bluuebunny/crossref_metadata_2025 huggingface dataset:
Concentration Sensing in Crowded Environments
Authors: Stroberg Wylie , Schnell Santiago
Published: October 2020

Signal transduction within crowded cellular compartments is essential for the physiological function of cells and organisms. While the accuracy with which receptors can probe the concentration of ligands has been thoroughly investigated in dilute systems, the effect of macromolecular crowding on the inference of concentration remains unknown. In this work we develop a novel algorithm to simulate reversible reactions between reacting Brownian particles. This facilitates the calculation of reaction rates and correlation times for ligand-receptor systems in the presence of macromolecular crowding. Using this method, we show that it is possible for crowding to increase the accuracy of estimated ligand concentration based on receptor occupancy. In particular, we find that crowding can enhance the effective association rates between small ligands and receptors to a large enough degree to overcome the increased chance of rebinding due to caging by crowding molecules. For larger ligands, crowding decreases the accuracy of the receptor’s estimate primarily by decreasing the microscopic association and dissociation rates.

SIGNIFICANCE

Developing an understanding of how cells effectively transmit signals within or between compartments under physical constraints is an important challenge for biophysics. This work investigates the effect that macromolecular crowding can have on the accuracy of a simple ligand-receptor signaling system. We show that the accuracy of an inferred ligand concentration based on the occupancy of the receptor can be enhanced by crowding under certain circumstances. Additionally, we develop a simulation algorithm that speeds the calculation of reaction rates in crowded environments and can be readily applied to other, more complex systems.
Increased wheat protein content via introgression of a HMW glutenin selectively reshapes the grain proteome
Authors: Cao Hui , Duncan Owen , Islam Shahidul , Zhang Jingjuan , Ma Wujun , Millar A. Harvey
Published: October 2020

Introgression of a high molecular weight glutenin subunit (HMW-GS) gene,1Ay21*, into commercial wheat cultivars increased overall grain protein content and bread-making quality by unknown mechanisms. As well as increased abundance of 1Ay HMW-GS, 115 differentially expressed proteins (DEPs) were discovered between three cultivars and corresponding introgressed near-isogenic lines (NILs). Functional category analysis showed that the DEPs were predominantly other storage proteins, and proteins involved in protein synthesis, protein folding, protein degradation, stress response and grain development. Nearly half the genes encoding the DEPs showed strong co-expression patterns during grain development. Promoters of these genes are enriched in elements associated with transcription initiation and light response, indicating a potential connection between thesecis-elements and grain protein accumulation. A model of how this HMW-GS enhances the abundance of machinery for protein synthesis and maturation during grain filling is proposed. This analysis not only provides insights into how introgression of the1Ay21*improves grain protein content, but also directs selection of protein candidates for future wheat quality breeding programmes.

One sentence summary

Introgression of the 1Ay21* HMW-GS increases wheat grain protein content and improves bread-making quality in association with a broad reshaping of the grain proteome network.
Birth timing after the long feeding migration in elephant seals
Authors: Condit Richard , Beltran Roxanne S. , Robinson Patrick W. , Crocker Daniel E. , Costa Daniel P.
Published: October 2020

Northern elephant seals migrate long distances from feeding grounds to raise pups during a brief period on breeding beaches. Since gestation sets a parturition date months in advance, timing of the arrival must be precise. We used satellite-tracked animals to examine this timing, establishing arrival and birth dates in 106 migrating females and estimating how far they traveled in the days just before birth. Females arrived a mean of 5.5 days prior to birth (range 1-11, sd=1.6), and females arriving later in the breeding season cut that pre-birth interval by 1.8 days relative to early arrivers. There was no correlation between female body condition, nor female age, and the pre-birth interval. The last 15 days prior to birth, animals traveled as far as 1465 km. Those furthest from the colony traveled > 100 km per day, three times faster than animals near the colony at the same time. Despite migrations covering several thousand kilometers while pregnant, female elephant seals were able to time their arrival within 6 days, swimming steadily at high speed if needed. This allows them to maintain a precise annual cycle for many years consecutively.
Decolonizing Psocopteran Systematics: Holarctic Lineages Cannot Inform Diversity and Evolution in Tropics
Authors: Sarria-Rodríguez Valentina , Gonzalez-Obando Ranulfo , Rivera-Franco Nelson , Cardenas-Henao Heiber , Román-Palacios Cristian
Published: October 2020

Despite tropical psocids comprise ~60% of species diversity within the Psocidae (Insecta, Psocodea), previous studies on the Psocidae phylogeny have poorly sampled tropical species (<40% species in trees). Here we discuss the evolution and systematics of the Psocidae based on the most comprehensive species-level sampling of the Psocidae. We sequenced and inferred the phylogenetic position of 43 previously unsampled Neotropical species from COI, H3, WNT, 18S, 16S, and 12S. Based on our phylogenies we found that Neotropical psocids are generally not closely related to morphologically similar taxa in the Holarctic region. Consequently, the monophyletic status for the major groups within Psocidae (subfamilies and tribes) is recovered only when Holarctic groups are sampled (7–10 of 11 higher-level groups are monophyletic) but violated when Neotropical species are included in the dataset (1 of 11 higher-level groups are monophyletic). Leveraging the largest phylogeny of the Psocidae, our study pinpoints the downfalls of simply extending taxonomic knowledge from lineages of a certain area to inform diversity and evolution of lineages in other regions.

Highlights

Tropical psocids comprise >60% of the extant family richness

Previous phylogenies have undersampled Tropical psocids

Holarctic and Neotropical species are classified under the same morphological groups

Holarctic and Neotropical generally correspond to evolutionarily distinct lineages

Phylogenies based on Holarctic psocids poorly inform evolution in the Neotropics
A single cell view of the transcriptome during lateral root initiation inArabidopsis thaliana
Authors: Gala Hardik P. , Lanctot Amy , Jean-Baptiste Ken , Guiziou Sarah , Chu Jonah C. , Zemke Joseph E. , George Wesley , Queitsch Christine , Cuperus Josh T. , Nemhauser Jennifer L.
Published: October 2020

Root architecture is a major determinant of fitness, and is under constant modification in response to favorable and unfavorable environmental stimuli. Beyond impacts on the primary root, the environment can alter the position, spacing, density and length of secondary or lateral roots. Lateral root development is among the best-studied examples of plant organogenesis, yet there are still many unanswered questions about its earliest steps. Among the challenges faced in capturing these first molecular events is the fact that this process occurs in a small number of cells with unpredictable timing. Single-cell sequencing methods afford the opportunity to isolate the specific transcriptional changes occurring in cells undergoing this fate transition. Using this approach, we successfully captured the transcriptomes of initiating lateral root primordia, and discovered many previously unreported upregulated genes associated with this process. We developed a method to selectively repress target gene transcription in the xylem pole pericycle cells where lateral roots originate, and demonstrated that expression of several of these targets was required for normal root development. We also discovered novel subpopulations of cells in the pericycle and endodermal cell files that respond to lateral root initiation, highlighting the coordination across cell files required for this fate transition.

One sentence summary

Single cell RNA sequencing reveals new molecular details about lateral root initiation, including the transcriptional impacts of the primordia on bordering cells.
Sequential development of embryoblast-like memory entities in human cancer tissues: An evolutionary self-repair structure with pluripotentiality
Authors: Diaz Jairo A , Sánchez Liliana , Diaz Luis A , Murillo Mauricio F , Poveda Laura , Suescun Oscar F , Castro Laura
Published: October 2020

Hidden collective organization of cancer cells can partially or completely return to embryoid genotype-phenotype with the plasticity to transform their morphology on cell embryoblast-like memory entities by expression of dormant genes that arise from embryogenesis.

After hundreds of driver mutations, cancer cells gain new abilities or attributes and recapitulate early stages of embryogenesis. Our findings document how malignant tissues reactivated ancestral storage memory and elaborate inside tumor glands spiral- pyramidal-fractal chiral crystals (Tc) as geometric attractors proteins and biomimicry the primitive cellular blastocyst embryoblast fluid-filled cavity. The resultant evolutionary embryoblast-like entity has higher survivability and spatial cephalic-caudal growth organization with pluripotentiality that carry the correct DNA instructions to repair, and regenerate. The isolation and manipulation of these order structures can guide and control the regenerative pathway mechanism in human tumors as follows: modify and reprogram the phenotype of the tumor where these entities are generated, establish a reverse primordial microscopic mold to use the swirlonic collective behavior of cellular building blocks to regenerate injured tissues, convert cancer cells to a normal phenotype through regeneration using the organizational level and scale properties of reverse genetic guidance, global control of mitotic activity and morphogenetic movements avoiding their spread and metastasis, determining a better life prognosis for patients who incubate these entities in their tumors compared to those who do not express them. An emergent self-repair order structure, biological template to develop targeted therapeutic alternatives not only in cancer but also in treatment of autoimmune, viral diseases, and in regenerative medicine and rejuvenation.
Look where you go: characterizing eye movements toward optic flow
Authors: Chow Hiu Mei , Knöll Jonas , Madsen Matthew , Spering Miriam
Published: October 2020

When we move through our environment, objects in the visual scene create optic flow patterns on the retina. Even though optic flow is ubiquitous in everyday life, it is not well understood how our eyes naturally respond to it. In small groups of human and non-human primates, optic flow triggers intuitive, uninstructed eye movements to the pattern’s focus of expansion (Knöll, Pillow & Huk, 2018). Here we investigate whether such intuitive oculomotor responses to optic flow are generalizable to a larger group of human observers, and how eye movements are affected by motion signal strength and task instructions. Observers (n= 43) viewed expanding or contracting optic flow constructed by a cloud of moving dots radiating from or converging toward a focus of expansion that could randomly shift. Results show that 84% of observers tracked the focus of expansion with their eyes without being explicitly instructed to track. Intuitive tracking was tuned to motion signal strength: saccades landed closer to the focus of expansion and smooth tracking was more accurate when dot contrast, motion coherence, and translational speed were high. Under explicit tracking instruction, the eyes aligned with the focus of expansion more closely than without instruction. Our results highlight the sensitivity of intuitive eye movements as indicators of visual motion processing in dynamic contexts.
Implementing and assessing an alchemical method for calculating protein-protein binding free energy
Authors: Patel Dharmeshkumar , Patel Jagdish Suresh , Ytreberg F. Marty
Published: October 2020

Protein-protein binding is fundamental to most biological processes. It is important to be able to use computation to accurately estimate the change in protein-protein binding free energy due to mutations in order to answer biological questions that would be experimentally challenging, laborious or time consuming. Although non-rigorous free energy methods are faster, rigorous alchemical molecular dynamics-based methods are considerably more accurate and are becoming more feasible with the advancement of computer hardware and molecular simulation software. Even with sufficient computational resources, there are still major challenges to using alchemical free energy methods for protein-protein complexes, such as generating hybrid structures and topologies, maintaining a neutral net charge of the system when there is a charge-changing mutation, and setting up the simulation. In the current study, we have used thepmxpackage to generate hybrid structures and topologies, and a double-system/single-box approach to maintain the net charge of the system. To test the approach, we predicted relative binding affinities for two protein-protein complexes using a non-equilibrium alchemical method based on the Crooks fluctuation theorem and compared the results with experimental values. The method correctly identified stabilizing from destabilizing mutations for a small protein-protein complex, but was not as successful to the larger, more challenging antibody complex. In addition, the correlation between predicted and experimental relative binding affinities was high for smaller complex, and low for the other larger complex.
Differences in external, internal oral and chondrocranial morphology of the tadpole ofCorythomantis greeningiBoulenger, 1896 (Anura: Hylidae)
Authors: Uchôa Lucas Rafael , Costa Claylton A. , Santos Antonia Joyce S. , Silva Rayone A. , Sena Felipe P. , Andrade Etielle B.
Published: October 2020

The genusCorythomantiscurrently comprises a single species,Corythomantis greeningi, a hylid widely distributed in xerophilic and subhumid morphoclimatic regions of Brazil, mainly in the Northeast region. Recently the external morphology, internal oral anatomy, and chondrocranium ofC. greeningitadpoles were described from specimens collected in the state of Bahia, however, we observed some differences in morphology of individuals from the state of Piauí, northeastern Brazil. The tadpoles were collected during the 2019 rainy season and 14 individuals were used to describe and compare the larval characters. We observed differences in external, internal oral and chondrocranial morphology in relation to specimens previously described, especially in oral disc, number and shape of oral cavity papillae, and some chondrocranium structures, as:cartilago suprarostralis,cornua trabeculae,fontanella frontoparietalis,cartilago orbitaliseplanum hypobranchiale. Our results point to the occurrence of heterochrony inC. greeningi, but we do not rule out the possibility that tadpoles belong to different species. Further studies involving a greater number of tadpoles at different stages, combined with genetic, acoustic, and morphological factors of adult specimens may establish the variation degree ofC. greeningiin different regions of northeastern Brazil.

O gêneroCorythomantiscompreende atualmente uma única espécie,Corythomantis greeningi, um hilídeo amplamente distribuído nas regiões morfoclimáticas xerofílicas e subúmidas do Brasil, principalmente na região Nordeste. Recentimente foram descritas a morfologia externa, anatomia oral interna e condrocrânio do girino deC. greeningia partir de espécimes coletados no estado da Bahia, no entanto, observamos algumas diferenças na morfologia dos indivíduos coletados na região norte do estado do Piauí, Nordeste do Brasil. Os girinos foram coletados durante o período chuvoso de 2019 e 14 indivíduos foram utilizados para descrição e comparação dos caracteres larvais. Observamos diferenças na morfologia externa, oral interna e no condrocranio do girino em relação ao descrito anteriormente, sobretudo no disco oral, no número e formato de papilas cavidade oral e algumas estruturas do condrocrânio, como:cartilago suprarostralis,cornua trabeculae,fontanella frontoparietalis,cartilago orbitaliseplanum hypobranchiale. Nossos resultados apontam a ocorrência de heterocronia emC. greeningi, porém não descartamos a possibilidade dos girinos pertencerem a espécies diferentes. Estudos futuros envolvendo uma maior área de distribuição e maior número de indivíduos em estágios diferentes, aliados a fatores genéticos, acústico e morfológicos dos espécimes adultos poderão estabelecer o grau de variação deC. greeningiem diferentes regiões do Nordeste brasileiro.
Proteomic analysis of microtubule inner proteins (MIPs) in Rib72 nullTetrahymenacells reveals functional MIPs
Authors: Fabritius Amy S. , Bayless Brian A. , Li Sam , Stoddard Daniel , Heydeck Westley , Ebmeier Christopher C. , Anderson Lauren , Gunnels Tess , Nachiappan Chidambaram , Whittall Justen B. , Old William , Agard David A. , Nicastro Daniela , Winey Mark
Published: October 2020

Motile cilia and flagella are built from stable populations of doublet microtubules that comprise their axonemes. Their unique stability is brought about, at least in part, by a network ofMicrotubuleInnerProteins (MIPs) found in the lumen of their doublet microtubules. Rib72A and Rib72B were identified as microtubule inner proteins (MIPs) in the motile cilia ofTetrahymena thermophila. Loss of these proteins leads to ciliary defects and loss of multiple MIPs. We performed mass spectrometry coupled with proteomic analysis and bioinformatics to identify the MIPs lost inRIB72A/Bknockout (KO)Tetrahymenacells. From this analysis we identified a number of candidate MIPs and pursued one, Fap115, for functional characterization. We find that loss of Fap115 results in disrupted cell swimming and aberrant ciliary beating. Cryo-electron tomography reveals that Fap115 localizes to MIP6a in the A-tubule of the doublet microtubules. Overall, our results highlight the complex relationship between MIPs, ciliary structure, and ciliary function.
Combined analysis of the time-resolved transcriptome and proteome of plant pathogenXanthomonas oryzaepv.oryzae
Authors: Kim Seunghwan , Jang Wooyoung Eric , Kim Min-Sik , Kim Jeong-Gu , Kang Lin-Woo
Published: October 2020

Xanthomonas oryzaepv.oryzae(Xoo) is a plant pathogen responsible for causing bacterial blight in rice. The immediate alterations in Xoo upon initial contact with rice are essential for pathogenesis. We studied time-resolved genome-wide gene expression in pathogenicity-activated Xoo cells at the transcriptome and proteome levels. The early response genes of Xoo include genes related to cell motility, inorganic ion transport, and effectors. The alteration of gene expression is initiated as early as few minutes after the initial interaction and changes with time. The time-resolved comparison of the transcriptome and proteome shows the differences between transcriptional and translational expression peaks in many genes, although the overall expression pattern of mRNAs and proteins is conserved. The discrepancy suggests an important role of translational regulation in Xoo at the early stages of pathogenesis. The gene expression analysis using time-resolved transcriptome and proteome provides unprecedented valuable information regarding Xoo pathogenesis.
Evolution of co-regulatory network of C4metabolic genes and TFs in the genus Flaveria: go anear or away in the intermediate species?
Authors: Lyu Ming-Ju Amy , Essemine Jemaa , Chen Faming , Chen Genyun , Zhu Xin-Guang
Published: October 2020

C4photosynthesis evolved from the ancestral C3photosynthesis by recruiting pre-existing genes to fulfill new functions. The enzymes and transporters required for the C4photosynthesis have been intensively studied; however, the transcription factors (TFs) regulating these C4metabolic genes are not well understood. In particular, how the TF regulatory network of C4metabolic genes was rewired during the evolution is unclear. Here, we constructed TFs co-regulatory networks for core C4metabolic genes (C4GRN) for four evolutionarily closely related species from the genus Flaveria, which represent four different evolutionary stages of the C4photosynthesis, namely, C3, type I C3-C4, type II C3-C4and C4. Our results show that more than half of the co-regulations of TFs and C4core metabolic genes were species specific. The counterparts of C4genes in C3species were already co-regulated with the photosynthesis-related genes; whereas the required TFs for the C4photosynthesis were recruited later. The type I C3-C4species recruited 40% of C4required TFs which co-regulated all core C4metabolic genes but PEPC; nevertheless, the type II C3-C4species took on a high divergent C4GRN with C4species itself. In C4species, PEPC and PPDK-RP possessed much more co-regulated TFs than other C4metabolic genes. This study provides for the first time the TFs profiles of the C4metabolic genes in species with different photosynthetic types and reveal the dynamic of C4genes-TFs co-regulations along the evolutionary process, providing thereby new insights into the evolution of C4photosynthesis.
Postharvest properties of ultra-late maturing peach cultivars and their attributions toMelting Flesh(M) locus: Re-evaluation ofMlocus in association with flesh texture
Authors: Nakano Ryohei , Kawai Takashi , Fukamatsu Yosuke , Akita Kagari , Watanabe Sakine , Asano Takahiro , Takata Daisuke , Sato Mamoru , Fukuda Fumio , Ushijima Koichiro
Published: October 2020

The postharvest properties of two ultra-late maturing peach cultivars, ‘Tobihaku’ (TH) and ‘Daijumitsuto’ (DJ), were investigated. Fruit were harvested at commercial maturity and held at 25°C. TH exhibited the characteristics of normal melting flesh (MF) peach, including rapid fruit softening associated with an increase in endogenous ethylene production In contrast, DJ did not soften at all during three-week experimental period even though substantial ethylene production was observed. Fruit of TH and DJ were treated with 5000 ppm of propylene, an ethylene analog, continuously for seven days. TH softened rapidly whereas DJ maintained high flesh firmness in spite of an increase in endogenous ethylene production, suggesting that DJ but not TH lacked the ability to be softened in response to endogenous and exogenous ethylene/propylene. DNA-seq analysis showed that tandem endo-polygalacturonase (endoPG) genes located atmelting flesh(M) locus,Pp-endoPGM(PGM) andPp-endoPGF(PGF), were deleted in DJ. TheendoPGgenes atMlocus are known to control flesh texture of peach fruit, and it was suggested that the non-softening property of DJ is due to the lack ofendoPGgenes. On the other hand, TH possessed an unidentifiedMhaplotype that is involved in determination of MF phenotype. Structural identification of the unknownMhaplotype, designated asM0, through comparison with previously reportedMhaplotypes revealed distinct differences betweenPGMonM0haplotype (PGM-M0) andPGMon other haplotypes (PGM-M1). PeachMhaplotypes were classified into four main haplotypes:M0withPGM-M0;M1with bothPGM-M1andPGF;M2withPGM-M1; andM3lacking bothPGMandPGF. Re-evaluation ofMlocus in association with MF/non-melting flesh (NMF) phenotypes in more than 400 accessions by using whole genome shotgun sequencing data on database and/or by PCR genotyping demonstrated thatM0haplotype was the common haplotype in MF accessions, andM0andM1haplotypes were dominant overM2andM3haplotypes and co-dominantly determined the MF trait. It was also assumed on the basis of structural comparison ofMhaplotypes amongPrunusspecies that the ancestral haplotype ofM0diverged from those of the other haplotypes before the speciation ofPrunus persica.
Spermidine and spermine are the natural substrates of theAcinetobacter baumanniiAmvA multidrug efflux pump
Authors: Short Francesca L. , Liu Qi , Ashwood Heather E. , Naidu Varsha , Li Liping , Mabbutt Bridget C. , Hassan Karl A. , Paulsen Ian T.
Published: October 2020

Multidrug efflux pumps are important drivers of antibiotic resistance inAcinetobacter baumanniiand other pathogens, however their ‘natural’ roles beyond transport of clinical antimicrobials are poorly described. Polyamines are an ancient class of molecules with broad roles in all three kingdoms of life, and are the likely natural substrate of at least one efflux pump family. We have defined the transcriptome ofA. baumanniifollowing treatment with high levels of the polyamines putrescine, cadaverine, spermidine and spermine. These molecules influenced expression of multiple gene classes inA. baumanniiincluding those associated with virulence, and the four polyamines induced distinct but overlapping transcriptional responses. Polyamine shock also induced expression of the MFS-family efflux pump geneamvAand its repressor geneamvR. Loss ofamvAdramatically reduced tolerance to the long-chain triaamine spermidine, but caused only modest changes in resistance to known AmvA substrates such as acriflavine. We confirmed reduced accumulation of spermidine inamvA-deficientA. baumannii, and showed that its expression is induced by long-chain polyamines through its cognate regulator AmvR. Our findings suggest that the conservedA. baumanniiefflux pump AmvA has evolved to export spermidine from the cell, but that its substrate recognition promiscuity also allows activity against clinically-important biocides and antibiotics.

Importance

AMR genes, including multidrug efflux pumps, evolved long before the ubiquitous use of antimicrobials in medicine and infection control. Multidrug efflux pumps often transport metabolites, signals and host-derived molecules in addition to antibiotics or biocides. Understanding the ancestral physiological roles of multidrug efflux pumps could help to inform the development of strategies to subvert their activity. In this study, we investigated the response ofAcinetobacter baumanniito polyamines, a widespread, abundant class of amino acid-derived metabolites, which led us to identify long-chain polyamines as natural substrates of the disinfectant efflux pump AmvA. A second clinically-important efflux pump, AdeABC, also contributed to polyamine tolerance. Our results suggest that the disinfectant resistance capability that allowsA. baumanniito survive in hospitals may have evolutionary origins in the transport of polyamine metabolites.
Effects of various carbohydrates on the in vitro pollen germination ofVinca roseaandCucumis melo var. utilissimus
Authors: Sharma S , Marni A D , Sharma V , Manchanda P
Published: October 2020

Pollen germination is crucial for the process of plant development which strongly depends on the presence of carbohydrates as a primary source of energy. In this study, we analyzed the differential effects of four sugars with varying concentrations on the pollen germination ofVinca rosea Linn. andCucumis melo var. utilissimus(Duth. & Fuller) using Brewbaker and Kwack’s medium as germination medium and hanging drop method after an incubation period of 1 hour. Sucrose and glucose supported the pollen germination but galactose and fructose did not support and even considerably inhibited the pollen germination ofVinca rosea. However in pollen germination ofCucumis melo var. utilissimus, all the four sugars supported the pollen germination. The study suggests that 15% sucrose, forVinca rosea, and 12% galactose, forCucumis melo var. utilissimus, supports in achieving the highest pollen germination percentage when added to the pollen germination medium.
Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture
Authors: Bashirzadeh Yashar , Redford Steven A. , Lorpaiboon Chatipat , Groaz Alessandro , Litschel Thomas , Schwille Petra , Hocky Glen M. , Dinner Aaron R. , Liu Allen P.
Published: October 2020

How complex actin network architectures arise and coexist in membrane-enclosed cell environment remains unknown. By encapsulating actin and crosslinking proteins α-actinin and fascin in giant unilamellar vesicles (GUVs), we show that physical confinement and its size can lead to formation of complex actin structures, including rings and asters at GUV peripheries and centers. Strikingly, we find that the materials properties of the aster structures depend on the ratio of the relative concentrations of α-actinin and fascin, and we demonstrate that this results from α-actinin and fascin sorting into separate domains in the structures. We complement our experiments with molecular simulations that capture the spontaneous formation of competing network architectures; these provide a microscopic view of the dynamics and delineate the molecular features that promote sorting. We propose that the observed boundary-imposed effect on protein sorting is a general mechanism for creating emergent structures in biopolymer networks with multiple crosslinkers.
Loss of α-actinin-3 during human evolution provides superior cold resilience and muscle heat generation
Authors: Wyckelsma VL , Venckunas T , Houweling PJ , Schlittler M , Lauschke VM , Tiong CF , Wood H , Ivarsson N , Paulauskas H , Eimantas N , Andersson DC , North KN , Brazaitis M , Westerblad H
Published: October 2020

The fast skeletal muscle protein α-actinin-3 is absent in 1.5 billion people worldwide due to homozygosity for a nonsense polymorphism in theACTN3gene (R577X)1. The prevalence of the 577X allele increased as modern humans moved to colder climates, suggesting a link between α-actinin-3 deficiency and improved cold tolerance1,2. Here, we show that humans lacking α-actinin-3 (XX) are superior in maintaining core body temperature during cold-water immersion due to changes in skeletal muscle thermogenesis. Muscles of XX individuals displayed a shift towards more slow-twitch isoforms of myosin heavy chain (MyHC) and sarcoplasmic reticulum (SR) proteins, accompanied by altered neuronal muscle activation resulting in increased tone rather than overt shivering3,4. Experiments onActn3knockout mice showed no alterations in brown adipose tissue (BAT) properties that could explain the improved cold tolerance in XX individuals. Thus, this study provides a clear mechanism for the positive selection of theACTN3X-allele in cold climates and supports a key thermogenic role of skeletal muscle during cold exposure in humans.
Scaffolded Learning of Bipedal Walkers: Bootstrapping Ontogenetic Development
Authors: Zhu Jiahui , Rong Chunyan , Iida Fumiya , Rosendo Andre
Published: October 2020

Bipedal locomotion has several key challenges, such as balancing, foot placement, and gait optimization. We reach optimality from a very early age by using natural supports, such as our parent’s hands, chairs, and training wheels, and bootstrap a new knowledge from the recently acquired one. In this paper, we propose a scaffolded learning method from an evolutionary robotics perspective, where a biped creature achieves stable and independent bipedal walking while exploiting the natural scaffold of its changing morphology to create a third limb. Hence, we compare three conditions of scaffolded learning to reach bipedalism, and we prove that a performance-based scaffold is the most conducive to accelerate the learning of ontogenetic bipedal walking. Beyond a pedagogical experiment, this work presents a powerful tool to accelerate learning on robots.
Impaired dynamic profile of brain recurring functional connectivity states in Alzheimer’s disease
Authors: Maleki-Balajoo Somayeh , Asemani Davud , Khadem Ali , Soltanian-Zadeh Hamid
Published: October 2020

Up to now, disrupted functional organization of the brain in Alzheimer’s disease (AD) has mostly been examined by assessing “static” functional connectivity (FC). However, recent studies have provided clear evidence that brain FC exhibits intrinsic spatiotemporal “dynamic” organization also being significantly affected in AD. However, inconsistency in former studies is a motivation for further investigation of impaired dynamic profile of brain FC networks in Alzheimer’s disease._In this work, we identified recurring FC states during rest (eyes-open) in 24 AD patients and 37 healthy controls (HC) by combining sliding window-based method (examining dynamic FC) and k-means clustering algorithm (identifying recurring FC states over time). To define the optimum number of recurring FC states in k-means algorithm, we employed non-supervised validity criteria such as silhouette value and Dunn index over bootstrap samples. Then, we examined differences in dynamic properties of recurring FC states including probability of occurrence, lifetime and switching profile between groups. Afterward, association between impaired dynamic profile of recurring FC states and cognitive performance was assessed in AD patients. Our findings revealed three recurring FC states and among them, FC state with the most significant differences in probability of occurrence (corrected p-value < 0.0001) included brain regions involved in default mode, frontoparietal and salience networks. This recurring FC state occurred significantly less and lasted shorter in patients with AD than in the HC. Further, the probability of occurrence in this recurring FC state significantly correlated positively with cognitive decline in patients with AD. Our findings suggest more decreased in cognitive performance in patients with AD associated with more reduced ability of AD patients to access clinically relevant impaired brain FC networks. Impaired dynamic profile of recurring FC states in AD provide greater understanding of AD’s pathophysiology.
Phenomenon of music-induced opening of the blood-brain barrier in healthy mice
Authors: Semyachkina-Glushkovskaya O. , Esmat A. , Bragin D. , Bragina O. , Shirokov A. A. , Navolokin N. , Yang Y. , Abdurashitov A. , Khorovodov A. , Terskov A. , Klimova M. , Mamedova A. , Fedosov I. , Tuchin V. , Kurths J.
Published: October 2020

Music plays a more important role in our life than just being an entertainment. It is an even anti-anxiety therapy of human and animals. However, the unsafe listening of loud music triggers hearing loss in millions of young people and professional musicians (rock, jazz, and symphony orchestra) due to exposure to damaging levels of sound using personal audio devices or at noisy entertainment venues including nightclubs, discotheques, bars, and concerts. Therefore, it is important to understand how loud music affects us.

In this pioneering study on healthy mice, we discover that loud rock music below the safety threshold causes opening of the blood-brain barrier (OBBB), which plays an important role in protecting the brain from viruses, bacteria and toxins. We clearly demonstrate that listening loud music during 2 hrs in an intermittent adaptive regime is accompanied by delayed (1h after music exposure) and short-lasting (during 1-4 hrs) OBBB to low and high molecular weight compounds without cochlear and brain impairments. We present the systemic and molecular mechanisms responsible for music-induced OBBB. Finally, a revision of our traditional knowledge about the BBB nature and the novel strategies in optimization of sound-mediated methods for brain drug delivery are discussed.
Sequence- and structure-selective mRNA m5C methylation by NSUN6 in animals
Authors: Liu Jianheng , Huang Tao , Zhang Yusen , Zhao Tianxuan , Zhao Xueni , Chen Wanying , Zhang Rui
Published: October 2020

mRNA m5C, which has recently been implicated in the regulation of mRNA mobility, metabolism, and translation, plays important regulatory roles in various biological events. Two types of m5C sites are found in mRNAs. Type I m5C sites, which contain a downstream G-rich triplet motif and are computationally predicted to locate in the 5’ end of putative hairpin structures, are methylated by NSUN2. Type II m5C sites contain a downstream UCCA motif and are computationally predicted to locate in the loops of putative hairpin structures. However, their biogenesis remains unknown. Here we identified NSUN6, a methyltransferase that is known to methylate C72 of tRNAThrand tRNACys, as an mRNA methyltransferase that targets Type II m5C sites. Combining the RNA secondary structure prediction, miCLIP, and results from a high-throughput mutagenesis analysis, we determined the RNA sequence and structural features governing the specificity of NSUN6-mediated mRNA methylation. Integrating these features into an NSUN6-RNA structural model, we identified an NSUN6 variant that largely loses tRNA methylation but retains mRNA methylation ability. Finally, we revealed a negative correlation between m5C methylation and translation efficiency. Our findings uncover that mRNA m5C is tightly controlled by an elaborate two-enzyme system, and the protein-RNA structure analysis strategy established may be applied to other RNA modification writers to distinguish the functions of different RNA substrates of a writer protein.
CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators
Authors: Fang Liang , Wang Wen , Li Guipeng , Zhang Li , Li Jun , Gan Diwen , Yang Jiao , Tang Yisen , Ding Zewen , Zhang Min , Zhang Wenhao , Deng Daqi , Song Zhengyu , Zhu Qionghua , Cui Huanhuan , Hu Yuhui , Chen Wei
Published: October 2020

Cellular RNA is decorated with over 170 types of chemical modifications. Many modifications in mRNA, including m6A and m5C, have been associated with critical cellular functions under physiological and/or pathological conditions. To understand the biological functions of these modifications, it is vital to identify the regulators that modulate the modification rate. However, a high-throughput method for unbiased screening of these regulators is so far lacking. Here, we report such a method combining pooled CRISPR screen and reporters with RNA modification readout, termedCRISPRintegratedgRNAandreporter sequencing (CIGAR-seq). Using CIGAR-seq, we discovered NSUN6 as a novel mRNA m5C methyltransferase. Subsequent mRNA bisulfite sequencing in HAP1 cells without or with NSUN6 and/or NSUN2 knockout showed that NSUN6 and NSUN2 worked on non-overlapping subsets of mRNA m5C sites, and together contributed to almost all the m5C modification in mRNA. Finally, using m1A as an example, we demonstrated that CIGAR-seq can be easily adapted for identifying regulators of other mRNA modification.
A transposon surveillance mechanism that safeguards plant male fertility during stress
Authors: Lee Yang-Seok , Maple Robert , Dürr Julius , Dawson Alexander , Tamim Saleh , Genio Charo del , Papareddy Ranjith , Luo Anding , Lamb Jonathan C. , Sylvester Anne W. , Birchler James A. , Meyers Blake C. , Nodine Michael D. , Rouster Jacques , Gutierrez-Marcos Jose
Published: October 2020

Although plants are able to withstand a range of environmental conditions, spikes in ambient temperature can impact plant fertility causing reductions in seed yield and significant economic losses1,2. Therefore, understanding the precise molecular mechanisms that underpin plant fertility under environmental constraints is critical to safeguard future food production3. Here, we identified two Argonaute-like proteins whose activities are required to sustain male fertility in maize plants under high temperatures. We found that MALE-ASSOCIATED ARGONAUTE 1 and 2 (MAGO1 and MAGO2) associate with temperature-induced phased secondary small RNAs in pre-meiotic anthers and are essential to control the activity of retrotransposons in male meiocyte initials. Biochemical and structural analyses revealed how MAGO2 activity and its interaction with retrotransposon RNA targets are modulated through the dynamic phosphorylation of a set of highly conserved surface-located serine residues. Our results demonstrate that an Argonaute-dependent RNA-guided surveillance mechanism is critical in plants to sustain male fertility under environmentally constrained conditions by controlling the mutagenic activity of transposons in male germ cells.
Comprehensive Comparative Genomics Reveals Over 50 Phyla of Free-living and Pathogenic Bacteria are Associated with Diverse Members of the Amoebozoa
Authors: Tekle Yonas I. , Lyttle Janae M. , Blasingame Maya G.
Published: October 2020

The association of bacteria with microbial eukaryotes has been extensively studied. Among these the supergroup Amoebozoa containing predominantly amoeboid unicellular protists has been shown to play an important ecological role in controlling environmental bacteria. Amoebozoans not only graze bacteria but also serve as a safe niche for bacterial replication and harbor endosymbiotic bacteria including dangerous human pathogens. Despite their importance, only a few lineages of Amoebozoa have been studied in this regard. Amoebozoa encompasses lineages of extreme diversity in ecology, morphology and evolutionary history. The limited amoebozoans studied are not representative of the high diversity known in the supergroup, and could undermine our understanding of their role as key players in environmental ecosystems and as emerging public health threats. In this research, we conducted a comprehensive genomic and transcriptomic study with expansive taxon sampling by including representatives from the three known clades of the Amoebozoa. We used culture independent whole culture and single cell genomics maintained in our laboratory cultures, and additionally published RNA-Seq data to investigate the association of bacteria with diverse amoebozoans. Relative to current published evidence, we recovered the largest number of bacterial phyla (57) and pathogen genera (49) associated with the Amoebozoa. Using single cell genomics we were able to determine up to 24 potential endobiotic bacterial phyla, some potentially endosymbionts. This includes the majority of multidrug-resistant pathogens designated as major public health threats. Our study demonstrates amoebozoans are associated with many more phylogenetically diverse bacterial phyla than previously recognized. It also shows that all amoebozoans are capable of harboring far more dangerous human pathogens than presently documented, making them of primal public health concern.
A potent neutralizing mouse monoclonal antibody specific to dengue virus type 1 Mochizuki strain recognized a novel epitope around the N-67 glycan on the E protein: a possible explanation of dengue virus evolution regarding the acquisition of N-67 glycan
Authors: Kotaki Tomohiro , Yamanaka Atsushi , Konishi Eiji , Kameoka Masanori
Published: October 2020

Analysis of the neutralizing epitope of dengue virus (DENV) is important for the development of an effective dengue vaccine. A potent neutralizing mouse monoclonal antibody named 7F4 was previously reported and, here, we further analyze the detailed epitope of this antibody. 7F4 recognized a novel conformational epitope close to the N-67 glycan on the E protein. This antibody was specific to the DENV that lacks N-67 glycan, including the Mochizuki strain. Interestingly, the Mochizuki strain acquired N-67 glycan by 7F4 selective pressure. DENVs might have evolved to escape from this antibody considering that most of currently circulating DENVs possess N-67 glycan. However, this suggests that 7F4 epitope might be useless as a vaccine target. Nevertheless, this study demonstrated the existence of epitopes competing for 7F4 epitope, which are involved in neutralization. This study describes the importance of antibodies recognizing epitopes near the N-67 glycan for future dengue vaccine development.
A Universal Stress Protein upregulated by hypoxia may contribute to chronic lung colonisation and intramacrophage survival in cystic fibrosis
Authors: O’Connor Andrew , Berisio Rita , Lucey Mary , Schaffer Kirsten , McClean Siobhán
Published: October 2020

Universal stress proteins (USPs) are ubiquitously expressed in bacteria, plants and eukaryotes and play a lead role in adaptation to environmental conditions. In Gram negative bacteria they enable adaption of bacterial pathogens to the conditions encountered in the human niche, including hypoxia, oxidative stress, osmotic stress, nutrient deficiency or acid stress, thereby facilitating colonisation. We previously reported that all six USP proteins encoded within a low-oxygen responsive locus inBurkholderia cenocepaciashowed increased abundance during chronic colonisation of the CF lung. However, the role of USPs in chronic infection is not known. Using mutants derived fromB. cenocepaciastrain, K56-2, we show that USP76 is required for growth and survival in many conditions associated with the CF lung including, hypoxia, acidic conditions, oxidative stress. Moreover, it is involved in attachment to host epithelial cells, but not virulence. It also has a role in survival in macrophages isolated from people with CF. In contrast, another USP encoded in the same locus, USP92 had no effect on host cell attachment or oxidative stress, but was responsible for a 3-fold increase in virulence. Overall this shows that these USPs, both upregulated during chronic infection, have distinct roles inBurkholderiapathogenesis and may support the survival ofB. cenocepaciain the CF lung. Specifically, USP76 is involved in its survival within CF macrophages, a hallmark ofBurkholderiainfection.
Spectrin Interactome under normal and HbE-disease conditions
Authors: Bose Dipayan , Islam Sk Ramiz , Saha Sutapa , Chakrabarti Abhijit
Published: October 2020

Spectrin, the major component of the erythrocyte membrane skeleton is a key player in red cell biology. It has a significant role in signalling pathways and as such knowledge of spectrin interactors becomes crucial. Here we report the cytosolic interactome of human erythroid spectrin (ProteomeXchange id: PXD021525). This is to the best of our knowledge the first report of the interactome of human erythroid spectrin. We have further investigated the spectrin interactome under HbE disease conditions. Our findings indicate that there is no difference in the identity of the proteins interacting with spectrin between normal and disease conditions. However relative abundance of the interacting partners is seen to change. Very interestingly the interacting chaperone proteins, heme-containing proteins and redox active proteins are seen to be up-regulated in HbE disease state. This is consistent with our previous observation that presence of oxidation prone hemoglobin variants leads to an increase of redox regulators and chaperones in the red cell proteome. Spectrin can also interact with horse radish peroxidase and oxidatively crosslink hemoglobin, which has possible implications in oxidative stress management. Since a large fraction of spectrin interacting proteins are chaperones and redox active proteins, it is possible that spectrin may have a broader role in redox regulation, especially in cases where there are unstable hemoglobin variants present.
Spatial modulation of hippocampal activity in freely moving macaques
Authors: Mao D. , Avila E. , Caziot B. , Laurens J. , Dickman J.D. , Angelaki D.E.
Published: October 2020

The hippocampal formation is linked to spatial navigation, but there is little corroboration from freely-moving primates with concurrent monitoring of three-dimensional head and gaze stances. We recorded neurons and local field potentials across hippocampal regions in rhesus macaques during free foraging in an open environment while tracking their head and eye. Theta band activity was intermittently present at movement onset and modulated by saccades. Many cells were phase-locked to theta, with few showing theta phase precession. Most hippocampal neurons encoded a mixture of spatial variables beyond place fields and a negligible number showed prominent grid tuning. Spatial representations were dominated by facing location and allocentric direction, mostly in head, rather than gaze, coordinates. Importantly, eye movements strongly modulated neural activity in all regions. These findings reveal that the macaque hippocampal formation represents three-dimensional space using a multiplexed code, with head orientation and eye movement properties dominating over simple place and grid coding during free exploration.