Exploring the Molecular Tapestry: Organ-Specific Peptide and Protein Ultrafiltrates and Their Role in Therapeutics.

This study aims to characterize the proteome composition of organ-derived protein extracts from rabbits. Protein isolation was performed using soft homogenization and size exclusion via ultrafiltration. The proteome analysis of the ultrafiltrates was conducted using gel electrophoresis, and the mass spectrometry data were subjected to gene ontology analysis. Proteomic profiling revealed comprehensive protein profiles associated with RNA regulation, fatty acid binding, inflammatory response, oxidative stress, and metabolism. Additionally, our results demonstrate the presence of abundant small proteins, as observed in the mass spectrometry datasets. Small proteins and peptides are crucial in transcription modulation and various biological processes. The protein networks identified in the ultrafiltrates have the potential to enhance and complement biological therapeutic interventions. Data are available via ProteomeXchange with identifier PXD050039.

Heavy metal concentration according to shrimp species and organ specificity: Monitoring and human risk assessment.

This study assessed heavy metal levels (lead (Pb), cadmium (Cd), total arsenic (tAs), arsenite (As (III)), arsenate (As (V)), monomethyl arsenic acid (MMA), dimethylarsinic acid (DMA), total mercury (tHg), and methylmercury (MeHg)) in six organs (total portion, head, body, shell, muscle, and intestine) of 11 shrimp species distributed in Korea. Shrimp exhibited significant variability in heavy metal accumulation, with Alaskan pink and dried shrimp (Lesser glass, Southern rough, and Chinese ditch prawn) showing the highest metal concentrations. Notably, the intestine having the highest overall metal content, while Cd was most prominent in the head, tHg was highest in the muscle. The Hazard Quotient values of 11 shrimp species in South Korea were below the European Food Safety Authority's allowable limits for heavy metals. This study illuminates the heavy metal profiles of distributed shrimp in Korea and emphasizes the ongoing need for monitoring heavy metals on seafood to ensure consumer safety.

Insights on the Organ-Dependent, Molecular Sexual Dimorphism in the Zebra Mussel, Dreissena polymorpha, Revealed by Ultra-High-Performance Liquid Chromatography-Tandem Mass Spectrometry Metabolomics.

The zebra mussel, Dreissena polymorpha, is extensively used as a sentinel species for biosurveys of environmental contaminants in freshwater ecosystems and for ecotoxicological studies. However, its metabolome remains poorly understood, particularly in light of the potential molecular sexual dimorphism between its different tissues. From an ecotoxicological point of view, inter-sex and inter-organ differences in the metabolome suggest variability in responsiveness, which can influence the analysis and interpretation of data, particularly in the case where males and females would be analyzed indifferently. This study aimed to assess the extent to which the molecular fingerprints of functionally diverse tissues like the digestive glands, gonads, gills, and mantle of D. polymorpha can reveal tissue-specific molecular sexual dimorphism. We employed a non-targeted metabolomic approach using liquid chromatography high-resolution mass spectrometry and revealed a significant sexual molecular dimorphism in the gonads, and to a lesser extent in the digestive glands, of D. polymorpha. Our results highlight the critical need to consider inter-sex differences in the metabolome of D. polymorpha to avoid confounding factors, particularly when investigating environmental effects on molecular regulation in the gonads, and to a lesser extent in the digestive glands.

Synthesis of multivalent fatty acid-conjugated antisense oligonucleotides: Cell internalization, physical properties, and in vitro and in vivo activities.

Herein, we describe the design and synthesis of multi-conjugatable fatty acid monomer phosphoramidites and their conjugation to antisense oligonucleotides (ASOs). Multivalent long-chain fatty acid conjugation improved the cellular uptake of ASOs but decreased in vitro activity due to alterations in physical properties and cellular localization. In addition, multivalently fatty acid-conjugated ASOs showed different organ specificity compared with that of unconjugated ASO in in vivo experiment. Although optimization of the linker structure between the fatty acid moiety and the ASO may be required, divalent long-chain fatty acid conjugation provides a new approach to increase endocytosis, thereby potentially improving the activity of therapeutic ASOs.

Comprehensive Analysis of Differentially Expressed Genes and Epigenetic Modification-Related Expression Variation Induced by Saline Stress at Seedling Stage in Fiber and Oil Flax, Linum usitatissimum L.

The ability of different germplasm to adapt to a saline-alkali environment is critical to learning about the tolerance mechanism of saline-alkali stress in plants. Flax is an important oil and fiber crop in many countries. However, its molecular tolerance mechanism under saline stress is still not clear. In this study, we studied morphological, physiological characteristics, and gene expression variation in the root and leaf in oil and fiber flax types under saline stress, respectively. Abundant differentially expressed genes (DEGs) induced by saline stress, tissue/organ specificity, and different genotypes involved in plant hormones synthesis and metabolism and transcription factors and epigenetic modifications were detected. The present report provides useful information about the mechanism of flax response to saline stress and could lead to the future elucidation of the specific functions of these genes and help to breed suitable flax varieties for saline/alkaline soil conditions.

Site and Organ-Specific Culture-Dependent Endophytic Diversity of Crocus sativus L. (Saffron) in Kashmir Himalaya, India.

The endophytic diversity of a host plant has been shown to vary across various spatio-temporal scales and between different organs of a plant, but no such study has been carried out on the economically important plant Crocus sativus (saffron). To fill this knowledge gap, the present study was undertaken to document the diversity of culturable bacterial, actinomycete and fungal endophytes at multiple sites from vegetative and reproductive organs of C. sativus. A total of 1170 culturable endophytic isolates were recovered from 6480 tissue segments of C. sativus collected from six different study sites in Pampore region of Kashmir valley in India. These isolates were identified using 16S and ITS (internal transcribed spacer) rDNA barcode sequence analysis and were classified into 84 operational taxonomic units (OTUs), including 52 bacterial OTUs, 7 actinomycete OTUs and 25 fungal OTUs. The phylogenetic analysis of sequences separated them into four phyla, namely, Firmicutes (46%), Ascomycota (30%), Proteobacteria (16%) and Actinobacteria (8%). Significant differences were observed in the diversity of endophytic assemblages across various study sites and different plant organs (P ≤ 0.001). Species richness was highest at the Baroosa site and lowest at the Chandhar site while the Shannon index was highest at the Baroosa site and lowest at the Letpur site. Among organs, species richness was highest in stigma and lowest in leaf. Similarly, Shannon index was highest for root and lowest for leaf. Further, 15 culturable endophytic OTUs showed organ specificity. The present study is the first comprehensive report that not only brings out differences in the diversity of endophytes associated with different organs and at different sites but also highlights the complexity of host-endophyte interaction at multiple scales.

Biofabrication of 3D Human Muscle Model with Vascularization and Endomysium.

This protocol describes the biofabrication of 3D millimeter-scale human muscle units, embedding non-planar muscle fibers wrapped by fibroblasts-rich endomysium and intertwined with microvascular networks. Suspended muscle fibers are formed through the self-assembly of human myoblasts within cylindrical cavities generated in a sacrificial gelatin template cast in a 3D printed frame. Following myotube differentiation, muscle fibers are embedded in a 3D matrix containing endothelial cells and muscle-derived fibroblasts. The cellular complexity of the environment is instrumental to drive fibroblast migration towards muscle fibers and to induce the organ-specific differentiation of endothelial cells. This advanced 3D muscle model can be applied to analyze the biological mechanisms underlying specific muscle diseases which involve a complex remodeling of the muscle environment (e.g., muscular dystrophies and fibrosis) whereby the pathological interplay among different cell populations drives the onset and progression of the disease.

Viral Metagenome-Based Precision Surveillance of Pig Population at Large Scale Reveals Viromic Signatures of Sample Types and Influence of Farming Management on Pig Virome.

Pigs are a major meat source worldwide and a pillar of Chinese animal husbandry; hence, their health and safety are a prioritized concern of the national economy. Although pig viruses have been continuously investigated, the full extent of the pig virome has remained unknown and emerging viruses are still a major threat to the pig industry. Here, we report a comprehensive study to delineate the pig virome of 1,841 healthy weaned pigs from 45 commercial farms collected from 25 major pig-producing regions across China. A viromic sequence data set, named Pigs_VIRES, which matched 96,586 viral genes from at least 249 genera within 66 families and which almost tripled the number of previously published pig viromic genes, was established. The majority of the mammalian viruses were closely related to currently known ones. A comparison with previously published viromes of bovines, avians, and humans has revealed the distinct composition of Pigs_VIRES, which has provided characteristic viromic signatures of serum, pharyngeal, and anal samples that were significantly influenced by farming management and disease control measures. Taken together, Pigs_VIRES has revealed the most complete viromic data set of healthy pigs to date. The compiled data also provide useful guidance to pig viral disease control and prevention and the biosafety management of pig farms. Especially, the established viromic protocol has created a precision surveillance strategy to potentially innovate currently used surveillance methods of animal infectious diseases, particularly by making precision surveillance available to other animal species on a large scale or even during a nationwide surveillance campaign. IMPORTANCE Pigs are deeply involved in human lives; hence, their viruses are associated with public health. Here, we established the most comprehensive virome of healthy piglets to date, which provides a viromic baseline of weaned pigs for disease prevention and control, highlighting that longitudinal viromic monitoring is needed to better understand the dynamics of the virome in pig development and disease occurrence. The present study also shows how high standards of animal farm management with strict biosafety measures can significantly minimize the risk of introduction of pathogenic viruses into pig farms. Particularly, the viromic strategy established, i.e., high-throughput detection and analyses of various known and unknown pathogenic viruses in a single test at large scale, has completely innovated current surveillance measures in provision of timely and precise detection of all potentially existing pathogenic viruses and can be widely applied in other animal species.

Aging features of the migratory locust at physiological and transcriptional levels.

BACKGROUND: Non-Drosophila insects provide diverse aging types and important complementary systems for studies of aging biology. However, little attention has been paid to the special roles of non-Drosophila insects in aging research. Here, the aging-related features of the migratory locust, Locusta migratoria, were determined at the physiological, cellular, and transcriptional levels. RESULTS: In physiological assessments, the flight performance and sperm state of locusts displayed clear aging-related decline in male adults. Transcriptional analyses demonstrated locusts have similar aging-related genes with model species. However, different from those of Drosophila and mammals, the organ-specific aging transcriptional features of locusts were characterized by intensive expression changes in flight muscle and fat body and little transcriptional changes in brain. The predominant transcriptional characteristics of flight muscle and fat body aging were changes in expression of mitochondrion-related genes and detoxification and phagocytosis genes, respectively. Cellular assessments revealed the incidence of mitochondrial abnormalities significantly increased in aged flight muscle, and apoptotic signals and nuclear abnormalities were enhanced in aged fat body but not in brain. In addition, some well-known aging genes and locust aging-related genes (i.e., IAP1, PGRP-SA, and LIPT1), whose roles in aging regulation were rarely reported, were demonstrated to affect lifespan, metabolism, and flight ability of locusts after RNAi. CONCLUSION: This study revealed multi-level aging signatures of locust, thus laying a foundation for further investigation of aging mechanisms in this famous insect in the future.

Comprehensive analysis of the isomiRome in the vegetative organs of the conifer Pinus pinaster under contrasting water availability.

An increasing number of microRNAs (miRNAs) and miRNA-related sequences produced during miRNA biogenesis, comprising the isomiRome, have been recently highlighted in different species as critical mediators of environmental stress responses. Conifers have some of the largest known genomes but an extensive characterization of the isomiRome from any conifer species has been lacking. We provide here a comprehensive overview of the Pinus pinaster isomiRome expressed in roots, stem and needles under well-watered and drought conditions. From the 13,441 unique small RNA sequences identified, 2,980 were annotated as canonical miRNAs or miRNA* and the remaining were classified as isomiRNA or miRNA-like sequences. A survey of their expression patterns highlighted roots as the most responsive organ under drought, where specific sequences of which a 24-nt novel miRNA stood out, were strongly down-regulated. Given the putative roles of the miRNA-targeted transcripts validated specifically in root tissues, some of the miRNAs, conserved and novel, are shortlisted as potential regulators of drought response. These results provide a valuable resource for comparative studies between gymnosperms and angiosperms. Furthermore, it evidences high transferability of the isomiRome between pine species being a useful basis for further molecular regulation and physiological studies, and especially those focused on adaptation to drought conditions.

PTBP1-targeting microRNAs regulate cancer-specific energy metabolism through the modulation of PKM1/M2 splicing.

Understanding of the microRNAs (miRNAs) regulatory system has become indispensable for physiological/oncological research. Tissue and organ specificities are key features of miRNAs that should be accounted for in cancer research. Further, cancer-specific energy metabolism, referred to as the Warburg effect, has been positioned as a key cancer feature. Enhancement of the glycolysis pathway in cancer cells is what primarily characterizes the Warburg effect. Pyruvate kinase M1/2 (PKM1/2) are key molecules of the complex glycolytic system; their distribution is organ-specific. In fact, PKM2 overexpression has been detected in various cancer cells. PKM isoforms are generated by alternative splicing by heterogeneous nuclear ribonucleoproteins. In addition, polypyrimidine tract-binding protein 1 (PTBP1) is essential for the production of PKM2 in cancer cells. Recently, several studies focusing on non-coding RNA elucidated PTBP1 or PKM2 regulatory mechanisms, including control by miRNAs, and their association with cancer. In this review, we discuss the strong relationship between the organ-specific distribution of miRNAs and the expression of PKM in the context of PTBP1 gene regulation. Moreover, we focus on the impact of PTBP1-targeting miRNA dysregulation on the Warburg effect.

Synanthropic Plants as an Underestimated Source of Bioactive Phytochemicals: A Case of Galeopsis bifida (Lamiaceae).

Hemp nettle (Galeopsis bifida Boenn.) is a synanthropic species of the Lamiaceae family that is widely distributed across Europe, Asia, and Siberia. Galeopsis bifida is deeply embedded in the ethnomedical tradition of Asian healers; however, this plant is still poorly characterized, both chemically and pharmacologically. To study Siberian populations of G. bifida, we used high-performance liquid chromatography with photodiode array and electrospray triple quadrupole mass detection for metabolic profiling. Ninety compounds were identified, including iridoid glycosides, phenylethanoid glycosides, hydroxycinnamates, and flavone glycosides, most of which were identified in G. bifida for the first time, while some phenolics were found to have potential chemotaxonomic significance in the Lamiaceae family and Galeopsis genus. An unequal quantitative distribution of the selected metabolites was observed within separate organs of the G. bifida plant, characterized by high accumulation of most compounds within the aerial part of the plant (leaves, flowers). Analysis of the content of specific chosen compounds within the leaves of different populations of G. bifida from Eastern Siberia revealed the existence of two chemical types based on metabolic specifics: the southern type accumulates flavone glucuronides, while the northern type tends to accumulate high levels of phenylpropanoids and acylated flavone glucosides. The first study of the bioactivity of G. bifida extract demonstrated that the herb has low toxicity in acute experiments and expresses antioxidant potential against free radicals in the form of DPPH˙, ABTS˙+, and superoxide radical, as well as high ferric reducing antioxidant power, oxygen radical absorbance capacity, and protective action in the carotene bleaching assay. In general, our results suggest the herb of G. bifida as a new, prospective synanthropic plant for medical application.

Organ-Specific Effects of Low Dose Radiation Exposure: A Comprehensive Review.

Ionizing radiation (IR) is a high-energy radiation whose biological effects depend on the irradiation doses. Low-dose radiation (LDR) is delivered during medical diagnoses or by an exposure to radioactive elements and has been linked to the occurrence of chronic diseases, such as leukemia and cardiovascular diseases. Though epidemiological research is indispensable for predicting and dealing with LDR-induced abnormalities in individuals exposed to LDR, little is known about epidemiological markers of LDR exposure. Moreover, difference in the LDR-induced molecular events in each organ has been an obstacle to a thorough investigation of the LDR effects and a validation of the experimental results in in vivo models. In this review, we summarized the recent reports on LDR-induced risk of organ-specifically arranged the alterations for a comprehensive understanding of the biological effects of LDR. We suggested that LDR basically caused the accumulation of DNA damages, controlled systemic immune systems, induced oxidative damages on peripheral organs, and even benefited the viability in some organs. Furthermore, we concluded that understanding of organ-specific responses and the biological markers involved in the responses is needed to investigate the precise biological effects of LDR.

Proteomics Analysis of Plasma Membrane Fractions of the Root, Leaf, and Flower of Rice.

The plasma membrane regulates biological processes such as ion transport, signal transduction, endocytosis, and cell differentiation/proliferation. To understand the functional characteristics and organ specificity of plasma membranes, plasma membrane protein fractions from rice root, etiolated leaf, green leaf, developing leaf sheath, and flower were analyzed by proteomics. Among the proteins identified, 511 were commonly accumulated in the five organs, whereas 270, 132, 359, 146, and 149 proteins were specifically accumulated in the root, etiolated leaf, green leaf, developing leaf sheath, and developing flower, respectively. The principle component analysis revealed that the functions of the plasma membrane in the root was different from those of green and etiolated leaves and that the plasma membrane protein composition of the leaf sheath was similar to that of the flower, but not that of the green leaf. Functional classification revealed that the root plasma membrane has more transport-related proteins than the leaf plasma membrane. Furthermore, the leaf sheath and flower plasma membranes were found to be richer in proteins involved in signaling and cell function than the green leaf plasma membrane. To validate the proteomics data, immunoblot analysis was carried out, focusing on four heterotrimeric G protein subunits, Gα, Gß, Gγ1, and Gγ2. All subunits could be detected by both methods and, in particular, Gγ1 and Gγ2 required concentration by immunoprecipitation for mass spectrometry detection.

Critical steps to tumor metastasis: alterations of tumor microenvironment and extracellular matrix in the formation of pre-metastatic and metastatic niche.

For decades, cancer metastasis has been a heated topic for its high mortality. Previous research has shown that pre-metastatic niche and metastatic niche are the 2 crucial steps in cancer metastasis, assisting cancerous cells' infiltration, survival, and colonization at target sites. More recent studies have unraveled details about the specific mechanisms related to the modification of pro-invasion environments. Here, we will review literatures on extracellular matrix (ECM) alterations, general cancer metastasis, organ specificity, pre-metastatic niche, metastatic niche, colony formation and impact on the course of metastasis. Respectively, the metastatic mechanisms like effect of hypoxia or inflammation on pre-metastatic niche construction, as well as the interaction between cancer cells and local milieu will be discussed. Based on the evidences of metastatic niches, we revisit and discussed the "Seed and Soil" hypothesis by Paget. This review will seek to provide insight into the mechanism of metastatic organ specificity which pre-metastatic niche and metastatic niche might suggest from an evolutionary aspect.

Matrix decoded - A pancreatic extracellular matrix with organ specific cues guiding human iPSC differentiation.

The extracellular matrix represents a dynamic microenvironment regulating essential cell functions in vivo. Tissue engineering approaches aim to recreate the native niche in vitro using biological scaffolds generated by organ decellularization. So far, the organ specific origin of such scaffolds was less considered and potential consequences for in vitro cell culture remain largely elusive. Here, we show that organ specific cues of biological scaffolds affect cellular behavior. In detail, we report on the generation of a well-preserved pancreatic bioscaffold and introduce a scoring system allowing standardized inter-study quality assessment. Using multiple analysis tools for in-depth-characterization of the biological scaffold, we reveal unique compositional, physico-structural, and biophysical properties. Finally, we prove the functional relevance of the biological origin by demonstrating a regulatory effect of the matrix on multi-lineage differentiation of human induced pluripotent stem cells emphasizing the significance of matrix specificity for cellular behavior in artificial microenvironments.

Blood and Lymphatic Vasculatures On-Chip Platforms and Their Applications for Organ-Specific In Vitro Modeling.

The human circulatory system is divided into two complementary and different systems, the cardiovascular and the lymphatic system. The cardiovascular system is mainly concerned with providing nutrients to the body via blood and transporting wastes away from the tissues to be released from the body. The lymphatic system focuses on the transport of fluid, cells, and lipid from interstitial tissue spaces to lymph nodes and, ultimately, to the cardiovascular system, as well as helps coordinate interstitial fluid and lipid homeostasis and immune responses. In addition to having distinct structures from each other, each system also has organ-specific variations throughout the body and both systems play important roles in maintaining homeostasis. Dysfunction of either system leads to devastating and potentially fatal diseases, warranting accurate models of both blood and lymphatic vessels for better studies. As these models also require physiological flow (luminal and interstitial), extracellular matrix conditions, dimensionality, chemotactic biochemical gradient, and stiffness, to better reflect in vivo, three dimensional (3D) microfluidic (on-a-chip) devices are promising platforms to model human physiology and pathology. In this review, we discuss the heterogeneity of both blood and lymphatic vessels, as well as current in vitro models. We, then, explore the organ-specific features of each system with examples in the gut and the brain and the implications of dysfunction of either vasculature in these organs. We close the review with discussions on current in vitro models for specific diseases with an emphasis on on-chip techniques.

Epiphytic and Endophytic Bacteria on Olive Tree Phyllosphere: Exploring Tissue and Cultivar Effect.

Variation on bacterial communities living in the phyllosphere as epiphytes and endophytes has been attributed to plant host effects. However, there is contradictory or inconclusive evidence regarding the effect of plant genetics (below the species' level) and of plant tissue type on phyllosphere bacterial community assembly, in particular when epiphytes and endophytes are considered simultaneously. Here, both surface and internal bacterial communities of two olive (Olea europaea) cultivars were evaluated in twigs and leaves by molecular identification of cultivable isolates, with an attempt to answer these questions. Overall, Proteobacteria, Actinobacteria and Firmicutes were the dominant phyla, being epiphytes more diverse and abundant than endophytes. Host genotype (at cultivar level) had a structuring effect on the composition of bacterial communities and, in a similar way, for both epiphytes and endophytes. Plant organ (leaf vs. twig) control of the bacterial communities was less evident when compared with plant genotype and with a greater influence on epiphytic than on endophytic community structure. Each olive genotype/plant organ was apparently selective towards specific bacterial operational taxonomic units (OTUs), which may lead to specific feedbacks on fitness of plant genotypes. Bacterial recruitment was observed to happen mainly within epiphytes than in endophytes and in leaves as compared with twigs. Such host specificity suggested that the benefits derived from the plant-bacteria interaction should be considered at genetic levels below the species.

Host tree organ is the primary driver of endophytic fungal community structure in a hemiboreal forest.

Despite numerous studies on plant endophytes, little is known about fungal communities associated with different aboveground tissues of living trees. We used high-throughput sequencing to compare the diversity and community structure of fungi inhabiting leaves, branches and trunks of Alnus incana and Corylus avellana growing at three hemiboreal forest sites. Our analysis revealed that tree organs are the main determinants of the structure of fungal communities, whereas the effects of host species and locality remained secondary and negligible, respectively. The structure of fungal communities in trunks was the most distinct compared to that in leaves and branches. The foliar fungal communities were more similar within than between individual trees, implying that certain fungi may grow through parts of the tree crown. The weak effect of locality compared to host organs and species identity suggests that the structural variation of fungal communities in the aboveground parts of trees depends mainly on deterministic factors rather than dispersal limitation.