bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon
Authors: Verta Jukka-Pekka , Barton Henry , Pritchard Victoria , Primmer Craig
Published: November 2020

Whole genome duplications (WGD) have been considered as springboards that potentiate lineage diversification through increasing functional redundancy. Divergence in gene regulatory elements is a central mechanism for evolutionary diversification, yet the patterns and processes governing regulatory divergence following events that lead to massive functional redundancy, such as WGD, remain largely unknown. We studied the patterns of divergence and strength of natural selection on regulatory elements in the Atlantic salmon (Salmo salar) genome, which has undergone WGD 100-80 Mya. Using ChIPmentation, we first show that H3K27ac, a histone modification typical to enhancers and promoters, is associated with genic regions, tissue specific transcription factor binding motifs, and with gene transcription levels in immature testes. Divergence in transcription between duplicated genes from WGD (ohnologs) correlated with difference in the number of proximal regulatory elements, but not with promoter elements, suggesting that functional divergence between ohnologs after WGD is mainly driven by enhancers. By comparing H3K27ac regions between duplicated genome blocks, we further show that a longer polyploid state post-WGD has constrained asymmetric regulatory evolution. Patterns of genetic diversity across natural populations inferred from re-sequencing indicate that recent evolutionary pressures on H3K27ac regions are dominated by largely neutral evolution. In sum, our results suggest that post-WGD functional redundancy in regulatory elements continues to have an impact on the evolution of the salmon genome, promoting largely neutral evolution of regulatory elements despite their association with transcription levels. These results highlight a case where genome-wide regulatory evolution following an ancient WGD is dominated by genetic drift.

Significance statement

Regulatory evolution following whole genome duplications (WGD) has been investigated at the gene expression level, but studies of the regulatory elements that control expression have been lacking. By investigating regulatory elements in the Atlantic salmon genome, which has undergone a whole genome duplication 100-80 million years ago, we discovered patterns suggesting that neutral divergence is the prevalent mode of regulatory element evolution post-WGD. Our results suggest mechanisms for explaining the prevalence of asymmetric gene expression evolution following whole genome duplication, as well as the mismatch between evolutionary rates in enhancers versus that of promoters.
Exploring the limits of ComBat method for multi-site diffusion MRI harmonization
Authors: Cetin-Karayumak Suheyla , Stegmayer Katharina , Walther Sebastian , Szeszko Philip R. , Crow Tim , James Anthony , Keshavan Matcheri , Kubicki Marek , Rathi Yogesh
Published: November 2020

The findings from diffusion-weighted magnetic resonance imaging (dMRI) studies often show inconsistent and sometimes contradictory results due to small sample sizes as well as differences in acquisition parameters and pre-/post-processing methods. To address these challenges, collaborative multi-site initiatives have provided an opportunity to collect larger and more diverse groups of subjects, including those with neuropsychiatric disorders, leading to increased power and findings that may be more representative at the group and individual level. With the availability of these datasets openly, the ability of joint analysis of multi-site dMRI data has become more important than ever. However, intrinsic- or acquisition-related variability in scanner models, acquisition protocols, and reconstruction settings hinder pooling multi-site dMRI directly. One powerful and fast statistical harmonization method called ComBat (https://github.com/Jfortin1/ComBatHarmonization) was developed to mitigate the “batch effect” in gene expression microarray data and was adapted for multi-site dMRI harmonization to reduce scanner/site effect. Our goal is to evaluate this commonly used harmonization approach using a large diffusion MRI dataset involving 542 individuals from 5 sites. We investigated two important aspects of using ComBat for harmonization of fractional anisotropy (FA) across sites: First, we assessed how well ComBat preserves the inter-subject biological variability (measured by the effect sizes of between-group FA differences) after harmonization. Second, we evaluated the effect of minor differences in pre-processing on ComBat’s performance. While the majority of effect sizes are mostly preserved in some sites after harmonization, they are not well-preserved at other sites where non-linear scanner contributions exist. Further, even minor differences in pre-processing can yield unwanted effects during ComBat harmonization. Thus, our findings suggest paying careful attention to the data being harmonized as well as using the same processing pipeline while using ComBat for data harmonization.
Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation
Authors: Bonora Giancarlo , Ramani Vijay , Singh Ritambhara , Fang He , Jackson Dana , Srivatsan Sanjay , Qiu Ruolan , Lee Choli , Trapnell Cole , Shendure Jay , Duan Zhijun , Deng Xinxian , Noble William S. , Disteche Christine M.
Published: November 2020

Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentiation and X inactivation by integrating, for the first time, allele-specific data obtained by high-throughput single-cell RNA-seq, ATAC-seq, and Hi-C. In differentiated cells, contact decay profiles, which clearly distinguish the active and inactive X chromosomes, reveal loss of the inactive X-specific structure at mitosis followed by a rapid reappearance, suggesting a ‘bookkeeping’ mechanism. In differentiating embryonic stem cells, changes in contact decay profiles are detected in parallel on both the X chromosomes and autosomes, suggesting profound simultaneous reorganization. The onset of the inactive X-specific structure in single cells is notably delayed relative to that of gene silencing, consistent with the idea that chromatin compaction is a late event of X inactivation. Novel computational approaches to effectively align single-cell gene expression, chromatin accessibility, and 3D chromosome structure reveal that long-range structural changes to chromosomes appear as discrete events, unlike progressive changes in gene expression and chromatin accessibility.
Virus-derived variation in diverse human genomes
Authors: Kojima Shohei , Kamada Anselmo Jiro , Parrish Nicholas F.
Published: November 2020

Acquisition of genetic material from viruses by their hosts can generate inter-host structural genome variation. We developed computational tools enabling us to study virus-derived structural variants (SVs) in population-scale whole genome sequencing (WGS) datasets and applied them to 3,332 humans. Although SVs had already been cataloged in these subjects, we found previously-overlooked virus-derived SVs. We detected somatic SVs present in the sequenced lymphoblastoid cell lines (LCLs) derived from squirrel monkey retrovirus (SMRV), human immunodeficiency virus 1 (HIV-1), and human T lymphotropic virus (HTLV-1); these variants are attributable to infection of LCLs or their progenitor cells and may impact gene expression results and the biosafety of experiments using these cells. In addition, we detected new heritable SVs derived from human herpesvirus 6 (HHV-6) and human endogenous retrovirus-K (HERV-K). We report the first solo-DR HHV-6 that likely to reflects rearrangement of a known full-length endogenous HHV-6. We used linkage disequilibrium between single nucleotide variants (SNVs) and variants in reads that align to HERV-K, which often cannot be mapped uniquely using conventional short-read sequencing analysis methods, to locate previously-unknown polymorphic HERV-K loci. Some of these loci are tightly linked to trait-associated SNVs, some are in complex genome regions inaccessible to prior methods, and some contain novel HERV-K haplotypes likely derived from gene conversion from an unknown source or introgression. These tools and results broaden our perspective on the coevolution between viruses and humans, including ongoing virus-to-human gene transfer contributing to genetic variation between humans.
Chromosomal neighbourhoods allowidentification of organ specific changesin gene expression
Authors: Roy Rishi Das , Hallikas Outi , Christensen Mona M. , Renvoisé Elodie , Jernvall Jukka
Published: November 2020

Although most genes share their chromosomal neighbourhood with other genes, distribution of genes has not been explored in the context of individual organ development; the common focus of developmental biology studies. Because developmental processes are often associated with initially subtle changes in gene expression, here we explored whether neighbouring genes are informative in the identification of differentially expressed genes. First, we quantified the chromosomal neighbourhood patterns of genes having related functional roles in the mammalian genome. Although the majority of protein coding genes have at least five neighbours within 1 Mb window around each gene, very few of these neighbours regulate development of the same organ. Analyses of transcriptomes of developing mouse molar teeth revealed that whereas expression of genes regulating tooth development changes, their neighbouring genes show no marked changes, irrespective of their level of expression. Finally, we test whether inclusion of gene neighbourhood in the analyses of differential expression could provide additional benefits. For the analyses, we developed an algorithm, called DELocal that identifies differentially expressed genes by comparing their expression changes to changes in adjacent genes in their chromosomal regions. Our results show that DELocal removes detection bias towards large changes in expression, thereby allowing identification of even subtle changes in development. Future studies, including the detection of differential expression, may benefit from, and further characterize the significance of gene-gene neighbour relationships.

Author Summary

Development of organs is typically associated with small and hard to detect changes in gene expression. Here we examined how often genes regulating specific organs are neighbours to each other in the genome, and whether this gene neighbourhood helps in the detection of changes in gene expression. We found that genes regulating individual organ development are very rarely close to each other in the mouse and human genomes. We built an algorithm, called DELocal, to detect changes in gene expression that incorporates information about neighbouring genes. Using transcriptomes of developing mouse molar teeth containing gene expression profiles of thousands of genes, we show how genes regulating tooth development are ranked high by DELocal even if their expression level changes are subtle. We propose that developmental biology studies can benefit from gene neighbourhood analyses in the detection of differential expression and identification of organ specific genes.
Quantitative dSTORM super-resolution microscopy localizes Aurora kinase A/AURKA in the mitochondrial matrix
Authors: Durel Béatrice , Kervrann Charles , Bertolin Giulia
Published: November 2020

Mitochondria are dynamic organelles playing essential metabolic and signaling functions in cells. Their ultrastructure has largely been investigated with electron microscopy (EM) techniques, which provided a wide range of information on how mitochondria acquire a tissue-specific shape, how they change during development, and how they are altered in disease conditions. However, quantifying protein-protein proximities using EM is extremely challenging. Super-resolution microscopy techniques as direct stochastic optical reconstruction microscopy (dSTORM) now provide a fluorescent-based alternative to EM with a higher quantitative throughput. Recently, super-resolution microscopy approaches including dSTORM led to valuable advances in our knowledge of mitochondrial ultrastructure, and in linking it with new insights in organelle functions. Nevertheless, dSTORM is currently used to image integral mitochondrial proteins only, and there is little or no information on proteins transiently present at this compartment. The cancer-related Aurora kinase A/AURKA is a protein localized at various subcellular locations, including mitochondria. After performing dSTORM, we here use the Geo-coPositioning System (GcoPS) image analysis method to quantify the degree of colocalization of AURKA with compartment-specific mitochondrial markers. We show that two-color dSTORM provides sufficient spatial resolution to visualize AURKA in the mitochondrial matrix. We conclude by demonstrating that optimizing fixation procedures is a key step to follow AURKA in the matrix. In this light, we show that a methanol-based fixation leads to a better detection of the matrix pool of AURKA than an aldehyde-based fixation. Our results indicate that dSTORM coupled to GcoPS colocalization analysis is a suitable approach to explore the compartmentalization of non-integral mitochondrial proteins as AURKA, in a qualitative and quantitative manner. This method also opens up the possibility of analyzing the proximity between AURKA and its multiple mitochondrial partners with exquisite spatial resolution, thereby allowing novel insights into the mitochondrial functions controlled by AURKA.
The effects of different frequencies of rhythmic acoustic stimulation on gait kinematics and trunk sway in healthy elderly population
Authors: Minino Roberta , Lopez Emahnuel Troisi , Sorrentino Pierpaolo , Rucco Rosaria , Lardone Anna , Pesoli Matteo , Tafuri Domenico , Mandolesi Laura , Sorrentino Giuseppe , Liparoti Marianna
Published: November 2020

The use of rhythmic acoustic stimulation (RAS) in improving gait and balance in healthy elderly subjects has been widely investigated. However, methodologies and results are often controversial. In this study, we hypothesize that both the kinematic features of gait and stability, depend on the frequency at which RAS is administered. Our aim was to observe, through 3D Gait Analysis, the effect of different types of RAS (at a fixed frequency or based on the average cadence of each subject) on both gait spatio-temporal parameters and stability. The latter was estimated through an innovative measure, the trunk displacement index (TDI) that we have recently implemented. We observed that the low frequencies RAS led to a general slowdown of gait, which did not provide any clear benefit and produced harmful effects on stability when the frequency became too low compared to the individual natural frequency. On the contrary, the high frequencies of RAS showed a slight acceleration of gait, accompanied by better stability (as documented by a lower TDI value), regardless of the type of RAS. Finally, the RAS equal to the individual natural cadence also produced an increase in stability.
Bayesian optimization of multivariate genomic prediction models based on secondary traits for improved accuracy gains and phenotyping costs
Authors: Hamazaki Kosuke , Iwata Hiroyoshi
Published: November 2020

Key message

We propose a novel approach to the Bayesian optimization of multi-variate genomic prediction models based on secondary traits to improve accuracy gains and phenotyping costs via efficient Pareto frontier estimation.

Multivariate genomic prediction based on secondary traits, such as data from various omics technologies including high-throughput phenotyping (e.g., unmanned aerial vehicle-based remote sensing), has attracted much attention because it offers improved accuracy gains compared with genomic prediction based only on marker genotypes. Although there is a trade-off between accuracy gains and phenotyping costs of secondary traits, no attempt has been made to optimize these trade-offs. In this study, we propose a novel approach to optimize multivariate genomic prediction models for secondary traits measurable at early growth stages for improved accuracy gains and phenotyping costs. The proposed approach employs Bayesian optimization for efficient Pareto frontier estimation, representing the maximum accuracy at a given cost. The proposed approach successfully estimated the optimal secondary trait combinations across a range of costs while providing genomic predictions for only about 20% of all possible combinations. The simulation results reflecting the characteristics of each scenario of the simulated target traits showed that the obtained optimal combinations were reasonable. Analysis of real-time target trait data showed that the proposed multivariate genomic prediction model had significantly superior accuracy compared to the univariate genomic prediction model.
Modeling the frequency and number of persons to test to detect and control COVID-19 outbreaks in congregate settings
Authors: Paul Prabasaj , Mosites Emily , Laws Rebecca L. , Scobie Heather , Slayton Rachel B. , Clarke Kristie E. N.
Published: November 2020

Background

Congregate settings are at risk for coronavirus disease 2019 (COVID-19) outbreaks. Diagnostic testing can be used as a tool in these settings to identify outbreaks and to control transmission.

Methods

We used transmission modeling to estimate the minimum number of persons to test and the optimal frequency to detect small outbreaks of COVID-19 in a congregate facility. We also estimated the frequency of testing needed to interrupt transmission within a facility.

Results

The number of people to test and frequency of testing needed depended on turnaround time, facility size, and test characteristics. Parameters are calculated for a variety of scenarios. In a facility of 100 people, 26 randomly selected individuals would need to be tested at least every 6 days to identify a true underlying prevalence of at least 5%, with test sensitivity of 85%, and greater than 95% outbreak detection sensitivity. Disease transmission could be interrupted with universal, facility-wide testing with rapid turnaround every three days.

Conclusions

Testing a subset of individuals in congregate settings can improve early detection of small outbreaks of COVID-19. Frequent universal diagnostic testing can be used to interrupt transmission within a facility, but its efficacy is reliant on rapid turnaround of results for isolation of infected individuals.
Interaction of Amphiphilic Lipoarabinomannan with Host Carrier Lipoproteins in Tuberculosis Patients: Implications for Blood-based Diagnostics
Authors: Jakhar Shailja , Sakamuri Ramamurthy , Vu Dung , Dighe Priya , Stromberg Loreen R. , Lilley Laura , Hengartner Nicolas , Swanson Basil I. , Moreau Emmanuel , Dorman Susan E. , Mukundan Harshini
Published: November 2020

Lipoarabinomannan (LAM), an amphiphilic lipoglycan of theMycobacterium tuberculosiscell wall, is a diagnostic target for tuberculosis. Previous work from our laboratory and others suggests that LAM is associated with host serum lipoproteins, which may in turn have implications for diagnostic assays. Our team has developed two serum assays for amphiphile detection: lipoprotein capture and membrane insertion. The lipoprotein capture assay relies on capture of the host lipoproteins, exploiting the biological association of host lipoprotein with microbial amphiphilic biomarkers to “concentrate” LAM. In contrast, the membrane insertion assay is independent of the association between pathogen amphiphiles and host lipoprotein association, and directly captures LAM based on its thermodynamic propensity for association with a supported lipid membrane, which forms the functional surface of an optical biosensor. In this manuscript, we explored the use of these assays for the detection of LAM in sera from adults whose tuberculosis status had been well-characterized using conventional microbiological tests, and endemic controls. Using the lipoprotein capture assay, LAM signal/noise ratios were >1.0 in 29/35 (83%) individuals with culture-confirmed active tuberculosis, 8/13 (62%) individuals with tuberculosis symptoms but no positive culture forM. tuberculosis, and 0/6 (0%) symptom-free endemic controls. To evaluate serum LAM levels without bias associated with potential differences in circulating host lipoprotein concentrations between individuals, we subsequently processed available samples to liberate LAM from associated host lipoprotein assemblies followed by direct detection of the pathogen biomarker using the membrane insertion approach. Using the membrane insertion assay, signal/noise for detection of serum LAM was greater than that observed using the lipoprotein capture method for culture-confirmed TB patients (6/6), yet remained negative for controls (2/2). Taken together, these results suggest that detection of serum LAM is a promising TB diagnostic approach. Further work is required to optimize assay performance and to decipher the implications of LAM/host lipoprotein associations for diagnostic assay performance and TB pathogenesis.
Could TDX-1 explain the changes observed in endocrine pancreas due to chronic cola drink consumption in rats? A global point of view
Authors: Cao Gabriel , González Julián , Fragola Juan P. Ortiz , Muller Angélica , Tumarkin Mariano , Moriondo Marisa , Azzato Francisco , Blanco Manuel Vazquez , Milei José
Published: November 2020

In previous studies, we reported evidence showing that chronic cola consumption in rats impairs pancreatic metabolism of insulin and glucagon and produces some alterations typically observed in the metabolic syndrome (i.e, hyperglycemia, and hypertriglyceridemia) with an increase in oxidative stress. Of note, no apoptosis nor proliferation of islet cells could be demonstrated. In the present study, 36 male Wistar rats were divided in three groups to freely drink regular cola, light cola, or water (controls). We assessed the impact of the three different beverages in glucose tolerance, lipid levels, creatinine levels and immunohistochemical changes addressed for the expression of insulin, glucagon, PDX-1 and NGN3 in islet cells, to evaluate the possible participation of PDX-1 in the changes observed in α and β cells after 6 months of treatment. On the other hand, we assessed by stereological methods, the mean volume of islets (Vi) and three important variables, the fractional β-cell area, the cross-sectional area of alpha (A α-cell) and beta cells (A β-cell), and the number of β and α cell per body weight.

Cola drinking caused impaired glucose tolerance as well as fasting hyperglycemia and increase of insulin immunolabeling. Immunohistochemical expression for PDX-1 was significantly high in regular cola consumption group compared to control. In this case, we observed cytoplasmatic and nuclear localization. Likewise, a mild but significant decrease of Vi was detected after 6 months of cola drink consumption compared with control group. Also, we observed a significant decrease of fractional β cell area compared with control rats. Accordingly, a reduced mean value of islet α and β cell number per body weight compared to control was detected. Interestingly, consumption of light cola increased the Vi compared to control. In line with this, a decreased cross-sectional area of β-cells was observed after chronic consumption of both, regular and light cola, compared to controls. On the other hand, NGN3 was negative in all three groups. Our results support for the first time, the idea that TDX-1 plays a key role in the dynamics of the pancreatic islets after chronic consumption of sweetened beverages. The loss of islets cells might be attributed to autophagy, favored by the local metabolic conditions.
Genetically controlled mtDNA editing prevents ROS damage by arresting oxidative phosphorylation
Authors: Stenberg Simon , Li Jing , Gjuvsland Arne B. , Persson Karl , Demitz-Helin Erik , Peña Carles Gonzalez , Yue Jia-Xing , Gilchrist Ciaran , Ärengård Timmy , Ghiaci Payam , Larsson-Berglund Lisa , Zackrisson Martin , Höög Johanna L. , Molin Mikael , Liti Gianni , Omholt Stig W. , Warringer Jonas
Published: November 2020

Deletion of mitochondrial DNA in eukaryotes is mainly attributed to rare accidental events associated with mitochondrial replication or repair of double-strand breaks. We report the discovery that yeast cells arrest harmful intramitochondrial superoxide production by shutting down respiration through genetically controlled deletion of mitochondrial oxidative phosphorylation genes. We show that the regulatory circuitry underlying this editing critically involves the antioxidant enzyme superoxide dismutase 2 and two-way mitochondrial-nuclear communication. While mitochondrial DNA homeostasis is rapidly restored after cessation of a short-term superoxide stress, long-term stress causes maladaptive persistence of the deletion process, leading to complete annihilation of the cellular pool of intact mitochondrial genomes and irrevocable loss of respiratory ability. Our results may therefore be of etiological as well as therapeutic importance with regard to age-related mitochondrial impairment and disease.

One-Sentence Summary

Genetically controlled editing of mitochondrial DNA is an integral part of the yeast’s defenses against oxidative damage.
Agreement Test Between The Six Minutes Walking Test And Four Meter Gait Speed
Authors: Nusdwinuringtyas Nury , Fransiska Tresia , Sunarjo Peggy , Triangto Kevin , Dahlan Sopiyudin
Published: November 2020

Background/Objective

In the field of Physical Medicine and Rehabilitation, it is essential to measure individual functional capacity, which could be evaluated through walking tests. Aside from the commonly used six minutes walking test (6MWT), four meter gait speed (4MGS) are widely used for its practicality. This study aimed to assess the agreement between 4 MGS and the 6MWT in Indonesian healthy adults.

Methods

This agreement analysis study had recruited 61 healthy and sedentary Indonesians aged 18 until 50 years old, and they were instructed to perform three tests, namely 6MWT and 4MGS with six meters and eight meters track. These gait speed were then compared to assess validity.

Results

Mean gait speed results for males in 6MWT is 1.602 m/s, whereas 4MGS in six meter track is 2.114 m/s and similarly 2.108 m/s in the eight meter track. Females on the other hand, achieved 1.462 m/s for 6MWT, 1.908 m/s and 1.986 m/s for 4MGS in six and eight meter simultaneously. Bland Altman Agreement test between the 6MWT and 4MGS shows scatter dots with close limit of agreement, thus showing a good agreement between the 6MWT and 4 MGS with both tracks.

Discussion

Both track length of 4 MGS were in a good agreement with 6MWT for functional capacity assessment.

Conclusions

In response to the COVID-19 pandemic era, shorter track of 4MGS (six meters) can be feasibly utilized. It is evident that shorter duration and track will boost the tests practicality in assessing functional capacity for both inpatient and outpatient settings.
Effects of Na+channel isoforms and lipid membrane environment on temperature tolerance of cardiac Na+current in zebrafish (Danio rerio) and rainbow trout (Oncorhynchus mykiss)
Authors: Haverinen Jaakko , Dzhumaniiazova Irina , Abramochkin Denis V. , Hassinen Minna , Vornanen Matti
Published: November 2020

Heat tolerance of heart rate in fish is suggested to be limited by impaired electrical excitation of the ventricle due to the antagonistic effects of high temperature on Na+(INa) and K+(IK1) ion currents (INais depressed at high temperatures while IK1is resistant to them). To examine the role of Na+channel proteins and the lipid matrix of the channels in heat tolerance of INa, we compared temperature-dependencies of zebrafish (Danio rerio) and rainbow trout (Oncorhynchus mykiss) ventricular INa, and INagenerated by the cloned zebrafish and rainbow trout NaV1.4 and NaV1.5 Na+channels in HEK cells. Whole-cell patch clamp recordings showed that zebrafish ventricular INahas better heat tolerance and slower inactivation kinetics than rainbow trout ventricular INa. In contrast, heat tolerance and inactivation kinetics of zebrafish and rainbow trout NaV1.4 channels are similar when expressed in the identical plasma membrane lipid matrix of HEK cells. The same applies to NaV1.5 channels. Thermal adaptation of the ventricular INais largely achieved by differential expression of Na+channel alpha subunits: zebrafish which tolerate well high temperatures mainly express the slower NaV1.5 isoform, while rainbow trout which prefer cold waters mainly express the faster NaV1.4 isoform. Differences in elasticity (stiffness) of the lipid bilayer may be also involved in thermal adaptation of INa. These findings suggest that both the protein component and its lipid bilayer matrix are involved in thermal adaptation of the voltage-gated Na+channels and therefore in heart rate regulation under thermal stress in fish.
Fecundity determines the outcome of founding queen associations in ants
Authors: Teggers Eva-Maria , Deegener Falk , Libbrecht Romain
Published: November 2020

Animal cooperation evolved because of its benefits to the cooperators. Pleometrosis in ants - the cooperation of queens to found a colony - benefits colony growth, but also incurs costs for some of the cooperators because only one queen usually survives the association. While several traits are associated with queen survival, they tend to be confounded and it is unclear which factor specifically determines the outcome of pleometrosis. In this study, we used the antLasius nigerto monitor offspring production in colonies founded by one or two queens. Then, we experimentally paired queens that differed in fecundity but not in size, andvice versa, to disentangle the effect of these factors on queen survival. Finally, we investigated how fecundity and size differed between queens depending on whether they were chosen as pleometrotic partners. Our results indicate that pleometrosis increased and accelerated worker production via a nutritional boost to the larvae. The most fecund queens more frequently survived the associations, even when controlling for size and worker parentage, and queens selected as pleometrotic partners were less fecund. Our results are consistent with fecundity being central to the onset and outcome of pleometrosis, a typical case of cooperation among unrelated animals.
μ Opioid Receptors Modulate Action Potential Kinetics and Firing Frequency in Neocortical Interneurons
Authors: Dutkiewicz Adrian P , Morielli Anthony D.
Published: November 2020

The endogenous opioid system of the cerebral cortex is an important feature of antinociception and reward valuation through its modulation of inhibitory neocortical interneurons. Dysregulation of this system, through disease or drugs, disrupts the reward system and contributes to eating and mood disorders, impulsive actions, and addiction. Impulsive behaviors can be induced experimentally through infusion of the μ opioid receptor specific agonist [D-Ala2, N-Me-Phe4, Gly5-ol]-Enkephalin (DAMGO) into the frontal cortex in animal models. The mechanism involves increased potassium channel function, which suppresses neocortical interneuron activity. However, much of the data on the effect of this receptor on ion channels have been derived from noncortical μORs, and the identity and effects of the ion channels that the μOR targets in neocortical neurons have not been thoroughly investigated. Based on previous experiments by other labs, we hypothesized that the μOR could activate α-dendrotoxin (αDTX) sensitive channels (Kv1.1, Kv1.2, and Kv1.6 subunits) to exert its inhibitory effects in cortical interneurons. This, in turn, is expected to confer a variety of effects on passive and active electrical properties of the cell. We performed patch-clamp electrophysiology to examine the electrophysiological effects of μORs in cultured neocortical interneurons. We found that a range of features among the 54 membrane and action potential properties we analyzed were modulated by μORs, including action potential kinetics and frequency. The Kv1.1, Kv1.2, and Kv1.6 inhibitor αDTX reversed some effects on action potential frequency, but not effects on their kinetics. Therefore, μORs in neocortical interneurons influence αDTX-sensitive channels, as well as other channels, to modulate action potential kinetics and firing properties.
Dynamics of gene expression and chromatin marking during cell state transition
Authors: Borsari Beatrice , Abad Amaya , Klein Cecilia C. , Nurtdinov Ramil , Esteban Alexandre , Palumbo Emilio , Ruiz-Romero Marina , Sanz María , Correa Bruna R. , Johnson Rory , Pérez-Lluch Sílvia , Guigó Roderic
Published: November 2020

We have monitored the transcriptomic and epigenomic status of cells at twelve time-points during the transdifferentiation of human pre-B cells into macrophages. Using this data, we have investigated some fundamental questions regarding the role of chromatin in gene expression. We have found that, over time, genes are characterized by a limited number of chromatin states (combinations of histone modifications), and that, consistently, chromatin changes over genes tend to occur in a coordinated manner. We have observed strong association between these changes and gene expression only at the time of initial gene activation. Activation is preceded by H3K4me1 and H3K4me2, and followed in a precise order by most other histone modifications. Further changes in gene expression, comparable or even stronger than those at initial activation, occur without associated changes in histone modifications. The data generated here constitutes, thus, a unique resource to investigate transcriptomic and epigenomic dynamics during a differentiation process.
Molecular engineering improves antigen quality and enables integrated manufacturing of a trivalent subunit vaccine candidate for rotavirus
Authors: Dalvie Neil C. , Brady Joseph R. , Crowell Laura E. , Tracey Mary Kate , Biedermann Andrew M. , Kaur Kawaljit , Hickey John M. , Kristensen D. Lee , Bonnyman Alexandra , Rodriguez-Aponte Sergio A. , Whittaker Charles A. , Bok Marina , Vega Celina , Mukhopadhyay Tarit , Joshi Sangeeta B. , Volkin David B. , Parreño Viviana , Love Kerry R. , Love J. Christopher
Published: November 2020

Background

Vaccines comprising recombinant subunit proteins are well-suited to low-cost and high-volume production for global use. The design of manufacturing processes to produce subunit vaccines depends, however, on the inherent biophysical traits presented by an individual antigen of interest. New candidate antigens typically require developing custom processes for each one and may require unique steps to ensure sufficient yields without product-related variants.

Results

We describe a holistic approach for the molecular design of recombinant protein antigens—considering both their manufacturability and antigenicity—informed by bioinformatic analyses such as RNA-seq, ribosome profiling, and sequence-based prediction tools. We demonstrate this approach by engineering the product sequences of a trivalent non-replicating rotavirus vaccine (NRRV) candidate to improve titers and mitigate product variants caused by N-terminal truncation, hypermannosylation, and aggregation. The three engineered NRRV antigens retained their original antigenicity and immunogenicity, while their improved manufacturability enabled concomitant production and purification of all three serotypes in a single, end-to-end perfusion-based process using the biotechnical yeast Komagataella phaffii.

Conclusions

This study demonstrates that molecular engineering of subunit antigens using advanced genomic methods can facilitate their manufacturing in continuous production. Such capabilities have potential to lower the cost and volumetric requirements in manufacturing vaccines based on recombinant protein subunits.
Convergent consequences of parthenogenesis on stick insect genomes
Authors: Jaron Kamil S. , Parker Darren J. , Anselmetti Yoann , Tran Van Patrick , Bast Jens , Dumas Zoé , Figuet Emeric , François Clémentine M. , Hayward Keith , Rossier Victor , Simion Paul , Robinson-Rechavi Marc , Galtier Nicolas , Schwander Tanja
Published: November 2020

The shift from sexual reproduction to parthenogenesis has occurred repeatedly in animals, but how the loss of sex affects genome evolution remains poorly understood. We generatedde novoreference genomes for five independently evolved parthenogenetic species in the stick insect genusTimemaand their closest sexual relatives. Using these references in combination with population genomic data, we show that parthenogenesis results in an extreme reduction of heterozygosity, and often leads to genetically uniform populations. We also find evidence for less effective positive selection in parthenogenetic species, supporting the view that sex is ubiquitous in natural populations because it facilitates fast rates of adaptation. Contrary to studies of non-recombining genome portions in sexual species, genomes of parthenogenetic species do not accumulate transposable elements (TEs), likely because successful parthenogens derive from sexual ancestors with inactive TEs. Because we are able to conduct replicated comparisons across five species pairs, our study reveals, for the first time, how animal genomes evolve in the absence of sex in natural populations, providing empirical support for the negative consequences of parthenogenetic reproduction as predicted by theory.
Multiple latent clustering model for the inference of RNA life-cycle kinetic rates from sequencing data
Authors: Mastrantonio Gianluca , Bibbona Enrico , Furlan Mattia
Published: November 2020

We here propose a hierarchical Bayesian model to infer RNA synthesis, processing, and degradation rates from sequencing data, based on an ordinary differential equation system that models the RNA life cycle. We parametrize the latent kinetic rates, that rule the system, with a novel functional form, and estimate their parameters through 6 Dirichlet process mixture models. Owing to the complexity of this approach, we are able to simultaneously perform inference, clustering and model selection. We apply our method to investigate transcriptional and post-transcriptional responses of murine fibroblasts to the activation of proto-oncogene Myc. Our approach uncovers simultaneous regulations of the rates, which had not previously been observed in this biological system.
KIR2DL4genetic diversity in a Brazilian population sample: implications for transcription regulation and protein diversity in samples with different ancestry backgrounds
Authors: Weiss Emiliana , Andrade Heloisa S. , Lara Juliana Rodrigues , Souza Andreia S. , Paz Michelle A. , Lima Thálitta H. A. , Porto Iane O. P. , Silva Nayane dos S. B. , Castro Camila F. Bannwart , Grotto Rejane M. T. , Donadi Eduardo A. , Mendes-Junior Celso T. , Castelli Erick C.
Published: November 2020

KIR2DL4 is an important immune modulator expressed in Natural Killer cells, being HLA-G its main ligand. We characterizeKIR2DL4gene diversity considering the promoter, all exons, and all introns, in a highly admixed Brazilian population sample using massively parallel sequencing. We also introduce a molecular method to amplify and sequence the completeKIR2DL4gene. To avoid mapping bias and genotype errors commonly observed in gene families, we have developed a bioinformatic pipeline designed to minimize mapping, genotyping, and haplotyping errors. We have applied this method to survey the variability of 220 samples from the State of São Paulo, southeastern Brazil. We have also compared theKIR2DL4genetic diversity in Brazilian samples with the previously reported by the 1000Genomes consortium.KIR2DL4presents high linkage disequilibrium throughout the gene, with coding sequences associated with specific promoters. There were few, but divergent, promoter haplotypes. We have also detected many newKIR2DL4sequences, all with nucleotide exchanges in introns and encoding previously described proteins. Exons 3 and 4, which encode the external domains, were the most variable ones. The ancestry background influencesKIR2DL4allele frequencies and must be considered for association studies regardingKIR2DL4.
Recruitment of CTCF to anFtoenhancer is responsible for transgenerational inheritance of obesity
Authors: Jung Yoon Hee , Wang Hsiao-Lin V. , Ruiz Daniel , Grandi Fiorella C. , Bixler Brianna J. , Linsenbaum Hannah , Xiang Jian-Feng , Forestier Samantha , Shafik Andrew M. , Jin Peng , Corces M. Ryan , Corces Victor G.
Published: November 2020

Transgenerational transmission of epiphenotypes is poorly understood. Here we show that exposure of pregnant mouse F0 females to BPA results in obesity in the F2 progeny due to increased food intake and leptin resistance. This epiphenotype can be transmitted up to the F6 generation and disappears in F7. Analyses of chromatin accessibility in sperm of the F1-F6 generations reveals alterations in the binding of CTCF at two enhancers of theFtogene in obese but not control animals that correlates with transmission of obesity. Deletion of the CTCF site inFtoresults in mice that fail to become obese when exposed to BPA. TheseFtoenhancers show increased interactions in sperm of obese mice with theIrx3andIrx5genes, which are involved in the differentiation of appetite controlling AgRP/NPY neurons. Single-nucleus and immunofluorescence analyses in the arcuate nucleus of the hypothalamus suggest that exposure to BPA results in expansion of the number of orexigenic AgRP neurons. This expansion correlates with increased accessibility of theFtoproximal enhancer in radial glia-like neural stem cells (RG-NSCs), which give rise to AgRP/NPY neurons, and in mature oligodendrocytes. The results provide a molecular mechanism for transgenerational inheritance in mammals and suggest that both genetic and epigenetic alterations ofFtocan lead to the same phenotypic outcomes.
High-Grade Serous Ovarian Tumor Cells Modulate NK Cell Function to Create an Immune-Tolerant Microenvironment
Authors: Gonzalez Veronica D. , Huang Ying-Wen , Chen Shih-Yu , Delgado-Gonzalez Antonio , Donoso Kenyi , Gentles Andrew , Sachs Karen , Porpiglia Ermelinda , Fantl Wendy J.
Published: November 2020

Tubo-ovarian high-grade serous cancer (HGSC) is unresponsive to immune checkpoint blockade despite significant frequencies of exhausted T cells. Here we applied mass cytometry to uncover decidual-like (dl)-NK cell subpopulations (CD56+CD9+CXCR3+KIR+CD3-CD16-) in chemo-naïve HGSC tumors that correlated with both tumor and transitioning epithelial-mesenchymal cell abundance. We showed different combinatorial expression patterns of ligands for activating and inhibitory NK receptors within the three HGSC tumor cell compartments; epithelial (E), transitioning epithelial-mesenchymal (EV) and mesenchymal (vimentin-expressing cells, V) with a more inhibitory ligand phenotype in V cells. When co-cultured with HGSC cell lines the NK-92 cell line acquired CD9 from tumor cells by trogocytosis with a resultant reduction in both anti-tumor cytokine production and cytotoxicity. Critically, a CD9 blocking antibody restored the killing activity of CD9+-NK-92 cells. These findings identify previously unrecognized mechanisms of immune suppression in HGSC. Furthermore, since CD9 is widely expressed in HGSC tumors it represents an important new therapeutic target with immediate relevance for NK immunotherapy.
Quantifying biofilm propagation on chemically modified surfaces
Authors: Halsted Michelle C. , Bible Amber N. , Morrell-Falvey Jennifer L. , Retterer Scott T.
Published: November 2020

Conditions affecting biofilm formation differ among bacterial species and this presents a challenge to studying biofilms in the lab. This work leverages functionalized silanes to control surface chemistry in the study of early biofilm propagation, quantified with a semi-automated image processing algorithm. These methods support the study ofPantoeasp. YR343, a gram-negative bacterium isolated from the poplar rhizosphere. We found thatPantoeasp. YR343 does not readily attach to hydrophilic surfaces but will form biofilms with a “honeycomb” morphology on hydrophobic surfaces. Our image processing algorithm described here was used to quantify this honeycomb morphology over time and displayed a logarithmic behavior in the propagation of the honeycomb biofilm. This methodology was repeated with a flagella-deficientfliRmutant ofPantoeasp. YR343 which resulted in reduced surface attachment. Quantifiable differences betweenPantoeaWT and ΔfliRbiofilm morphologies were captured by the image processing algorithm, further demonstrating the insight gained from these methods.
Comparative biochemistry of four polyester (PET) hydrolases
Authors: Bååth Jenny Arnling , Borch Kim , Jensen Kenneth , Brask Jesper , Westh Peter
Published: November 2020

The potential of bioprocessing in a circular plastic economy has strongly stimulated research in enzymatic degradation of different synthetic resins. Particular interest has been devoted to the commonly used polyester, poly(ethylene terephthalate) (PET), and a number of PET hydrolases have been described. However, a kinetic framework for comparisons of PET hydrolases (or other plastic degrading enzymes) acting on the insoluble substrate, has not been established. Here, we propose such a framework and test it against kinetic measurements on four PET hydrolases. The analysis provided values of kcatand KM, as well as an apparent specificity constant in the conventional units of M−1s−1. These parameters, together with experimental values for the number of enzyme attack sites on the PET surface, enabled comparative analyses. We found that the PET hydrolase fromIdeonella sakaiensiswas the most efficient enzyme at ambient conditions, and that this relied on a high kcatrather than a low KM. Moreover, both soluble and insoluble PET fragments were consistently hydrolyzed much faster than intact PET. This suggests that interactions between polymer strands slow down PET degradation, while the chemical steps of catalysis and the low accessibility associated with solid substrate were less important for the overall rate. Finally, the investigated enzymes showed a remarkable substrate affinity, and reached half the saturation rate on PET, when the concentration of attack sites in the suspension was only about 50 nM. We propose that this is linked to nonspecific adsorption, which promotes the nearness of enzyme and attack sites.