bluuebunny/crossref_metadata_2025 huggingface dataset:
Epigenome-wide contributions to individual differences in childhood phenotypes: A GREML approach
Authors: Neumann Alexander , Pingault Jean-Baptiste , Felix Janine F. , Jaddoe Vincent W. V. , Tiemeier Henning , Cecil Charlotte , Walton Esther
Published: June 2021

Background

DNA methylation is an epigenetic mechanism involved in human development. Numerous epigenome-wide association studies (EWAS) have investigated the associations of DNA methylation at single CpG sites with childhood outcomes. However, the overall contribution of DNA methylation across the genome (R2Methylation) towards childhood phenotypes is unknown. An estimate of R2Methylationwould provide context regarding the importance of DNA methylation explaining variance in health outcomes.

Methods

We estimated the variance explained by epigenome-wide cord blood methylation (R2Methylation) for five childhood phenotypes: gestational age, birth weight, and body mass index (BMI), IQ and ADHD symptoms at school age. We adapted a genome-based restricted maximum likelihood (GREML) approach with cross-validation (CV) to DNA methylation data and applied it in two population-based birth cohorts: ALSPAC (n=775) and Generation R (n=1382).

Results

Using information from >470,000 autosomal probes we estimated that DNA methylation at birth explains 45% (SDCV= 0.07) of gestational age variance and 16% (SDCV= 0.05) of birth weight variance. The R2Methylationestimates for BMI, IQ and ADHD symptoms at school age estimates were near 0% across almost all cross-validation iterations.

Conclusions

The results suggest that cord blood methylation explains a moderate to large degree of variance in gestational age and birth weight, in line with the success of previous EWAS in identifying numerous CpG sites associated with these phenotypes. In contrast, we could not obtain a reliable estimate for school-age BMI, IQ and ADHD symptoms. This may reflect a null bias due to insufficient sample size to detect variance explained in more weakly associated phenotypes, although the true R2Methylationfor these phenotypes is likely below that of gestational age and birth weight when using DNA methylation at birth.
The effect ofStachys inflataon the performance of broiler chickens and Newcastle Disease Antibody Titer
Authors: Attaran Hamidreza , Zamanimoghaddam Abdolkarim , Ghannadi Alireza , Namjoo Abdolrasool , Zamani Farshad
Published: June 2021

This study shows how performance and NDHI titers of broiler chickens are affected by the plantStachys inflatay. One hundred and eighty, one day old Ross male broiler chickens were randomly divided into 5 groups of 36 (consisting of 3 replicates) and placed in 12 separate pens. Groups 1, 2, 3, 4 and 5 received 0, 0.15, 0.3, 0.45 and 0.6%S.inflatain their feed respectively from 8 to 42 days of age. Performance indexes were recorded on a weekly basis. At 42 days of age, serum and mid gut samples were taken for NDHI test and histopathological studies. The results were analyzed by the One Way ANOVA, Tukey test. The body weight of the second group was significantly (P ≤ 0.05) higher than the control from the third week to the end. All treatment groups had HI titers higher than the control but the differences were not significant (P > 0.05). In the third group (0.3%S.inflata), relative liver and heart weight were significantly lower than control. No microscopic lesions were observed in mid gut in all experimental groups. It seems thatS. inflatareduces harmful intestinal flora which causes better use of feed.
Transfer learning improves outcome predictions for ASD from gene expression in blood
Authors: Robasky Kimberly , Kim Raphael , Yi Hong , Xu Hao , Bao Bokan , Chiang Austin W.T. , Courchesne Eric , Lewis Nathan E.
Published: June 2021

Background

Predicting outcomes on human genetic studies is difficult because the number of variables (genes) is often much larger than the number of observations (human subject tissue samples). We investigated means for improving model performance on the types of under-constrained problems that are typical in human genetics, where the number of strongly correlated genes (features) may exceed 10,000, and the number of study participants (observations) may be limited to under 1,000.

Methods

We created ‘train’, ‘validate’ and ‘test’ datasets from 240 microarray observations from 127 subjects diagnosed with autism spectrum disorder (ASD) and 113 ‘typically developing’ (TD) subjects. We trained a neural network model (a.k.a., the ‘naive’ model) on 10,422 genes using the ‘train’ dataset, composed of 70 ASD and 65 TD subjects, and we restricted the model to one, fully-connected hidden layer to minimize the number of trainable parameters, including a dropout layer to help prevent overfitting. We experimented with alternative network architectures and tuned the hyperparameters using the ‘validate’ dataset, and performed a single, final evaluation using the holdout ‘test’ dataset. Next, we trained a neural network model using the identical architecture and identical genes to predict tissue type in GTEx data. We transferred that learning by replacing the top layer of the GTEx model with a layer to predict ASD outcome and we retrained the new layer on the ASD dataset, again using the identical 10,422 genes.

Findings

The ‘naive’ neural network model had AUROC=0.58 for the task of predicting ASD outcomes, which saw a statistically significant 7.8% improvement from transfer learning.

Interpretation

We demonstrated that neural network learning could be transferred from models trained on large RNA-Seq gene expression to a model trained on a small, microarray gene expression dataset with clinical utility for mitigating over-training on small sample sizes. Incidentally, we built a highly accurate classifier of tissue type with which to perform the transfer learning.

Funding

This work was supported in part by NIMH R01-MH110558 (E.C., N.E.L.)

Author Summary

Image recognition and natural language processing have enjoyed great success in reusing the computational efforts and data sources to overcome the problem of over-training a neural network on a limited dataset. Other domains using deep learning, including genomics and clinical applications, have been slower to benefit from transfer learning. Here we demonstrate data preparation and modeling techniques that allow genomics researchers to take advantage of transfer learning in order to increase the utility of limited clinical datasets. We show that a non-pre-trained, ‘naive’ model performance can be improved by 7.8% by transferring learning from a highly performant model trained on GTEx data to solve a similar problem.
tACS phase-specifically biases brightness perception of flickering light
Authors: Fiene Marina , Radecke Jan-Ole , Misselhorn Jonas , Sengelmann Malte , Herrmann Christoph S. , Schneider Till R. , Schwab Bettina C. , Engel Andreas K.
Published: June 2021

Background

Visual phenomena like brightness illusions impressively demonstrate the highly constructive nature of perception. In addition to physical illumination, the subjective experience of brightness is related to temporal neural dynamics in visual cortex.

Objective

Here, we asked whether biasing the temporal pattern of neural excitability in visual cortex by transcranial alternating current stimulation (tACS) modulates brightness perception of concurrent rhythmic visual stimuli.

Methods

Participants performed a brightness discrimination task of two flickering lights, one of which was targeted by same-frequency electrical stimulation at varying phase shifts. tACS was applied with an occipital and a periorbital active control montage, based on simulations of electrical currents using finite-element head models.

Results

Experimental results reveal that flicker brightness perception is modulated dependent on the phase shift between sensory and electrical stimulation, solely under occipital tACS. Phase-specific modulatory effects by tACS were dependent on flicker-evoked neural phase stability at the tACS-targeted frequency, recorded prior to electrical stimulation. The optimal timing of tACS application leading to enhanced brightness perception was further correlated with the neural phase delay of the cortical flicker response.

Conclusions

Our results corroborate the role of temporally coordinated neural activity in visual cortex for brightness perception of rhythmic visual input in humans. Phase-specific behavioral modulations by tACS emphasize its efficacy to transfer perceptually relevant temporal information to the cortex. These findings provide an important step towards understanding the basis of visual perception and further confirm electrical stimulation as a tool for advancing controlled modulations of neural activity and related behavior.
Probing Specificities of Alcohol Acyltransferases for Designer Ester Biosynthesis with a High-Throughput Microbial Screening Platform
Authors: Lee Jong-Won , Seo Hyeongmin , Young Caleb , Trinh Cong T.
Published: June 2021

Alcohol acyltransferases (AATs) enables microbial biosynthesis of a large space of esters by condensing an alcohol and an acyl CoA. However, substrate promiscuity of AATs prevents microbial biosynthesis of designer esters with high selectivity. Here, we developed a high-throughput microbial screening platform that facilitates rapid identification of AATs for designer ester biosynthesis. First, we established a microplate-based culturing technique with in situ fermentation and extraction of esters. We validated its capability in rapid profiling of the alcohol substrate specificity of 20 chloramphenicol acetyltransferase variants derived from Staphylococcus aureus (CATSa) for microbial biosynthesis of acetate esters with various exogeneous alcohol supply. By coupling the microplate-based culturing technique with a previously established colorimetric assay, we developed a high-throughput microbial screening platform for AATs. We demonstrated that this platform could not only confirm CATSa F97W with enhanced isobutyl acetate synthesis but also identify three ATF1Sc (P348M, P348A, and P348S) variants, derived from Saccharomyces cerevisiae’s AAT and engineered by model-guided protein design, for enhanced butyl acetate production. We anticipate the high-throughput microbial screening platform is a useful tool to identify novel AATs that have important roles in nature and industrial biocatalysis for designer bioester production.
MicroRNA-202 prevents precocious spermatogonial differentiation and meiotic initiation during mouse spermatogenesis
Authors: Chen Jian , Gao Chenxu , Lin Xiwen , Ning Yan , He Wei , Zheng Chunwei , Zhang Daoqin , Yan Lin , Jiang Binjie , Zhao Yuting , Hossen Md Alim , Han Chunsheng
Published: June 2021

Spermatogonial differentiation and meiotic initiation during spermatogenesis are tightly regulated by a number of genes including those coding enzymes for miRNA biogenesis. However, whether and how single miRNAs regulate these processes remain unclear. Here, we report that miR-202, a member of the let-7 family, prevents precocious spermatogonial differentiation and meiotic initiation in spermatogenesis by regulating the timely expression of many genes including those for other key regulators. In miR-202 knockout (KO) mice, the undifferentiated spermatogonial pool is reduced, ultimately causing agametic seminiferous tubules. SYCP3, STRA8 and DMRT6 are expressed earlier in KO mice than in wild-type (WT) littermates, and Dmrt6 mRNA is a direct target of miR-202-5p. Moreover, the precocious spermatogonial differentiation and meiotic initiation were also observed in KO spermatogonial stem cells when cultured and induced in vitro, and could be rescued by the knockdown of Dmrt6. Therefore, we have not only shown that miR-202 is a novel regulator of meiotic initiation but also added a new module to the underlying regulatory network.

Summary statement

A single miRNA, miR-202, prevents precocious differentiation and meiotic initiation during spermatogenesis. miR-202, DMRT6 and STRA8 act together as a novel module in the regulatory network of meiotic initiation.
Herbivore feeding behavior validates optimal defense theory for specialized metabolites within plants
Authors: Hunziker Pascal , Lambertz Sophie Konstanze , Weber Konrad , Crocoll Christoph , Halkier Barbara Ann , Schulz Alexander
Published: June 2021

Numerous plants protect themselves from attackers using specialized metabolites. The biosynthesis of these deterrent, often toxic metabolites is costly, as their synthesis diverts energy and resources on account of growth and development. How plants diversify investments into growth and defense is explained by the optimal defense theory. The central prediction of the optimal defense theory is that plants maximize growth and defense by concentrating specialized metabolites in tissues that are decisive for fitness. To date, supporting physiological evidence merely relies on the correlation between plant metabolite distribution and animal feeding preference. Here, we use glucosinolates as a model to examine the effect of changes in chemical defense distribution on actual feeding behavior. Taking advantage of the uniform glucosinolate distribution in transporter mutants, we show that high glucosinolate accumulation in tissues important to fitness protects them by guiding larvae of a generalist herbivore to feed on other tissues. Moreover, we show that mature leaves of Arabidopsis thaliana supply young leaves with glucosinolates to optimize defense against herbivores. Our study provides physiological evidence for the central hypothesis of the optimal defense theory and sheds light on the importance of integrating glucosinolate biosynthesis and transport for optimizing plant defense.
Kidney organoids: A system to study human basement membrane assembly in health and disease
Authors: Morais Mychel Raony Paiva Teixeira , Tian Pinyuan , Lawless Craig , Murtuza-Baker Syed , Hopkinson Louise , Woods Steven , Mironov Aleksandr , Long David Andrew , Gale Daniel , Zorn Telma Maria Tenorio , Kimber Susan , Zent Roy , Lennon Rachel
Published: June 2021

Basement membranes (BMs) are complex macromolecular networks underlying all continuous layers of cells. Essential components include type IV collagen and laminins, which are affected by human genetic defects leading to a range of debilitating conditions including kidney, muscle, and cerebrovascular phenotypes. We investigated the dynamics of BM assembly in human pluripotent stem cell-derived kidney organoids. We resolved their global BM composition and discovered a conserved temporal sequence in BM assembly that paralleled mammalian fetal kidneys. We identified the emergence of key BM isoforms, which were altered by a pathogenic variant in COL4A5. Integrating organoid, fetal and adult kidney proteomes we found dynamic regulation of BM composition through development to adulthood, and with single-cell transcriptomic analysis we mapped the cellular origins of BM components. Overall, we define the complex and dynamic nature of vertebrate BM assembly and provide a platform for understanding its wider relevance in human development and disease.
LIM domain-wide comprehensive mutagenesis reveals the role of leucine in CSRP3 protein stability
Authors: Chauhan Pankaj Kumar , Sowdhamini R.
Published: June 2021

Cardiomyopathies are a severe and chronic cardiovascular burden worldwide, affecting a large cohort in the general population. Cysteine and glycine-rich protein 3 (CSRP3) is one of key proteins implicated in dominant dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM). In this study, we device a rapid in-silico screening protocol that creates a mutational landscape map for all possible allowed and disallowed substitutions in the protein of interest. This map provides the structural and functional insights on the stability of LIM domains of CSRP3. Further, the sequence analysis delineates the eukaryotic CSRP3 protein orthologs which complements the mutational map. Next, we also evaluated the effect of HCM/DCM mutations on these domains. One of highly destabilising mutations - L44P (also disease causing) and a neutral mutation - L44M were further subjected to molecular dynamics (MD) simulations. The results establish that L44P substitution affects the LIM domain structure. The present study provides a useful perspective to our understanding of the role of mutations in the CSRP3 LIM domains and their evolution. Experimentally verifying every reported mutation can become challenging both in time and resources used. This study provides a novel screening method for quick identification of key mutation sites for specific protein structures that can reduce the burden on experimental research.
Contraction-dependent intracortical inhibition supports gravity-efficient motor control
Authors: Gueugneau Nicolas , Martin Alain , Gaveau Jérémie , Papaxanthis Charalambos
Published: June 2021

Efficient control of voluntary movements along the gravity axis requires adapted shifts in muscular contraction modes. In daily life, rising the arm up involves shortening (i.e., concentric) contractions of arm flexors, while the reverse movement can rely on lengthening (i.e., eccentric) contractions of the same muscles with the help of gravity force. Although this muscular-control mode is universal, the neuromuscular mechanisms that subserve the control of such gravity-oriented movements remain unknown. In this study, we designed two neurophysiological experiments that allowed tracking modulations of cortical, spinal, and muscular outputs of arm flexors while healthy humans carried out vertical pointing movements. In conditions where upward and downward movements revealed kinematic features reminiscent of optimal motor commands (i.e., directional asymmetries), we report fine contraction-dependent modulations of the corticospinal output. The overall corticospinal excitability dropped during lengthening contractions (downward movements) compared with shortening contractions (upward movements). Specifically, we did not observe any change in spinal motoneuron responsiveness from cervicomedullary stimulations but a specific increase in intracortical inhibition during lengthening vs. shortening contractions. We discuss these fine contraction-dependent modulations of the supraspinal motor output in the light of feedforward mechanisms that may support gravity-tuned motor control. Generally, these results shed a new perspective on the neural policy that optimize movement control along the gravity axis.
Identification and characterisation of splicing regulators in Toxoplasma gondii
Authors: Lee V Vern , Seizova Simona , McMillan Paul J. , McHugh Emma , Tonkin Christopher J. , Ralph Stuart A.
Published: June 2021

The splicing of mRNA constitutes a major source of co- and post-transcriptional regulation in metazoans. In particular, members of the serine/arginine (SR) protein family are essential splicing factors that are implicated in the regulation of gene expression and RNA metabolism. However, very little is known about these proteins in apicomplexans, a phylum that includes some of the most important global parasites. In this study, we investigated the suite of three uncharacterised SR proteins in Toxoplasma gondii and show that all three are found localised to nuclear speckles. We show, by genetic ablation, that TgSR1 is particularly important for T. gondii growth. Using RNA-seq, we also characterised the global gene expression and splicing regulation of these proteins. We find that the SR proteins regulate several types of alternative splicing of distinct but overlapping subsets of transcripts, as well as impacting transcript abundance. Most of the alternative splicing events are non-productive intron retention events that do not appear to affect transcript abundance. The splicing sites of the impacted transcripts are enriched in characteristic SR binding motifs. We also identified and conditionally knocked down two putative kinases of SR proteins. The kinases are localised to nuclear speckles and are essential to parasite survival. Their perturbation resulted in widespread changes to splicing, but the affected transcripts did not mirror the patterns seen in knockouts of individual SRs, suggesting an absence of a simple relationship between SRs and these putative kinase regulators. Overall, this study reveals a complex system of splicing factors and kinases that post-transcriptionally regulate gene expression in T. gondii.
Evolution and favored change: a principle of least selection
Authors: Yarus Michael
Published: June 2021

Favored biological characteristics can evolve by a subtle path, but beneficial selection has predictable qualities to guide thought. These favored pathways are paths of “least selection”. Faster evolution is least selection, more probable because earlier evolutionary success is simply, “success”. A more likely path also requires least selection in the form of least selected change. Truncation selections, accepting only extreme values of a distributed quantity, produce greater change in population means. Truncation selection therefore readily offers a least selection. Assuming selection for a Normally-distributed quality, truncation is enhanced via simple dependences on increased standard deviation and higher selection threshold (consistent with some population survival). Least selection applies to both chemical and biological evolution, and can be estimated in general form, without reference to its genetics, from an underlying phenotypic distribution. Chemical truncation selection is free of the Haldane cost of natural selection; potentially yielding very rapid early evolution. Notably, a principle of least selection unifies prior examples of quick evolution. For example: the ‘crescendo’ of accurate codes leading to the Standard Genetic Code facilitates a least selection. More generally, evolutionary extinctions and radiations are events with multiple coercive thresholds; thus Earth’s history offers many wide-ranging truncation/least selection events.
Stress decreases serotonin tone in the nucleus accumbens to promote aversion and potentiate cocaine preference via decreased stimulation of 5-HT1B receptors
Authors: Fontaine Harrison M , Silva Phillip R , Neiswanger Carlie , Tran Rachelle , Abraham Antony D , Land Benjamin B , Neumaier John F , Chavkin Charles
Published: June 2021

Stress-induced release of dynorphins (Dyn) activates kappa opioid receptors (KOR) in monoaminergic neurons to produce dysphoria and potentiate drug reward; however, the circuit mechanisms responsible for this effect are not known. We found that conditional deletion of KOR from Slc6a4 (SERT)-expressing neurons blocked stress-induced potentiation of cocaine conditioned place preference (CPP). Within the dorsal raphe nucleus (DRN), two overlapping populations of KOR-expressing neurons: Slc17a8 (VGluT3) and SERT, were distinguished functionally and anatomically. Optogenetic inhibition of these SERT+ neurons potentiated subsequent cocaine CPP, whereas optical inhibition of the VGluT3+ neurons blocked subsequent cocaine CPP. SERT+/VGluT3− expressing neurons were concentrated in the lateral aspect of the DRN. SERT projections from the DRN were observed in the medial nucleus accumbens (mNAc), but VGluT3 projections were not. Optical inhibition of SERT+ neurons produced place aversion, whereas optical stimulation of SERT+ terminals in the mNAc attenuated stress-induced increases in forced swim immobility and subsequent cocaine CPP. KOR neurons projecting to mNAc were confined to the lateral aspect of the DRN, and the principal source of dynorphinergic (Pdyn) afferents in the mNAc was from local neurons. Excision of Pdyn from the mNAc blocked stress-potentiation of cocaine CPP. Prior studies suggested that stress-induced dynorphin release within the mNAc activates KOR to potentiate cocaine preference by a reduction in 5-HT tone. Consistent with this hypothesis, a transient pharmacological blockade of mNAc 5-HT1B receptors potentiated subsequent cocaine CPP. 5-HT1B is known to be expressed on 5-HT terminals in NAc, and 5-HT1B transcript was also detected in Pdyn+, Adora2a+ and ChAT+ (markers for direct pathway, indirect pathway, and cholinergic interneurons, respectively). Following stress exposure, 5-HT1B transcript was selectively elevated in Pdyn+ cells of the mNAc. These findings suggest that Dyn/KOR regulates serotonin activation of 5HT1B receptors within the mNAc and dynamically controls stress response, affect, and drug reward.
Clinical recovery of Macaca fascicularis infected with Plasmodium knowlesi
Authors: Peterson Mariko S. , Joyner Chester J. , Brady Jessica A. , Wood Jennifer S. , Cabrera-Mora Monica , Saney Celia L. , Fonseca Luis L. , Cheng Wayne T. , Jang Jianlin , Lapp Stacey A. , Soderberg Stephanie R. , Nural Mustafa V. , Humphrey Jay C. , Hankus Allison , Machiah Deepa , Karpuzoglu Ebru , DeBarry Jeremy D. ,   MaHPIC-Consortium, Tirouvanziam Rabindra , Kissinger Jessica C. , Moreno Alberto , Gumber Sanjeev , Voit Eberhard O. , Gutiérrez Juan B. , Cordy Regina Joice , Galinski Mary R.
Published: June 2021

Background

Kra monkeys (Macaca fascicularis), a natural host of Plasmodium knowlesi, control parasitaemia caused by this parasite species and escape death without treatment. Knowledge of the disease progression and resilience in kra monkeys will aid the effective use of this species to study mechanisms of resilience to malaria. This longitudinal study aimed to define clinical, physiological and pathological changes in kra monkeys infected with P. knowlesi, which could explain their resilient phenotype.

Methods

Kra monkeys (n = 15, male, young adults) were infected intravenously with cryopreserved P. knowlesi sporozoites and the resulting parasitaemias were monitored daily. Complete blood counts, reticulocyte counts, blood chemistry and physiological telemetry data (n = 7) were acquired as described prior to infection to establish baseline values and then daily after inoculation for up to 50 days. Bone marrow aspirates, plasma samples, and 22 tissue samples were collected at specific time points to evaluate longitudinal clinical, physiological and pathological effects of P. knowlesi infections.

Results

As expected, the kra monkeys controlled parasitaemia and remained with low-level, persistent parasitaemias without antimalarial intervention. Unexpectedly, early in the infection, fevers developed, which ultimately returned to baseline, as well as mild to moderate thrombocytopaenia, and moderate to severe anaemia. Mathematical modeling and the reticulocyte production index indicated that the anaemia was largely due to the removal of uninfected erythrocytes and not impaired production of erythrocytes. Mild tissue damage was observed, and tissue parasite load was associated with tissue damage even though parasite accumulation in the tissues was generally low.

Conclusions

Kra monkeys experimentally infected with P. knowlesi sporozoites presented with multiple clinical signs of malaria that varied in severity among individuals. Overall, the animals shared common mechanisms of resilience characterized by controlling parasitaemia 3-5 days after patency, and controlling fever, coupled with physiological and bone marrow responses to compensate for anaemia. Together, these responses likely minimized tissue damage while supporting the establishment of chronic infections, which may be important for transmission in natural endemic settings. These results provide new foundational insights into malaria pathogenesis and resilience in kra monkeys, which may improve understanding of human infections.
A novel small molecule that induces cytotoxicity in lung cancer cells inhibits disulfide reductases GSR and TXNRD1
Authors: Johnson Fraser D. , Ferrarone John , Liu Alvin , Brandstädter Christina , Munuganti Ravi , Farnsworth Dylan , Lu Daniel , Luu Jennifer , Sihota Tianna , Jansen Sophie , Nagelberg Amy , Shi Rocky , Forcina Giovanni C. , Zhang Xu , Cheng Grace S. W. , Spencer Miko Sandra E. , de Rappard-Yuswack Georgia , Sorensen Poul H. , Dixon Scott J. , Guha Udayan , Becker Katja , Djaballah Hakim , Somwar Romel , Varmus Harold , Morin Gregg B. , Lockwood William W.
Published: June 2021

High-throughput phenotype-based screening of large libraries of novel compounds without known targets can identify small molecules that elicit a desired cellular response, but additional approaches are required to find and characterize their targets and mechanisms of action. Here we show that a compound termed lung cancer screen 3 (LCS3), previously selected for its ability to impair the growth of human lung adenocarcinoma (LUAD) cell lines, but not normal lung cells, induces oxidative stress and activates the NRF2 signaling pathway by generating reactive oxygen species (ROS) in sensitive LUAD cell lines. To identify the target that mediates this effect, we applied thermal proteome profiling (TPP) and uncovered the disulfide reductases GSR and TXNRD1 as LCS3 targets. Through enzymatic assays using purified protein, we confirmed that LCS3 inhibits disulfide reductase activity through a reversible, uncompetitive mechanism. Further, we demonstrate that LCS3-sensitive LUAD cells are correspondingly sensitive to the synergistic inhibition of glutathione and thioredoxin pathways. Lastly, a genome-wide CRISPR knockout screen identified the loss of NQO1 as a mechanism of LCS3 resistance. This work highlights the ability of TPP to uncover targets of small molecules identified by high-throughput screens and demonstrates the potential utility of inhibiting disulfide reductases as a therapeutic strategy for LUAD.
Repurposing of the enhancer-promoter communication underlies the compensation of Mesp2 by Mesp1
Authors: Okada Hajime , Saga Yumiko
Published: June 2021

Organisms are inherently equipped with buffering systems against genetic perturbations. Upregulation of homologous genes responding to gene loss, termed genetic compensation, is one such buffering mechanism. Recently, a well-conserved compensatory mechanism was proposed: transcriptional adaptation of homologs under the nonsense-mediated mRNA decay pathways. However, this model cannot explain the onset of all compensatory events. We report a novel genetic compensation mechanism operating over the Mesp gene locus. Mesp1 and Mesp2 are homologs located adjacently in the genome. Mesp2 loss is partially rescued by Mesp1 upregulation in the presomitic mesoderm (PSM). Using a cultured PSM induction system, we reproduced the compensatory response in vitro and found that the Mesp2-enhancer is required to promote Mesp1. We revealed that the Mesp2-enhancer directly interacts with the Mesp1 promoter, thereby upregulating Mesp1 expression upon the loss of Mesp2. Of note, this interaction is established by genomic arrangement upon PSM development independently of Mesp2 disruption. We propose that the repurposing of this established enhancer-promoter communication is the mechanism underlying this compensatory response for the upregulation of the adjacent homolog.
DAB2IP inhibits p53 ubiquitin-mediated degradation by competitively binding to GRP75 and suppresses tumor malignancy in colon cancer
Authors: Shen Jie , Feng Shengjie , Deng Jiao , Huang Qingwen , Zhao Dayong , Jia Weiyi , Li Xiaolan , Tao Deding , Gong Jianping , Xie Daxing , Liu Liang
Published: June 2021

Increasing evidence has shown that DAB2IP acts as a tumor suppressor and plays an inhibition role in many tumors. However, the underlying mechanism is still uncertain. Our study shows that DAB2IP is positively associated with a better prognosis in colon cancer patients with wild-type TP53 expression. In vitro assay shows that DAB2IP elicits potent tumor-suppressive effects on inhibiting cell invasiveness, colony formation and promoting cell apoptosis in wild-type TP53 colon cancer cell lines. Subsequently, DAB2IP is demonstrated to up-regulate the stability of wild-type TP53 by inhibiting its degradation in a ubiquitin-proteasome-dependent manner. Using mass spectrometry profiling, we unveil that DAB2IP and p53 could both interact with the ubiquitin ligase-related protein, GRP75. Mechanistically, DAB2IP could competitively bind with GRP75, thus reducing GRP75-mediated p53 ubiquitination and degradation. Finally, animal experiments also reveal that DAB2IP inhibits the tumor progression in vivo. In conclusion, our study presents a novel function of DAB2IP in GRP75-driven wild-type p53 degradation, which provides a new insight in DAB2IP-induced tumor suppression and provides a novel molecular aspect of the p53 pathway.
Nanoscopical analysis reveals an orderly arrangement of the presynaptic scaffold protein Bassoon at the Golgi-apparatus
Authors: Ghelani Tina , Montenegro-Venegas Carolina , Fejtova Anna , Dresbach Thomas
Published: June 2021

1.

Bassoon is a large, 440 kDa, scaffold protein of the specialized sites mediating neurotransmitter release from presynaptic nerve terminals, called active zones. At active zones of the brain, Bassoon is arranged with its C-terminus facing the plasma membrane. In young, cultured neurons Bassoon is associated with the Golgi-apparatus, where it may assemble active zone precursors structures, but whether or not Bassoon is an extended protein at the Golgi-apparatus and whether it is arranged in an orderly fashion is unknown. Understanding the topology of this large scaffold protein is important for models of active zone biogenesis.

Here, we generated recombinant Bassoon constructs for expression in neurons, with tags positioned to allow for the specific detection of N- and C-terminal regions of Bassoon by single-domain antibodies, called nanobodies. Using stimulated emission depletion (STED) nanoscopy in cultured hippocampal neurons, we confirmed that recombinant Bassoon is oriented with its C-terminus towards the active zone plasma membrane at synapses. Focusing on the soma, we found that an intramolecular tag located immediately downstream of amino acid 97 of Bassoon, showed prominent colocalization with markers of the trans Golgi network, including TGN38 and syntaxin-6. In contrast, tags located immediately downstream of the C-terminal amino acid 3938 of Bassoon showed significantly less colocalization with these Golgi-markers. The intramolecular N-terminal tag was located between 48 and 69 nm away from TGN38, while C-terminal tags were located between 100 and 115 nm away from TGN38. Sequences within the first 95 amino acids of Bassoon, but not its N-myristoylation sequence, were required for this arrangement.

Our results indicate that at the Golgi-apparatus Bassoon is oriented with its N-terminus towards and its C-terminus away from the trans Golgi network membrane. Moreover, they suggest that Bassoon is an extended molecule at the trans Golgi network with the distance between amino acids 97 and 3938 estimated to be between 46 and 52 nm. Our data are consistent with a model, in which the N-terminus of Bassoon binds to the membranes of the trans-Golgi network, while the C-terminus associates with active zone components, thus reflecting the topographic arrangement characteristic of synapses also at the Golgi-apparatus.
Sleep spindle frequency: overnight dynamics, afternoon nap effects, and possible circadian modulation
Authors: Bódizs Róbert , Horváth Csenge G. , Szalárdy Orsolya , Ujma Péter P. , Simor Péter , Gombos Ferenc , Kovács Ilona , Genzel Lisa , Dresler Martin
Published: June 2021

Homeostatic and circadian processes play a pivotal role in determining sleep structure, timing and quality. In sharp contrast with the wide accessibility of the EEG index of sleep homeostasis, an electrophysological measure of the circadian modulation of sleep is still non-available. Evidence suggests that sleep spindle frequencies decelerate during biological night. In order to test the feasibility of measuring this marker in common polysomnographic protocols, the Budapest-Munich database of sleep records (N = 251 healthy subjects, 122 females, age range: 4–69 years), as well as an afternoon nap sleep record database (N = 112 healthy subjects, 30 females, age range: 18–30 years) were analysed by the Individual Adjustment Method of sleep spindle analysis. Slow and fast sleep spindle frequencies were characterized by U-shaped overnight dynamics, with highest values in the first and the fourth-to-fifth sleep cycle and the lowest values in the middle of the sleeping period (cycles 2–3). Age-related attenuation of sleep spindle deceleration was evident. Estimated phases of the nadirs in sleep spindle frequencies were advanced in children as compared to other age groups. Additionally, nap sleep spindles were faster than night sleep spindles (0.57 and 0.39 Hz difference for slow and fast types, respectively). The fine frequency resolution analysis of sleep spindles is a feasible method of measuring the assumed circadian modulation of sleep. Moreover, age-related attenuation of circadian sleep modulation might be measurable by assessing the overnight dynamics in sleep spindle frequency. Phase of the minimal sleep spindle frequency is a putative biomarker of chronotype.
Inhibition of Casein Kinase 2 induces cell death in chronic myelogenous leukemia cells resistant to tyrosine kinase inhibitors
Authors: Mitrovský Ondřej , Myslivcová Denisa , Macháčková-Lopotová Tereza , Obr Adam , Čermáková Kamila , Ransdorfová Šárka , Březinová Jana , Klamová Hana , Žáčková Markéta
Published: June 2021

Chronic myelogenous leukemia (CML) is a myeloproliferative disease characterized by the presence of a BCR-ABL oncogene. Despite the high performance of treatment with tyrosine kinase inhibitors (TKI), about 30 % of patients develop resistance to the therapy. To improve the outcomes, identification of new targets of treatment is needed. Here, we explored the Casein Kinase 2 (CK2) as a potential target for CML therapy. Previously, we detected increased phosphorylation of HSP90β Serine 226 in patients non-responding to TKIs imatinib and dasatinib. This site is known to be phosphorylated by CK2, which was also linked to CML resistance to imatinib. In the present work, we established six novel imatinib- and dasatinib-resistant CML cell lines, all of which had increased CK2 activation. A CK2 inhibitor, CX-4945, induced cell death of CML cells in both parental and resistant cell lines. In some cases, CK2 inhibition also potentiated the effects of TKI on the cell metabolic activity. No effects of CK2 inhibition were observed in normal mononuclear blood cells from healthy donors and BCR-ABL negative HL60 cell line. Our data indicate that CK2 kinase supports CML cell viability even in cells with different mechanisms of resistance to TKI, and thus represents a potential target for treatment.
Global analysis of putative phospholipases in the malaria parasite Plasmodium falciparum reveals critical factors for parasite proliferation
Authors: Burda Paul-Christian , Ramaprasad Abhinay , Pietsch Emma , Bielfeld Sabrina , Söhnchen Christoph , Wilcke Louisa , Strauss Jan , Schwudke Dominik , Sait Aaron , Collinson Lucy M , Blackman Michael J , Gilberger Tim-Wolf
Published: June 2021

For its replication within red blood cells, the malaria parasite is highly dependent on correctly regulated lipid metabolism. Enzymes involved in lipid metabolic processes are therefore potential drug targets. We here provide a functional analysis of the 20 putative phospholipases that are expressed by asexual blood stages of Plasmodium falciparum. We reveal a high level of redundancy among members of this group, but using conditional mislocalization and gene disruption techniques we show that the phosphoinositide-specific phospholipase C (PF3D7_1013500) has a previously unrecognized essential role in intracellular parasite maturation. In addition, we demonstrate that the patatin-like phospholipase PF3D7_1358000 localizes to the mitochondrion. Parasites lacking this enzyme display a severe growth phenotype and defects in mitochondrial morphogenesis and function leading to hypersensitivity towards proguanil and inhibitors of the mitochondrial electron transport chain including atovaquone. This demonstrates that regulated mitochondrial lipid homeostasis is necessary for mitochondrial function and coordinated division during parasite multiplication.
Identification and verification of the potential effect of therapeutic miRNA-mRNA pairs on ferroptosis in small cell lung cancer by bioinformatics analysis
Authors: Wu Yuefeng
Published: June 2021

Owing to the high mortality rate of small cell lung cancer (SCLC), it is essential to determine a novel therapeutic approach for treating patients with SCLC. miRNA is a type of non-coding RNA that plays a role in translational control. By applying this identity, it is applicable for treating patients using miRNA and nanotechnology. Ferroptosis is a newly discovered type of programmed cell death. Accumulated evidence suggests the possibility of using ferroptosis in treating patients with SCLC. Thus, identifying potential therapeutic miRNA-mRNA pairs that have an impact on ferroptosis will be valuable. In the in silico analysis, several Gene Expression Omnibus datasets were analyzed. The results were verified using other data. Here, we report that the miR-30 family and KIF11 pair have a crucial influence on SCLC cells, which may also affect ferroptosis.
Regulation of Myoepithelial Differentiation in 3-Dimensional Culture
Authors: Thiemann Renee F. , Varney Scott , Moskwa Nicholas , Lamar John , Larsen Melinda , LaFlamme Susan E.
Published: June 2021

The salivary gland can be permanently impaired by radiation treatment for head and neck cancers. Efforts at tissue regeneration have focused on saliva-producing acinar cells. However, myoepithelial cells are also critical to gland function, but mechanisms that regulate their differentiation are poorly defined. To study myoepithelial differentiation, we employed mSG-PAC1 murine salivary gland epithelial cells. We demonstrate that mSG-PAC1 spheroids exhibit phenotypic plasticity between pro-acinar and myoepithelial cell fates. Increased expression of pro-acinar/acinar or myoepithelial RNAs was identified from spheroids cultured under different media conditions by microarray followed by gene-set enrichment analysis. Spheroids cultured with different medium components expressed proteins typical of either acinar or myoepithelial cells, as detected by immunocytochemistry. We demonstrate that the pattern of TAZ expression in the epithelial compartment of the differentiating murine salivary gland correlates with the expression of the myoepithelial marker alpha-SMA, as is the case for TAZ expression in mSG-PAC1 spheroids. Our analysis also indicates that YAP/TAZ target genes are upregulated together with myoepithelial markers. Importantly, siRNA targeting of TAZ expression in mSG-PAC1 spheroids diminished the expression of myoepithelial markers. Our results in thisin vitrocell model implicate TAZ signaling in myoepithelial differentiation.
Assessment of Molecular Mechanics-based Zn2+ Models in Mono- and Bimetallic Ligand Binding Sites
Authors: Melse Okke , Antes Iris
Published: June 2021

Zn2+ ions play an important role in biology, but accurate sampling of metalloproteins using Molecular Mechanics remains challenging. Several models have been proposed to describe Zn2+ in biomolecular simulations, ranging from nonbonded models, employing classical 12-6 Lennard-Jones (LJ) potentials or extended LJ-potentials, to dummy-atom models and bonded models. We evaluated the performance of a large variety of these Zn2+ models in two challenging environments for which little is known about the performance of these methods, namely in a monometallic (Carbonic Anhydrase II) and a bimetallic ligand binding site (metallo-β-lactamase VIM-2). We focused on properties which are important for a stable, correct binding site description during molecular dynamics (MD) simulations, because a proper treatment of the metal coordination and forces are here essential. We observed that the strongest difference in performance of these Zn2+ models can be found in the description of interactions between Zn2+ and non-charged ligating atoms, such as the imidazole nitrogen in histidine residues. We further show that the nonbonded (12-6 LJ) models struggle most in the description of Zn2+-biomolecule interactions, while the inclusion of ion-induced dipole effects strongly improves the description between Zn2+ and non-charged ligating atoms. The octahedral dummy-atom models result in highly stable simulations and correct Zn2+ coordination, and are therefore highly suitable for binding sites containing an octahedral coordinated Zn2+ ion. The results from this evaluation study in ligand binding sites can guide structural studies of Zn2+ containing proteins, such as MD-refinement of docked ligand poses and long-term MD simulations.
Glypican-6 deficiency causes dose-dependent conotruncal congenital heart malformations through abnormal remodelling of the endocardial cushions
Authors: Tenin Gennadiy , Crozier Alexander , Hentges Kathryn E. , Keavney Bernard
Published: June 2021

Tetralogy of Fallot (TOF) is considered to be the commonest type of cyanotic congenital heart disease (CHD). A previous GWAS showed significant association between TOF and single nucleotide polymorphisms in chromosome 13q31. Here through integration of population genomic and chromosomal interaction data we identify the heparan sulfate proteoglycan glypican-6 (GPC6) as the potentially responsible gene at the associated locus. We showed that GPC6 is expressed in the endocardial cushions at the appropriate time in development to contribute to TOF risk. We generated mice homozygous for a Gpc6 KO allele, which exhibit 100% neonatal lethality with severe cardiac malformations, namely TOF-type double outlet right ventricle (DORV) with rightward mal-positioned aorta and perimembranous ventricular septal defect (VSD), together with right ventricular (RV) hypertrophy and narrowing of the pulmonary artery. We established a dose-response relationship between Gpc6 expression and the anatomical severity of cardiac malformations. We showed the mouse knockout phenotype arises from abnormal morphology of the endocardial cushions, and tissue-specific knockout of Gpc6 in endothelial and neural crest cell lineages produces a phenotype featuring VSD and aortic malposition analogous to human TOF. This successful identification of a CHD gene from GWAS data suggests that larger GWA studies may find additional causative genes.
Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs
Authors: Smith Zachary , Tiwary Pratyush
Published: June 2021

Molecular dynamics (MD) simulations provide a wealth of high-dimensional data at all-atom and femtosecond resolution but deciphering mechanistic information from this data is an ongoing challenge in physical chemistry and biophysics. Theoretically speaking, joint probabilities of the equilibrium distribution contain all thermodynamic information, but they prove increasingly difficult to compute and interpret as the dimensionality increases. Here, inspired by tools in probabilistic graphical modeling, we develop a factor graph trained through belief propagation that helps factorize the joint probability into an approximate tractable form that can be easily visualized and used. We validate the study through the analysis of the conformational dynamics of two small peptides with 5 and 9 residues. Our validations include testing the conditional dependency predictions through an intervention scheme inspired by Judea Pearl. Secondly we directly use the belief propagation based approximate probability distribution as a high-dimensional static bias for enhanced sampling, where we achieve spontaneous back-and-forth motion between metastable states that is up to 350 times faster than unbiased MD. We believe this work opens up useful ways to thinking about and dealing with high-dimensional molecular simulations.