Molecular Processes Research Articles

High-speed and low-power molecular dynamics processing unit (MDPU) with ab initio accuracy

Molecular dynamics (MD) is an indispensable atomistic-scale computational tool widely-used in various disciplines. In the past decades, nearly all ab initio MD and machine-learning MD have been based on the general-purpose central/graphics processing units (CPU/GPU), which are well-known to suffer from their intrinsic “memory wall” and “power wall” bottlenecks. Consequently, nowadays MD calculations with ab initio accuracy are extremely time-consuming and power-consuming, imposing serious restrictions on the MD simulation size and duration. To solve this problem, here we propose a special-purpose MD processing unit (MDPU), which could reduce MD time and power consumption by about 103 times (109 times) compared to state-of-the-art machine-learning MD (ab initio MD) based on CPU/GPU, while keeping ab initio accuracy. With significantly-enhanced performance, the proposed MDPU may pave a way for the accurate atomistic-scale analysis of large-size and/or long-duration problems which were impossible/impractical to compute before.

Impact of Peritoneal Neutrophil Extracellular Traps on Peritoneal Characteristics and Technical Failure in Patients Undergoing Peritoneal Dialysis.

Peritoneal dialysis (PD) is an effective home therapy for end-stage kidney disease. However, continuous exposure to PD fluids with high glucose concentration and recurrent peritonitis may lead to the activation of cellular and molecular processes of peritoneal damage, including inflammation and fibrosis. In particular, recent studies have highlighted the role of neutrophils in chronic inflammation. This study explores how neutrophil extracellular traps (NETs) affect peritoneal membrane function and contribute to technical failures in PD patients. We conducted a prospective observational study involving 250 non-infectious and 30 acute peritonitis patients. NETs were measured using nucleosome and myeloperoxidase DNA levels in PD fluids. Monocyte chemoattractant protein-1 (MCP-1) and matrix metalloproteinase-8 (MMP-8) were also measured to assess peritoneal inflammation and damage. A significant increase in peritoneal NETs, as determined by nucleosome and myeloperoxidase DNA levels, was observed in patients with acute peritonitis compared to patients without peritonitis. Even in non-infectious samples, NET levels were widely distributed and closely correlated with levels of MCP-1 and MMP-8. Higher levels of peritoneal NETs were closely associated with increased 4-hour dialysate/peritoneal (D/P) creatinine ratio and 1-hour D/P sodium levels, indicating a higher prevalence of fast transport and limited free water transport. These factors were associated with a higher risk of technical failure. During a mean follow-up of 34 months, 39.2% (98 patients) switched from PD to hemodialysis, with higher NET levels significantly increasing the risk by 1.9 times (95% confidence interval 1.27-2.83, p=0.020). This study suggests the importance of peritoneal NETs not only as markers of acute inflammation but also as significant immunological predictors of chronic peritoneal membrane inflammation and dysfunction, and as potential risk factors for technical failure.

Odorant Binding Proteins Facilitate the Gas-Phase Uptake of Odorants Through the Nasal Mucus.

Mammalian odorant binding proteins (OBPs) have long been suggested to transport hydrophobic odorant molecules through the aqueous environment of the nasal mucus. While the function of OBPs as odorant transporters is supported by their hydrophobic beta-barrel structure, no rationale has been provided on why and how these proteins facilitate the uptake of odorants from the gas phase. Here, a multi-scale computational approach validated through available high-resolution spectroscopy experiments reveals that the conformational space explored by carvone inside the binding cavity of porcine OBP (pOBP) is much closer to the gas than the aqueous phase, and that pOBP effectively manages to transport odorants by lowering the free energy barrier of odorant uptake. Understanding such perireceptor events is crucial to fully unravel the molecular processes underlying the olfactory senseand move towards the development of protein-based biomimetic sensor units that can serve as artificial noses.

Gradual chromosomal lagging drive programmed genome elimination in hemiclonal fishes from the genus Hypseleotris

Most eukaryotes maintain the stability of their cellular genome sizes to ensure genome transmission to offspring through sexual reproduction. However, some alter their genome size by selectively eliminating parts or increasing ploidy at specific developmental stages. This phenomenon of genome elimination or whole genome duplication occurs in animal hybrids reproducing asexually. Such genome alterations occur during gonocyte development ensuring successful reproduction of these hybrids. Although multiple examples of genome alterations are known, the underlying molecular and cellular processes involved in selective genome elimination and duplication remain largely unknown. Here, we uncovered the process of selective genome elimination and genome endoreplication in hemiclonal fish hybrids from the genus Hypseleotris. Specifically, we examined parental sexual species H. bucephala and hybrid H. bucephala × H. gymnocephala (HB × HX). We observed micronuclei in the cytoplasm of gonial cells in the gonads of hybrids, but not in the parental sexual species. We also observed misaligned chromosomes during mitosis which were unable to attach to the spindle. Moreover, we found that misaligned chromosomes lag during anaphase and subsequently enclose in the micronuclei. Using whole mount immunofluorescent staining, we showed that chromatid segregation has failed in lagging chromosomes. We also performed three-dimensional comparative genomic hybridization (3D-CGH) using species-specific probes to determine the role of micronuclei in selective genome elimination. We repeatedly observed that misaligned chromosomes of the H. bucephala genome were preferentially enclosed in micronuclei of hybrids. In addition, we detected mitotic cells without a mitotic spindle as a potential cause of genome duplication. We conclude that selective genome elimination in the gonads of hybrids occurs through gradual elimination of individual chromosomes of one parental genome. Such chromosomes, unable to attach to the spindle, lag and become enclosed in micronuclei.

Molecular Impact of Sublethal Spinetoram Exposure on Honeybee (Apis mellifera) Larval and Adult Transcriptomes

Pesticide toxicity is a global concern for honeybee populations, and understanding these effects at the molecular level is critical. This study analyzed the transcriptome of honeybees at larval and adult stages after chronic exposure to a sublethal dose (0.0017 µg a.i./larva) of spinetoram (SPI) during the larval phase. Four groups were used: acetone-treated honeybee larvae (ATL), acetone-treated honeybee adults (ATAs), SPI-treated honeybee larvae (STL), and SPI-treated honeybee adults (STAs). In total, 5719 differentially expressed genes (DEGs) were identified for ATL vs. ATAs, 5754 for STL vs. STAs, 273 for ATL vs. STL, and 203 for ATAs vs. STAs (FC ≤ 1.5, p < 0.05). In response to SPI, 29 unique DEGs were identified in larvae and 42 in adults, with 23 overlapping between comparisons, suggesting genes linked to SPI toxicity. Gene ontology analysis showed that SPI affected metabolism-related genes in larvae and lipid-transport-associated genes in adults. KEGG pathway analysis revealed an enrichment of pathways predominantly associated with metabolism, hormone biosynthesis, and motor proteins in STL. The transcriptomic data were validated by qPCR. These findings demonstrated that SPI disrupts essential molecular processes, potentially harming honeybee development and behavior, underscoring the need for safer agricultural practices.

Extensive import of nucleus-encoded tRNAs into chloroplasts of the photosynthetic lycophyte, Selaginella kraussiana

Over the course of evolution, land plant mitochondrial genomes have lost many transfer RNA (tRNA) genes and the import of nucleus-encoded tRNAs is essential for mitochondrial protein synthesis. By contrast, plastidial genomes of photosynthetic land plants generally possess a complete set of tRNA genes and the existence of plastidial tRNA import remains a long-standing question. The early vascular plants of the Selaginella genus show an extensive loss of plastidial tRNA genes while retaining photosynthetic capacity, and represent an ideal model for answering this question. Using purification, northern blot hybridization, and high-throughput tRNA sequencing, a global analysis of total and plastidial tRNA populations was undertaken in Selaginella kraussiana. We confirmed the expression of all plastidial tRNA genes and, conversely, observed that nucleus-encoded tRNAs corresponding to these plastidial tRNAs were generally excluded from the chloroplasts. We then demonstrated a selective and differential plastidial import of around forty nucleus-encoded tRNA species, likely compensating for the insufficient coding capacity of plastidial-encoded tRNAs. In-depth analysis revealed differential import of tRNA isodecoders, leading to the identification of specific situations. This includes the expression and import of nucleus-encoded tRNAs expressed from plastidial or bacterial-like genes inserted into the nuclear genome. Overall, our results confirm the existence of molecular processes that enable tRNAs to be selectively imported not only into mitochondria, as previously described, but also into chloroplasts, when necessary.

Effect of detachment on Magnum-PSI ELM-like pulses: direct observations and qualitative results

Abstract Conditions similar to those at the end of the divertor leg in a tokamak were replicated in the linear plasma machine Magnum-PSI. The neutral pressure in the target chamber is then increased to cause the target to transition from an attached to a detached state. Superimposed to this steady state regime, edge localised mode (ELM)-like pulses are reproduced, resulting in a sudden increase in plasma temperature and density, such that the heat flux increases transiently by half an order of magnitude. Visible light emission, target thermography, and Thomson scattering are used to demonstrate that the higher the neutral pressure the more energy is removed from the ELM-like pulse in the volume. If the neutral pressure is sufficiently high, the ELM-like pulse can be prevented from affecting the target and the plasma energy is fully dissipated in the volume instead (ID 4 in table 1). The visible light images allow the division of the ELM-plasma interaction process of ELM energy dissipation into 3 ‘stages’ ranging from no dissipation to full dissipation (the target plasma is detached). In the second publication related to this study, spectroscopic data is analysed with a Bayesian approach, to acquire insights into the significance of molecular processes in dissipating the plasma energy and particles.

Transcriptome analysis of mammary epithelial cell between Sewa sheep and East FriEsian sheep from different localities.

Mammary epithelial cells, the only milk-producing cell type in the mammary gland, undergo dynamic proliferation and differentiation during pregnancy, culminating in lactation postpartum. The East FriEsian sheep ranks among the world's most prolific dairy breeds, while the Sewa sheep, a unique dual-purpose breed autochthonous to the Qinghai-Tibet Plateau, exhibits significantly lower milk production. Employing tissue culture methods, we successfully established mammary epithelial cell lines from both breeds. Morphological assessment of mammary epithelial cells and immunofluorescence identification of Cytokeratin 7 and Cytokeratin 8 confirmed the epithelial identity of the isolated cells. Subsequent RNA-seq analysis of these in vitro epithelial cell lines revealed 1813 differentially expressed genes (DEGs). Among these, 1108 were significantly up-regulated and 705 were down-regulated in Sewa epithelial sheep cells compared to East FriEsian epithelial cells. KEGG enrichment analysis identified cellular processes, environmental information processing, human diseases, metabolism, and organismal systems as the primary functional categories associated with DEGs. Gene ontology (GO) terms annotation, categorized into molecular function, biological processes, and cellular component, yielded "binding and catalytic activity," "molecular function regulator activity," and "cellular process," "biological regulation," and "regulation of biological process" as the top three terms within each domain, respectively. Clusters of Orthologous Groups of proteins (KOG) classification further revealed that "signal transduction mechanisms" accounted for the largest proportion of DEGs among all KOG categories. Finally, based on these analyses, ATF3 and MPP7 were identified as promising candidate genes for regulating lactation.

Advance in Nrf2 Signaling Pathway in Leishmaniasis

One of the main components of innate defense against invasive parasites is oxidative stress, which is brought on by reactive oxygen species (ROS). On the other hand, oxidative stressors serve two purposes: free radicals aid in the elimination of pathogens, but they can also set off inflammation, which leads to tissue damage. Nuclear factor erythroid 2-related factor 2 (Nrf2) is a transcription factor that controls the expression of numerous genes involved in the body’s defense against oxidative stress brought on by aging, inflammation, tissue damage, and other pathological consequences. From cutaneous to visceral forms, Leishmania parasites invade macrophages and cause a wide range of human pathologies. Leishmania parasites have a wide range of adaptive mechanisms that disrupt several macrophage functions by altering host signaling pathways. An increasing amount of data are corroborating the idea that one of the primary antioxidant routes to counteract this oxidative burst against parasites is NRF2 signaling, which also interferes with immune responses. The nature and potency of the host immune response, as well as interactions between the invading Leishmania spp., will ascertain the course of infection and the parasites’ eventual survival or eradication. The molecular processes via which Nrf2 coordinates such intricate networks comprising various pathways remain to be completely understood. In light of NRF2’s significant contribution to oxidative stress, we examine the NRF2 antioxidant pathway’s activation mechanism in Leishmania infection in this review. Thus, this review will examine the relationship between Nrf2 signaling and leishmaniasis, as well as explore potential therapeutic strategies for modifying this system.

The characterization of ancient Methanococcales malate dehydrogenases reveals that strong thermal stability prevents unfolding under intense γ-irradiation.

Malate dehydrogenases (MalDH) (EC.1.1.1.37), which are involved in the conversion of oxaloacetate to pyruvate in the tricarboxylic acid cycle, are a relevant model for the study of enzyme evolution and adaptation. Likewise, a recent study showed that Methanococcales, a major lineage of Archaea, is a good model to study the molecular processes of proteome thermoadaptation in prokaryotes. Here, we use ancestral sequence reconstruction and paleoenzymology to characterize both ancient and extant MalDHs. We observe a good correlation between inferred optimal growth temperatures (OGTs) and experimental optimal temperatures for activity (A-Topt). In particular, we show that the MalDH present in the ancestor of Methanococcales was hyperthermostable and had an A-Topt of 80°C, consistent with a hyperthermophilic lifestyle. This ancestor gave rise to two lineages with different thermal constraints, one remaining hyperthermophilic while the other underwent several independent adaptations to colder environments. Surprisingly, the enzymes of the first lineage have retained a thermoresistant behavior (i.e., strong thermostability and high A-Topt), whereas the ancestor of the second lineage shows a strong thermostability, but a reduced A-Topt. Using mutants, we mimic the adaptation trajectory towards mesophily and show that it is possible to significantly reduce the A-Topt without altering the thermostability of the enzyme by introducing a few mutations. Finally, we reveal an unexpected link between thermostability and the ability to resist γ-irradiation-induced unfolding.

Insight into the direct carbonation process of Ca2SiO4 based on ReaxFF MD simulation and experiments

Ca2SiO4 is the primary carbonation-reactive mineral in steel slag, and demonstrates significant carbon sequestration potential, yet its microscopic reaction processes remain unclear. This study investigated the carbonation behavior of Ca2SiO4 using ReaxFF MD simulations. The results indicated that as CO2 concentration increased, the capture rate of Ca2SiO4 decreased, and the molecular structure of the resulting CaCO3 varied in oxygen origin. At room temperature, the carbonation rate of Ca₂SiO₄ gradually decreased over time until it reached equilibrium. Increasing the temperature could reactivate the carbonation, but the rate would still decline until it reached equilibrium again. Higher temperatures could accelerate the formation of the intermediate C2O52− and internal CO32− diffusion, thereby boosting the carbonation and increasing CO2 adsorption. This study investigated the carbonation of Ca2SiO4 at the atomic level, aiming to link microscopic molecular processes with macroscopic experimental phenomena, thereby providing a theoretical foundation for enhancing the carbonation efficiency of steel slag.

Whole transcriptome sequencing of testis and epididymis reveals genes associated with sperm development in roosters

BackgroundChickens play a crucial role as the primary global source of eggs and poultry, and the quality of rooster semen significantly impacts poultry reproductive efficiency. Therefore, it is imperative to comprehend the regulatory mechanisms underlying sperm development.ResultsIn this study, we established transcriptome profiles of lncRNAs, miRNAs, and mRNAs in 3 testis tissues and 3 epididymis tissues from “Jing Hong No.1” roosters at 24, 35, and 64 weeks of age. Using the data, we conducted whole transcriptome analysis and constructed a ceRNA network. We detected 10 differentially expressed mRNAs (DEmRNAs), 33 differentially expressed lncRNAs (DElncRNAs), and 10 differentially expressed miRNAs (DEmiRNAs) in the testis, as well as 149 DEmRNAs, 12 DElncRNAs, and 10 DEmiRNAs in the epididymis. These genes were found to be involved in cell differentiation and development, as well as various signaling pathways such as GnRH, MAPK, TGF-β, mTOR, VEGF, and calcium ion pathways. Subsequently, we constructed two competing endogenous RNA (ceRNA) networks comprising DEmRNAs, DElncRNAs, and DEmiRNAs. Furthermore, we identified four crucial lncRNA-mRNA-miRNA interactions that govern specific biological processes in the chicken reproductive system: MSTRG.2423.1-gga-miR-1563-PPP3CA and MSTRG.10064.2-gga-miR-32-5p-GPR12 regulating sperm motility in the testis; MSTRG.152556.1-gga-miR-9-3p-GREM1/THYN1 governing immunomodulation in the epididymis; and MSTRG.124708.1-gga-miR-375-NDUFB9/YBX1 controlling epididymal sperm maturation and motility.ConclusionsWhole transcriptome sequencing of chicken testis and epididymis screened several key genes and ceRNA regulatory networks, which may be involved in the regulation of epididymal immunity, spermatogenesis and sperm viability through the pathways of MAPK, TGF-β, mTOR, and calcium ion. These findings contribute to our comprehensive understanding of the intricate molecular processes underlying rooster spermatogenesis, maturation and motility.

Interrogating the photoluminescent properties of carbon dots using quantitative 13C NMR combined with systematic photobleaching

In this work, molecular-level events accompanying the photobleaching of carbon dots (CDs) synthesized from ethylenediamine and citric acid (CACDs) were identified using solution-phase NMR. By combining quantitative 13C NMR data with fluorescence measurements we show that this new approach is capable of identifying not only molecular fluorophores in CACDs, but also their contribution to the overall CACD fluorescence and their relative photostability. Specifically, imidazo[1,2-a]pyridine-7-carboxylic acid (IPCA) is found to be the dominant (84 %) species responsible for fluorescence in CACDs along with a second undetermined source, most likely associated with the aromatic core which is significantly (approximately 20 times) more photostable than IPCA. The presence of these two fluorescent species with different photostabilities rationalizes not only the photobleaching kinetics but also the evolution of the fluorescence spectrum during photobleaching Diffusion-ordered spectroscopy (DOSY) also reveals that all of the IPCA molecules are trapped within or covalently bound to the CACD, but are not present as isolated molecules freely rotating in solution. Singlet oxygen is confirmed as a key ROS responsible for photobleaching, with prototypical photoproducts identified from mass spectrometry studies of citrazinic acid. Quantitative 13C NMR of CACDs is possible because their extremely high colloidal stability enables high concentrations (667 mg/mL) to remain stable in solution. The approach described in this study could be extended to identify the structure of chromophores in other CDs and interrogate molecular level processes that accompany CD sensing.

A Systems Biology Approach Towards a Comprehensive Understanding of Ferroptosis.

Ferroptosis is a regulated cell death process characterized by iron ion catalysis and reactive oxygen species, leading to lipid peroxidation. This mechanism plays a crucial role in age-related diseases, including cancer and cardiovascular and neurological disorders. To better mimic iron-induced cell death, predict the effects of various elements, and identify drugs capable of regulating ferroptosis, it is essential to develop precise models of this process. Such drugs can be tested on cellular models. Systems biology offers a powerful approach to studying biological processes through modeling, which involves accumulating and analyzing comprehensive research data. Once a model is created, it allows for examining the system's response to various stimuli. Our goal is to develop a modular framework for ferroptosis, enabling the prediction and screening of compounds with geroprotective and antiferroptotic effects. For modeling and analysis, we utilized BioUML (Biological Universal Modeling Language), which supports key standards in systems biology, modular and visual modeling, rapid simulation, parameter estimation, and a variety of numerical methods. This combination fulfills the requirements for modeling complex biological systems. The integrated modular model was validated on diverse datasets, including original experimental data. This framework encompasses essential molecular genetic processes such as the Fenton reaction, iron metabolism, lipid synthesis, and the antioxidant system. We identified structural relationships between molecular agents within each module and compared them to our proposed system for regulating the initiation and progression of ferroptosis. Our research highlights that no current models comprehensively cover all regulatory mechanisms of ferroptosis. By integrating data on ferroptosis modules into an integrated modular model, we can enhance our understanding of its mechanisms and assist in the discovery of new treatment targets for age-related diseases. A computational model of ferroptosis was developed based on a modular modeling approach and included 73 differential equations and 93 species.

Transcriptomics changes of calcitonin gene-related peptide in mitigating lipopolysaccharide-induced septic cardiomyopathy

Septic cardiomyopathy (SCM), a complication initiated by sepsis, presents a significant clinical challenge, leading to increased mortality rates. However, the mechanisms of SCM have not been fully uncovered. Our study involved analyzing RNA sequencing (RNA-seq) data from rat heart tissue, along with utilizing molecular docking and molecular dynamics (MD) simulations, to discover key targets and potential pharmacological actions of the calcitonin gene-related peptide (CGRP) against SCM. A lipopolysaccharide-induced SCM model was established in rats (LPS 10 mg/kg, intraperitoneal (i.p.)). Thereafter, the myocardial tissues from the three groups of rats (Ctrl group, LPS group, and CGRP group) (n = 5) were extracted and underwent RNA-seq, followed by bioinformatics analyses. The qPCR-validated hub targets potentially interacting with CGRP were identified. Following this, homology modeling was utilized to obtain the 3D structure of hub targets, and molecular docking was conducted to evaluate the interaction between CGRP and hub targets. MD simulations (300 ns) were performed to confirm the findings further. Our findings demonstrated that CGRP significantly lowered mortality in SCM rats. 633 DEGs were affected by LPS, contrasted with the Ctrl group. 96 DEGs were affected by CGRP compared to the LPS group. In total, ten fully annotated CGRP-triggered hub genes were obtained. The molecular docking and MD simulations indicate that the relationship between CGRP and eight hub genes is extremely strong. This research offers a thorough examination of the possible objectives and fundamental molecular processes of CGRP in combating SCM, laying the groundwork for investigating the potential protective mechanisms of CGRP against SCM.

Advances in molecular imaging of kidney diseases.

Background Diagnosing and monitoring kidney diseases traditionally rely on blood and urine analyses and invasive procedures such as kidney biopsies, the latter offering limited possibilities for longitudinal monitoring and a comprehensive understanding of disease dynamics. Current non-invasive methods lack specificity in capturing intrarenal molecular processes, hindering patient stratification and patient monitoring in clinical practice and clinical trials. Summary Molecular imaging enables non-invasive and quantitative assessment of physiological and pathological molecular processes. By using specific molecular probes and imaging technologies, e.g., magnetic resonance imaging (MRI), positron emission tomography (PET), single-photon emission computed tomography (SPECT), or ultrasound (US), molecular imaging allows the detection and longitudinal monitoring of disease activity with spatial and temporal resolution of different kidney diseases and disease-specific pathways. Several approaches have already shown promising results in kidneys and exploratory clinical studies, and validation is needed before implementation in clinical practice. Key messages Molecular imaging offers a non-invasive assessment of intrarenal molecular processes, overcoming the limitations of current diagnostic methods. It has the potential to serve as companion diagnostics, not only in clinical trials, aiding in patient stratification and treatment response assessment. By guiding therapeutic interventions, molecular imaging might contribute to the development of targeted therapies for kidney diseases.

New Horizons in Nuclear Cardiology: Imaging of Peripheral Arterial Disease.

Lower extremity peripheral artery disease (PAD) is characterized by impairment of blood flow associated with arterial stenosis and frequently coexisting microvascular disease and is associated with high rates of morbidity and mortality. Current diagnostic modalities have limited accuracy in early diagnosis, risk stratification, preprocedural assessment, and evaluation of therapy and are focused on the detection of obstructive atherosclerotic disease. Early diagnosis and assessment of both large vessels and microcirculation may improve risk stratification and guide therapeutic interventions. SPECT and PET imaging have been shown to be accurate to detect changes in perfusion in preclinical models and clinical disease, and have the potential to overcome limitations of existing diagnostic modalities, while offering novel information about perfusion, metabolic, and molecular processes. This review provides a comprehensive reassessment of radiotracer-based imaging of PAD in preclinical and clinical studies, emphasizing the challenges that arise due to the complex physiology in the peripheral vasculature. We will also highlight the latest advancements, underscoring emerging artificial intelligence and big data analysis, as well as clinically relevant areas where the field could advance in the next decade.

TRBP2, a Major Component of the RNAi Machinery, Is Subjected to Cell Cycle-Dependent Regulation in Human Cancer Cells of Diverse Tissue Origin.

Transactivation Response Element RNA-binding Protein (TRBP2) is a double-stranded RNA-binding protein widely known for its critical contribution to RNA interference (RNAi), a conserved mechanism of gene-expression regulation mediated through small non-coding RNA moieties (ncRNAs). Nevertheless, TRBP2 has also proved to be involved in other molecular pathways and biological processes, such as cell growth, organism development, spermatogenesis, and stress response. Mutations or aberrant expression of TRBP2 have been previously associated with diverse human pathologies, including Alzheimer's disease, cardiomyopathy, and cancer, with TRBP2 playing an essential role(s) in proliferation, invasion, and metastasis of tumor cells. Hence, the present study aims to investigate, via employment of advanced flow cytometry, immunofluorescence, cell transgenesis and bioinformatics technologies, new, still elusive, functions and properties of TRBP2, particularly regarding its cell cycle-specific control during cancer cell division. We have identified a novel, mitosis-dependent regulation of TRBP2 protein expression, as clearly evidenced by the lack of its immunofluorescence-facilitated detection during mitotic phases, in several human cancer cell lines of different tissue origin. Notably, the obtained TRBP2-downregulation patterns seem to derive from molecular mechanisms that act independently of oncogenic activities (e.g., malignancy grade), metastatic capacities (e.g., low versus high), and mutational signatures (e.g., p53-/- or p53ΔΥ126) of cancer cells. Taken together, we herein propose that TRBP2 serves as a novel cell cycle-dependent regulator, likely exerting mitosis-suppression functions, and, thus, its mitosis-specific downregulation can hold strong promise to be exploited for the efficient and successful prognosis, diagnosis, and (radio-/chemo-)therapy of diverse human malignancies, in the clinic.

High-quality InAs homoepitaxial layers grown by molecular beam epitaxy

The growth conditions for InAs homoepitaxy by molecular beam epitaxy were comprehensively studied across a broad spectrum of substrate temperatures, As2/In flux ratios, and growth rates. It was found that the surface morphology and overall quality of the InAs layers were significantly influenced by these parameters. Optimal conditions, including a lower growth temperature, reduced As2 flux, and slower growth rate, were pivotal in achieving high-quality InAs layers. Two primary characterization techniques, differential interference contrast microscopy and atomic force microscopy, were employed to evaluate the material quality. High-quality InAs homoepitaxial layers were successfully grown at a substrate temperature of 455 °C and a growth rate of 0.33 monolayers per second (ML/s). These layers exhibited a remarkably low defect density of approximately 300 defects per square centimeter, which is over an order of magnitude lower than previously reported, and a notably low root-mean-square roughness of 0.116 nm. At a growth rate of 0.33 ML/s, the growth temperature range for InAs homoepitaxial layers was found to be quite broad, whereas the As2/In flux ratio remained within a narrow range. This study underscores the critical role of precise control over growth parameters in the molecular beam epitaxy process for producing high-quality InAs homoepitaxial layers.

Time-resolved photoelectron spectroscopy at surfaces

Light is still an important spectroscopic tool for investigating the electronic structure of surfaces. Time-resolved photoelectron spectroscopy has mainly been developed in the last 30 years. It is therefore not surprising that the topic was hardly mentioned in the last issue on “The first thirty years” of surface science. In the second thirty years, however, we have seen tremendous progress in the development of time-resolved photoelectron spectroscopy on surfaces. Femtosecond light pulses and advanced photoelectron detection schemes are increasingly being used to study the electronic structure and dynamics of occupied and unoccupied electronic states and dynamic processes such as the energy and momentum relaxation of electrons, charge transfer at interfaces and collective processes such as plasmonic excitation and optical field screening. Using spin- and time-resolved photoelectron spectroscopy, we were able to study ultrafast spin dynamics, electron-magnon scattering and spin structures in magnetic and topological materials. Light also provides photon energy as well as electric and magnetic fields that can influence molecular surface processes to steer surface photochemistry and hot-electron-driven catalysis. In addition, we can consider light as a chemical reagent that can alter the properties of matter by creating non-equilibrium states and ultrafast phase transitions in correlated materials through the coupling of electrons, phonons and spins. Electric fields have also been used to temporarily change the electronic structure. This opened up new methods and areas such as high harmonic generation, light wave electronics and attosecond physics. This overview certainly cannot cover all these interesting topics. But also as a testimony to the cohesion and constructive exchange in our ultrafast community, a number of colleagues have come together to share their expertise and views on the very vital field of dynamics at surfaces. Following the introduction, the interested reader will find a list of contributions and a brief summary in Section 1.3.