationary neural data to a consistent set of neural dynamics, thereby providing stable input to the iBCI decoder. In applications to data from monkey motor cortex collected during motor tasks, NoMAD enables accurate behavioral decoding with unparalleled stability over weeks-to months-long timescales without any supervised recalibration.
A transcriptional network required for Toxoplasma gondii tissue cyst formation is dispensable for long-term persistence
Authors: Borrelli Sarah Sokol , Reilly Sarah M. , Sharp Katherine G. , Cabo Leah F. , Alrubaye Hisham S. , Di Genova Bruno Martorelli , Boyle Jon P.
Published: April 2022

Cyst formation is a key feature of the T. gondii life cycle but the genetic networks that drive this process are not yet fully characterized. To identify new components of this network, we compared T. gondii to its nearest extant relative Hammondia hammondi given the critical differences between these species in the timing and efficiency of cyst formation. Using transcriptional data from critical developmental and pH exposure time points from both species, we identified the gene TGVEG_311100, which we named Regulator of Cystogenesis 1 (ROCY1), as being both necessary and sufficient for cyst formation in T. gondii. Compared to WT parasites, TGVEGΔROCY1 parasites formed significantly fewer tissue cysts in response to alkaline pH stress in vitro and cysts were nearly undetectable in mouse brains for up to 9 weeks post-infection. Overexpression of tagged ROCY1 in WT parasites was sufficient to induce cyst formation in vitro in both WT and ROCY1-deficient parasites, demonstrating that ROCY1 is both necessary and sufficient for cyst formation. Moreover this induction of cyst formation required at least 1 of 3 predicted CCCH Zinc finger domains. Mice chronically infected with ΔROCY1 parasites had detectable tachyzoites in the brain for up to 37 days post-infection (while mice infected with WT parasites did not), and CNS transcriptional analyses at day 30 post-infection throughout the chronic phase of infection revealed inflammatory signatures consistent with acute infection in ΔROCY1 parasites compared to WT. Despite our inability to detect brain cysts in infected mice, both WT and ΔROCY1 knockout parasites reactivated after dexamethasone treatment with similar timing and magnitude for up to 5 months post infection, challenging the paradigm that long term parasite persistence in the CNS requires cyst formation. These data identify a new regulator of cyst formation in T. gondii that is both necessary and sufficient for cyst formation, and whose function relies on its conserved nucleic acid binding motif.
Structures and comparison of endogenous 2-oxoglutarate and pyruvate dehydrogenase complexes from bovine kidney
Authors: Liu Shiheng , Xia Xian , Zhen James , Li Zihang , Zhou Z. Hong
Published: April 2022

The α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members of the family have different component structures and structural organization between each other and across phylogenetic species. While native structures of α-keto acid dehydrogenase complexes from bacteria and fungi became available recently, the atomic structure and organization of their mammalian counterparts in their native states remain unknown. Here, we report the cryo electron microscopy (cryoEM) structures of the endogenous cubic 2-oxoglutarate dehydrogenase complex (OGDC) and icosahedral pyruvate dehydrogenase complex (PDC) cores from bovine kidney determined at 3.5 Å and 3.8 Å resolution, respectively. The structures of multiple protein were reconstructed from a single lysate sample, allowing direct structural comparison without the concerns of differences arising from sample preparation and structure determination. Although native and recombinant E2 core scaffold structures are similar, native structures are decorated with their peripheral E1 and E3 subunits. Asymmetric sub-particle reconstructions support heterogeneity in the arrangements of these peripheral subunits. Additionally, despite sharing a similar monomeric fold, OGDC and PDC E2 cores have distinct interdomain and intertrimer interactions, which suggests a means of modulating self-assembly to mitigate heterologous binding between mismatched E2 species. The lipoyl moiety lies near a mobile gatekeeper within the interdomain active site of OGDC E2 and PDC E2. Analysis of the two-fold related intertrimer interface identified secondary structural differences and chemical interactions between icosahedral and cubic geometries of the core. Taken together, our study provides direct structural comparison of OGDC and PDC from the same source and offers new insights into determinants of interdomain interactions and of architecture diversity among α-keto acid dehydrogenase complexes.
Inhibition of mutant IDH1 promotes cycling of acute myeloid leukemia stem cells
Authors: Gruber Emily , So Joan , Lewis Alexander C. , Franich Rheana , Cole Rachel , Martelotto Luciano G. , Rogers Amy J. , Vidacs Eva , Fraser Peter , Stanley Kym , Jones Lisa , Trigos Anna , Thio Niko , Li Jason , Nicolay Brandon , Daigle Scott , Tron Adriana E. , Hyer Marc L. , Shortt Jake , Johnstone Ricky W. , Kats Lev M.
Published: April 2022

Acute myeloid leukemias (AML) are comprised of multiple cell types with distinct capabilities to propagate the disease and resist therapy. Approximately 20% of AML patients carry gain- of-function mutations in IDH1 or IDH2 that result in over-production of the onco-metabolite 2-HG. Although IDH inhibitors can induce complete morphological remission, almost all patients eventually relapse. Analysis of clinical samples suggests that a population of IDH mutant cells is able to persist during treatment eventually acquiring 2-HG independence and drug resistance. Herein we characterized the molecular and cellular responses to the clinical IDH1 inhibitor AG-120 at high resolution using a novel multi-allelic mouse model of IDH1 mutant AML. We demonstrate that AG-120 exerts cell type-dependent effects on leukemic cells promoting delayed disease regression. Although IDH1 inhibition alone was not able to fully eradicate the disease, we uncovered that it increases cycling of rare leukemic stem cells and triggers transcriptional upregulation of the pyrimidine salvage pathway. Accordingly, AG-120 sensitized IDH1 mutant AML to azacitidine with the combination of AG-120 and azacitidine showing vastly improved efficacy in vivo. Our data highlight the impact of non- genetic heterogeneity on treatment response and provide mechanistic rationale for a drug combination that is being tested in clinical trials.

STATEMENT OF SIGNIFICANCE

Inhibition of mutant IDH1 in AML is insufficient to eliminate the disease but promotes proliferation of quiescent leukemic stem cells. Our data provide a mechanistic explanation for the observed synergy between IDH inhibitors and azacitidine and suggest that IDH inhibitors may also synergize with other drugs that preferentially target actively dividing cells.
Secreted dengue virus NS1 from infection is predominantly dimeric and in complex with high-density lipoprotein
Authors: Chew Bing Liang Alvin , Ngoh An Qi , Phoo Wint Wint , Chan Kitti Wing Ki , Ser Zheng , Tulsian Nikhil K , Lim Shiao See , Weng Mei Jie Grace , Watanabe Satoru , Choy Milly M. , Low Jenny G. , Ooi Eng Eong , Ruedl Christiane , Sobota Radoslaw M. , Vasudevan Subhash G. , Luo Dahai
Published: April 2022

Severe dengue infections are characterized by endothelial dysfunction shown to be associated with the secreted nonstructural protein 1 (sNS1), making it an attractive vaccine antigen and biotherapeutic target. To uncover the biologically relevant structure of sNS1, we obtained infection-derived sNS1 (isNS1) from DENV-infected Vero cells through immunoffinity purification instead of recombinant sNS1 (rsNS1) overexpressed in insect or mammalian cell lines. We found that isNS1 appeared as an approximately 250 kDa complex of NS1 and ApoA1 and further determined the cryoEM structures of isNS1 and its complex with a monoclonal antibody/Fab. Indeed, we found that the major species of isNS1 is a complex of the NS1 dimer partially embedded in a High-Density Lipoprotein (HDL) particle. Cross-linking mass spectrometry (XL-MS) studies confirmed that the isNS1 interacts with the major HDL component ApoA1 through interactions that map to the NS1 wing and hydrophobic domains. Furthermore, our studies demonstrated that the sNS1 in sera from DENV-infected mice and a human patient form a similar complex as isNS1. Our results report the molecular architecture of a biological form of sNS1 which may have implications for the molecular pathogenesis of dengue.

CryoEM structures of secreted dengue virus NS1 protein reveal dimers in complex with high-density lipoprotein.
Bio-electric potentials in superior plants: electric collective behaviour
Authors: Chiolerio Alessandro , Dehshibi Mohammad Mahdi , Vitiello Giuseppe , Bernard Alessandro , Ceretto Paolo , Arvat Massimo , Adamatzky Andrew
Published: April 2022

Electrical activity is used by plants in long term signalling and information transfer between the distant parts of the plant. Biopotential recordings from trees in a natural environment have been so far less discussed in scientific literature. Here we present our data about the open science experiment TRee-hUMAn iNterface (TRUMAN) located in Paneveggio forest (Valle di Fiemme, Trento, Italy), cultivated since one thousand years for the production of harmonic wood from Picea abies (red fir). We show that: i) biopotential features based on xylem can be correlated with the solar (and lunar) cycle ii) dead tree logs show an electrical activity that is correlated with that of neighbouring trees iii) statistical features of the spike-like peaks are evidenced, including amplitude, frequency, propagation speed, entropy iv) a quantum field theory is presented to highlight the collective behaviour of the forest, supported by preliminar correlation analyses between electrical signal Kolmogorov entropy and thermographies Shannon entropy.
LILAC: Enhanced actin imaging with an optogenetic Lifeact
Authors: Kroll Kourtney L. , French Alexander R. , Sosnick Tobin R. , Rock Ronald S.
Published: April 2022

We have designed an improved Lifeact variant that binds to actin under the control of light using the LOV2 protein. Light control enables one to subtract the pre-illumination signal of the unbound label, yielding an enhanced view of F-actin dynamics in cells. Furthermore, the tool eliminates actin network perturbations and cell sickness caused by Lifeact overexpression.
Recycling of uridylated mRNAs in starfish embryos
Authors: Yamazaki Haruka , Furuichi Megumi , Katagiri Mikoto , Kajitani Rei , Itoh Takehiko , Chiba Kazuyoshi
Published: April 2022

In eukaryotes, mRNAs with long poly(A) tails are translationally active, whereas deadenylation of the tails decreases translation and uridylation of the short poly(A) tails causes the mRNA to be degraded. In this study, we confirmed that maternalcyclin BmRNAs with long poly(A) tails in blastula embryos of invertebrate starfish were deadenylated and uridylated, followed by decay. In starfish oocytes, however,cyclin BmRNAs with uridylated short poly(A) tails are stable. They are polyadenylated and translationally active immediately following hormonal stimulation for resumption of meiosis. Similarly, maternal ribosomal protein mRNAs,Rps29andRpl27a, which become uridylated following deadenylation upon hormonal stimulation, remain stable even after fertilisation and early development. At the morula stage, the uridylated maternal ribosomal protein mRNAs are modified to yield non-canonical poly (A) tails rich in U and G residues in the 5’ region and in A residues at the 3’ end, rendering them translationally active. These results indicate that the fates of uridylated mRNAs in starfish are decay and/or recycling.
The production of diverse brGDGTs by an Acidobacterium allows a direct test of temperature and pH controls on their distribution
Authors: Chen Yufei , Zheng Fengfeng , Yang Huan , Yang Wei , Wu Ruijie , Liu Xinyu , Liang Huayang , Chen Huahui , Pei Hongye , Zhang Chuanlun , Pancost Richard D. , Zeng Zhirui
Published: April 2022

Microbial lipid biomarkers preserved in geological archives can be used to explore past climate changes. Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are unique bacterial biomarkers that have been used as molecular tools for the quantitative determination of terrestrial temperatures and the pH of depositional environments over a range of geological timescales. However, the exact biological source organisms – especially of the entire suite of brGDGTs found in the environment – remains unclear; by extension, so do the mechanisms that govern these proxies. Here, we identified a brGDGT-producing strainCandidatus Solibacter usitatusEllin6076, by identifying archaeal tetraether synthase homologs in bacterial genomes. This strain synthesizes diverse brGDGTs, including regular C5-methylated and cyclic brGDGTs, and brGDGTs comprise up to 66% of the major lipids, far exceeding the proportions found in previous studies. The degree of C5-methylation in cultured strain Ellin6076 is primarily determined by temperature, whereas cyclization appears to be influenced by multiple factors. Consequently, culture-derived paleoclimate indices are in agreement with the global soil-derived MBT’5ME(methylation index of C5-methyl brGDGTs) proxy for temperature but not the CBT5ME(cyclization index of C5-methyl brGDGTs) proxy for pH. Our findings provide important insights from a physiological perspective into the underlying mechanism of brGDGT-based proxies.

Significance Statement

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are biomarkers widely used for the quantitative estimation of past climatic changes due to their ubiquitous occurrence in the environment and the relationships between their distributions and temperature and pH. However, the ecophysiology of brGDGT-producing bacteria and the mechanistic basis for brGDGT-based climate proxies remain unknown. Here, we identify a brGDGT-producing Acidobacterium and present a physiological study of brGDGTs in response to cultivation variables, which provides pivotal insights into how brGDGT producers modulate methylation and cyclization under different culturing conditions. Our study represents a significant advancement in understanding the physiological role of lipid structures in microbial adaptation and helps us interpret the relationships between brGDGT-based proxies and environmental conditions of the geological environment.
AGC: Compact representation of assembled genomes
Authors: Deorowicz Sebastian , Danek Agnieszka , Li Heng
Published: April 2022

High-quality sequence assembly is the ultimate representation of complete genetic information of an individual. Several ongoing pangenome projects are producing collections of high-quality assemblies of various species. Here, we show how to represent the sequenced genomes in 2–3 orders of magnitude smaller space, allowing easy and fast extraction of any contig or its part.
ARP2/3 complex associates with peroxisomes to participate in pexophagy in plants
Authors: Martinek Jan , Cifrová Petra , Vosolsobě Stanislav , Krtková Jana , Sikorová Lenka , Malínská Kateřina , Mauerová Zdeňka , Leaves Ian , Sparkes Imogen , Schwarzerová Kateřina
Published: April 2022

ARP2/3 is a heteroheptameric protein complex evolutionary conserved in all eukaryotic organisms. Its conserved role is based on the induction of actin polymerization at the interface between membranes and the cytoplasm. Plant ARP2/3 has been reported to participate in actin reorganization at the plasma membrane during polarized growth of trichomes and at the plasma membrane-endoplasmic reticulum contact sites. We demonstrate here that individual plant subunits of ARP2/3 fused to fluorescent proteins form motile dot-like structures in the cytoplasm that are associated with plant peroxisomes. ARP2/3 dot structure is found at the peroxisome periphery and contains assembled ARP2/3 complex and WAVE/SCAR complex subunit NAP1. This dot occasionally colocalizes with the autophagosome, and under conditions that affect the autophagy, colocalization between ARP2/3 and the autophagosome increases. ARP2/3 subunits co-immunoprecipitate with ATG8f marker. Since mutants lacking functional ARP2/3 complex have more peroxisomes than WT, we link the ARP2/3 complex on peroxisomes to the process of peroxisome degradation by autophagy called pexophagy. Additionally, several other peroxisomal proteins colocalize with ARP2/3 dot on plant peroxisomes. Our results suggest a specific role of ARP2/3 and actin in the peroxisome periphery, presumably in membrane remodelling. We hypothesize that this role of ARP2/3 aids processes at the peroxisome periphery such as peroxisome degradation through autophagy or regulation of peroxisomal proteins localization or function.

Significance statement

ARP2/3 complex-positive dots associate exclusively with peroxisomes in plant cells, where it colocalizes with autophagosome marker ATG8f and several other proteins. Our experiments link ARP2/3 to pexophagy: colocalization between ARP2/3 dots and autophagosome increases when autophagy processes are induced or inhibited; ARP2/3 and ATG8f colocalize and co-immunoprecipitate, and finally, ARP2/3 mutants’ cells contain more peroxisomes than WT. Our results suggest a novel role of ARP2/3 in peroxisome structure and function regulation.
Plant N-glycan breakdown by human gut Bacteroides
Authors: Crouch Lucy I. , Urbanowicz Paulina A. , Baslé Arnaud , Cai Zhi-Peng , Liu Li , Voglmeir Josef , Diaz Javier M. Melo , Benedict Samuel T. , Spencer Daniel I.R. , Bolam David N.
Published: April 2022

The major nutrients available to the human colonic microbiota are complex glycans derived from the diet. To degrade this highly variable mix of sugar structures, gut microbes have acquired a huge array of different carbohydrate-active enzymes (CAZymes), predominantly glycoside hydrolases, many of which have specificities that can be exploited for a range of different applications. Plant N-glycans are prevalent on proteins produced by plants and thus components of the diet, but the breakdown of these complex molecules by the gut microbiota has not been explored. Plant N-glycans are also well characterised allergens in pollen and some plant-based foods, and when plants are used in heterologous protein production for medical applications, the N-glycans present can pose a risk to therapeutic function and stability. Here we use a novel genome association approach for enzyme discovery to identify a breakdown pathway for plant complex N-glycans encoded by a gut Bacteroides species and biochemically characterise five CAZymes involved, including structures of the PNGase and GH92 α-mannosidase. These enzymes provide a toolbox for the modification of plant N-glycans for a range of potential applications. Furthermore, the keystone PNGase also has activity against insect-type N-glycans, which we discuss from the perspective of insects as a nutrient source.
Streptococcus Pneumoniae Promotes Lung Tumorigenesis by Activating PI3K/AKT and NF-kB Pathways via Binding PspC to PAFR
Authors: Li Ning , Zhou Huifen , Holden Van K , Deepak Janaki , Dhilipkannah Pushpa , Todd Nevins W , Jiang Feng
Published: April 2022

Streptococcus pneumoniae (SP) is associated with lung cancer, yet its role in the tumorigenesis remains uncertain. Herein we find that SP attaches to lung cancer cells via binding pneumococcal surface protein C (PspC) to platelet-activating factor receptor (PAFR), a receptor overexpressed in lung tumors. Interaction between PspC and PAFR stimulates cell proliferation and activates PI3K/AKT and NF-kB signaling pathways, which triggers a pro-inflammatory response. Lung cancer cells infected with SP rapidly form larger tumors in BALB/C mice compared to untreated cells. Mice treated with tobacco carcinogen and SP develop more lung tumors and had shorter survival than mice treated with the carcinogen alone. Mutating PspC or deleting PAFR abolishes the tumor-promoting effects of SP. Overabundance of SP is found in lung tumors of patients with lung cancer and associated with the survival. SP plays a driving role in lung tumorigenesis by activating PI3K/AKT and NF-kB pathways via binding PspC to PAFR and provides a microbial target for diagnosis and treatment of the disease.
Probing the role of macromolecular crowding in cell volume regulation using fluorescence anisotropy
Authors: Biswas Parijat , Ray Dipanjan , Jana Subhamoy , Das Jibitesh , Sinha Bidisha , Sinha Deepak Kumar
Published: April 2022

Cytoplasmic macromolecular crowding (MMC) influences multiple cellular functions. Using fluorescence anisotropy of EGFP, we explore the homeostasis of MMC in the cytoplasm and its role in cell volume regulation. Individual cells of different lineages maintain a distinctly unique average cytoplasmic MMC for considerably long durations. Despite diffusion, actin cytoskeleton facilitates spatially heterogeneous MMC in the cytoplasm. While hypertonic-stress triggers regulatory volume increase (RVI), other methods of increasing cytoplasmic MMC fail to start RVI, suggesting that cells lack capabilities for MMC homeostasis. During spreading or microtubule-depolymerized state, cells neglect changes in cytoplasmic MMC to undergo volume regulation. Inhibition of TNFR1 increases the membrane tension and deprives cells of their ability to undergo volume regulation. Current understanding contemplates that cytoplasmic MMC, the mechanical state of the plasma membrane or the actin cytoskeleton, could be sensors for cell volume regulation. Our observations establish the irrelevance of cytoplasmic MMC and the significance of plasma membrane tension in setting off the cell volume regulation machinery.
Extended functional connectivity of convergent structural alterations among individuals with PTSD: A neuroimaging meta-analysis
Authors: Pankey Brianna S. , Riedel Michael C. , Cowan Isis , Bartley Jessica E. , Lobo Rosario Pintos , Hill-Bowen Lauren D. , Salo Taylor , Musser Erica D. , Sutherland Matthew T. , Laird Angela R.
Published: April 2022

Background

Post-traumatic stress disorder (PTSD) is a debilitating disorder defined by the onset of intrusive, avoidant, negative cognitive or affective, and/or hyperarousal symptoms after witnessing or experiencing a traumatic event. Previous voxel-based morphometry studies have provided insight into structural brain alterations associated with PTSD with notable heterogeneity across these studies. Furthermore, how structural alterations may be associated with brain function, as measured by task-free and task-based functional connectivity, remains to be elucidated.

Methods

Using emergent metaanalytic techniques, we sought to first identify a consensus of structural alterations in PTSD using the anatomical likelihood estimation (ALE) approach. Next, we generated functional profiles of identified convergent structural regions utilizing resting-state functional connectivity (rsFC) and meta-analytic coactivation modeling (MACM) methods. Finally, we performed functional decoding to examine mental functions associated with our ALE, rsFC, and MACM brain characterizations.

Results

We observed convergent structural alterations in a single region located in the medial prefrontal cortex. The resultant rsFC and MACM maps identified functional connectivity across a widespread, whole-brain network that included frontoparietal and limbic regions. Functional decoding revealed overlapping associations with attention, memory, and emotion processes.

Conclusions

Consensus-based functional connectivity was observed in regions of the default mode, salience, and central executive networks, which play a role in the tripartite model of psychopathology. Taken together, these findings have important implications in understanding the neurobiological mechanisms associated with PTSD.
Long lifespan is maintained by a unique Heat Shock Factor in reproductive ants
Authors: Glastad Karl M. , Roessler Julian , Gospocic Janko , Berger Shelley L.
Published: April 2022

Among eusocial insects, reproductive females show longer lifespan than non-reproductive female workers despite high genetic similarity. Using an ant species (Harpegnathos saltator, Hsal) featuring inducible worker reproduction and correlated extended lifespan, we find that long-lived reproductive individuals (called “gamergates”) show elevated expression of heat shock response (HSR) genes specifically in the absence of heat stress. This HSR gene elevation is driven in part by gamergate-specific constitutive upregulation of a heat shock transcription factor gene most similar to mammalian HSF2 (called hsalHSF2). In sterile workers hsalHSF2 is bound to DNA only upon heat stress, but in gamergates hsalHSF2 binds to DNA in the absence of heat stress, and correlates with caste-biased gene expression of a subset of heat-inducible genes, thus showing natural bias to gamergates. Remarkably, ectopic expression in D. melanogaster of hsalHSF2 leads to enhanced survival compared to hsalHSF1 following heat stress, as well as extended lifespan. Molecular characterization of these longer-lived flies illustrates multiple parallels between long-lived flies and gamergates, underscoring the centrality of hsalHSF2 to extended lifespan in gamergates. Hence, ant caste-specific heat stress resilience and excessive longevity is, remarkably, transferrable to flies via a specialized ant heat shock factor, HSF2. These findings reinforce the critical role of proteostasis to health and to aging, and reveal novel mechanisms underlying facultative lifespan extension.
A generic framework for hierarchical de novo protein design
Authors: Harteveld Zander , Bonet Jaume , Rosset Stéphane , Yang Che , Sesterhenn Fabian , Correia Bruno E.
Published: April 2022

De novo protein design enables the exploration of novel sequences and structures absent from the natural protein universe. De novo design also stands as a stringent test to our understanding of the underlying physical principles of protein folding and may lead to the development of proteins with unmatched functional characteristics. The first fundamental challenge of de novo design is to devise “designable” structural templates leading to sequences that will adopt the predicted fold. Here, we built on the TopoBuilder de novo design method to automatically assemble structural templates with native-like features starting from string descriptors that capture the overall topology of proteins. Our framework eliminates the dependency of hand-crafted and fold-specific rules through an iterative, data-driven approach that extracts geometrical parameters from structural tertiary motifs. We evaluated the TopoBuilder framework by designing sequences for a set of five protein folds and experimental characterization revealed that several sequences were folded and stable in solution. The TopoBuilder de novo design framework will be broadly useful to guide the generation of artificial proteins with customized geometries, enabling the exploration of the protein universe.
High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation
Authors: Laine Romain F. , Heil Hannah S. , Coelho Simao , Nixon-Abell Jonathon , Jimenez Angélique , Galgani Tommaso , Stubb Aki , Follain Gautier , Webster Samantha , Goyette Jesse , Culley Siân , Jacquemet Guillaume , Hajj Bassam , Leterrier Christophe , Henriques Ricardo
Published: April 2022

In recent years, the development of new image analysis approaches has highlighted the possibility of recovering superresolution information from short sequences of wide-field images. Our recently developed method, SRRF (Super-Resolution Radial Fluctuations), enables long-term live-cell imaging beyond the resolution limit without specialized hardware. Here, we present eSRRF (enhanced-SRRF), a significant improvement over our initial method, enhancing image fidelity to the underlying structure and resolution. Especially, eSRRF uses automated data-driven parameter optimization, including an estimation of the number of frames necessary for optimal reconstruction. We demonstrate the improved fidelity of the images reconstructed with eSRRF and highlight its versatility and ease of use over a wide range of microscopy techniques and biological systems. We also extend eSRRF to 3D super-resolution microscopy by combining it with multi-focus microscopy (MFM), obtaining volumetric super-resolution imaging of live cells with acquisition speed of ~1 volume/second.
Oncogenic signalling is coupled to colorectal cancer cell differentiation state
Authors: Sell Thomas , Klotz Christian , Fischer Matthias M. , Astaburuaga-García Rosario , Krug Susanne , Drost Jarno , Clevers Hans , Morkel Markus , Blüthgen Nils
Published: April 2022

Colorectal cancer progression is intrinsically linked to stepwise deregulation of the intestinal differentiation trajectory. In this process, sequential mutations of APC/Wnt, KRAS, TP53 and SMAD4 stepwisely enable an oncogenic signalling network. Here, we developed a novel mass cytometry antibody panel to analyse colorectal cancer cell differentiation and signalling in human isogenic colorectal cancer organoids and in patient-derived cultures. We define a differentiation axis following EphrinB2 abundance in all tumour progression states from normal to cancer. We show that during colorectal cancer progression, oncogenes decrease dependence on external factors and shape distribution of cells along the differentiation axis. In this regard, subsequent mutations can have stem cell-promoting or restricting effects. Individual nodes of the signalling network remain coupled to the differentiation state, regardless of the presence of oncogenic signals. Our work underscores the key role of cell plasticity as a hallmark of cancer that is gradually unlocked during colorectal cancer progression.
Functional Contribution of Cancer-Associated Fibroblasts in Glioblastoma
Authors: Galbo Phillip M. , Liu Yang , Peng Mou , Wei Yao , Madsen Anne Tranberg , Graff Sarah , Montagna Cristina , Segall Jeffrey E. , Sidoli Simone , Zang Xingxing , Zheng Deyou
Published: April 2022

The abundance and biological contribution of cancer associated fibroblasts (CAFs) in glioblastoma are poorly understood. Here, we applied single-cell RNA sequencing and spatial transcriptomics analyses to identify and characterize CAFs in human glioblastoma tumors and then performed functional enrichment analysis and in vitro assays to investigate their interactions with malignant glioblastoma cells. We found that CAF abundance was significantly correlated with tumor grade, poor clinical outcome, and activation of extracellular matrix remodeling, using three large databases containing bulk RNA-sequencing data and clinical information. Proteomic analysis of the CAFs and their secretome revealed fibronectin (FN1) as a strong candidate mediating CAF functions. This was validated using in vitro cellular models, which demonstrated that CAF conditioned media and recombinant FN1 could facilitate the migration and invasion of glioblastoma cells. In addition, we showed that CAFs were more abundant in the mesenchymal-like state (or subtype) than in other states of glioblastomas, while cell lines resembling the proneural-state responded to the CAF signaling better in terms of the migratory and invasive phenotypes. Investigating the in-situ expression of gene markers specifically associated with CAFs and mesenchymal malignant cells further indicated that CAFs were enriched in the perinecrotic and pseudopalisading zones of human tumors, where mesenchymal-like glioblastoma cells co-resided and thus likely interacted. Overall, this study characterized the molecular features and functional impacts of CAFs in glioblastoma, alluding to a novel cell-to-cell interaction axis mediated by CAFs in the glioblastoma microenvironment.
Discovery of a novel human antibody VH domain with potent activity against mesothelin expressing cancer cells in both CAR T-cell and antibody drug conjugate formats
Authors: Sun Zehua , Chu Xiaojie , Adams Cynthia , Ilina Tatiana V. , Guerrero Michel , Lin Guowu , Chen Chuan , Jelev Dontcho , Ishima Rieko , Li Wei , Mellors John W , Calero Guillermo , Dimitrov Dimiter S
Published: April 2022

Antibody based therapeutics targeting mesothelin (MSLN) have shown limited anticancer activity in clinical trials. Novel antibodies with high affinity and better therapeutic properties are needed. In the current study, we have isolated and characterized a novel VH domain 3C9 from a large size human immunoglobulin heavy chain variable (VH) domain library. 3C9 exhibited high affinity [KD (dissociation constant) < 3 nM] and binding specificity in a membrane proteome array (MPA). In a mouse xenograft model, 3C9 fused to human Fc became visible at tumor sites as early as 8 hours post infusion and persisted at the tumor site for more than 10 days. Both CAR-T cells and antibody domain drug conjugations (DDCs) generated with 3C9 were highly effective at killing MSLN positive cells in vitro without off-target effects. The X-ray crystal structure of full-length MSLN in complex with 3C9 reveals interaction of the 3C9 domains with two distinctive residues patches on the MSLN surface. 3C9 fused to human Fc domain drug conjugate was efficacious to inhibit tumor growth in a mouse xenograft model. This newly discovered VH antibody domain holds promise as a therapeutic candidate for MSLN-expressing cancers.
Structural insights into the mechanism of the sodium/iodide symporter (NIS)
Authors: Ravera Silvia , Nicola Juan Pablo , de Simone Glicella Salazar , Sigworth Fred J. , Karakas Erkan , Amzel L. Mario , Bianchet Mario A. , Carrasco Nancy
Published: April 2022

The sodium/iodide symporter (NIS) is the essential plasma membrane protein that mediates active iodide (I-) transport into the thyroid gland, the first step in the biosynthesis of the thyroid hormones—the master regulators of intermediary metabolism. NIS couples the inward translocation of I- against its electrochemical gradient to the inward transport of Na+ down its electrochemical gradient. For nearly 50 years before its molecular identification, NIS was already the molecule at the center of the single most effective internal radiation cancer therapy ever devised: radioiodide (131I-) treatment for thyroid cancer. Mutations in NIS cause congenital hypothyroidism, which must be treated immediately after birth to prevent stunted growth and cognitive deficiency. To date, the structure of NIS has been unknown. Here, we report three structures of rat NIS, determined by single-particle cryo-electron microscopy (cryo-EM): one with no substrates bound, one with 2 Na+ and 1 I- bound, and one with 1 Na+ and the oxyanion perrhenate bound. Structural analyses, functional characterization, and computational studies reveal the substrate binding sites and residues key for transport activity. Our results yield insights into how NIS selects, couples, and translocates anions—thereby establishing a framework for understanding NIS function—and into how it transports different substrates with different stoichiometries and releases substrates from its substrate-binding cavity into the cytosol.
Impairments in SHMT2 expression or cellular folate availability reduce oxidative phosphorylation and pyruvate kinase activity
Authors: Fiddler Joanna L. , Blum Jamie E. , Castillo Luisa F. , Thalacker-Mercer Anna E. , Field Martha S.
Published: April 2022

Background

Serine hydroxymethyltransferase 2 (SHMT2) catalyzes the reversible conversion of tetrahydrofolate (THF) and serine producing THF-conjugated one-carbon units and glycine in the mitochondria. Biallelic SHMT2 variants were identified in humans and suggested to alter the protein’s active site, potentially disrupting enzymatic function. SHMT2 expression has also been shown to decrease with aging in human fibroblasts. Immortalized cells models of total SHMT2 loss or folate deficiency exhibit decreased oxidative capacity and impaired mitochondrial complex I assembly and protein levels, suggesting folate-mediated one-carbon metabolism (FOCM) and the oxidative phosphorylation system are functionally coordinated. This study examined the role of SHMT2 and folate availability in regulating mitochondrial function, energy metabolism, and cellular proliferative capacity in both heterozygous and homozygous cell models of reduced SHMT2 expression.

Methods

Primary mouse embryonic fibroblasts (MEF) were isolated from a C57Bl/6 dam crossed with a heterozygous Shmt2+/- male to generate Shmt2+/+ (wild-type) or Shmt2+/- (HET) MEF cells. In addition, haploid chronic myeloid leukemia cells (HAP1, wild-type) or HAP1 cells lacking SHMT2 expression (ΔSHMT2) were cultured for 4 doublings in either low-folate or folate-sufficient culture media. Cells were examined for proliferation, total folate levels, mtDNA content, protein levels of pyruvate kinase and PGC1α, pyruvate kinase enzyme activity, mitochondrial membrane potential, and mitochondrial function.

Results

Homozygous loss of SHMT2 in HAP1 cells impaired cellular folate accumulation and altered mitochondrial DNA content, membrane potential, and basal respiration. Formate rescued proliferation in HAP1, but not ΔSHMT2, cells cultured in low-folate medium. Pyruvate kinase activity and protein levels were impaired in ΔSHMT2 cells and in MEF cells exposed to low-folate medium. Mitochondrial biogenesis protein levels were elevated in Shmt2+/- MEF cells, while mitochondrial mass was increased in both homozygous and heterozygous models of SHMT2 loss.

Conclusions

The results from this study indicate disrupted mitochondrial FOCM impairs mitochondrial folate accumulation and respiration, glycolytic activity, and cellular proliferation. These changes persist even after a potentially compensatory increase in mitochondrial biogenesis as a result of decreased SHMT2 levels.
The impact of AlphaFold on experimental structure solution
Authors: Edich Maximilian , Briggs David C. , Kippes Oliver , Gao Yunyun , Thorn Andrea
Published: April 2022

AlphaFold2 is a machine-learning based program that predicts a protein structure based on the amino acid sequence. In this article, we report on the current usages of this new tool and give examples from our work in the Coronavirus Structural Task Force. With its unprecedented accuracy, it can be utilized for the design of expression constructs, de novo protein design and the interpretation of Cryo-EM data with an atomic model. However, these methods are limited by their training data and are of limited use to predict conformational variability and fold flexibility; they also lack co-factors, posttranslational modifications and multimeric complexes with oligonucleotides. They also are not always perfect in terms of chemical geometry. Nevertheless, machine learning based fold prediction are a game changer for structural bioinformatics and experimentalists alike, with exciting developments ahead.
The Gene Knockout of Angiotensin II Type 1a Receptor Improves High-fat Diet-Induced Obesity in rat via Promoting Adipose Lipolysis
Authors: Li Aiyun , Shi Wenjuan , Wang Jin , Wang Xuejiao , Zhang Yan , Lei Zhandong , Jiao Xiang-Ying
Published: April 2022

Aims

The renin-angiotensin system (RAS) is over-activated and the serum angiotensin II (Ang II) level increased in obese patients, while their correlations were incompletely understood. This study aims to explore the role of Ang II in diet-induced obesity by focusing on adipose lipolysis.

Methods

Rat model of AT1aR gene knockout were established to investigate the special role of Ang II. Wild-type (WT) and AT1aR gene knockout (AT1aR-/-) SD rats were fed with normal diet or high-fat diet for 12 weeks. Adipose morphology and adipose lipolysis were examined.

Results

AT1aR deficiency activated lipolysis-related enzymes and increased the levels of NEFAs and glycerol released from adipose tissue in high-fat diet rats, while did not affect triglycerides synthesis. Besides, AT1aR knockout promoted energy expenditure and fatty acids oxidation in adipose tissue. cAMP levels and PKA phosphorylation in the adipose tissue were significantly increased in AT1aR-/- rats fed with high-fat. Activated PKA could promote adipose lipolysis and thus improved adipose histomorphology and insulin sensitivity in high-fat diet rats.

Conclusions

AT1aR deficiency alleviated adipocyte hypertrophy in high-fat diet rats by promoting adipose lipolysis via cAMP/PKA pathway, and thereby delayed the onset of obesity and related metabolic diseases.
Biogeography and taxonomy of theHemileuca maia-nevadensisStretch species complex (Lepidoptera: Saturniidae): insights to the midcontinental populations
Authors: Schmidt Christian
Published: April 2022

An integrated assessment of geographic distribution, genetic variation and interpopulation reproductive barriers of the Great Plains and Great Lakes populations of theHemileuca maia-nevadensisspecies complex is presented. The taxonomic circumscription ofHemileuca nevadensisStretch, key to understanding the complex evolutionary history of the group, has previously been misinterpreted. Detailed distribution maps based on historic, literature, and contemporary occurrence records, combined with analysis of genetic variation using mtDNA-COI barcode sequences and pheromone compatibility trials, indicate that Great PlainsH. “nevadensis” are disjunct and genetically divergent from nominateH. nevadensis, instead being more closely related to Great Lakes populations. Despite the genomic differentiation of the bog buckmoth established in recent studies, similar or identical mtDNA-COI haplotypes indicate past genetic linkages among now-isolated populations across the northern range periphery of themaia-complex. Based on the current evidence, northern Great PlainsHemileuca latifasciaBarnes & McDunnoughstat. nov. and eastern Great Lakes (bog buckmoth)Hemileuca menyanthevoraPavulaanstat. nov. (=Hemileuca iroquoisDirig & Cryansyn. nov.) should be considered as species distinct from others in themaia-group. Post-glacial dispersal hypotheses are evaluated in light of molecular variation and ecology, and key knowledge gaps are identified to guide future research.