Molecular Techniques Research Articles

Exploring the Mechanism of Action of the "Scutellaria Barbata D.Don-Prunella Vulgaris L." Herb Pair in the Treatment of Lung Cancer Using Network Pharmacology and Molecular Docking Techniques

Objective: To explore the mechanism of action of the herbal pair "Scutellaria barbata D.Don-Prunella vulgaris L." in the treatment of lung cancer through network pharmacology and molecular docking techniques. Methods: Active ingredients and their targets of Scutellaria barbata D.Don and Prunella vulgaris L. were collected and screened from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Disease-related targets were obtained and screened from the Genecards and OMIM databases. The intersection Venn diagram of the targets of "Scutellaria barbata D.Don-Prunella vulgaris L." and lung cancer disease targets was obtained using R 4.4.1 software and packages such as "ggvenn". A drug-active ingredient-target-disease association network was constructed in Cytoscape 3.10.0, and core active ingredients were screened using the Analyze Network function. A PPI network for drug-disease common targets was constructed using the String database website, and the TSV format of protein interaction relationship files was imported into Cytoscape 3.10.0 software,install and run CytoHubba to calculate and obtain the core targets in the network. GO function and KEGG pathway enrichment analyses were performed on drug-disease common targets using R 4.4.1 software. Finally, molecular docking validation was performed on core ingredients and core targets using AutoDock, and the three best binding molecular docking patterns were displayed using PyMol software. Results: A total of 33 active drug components and 108 drug-disease common targets were obtained. Among them, there are 5 core active components: quercetin, luteolin, wogonin, kaempferol, and baicalein; core targets include TP53, AKT1, JUN, HSP90AA1, etc. GO analysis yielded 2, 010 related entries. KEGG analysis identified 147 signaling pathways. Molecular docking showed that the core active components have strong affinity with the core targets. Conclusion: The drug pair of Scutellaria barbata D.Don and Prunella vulgaris L. may exert anti-tumor effects by acting on targets such as TP53, AKT1, JUN, HSP90AA1, and through signaling pathways like PI3K-AKT, inhibiting tumor cell proliferation, promoting tumor cell apoptosis, suppressing its proliferation, differentiation, and metastasis, thereby achieving therapeutic effects on lung cancer.

Exploring the Potential of Moringa Oleifera Phytochemicals as Inhibitors of Dipeptidyl Peptidase-4 (DPP-4) in Diabetes Mellitus: A Molecular Docking Approach

Abstract Diabetes mellitus (DM) is a global health concern characterized by chronic hyperglycemia due to defects in insulin secretion, insulin action, or both. Type 2 diabetes (T2DM), the most prevalent form, is largely driven by obesity and a sedentary lifestyle, contributing to over 95% of diabetes cases worldwide. The current treatment regimens for T2DM, including Dipeptidyl Peptidase-4 (DPP-4) inhibitors, aim to enhance insulin secretion but are often associated with adverse side effects. This has intensified the search for natural, safer alternatives with comparable efficacy. Moringa oleifera, a highly valued plant with an extensive history in traditional medicine, has shown promising antidiabetic properties. This research explores the potential of Moringa oleifera-derived phytochemicals as natural DPP-4 inhibitors using in-silico molecular docking techniques. The study identifies and evaluates the binding affinities of these phytochemicals to the DPP-4 enzyme, aiming to predict their inhibitory potential and minimal side effects, thereby contributing to the development of novel, safer hypoglycemic drugs. The results indicate the compounds’ potential as effective DPP-4 inhibitors with promising hypoglycemic properties. Specifically, piceatannol exhibited the highest binding affinity of -7.9 kcal/mol, whereas vanillic acid had the lowest at -5.7 kcal/mol. This study underscores the potential of Moringa oleifera as a natural, safer alternative in the development of novel anti-diabetic drugs, contributing to the growing body of research on plant-based therapeutics for diabetes management.

Exploring marine compounds as potential biocontrol agents against powdery mildew for agricultural sustainability: a computer-based approach

Powdery mildew is a pervasive fungal disease causing significant economic losses globally. Continuous use of synthetic fungicides has led to environmental concerns and resistant fungal strains. This study explores marine-derived cephalostatins from the South African Natural Compounds Database as novel fungicidal agents for managing powdery mildew. Using molecular docking techniques, we investigated the interaction between selected cephalostatins and critical proteins involved in powdery mildew pathogenesis. Compounds were selected based on drug-likeness and bioactivity, adhering to Lipinski’s Rule of Five. Molecular interactions, binding affinities, and stability were analysed using AutoDock Vina, PyMOL, and Discovery Studio. Cephalostatin 17 exhibited the highest binding affinity (−10.4 kcal/mol), indicating strong potential for inhibiting fungal growth through significant hydrogen bonding and hydrophobic interactions. The study’s primary limitation is the reliance on computational predictions, necessitating experimental validation. Cephalostatin 17 stands out as a promising candidate for sustainable agricultural practices.

Evaluation on the diffusion-fusion properties and interfacial mechanical behavior of virgin and aged asphalt

To investigate the regeneration mechanisms of rejuvenated asphalt mixtures, molecular simulation techniques were employed to research virgin and aged asphalt's fusion characteristics and interface mechanical properties. The blended zone was identified based on relative density distribution, and a molecular-scale calculation method for the Degree of binder Blended (DOB) between virgin and aged asphalt was proposed. Finally, the influence of DOB on the mechanical properties of the asphalt-aggregate interface was evaluated through interface pull-out tests. The results revealed that the proposed molecular-scale DOB calculation method effectively assessed the blending effectiveness between virgin and aged asphalt. Higher degrees of asphalt aging made it more challenging for aged asphalt to fuse with virgin asphalt, while elevated temperatures facilitated diffusion fusion between them. Under tensile loading, initial cracks were primarily initiated from the rejuvenated asphalt's blended zone. This region represented the weakest area within the interface system and was prone to fracture under load. The increase in DOB significantly improved the interfacial properties of recycled asphalt, with the increase in DOB the interfacial tensile strength increased by 4%–14% and the fracture energy increased by 10%–19%. However, this enhancement effect diminished with an increased degree of asphalt aging. At the molecular scale, increasing DOB improved the interface strength and deformation resistance of rejuvenated asphalt. The molecular simulation results provide theoretical guidance for evaluating the fusion degree of aged asphalt in RAP materials and determining the utilization efficiency of aged asphalt.

Detection of Bartonella henselae in feline erythrocytes in Egypt by using Giemsa staining, transmission electron microscopy, and polymerase chain reaction.

Bartonella species (Bartonella spp.) have gained recognition as a significant human pathogen, implicated in a wide range of diseases. Among these, Bartonella henselae infection has been extensively studied for its primary occurrence in cats and its role in the development of cat-scratch disease in humans. While light microscopy and transmission electron microscopy (TEM) have traditionally played crucial roles in identifying causative agents of infectious diseases, including Bartonella spp., the accuracy of these methods in identifying Bartonella spp. remains undefined. Therefore, this study aims to bridge this gap by employing both light microscopy and TEM to detect Bartonella in feline blood samples and to confirm B. henselae with polymerase chain reaction (PCR). Examination of blood smears stained with Giemsa and toluidine blue semithin sections by using light microscopy revealed the presence of intraerythrocytic corpuscles, suggesting Bartonella infection in six out of 33 examined cat blood samples. TEM findings corroborated these observations, showcasing the engulfment of bacteria by the erythrocyte membrane, along with the presence of some Bartonella spp., adhering to the erythrocyte wall. PCR-based molecular detection confirmed the presence of B. henselae in these six samples. It is concluded that light microscopy and TEM are considered valuable in the screening of cats' blood for the potential presence of Bartonella. However, further molecular techniques are essential for precise identification and confirmation of specific Bartonella spp. RESEARCH HIGHLIGHTS: Giemsa-stained blood smear and semithin section showed potential intraerythrocytic Bartonella spp. corpuscles. TEM demonstrated the engulfment of Bartonella spp. by the erythrocyte membrane, along with the presence of some Bartonella spp. adhering to the erythrocyte wall. Molecular analysis of blood samples from cats by PCR unveiled that six out of 33 (18.18%) samples tested positive for B. henselae infection.

Recent Advances and Future Perspectives in Radiolabeled Antibody Fragments for Breast Cancer Molecular Imaging

Breast Cancer (BC) is the leading cause of cancer-related deaths in women and the most common cancer worldwide. It is classified based on its anatomical origin, the presence of Human Epidermal Growth Factor Receptor 2 (HER-2), and the presence of Estrogen Receptor (ER) and/or Progesterone Receptor (PR). Around 20% of breast cancers are HER-2 positive. While biopsy-based diagnoses are valuable in clinical settings, they have limitations in terms of sampling and interpretation. However, laboratory tests such as Immunohistochemistry (IHC) or Fluorescence In Situ Hybridization (FISH) are also limited, including being time-consuming, expensive, and requiring specialized equipment. Ongoing research and technological advancements aim to address the challenges associated with biopsy-based diagnoses and laboratory tests to develop more accurate and efficient methods for assessing HER-2 status. To this end, various radioactively labeled proteins and small compounds, such as single-chain variable Fragments (scFv), F(ab')2, affibody, and nanobody, have been developed to target HER-2 using molecular array techniques. These smaller targeted compounds offer improved image quality, shorter circulating half-life, and reduced immunogenicity compared to their larger counterparts. This is due to their better biodistribution, clearance, and stability. This study investigates the current understanding and ongoing efforts in utilizing antibody fragments for molecular imaging. The specific objectives were to evaluate the advantages of antibody fragments over full-length antibodies regarding biodistribution, clearance, and stability. Additionally, this study aims to assess the current knowledge and ongoing research in utilizing antibody fragments for molecular imaging.

Advancing Oncology through Imaging: Evaluating FDG-PET's Role in Cancer Diagnosis and Staging

Purpose: Fluorine-18 fluorodeoxyglucose positron emission tomography (18F-FDG PET) represents a valuable functional molecular imaging technique. Through non-invasive means, 18F-FDG PET allows for the assessment of glucose metabolic activity in living biological systems. Its utility in oncology is well established, with applications in tumor diagnosis, staging, and treatment monitoring. The purpose of this study is to conduct a systematic review assessing the indicative value and effect on the clinical management of 18F-FDG PET/CT for various cancer types based on the current literature. Materials and Methods: An inclusive search of the PubMed, Google Scholar, and Science Direct databases was performed to identify relevant studies published from 2022 to the present. Records were screened according to predefined inclusion and exclusion criteria. A full-text review of the eligible studies was independently conducted by two reviewers. Results: Twenty-one primary research articles met the inclusion criteria and encompassed several cancer types. Evidence demonstrates superior detection, characterization, and staging compared with anatomical imaging alone. Advantages have been substantiated for head/neck, lung, and brain cancers, as well as lymphomas. The significant associations between 18F-FDG uptake and clinical features validated the molecular profiling capacity. Conclusion: 18F-FDG PET provides crucial metabolic tumor information, augmenting conventional approaches. Specific diagnostic values have been established for diverse oncological applications. While technical refinements are ongoing, 18F-FDG PET plays an expanding role in multimodal cancer algorithms according to guidelines. Continued investigation aims to further optimize these techniques and clarify their comparative effectiveness.

Neglected Tropical Diseases in India: Enhancing POC based Diagnosis towards Elimination

Neglected tropical diseases (NTDs) represent a significant global health challenge, particularly in regions with limited access to healthcare and sanitation facilities. India, with its vast population and diverse landscape, faces a substantial burden of NTDs, including lymphatic filariasis (LF), visceral leishmaniasis (VL), and dengue along with other coinfections. The Government of India has undertaken various initiatives to eliminate these diseases, aligning with global objectives. However, challenges persist, including the need for accurate disease burden estimation, resource allocation, and disease diagnosis.Efforts to eliminate NTDs in India require comprehensive strategies, including mass drug administration and vector control programs. Thus, accurate and accessible diagnostic tools are essential for disease surveillance and treatment monitoring. Point-of-care testing including molecular and serological-based techniques facilitates swift diagnosis and disease surveillance, particularly in resource-limited settings. Thus, by prioritizing investments in innovative diagnostic and therapeutic strategies, India can make significant strides toward improving patient survival and decrease mortality rates.

Clinical Applications and Advancements of Positron Emission Tomography/Computed Tomography in Cardio-Oncology: A Comprehensive Literature Review and Emerging Perspectives.

Recent advancements in molecular biology, biotechnology, chemistry/radiochemistry, artificial intelligence, and imaging techniques have significantly propelled the field of cardiovascular molecular imaging. This review aims to provide a comprehensive overview of the current state of cardiovascular positron emission tomography (PET) imaging and cardiac computed tomography (CT), exploring their roles in elucidating molecular and cellular processes, enabling early disease detection, and guiding novel therapeutic interventions for cardiovascular conditions. Cardiovascular PET imaging strives to uncover molecular and cellular events preceding visible anatomical manifestations or physiological changes. Meanwhile, cardiac CT has evolved into a multifaceted modality, offering insights into both anatomy and function. Utilizing advanced CT technologies allows for a thorough evaluation, encompassing fractional flow reserve, perfusion imaging, pericoronary adipose tissue attenuation, atherosclerotic plaque characterization, cardiomyopathies, structural cardiac abnormalities, and congenital heart anomalies. The emergence of hybrid imaging, combining PET and CT, presents innovative prospects in cardiology. This approach enables the simultaneous assessment of cardiac perfusion and coronary anatomy in a singular scan, providing complementary insights relevant to potential coronary artery disease. Despite the substantial potential impact, operational familiarity with this hybrid tool remains limited, and its integration into routine clinical practice warrants further exploration. In summary, the review underscores the transformative impact of recent technological advancements on cardiovascular molecular imaging. The integration of PET and CT, along with their individual capabilities, holds promise for early disease detection and informed clinical decision-making. While acknowledging the potential of hybrid imaging, it emphasizes the need for increased operational familiarity and continued exploration to facilitate its seamless integration into routine clinical practice. The insights gained from this review contribute to the ongoing dialogue in the field, offering a foundation for future research and advancements in cardiovascular imaging.

Isolation and characterization of alginate producing Azotobacter sp, isolated from rhizospheric soil of Oryza sativa (L.) and Triticum aestivum (L.)

Alginate as biopolymer consisting of β-D Mannuronic acid and α-L Guluronic acid monomer residues linked by (1-4) glycosidic bond. Brown seaweeds mostly Laminaria sp, Ascophyllum nodosum, Eclonia maxima, Sargassum sp. and Macrocystis pyrifera were earlier used for commercial alginate production. Major drawback of using sea weeds for alginate production were high production cost, impurity issue and safety concerns includes the reasons behind discovery of novel bacterial sources to make an efficient alginate production system. Later two bacterial genera Pseudomonas and Azotobacter were reported for alginate production. However, due to pathogenicity, and quality issue associated with some Pseudomonas strains, Azotobacter sp. was found to be most reliable and prioritized bacterial sources for alginate production with appreciable qualities which will be ready to be used for industrial applications. Therefore, current research aims to isolate and characterize a new strain of Azotobacter sp. with alginate-producing ability. Two different soil samples were collected from two places Deokali and Parsurampur, Jaunpur district in the spring (06 August 2022) and winter (06 February, 2023) seasons from Oryza sativa and Triticum aestivum rhizospheric region respectively. Azotobacter sp. was isolated by using Nitrogen Free Burk’s medium and alginate production was confirmed by gel formation assay method in the presence of CuSO4 and CaCl2 solutions. The carbohydrate qualitative test was done by using Molisch’s Test. Two novel strains Azotobacter chroococcum PU-RSD01 and Azotobacter chroococcum PU-RSD02 were isolated on the basis of high alginate producing ability. Morphological, biochemical and molecular techniques further characterized the isolates.

Identification and In silico analysis of fungal species from plant pathogens

The study aimed to identify, characterize and analyze fungal species associated with two economically significant plant species, Pongamia pinnata and Asclepias syriaca. Through molecular technique, fungal isolates were identified.The study employed DNA sequencing and phylogenetic analysis to classify the fungal isolates accurately. Furthermore, in silico analyses provided insights into the pathogenicity mechanisms and genetic diversity of the identified fungal species. Functional annotation and pathway analysis elucidated metabolic pathways associated with pathogenesis and host interactions. Overall, our integrated approach provides a comprehensive understand of fungal diversity, evolution, and pathogenicity in P.pinnata and A.syriaca. These findings lay the foundation of future research aimed at developing sustainable strategies for disease management and crop improvement in agricultural systems.

Comparing Typing Methods for Foot-and-Mouth Disease Virus Serotypes: Sandwich ELISA, Multiplex PCR, RT-LAMP and SYBR Green Real-time PCR

Background: Foot and Mouth Disease (FMD) poses a significant economic threat to the cattle population in Assam, with recurrent outbreaks occurring annually. Methods: This study aimed to compare different diagnostic techniques for the molecular detection and serotyping of Foot and Mouth Disease Virus (FMDV) outbreaks in the region. Epithelial tissue samples (n=29) were collected following standard procedures. SYBR Green real-time PCR targeting the 3D gene, sandwich enzyme-linked immunosorbent assay (S-ELISA), multiplex PCR (mPCR), and reverse transcription loop-mediated isothermal amplification (RT-LAMP) were utilized for detection and serotyping. Results: All 29 tissue samples tested positive for FMDV using SYBR Green real-time PCR, mPCR, and RT-LAMP, with 100% congruence in serotyping (20 serotype O, 9 serotype A). In contrast, S-ELISA detected only 86.21% of samples as positive (17 serotype O, 8 serotype A). Statistical analysis revealed significant differences between the sensitivity of S-ELISA and molecular techniques (p = 2.91×10-7).The findings underscore the superior sensitivity of SYBR Green real-time PCR, mPCR, and RT-LAMP, highlighting their potential for enhancing FMDV surveillance and control efforts in Assam.

Exploring the anti‑oxidative mechanisms of Rhodiola rosea in ameliorating myocardial fibrosis through network pharmacology and in vitro experiments.

Myocardial fibrosis (MF) significantly compromises cardiovascular health by affecting cardiac function through excessive collagen deposition. This impairs myocardial contraction and relaxation and leads to severe complications and increased mortality. The present study employed network pharmacology and in vitro assays to investigate the bioactive compounds of Rhodiola rosea and their targets. Using databases such as HERB, the Encyclopedia of Traditional Chinese Medicine, Pubchem, OMIM and GeneCards, the present study identified effective components and MF‑related targets. Network analysis was conducted with Cytoscape to develop a Drug‑Ingredient‑Target‑Disease network and the STRING database was utilized to construct a protein‑protein interaction network. Key nodes were analyzed for pathway enrichment using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Molecular interactions were further explored through molecular docking techniques. The bioactivity of salidroside (SAL), the principal component of Rhodiola rosea, against MF was experimentally validated in H9c2 cardiomyocytes treated with angiotensin II and assessed for cell viability, protein expression and oxidative stress markers. Network pharmacology identified 25 active ingredients and 372 targets in Rhodiola rosea, linking SAL with pathways such as MAPK, EGFR, advanced glycosylation end products‑advanced glycosylation end products receptor and Forkhead box O. SAL showed significant interactions with core targets such as albumin, IL6, AKT serine/threonine kinase 1, MMP9 and caspase‑3. In vitro, SAL mitigated AngII‑induced increases in collagen I and alpha smooth muscle actin protein levels and oxidative stress markers, demonstrating dose‑dependent effectiveness in reversing MF. SAL from Rhodiola rosea exhibited potent anti‑oxidative properties that mitigated MF by modulating multiple molecular targets and signaling pathways. The present study underscored the therapeutic potential of SAL in treating oxidative stress‑related cardiovascular diseases.

The Potential of Molecular Docking for Predictive Toxicology.

Molecular modeling techniques are widely used in medicinal chemistry for the study of biological targets, the rational design of new drugs, or the investigation of their mechanism of action.They are also applied in toxicology to identify chemical potential harmful effects.Molecular docking is a computational technique to predict the ligand binding mode and evaluate the interaction energy with a biological target.This chapter describes a computational workflow to predict possible endocrine disruptors on peroxisome proliferator-activated receptor alpha (PPARα), a nuclear receptor involved in glucose and lipid metabolism. The analyzed compounds are food contact chemicals, natural or synthetic substances intentionally added to food or released from the package or during production or technological processes.

In silico design and ADMET evaluation of new inhibitors for PIM1 kinase using QSAR studies, molecular docking, and molecular dynamic simulation

The proviral Integration site of Moloney (PIM) kinase is highly expressed in various diseases, including cancer, making the development of selective inhibitors for this protein important. A series of PIM1 inhibitors, triazolo [4, 3-b] pyridazin-3-yl-quinoline derivatives, have been studied to design new inhibitors. The activity and structural features of these derivatives were investigated to understand their interactions with PIM1 using molecular docking, molecular dynamic simulation, and QSAR techniques.In a study of 30 compounds using the structure-activity technique and the MLR method, a linear model with R2train = 0.91 and R2test = 0.96 was obtained. The model utilized descriptors such as RDF080v, RDF105v, RDF135v, Mor03v, and H046 to express the structural characteristics of the inhibitors. To enhance the model, the SVR non-linear method with the RBF function was also used, resulting in an improved model with R2train = 0.98 and R2test = 0.98.Furthermore, the molecular docking technique was employed to investigate the interaction of compounds with high (compound 25) and low (compound 13) inhibitory activity. It was observed that the rings with nitrogen atoms interacted with the protein. The molecular binding results indicate that groups such as OMe and rings with Nitrogen can enhance the inhibitory activity of the compounds. Additionally, oxygen and nitrogen atoms contribute to an increased number of hydrogen bonds, thereby increasing the inhibitory activity of the compounds.Additionally, the stability and bonding modes of active and inactive compounds were studied using molecular dynamic simulation. Based on the results, four new inhibitors were designed, demonstrating better inhibition efficiency with the PIM1 kinase compared to the reference compounds. Moreover, the designed compounds underwent evaluation for ADMET, yielding promising results.

Synthesis and InhA Inhibition of Imidazo[1,2-a]pyridine Derivatives as Anti-Tuberculosis Agents

Abstract: Imidazopyridine holds significance as a crucial fused bicyclic heterocycle within the realm of medicinal chemistry, being acknowledged as a "privileged scaffold" owing to its extensive utility. Numerous methodologies for the synthesis of imidazo[1,2-a]pyridines have been documented, with a considerable focus on strategies aimed at functionalizing these compounds. This study aimed to explore the potential of novel imidazo[1,2- a] pyridine derivatives as agents against drug-resistant Mycobacterium tuberculosis, which poses significant challenges in tuberculosis (TB) treatment. The research involved the synthesis of substituted imidazo[1,2- a]pyridine derivatives using site identification and molecular docking techniques. Characterization of the synthesized compounds was carried out using FT-IR, LC-MS, 1H NMR, and 13C NMR analysis. Compounds 6a and 6k showed good anti-TB activity against the H37Rv strain of Mycobacterium tuberculosis, with MIC values of 0.6 μM and 0.9 μM, respectively, which were comparable with the standard drug isoniazid. These findings suggest that imidazo[1,2-a]pyridine derivatives, especially compounds 6a and 6k, have potential as agents against drug-resistant TB, providing valuable insights for ongoing efforts in developing effective TB treatments.

Molecular Mechanisms Underlying the Spectral Shift in Zebrafish Cone Opsins.

Visual pigments are essential for converting light into electrical signals during vision. Composed of an opsin protein and a retinal-based chromophore, pigments in vertebrate rods (Rh1) and cones (Rh2) have different spectral sensitivities, with distinct peak absorption wavelengths determined by the shape and composition of the chromophore binding pocket. Despite advances in understanding Rh1 pigments such as bovine rhodopsin, the molecular basis of spectral shifts in Rh2 cone opsins has been less studied, particularly the E122Q mutation, which accounts for about half of the observed spectral shift in these pigments. In this study, we employed molecular modeling and quantum mechanical techniques to investigate the molecular mechanisms behind the spectral difference in blue-shifted Rh2-1 (absorption peak = 467 nm, 122Q) and green-shifted Rh2-4 (absorption peak = 505 nm, 122E) zebrafish cone opsins. We modeled the pigments 3D structures based on their sequences and conducted all-atom molecular dynamics simulations totaling 2 microseconds. Distance analysis of the trajectories identified three key sites: E113, E181, and E122. The E122Q mutation, previously known, validates our findings, while E181 and E113 are newly identified contributors. Structural analysis revealed key features with differing values that explain the divergent spectral sensitivities of Rh2-1 and Rh2-4: 1) chromophore atom fluctuations and C5-C6 torsion angle, 2) binding pocket volume, 3) hydration patterns, and 4) E113-chromophore interaction stability. Quantum mechanics further confirms the critical role of residue E181 in Rh2-1 and E122 in Rh2-4 for their spectral behavior. Our study provides new insights into the molecular determinants of spectral shifts in cone opsins, and we anticipate that it will serve as a starting point for a broader understanding of the functional diversity of visual pigments.

Digital PCR threshold robustness analysis and optimization using dipcensR.

Digital polymerase chain reaction (dPCR) is a best-in-class molecular biology technique for the accurate and precise quantification of nucleic acids. The recent maturation of dPCR technology allows the quantification of up to thousands of targeted nucleic acids per instrument per day. A key step in the dPCR data analysis workflow is the classification of partitions into two classes based on their partition intensities: partitions either containing or lacking target nucleic acids of interest. Much effort has been invested in the design and tailoring of automated dPCR partition classification procedures, and such procedures will be increasingly important as the technology ventures into high-throughput applications. However, automated partition classification is not fail-safe, and evaluation of its accuracy ishighly advised. This accuracy evaluation is a manual endeavor and is becoming a bottleneck for high-throughput dPCR applications. Here, we introduce dipcensR, the first data-analysis procedure that automates the assessment of any linear partition classifier's partition classification accuracy, offering potentially substantial efficiency gains. dipcensR is based on a robustness evaluation of said partition classification and flags classifications with low robustness as needing review. Additionally, dipcensR's robustness analysis underpins (optional) automatic optimization of partition classification to achieve maximal robustness. A freely available R implementation supports dipcensR's use.

The use of PCR method for adulteration detection of goat dairy products manufactured by smallholders

The analysis of food adulteration is an important element of improving health safety. Both accidental and intentional adulteration of food, can cause serious health consequences for humans and can be considered as health hazard. In recent years, molecular biology techniques has been increasingly used in food analysis due to their high precision and the ability to obtain results in a short time, as well as the identification and quantitative determination of food adulterants. The samples tested in the study were goat's milk, yogurts, fresh and ripening cheeses produced by smallholders all over Poland. The analysis included DNA isolation, which was used as template for duplex PCR and detection of goat’s and cow’s mitochondrial DNA fragments. The obtained results indicate that the applied technique enabled the rapid identification of adulteration in analyzed goat’s milk products, among which in only one product out of thirty five the presence of undeclared cow’s milk was detected. This indicates good food safety standards applied on small-scale farms.

Investigating the active components and mechanistic effects of Forsythia suspensa Leaf against RSV via the PI3K/Akt-NLRP3 pathway

BackgroundPulmonary infections resulting from respiratory syncytial virus (RSV) continue to pose a significant threat to the well-being of infants and the elderly, but there is no safe, effective and specific treatment except symptomatic treatment. Forsythia Suspensa Leaf (FSL) is cold in nature and bitter in taste, and has the efficacy of clearing away heat and toxic materials. Previous research by our research group showed that the active components in FSL have the pharmacological effect of anti-RSV. Based on that, this study aims further to clarify the anti-RSV active components and mechanism of FSL. MethodsFirstly, we established the BALB/c mouse model of RSV infection, assessed the in vivo anti-RSV efficacy, and determined the optimal dosage of FSL and its active components. Evaluation parameters included body weight changes, organ indices, lung tissue pathological sections, lung tissue viral load, and inflammatory factors. Additionally, we used RT-PCR, Western Blot and other molecular biology techniques to determine the expression changes of key factors such as Nrf2 and NLRP3 in PI3K/Akt-NLRP3 pathway, and revealed the anti-RSV mechanism of FSL and its active components. ResultsPharmacodynamic experiments in animals showed that the FSL Low (0.4 g/kg·d), RosA Low (100 mg/kg·d) and Phillyrin Medium (100 mg/kg·d) groups could effectively improve the pathological conditions of mice with RSV pneumonia, such as weight loss, the level of pulmonary inflammatory factors and the increase of viral load. In addition, oral administration of Phillyrin at a dose of 100 mg/kg d to RSV-infected mice can effectively control the trend that the expression of Nrf2 protein decreases and the expression of NLRP3 protein increases in RSV pneumonia mice. ConclusionPhillyrin, the active component in FSL, can not only directly inhibit the replication of RSV, but also effectively control the inflammatory reaction caused by RSV infection and improve lung injury, which is expected to become a potential drug against RSV pneumonia.