Search

Metazoan development requires the robust proliferation of progenitor cells, the identities of which are established by tightly controlled transcriptional networks.sup.1. As gene expression is globally inhibited during mitosis, the transcriptional programs that define cell identity must be restarted in each cell cycle.sup.2-5 but how this is accomplished is poorly understood. Here we identify a ubiquitin-dependent mechanism that integrates gene expression with cell division to preserve cell identity. We found that WDR5 and TBP, which bind active interphase promoters.sup.6,7, recruit the anaphase-promoting complex (APC/C) to specific transcription start sites during mitosis. This allows APC/C to decorate histones with ubiquitin chains branched at Lys11 and Lys48 (K11/K48-branched ubiquitin chains) that recruit p97 (also known as VCP) and the proteasome, which ensures the rapid expression of pluripotency genes in the next cell cycle. Mitotic exit and the re-initiation of transcription are thus controlled by a single regulator (APC/C), which provides a robust mechanism for maintaining cell identity throughout cell division. WDR5 and TBP recruit anaphase-promoting complex to specific transcription start sites in mitosis, initiating a ubiquitin-dependent mechanism that preserves cell identity by linking gene expression and cell division., Author(s): Eugene Oh [sup.1] [sup.2] , Kevin G. Mark [sup.1] [sup.2] , Annamaria Mocciaro [sup.1] [sup.2] [sup.7] , Edmond R. Watson [sup.3] , J. Rajan Prabu [sup.3] , Denny D. [...]

This article discusses the impact of a highly effective modulator therapy, elexacaftor/tezacaftor/ivacaftor (ETI), on olfactory dysfunction (OD) in individuals with chronic rhinosinusitis (CRS) and cystic fibrosis (CF). The study found that after 2 years of ETI treatment, OD did not improve significantly in adults with CF. However, there was a modest improvement in the questionnaire scores related to olfactory-specific quality of life (QOL). The study suggests that OD in adults with CF may be irreversible, and further research is needed to understand the mechanisms of olfactory loss and the potential for early intervention to improve OD. [Extracted from the article]

Simple Summary: Belzutifan, a hypoxia-inducible factor-2 alpha (HIF-2α) inhibitor, has emerged as an exciting new treatment option not only for patients with Von Hippel-Lindau (VHL)-related renal cell carcinoma (RCC) but also for sporadic RCC. While initial clinical data are promising, potential resistance with HIF-2α inhibitors may occur with increased understanding of this class of therapy. Potential ways to further increase the antitumor activity of HIF-2α targeting include combination strategies with immune checkpoint inhibitors and other targeted agents as well as newer generation HIF-2α inhibitors that are currently under development. Germline inactivation of the Von Hippel-Lindau (VHL) tumor suppressor is the defining hallmark in hereditary VHL disease and VHL-associated renal cell carcinoma (RCC). However, somatic VHL mutations are also observed in patients with sporadic RCC. Loss of function VHL mutations result in constitutive activation of hypoxia-inducible factor-2 alpha (HIF-2α), which leads to increased expression of HIF target genes that promote angiogenesis and tumor growth. As of 2023, belzutifan is currently the only approved HIF-2α inhibitor for both VHL-associated and sporadic metastatic RCC (mRCC). However, there is potential for resistance with HIF-2α inhibitors which warrants novel HIF-2α-targeting strategies. In this review, we discuss the potential resistance mechanisms with belzutifan and current clinical trials evaluating novel combinations of belzutifan with other targeted therapies and immune checkpoint inhibitors which may enhance the efficacy of HIF-2α targeting. Lastly, we also discuss newer generation HIF-2α inhibitors that are currently under early investigation and outline future directions and challenges with HIF-2α inhibitors for mRCC. [ABSTRACT FROM AUTHOR]

Early and precise detection of parathyroid glands (PGs) is a challenging problem in thyroidectomy due to their small size and similar appearance to surrounding tissues. Near‐infrared autofluorescence (NIRAF) has stimulated interest as a method to localize PGs. However, high incidence of false positives for PGs has been reported with this technique. We introduce a prototype equipped with a coaxial excitation light (785 nm) and a dual‐sensor to address the issue of false positives with the NIRAF technique. We test the clinical feasibility of our prototype in situ and ex vivo using sterile drapes on 10 human subjects. Video data (1287 images) of detected PGs were collected to train, validate and compare the performance for PG detection. We achieved a mean average precision of 94.7% and a 19.5‐millisecond processing time/detection. This feasibility study supports the effectiveness of the optical design and may open new doors for a deep learning‐based PG detection method. [ABSTRACT FROM AUTHOR]

A detailed study on the effects of (methylenecyclopropyl)formyl-CoA (MCPF-CoA), a toxic metabolite of methylenecyclopropylglycine, on a number of enzymes involved in the metabolism of fatty acids has been conducted. The results confirmed the role of MCPF-CoA as a potent inactivator of enoyl-CoA hydratases (ECHs) despite its minimal effect on the beta-oxidation enzymes used in the study. The function of MCPF-CoA as a rare irreversible inhibitor for ECHs has potential applications in the design of new drugs for controlling fatty acid metabolism.

Acyl-CoA dehydrogenases (ACDs) are FAD-dependent enzymes that catalyze the conversion of an appropriate fatty acyl-CoA thioester substrate to the corresponding trans-[Alpha],[Beta]-enoyl-CoA product. Early studies have shown that the dehydrogenation is stereospecific and is initiated by the abstraction of the pro-R [Alpha]-H, followed by the transfer of the pro-R [Beta]-H, as a hydride equivalent, to the bound FAD. However, recent studies of the inactivation of ACDs by a metabolite of hypoglycin A, (methylenecyclopropyl)acetyl-CoA (MCPA-CoA), led to an alternative mechanism in which the reducing equivalent is delivered from the initially formed [Alpha]-anion to the bound FAD via a single electron transfer process. To further explore the observed mechanistic discrepancy, we have reexamined the inhibitory properties of a closely related MCPA-CoA analogue, spiropentylacetyl-CoA (SPA-CoA), which was previously reported as a tight-binding inhibitor for ACDs. In contrast to early results, our data showed that SPA-CoA is a mechanism-based inhibitor for pig kidney medium-chain acyl-CoA dehydrogenase (MCAD) and Megasphaera elsdenii short-chain acyl-CoA dehydrogenase (SCAD) and that the inactivation is time-dependent, active-site-directed, and irreversible. More importantly, both (R)- and (S)-SPA-CoA could effectively inactivate MCAD, and the resulting inhibitor - FAD adducts appear to have one of the three-membered rings of the spiropentyl moiety cleaved. Since the inactivation is nonstereospecific with respect to [C.sub.[Beta]]-C bond scission, the ring opening of SPA-CoA leading to enzyme inactivation is likely initiated by a spiropentylcarbinyl radical. Such a radical-induced ring fragmentation is expected to be extremely facile and may bypass the chiral discrimination normally imposed by the enzyme. Thus, these results are consistent with our early notion that MCAD is capable of mediating one-electron redox chemistry. Interestingly, it was also found that (R)-SPA-CoA is an irreversible inhibitor for SCAD, while the S-epimer is only a competitive inhibitor for the same enzyme. The selective inhibition exhibited by these compounds against two closely related dehydrogenases is likely a consequence of the distinct steric and electronic demands imposed by the active sites of MCAD and SCAD. Such information is important for the design of novel class-selective inhibitors to control and/or regulate fatty acid metabolism.

A study was done on the major turnover product from the enzymatic incubation of (methylenecyclopropyl)acetyl-CoA under aerobic conditions. The turnover product was characterized to be a CoA ester composed of a disubstituted terminal olefin, an epoxide and a hydroxymethyl group. This product was formed after trapping the acyclical radical intermediate with O2 forming a transient peroxy radical. Anaerobic studies have uncovered a minor inactivation pathway which involves the covalent modification of flavin.

The successful preparation of (1R)-(methylenecyclopropyl)acetonitrile provides a new route for the synthetic derivation of MCPA-CoA in enantiomerically pure form. The MCPA-CoA precursor can be obtained in an overall yield of more than 40% from the asymmetric synthesis of (S)-glycidyl benzyl ether. The process does not involve any additional chemical resolution procedures to isolate the desired product. Moreover, the process can be applied in deriving synthetic products containing methylenecyclopropane units in enantiomerically pure form.

Background Achalasia is an incurable neurodegenerative disease of the esophagus. Palliative treatment includes disruption of the lower esophageal sphincter via multiple techniques, including open Heller myotomy (OHM), laparoscopic Heller myotomy (LHM), and per-oral esophageal myotomy (POEM). There is a paucity of data comparing long-term outcomes between OHM, LHM, and POEM. We sought to evaluate the relationship of these methods with clinical outcome parameters using our institution's experience. Methods Patients greater than 3 years removed from myotomy for achalasia were studied. Post-operative Eckardt Symptom (ES) score and daily proton pump inhibitor (PPI) usage was recorded. Patients underwent timed barium esophagram (TBE) as clinically indicated. Retention was defined as a persistent column >5 cm at 5 minutes. Post-operative interventions included Savary dilation, Botox injection, pneumatic dilation, surgical myotomy, and esophagectomy. Groups were stratified by surgery type (OHM, LHM, POEM) and by time since surgery (3–6 years, 6–10 years, >10 years). A logistic regression analysis was performed examining the relationship of surgery type, time, symptomatic/objective outcomes, and post-operative interventions. Results 172 patients had long-term data available. Mean follow up was 7.8 years (3.1–19.5 years). Nearly one-third of patients had a post-operative intervention (31%, 53/172). On regression analysis, OHM was associated with a higher risk of intervention (OR 9.4, p < 0.05). Barium retention was significantly associated with LHM (OR 15.9, p < 0.05) and the 3–6 year post-operative period (OR 11.1, p < 0.05). PPI usage was not associated with surgery type, but was associated with the 3–6 year post-operative period (OR 3.2, p < 0.05). There was no significant association of dysphagia with surgery type or time. Conclusion Post-operative barium retention and interventions are associated with specific myotomy techniques, but not time. PPI usage is associated with the early post-operative period, but not technique. Neither myotomy technique nor time alone are sufficient to predict risk of abnormal ES or dysphagia. [ABSTRACT FROM AUTHOR]

Ubiquitylation is an essential posttranslational modification that controls cell division, differentiation, and survival in all eukaryotes. By combining multiple E3 ligases (writers), ubiquitin-binding effectors (readers), and de-ubiquitylases (erasers) with functionally distinct ubiquitylation tags, the ubiquitin system constitutes a powerful signaling network that is employed in similar ways from yeast to humans. Here, we discuss conserved principles of ubiquitin-dependent signaling that illustrate how this posttranslational modification shapes intracellular signaling networks to establish robust development and homeostasis throughout the eukaryotic kingdom. [ABSTRACT FROM AUTHOR]

Rationale: Findings from animal studies and human PET imaging indicate that nicotine and cigarette smoking affect glutamate (Glu) and related neurochemical markers in the brain and imply that smoking reduces extracellular Glu. As Glu release is mediated by nicotinic acetylcholine receptors (nAChRs), which are present at high concentrations in the thalamus, we examined the effects of smoking on thalamic Glu. Objective: To determine the effects of tobacco smoking on thalamic glutamate levels. Methods: Thalamic Glu levels were measured in vivo in 18 smokers and 16 nonsmokers using proton magnetic resonance spectroscopic imaging (H MRSI) at 1.5 T. Results: Mean Glu levels did not differ significantly between the subject groups. However, within smokers, Glu levels were negatively correlated with self-reports of both cigarettes/day over the last 30 days ( r = −0.64, p = 0.006) and pack-years of smoking ( r = −0.66, p = 0.005). Conclusions: Consistent with expectations based on preclinical studies, within smokers, cigarettes/day and pack-years are associated with reduced Glu in thalamus, a brain region rich in nAchRs. These results encourage work on candidate glutamatergic therapies for smoking cessation and suggest a noninvasive metric for their action in the brain. [ABSTRACT FROM AUTHOR]

A novel and effective method was devised for synthesizing a vertically aligned carbon nanotube (CNT) forest on a substrate using waste plastic obtained from commercially available water bottles. The advantages of the proposed method are the speed of processing and the use of waste as a raw material. A mechanism for the CNT growth was also proposed. The growth rate of the CNT forest was ∼2.5µm min-1. Transmission electron microscopy images indicated that the outer diameters of the CNTs were 20-30 nm on average. The intensity ratio of the G and D Raman bands was 1.27 for the vertically aligned CNT forest. The Raman spectrum showed that the wall graphitization of the CNTs, synthesized via the proposed method was slightly higher than that of commercially available multi-walled carbon nanotubes (MWCNTs). We expect that the proposed method can be easily adapted to the disposal of other refuse materials and applied to MWCNT production industries. [ABSTRACT FROM AUTHOR]

Summary: As nascent polypeptides exit ribosomes, they are engaged by a series of processing, targeting, and folding factors. Here, we present a selective ribosome profiling strategy that enables global monitoring of when these factors engage polypeptides in the complex cellular environment. Studies of the Escherichia coli chaperone trigger factor (TF) reveal that, though TF can interact with many polypeptides, β-barrel outer-membrane proteins are the most prominent substrates. Loss of TF leads to broad outer-membrane defects and premature, cotranslational protein translocation. Whereas in vitro studies suggested that TF is prebound to ribosomes waiting for polypeptides to emerge from the exit channel, we find that in vivo TF engages ribosomes only after ∼100 amino acids are translated. Moreover, excess TF interferes with cotranslational removal of the N-terminal formyl methionine. Our studies support a triaging model in which proper protein biogenesis relies on the fine-tuned, sequential engagement of processing, targeting, and folding factors. PaperClip: Display Omitted [Copyright &y& Elsevier]

The packaging of eukaryotic DNA into chromatin sterically occludes polymerases, recombinases and repair enzymes. How chromatin structure changes to allow their actions is unknown. We constructed defined fluorescently labeled trinucleosome arrays, allowing analysis of chromatin conformational dynamics via fluorescence resonance energy transfer (FRET). The arrays undergo reversible Mg2+-dependent folding similar to that of longer arrays studied previously. We define two intermediate conformational states in the reversible folding of the nucleosome arrays and characterize the microscopic rate constants. Nucleosome arrays are highly dynamic even when compact, undergoing conformational fluctuations on timescales in the second to microsecond range. Compact states of the arrays allow binding to DNA within the central nucleosome via site exposure. Protein binding can also drive decompaction of the arrays. Thus, our results reveal multiple modes by which spontaneous chromatin fiber dynamics allow for the invasion and action of DNA-processing protein complexes. [ABSTRACT FROM AUTHOR]

Abstract: A facile and fast sonochemical route for the fabrication of a resistive-type ZnO gas sensor has been demonstrated. Vertically aligned ZnO nanorod arrays were grown on a Pt-electrode patterned alumina substrate under ambient conditions. The average diameter and length of the ZnO nanorods were 50 and 500nm, respectively. Sonochemically grown ZnO nanorod gas sensor was highly sensitive to NO2 gas with a very low detection limit of 10ppb at 250°C; further, its response and recovery time were short. Considering the advantageous properties of this sonochemical technique, we believe that it can be used to fabricate high-performance gas sensors. [Copyright &y& Elsevier]

Significant insight about biological networks arises from the study of network motifs—overly abundant network subgraphs—but such wiring patterns do not specify when and how potential routes within a cellular network are used. To address this limitation, we introduce activity motifs, which capture patterns in the dynamic use of a network. Using this framework to analyze transcription in Saccharomyces cerevisiae metabolism, we find that cells use different timing activity motifs to optimize transcription timing in response to changing conditions: forward activation to produce metabolic compounds efficiently, backward shutoff to rapidly stop production of a detrimental product and synchronized activation for co-production of metabolites required for the same reaction. Measuring protein abundance over a time course reveals that mRNA timing motifs also occur at the protein level. Timing motifs significantly overlap with binding activity motifs, where genes in a linear chain have ordered binding affinity to a transcription factor, suggesting a mechanism for ordered transcription. Finely timed transcriptional regulation is therefore abundant in yeast metabolism, optimizing the organism's adaptation to new environmental conditions. [ABSTRACT FROM AUTHOR]