Sequencing Research Articles

Reassessing the Diversity of the Arthropod-Pathogenic Genus Pandora Batko (Entomophthoromycotina; Erynioideae)

The fungal order Entomophthorales occurs worldwide, with most species infecting arthropods as pathogens. Species in this order can cause epizootics and change the behavior of infected hosts. Molecular data are available only for 20% of the known species, and distributions of species are seldom summarized. Significant diversity of hosts, poor molecular data availability, and poor resolution of the phylogenetic relationships within this fungal order suggest that the diversity of these fungi is not sufficiently described. The subfamily Erynioideae includes 111 arthropod pathogens, divided among six genera, with the genus Pandora being one of the most diverse genera. Sequences of 18S, 28S, and ITS for two species are used to place these Pandora species in a phylogenic tree of the subfamily; this tree also supports our synonymy of the genus Furia with Pandora. Among the two species specifically covered in this paper, Pandora gloeospora was observed during epizootics occurring in mushroom flies (Diptera: Sciaridae) on Agaricus bisporus cultures in Pennsylvania, Delaware, and Maryland (US) mushroom farms and also in Florida on Pleurotus sp. Outside the US, P. gloeospora was found infecting several Nematocera (Diptera) in Europe (France) and Asia (China). Pandora sylvestris n. sp. was collected during epizootics occurring in larvae of hickory tussock moths, Lophocampa caryae (Lepidoptera: Erebidae), in hardwood forests in Michigan and Vermont.

Phylogenomic insights into the worldwide evolutionary relationships of the stingless bees (Apidae, Meliponini)

Stingless bees (tribe Meliponini) are remarkable for their characteristically large social colonies, their capacity to produce honey and other useful products, and their morphological and behavioral diversity. They have a disjunct pan-tropical distribution, primarily occurring in warm and humid environments in the Neotropical, Afrotropical, and Indo-Australasian regions. Even though phylogenetic hypotheses have been proposed for Meliponini based on morphology and molecular data, many questions are still unsolved regarding the evolutionary relationships and systematics of the tribe. In this contribution, we present a large phylogenomic dataset comprising over 2,500 ultra-conserved element (UCE) loci sequenced for 153 species of Meliponini, representing all known genera of stingless bees. The genera Camargoia, Paratrigonoides, Plectoplebeia, Cleptotrigona, Ebaiotrigona, Papuatrigona, Pariotrigona, Platytrigona, and Sahulotrigona were included in molecular phylogenetic analyses for the first time. Concatenated and species-tree analyses were performed using different partitioning strategies and summary methods. We performed gene-genealogy interrogation (GGI) on several recalcitrant nodes to resolve discordances among recovered tree topologies. Results were mostly consistent among analyses, recovering three main lineages of Meliponini congruent with the biogeographic domains to which they are associated. Within major clades, discordances were found in relation to previous works. The genus Frieseomelitta was recovered as paraphyletic in relation to Trichotrigona, and the genus Lepidotrigona was revealed to be composed of two independent lineages. Even though concatenated and weighted ASTRAL analyses were mostly effective in recovering the relationships favored by GGI, they retrieved different results in relation to the phylogenetic placements of Oxytrigona and Cephalotrigona. The most favored hypothesis in GGI analyses was not found in any other analyses, being more congruent with morphological evidence and highlighting the relevance of exploring the support given to alternative hypotheses through topological tests. Recent advances in our capacity to generate molecular sequences from old specimens using modern sequencing methods allowed for unparalleled sampling across genera, yielding a backbone for the phylogenetic relationships of stingless bees, which will further investigations into their systematics and evolution.

Prevalence and identification of cyathocotylid trematodes infecting African catfish in Egypt.

The trematode family Cyathocotylidae infects various hosts worldwide, including birds, mammals, reptiles, and fish. However, the lack of molecular data from adult worms hinders phylogenetic, epidemiological, and host association studies. This study aims to identify the common cyathocotylid trematodes infecting African catfish in Egypt using morphological and molecular evidence. Out of 142Clarias gariepinus, 123 fish (86.6%) harbored cyathocotylid metacercariae, with a mean metacercarial intensity of 201 ± 38.5/g. Cyathocotylid metacercariae prevalence gradually rose as host size increased. Although there was no significant difference between groups, larger fish had a higher mean metacercarial intensity. The prevalence and intensity were unrelated to the fish gender. Histopathological examination of metacercariae-infected catfish revealed varying degrees of degenerative changes, including intermuscular edema leading to muscle fiber dispersion and atrophy, involving 11% to over 81% of muscle sections. We identified three cyathocotylid metacercariae and eight cyathocotylid adult species from experimental infection using morphometric and molecular data, including internal transcribed spacer (ITS) and/or mitochondrial cytochrome c oxidase subunit 1 (cox1) sequences. We determined the phylogenetic position of these cyathocotylid samples.The ITS sequence analysis linked the isolated Cyathocotylidae sp. 1 and 2 metacercariae to Prohemistomum vivax adults. Mesostephanus appendiculatoides and Paracoenogonimus ovatus were reported for the first time in Egypt. These findings may provide valuable genetic data for future molecular epidemiological and phylogenetic studies of cyathocotylid trematodes.

Phylogeny and biogeography support ancient vicariance and subsequent dispersal out of Africa in Palpimanidae spiders (Araneae)

Abstract The Palpimanidae are one of five extant Palpimanoidea families that occur mainly in South America and Africa, although there are lineages in Madagascar, islands of the Indian Ocean, and parts of Asia. Here we examine the role of plate tectonics in shaping the distribution of Palpimanidae. We perform molecular sequencing via target enrichment, which makes use of fragmented DNA, because most specimens are stored in natural history museum collections and were not properly preserved for molecular sequencing. We perform phylogenetic analysis, divergence dating, and ancestral range reconstructions to assess whether continental vicariance shaped the evolution of Palpimanidae. We also examine evolution of eye loss via ancestral character reconstruction. We report the first Palpimanidae phylogeny based on genomic data that samples the majority of Chediminae genera. Results suggest that Palpimanidae originated in the Triassic, with diversification spanning the Jurassic to the Cretaceous. Vicarance played a role in early diversification, with later range expansion out of Africa. Based on morphology and phylogenetic analysis, Sceliraptor is synonymized with Sarascelis, Sceliscelis is synonymized with Scelidocteus, and the new genus and species Sitamacho tao gen. nov., sp. nov. is described, with three species transferred from Hybosida.

Accelerating DNA Sequence Alignment using Altera DE2-115

DNA sequence alignment is a technique for discovering information between two base sequences which the Smith-Waterman algorithm is the accurate method that provides a precise result for alignment compared to others. However, the performance was influence by size of dataset and a long DNA base sequence which resulted the time required for the alignment process is much longer in relation to the number of DNA sequence samples. There are many ways to accelerate DNA sequence alignment, and Field Programmable Gate Array (FPGA) is a good choice due to its parallel processing and cost efficiency. Although FPGA acceleration approaches are not new, this work investigates a purely software-based FPGA acceleration using the Altera Cyclone IV EP4CE115F29C7N FPGA as the target device. The SW algorithm was developed using the C language in Quartus II version 18.1 and the Nios II software build tools for Eclipse. The development starts with setting up the Qsys architecture before developing the code in Eclipse to determine the computational performance. The result shows the computational timing and speed of the implementation, with the highest speed achieved being 198.76 cells per millisecond. To summarise, the computational performance ultimately depends on the maximum matrix size of the FPGA, which is also influenced by the DNA-based pair length and able to complete using low-cost FPGA.

The Characteristics of Microsatellites and Development of SSR Markers in the Genome of Periplaneta americana

The research was to analyze the number and pattern of microsatellites in Periplaneta americana’s genome, and also developed tetranucleotide SSR markers. We thoroughly scrutinized and dissected the inherent traits that govern the allocation of microsatellite sequences within the profound domain of P. americana’s genome, software MSDBv2 allowed for the utilization of 2.67 Gb. There were precisely 1,498,458 flawless microsatellite sequences, encompassed approximately 1.57%. The cumulative length of microsatellites was 45,076,707 bp, and the abundance of microsatellites was 16889.577 loci/Mb. Out of all the microsatellite repeat variations, the trinucleotide repeats accounted for 44.83% of the total, with a count of 671,830, which were the most abundant type. The tetranucleotide, mononucleotide, pentanucleotide, dinucleotide, and hexanucleotide repeats accounted for 29.01%, 13.62%, 8.37%, 3.70% and 0.47%, respectively. The numbers of different repeat copy categories in each repeat type were also quite different, such as the A in mononucleotide repeat type, the AT in dinucleotides, the AAT in trinucleotides, and AAAT in tetranucleotide were the most of each categories. 143 primers were designed. After undertaking the arduous task of enhancing the initial PCR conditions to perfection, we successfully determined and analyzed a gargantuan number of 38 different polymorphic tetranucleotide microsatellite markers with utmost precision, employed the assistance of two-color fluorescence markers and ingenious genotyping scaned for their comprehensive characterization. The genetic variation in P. americana population involved analyzing the diversity of microsatellite loci, which exhibited varying numbers of alleles per locus ranging from 4 to 21 among the 32 individuals studied. Among them, there were 24 microsatellite loci whose alleles were greater than 10, accounted for 63.16% of the total number of polymorphic microsatellite. The calculated degrees of genetic diversity varied between 0 and 1, the observed heterozygosities was between 0.219 and 1.0, with a mean of 0.6391. The expected heterozygosities was between 0.312 and 0.942, with a mean of 0.7663. The PIC was between 0.296 and 0.923, with a mean of 0.7294, and there were 36 microsatellite loci whose PIC was greater than 0.5, accounted for 94.74%. This study indicated that new development of microsatellite markers for P. americana was feasible. Furthermore, these new development microsatellite markers will provide adequate and reliable molecular genetics data for carrying out the research of molecular ecology and conservation genetics for P. americana.

Research on the Regulatory Mechanism of Ginseng on the Tumor Microenvironment of Colorectal Cancer based on Network Pharmacology and Bioinformatics Validation.

A network pharmacology study on the biological action of ginseng in the treatment of colorectal cancer (CRC) by regulating the tumor microenvironment (TME). To investigate the potential mechanism of action of ginseng in the treatment of CRC by regulating TME. This research employed network pharmacology, molecular docking techniques, and bioinformatics validation. Firstly, the active ingredients and the corresponding targets of ginseng were retrieved using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), the Traditional Chinese Medicine Integrated Database (TCMID), and the Traditional Chinese Medicine Database@Taiwan (TCM Database@Taiwan). Secondly, the targets related to CRC were retrieved using Genecards, Therapeutic Target Database (TTD), and Online Mendelian Inheritance in Man (OMIM). Tertiary, the targets related to TME were derived from screening the GeneCards and National Center for Biotechnology Information (NCBI)-Gene. Then the common targets of ginseng, CRC, and TME were obtained by Venn diagram. Afterward, the Protein-protein interaction (PPI) network was constructed in the STRING 11.5 database, intersecting targets identified by PPI analysis were introduced into Cytoscape 3.8.2 software cytoHubba plugin, and the final determination of core targets was based on degree value. The OmicShare Tools platform was used to analyze the Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the core targets. Autodock and PyMOL were used for molecular docking verification and visual data analysis of docking results. Finally, we verified the core targets by Gene Expression Profiling Interactive Analysis (GEPIA) and Human Protein Atlas (HPA) databases in bioinformatics. A total of 22 active ingredients and 202 targets were identified to be closely related to the TME of CRC. PPI network mapping identified SRC, STAT3, PIK3R1, HSP90AA1, and AKT1 as possible core targets. Go enrichment analysis showed that it was mainly involved in T cell co-stimulation, lymphocyte co-stimulation, growth hormone response, protein input, and other biological processes; KEGG pathway analysis found 123 related signal pathways, including EGFR tyrosine kinase inhibitor resistance, chemokine signaling pathway, VEGF signaling pathway, ErbB signaling pathway, PD-L1 expression and PD-1 checkpoint pathway in cancer, etc. The molecular docking results showed that the main chemical components of ginseng have a stable binding activity to the core targets. The results of the GEPIA database showed that the mRNA levels of PIK3R1 were significantly lowly expressed and HSP90AA1 was significantly highly expressed in CRC tissues. Analysis of the relationship between core target mRNA levels and the pathological stage of CRC showed that the levels of SRC changed significantly with the pathological stage. The HPA database results showed that the expression levels of SRC were increased in CRC tissues, while the expression of STAT3, PIK3R1, HSP90AA1, and AKT1 were decreased in CRC tissues. Ginseng may act on SRC, STAT3, PIK3R1, HSP90AA1, and AKT1 to regulate T cell costimulation, lymphocyte costimulation, growth hormone response, protein input as a molecular mechanism regulating TME for CRC. It reflects the multi-target and multi-pathway role of ginseng in modulating TME for CRC, which provides new ideas to further reveal its pharmacological basis, mechanism of action and new drug design and development.

Globally Distributed Arbuscular Mycorrhizal Fungi Associated With Invasive Cinchona pubescens on Santa Cruz Island, Galápagos.

The presence of arbuscular mycorrhizal fungi (AMF) is essential for the survival and establishment of most plant species in nature. The reproductive success of invasive plant species in a particular habitat could also depend on these AM fungi. Cinchona pubescens, commonly known as quinine, is highly invasive on Santa Cruz Island, Galápagos, but at the same time severely endangered in its native range on mainland Ecuador due to overexploitation in the past. In this study, we aim at determining the AMF communities associated with C. pubescens at both locations to investigate whether the successful invasion of C. pubescens on Santa Cruz is related to its association with a particular community of AMF. For this, roots of C. pubescens trees were sampled at three sites, one site on Santa Cruz and two sites in the province of Loja, on mainland Ecuador. Communities of AM fungi were determined through the molecular cloning and sequencing of the 18S nrDNA gene and through the delimitation of Operational Taxonomic Units (OTUs), associated with the plant roots. We found 36 AMF OTUs associated with C. pubescens, most of them belonging to the genus Glomus. The highest richness of AMF OTUs was detected in samples from sites located on mainland Ecuador. The AMF communities between Santa Cruz and mainland Ecuador were significantly different, and only five OTUs were shared between both locations. Two dominant OTUs in C. pubescens from Santa Cruz were detected but no dominant OTUs from mainland Ecuador. Almost two thirds of the OTUs associated with C. pubescens had a wide global distribution. Our results suggest that the successful invasion of C. pubescens on Santa Cruz could have been facilitated by local generalist AMF and not by particular AMF. The observed generalist AMF from both locations could be important for conservation plans of restoring the endangered C. pubescens in the native forests on mainland Ecuador.

Cepharanthine sensitizes gastric cancer cells to chemotherapy by targeting TRIB3-FOXO3-FOXM1 axis to inhibit autophagy

BackgroundGastric cancer is among the common solid tumors. Chemotherapy resistance is the most common issue in gastric cancer treatment. Inhibiting intracellular autophagy may be a feasible method for overcoming chemotherapy resistance. Cepharanthine (CEP), a natural small molecule extracted from the stephania cephalantha Hayata plant, has been demonstrated to significantly inhibit cancer growth and can regulate autophagy. Although CEP can significantly inhibit cancer growth, it remains unclear whether CEP can regulate autophagy in gastric cancer. This study aimed to investigate whether CEP can enhance the sensitivity of gastric cancer to chemotherapy and elucidate its molecular mechanism. MethodsThree gastric cancer cell lines (AGS, SGC7901, and MFC) and one normal gastric mucosal epithelial cell line (GES-1) were used for in vitro experiments. The characterization of autophagy in gastric cancer cells included the detection of autophagy markers and autophagy flux through immunofluorescence staining and Western blotting, as well as the assessment of lysosomal function using fluorescence staining (LysoTracker Red DND-99, Acridine Orange staining) and Western blotting. The cytotoxicity of CEP, autophagy inhibitors (chloroquine [CQ] and 3-methyladenine [3MA]), and chemotherapy drugs (doxorubicin [DOX] and cisplatin [CIS]) was evaluated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, cell colony formation, and fluorescence staining techniques (H2DCFDA, Dihydroethidium, and JC-1 staining). The interaction between CEP and autophagy inhibitors was tested in a 615 mice model, and changes in the gut microbiota were determined through accurate 16S absolute quantification sequencing. The signaling pathway and autophagy regulatory target TRIB3-FOXO3-FOXM1 were confirmed through molecular docking, RNA sequencing, bioinformatic analysis, transfection techniques, and Western blotting. ResultsCEP blocked autophagic flux in gastric cancer cells without affecting lysosomal function. As a novel autophagy inhibitor, CEP could combine with conventional autophagy inhibitors (CQ and 3MA) to block intracellular autophagy, thereby inhibiting gastric cancer growth. During this process, changes in the gut microbiota were observed, including low-level changes in Odoribacterium, Erysipelatoclostridium, and ParaPrevotella and high-level changes in Ileibacterium, Enterorhabdus, and Bifidobacterium. Additionally, CEP synergistically inhibited the growth of gastric cancer when combined with chemotherapy drugs. Mechanistically, the TRIB3-FOXO3-FOXM1 signaling axis was found to be involved in the inhibition of gastric cancer by CEP combined with autophagy inhibitors and chemotherapy drugs, thereby mediating cell apoptosis. ConclusionThis study links the TRIB3-FOXO3-FOXM1 axis with chemotherapy efficacy. Our findings demonstrated that CEP inhibits autophagy by modulating the FOXO3-FOXM1 axis. When combined with chemotherapy drugs (DOX and CIS), CEP, as an autophagy inhibitor, can limit TRIB3 protein expression, thereby regulating the FOXO3-FOXM1 axis and enhancing its ability to prevent gastric cancer growth. These findings may contribute to improving the prognosis of patients with gastric cancer. Furthermore, these results enrich the fundamental understanding of how autophagy inhibition can enhance clinical cancer treatment efficacy and provide insights into the potential mechanisms by which CEP functions as an anti-tumor drug, thereby exploring its value for clinical application.

Beta-Thalassemia Haplotypes in Southwest of Iran

Background: Thalassemia is a widespread disease affecting people across various ethnicities and regions. In comparison to previous studies conducted in different regions of Iran, such as those in Lorestan and Sistan-Baluchestan, this study highlights unique mutation patterns prevalent in the southwestern population, emphasizing the genetic heterogeneity in this region. The identification of common mutations of beta-thalassemia in various ethnic groups within the nation is regarded as a practical solution for thalassemia prevention and prenatal diagnosis. Materials and Methods: In this retrospective observational study, the medical records of 545 patients with various types of beta-thalassemia (silent, minor, intermediate, and major), referred to the center at Baqaei 2 hospital over a 14-year period (2008–2022), were examined. The age range of patients spanned from a 2-month-old fetus to a 34-year-old individual. Their mutations and thalassemia types were determined and confirmed using molecular methods, including PCR-ARMS (polymerase chain reaction-amplification refractory mutation system) and sequencing. The results were analyzed using SPSS software. Results: The study examined 545 patients and identified 81 types of mutations. The most frequent mutations observed were CD36-37(-T)/N, IVSII-1/N, and IVS1-110(G>A). The study also noted population heterogeneity, reflected in the wide range of mutations found in the region. Among the patients, 6 had the silent form of beta-thalassemia, 488 had the minor form (464 patients and 24 fetuses), 9 had the intermediate form (8 patients and 1 fetus), and 42 had the major form (26 fetuses and 16 adults). Conclusion: The identification of prevalent beta-thalassemia mutations facilitates disease control and prevention programs and is crucial for the identification of various beta-thalassemia gene mutations. This should be re-evaluated periodically. Observing a wide range of beta-thalassemia genotypes in the southwestern region of Iran suggests gene flow; thus, identifying these genotypes is instrumental in preventing and controlling the disease.

Selective degradation of organic pollutants in the aquatic environment by microplastic-derived dissolved organic matter through molecular photoresponse sequence transformation

The photochemical behavior of microplastics (MPs)-dissolved organic matter (PDOM) has received considerable attention, the molecular mechanism by which it undergoes photoresponsive transformation to generate reactive oxygen species (ROS) for the removal of organic pollutants remains unclear. This study combines fluorescence, mass spectrometry, and theoretical models to analyse the differences in the molecular mechanisms of PDOM, biochar-DOM (BDOM) and soil-DOM (SDOM) photoresponsive releasing ROS for selective degradation of organic pollutants. During the photoresponse process, molecular compounds in DOMs mainly undergo demethylation, decarboxylation, deoxygenation reactions to selectively degrade organic pollutants. However, differences in DOMs’ molecular structure composition and transformation patterns lead to varying ROS production. BDOMs containing higher proportion of aromatic compounds (26.68 %) exhibit stronger photoreactivity, resulting in better degradation efficiency of pollutants (>90 %). The high selectivity of PDOM for degradation of organic pollutants stems from the interconversion mode between its high and low oxygen compounds. PDOM degrades large molecular pollutants into less biotoxic small molecular intermediates through both radical and non-radical pathways, thereby reducing environmental hazards (1.5–948 times) posed by pollutants. The results show that although MPs is harmful to aquatic environment, it plays a positive role in regulating the structure of organic carbon pool and reducing environmental risks of other pollutants.

Characterization of the Complete Mitochondrial Genome of Pleurogenoides japonicus (Digenea, Pleurogenidae): Comparison With the Members of Microphalloidea and Phylogenetic Implications.

Pleurogenoides japonicus (Trematoda: Microphalloidea) is an important parasite in wood frogs with high infection rates and significant ecological, economic, and societal importance. The scarcity of molecular data for these parasites severely limits population genetics and phylogenetic studies. In the present study, for the first time, we determined and described the entire mitochondrial (mt) genome of P. japonicus as the first representative of the family Pleurogenidae. The entire mt genome of P. japonicus was circular, with 15,043 bp (GenBank accession number OR900118), containing 36 genes, comprising 12 protein-coding genes (cox1-3, nad1-6, nad4L, cytb, and atp6), two ribosomal RNA genes, 22 transfer RNA genes, and two non-coding regions. There were 23 intergenic spacers, ranging from 2 to 162 bp, and only one 40 bp overlap between nad4L and nad4 genes in the P. japonicus mt genome. The nucleotide composition of P. japonicus mt genome exhibited a strong AT bias with a 63.75% A + T content, while the AT- and GC-skews were - 0.435 and 0.407, respectively. Comparative analysis demonstrated that the P. japonicus mt genome shared the most common characteristics with Microphalloidea trematodes, and the cox1 gene was the longest and most conserved gene in Microphalloidea trematodes. The gene arrangements of Xiphidiata trematodes were of the same order based on protein-coding genes and rRNA genes, except for tRNA. More than two gene arrangement types exist in Echinostomata and Xiphidiata, and the gene rearrangement events mainly occurred in "trnE-trnG" and "trnG-trnE". Phylogenetic analysis suggested that trematodes of the family Pleurogenidae clustered more with Prosthogonimidae than Eucotylidae. The mt genome data of P. japonicus provide an accurate genetic marker for further studies of Xiphidiata trematodes.

A snow-dwelling tropical butterfly? An unprecedented discovery of a new genus of the Pedaliodes clade in an extreme, high-altitude Andean environment (Lepidoptera: Nymphalidae: Satyrinae)

Abstract A new genus of satyrine butterflies, Nivaliodes gen. nov., is described for three species, all new: Nivaliodes negrobueno sp. nov., Nivaliodes viracocha sp. nov., and Nivaliodes puriq sp. nov. (Lepidoptera: Nymphalidae), with the support of molecular data and adult morphology. A target enrichment-based phylogeny indicates that Nivaliodes gen. nov. is sister to the genus Pherepedaliodes within an extremely diverse Pedaliodes clade of the predominantly Andean subtribe Pronophilina. Although an overwhelming majority of species of this group occur in tropical montane forests, N. negrobueno sp. nov. was discovered in a central Peruvian desert puna at some 4600–4800 m a.s.l., the highest elevation reported for any species of the Pronophilina. Individuals were observed overflying rocky slopes and resting directly on snow-covered surfaces, which is an exceptionally unusual behaviour among butterflies. The other two species of the new genus were found at lower elevations, some 3300–4200 m a.s.l., at the timberline and in puna grassland.

Data Harmonization, Standardization, and Collaboration for Diabetic Retinal Disease (DRD) Research: Report From the 2024 Mary Tyler Moore Vision Initiative Workshop on Data.

The 2024 Mary Tyler Moore Vision Initiative (MTM Vision) Workshop on Data convened to discuss best practices and specific considerations for building a comprehensive, shareable MTM Vision data lake. The workshop aimed to accelerate the development of new indications, therapies, and regulatory pathways for diabetic retinal disease (DRD) by standardizing and harmonizing clinical data and ocular 'omics analyses. Standardization of data collection, the use of common data elements, and data interoperability were emphasized, alongside federated learning approaches to promote data sharing and collaboration while maintaining data privacy and security. The integration of molecular data with other multimodal data types was recognized as a promising strategy for leveraging machine learning and AI approaches to advancing therapeutics development and improving treatment outcomes for DRD patients. Partnerships with entities such as the National Eye Institute, part of the National Institutes of Health, foundations, and industry were deemed vital for the successful implementation of these initiatives.

Lignans of Schisandra chinensis (Turcz.) Baill inhibits Parkinson's disease progression through mediated neuroinflammation-TRPV1 expression in microglia

BackgroundSchisandra chinensis (Turcz.) Baill (S. chinensis), a member of the Magnoliaceae family, is renowned for its distinctive medicinal attributes and is commonly employed in the treatment of disorders affecting the CNS. PurposeThe potential therapeutic effects of a lignan-enriched extract derived from Schisandra chinensis (Turcz.) Baill (LSC) on PD is assessed, which focuses on its mechanisms of action in addressing neuroinflammation. MethodsThe LSC has been obtained by purifying the ethyl alcohol extract of S. chinensis. The Orbitrap-MS method has been employed to analyze the chemical composition of the LSC. In LPS-induced BV2 cells, LSC-induced changes in M1/M2 type inflammatory cytokines have been examined using the Griess reaction, Elisa, JC-1, flow cytometry, IF, and WB methods. A model of PD has been established by treatment of MPTP in C57BL/6 mice. The effect of LSC on behavioral changes, inflammatory factor levels, expression of TH and IBA-1, and production of autophagy in the midbrain has been investigated by TEM, immunohistochemistry, Elisa, and WB. ResultsLSC has relieved sports injuries and pathological damage, and targeted the TRPV1-AMPK-NLRP3 signaling pathway, which affected neuroinflammation and autophagy in vivo. Furthermore, in vitro investigations demonstrated that LSC has activated M1/M2 transformation, its related inflammatory factors, and protein expressions of the NLRP3-Caspase1 signaling pathway in LPS-BV2 cells. The research notably demonstrated that the LSC promoted autophagy and suppressed inflammation through targeting TRPV1. ConclusionIn the investigation, LSC focused on TRPV1 and controlled neuroinflammation-autophagy by regulating AMPK-NLRP3, which has been proven for the first time. The study has presented molecular data supporting the use of LSC in treating PD and offers references for developing drugs. Remarkably, LSC has the potential to be utilized as a therapeutic or health medication that could significantly decrease PD.

Non-receipt of targeted and immunotherapies in diverse patients with metastatic cancers.

93 Background: The rapid evolution of molecularly targeted kinase inhibitors (TKIs) and immune checkpoint inhibitors (ICIs) in the treatment of metastatic cancer, coupled with high drug costs, raises potential for unwarranted variation in patient management. We evaluated correlates of non-receipt of TKIs and ICIs in a diverse, population-based sample of patients with metastatic non-small cell lung cancer (NSCLC), kidney and bladder (GU) cancer, and melanoma. Methods: We identified 2240 patients diagnosed in 2019 with metastatic NSCLC, GU cancer, or melanoma and reported to the Georgia or Los Angeles SEER registries. Using SEER registry data, we linked all patients to a managing oncology physician. We collected data from the managing physician regarding receipt of TKIs and ICIs. We used bivariate analyses and multivariable logistic regression models to assess associations between non-receipt of TKIs and ICIs and patient-level factors. Results: We present results for a preliminary sample (N=894). About half (55%) of the patients had NSCLC, 31% had GU cancer, and 14% had melanoma. The mean age was 62 (SD 12); 59% were male; 65% were White, 16% were Black, 11% were Hispanic, and 7% were Asian; 52% had Medicare, 29% had private insurance, 9% had Medicaid, and 4% had no insurance; 89% resided in urban areas, 11% resided in rural areas. 22% lived in a census tract area with >20% of the population living below the poverty level. The Table shows that in bivariate analyses, non-receipt of TKIs was associated with NSCLC, older age, male sex, non-white race, and non-private or no insurance (all p<0.05). After adjustment, non-receipt of TKIs was associated with NSCLC, older age, male sex, and race. Asian and Hispanic patients had lower rates of non-receipt, and Black patients had higher rates. In bivariate analyses, non-receipt of ICIs was associated with NSCLC and GU cancer (p=0.004); this association remained significant after adjustment. Conclusions: Non-receipt of TKIs was associated with important non-clinical factors including race and sex. Non-receipt of ICIs was associated only with cancer type. These findings suggest that policy-relevant factors such as out-of-pocket costs for oral cancer therapies and differential access to molecular sequencing may contribute to unwarranted variation in receipt of TKIs. Bivariate analyses of non-receipt. Did not Receive TKI Did not Receive ICI % P % P Cancer type NSCLC GU Melanoma 786572 0.002 313015 0.004 Age <50 50-64 65-74 75-84 85+ 5471757986 <0.001 2625302940 0.385 Sex Male Female 7670 0.048 2631 0.085 Race & Ethnicity White Black Hispanic Asian Other 7579655860 0.002 2329312927 0.981 Marital Status Married Unmarried 7373 0.645 2630 0.158 Insurance Medicare Medicaid Private Other government None 7075637080 <0.001 3130215031 0.101 Geography Urban Rural 7375 0.784 2826 0.567 % population below poverty level 0-5% 5-<10% 10-<20% 20-100% 69717774 0.314 29273222 0.138

A new species of planthopper in the genus Eumyndus (Hemiptera: Cixiidae) from palms in eastern Madagascar and molecular evidence for the synonymy of Eumyndus kraussi and Eumyndus metcalfi

A new species of Eumyndus Synave, 1956, a genus endemic to Madagascar, is here described as Eumyndus jeanjacquei sp. nov. The new species was collected from the palm Vonitra fibrosa (C.H.Wright) Becc., 1911. Molecular data are provided for the new species from the barcoding region (5’ half) of the cytochrome c oxidase subunit I (COI) gene, 18S rRNA gene and D9-D10 expansion region of the 28S rRNA gene and support placement of the new species in Eumyndus. A new synonymy is proposed based on examination of type material: E. metcalfi Synave, 1956 equals E. kraussi Synave, 1956, new synonym.

La anatomía de la raíz como evidencia filogenética para los helechos Cheilanthoides (Pteridaceae)

Background and aims: To our hypothesis on the evolutionary relationships of Cheilanthoid ferns, based on molecular data and partially on morphological and reproductive data, we add here a study of root anatomy in the genera of the subfamily occurring in South America. M&M: Root characters were analyzed anatomically in 48 South American species representing the 12 genera of Cheilanthoideae occurring in South America. Techniques of plant histology were used for anatomical analysis and tissue characterization. Characters with possible diagnostic value were identified and mapped on a molecular phylogeny of Cheilanthoideae based on three plastidial markers (rbcL, trnL-F and rps4). Results: The character "type of root cortex" showed a distribution of states that fit to the major clades or genera in the phylogeny of the subfamily. The homogeneous cortex state was plesiomorphic for Cheilanthoideae, whereas the heterogeneous bark state was acquired by some genera of the hemionitoid clade: Hemionitis and the genera of the Adiantopsis-Doryopteris clade (except Mineirella). In addition, we discuss the role of different tissues in the root mechanics of this group. Conclusions: The character "type of root cortex" could contribute to the characterization of genera and the generic assignment of confusing species in the classification of Cheilanthoideae. However, the complete resolution of the relationship of hemionitds clade in the global phylogeny of the subfamily is necessary.

Present Understanding of Biodiversity of Anoxygenic Phototrophic Bacteria in the Relic Lake Mogilnoe (Kildin Island, Murmansk oblast, Russia)

The relic Lake Mogilnoe, separated from the Barents Sea by a sand and pebble dam, is located in the high Arctic on the Kildin island (Murmansk region). This lake is a classic example of a meromictic basin of marine origin. The data obtained during the 2018 expedition showed changes in the hydrochemical regime of the lake that have occurred over the past 20 years. Sulfide concentration in the monimolimnion of the lake was as high as 140 mg/L. A tendency for salinization of the surface waters to 7 g/L has been noted. The Lake Mogilnoe is characterized by a discrepancy between the halocline and thermocline levels. The chemocline zone in the lake is below the halocline level. In a narrow oxygen-containing layer between 3 and 7.5 m, aerobic microflora of the marine type and marine fauna were present. The bacterial plate was formed at the boundary of the sulfide layer at ~8 m and mainly consisted of green sulfur bacteria (GSB). Brown-colored GSB species containing bacteriochlorophyll e were predominant. The previously formed concept of anaerobic phototrophic bacteria (APB) biodiversity based on morphological characteristics was modified using metagenomic data obtained by analyzing DNA from two samples of lake water in the chemocline zone, and was also supplemented by identifying new GSB species. Molecular diagnostic data confirmed the absolute dominance of the brackish species of GSB Chlorobium phaeovibrioides. This is the first on isolation and identification of brown- and green-colored Prosthecochloris aestuarii morphotypes from Lake Mogilnoe and identified, as well as of bacteriochlorophyll c-containing Prosthecochloris sp. The taxonomic position of Pelodyction phaem, which was constantly present in the Lake Mogilnoe, is discussed in detail. Despite the partial isolation of the ecosystem of Lake Mogilnoe from the Barents Sea, the main properties of the dominant GSB species of GSB and Prosthecochloris aestuarii turned out to be similar to those of the phylotypes living in lakes on the White Sea coast of the, which remained connected with the Barents Sea.

Higher Order Structure Differences Among Insulin Crystalline Drugs Revealed by 2D heteronuclear NMR.

During therapeutic protein development, two-dimensional (2D) heteronuclear NMR spectra can be a powerful analytical method for measuring protein higher order structure (HOS) in solution since the spectra exhibit much higher resolution than homonuclear 1H spectra. However, 2D NMR capabilities for characterizing protein HOS in crystalline states remain to be assessed, given the low 13C natural abundance and intrinsically broader lines in solid-state NMR (SSNMR). Herein, high-resolution heteronuclear correlation (HETCOR) SSNMR was utilized to directly measure intact crystal drug products of insulin human, insulin analogs of insulin lispro and insulin aspart. The fingerprint regions in 2D 1H-13C HETCOR spectra were identified, which distinguished the insulin crystals in their primary structure, HOS heterogeneity and dynamics, as well as the manufacturing processes. The HOS heterogeneity in insulin analogs is consistent with their therapeutic effect of rapid action; while insulin human crystals showed more structural homogeneity, consistent with their slower pharmacokinetics (PK)peak time than insulin analogs. Therefore, heteronuclear NMR could be broadly applicable to study protein drug dosage forms from liquid to solid, yielding improved molecular level structure data for assessing drug HOS in biosimilar drug development.