Comparative transcriptome analysis between rhesus macaques(Macaca mulatta) and crab-eating macaques(M. fascicularis)

Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques(Macaca mulatta, MMU)and crab-eating macaques(M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from84 samples(41 MFA samples and 43 MMU samples)encompassing 14 common tissues. Our findings revealed a small fraction of genes(3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover,19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary,this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.

Deflections of photoelectron classical trajectories in screened Coulomb potentials of H_2^+

The photoelectron momentum distribution of H＋ in circularly polarized laser fields is studied based on classical trajectory calculations. We screen Coulomb potentials at different radii, and trace trajectories of an ensemble of electrons in such screened Coulomb potentials and circularly polarized laser fields. Simulations show that electron trajectories are bent by Coulomb fields, resulting in the laser-intensity-dependent drift of photoelectron momentum distributions in the laser polarization plane. This study intuitively explains how Coulomb potentials modify photoelectron momenta.

RsaL is a self-regulatory switch that controls alternative biosynthesis of two AHL-type quorum sensing signals in Pseudomonas aeruginosa PA1201

Pseudomonas aeruginosa is a ubiquitous and metabolically versatile microorganism naturally found in soil and water.It is also an opportunistic pathogen in plants,insects,animals,and humans.In response to increasing cell density,P.aeruginosa uses two acylhomoserine lactone(AHL)quorum-sensing(QS)signals(i.e.,N-3-oxo-dodecanoyl homoserine lactone[3-oxo-C12-HSL]and Nbutanoyl-homoserine lactone[C4-HsL]),which regulate the expression of hundreds of genes.However,how the biosynthesis of these two QS signals is coordinated remains unknown.We studied the regulation of these two QS signals in the rhizosphere strain PA1201.PA1201 sequentially produced 3-oxo-C12-HSL and C4-HSL at the early and late growth stages,respectively.The highest 3-oxo-C12-HSL-dependent elastase activity was observed at the early stage,while the highest C4-HSL-dependent rhamnolipid production was observed at the late stage.The atypical regulator RsaL played a pivotal role in coordinating 3-oxo-C12-HSL and C4-HSL biosynthesis and QS-associated virulence.RsaL repressed las/transcription by binding the-10 and-35 boxes of the lasl promoter.In contrast,RsaL activated rhll transcription by binding the region encoding the 5'-untranslated region of the rhll mRNA.Further,RsaL repressed its own expression by binding a nucleotide motif located in the-35 box of the rsaL promoter.Thus,RsaL acts as a molecular switch that coordinates the sequential biosynthesis of AHL QS signals and differential virulence in PA1201.Finally,C4-HSL activation by RsaL was independent of the Las and Pseudomonas quinolone signal(PQS)QS signaling systems.Therefore,we propose a new model of the QS regulatory network in PA1201,in which RsaL represents a superior player acting at the top of the hierarchy.

Vacuolar H^(+)-ATPase and BZR1 form a feedback loop to regulate the homeostasis of BR signaling inArabidopsis

Brassinosteroid(BR)is a vital plant hormone that regulates plant growth anddevelopment.BRASSINAZOLE RESISTANT1(BZR1)is a key transcription factor in BR signaling,and its nucleocytoplasmic localization is crucial for BR signaling.However,the mechanisms that regulate BzR1 nucleocytoplasmic distribution and thus the homeostasis of BR signaling remain largely unclear.The vacuole is the largest organelle in mature plantcells and plays a key role in maintenance of cell ular pH,storage of intracellular substances,and transport ofions.In this study,weuncovered anovel mechanismof BR signaling homeostasis regulatedbythe vacuolar H+-ATPase(V-ATPase)and BZR1 feedback loop.Our results revealed that the vha-a2 vha-a3 mutant(vha2,lacking V-ATPase activity)exhibits enhanced BR signaling with increased total amount of BZR1,nuclearlocalized BZR1,and the ratio of BZR1/phosphorylated BZR1 in the nucleus.Further biochemical assays revealed that VHA-a2 and VHA-a3 of V-ATPase interact with the BZR1 protein through a domain that is conserved across multiple species.VHA-a2 and VHA-a3 negatively regulate BR signaling by interacting with BzR1 and promoting its retention in the tonoplast.Interestingly,a series of molecular analyses demonstrated that nuclear-localized BZR1 could bind directlyto specific motifs in the promoters of VHA-a2 andVHAa3topromote their expression.Taken together,these results suggest that V-ATPase and BzR1 mayforma feedback regulatory loop to maintain thehomeostasis of BR signaling in Arabidopsis,providing new insights into vacuole-mediated regulation of hormone signaling.

The art of two-dimensional soft nanomaterials

The discovery of graphene has triggered the explosive development of two-dimensional(2D) nanomaterials, including both inorganic and organic species. Benefiting from the simple elemental composition, inorganic 2D nanomaterials were the center research in the past decade, which has long shadowed the research of 2D organic(or soft) nanomaterials. Although many kinds of2D soft nanomaterials have been successfully prepared, a unified definition for them is still impossible due to the complicate and quite different chemical structures between each other and even relying on totally different techniques to distinguish them. Since our first review on 2D soft nanomaterials in 2015, this field has moved forward with big success. In this review, we will focus on the development of 2D soft nanomaterials after 2015. In order to deliver better overview of this field, new and comprehensive classification is used in this review: 2D aromatic molecules, graphene and graphene nanoribbons, graphyne and graphdiyne,BxCyNznanosheets, 2D polymers, 2D supramolecules, crystalline 2D assemblies, 2D covalent organic frameworks, 2D metalorganic frameworks, sandwich-like 2D porous polymers, 2D polymer nanosheets, etc. The focus of this review lies on synthetic strategies and the challenges of characterization, definition and fundamental understanding.

Preliminary Assessment of the COVID-19 Outbreak Using 3-Staged Model e-ISHR

The outbreak of coronavirus disease 2019(COVID-19)in Wuhan has aroused widespread concern and attention from all over the world.Many articles have predicted the development of the epidemic.Most of them only use very basic SEIR model without considering the real situation.In this paper,we build a model called e-ISHR model based on SEIR model.Then we add hospital system and time delay system into the original model to simulate the spread of COVID-19 better.Besides,in order to take the government's control and people's awareness into consideration,we change our e-ISHR model into a 3-staged model which effectively shows the impact of these factors on the spread of the disease.By using this e-ISHR model,we fit and predict the number of confirmed cases in Wuhan and China except Hubei.We also change some of parameters in our model.The results indicate the importance of isolation and increasing the number of beds in hospital.

Adaptive Agent-Based Modeling Framework for Collective Decision-Making in Crowd Building Evacuation

Crowd evacuation in different situations is an important topic in the research field of safety. This paper presents a hybrid model for heterogeneous pedestrian evacuation simulation. Our adaptive agent-based model (ABM) combines the strength of human crowd behavior description from classical social force models with discrete dynamics expression from cellular automaton models by extending the conception of floor field. Several important factors which may influence the results of decision-making of pedestrians are taken into consideration, such as the location of sign, the attraction of exit, and the interaction among pedestrians. To compare the effect of information on the pedestrians, we construct three decision-making mechanisms with different assumptions. To validate these three simulation models, we compare the numerical results from different perspectives with rational range in the case study where the Tampere Theater evacuation was carried out. The ABM framework is open for rules modification and could be applied to different building plans and has implication for architectural design of gates and signs in order to increase the evacuation efficiency.

Development of a 6D Kalman filter for charged particle tracking in time projection chamber without magnetic field

Background Track reconstruction is necessary for time projection chamber(TPC),because TPCs usually face the measure-ment error that impedes gaining precise spacial and angular resolution.Purpose Kalman filter is a well-performed and applicable algorithm to denoise and reconstruct the event track.Methods In this paper,we develop a six-dimensional Kalman filter to reconstruct the particle track in high-energy physics experiments,while the most common form of Kalman filter used in many research fields is four-dimensional.The modelisation is based on a gaseous TPC,and the whole reconstruction process is first tested by a toy Monte Carlo simulation.Results The results show the Kalman filter can effectively reduce the noise and improve the detector resolution.Then,the performance of the Kalman filter is also verified with the data produced by the Geant4 toolkit.