On the Target Detection Performance of a Molecular Communication Network with Multiple Mobile Nanomachines.

A network of nanomachines (NMs) can be used to build a target detection system for a variety of promising applications. They have the potential to detect toxic chemicals, infectious bacteria, and biomarkers of dangerous diseases such as cancer within the human body. Many diseases and health disorders can be detected early and efficiently treated in the future by utilizing these systems. To fully grasp the potential of these systems, mathematical analysis is required. This paper describes an analytical framework for modeling and analyzing the performance of target detection systems composed of multiple mobile nanomachines of varying sizes with passive/ absorbing boundaries. We consider both direct contact detection, in which NMs must physically contact the target to detect it, and indirect sensing, in which NMs must detect the marker molecules emitted by the target. The detection performance of such systems is calculated for degradable and non-degradable targets, as well as mobile and stationary targets. The derived expressions provide various insights, such as the effect of NM density and target degradation on detection probability.

Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape.

Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy.

The FANCI/FANCD2 complex links DNA damage response to R-loop regulation through SRSF1-mediated mRNA export.

Fanconi anemia (FA) is characterized by congenital abnormalities, bone marrow failure, and cancer susceptibility. The central FA protein complex FANCI/FANCD2 (ID2) is activated by monoubiquitination and recruits DNA repair proteins for interstrand crosslink (ICL) repair and replication fork protection. Defects in the FA pathway lead to R-loop accumulation, which contributes to genomic instability. Here, we report that the splicing factor SRSF1 and FANCD2 interact physically and act together to suppress R-loop formation via mRNA export regulation. We show that SRSF1 stimulates FANCD2 monoubiquitination in an RNA-dependent fashion. In turn, FANCD2 monoubiquitination proves crucial for the assembly of the SRSF1-NXF1 nuclear export complex and mRNA export. Importantly, several SRSF1 cancer-associated mutants fail to interact with FANCD2, leading to inefficient FANCD2 monoubiquitination, decreased mRNA export, and R-loop accumulation. We propose a model wherein SRSF1 and FANCD2 interaction links DNA damage response to the avoidance of pathogenic R-loops via regulation of mRNA export.

Borylation-Reduction-Borylation for the Formation of 1,4-Azaborines.

Given the current interest in materials containing 1,4-azaborine units, the development of new routes to these structures is important. Carbonyl directed electrophilic borylation using BBr3 is a facile method for the ortho-borylation of N,N-diaryl-amide derivatives. Subsequent addition of Et3SiH results in carbonyl reduction and then formation of 1,4-azaborines that can be protected in situ using a Grignard reagent. Overall, borylation-reduction-borylation is a one-pot methodology to access 1,4-azaborines from simple precursors.

Properties of a Random Bipartite Geometric Associator Graph Inspired by Vehicular Networks.

We consider a point process (PP) generated by superimposing an independent Poisson point process (PPP) on each line of a 2D Poisson line process (PLP). Termed PLP-PPP, this PP is suitable for modeling networks formed on an irregular collection of lines, such as vehicles on a network of roads and sensors deployed along trails in a forest. Inspired by vehicular networks in which vehicles connect with their nearest wireless base stations (BSs), we consider a random bipartite associator graph in which each point of the PLP-PPP is associated with the nearest point of an independent PPP through an edge. This graph is equivalent to the partitioning of PLP-PPP by a Poisson Voronoi tessellation (PVT) formed by an independent PPP. We first characterize the exact distribution of the number of points of PLP-PPP falling inside the ball centered at an arbitrary location in R2 as well as the typical point of PLP-PPP. Using these distributions, we derive cumulative distribution functions (CDFs) and probability density functions (PDFs) of kth contact distance (CD) and the nearest neighbor distance (NND) of PLP-PPP. As intermediate results, we present the empirical distribution of the perimeter and approximate distribution of the length of the typical chord of the zero-cell of this PVT. Using these results, we present two close approximations of the distribution of node degree of the random bipartite associator graph. In a vehicular network setting, this result characterizes the number of vehicles connected to each BS, which models its load. Since each BS has to distribute its limited resources across all the vehicles connected to it, a good statistical understanding of load is important for an efficient system design. Several applications of these new results to different wireless network settings are also discussed.

Selective aerobic coupling of amines to imines using solar spectrum-responsive flower-like Nen-graphene quantum dots (GQDs) decorated with 2, 4-dinitrophenylhydrazine (PH) as a photocatalyst.

Indeed, the development of ecologically benign molecular fabrication methods for highly efficient graphene quantum dots-based photocatalysts is of great significant. Graphene quantum dots-based photocatalysts have promising applications in various field, including environmental remediation, energy conversion, and splitting of water. However, ensuring resource reusability and minimizing the environmental impact are crucial considerations in the development. From this perspective, attention has also been paid to the creation of easy to make solar light harvesting graphene quantum dots-based photocatalysts for synthesising pharmaceuticals and functional imines compounds. Imines are excellent significant building blocks in pharmaceutical chemistry and excellent examples of these valuable compounds' synthetic intermediates, and the environmentally friendly oxidative synthesis of imines from amines. Therefore, herein, we designed a facile and efficient condensation route to synthesize the Nen-GQDs@PH photocatalyst. This route involves coupling of 2,4-dinitrophenylhydrazine (PH) with nitrogen-enriched graphene quantum dots (Nen-GQDs). The Nen-GQDs@PH as photocatalyst functions in a highly selective and efficient manner, leading to high amines conversion efficiency to imines (95%). Our results highlight a novel and environmentally safe approach for generating highly selective imines from various types of amines, setting a new benchmark in the current research field.

Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry.

RNA-binding proteins (RBPs) are key post-transcriptional regulators of gene expression, and thus underlie many important biological processes. Here, we developed a strategy that entails extracting a "hotspot pharmacophore" from the structure of a protein-RNA complex, to create a template for designing small-molecule inhibitors and for exploring the selectivity of the resulting inhibitors. We demonstrate this approach by designing inhibitors of Musashi proteins MSI1 and MSI2, key regulators of mRNA stability and translation that are upregulated in many cancers. We report this novel series of MSI1/MSI2 inhibitors is specific and active in biochemical, biophysical, and cellular assays. This study extends the paradigm of "hotspots" from protein-protein complexes to protein-RNA complexes, supports the "druggability" of RNA-binding protein surfaces, and represents one of the first rationally-designed inhibitors of non-enzymatic RNA-binding proteins. Owing to its simplicity and generality, we anticipate that this approach may also be used to develop inhibitors of many other RNA-binding proteins; we also consider the prospects of identifying potential off-target interactions by searching for other RBPs that recognize their cognate RNAs using similar interaction geometries. Beyond inhibitors, we also expect that compounds designed using this approach can serve as warheads for new PROTACs that selectively degrade RNA-binding proteins.

Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry.

RNA-binding proteins (RBPs) are key post-transcriptional regulators of gene expression, and thus underlie many important biological processes. Here, we developed a strategy that entails extracting a "hotspot pharmacophore" from the structure of a protein-RNA complex, to create a template for designing small-molecule inhibitors and for exploring the selectivity of the resulting inhibitors. We demonstrate this approach by designing inhibitors of Musashi proteins MSI1 and MSI2, key regulators of mRNA stability and translation that are upregulated in many cancers. We report this novel series of MSI1/MSI2 inhibitors is specific and active in biochemical, biophysical, and cellular assays. This study extends the paradigm of "hotspots" from protein-protein complexes to protein-RNA complexes, supports the "druggability" of RNA-binding protein surfaces, and represents one of the first rationally-designed inhibitors of non-enzymatic RNA-binding proteins. Owing to its simplicity and generality, we anticipate that this approach may also be used to develop inhibitors of many other RNA-binding proteins; we also consider the prospects of identifying potential off-target interactions by searching for other RBPs that recognize their cognate RNAs using similar interaction geometries. Beyond inhibitors, we also expect that compounds designed using this approach can serve as warheads for new PROTACs that selectively degrade RNA-binding proteins.

Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2).

Musashi 2 (MSI2) is an RNA binding protein (RBP) that regulates asymmetric cell division and cell fate decisions in normal and cancer stem cells. MSI2 appears to repress translation by binding to 3' untranslated regions (3'UTRs) of mRNA, but the identity of functional targets remains unknown. Here, we used individual nucleotide resolution cross-linking and immunoprecipitation (iCLIP) to identify direct RNA binding partners of MSI2 and integrated these data with polysome profiling to obtain insights into MSI2 function. iCLIP revealed specific MSI2 binding to thousands of mRNAs largely in 3'UTRs, but translational differences were restricted to a small fraction of these transcripts, indicating that MSI2 regulation is not triggered by simple binding. Instead, the functional targets identified here were bound at higher density and contain more 'UAG' motifs compared to targets bound nonproductively. To further distinguish direct and indirect targets, MSI2 was acutely depleted. Surprisingly, only 50 transcripts were found to undergo translational induction on acute loss. Using complementary approaches, we determined eukaryotic translation initiation factor 3A (EIF3A) to be an immediate, direct target. We propose that MSI2 downregulation of EIF3A amplifies these effects on translation. Our results also underscore the challenges in defining functional targets of RBPs since mere binding does not imply a discernible functional interaction.

Generation of scalable cancer models by combining AAV-intron-trap, CRISPR/Cas9, and inducible Cre-recombinase.

Scalable isogenic models of cancer-associated mutations are critical to studying dysregulated gene function. Nonsynonymous mutations of splicing factors, which typically affect one allele, are common in many cancers, but paradoxically confer growth disadvantage to cell lines, making their generation and expansion challenging. Here, we combine AAV-intron trap, CRISPR/Cas9, and inducible Cre-recombinase systems to achieve >90% efficiency to introduce the oncogenic K700E mutation in SF3B1, a splicing factor commonly mutated in multiple cancers. The intron-trap design of AAV vector limits editing to one allele. CRISPR/Cas9-induced double stranded DNA breaks direct homologous recombination to the desired genomic locus. Inducible Cre-recombinase allows for the expansion of cells prior to loxp excision and expression of the mutant allele.  Importantly, AAV or CRISPR/Cas9 alone results in much lower editing efficiency and the edited cells do not expand due to toxicity of SF3B1-K700E. Our approach can be readily adapted to generate scalable isogenic systems where mutant oncogenes confer a growth disadvantage.

Postoperative pain: a review of emerging therapeutic options.

INTRODUCTION: Postoperative pain is often managed by opioid medications, even though they carry a risk of adverse effects such as vomiting, constipation, sedation, respiratory depression and physical dependence. Furthermore, opioid use in the healthcare setting has likely contributed to the epidemic. However, the mismanagement of postoperative pain can result in delayed recovery time, impaired physical function, increased risk of morbidity and mortality, chronic pain, and higher healthcare costs. AREAS COVERED: This review explores emerging therapeutic options and strategies in the management of acute postoperative pain and focuses on opioid-sparing, multimodal analgesia. This includes regional anesthetic techniques, non opioid pharmacotherapy, novel opioids and non-pharmacologic therapy. We have also discussed examples of novel analgesics and formulations which have potential benefits in reducing postoperative pain and opioid use after surgery. EXPERT OPINION: The development of novel regional anesthesia techniques allows for opioid minimization in increasing number of surgical procedures. This synergizes with the availability of novel non-opioid analgesic adjucts. In addition, several novel opioid drugs have been developed which may be pathway selective and associated with less adverse effect than conventional opioids.

Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells.

Cancer cells employ various defense mechanisms against drug-induced cell death. Investigating multi-omics landscapes of cancer cells before and after treatment can reveal resistance mechanisms and inform new therapeutic strategies. We assessed the effects of navitoclax, a BCL2 family inhibitor, on the transcriptome, methylome, chromatin structure, and copy number variations of MDA-MB-231 triple-negative breast cancer (TNBC) cells. Cells were sampled before treatment, at 72 h of exposure, and after 10-day drug-free recovery from treatment. We observed transient alterations in the expression of stress response genes that were accompanied by corresponding changes in chromatin accessibility. Most of these changes returned to baseline after the recovery period. We also detected lasting alterations in methylation states and genome structure that suggest permanent changes in cell population composition. Using single-cell analyses, we identified 2350 genes significantly upregulated in navitoclax-resistant cells and derived an 18-gene navitoclax resistance signature. We assessed the navitoclax-response-predictive function of this signature in four additional TNBC cell lines in vitro and in silico in 619 cell lines treated with 251 different drugs. We observed a drug-specific predictive value in both experiments, suggesting that this signature could help guiding clinical biomarker studies involving navitoclax.

Degenerate minigene library analysis enables identification of altered branch point utilization by mutant splicing factor 3B1 (SF3B1).

Cancer-associated mutations of the core splicing factor 3 B1 (SF3B1) result in selection of novel 3' splice sites (3'SS), but precise molecular mechanisms of oncogenesis remain unclear. SF3B1 stabilizes the interaction between U2 snRNP and branch point (BP) on the pre-mRNA. It has hence been speculated that a change in BP selection is the basis for novel 3'SS selection. Direct quantitative determination of BP utilization is however technically challenging. To define BP utilization by SF3B1-mutant spliceosomes, we used an overexpression approach in human cells as well as a complementary strategy using isogenic murine embryonic stem cells with monoallelic K700E mutations constructed via CRISPR/Cas9-based genome editing and a dual vector homology-directed repair methodology. A synthetic minigene library with degenerate regions in 3' intronic regions (3.4 million individual minigenes) was used to compare BP usage of SF3B1K700E and SF3B1WT. Using this model, we show that SF3B1K700E spliceosomes utilize non-canonical sequence variants (at position -1 relative to BP adenosine) more frequently than wild-type spliceosomes. These predictions were confirmed using minigene splicing assays. Our results suggest a model of BP utilization by mutant SF3B1 wherein it is able to utilize non-consensus alternative BP sequences by stabilizing weaker U2-BP interactions.

Cyclin-dependent kinase 1 (CDK1) and CDK2 have opposing roles in regulating interactions of splicing factor 3B1 with chromatin.

Splicing factor 3B1 (SF3B1) is a core splicing protein that stabilizes the interaction between the U2 snRNA and the branch point in the mRNA target during splicing. SF3B1 is heavily phosphorylated at its N terminus and a substrate of cyclin-dependent kinases (CDKs). Although SF3B1 phosphorylation coincides with splicing catalysis, the functional significance of SF3B1 phosphorylation is largely undefined. Here, we show that SF3B1 phosphorylation follows a dynamic pattern during cell cycle progression that depends on CDK activity. SF3B1 is known to interact with chromatin, and we found that SF3B1 maximally interacts with nucleosomes during G1/S and that this interaction requires CDK2 activity. In contrast, SF3B1 disassociates from nucleosomes at G2/M, coinciding with a peak in CDK1-mediated SF3B1 phosphorylation. Thus, CDK1 and CDK2 appear to have opposing roles in regulating SF3B1-nucleosome interactions. Importantly, these interactions were modified by the presence and phosphorylation status of linker histone H1, particularly the H1.4 isoform. Performing genome-wide analysis of SF3B1-chromatin binding in synchronized cells, we observed that SF3B1 preferentially bound exons. Differences in SF3B1 chromatin binding to specific sites, however, did not correlate with changes in RNA splicing, suggesting that the SF3B1-nucleosome interaction does not determine cell cycle-dependent changes to mRNA splicing. Our results define a cell cycle stage-specific interaction between SF3B1 and nucleosomes that is mediated by histone H1 and depends on SF3B1 phosphorylation. Importantly, this interaction does not seem to be related to SF3B1's splicing function and, rather, points toward its potential role as a chromatin modifier.

Crystal structure of {6,6'-dibenzoyl-4,4'-di-tert-butyl-2,2'-[(ethane-1,2-di-yl)di-nitrilo-bis-(phenyl-methanylyl-idene)]diphenolato-κ(4) O (1),N,N',O (1')}nickel(II).

The mononuclear title complex, [Ni(C50H46N2O4)], crystallizes in the triclinic space group P-1, with two mol-ecules in the asymmetric unit (Z' = 2). Each Ni(II) atom has a slightly distorted square-planar geometry [ω = 3.91 (5)° and 2.04 (7)°] defined by the two phenolate O and two imine N atoms of the tetra-dentate Schiff base ligand. The dihedral angles between the central phenolate ring and peripheral phenyl rings are 60.5 (2)/70.0 (2) and 86.4 (2)/56.1 (2)° in mol-ecule A, and 89.43 (19)/18.0 (2) and 63.87 (19)/68.2 (2)° in mol-ecule B. The two central phenolate rings are twisted by angles of 19.37 (19) and 19.36 (18)° in the two mol-ecules. The packing is stabilized through intra- and inter-molecular C-H⋯O and C-H⋯π inter-actions, forming chains parallel to the b axis. The tert-butyl groups in one of the two mol-ecules are positionally disordered with a refined occupancy ratio of 0.707 (13):0.293 (13).

Tris(2,6-dibenzoyl-4-methyl-phenolato-κ(2) O (1),O (2))cobalt(III).

In the title compound, [Co(C21H15O3)3], the Co(III) ion is coordinated in a slightly distorted octa-hedral environment by three phenolate O and three benzoyl O atoms from three monoanionic bidentate 2,6-dibenzoyl-4-methyl-phenolate ligands. The dihedral angles between the mean planes of the central phenolate rings and the peripheral phenyl rings are 46.62 (10)/87.06 (9), 60.44 (8)/23.13 (8) and 46.49 (6)/65.29 (6)°. The crystal packing is stabilized by weak inter-molecular C-H⋯O inter-actions. Mol-ecules are further linked by two π-π [centroid-centroid distances = 3.8612 (14) and 3.9479 (14) Å] and four C-H⋯π inter-actions, forming a three-dimensional network.

Differential distribution of a SINE element in the Entamoeba histolytica and Entamoeba dispar genomes: role of the LINE-encoded endonuclease.

BACKGROUND: Entamoeba histolytica and Entamoeba dispar are closely related protistan parasites but while E. histolytica can be invasive, E. dispar is completely non pathogenic. Transposable elements constitute a significant portion of the genome in these species; there being three families of LINEs and SINEs. These elements can profoundly influence the expression of neighboring genes. Thus their genomic location can have important phenotypic consequences. A genome-wide comparison of the location of these elements in the E. histolytica and E. dispar genomes has not been carried out. It is also not known whether the retrotransposition machinery works similarly in both species. The present study was undertaken to address these issues. RESULTS: Here we extracted all genomic occurrences of full-length copies of EhSINE1 in the E. histolytica genome and matched them with the homologous regions in E. dispar, and vice versa, wherever it was possible to establish synteny. We found that only about 20% of syntenic sites were occupied by SINE1 in both species. We checked whether the different genomic location in the two species was due to differences in the activity of the LINE-encoded endonuclease which is required for nicking the target site. We found that the endonucleases of both species were essentially very similar, both in their kinetic properties and in their substrate sequence specificity. Hence the differential distribution of SINEs in these species is not likely to be influenced by the endonuclease. Further we found that the physical properties of the DNA sequences adjoining the insertion sites were similar in both species. CONCLUSIONS: Our data shows that the basic retrotransposition machinery is conserved in these sibling species. SINEs may indeed have occupied all of the insertion sites in the genome of the common ancestor of E. histolytica and E. dispar but these may have been subsequently lost from some locations. Alternatively, SINE expansion took place after the divergence of the two species. The absence of SINE1 in 80% of syntenic loci could affect the phenotype of the two species, including their pathogenic properties, which needs to be explored.