A perspective of the dynamic structure of the nucleus explored at the single-molecule level

Cellular life can be described as a dynamic equilibrium of a highly complex network of interacting molecules. For this reason, it is no longer sufficient to “only” know the identity of the participants in a cellular process, but questions such as where, when, and for how long also have to be addressed to understand the mechanism being investigated. Additionally, ensemble measurements may not sufficiently describe individual steps of molecular mobility, spatial-temporal resolution, kinetic parameters, and geographical mapping. It is vital to investigate where individual steps exactly occur to enhance our understanding of the living cell. The nucleus, home too many highly complex multi-order processes, such as replication, transcription, splicing, etc., provides a complicated, heterogeneous landscape. Its dynamics were studied to a new level of detail by fluorescence correlation spectroscopy (FCS). Single-molecule tracking, while still in its infancy in cell biology, is becoming a more and more attractive method to deduce key elements of this organelle. Here we discuss the potential of tracking single RNAs and proteins in the nucleus. Their dynamics, localization, and interaction rates will be vital to our understanding of cellular life. To demonstrate this, we provide a review of the HIV life cycle, which is an extremely elegant balance of nuclear and cytoplasmic functions and provides an opportunity to study mechanisms deeply integrated within the structure of the nucleus. In summary, we aim to present a specific, dynamic view of nuclear cellular life based on single molecule and FCS data and provide a prospective for the future

Intelligent Lunar Landing Site Recommender

Space exploration is brewing to be one of the most sought after fields in today’s world with each country pooling in resources and skilled minds to be one step ahead of the other. The core aspect of space exploration is exoplanet exploration, i.e., by sending unmanned rovers or manned spaceships to planets and celestial bodies within and beyond our solar system to determine habitable planets. Landscape inspection and traversal is the core feature of any planetary exploration mission. It is often a strenuous task to carry out a machine learning experiment on an extraterrestrial surface like the Moon. Consequent lunar explorations undertaken by various space agencies in the last four decades have helped to analyze the nature of the Lunar Terrain through satellite images. The motion of the rovers has traditionally been governed by the use of sensors that achieve obstacle avoidance. In this project we aim to detect craters on the lunar landscape which in turn will be used to determine soft landing sites on the lunar landscape for exploring the terrain, based on the classified lunar landscape images

Autonomy and robustness of translocation through the nuclear pore complex: a single-molecule study

All molecular traffic between nucleus and cytoplasm occurs via the nuclear pore complex (NPC) within the nuclear envelope. In this study we analyzed the interactions of the nuclear transport receptors kapα2, kapβ1, kapβ1ΔN44, and kapβ2, and the model transport substrate, BSA-NLS, with NPCs to determine binding sites and kinetics using single-molecule microscopy in living cells. Recombinant transport receptors and BSA-NLS were fluorescently labeled by AlexaFluor 488, and microinjected into the cytoplasm of living HeLa cells expressing POM121-GFP as a nuclear pore marker. After bleaching the dominant GFP fluorescence the interactions of the microinjected molecules could be studied using video microscopy with a time resolution of 5 ms, achieving a colocalization precision of 30 nm. These measurements allowed defining the interaction sites with the NPCs with an unprecedented precision, and the comparison of the interaction kinetics with previous in vitro measurements revealed new insights into the translocation mechanism

Proteasomes associated with the Blm10 activator protein antagonize mitochondrial fission through degradation of the fission protein Dnm1

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Archaea in mammalian gut microbiomes

Background: Archaea are the most enigmatic domain of the three domains of life. Archaea are unique in that they share some characteristics with bacteria and others with eukaryotes while they are also distinct from these two domains. Mostarchaea are extremophiles that are found in highly acidic, high salt, or high- temperature environments. However, recent microbiome research has revealed that these prokaryotes are also a part of the gut microbiota, albeit their functional roles in gut health or disease are unclear. Archaea could be keystone species in the gut that engage in important syntrophic relationships with other gut microbes. The recent proposal of archaeal strains as a new class of probiotics (archaebiotics) could be of interest for improving gut pathophysiology and overall human health. The main aim of this study is to mine extant microbiome data sets in our laboratory for the presence of archaeal sequences.Method: Metagenomic data sets from mammalian microbiome studies (e.g., mouse, rat, prairie voles) based on 16S rRNA amplicon or whole-genome shotgun sequencing approaches are screened for archaeal sequences. Taxonomic profiling workflows in the Qiagen CLC Genomics Workbench and other bioinformatics software such as MetaPhlan are used to elucidate the relative abundances of these enigmatic microorganisms.Results: Archaeal sequences have been found in DNA isolated from digesta and feces at relatively low abundances. Most sequence variants are derived from methanogens, a subgroup of archaea, while we also found indications for the presence of halophilic archaea.Conclusion: Our experiments demonstrate that archaeal sequences, specifically from methanogens and halophiles, are found in our mammalian gut microbiome data sets. Future studies will include confirmation of archaeal presence using quantitative PCR (qPCR) and, if possible, in vitro culture. Predictions on the functional roles of archaea in the gut will also be conducted to help characterizethe impact of these microorganisms on gut healt

Survival Outcomes in T3 Laryngeal Cancers: Primary Total Laryngectomy vs. Concurrent Chemoradiation or Radiation Therapy-A Meta-Analysis

Background: The management of cT3 laryngeal cancers remains controversial, with studies recommending surgical or non-surgical approaches. Despite the many papers that have been published on the subject, there is a lack of studies showing which treatment has better results in terms of survival. Objective: To determine the difference in survival outcomes following total laryngectomy (TL), concurrent chemoradiation (CRT) or radiation therapy (RT) alone in T3 laryngeal cancers. Methods: Search of PubMed, Scopus, and Google Scholar databases from 1995 to 2023 employing specific keywords and Boolean operators to retrieve relevant articles. Statistical analysis was conducted using a random-effects model, and heterogeneity was evaluated using the Q-test and I2 statistic. Funnel plot asymmetry was assessed using rank correlation and regression tests. Results: The qualitative data synthesis comprised 10,940 patients from 16 included studies. TL was performed in 2149 (19.4%), CRT in 6723 (61.5%), RT in 295 (2.7%), while non-surgical treatment was not specified in 1773 (16.2%) patients. The pooled 2-year overall survival (OS) rates were TL = 73%, CRT = 74.7%, RT = 57.9%, 3-year OS rates were TL = 64.3%, CRT = 62.9%, RT = 52.4%, and 5-year OS rates were TL = 54.2%, CRT = 52.7%, RT = 40.8%. There was a significant heterogeneity in the included studies. There was no statistically significant difference in 2-year OS (logOR= -0.88 (95% confidence interval (CI): -1.99 to 0.23), p = 0.12), 3-year OS (logOR = -0.6 (95% CI: -1.34 to 0.15), p = 0.11), and 5-year OS (logOR = -0.54 (95% CI: -1.29 to 0.21), p = 0.16) between TL and CRT. Instead, there was significant difference in 2-year OS (logOR= -1.2383 (95% CI: -2.1679 to -0.3087), p = 0.009), 3-year OS (-1.1262 (95% CI: -1.6166 to -0.6358), p < 0.001), and 5-year OS (-0.99 (95% CI: -1.44 to -0.53)), p < 0.001) between TL and RT alone. Conclusions and Significance: TL followed with adjuvant (chemo)radiation on indication and CRT with salvage surgery in reserve appear to have similar OS outcomes. Both resulted in better OS outcomes compared to RT alone in the treatment of T3 laryngeal cancers. If patients are unfit for chemotherapy, making CRT impossible, surgery may become the choice of treatment

Comparative analysis of opioid-induced microbiome alterations in rat small intestine, cecum, and colon

Background: Trillions of bacteria, archaea, fungi, and viruses comprise the animal microbiome and virome. The composition and diversity of these complex communities have a profound impact on the health of their animal host. Conversely, microbiome profiles can be affected by multiple host factors such as diet, health, or medication. Embedded in these communities might be groupings such as individual bacterial species/strains or consortia that have key roles and could serve as biomarkers for host health and disease.Methods: We have been collecting microbiota and/or microbiome profiles from rat small intestine, cecum, and colon after chronic oxycodone administration to assess the impact of the drug on the resident microbial communities and identify such specific markers. Next-generation sequencing systems are used for 16S ribosomal RNA analyses and whole-genome shotgun metagenomics to determine taxonomic profiles and predict functional profiles of the microbial communities.Results: Alpha and beta diversity analyses of the microbiota showed differences in the gastrointestinal regions when using location, sex, or treatment as metadata. Differential abundance analyses of datasets from control and oxycodone-treated animals revealed specific alterations in the microbiota composition within these experimental groups. Examples of workflows and bioinformatic approaches are presented that illustrate how biomarker discovery within different gastrointestinal regions could lead to deeper understanding of the impact oxycodone has on the animal and human microbiomes.Conclusions: Correlation of microbiome profiles with host metadata will aid in the identification of potential biomarkers of oxycodone use in the different host organ environments. The resulting biomarker discoveries may aid in diagnosis, prevention, and treatment of drug-induced gastrointestinal dysbiosis

Geographic and behavioral differences associated with sexually transmitted infection prevalence among Indian men who have sex with men in Chennai and Mumbai

BACKGROUND: India has one of the largest numbers of men who have sex with men (MSM) globally, however, geographic data on sexually transmitted infection (STI) prevalence and associations with sexual behavior are limited. METHODS: Six-hundred-eight MSM in Chennai and Mumbai screening in for a behavioral trial and assessed bacterial STI (syphilis, chlamydia, gonorrhea), HIV, and past-month self-reported condomless anal sex (CAS). RESULTS: Mumbai (37.8%) had a greater prevalence of any STIs than Chennai (27.6%) (est=1.37, 95% CI:1.09,1.73). This pattern also emerged for gonorrhea and chlamydia separately but not syphilis. Conversely, Mumbai had lower CAS (M=2.2) compared to Chennai (M=14.0) (est=−11.8, 95% CI:−14.6,−9.1). The interaction of city by CAS on any STI prevalence (PR=2.09, 95% CI:1.45,3.01, p<.0001) revealed that in Chennai, higher CAS was not associated with STI prevalence, but in Mumbai it was (PR=2.49, 95% CI:1.65,3.76, p<.0001). DISCUSSION: Higher bacterial STIs but lower CAS in Mumbai versus Chennai, and the significant interaction of CAS with city on STIs suggests that either differences in disease burden or differences by city with respect to self-reported assessment of CAS. Regardless, the high prevalence rates of untreated STI and condomless sex among MSM suggests the need for additional prevention intervention efforts for MSM in urban India

Elevated Proteasome Capacity Extends Replicative Lifespan in Saccharomyces cerevisiae

Aging is characterized by the accumulation of damaged cellular macromolecules caused by declining repair and elimination pathways. An integral component employed by cells to counter toxic protein aggregates is the conserved ubiquitin/proteasome system (UPS). Previous studies have described an age-dependent decline of proteasomal function and increased longevity correlates with sustained proteasome capacity in centenarians and in naked mole rats, a long-lived rodent. Proof for a direct impact of enhanced proteasome function on longevity, however, is still lacking. To determine the importance of proteasome function in yeast aging, we established a method to modulate UPS capacity by manipulating levels of the UPS–related transcription factor Rpn4. While cells lacking RPN4 exhibit a decreased non-adaptable proteasome pool, loss of UBR2, an ubiquitin ligase that regulates Rpn4 turnover, results in elevated Rpn4 levels, which upregulates UPS components. Increased UPS capacity significantly enhances replicative lifespan (RLS) and resistance to proteotoxic stress, while reduced UPS capacity has opposing consequences. Despite tight transcriptional co-regulation of the UPS and oxidative detoxification systems, the impact of proteasome capacity on lifespan is independent of the latter, since elimination of Yap1, a key regulator of the oxidative stress response, does not affect lifespan extension of cells with higher proteasome capacity. Moreover, since elevated proteasome capacity results in improved clearance of toxic huntingtin fragments in a yeast model for neurodegenerative diseases, we speculate that the observed lifespan extension originates from prolonged elimination of damaged proteins in old mother cells. Epistasis analyses indicate that proteasome-mediated modulation of lifespan is at least partially distinct from dietary restriction, Tor1, and Sir2. These findings demonstrate that UPS capacity determines yeast RLS by a mechanism that is distinct from known longevity pathways and raise the possibility that interventions to promote enhanced proteasome function will have beneficial effects on longevity and age-related disease in humans