Tool For Molecular Analysis Research Articles

MolAR: Memory-Safe Library for Analysis of MD Simulations Written in Rust.

Transition to the memory safe natively compiled programming languages is a major software development trend in recent years, which eliminates memory-related security exploits, enables a fearless concurrency and parallelization, and drastically improves ergonomics and speed of software development. Modern memory-safe programing languages, such as Rust, are currently not used for developing molecular modeling and simulation software despite such obvious benefits as faster development cycle, better performance and smaller amount of bugs. This work introduces MolAR-the first memory-safe library for analysis of MD simulations written in Rust. MolAR is intended to explore the advantages and challenges of implementing molecular analysis software in the memory-safe natively compiled language and to develop specific memory-safe abstractions for this kind of software. MolAR demonstrates an excellent performance in benchmarks outperforming popular molecular analysis libraries and tools, which makes it attractive for implementing computationally intensive analysis tasks. MolAR is freely available under Artistic License 2.0 at https://github.com/yesint/molar.

Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling

Multiomic profiling of single cells by sequencing is a powerful technique for investigating cellular diversity. Existing droplet-based microfluidic methods produce many cell-free droplets, underutilizing bead barcodes and reagents. Combinatorial indexing on microplates is more efficient for barcoding but labor-intensive. Here we present Overloading And unpacKing (OAK), which uses a droplet-based barcoding system for initial compartmentalization followed by a second aliquoting round to achieve combinatorial indexing. We demonstrate OAK’s versatility with single-cell RNA sequencing as well as paired single-nucleus RNA sequencing and accessible chromatin profiling. We further showcase OAK’s performance on complex samples, including differentiated bronchial epithelial cells and primary retinal tissue. Finally, we examine transcriptomic responses of over 400,000 melanoma cells to a RAF inhibitor, belvarafenib, discovering a rare resistant cell population (0.12%). OAK’s ultra-high throughput, broad compatibility, high sensitivity, and simplified procedures make it a powerful tool for large-scale molecular analysis, even for rare cells.

Artificial intelligence tools for molecular analysis of sensitization profiles in patients with atopic dermatitis and bronchial asthma

Background. The variety of characteristics that should be taken into account in the clinical phenotyping of allergic diseases is currently being discussed. One of such characteristics is the individual spectrum of sensitization. An important stage in modern allergology has become the introduction of molecules / components for the detection of mediated reactions to specific class E immunoglobulins.Aim. To determine the dominant phenotypes of sensitization in patients with severe atopic dermatitis and bronchial asthma based on the results of molecular diagnostics by the ImmunoCAP Immuno Solid-phase Allergen Chip (ISAC) method using machine learning.Materials and methods. The study included 100 patients who were candidates for genetically engineered biological therapy (n = 63), severe atopic dermatitis (n = 20), or their combination (n = 17) were included. Allergodiagnosis was performed by the ImmunoCAP ISAC method.Results. Based on the results of the study, 6 phenotypes were identified. In phenotype 1, pollen molecules (Amb a1, Phl p4) and crossed reactive food molecules (Mal d1, Ara h8, Gly m4, Act d8, Pru p3) are the leading, among epidermal molecules only Fel d1 (epidermal allergen) and Asp f6 (fungal allergen) are found. For phenotype 2, the significant allergens were fungal (Asp f6), epidermal (Can f1, Can f5, Can f6, Fel d1), food (Gad c1) and cross reactive food molecules (Mal d1, Pru p1. Ara h8, Cor a1.0401). In phenotype 4, only 3 allergen groups are present:epidermal (Fel d1, Fel d2, Can f5, Can f6, Can f3), fungal (Asp f6), and cross food allergy (Jug r3, Pru p3). Phenotype 5 and 6 are dominated by epidermal molecules (Can f1 and Fel d1), true food allergies allergens (Gad c1 and Gal d1 and Gad c1, Gal d1, Gal d3, respectively). In phenotype 3, a combination of the previously labeled molecules is noted.Conclusion. Each of the identified phenotypes reveals a different set of molecules that can be used in real clinical practice to develop reduced panels, making them more accessible.

Methods used in sea turtle genetic and molecular studies

Sea turtles have a tropical and subtropical distribution and can be found in nearly all seas and oceans. They have been the subject of considerable genetic research. However, it does not yet appear that the molecular techniques used for these genetic studies follow a consensus or universal set of tools to be followed for subsequent studies. This is not desirable since it may preclude data exchange and use among studies. Thus, the aim of this review was to survey the main genetic and molecular methods used for sea turtle research worldwide. To achieve this goal, a total of 95 scientific papers were compiled from online databases. We considered articles that used molecular tools for genetic analysis and provided detailed locality data. The following aspects were assessed: species studied, local of sample collection, type of tissue used for molecular studies and type of genetic material used. The seven known sea turtle species have different distribution patterns, with some overlapping of occurrence. Chelonia mydas has been studied genetically along the coasts of all continents. Skin is the most common type of tissue used for molecular analyses. From genetic studies on sea turtles, it is possible to verify the occurrence of hybridism. This phenomenon is relevant to the conservation of the species and was reported in six articles on this topic. Therefore, it is considered that genetic and molecular assays in sea turtles are important tools for biological evaluation and protection. The aim was to survey the main methods used in genetic and molecular research on marine turtles. Keywords: DNA, Chelonian, Testudines, marine turtles

DNA Extraction and PCR Optimization of Coffea arabica L. and Coffea canephora Pierre ex A. Froehner

DNA isolation is an important step for further molecular analysis. Coffee plants contain polysaccharides, polyphenols, and secondary metabolites which can contaminate the results of DNA isolation. This study was conducted to isolate DNA from arabica and robusta coffee leaves using a modified CTAB method and PCR optimization for amplification of matK and rbcL genes. DNA was isolated using buffers (CTAB 10%, PVP 1%, β-mercaptoethanol 1%, Tris-HCl 1M, NaCl 5M, and EDTA 0.5%), and eluted with TE-RNase. Genomic DNA of ten coffee plants was successfully isolated with concentrations ranging from 33-146 nm/µL with purity (A260/A280) 1.7-1.9. Based on the genomic DNA isolated, matK and rbcL genes were amplified with initial denaturation conditions of 94°C (for 1 minute of matK and 4 minutes of rbcL) followed by 35 cycles of denaturation at 94°C for 30 seconds, annealing (adjusted to each primer), and extension at 72°C for 1 minute. The optimal PCR conditions were effective to amplify matK (900 bp) and rbcL (600 bp) genes. Thus, the modified DNA isolation method and PCR optimization can be used as an efficient tool for further molecular analysis of Coffea arabica L. and Coffea canephora Pierre ex A. Froehner.

Network Pharmacology-Based Virtual Screening of Chemical Constituents from Vitexnegundo Linn's Discovered Novel Molecular Targets for Breast Cancer Treatment.

The Chinese chaste tree Vitexnegundo (VN) is a popular herb in South and Southeast Asia that has several health benefits, including the ability to inhibit tumor growth and induce apoptosis in multiple tumors. Literature revealed scanty research on breast cancer, with little focus on the molecular mechanism of the disease and an emphasis on targets, biological networks, and active components. Exploring natural compounds as possible therapeutic options is an old but still promising approach for drug discovery and development. This study used a thorough computational and statistical method to screen potential drug candidates. The active ingredients and targets of VN were identified using SwissADME, SwissTargetPrediction, STITCH, IMPPAT database, KNapSAcK database, and literature. The OMIM and GeneCards databases were searched for possible targets related to breast cancer. The PASS online server was used to check the probability of active metabolite (Pa) against breast cancer. To build protein-protein interactions (PPI) networking, the intersection of disease and drug targets was uploaded to the STITCH database. Cytoscape software was used to analyze the topology parameters of networking to identify hub targets. Gene Ontology (GO) was analyzed using Metascape and ShinyGO, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed using the David database and SR plot, and the site of expression and protein domain were studied using FunRich. We employed AutoDockvina, Discovery Studio, and UCSF ChimeraX software and auxiliary tools for molecular docking and analysis. Zincpharmer was used for pharmacophore mapping. ADMET analysis was conducted using ADMETsar, Swiss ADME, ADMETLab servers, and mypresto using GROMACS for molecular dynamics simulation (MDS). A total of 65 targets and 21 active ingredients were identified. Further investigation was conducted on 20 hub targets selected through PPI networking construction. The enrichment analysis results indicated that the key factors were P, amyloid-beta response, cellular response to amyloid- beta, Pos. reg. of G2/M transition of the mitotic cell cycle, and response to a toxic substance. The molecular docking, pharmacophore mapping, and MD simulation results indicated that apigenin, kaempferol, and luteolin positively interacted with CDK1 and CDK6 proteins. This study is the first to use network pharmacology, molecular docking, pharmacophore mapping, and MD simulation to identify the active ingredients, molecular targets, and critical biological pathways responsible for VN anti-breast cancer. The study provides a theoretical basis for further research in this area.

Liquid Interfacial Gating of Superhydrophobic Plasmonic Metal-Organic Frameworks for Three-in-One Separation, Enrichment, and Recognition in Bacterial Quorum Sensing.

Poor adsorption properties of nonadsorbing targets and competing adsorption of nontargets at a liquid interface always hamper the development of interface sensing techniques. There is a need to fabricate materials that are applicable to various interface assemblies and, meanwhile, could be employed as interfacial gating to improve the performance of interface sensing by separating, enriching, and recognizing targets at the liquid interface. Here, superhydrophobic zeolite imidazole frameworks-8@gold nanoparticles-1H,1H,2H,2H-perfluorodecanethiol (ZIF-8@GNPs-PFDT) with a static water contact angle (WCA) of 155° was constructed via electrostatic self-assembly and surface graft modification. The plasmonic metal-organic framework (PMOF) nanohybrid realized all-purpose self-assembly at air/liquid and liquid/liquid interfaces and also facilely assembled on the surface of liquid droplets, hydrogels, and foams. The self-assembled porous materials displayed the capability for separating, enriching, and recognizing analytes at various oil/water interfaces and thus could be used to adsorb nonadsorbing targets and block the competing adsorption of nontargets. The self-assembled ZIF-8@GNPs-PFDT structures were employed as a three-in-one interfacial gating to endow the excellent surface-enhanced Raman scattering (SERS) sensing capability and has become a promising tool for dye molecular analysis, oil/water separation, organic phase identification, and in situ cultivation and monitoring of bacterial quorum sensing (QS).

Advancements in medical research: Exploring Fourier Transform Infrared (FTIR) spectroscopy for tissue, cell, and hair sample analysis.

Fourier Transform Infrared (FTIR) spectroscopy has emerged as a powerful analytical tool in medical research, offering non-invasive and precise examination of the molecular composition of biological samples. The primary objective of this review is to underscore the benefits of FTIR spectroscopy in medicinal research, emphasizing its ability to delineate molecular fingerprints and assist in the identification of biochemical structures and key peaks in biological samples. This review comprehensively explores the diverse applications of FTIR spectroscopy in medical investigations, with a specific focus on its utility in analyzing tissue, cells, and hair samples. Various sources, including Google Scholar, PubMed, WorledCat and Scopus, were utilized to conduct this comprehensive literature review. Recent advancements showcase the versatility of FTIR spectroscopy in elucidating cellular and molecular processes, facilitating disease diagnostics, and enabling treatment monitoring. Notably, FTIR spectroscopy has found significant utility in clinical assessment, particularly in screening counterfeit medicines, owing to its user-friendly operation and minimal sample preparation requirements. Furthermore, customs officials can leverage this technique for preliminary analysis of suspicious samples. This review aims to bridge a gap in the literature and serve as a valuable resource for future research endeavors in FTIR spectroscopy within the medical domain. Additionally, it presents fundamental concepts of FTIR spectroscopy and spectral data interpretation, highlighting its utility as a tool for molecular analysis using Mid-Infrared (MIR) radiation.

Photo-regulated PROTACs: A novel tool for temporal control of targeted protein degradation

PROTACs (Proteolysis targeting chimeras) are chimeric molecules designed to induce targeted protein degradation via the ubiquitin–proteasome system. These molecules catalytically degrade target proteins and sustainably inhibit their function. Therefore, PROTAC's unique mechanism of action is not only beneficial in medicine but also serves as a valuable tool for molecular biological analysis in fields like chemical biology, biochemistry, and drug discovery. This study presents a novel turn-off (ON-OFF) type PROTAC development strategy utilizing a photocleavable linker. The inclusion of this linker enables temporal control of the degradation activity targeting BRD4 protein upon UV light exposure. PROTAC-2 demonstrated the most potent degradation activity against BRD4 among the other synthesized PROTACs with varying linker lengths. The UV light-induced cleavage of PROTAC-2 was confirmed, leading to a reduction in its BRD4 degradation activity. Notably, this study introduces a novel linker capable of nullifying degradation activity of PROTACs which is activated by light irradiation. These findings offer a promising strategy for the development of turn-off type PROTACs, providing enhanced temporal control over protein degradation. The approach holds significant potential for applications in molecular function studies and drug discovery.

Dynamic cell photo-manipulation technology for the molecular and mechanical regulation analyses of collective cell migration

Collective cell migration is an essential biological process. Migration behaviors of multiple cellular units depend on the mechanical and chemical properties of their scaffolds and the geometry of the cells. However, the mechanisms by which these properties synergistically regulate the collective cell characteristics remain unknown. A robust method is required to analyze collective cell migration. Therefore, in this study, we developed a new method for collective cell migration analysis using defined chemical, mechanical, and geometrical properties. Our method is based on a poly(acrylic acid) hydrogel, whose surface is functionalized with photocleavable poly(ethylene glycol) and a cell-adhesive peptide. By controlling the UV irradiation of the photoactivatable hydrogel, we created geometrically controlled cellular clusters and induced collective migration. Furthermore, chemical and mechanical cues exposed to cell clusters were manipulated depending on the surface density of the cell-adhesive peptide and crosslinking density of the hydrogel. As a proof of concept, we also demonstrated that the collective migration of epithelial cells was synergistically regulated by the chemical and mechanical properties of the scaffold. Our results suggest the new photoactivatable substrate as a promising tool for advanced molecular and mechanobiological analyses of collective cell migration.

Prediction of deleterious non-synonymous SNPs of TMPRSS2 protein combined with Molecular Dynamics Simulations and free energy analysis to identify the potential peptide substrates against SARS-CoV-2.

Globally the SARS-CoV-2 viral infection demands for the new drugs, the TMPRSS2 target plays a vital role in facilitating the virus entry. The aim of the present study is to identify the potential peptide substrate from the Anti-viral database against TMPRSS2 of SARS-CoV-2. The compound screening and variation analysis were performed using molecular docking analysis and online tools such as PROVEAN and SNAP2 server, respectively. The re-docked crystal structure peptide substrate exhibits -128.151 kcal/mol whereas the RRKK peptide substrate shows -134.158 kcal/mol. Further, the selected compounds were proceeded with Molecular Dynamics Simulation, it explores the stability of the complex by revealing the hotspot residues (His296 and Ser441) were active for nucleophilic attack against TMPRSS2. The average Binding Free Energy values computed through MM/GBSA for RRKK, Camostat, and Crystal Structure were shown -69.9278 kcal/mol, -64.5983 kcal/mol, and -63.9755 kcal/mol, respectively against TMPRSS2. The 'rate of acylation' emerges as an indicator for RRKK's efficacy, it maintains the distance of 3.2 Å with Ser441 resembles, whilst its -NH backbone stabilizes at 2.5 Å 'Michaelis Complex' which leads to prevent the entry of SARS-CoV-2 to human cells. The sequence variation analysis explores that the V160 and G6 substitutions are essential to emphasize the uncover possibilities for the ongoing drug discovery research. Therefore, the identified peptide substrate found to be potent against SARS-CoV-2 and these results will be valuable for ongoing drug discovery research.Communicated by Ramaswamy H. Sarma.

Genetic Diversity of Brucella melitensis Isolated from Domestic Ruminants in Iraq.

The control and eradication of brucellosis represents a critical objective for Veterinary and Health Authorities across several countries globally. Efficient surveillance programs play a pivotal role in detecting and managing outbreaks. Epidemiological investigations significantly benefit from standardized and efficient molecular typing techniques and analytical tools, enabling public health laboratories to identify the origin of outbreaks. This study aimed to sequence Brucella spp. strains isolated in Iraq from different ruminant species to verify their molecular epidemiological correlations and, above all, to shed a light on how these Iraqi isolates are positioned in the phylogenetic context of Brucella spp. The 35 isolates under study were from abortion, milk, placenta, and the fetal membranes of sheep, cattle, and buffalo. Genotyping involved various techniques: MLVA-16, Whole Genome Sequencing, MLST, and cgMLST. All the Iraqi isolates from our study clustered in MLVA-16 within the East Mediterranean clade, and all but one grouped together in the same branch of the MST tree. MST analysis showed the minimum distance of one allele between the studied isolates, except for one strain from buffalo, which was positioned farther away from the rest of the isolates. In cgMLST, the majority of strains grouped within a large cluster predominantly comprising genotypes from the Middle East. The application of different control measures in different territories based on molecular epidemiological studies would increase the chances of maximizing public health benefits and minimizing the spread of infection to disease-free or lower prevalence areas.

Abstract A078: Characterization of normal human male mammary cells and their de novo transformed derivatives

Abstract Men normally develop and maintain bi-layered mammary glands that appear structurally and histologically similar to those that develop in women, but with reported deficient lobule formation. Men also develop breast cancer, mostly of the ER+ subtype and an age-associated increasing onset, but at a 100-fold lower incidence and overall worse outcome. However, the classification and treatment of male breast cancers are largely based on strategies developed for female patients, despite their known hormonal and other differences. This is likely due, at least in part, to the fact that adult male mice, unlike humans do not develop full mammary glands. Thus, experimental access to mouse models have been lacking and studies of “normal” male mammary tissue have thus been largely restricted to analysis of human male gynecomastia samples. We now report the utility of multiple systems for analyzing normal adult human female mammary cell properties to this source of freshly obtained and viably cryopreserved normal human male mammary tissue. Histological examination of male mammary tissues (3 donors) confirmed their reported bi-layered structure surrounded by fibroblasts and lack of gross evidence of lobules. Use of procedures created for analyzing female breast tissue indicates that the human male mammary glands contain the same subsets but in different relative proportions; i.e., the proportion of EpCAM+CD49f- mammary cells (Luminal Cells, LCs) is relatively increased and of the EpCAM+CD49f+ cells (Luminal Progenitors, LPs) and EpCAM-CD49f+ cells (Basal Cells, BCs) is correspondingly decreased, consistent with a lack of alveolae. However, the freshly isolated male LPs and BCs contain a similar frequency of EGF-responsive colony-forming cells (CFCs) as female LPs and BCs. Subcutaneous transplantation of the male mammary cells in both male and female immunodeficient mice resulted in the generation of hollow mammary structures 4 weeks later as previously shown for female cells, and these were also found to contain LC, LP and BC populations including some with detectable levels of CFCs suggesting their derivation from a male mammary stem cell population (Eirew et al Nat Med 2008). We have also found evidence from qPCR and RNA-seq analyses of reduced progesterone signaling and alveologenesis in male LPs and LCs. These findings suggest hormonal differences may play a major role in regulating the altered ratios of cell types present in the normal adult human male mammary gland in comparison to premenopausal female. Interestingly, preliminary experiments also indicate that normal human male mammary cells transduced with KRASG12D without, or with BMI1+MYC+TP53R273C , generate analogous slowly-growing ER+, and rapidly-growing, highly aggressive tumours, respectively, in male immunodeficient mice. Taken together, our findings demonstrate the potential of established cell culture, xenotransplantation and molecular analytical tools to reveal the altered mechanisms that account for the different structure and biology of human male mammary tissue. Citation Format: Shengsen Ding, Susanna Tan, Ebrahim Eskandari-Nasab, Shrinka Sen, Martin Hirst, Connie Eaves. Characterization of normal human male mammary cells and their de novo transformed derivatives [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A078.

Simultaneous Application of Raman and Laser-Induced Breakdown Spectroscopy in the Gas Phase with a Single Laser and Detector.

Raman spectroscopy and laser-induced breakdown spectroscopy (LIBS) are powerful tools for molecular and elemental analysis, respectively. Their combined application, however, is challenging due to the differences in the signal generation and detection characteristics. This note proposes three experimental schemes for the simultaneous application of Raman and LIBS for gas-phase diagnostics. Ring-cavity optical pulse stretchers facilitate shaping suitable pulse pairs from a Q-switched laser that enables the quasi-simultaneous detection of the Raman and LIBS signals on a single detector.

Distribution, source and potential biological impacts of polycyclic aromatic hydrocarbons in the core sediments of a networked aquatic system in the northwest coast of India – A special focus on Thane Creek Flamingo Sanctuary (Ramsar site)

Mumbai, one of the most industrialised and inhabited cities in the world, has been confronting an exponential increase in pollution brought about by anthropogenic activities throughout its coastal belt over the years. The historical accumulation of 16 polycyclic aromatic hydrocarbons (PAHs) in the sediments of Thane creek, Panvel creek and the Ulhas estuarine river system was examined in light of these circumstances. The present study has found that the PAHs were distributed vertically in the sediments of Thane Creek as 16.53 – 1317.02 ng/g dw and Ulhas Estuary as 105.44 – 1815.20 ng/g dw. Major sources of PAHs pollution to the system like petroleum spillages, biomass burning and vehicular exhaust was discernible based on molecular diagnostic ratio (MDR) and principal component analysis (PCA) tools, signifying petrogenic and pyrogenic origins. Based on the total toxicity equivalence (TEQ) and sediment quality guidelines (SQGs) indices, high or moderate contamination risks have been identified in the lower and middle regions of the Ulhas estuary, as well as in the lower regions of Thane creek. Specifically, high contamination risk of benzo[a]pyrene which has high cancerous potential, was identified in the above sites.

Molecular Epidemiological Study of a Human Brucellosis Outbreak - Weihai City, Shandong Province, China, 2022.

Brucellosis, mainly caused by Brucella melitensis (B. melitensis), is regarded as a significant zoonotic disease in China. In Weihai, located at the eastern end of the Shandong Peninsula, brucellosis has been in a low epidemic phase for the past five years. This was the initial report of a brucellosis outbreak in the last five years. Strains of B. melitensis bv. 3 from Weihai and other cities showed a close genetic relationship, suggesting a potential common ancestry. Epidemiological investigations depend on standardized and effective molecular typing methods and analysis tools for public health laboratories to identify and trace outbreaks. Understanding the circulation patterns of livestock in free-range households in heavily affected areas is essential for controlling the spread of brucellosis.

Single clonal tracking on biomimetic microtextured platforms for real-time guided migration analysis of myeloid-derived suppressor cell dissemination characteristics ex vivo.

Current strategies to undermine the deleterious influence of myeloid-derived suppressor cells (MDSCs) in the tumor microenvironment (TME) are lacking effective clinical solutions, in large part, due to insufficient knowledge on susceptible cellular and molecular targets. We describe here the application of biomimetic microfabricated platforms designed to analyze migratory phenotypes of MDSCs in the tumor niche ex vivo, which may enable accelerated therapeutic discovery. By mimicking the guided structural cues present in the physiological architecture of the TME, aligned microtopography substrates can elucidate potential interventions on migratory phenotypes of MDSCs at the single clonal level. Coupled with cellular and molecular biology analysis tools, our approach employs real-time tracking analysis of cell motility to probe the dissemination characteristics of MDSCs under guided migration conditions. These methods allow us to identify cellular subpopulations of interest based on their disseminative and suppressive capabilities. By doing so, we illustrate the potential of applying microscale engineering tools, in concert with dynamic live cell imaging and bioanalysis methods to uncover novel exploitable motility targets for advancing cancer therapy discovery. The inherent simplicity and extended application to a variety of contexts in tumor-associated cell migration render this method widely accessible to existing biological laboratory conditions and interests.

The Role of Artificial Intelligence in the Pharmaceutical Sector: A Comprehensive Analysis of its Application from the Discovery Phase to Industrial Implementation

The incorporation of artificial intelligence (AI) technology into the pharmaceutical sector is a groundbreaking revolution, promising to enhance drug development significantly by boosting speed, efficiency, and effectiveness. This transformative journey encompasses several key facets, notably the sophisticated analysis of complex data, the optimization of drug delivery systems, the acceleration of drug discovery, the identification of valuable biomarkers and drug candidates, and the fine-tuning of treatment outcomes. Beyond these crucial strides, AI is reshaping healthcare at large, elevating decision-making processes, and deepening our understanding of diseases and pharmaceuticals. The broader domains within this AI-driven transformation encompass themes such as “Revolutionizing Pharmaceutical Product Development Through AI,” where AI platforms like the Chemputer successfully synthesize compounds and estimate granulation completion times, improving production efficiency. In “Transforming Pharmaceutical Manufacturing with AI, “AI optimizes manufacturing processes, further enhancing efficiency.” Enhancing Clinical Trial Design Through AI” harnesses AI to improve patient selection and adherence, utilizing genome and exposome profiles for precise and efficient clinical trials. AI also proves valuable in preclinical phases, predicting lead compounds. Moreover, AI extends its influence to brand recognition and market positioning of pharmaceutical products, leveraging technology and e-commerce platforms for distinct product identities and effective marketing strategies. In “Convergence of AI and Nanomedicine,” AI delves into complex formulation development, optimizing drug delivery methods via molecular analysis and simulation tools. Furthermore, AI’s role in addressing challenges in the pharmaceutical market, such as reducing financial burdens and risks related to virtual screening, is pivotal. The sector’s substantial growth and its integration into pharmaceutical companies’ strategies through collaborations signify a promising future for AI in healthcare.In summary, the incorporation of AI in the pharmaceutical industry holds immense potential for enhancing production processes, clinical trial design, market positioning, nanomedicine, and overall industry efficiency. These collective advancements mark a transformative era in pharmaceutical innovation and patient care.

Defining Hereditary Pyropoikilocytosis (HPP) in the Molecular Diagnostic Era

Misconceptions continue in distinguishing hereditary elliptocytosis (HE) with hemolysis in early perinatal period and hereditary pyropoikilocytosis (HPP). In 1975, Zarkowsky and colleagues described a group of children with transfusion dependent congenital hemolytic anemia with the unique morphology of “microspherocytes, measuring 2-3 microns in diameter, and cells with blunted projections or triangular in shape”, a morphology resembling the heat induced damage to normal erythrocytes - hence the name hereditary pyropoikilocytosis (HPP). Subsequently, similar cases were described with or without demonstrable heat sensitivity (Ravindranath & Johnson, 1985). Regardless, the common denominators were 1) transfusion dependency early in infancy - resolved with splenectomy, 2) severe microcytosis, often <60 fL, and 3) a decrease in membrane bound spectrin (decreased spectrin/band3 ratio). Family studies showed normal RBC morphology in both parents (Ravindranath & Johnson, 1985) or in some cases, one parent with HE (Zarkowsky et al., 1975). Protein chemistry studies showed decreased tetramer formation and tryptic digests showed mutations within the n-terminal alpha 1 domain of alpha spectrin - the dimer/dimer interaction site. Thus, homozygosity or double heterozygosity of mutations in the dimer/dimer interaction site of alpha spectrin (alpha 1 domain of alpha spectrin) defined HPP while classical HE cases showed heterozygous mutations in the alpha 1 domain. A fact unexplained was how this results in spectrin deficiency, specifically, alpha spectrin deficiency (Ravindranath & Johnson, 1985). Using the molecular analytical tool AnemiaID (courtesy of Agios Pharmaceuticals, Inc.), we show that HPP is defined by the co-inheritance of two SPTA1 mutations and Alpha-LeLy polymorphism ( αLeLy rs28525570; SPTA1[c.5572C>G;c.6531-12C>T]) in one or both alleles, thus explaining the increased propensity for red cell fragmentation and the spectrin deficiency noted on acrylamide gels [Table: Clinical and molecular characteristics of our cases]. Of note, homozygosity for αLeLy polymorphism and one SPTA1 variant did not result in clinical HPP phenotype [HE-2 in Table]. At a clinical laboratory level, the extreme microcytosis in HPP is evident in the markedly diminished band3 content on eosin-5'-maleimide (EMA) binding test- mean channel fluorescence (MCF) of <275.0 (control: 473.0-549.0) while HE (including neonatal HE with hemolysis) show a double peak pattern in EMA (the minor peak representing the fragmented cells while the major peak had MCF higher than control MCF) and the characteristic trapezoid pattern on osmotic gradient ektacytometry (not shown).

The Why and How of Ultrasmall Nanoparticles.

ConspectusIn this Account, we describe our research into ultrasmall nanoparticles, including their unique properties, and outline some of the new opportunities they offer. We will summarize our perspective on the current state of the field and highlight what we see as key questions that remain to be solved. First, there are several nanostructure size-scale regimes, with qualitatively distinct functional biological attributes. Broadly generalized, larger particles (e.g., larger than 300 nm) tend to be more efficiently swept away by the first line of the immune system (for example macrophages). In the "middle-sized" regime (20-300 nm), nanoparticle surfaces and shapes can be recognized by energy-dependent cellular reorganizations, then organized locally in a spatial and temporally coherent way. That energy is gated and made available by specific cellular recognition processes. The relationship between particle surface design, endogenously derived nonspecific biomolecular corona, and architectural features recognized by the cell is complex and only purposefully and very precisely designed nanoparticle architectures are able to navigate to specific targets. At sufficiently small sizes (<10 nm including the ligand shell, associated with a core diameter of a few nm at most) we enter the "quasi-molecular regime" in which the endogenous biomolecular environment exchanges so rapidly with the ultrasmall particle surface that larger scale cellular and immune recognition events are often greatly simplified. As an example, ultrasmall particles can penetrate cellular and biological barriers within tissue architectures via passive diffusion, in much the same way as small molecule drugs do. An intriguing question arises: what happens at the interface of cellular recognition and ultrasmall quasi-molecular size regimes? Succinctly put, ultrasmall conjugates can evade defense mechanisms driven by larger scale cellular nanoscale recognition, enabling them to flexibly exploit molecular interaction motifs to interact with specific targets. Numerous advances in control of architecture that take advantage of these phenomena have taken place or are underway. For instance, syntheses can now be sufficiently controlled that it is possible to make nanoparticles of a few hundreds of atoms or metalloid clusters of several tens of atoms that can be characterized by single crystal X-ray structure analysis. While the synthesis of atomically precise clusters in organic solvents presents challenges, water-based syntheses of ultrasmall nanoparticles can be upscaled and lead to well-defined particle populations. The surface of ultrasmall nanoparticles can be covalently modified with a wide variety of ligands to control the interactions of these particles with biosystems, as well as drugs and fluorophores. And, in contrast to larger particles, many advanced molecular analytical and separation tools can be applied to understand their structure. For example, NMR spectroscopy allows us to obtain a detailed image of the particle surface and the attached ligands. These are considerable advantages that allow further elaboration of the level of architectural control and characterization of the ultrasmall structures required to access novel functional regimes and outcomes. The ultrasmall nanoparticle regime has a unique status and provides a potentially very interesting direction for development.