Cellular Functions Research Articles

Meeting the Needs of Underrepresented Female Students Using Innovative Molecular Models

The underrepresentation of women in science, technology, engineering, and math (STEM) fields is of national concern. Research shows that females begin to lose confidence in their math and science abilities in middle school and it worsens in high school. Developing and leveraging young women’s interest in these topics via active learning activities and hands on models can encourage pursuit of STEM degrees in college. The MIT Edgerton Center Models and Curriculum was incorporated into the EMPOWER Program, a four-week program engaging female research scholars in 10th-12th grade in a summer fellowship that provided hands-on research experience focused on in-depth understanding of how exposures to toxic environmental insults in the urban environment impact health and alter biologic processes. The models were used to teach about DNA/RNA and protein synthesis. The models are designed to teach processes, in addition to structure. They are made to be manipulated so learners can perform cellular functions with their own hands. We hypothesized that using a hands on activity would increase engagement and learning about the Central Dogma of Life. Methods: Participants were guided through exercises using the models. Students (n=5) and teachers (n=2) utilized the MIT Edgerton Center Models of DNA/RNA and protein synthesis. Results/Discussion: Surveys were completed at the end of the program to determine student’s perceived impact on their learning and overall experience using the hands-on models. A Likert scale was used to assess student learning. On a scale of 1 to 5, with 5 representing strongly agree, all participants strongly agreed the models helped them learn more about DNA/RNA and proteins. Conclusion: Innovative molecular models increased student engagement and learning creating an environment for student centered learning. NIEHS Project Number: 5R25ES030240-03. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Estrogen Metabolites Modulate Airway Hyperreactivity in a Murine Model of Asthma

Objective: Airway hyperreactivity (AHR) and remodeling are the key contributors to airway changes in asthma resulting in airway narrowing and resistance to airflow. Sex-steroid signaling, especially estrogen’s differential role in asthma undoubtedly questions its prime involvement in regulating airway structure and function in context to asthma. Evidence from cardiovascular (CV) and reproductive systems suggests that estrogen metabolites particularly 2-hydroxyestradiol (2HE) and 16α-hydroxyestradiol (16αHE2) influence a multitude of cellular functions. Accordingly, the aim of this study is to determine how estrogen metabolites regulate AHR and remodeling using a mouse model of asthma. Methods: WT C57BL/6J (male and female) mice were procured from Jackson Laboratory. Experimental animals were administered with PBS, 2-HE (2 mg/kg), 16αHE2 (2 mg/kg) with/without MA intranasally on alternate days for 28 days. On day 29, mice were anesthetized and subjected to SCIREQ flexiVent to measure Lung mechanics like airway resistance (Rrs), elastance (Ers), and compliance (Crs). Following this, broncho-alveolar lavage (BAL) was performed for differential leukocyte count (DLC) and lung tissue samples processed for histology using hematoxylin and eosin (H&E) staining and Sirius-red and fast-green (SRFG). Results: MA-challenged group increased airway Rrs and reduced Crs in response to methacholine (MCh) in both male and female mice with profound effects in female mice. Animals exposed to MA and administered with 16αHE2 showed significant increase the Rrs while 2-HE downregulated the MA effect. The exacerbated effect of 16αHE2 on Rrs was significantly higher in MA-challenged female mice compared to male mice. Histology study including H&E and SRFG stained lung sections show increased ASM mass in 16αHE2 exposed mixed MA challenged mice. Whereas 2HE reversed MA induced effect. DLC in BAL showed increased neutrophils and eosinophils in MA challenged mice, this was attenuated by 2HE. Conclusion: This study highlights the distinct role of estrogen metabolites in regulating airway hyperresponsiveness and remodeling in the context of asthma. Thus, providing possible therapeutic potential for observed sex differences in asthma. Acknowledgment: Supported by NIH grant R01-HL146705 (Sathish). This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Critical roles and clinical perspectives of RNA methylation in cancer.

RNA modification, especially RNA methylation, is a critical posttranscriptional process influencing cellular functions and disease progression, accounting for over 60% of all RNA modifications. It plays a significant role in RNA metabolism, affecting RNA processing, stability, and translation, thereby modulating gene expression and cell functions essential for proliferation, survival, and metastasis. Increasing studies have revealed the disruption in RNA metabolism mediated by RNA methylation has been implicated in various aspects of cancer progression, particularly in metabolic reprogramming and immunity. This disruption of RNA methylation has profound implications for tumor growth, metastasis, and therapy response. Herein, we elucidate the fundamental characteristics of RNA methylation and their impact on RNA metabolism and gene expression. We highlight the intricate relationship between RNA methylation, cancer metabolic reprogramming, and immunity, using the well-characterized phenomenon of cancer metabolic reprogramming as a framework to discuss RNA methylation's specific roles and mechanisms in cancer progression. Furthermore, we explore the potential of targeting RNA methylation regulators as a novel approach for cancer therapy. By underscoring the complex mechanisms by which RNA methylation contributes to cancer progression, this review provides a foundation for developing new prognostic markers and therapeutic strategies aimed at modulating RNA methylation in cancer treatment.

Phosphorylation Code of Human Nucleophosmin Includes Four Cryptic Sites for Hierarchical Binding of 14-3-3 Proteins

Nucleophosmin (NPM1) is the 46th most abundant human protein with many functions whose dysregulation leads to various cancers. Pentameric NPM1 resides in the nucleolus but can also shuttle to the cytosol. NPM1 is regulated by multisite phosphorylation, yet molecular consequences of site-specific NPM1 phosphorylation remain elusive. Here we identify four 14-3-3 protein binding sites in NPM1 concealed within its oligomerization and α-helical C-terminal domains that are found phosphorylated in vivo. By combining mutagenesis, in-cell phosphorylation and PermaPhos technology for site-directed incorporation of a non-hydrolyzable phosphoserine mimic, we show how phosphorylation promotes NPM1 monomerization and partial unfolding, to recruit 14-3-3 dimers with low-micromolar affinity. Using fluorescence anisotropy we quantified pairwise interactions of all seven human 14-3-3 isoforms with four recombinant NPM1 phosphopeptides and assessed their druggability by fusicoccin. This revealed a complex hierarchy of 14-3-3 affinities toward the primary (S48, S293) and secondary (S106, S260) sites, differentially modulated by the small molecule. As three of these 14-3-3 binding phosphosites in NPM1 reside within signal sequences, this work suggests a mechanism of NPM1 regulation by which NPM1 phosphorylation can promote 14-3-3 binding to affect NPM1 shuttling between cell compartments. It also provides further evidence that phosphorylation-induced structural rearrangements of globular proteins serve to expose otherwise cryptic 14-3-3-binding sites that are important for cellular function.

In vitro mRNA-S maternal vaccination induced altered immune regulation at the maternal-fetal interface.

Maternal-fetal immunology is intricate, and the effects of mRNA-S maternal vaccination on immune regulation at the maternal-fetal interface require further investigation. Our study endeavors to elucidate these immunological changes, enhancing our comprehension of maternal and fetal health outcomes. By analyzing immune profiles and cytokine responses, we aim to provide valuable insights into the impact of mRNA-S vaccination on the delicate balance of immune regulation during pregnancy, addressing critical questions in the field of reproductive pharmacology. This investigation sought to examine the prospective influence of mRNA-S-based vaccines and extracellular vesicles (EVs) containing the Spike (S) protein at the maternal-fetal interface. Our primary emphasis was on evaluating their effects on maternal decidua cells and fetal chorion trophoblast cells (hFM-CTCs). We validated the generation of EVs containing the S protein from small human airway epithelial cell lines (HSAECs) following mRNA-S vaccine exposure. We assessed the expression of angiotensin-converting enzyme 2 (ACE2) gene and protein in fetal membranes and the placenta, with specific attention to decidual cells and fetal membrane chorion cells. To assess cellular functionality, these cells were exposed to both recombinant S protein and EVs loaded with S proteins (eSPs). Our findings revealed that cells and EVs subjected to mRNA-S-based vaccination exhibited altered protein expression levels of S proteins. At the feto-maternal interface, both placental and fetal membrane tissues demonstrated similar ACE-2 expression levels. Among individual cellular layers, syncytiotrophoblast cells in the placenta and chorion cells in the fetal membrane exhibited elevated ACE-2 expression. Notably, EVs derived from HSAECs activated the MAPK pathway in decidual cells. Additionally, decidual cells displayed a substantial increase in gene expression of chemokines like CXCL-10 and CXCL-11, as well as proinflammatory cytokines such as IL-6 in response to eSPs. However, the levels of Ccl-2 and IL-1β remained unchanged in decidual cells under the same conditions. Conversely, hFM-CTCs demonstrated significant alterations in the proinflammatory cytokines and chemokines with respect to eSPs. In conclusion, our study indicates that mRNA-S-based maternal vaccination during pregnancy may influence the maternal-fetal interface's COVID-19 interaction and immune regulation. Further investigation is warranted to assess safety and implications.

Effects of aging and exercise on Mitochondria-ER contacts (MERCs) in skeletal muscle

Mitochondrial dysfunction is a prominent factor contributing to age-associated loss of muscle mass and force (a.k.a., sarcopenia). Yet, events preceding age-related mitochondrial dysfunction, which may allow the development of new therapies, remain poorly understood. Physical coupling of the outer mitochondrial membrane (OMM) to the endoplasmic or sarcoplasmic reticulum (ER), termed mitochondria ER contact sites (MERCs), modulate several mitochondrial processes influencing cellular function. In an energetically demanding and primarily post-mitotic tissue, we hypothesized that alterations in MERCs correlate with the development of sarcopenia. We also hypothesized that MERCs respond to exercise training and may contribute to beneficial muscular remodeling in older adults. To address these, we studied three age groups of male C57BL6N mice: young adults (Y, 5 mo. of age), old (O, 20 mo. of age), and very old (VO, 31 mo. of age). An additional group of old mice underwent 8-9 weeks of treadmill training (OET). Muscle mass and contractile function decreased with aging; VO animals displayed ~25% decline in maximum tetanic force vs. Y mice (p<0.0001). Fatigability (assessed via repetitive sub-maximal contractions) increased by ~10% with aging but was attenuated in the OET group (p<0.001). In saponin-permeabilized muscle fibers, aging did not affect mitochondrial oxidative capacity. However, H2O2 emission was nearly doubled in the O group (p<0.01) and this trend was partially alleviated by exercise training. Assessed via TEM, aging decreased the size of MERCs (i.e., length of SR and OMM apposition) by around 20% (p<0.01). Interestingly, OET animals displayed ~50% increase in MERC coverage (i.e., proportion of OMM covered by SR; p<0.0001). Immunoblots of cellular MERC fractions revealed that MERC proteins associated with calcium exchange were altered with age and exercise. The OMM channel, VDAC1, was reduced by 20% in O muscles (p=0.02), while Grp75, a tether protein, was ~25% higher in OET (p=0.02). Quantitative proteomic analyses revealed various MERC proteins being modified by aging and exercise. Our findings indicate that changes in MERC structure and protein composition may underlie early events preceding the development of sarcopenia and that exercise-mediated adaptations at MERCs may contribute to the beneficial adaptations in aging skeletal muscle. Supported by the University of Iowa Fraternal Order of Eagles Diabetes Research Center (UIowa FOEDRC). This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Effects of nanoparticles on sensitivity to injury and role of autophagy in alveolar epithelial cells

Autophagy, a housekeeping mechanism, is crucial in the maintenance of normal cellular function. Although the involvement of autophagic processes is recognized in numerous diseases, it is unknown how cellular homeostasis might be affected by alterations in available autophagic activity and/or autophagic capacity. In this study, we measured autophagic flux and cellular damage in primary cultured monolayers of rat alveolar epithelial cells (AEC) exposed separately and sequentially to two different autophagy inducers. Rat AEC monolayers were exposed apically for 24 hrs to (1) polystyrene nanoparticles (PNP, 20 nm, carboxylated, near-infrared dye-labeled), (2) tunicamycin (TN, a disruptor of protein synthesis and inducer of the unfolded protein response, at 1-15 μg/mL), or (3) TN (1-15 μg/mL) after 12 hrs of PNP pre-incubation. Release of the cytoplasmic enzyme lactate dehydrogenase (LDH) was used as an indicator of cellular damage and quantified by an LDH assay from Dojindo (Rockville, MD). Autophagic flux was assessed by live cell imaging using confocal microscopy and 0.1 μM DAPRed (Dojindo; Rockville, MD) in the presence (for 1 hr) and absence of 40 μM chloroquine. Serial z sections were collected over the entire cell volume of live single cells to detect DAPRed (autophagosome) fluorescence. PNP were taken up into AEC, where their cytosolic presence induced a gradually increased autophagic flux, reaching a steady state at ~10-24 hrs. When AEC were exposed to TN alone for 24 hrs, autophagy was also activated. Cellular damage in the presence of TN, determined by increased LDH release, revealed dose-dependent injury with LD50 of 8.12 μg/mL over 24 hr TN exposure. When AEC were pre-exposed to PNP for 12 hrs and subsequently exposed to TN, increased LDH release was seen with LD50 of 3.95 μg/mL. In summary, the intracellular presence of PNP taken up from apical fluid of rat AEC monolayers activated autophagy. When cellular protein synthesis was disrupted with TN alone, autophagy was also activated. Furthermore, TN induced dose-dependent cellular damage in AEC. However, after pre-exposure to PNP, TN induced greater cellular damage observed as increased LDH release. These results suggest that autophagic capacity is limited and that pre-induction of autophagy by inhaled PNP makes AEC more susceptible to secondary injury by TN. These findings are consistent with the hypothesis that environmental stressors (e.g., ambient air nanoparticles) exert their harmful effects, at least in part, by reducing available autophagic activity/capacity, thereby causing nanoparticle-exposed AEC to be more susceptible to secondary injury. Funding: NIH; WRMPPF. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Rational design of a bacterial import system for new-to-nature molecules

Integration of novel compounds into biological processes holds significant potential for modifying or expanding existing cellular functions. However, the cellular uptake of these compounds is often hindered by selectively permeable membranes. We present a novel bacterial transport system that has been rationally designed to address this challenge. Our approach utilizes a highly promiscuous sulfonate membrane transporter, which allows the passage of cargo molecules attached as amides to a sulfobutanoate transport vector molecule into the cytoplasm of the cell. These cargoes can then be unloaded from the sulfobutanoyl amides using an engineered variant of the enzyme γ-glutamyl transferase, which hydrolyzes the amide bond and releases the cargo molecule within the cell. Here, we provide evidence for the broad substrate specificity of both components of the system by evaluating a panel of structurally diverse sulfobutanoyl amides. Furthermore, we successfully implement the synthetic uptake system in vivo and showcase its functionality by importing an impermeant non-canonical amino acid.

Engineering of Genetically Encoded Calcium Channel Blockers

Calcium Release-Activated Calcium (CRAC) channel is a highly Ca2+-selective store-operated channel constituted by two-component mediators (STIM and ORAI) and controls a wide range of cellular functions in various tissues. Gain-of-function (GoF) mutations of CRAC channel cause excessive Ca2+ entry, which can lead to serious diseases such as tubular aggregate myopathy and Stormorken syndrome (TAM/STRMK). To solve this problem and to gain precise control of the CRAC channel, we have designed both an optogenetic and a chemogenetic strategy for engineering of CRAC channel blockers (designated Opto-CRAB and Chemo-CRAB), which can mediate Ca2+ influx and Ca2+-dependent signaling such as NFAT induced gene expression and T cell activation. Beyond in vitro applications, both Opto-CRAB and Chemo-CRAB have been applied in vivo experiments in a zebrafish model of Stormorken syndrome that resulted in the mitigation of thrombocytopenia and hemorrhage in light and chemical dependent manners. Welch Foundation (BE-1913-20220331 to Y.Z.), Leukemia & Lymphoma Society (LLS6680-24 to Y.Z.), the National Institutes of Health (R01GM144986 to Y.Z. and R21AI174606 to Y.Z.). This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Comparative study of molecular mechanisms of sucrose & trehalose mediated protection and stabilization of Escherichia coli lipid membrane during desiccation

Desiccation presents considerable challenges to the survival of various bacteria, disrupting cellular functions and damaging the structure of macromolecular assemblies. Dehydration can induce a phase transition in lipid membranes, shifting from a favorable fluid phase to an unfavorable gel-like structure. In response to this stress, various organisms evolve different types of protective mechanisms, among which an accumulation of disaccharides is particularly noteworthy. Despite large number studies are present in the literature, the detailed mechanism of how disaccharides mitigate the deleterious effect of desiccation on lipid membrane is still elusive. Our study examines how disaccharides, like sucrose and trehalose, protect lipid membranes derived from an Escherichia coli (E. coli) bacteria during desiccation, aiming to uncover the mechanisms behind membrane protection and its significance for bacterial survival. We have simulated the lipid membrane at six different hydration levels, ranging from fully hydrated (with a water-to-lipid ratio of 42) to severely dehydrated (with a ratio of 2), both in the presence and absence of sucrose. We monitor various structural and dynamical parameters of the lipid membrane with a reduction of the hydration level. We conduct a comparative analysis between sucrose and trehalose. Our findings indicate that dehydration negatively impacts the fluidity of the membrane, and both the disaccharides demonstrate nearly equal effectiveness in mitigating the adverse effects of extreme dehydration on the lipid membrane. Furthermore, we provide evidence supporting the validity of the vitrification and water replacement hypotheses in understanding the role of disaccharides in protecting lipid membranes.

Immobilization of hUC-MSCs Conditioned Medium on 3D PLLA Collagen-Coated Matrix Enhances Diabetic Wound Healing Progression

Conditioned medium (CM) derived from human umbilical cord-mesenchymal stem cells (hUC-MSCs) which contains numerous amounts of growth factors, has demonstrated potential in treatment of diabetic wounds. However, for practical application, a biodegradable supporting material is needed to hold the CM and fill in the injury site, where deep cavity wounds are often present in diabetic patients. Poly-L-lactic acid matrix coated with collagen (PLLA/CC) is a suitable carrier due to its biodegradability and biocompatibility. Thus, we present a method to immobilize the hUC-MSCs CM on PLLA/CC through freeze-drying process (PLLA/CC CM FD). When seeded on PLLA/CC CM FD, fibroblasts had an increased cellular function in producing collagen; although no enhancement in cell viability was observed. Moreover, implantation of PLLA/CC CM FD on the wound of diabetic rats showed improvement in wound closure and collagen deposition in the wound area. Altogether, this study exhibits the potential of PLLA/CC CM FD as a therapy for diabetic deep cavity wound.

Impaired Long-Chain Fatty Acid Metabolism in Carnitine Palmitoyltransferase II Knockout Mouse Leads to Chronic Pancreatitis

Background: To support high rates of protein synthesis, pancreatic acinar cells must generate large quantities of ATP. Mitochondrial dysfunction and impaired energy metabolism play a significant role in the development of pancreatitis. Patients with elevated plasma triglycerides are at increased risk for development of severe acute pancreatitis. Carnitine palmitoyltransferase II (CPT2) is required for importing and thus metabolizing long-chain fatty acids (LCFAs) in mitochondria. To inhibit LCFA metabolism, we utilized the CPT2acinarKO mouse to probe the consequences of impaired LCFA import on pancreatic function. Hypothesis: Loss of CPT2 causes an accumulation of long-chain acylcarnitines and disruption of the tissue acylcarnitine/free carnitine ratio which is thought to alter cellular function. Given acinar cells’ high metabolic requirement, impaired LCFA utilization would reduce energy production, secretory function, and alter pancreatic lipid composition. Methods: We generated mice lacking CPT2 specifically in acinar cells (CPT2acinarKO) by crossing tamoxifen-inducible, Elastase-Cre mice with CPT2 floxed mice. Mice were fed a high fat (60% kcal fat), low fat (10% kcal fat), or chow (14% kcal fat) diet for 12 weeks. Analysis of fat accumulation, edema, and fibrosis was performed with H&E and picrosirius staining. Mass Spec. lipid profiling was performed in pancreas and serum. Acinar cells were isolated from wildtype, CPT2 floxed, and CPT2acinarKO mice to assess secretory function, ATP levels, and necrosis via lactate dehydrogenase (LDH) release. Results: Histologic examination revealed CPT2acinarKO mice on all three diets displayed pancreatic fat accumulation. Strikingly, CPT2acinarKO mice fed a chow or low fat diet developed chronic pancreatitis with a 25% loss in pancreatic weight, immune cell infiltration, edema, and fibrosis. As anticipated, long-chain acylcarnitines were significantly elevated in CPT2acinarKO pancreas. Assessment of secretion in 2 weeks post tamoxifen cells revealed significantly reduced maximal (10 pM) and supramaximal (1 nM) cholecystokinin (CCK) stimulated amylase release as a percent of total cellular amylase. Acini isolated at 4 weeks post tamoxifen revealed significantly increased basal secretion and reduced maximal and supramaximal CCK stimulated amylase release. When normalized to cellular DNA, secretion was similar between CPT2acinarKO and CPT2 floxed acinar cells indicating CPT2acinarKO cells had reduced amylase levels. Wildtype acinar cells treated with unsaturated and saturated free fatty acid concentrations as low as 100 μM for 3 hours caused significant necrosis. CPT2acinarKO pancreas had significantly decreased ATP levels indicative of mitochondrial dysfunction. Conclusion: Loss of CPT2 in the pancreatic acinar cells impairs LCFA import, reduces ATP levels, disrupts the secretory pathway, promoting chronic pancreatitis. In contrast to other CPT2 knockout models, pancreatitis occurs independent of high fat feeding in CPT2acinarKO mice. Further investigation is needed to identify metabolic alterations leading to acinar damage and mitochondrial dysfunction following the loss of CPT2. UW-Madison Comprehensive Diabetes Center Pilot Grant. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

An evolutionarily conserved mechanism controls reversible amyloids of pyruvate kinase via pH-sensing regions.

Amyloids are known as irreversible aggregates associated with neurodegenerative diseases. However, recent evidence shows that a subset of amyloids can form reversibly and fulfill essential cellular functions. Yet, the molecular mechanisms regulating functional amyloids and distinguishing them from pathological aggregates remain unclear. Here, we investigate the conserved principles of amyloid reversibility by studying the essential metabolic enzyme pyruvate kinase (PK) in yeast and human cells. We demonstrate that yeast PK (Cdc19) and human PK (PKM2) form reversible amyloids through a pH-sensitive amyloid core. Stress-induced cytosolic acidification promotes aggregation via protonation of specific glutamate (yeast) or histidine (human) residues within the amyloid core. Mutations mimicking protonation cause constitutive PK aggregation, while non-protonatable PK mutants remain soluble even upon stress. Physiological PK aggregation is coupled to metabolic rewiring and glycolysis arrest, causing severe growth defects when misregulated. Our work thus identifies an evolutionarily conserved, potentially widespread mechanism regulating functional amyloids during stress.

Systematic evaluation of single-cell RNA-seq analyses performance based on long-read sequencing platforms

IntroductionThe rapid development of next-generation sequencing (NGS)-based single-cell RNA sequencing (scRNA-seq) allows for detecting and quantifying gene expression in a high-throughput manner, providing a powerful tool for comprehensively understanding cellular function in various biological processes. However, the NGS-based scRNA-seq only quantifies gene expression and cannot reveal the exact transcript structures (isoforms) of each gene due to the limited read length. On the other hand, the long read length of third-generation sequencing (TGS) technologies, including Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), enable direct reading of intact cDNA molecules. ObjectivesBoth ONT and PacBio have been used in conjunction with scRNA-seq, but their performance in single-cell analyses has not been systematically evaluated. MethodsTo address this, we generated ONT and PacBio data from the same single-cell cDNA libraries containing different amount of cells. ResultsUsing NGS as a control, we assessed the performance of each platform in cell type identification. Additionally, the reliability in identifying novel isoforms and allele-specific gene/isoform expression by both platforms was verified, providing a systematic evaluation to design the sequencing strategies in single-cell transcriptome studies. ConclusionBeyond gene expression analysis, which the NGS-based scRNA-seq only affords, TGS-based scRNA-seq achieved gene splicing analyses, identifying novel isoforms. Attribute to higher sequencing quality of PacBio, it outperforms ONT in accuracy of novel transcripts identification and allele-specific gene/isoform expression.

Mitochondria and Cancer.

Mitochondria are semiautonomous organelles with diverse metabolic and cellular functions including anabolism and energy production through oxidative phosphorylation. Following the pioneering observations of Otto Warburg nearly a century ago, an immense body of work has examined the role of mitochondria in cancer pathogenesis and progression. Here, we summarize the current state of the field, which has coalesced around the position that functional mitochondria are required for cancer cell proliferation. In this review, we discuss how mitochondria influence tumorigenesis by impacting anabolism, intracellular signaling, and the tumor microenvironment. Consistent with their critical functions in tumor formation, mitochondria have become an attractive target for cancer therapy. We provide a comprehensive update on the numerous therapeutic modalities targeting the mitochondria of cancer cells making their way through clinical trials.

Exploring the influence of microgravity on chemotherapeutic drug response in cancer: Unveiling new perspectives.

Microgravity, an altered gravity condition prevailing in space, has been reported to have a profound impact on human health. Researchers are very keen to comprehensively investigate the impact of microgravity and its intricate involvement in inducing physiological changes. Evidenced transformations were observed in the internal architecture including cytoskeletal organization and cell membrane morphology. These alterations can significantly influence cellular function, signalling pathways and overall cellular behaviour. Further, microgravity has been reported to alter in the expression profile of genes and metabolic pathways related to cellular processes, signalling cascades and structural proteins in cancer cells contributing to the overall changes in the cellular architecture. To investigate the effect of microgravity on cellular and molecular levels numerous ground-based simulation systems employing both invitro and invivo models are used. Recently, researchers have explored the possibility of leveraging microgravity to potentially modulate cancer cells against chemotherapy. These findings hold promise for both understanding fundamental processes and could potentially lead to the development of more effective, personalized and innovative approaches in therapeutic advancements against cancer.

Virtually identical does not mean exactly identical: Discrepancy in energy metabolism between glucose and fructose fermentation influences the reproductive potential of yeast cells

The physiological efficiency of cells largely depends on the possibility of metabolic adaptations to changing conditions, especially on the availability of nutrients. Central carbon metabolism has an essential role in cellular function. In most cells is based on glucose, which is the primary energy source, provides the carbon skeleton for the biosynthesis of important cell macromolecules, and acts as a signaling molecule. The metabolic flux between pathways of carbon metabolism such as glycolysis, pentose phosphate pathway, and mitochondrial oxidative phosphorylation is dynamically adjusted by specific cellular economics responding to extracellular conditions and intracellular demands. Using Saccharomyces cerevisiae yeast cells and potentially similar fermentable carbon sources i.e. glucose and fructose we analyzed the parameters concerning the metabolic status of the cells and connected with them alteration in cell reproductive potential. Those parameters were related to the specific metabolic network: the hexose uptake - glycolysis and activity of the cAMP/PKA pathway - pentose phosphate pathway and biosynthetic capacities - the oxidative respiration and energy generation. The results showed that yeast cells growing in a fructose medium slightly increased metabolism redirection toward respiratory activity, which decreased pentose phosphate pathway activity and cellular biosynthetic capabilities. These differences between the fermentative metabolism of glucose and fructose, lead to long-term effects, manifested by changes in the maximum reproductive potential of cells.

Me31B: a key repressor in germline regulation and beyond.

Maternally Expressed at 31B (Me31B), an evolutionarily conserved ATP-dependent RNA helicase, plays an important role in the development of the germline across diverse animal species. Its cellular functionality has been posited as a translational repressor, participating in various RNA metabolism pathways to intricately regulate the spatiotemporal expression of RNAs. Despite its evident significance, the precise role and mechanistic underpinnings of Me31B remain insufficiently understood. This article endeavors to comprehensively review historic and recent research on Me31B, distill the major findings, discern generalizable patterns in Me31B's functions across different research contexts, and provide insights into its fundamental role and mechanism of action. The primary focus of this article centers on elucidating the role of Drosophila Me31B within the germline, while concurrently delving into pertinent research on its orthologs within other species and cellular systems.

Periodontal granulation tissue - To remove or not to remove, that is the question.

Formation of granulation tissue is a fundamental phase in periodontal wound healing with subsequent maturation leading to regeneration or repair. However, persistently inflamed granulation tissue presents in osseous defects as a result of periodontitis and is routinely disrupted and discarded with non-surgical and surgical therapy to facilitate wound healing or improve chances of regeneration. Histological assessment suggests that granulation tissue from periodontitis-affected sites is effectively a chronic inflammatory tissue resulting from impaired wound healing due to persistence of bacterial dysbiotic bioflim. Nevertheless, the immunomodulatory potential and stem cell characteristics in granulation tissue have also raised speculation about the tissue's regenerative potential. This has led to the conception and recent implementation of surgical techniques which preserve granulation tissue with the intention of enhancing innate regenerative potential and improve clinical outcomes. As knowledge of fundamental cellular and molecular functions regulating periodontitis-affected granulation tissue is still scarce, this review aimed to provide a summary of current understanding of granulation tissue in the context of periodontal wound healing. This may provide new insights into clinical practice related to the management of granulation tissue and stimulate further investigation.

A Simple Nonviral Method to Generate Human Induced Pluripotent Stem Cells Using SMAR DNA Vectors.

Induced pluripotent stem cells (iPSCs) are a powerful tool for biomedical research, but their production presents challenges and safety concerns. Yamanaka and Takahashi revolutionised the field by demonstrating that somatic cells could be reprogrammed into pluripotent cells by overexpressing four key factors for a sufficient time. iPSCs are typically generated using viruses or virus-based methods, which have drawbacks such as vector persistence, risk of insertional mutagenesis, and oncogenesis. The application of less harmful nonviral vectors is limited as conventional plasmids cannot deliver the levels or duration of the factors necessary from a single transfection. Hence, plasmids that are most often used for reprogramming employ the potentially oncogenic Epstein-Barr nuclear antigen 1 (EBNA-1) system to ensure adequate levels and persistence of expression. In this study, we explored the use of nonviral SMAR DNA vectors to reprogram human fibroblasts into iPSCs. We show for the first time that iPSCs can be generated using nonviral plasmids without the use of EBNA-1 and that these DNA vectors can provide sufficient expression to induce pluripotency. We describe an optimised reprogramming protocol using these vectors that can produce high-quality iPSCs with comparable pluripotency and cellular function to those generated with viruses or EBNA-1 vectors.