Long non-coding RNA (lncRNA) biology is a rapidly growing area of study. Thousands of lncRNAs are implicated as key players in cellular pathways and cancer biology. However, the structure-function relationships of these novel biomolecules are not well understood. Recent structural studies suggest that lncRNAs contain modular structural domains, which play a crucial role in their function. Here, we hypothesized that such structural domains exist in lncTCF7, a conserved lncRNA implicated in the development and progression of several cancers. To understand the structure-function relationship of lncTCF7, we characterized its secondary structure using chemical probing methods. Our model revealed structural domains and conserved regions in lncTCF7. One of the modular domains identified here coincides with a known protein-interacting domain. The model reported herein is, to our knowledge, the first structural model of lncTCF7 and thus will serve to direct future studies that will provide fundamental insights into the function of this lncRNA.

Transcriptional responses to the appropriate temporal pattern of action potential firing are essential for long-term adaption of neuronal properties to the functional activity of neural circuits and environmental experience. However, standard transcriptome analysis methods can be too limited in identifying critical aspects that coordinate temporal coding of action potential firing with transcriptome response. A Pearson correlation analysis was applied to determine how pairs of genes in the mouse dorsal root ganglion (DRG) neurons are coordinately expressed in response to stimulation producing the same number of action potentials by two different temporal patterns. Analysis of 4728 distinct gene-pairs related to calcium signaling, 435,711 pairs of transcription factors, 820 pairs of voltage-gated ion channels, and 86,862 pairs of calcium signaling genes with transcription factors indicated that genes become coordinately activated by distinct action potential firing patterns and this depends on the duration of stimulation. Moreover, a measure of expression variance revealed that the control of transcripts abundances is sensitive to the pattern of stimulation. Thus, action potentials impact intracellular signaling and the transcriptome in dynamic manner that not only alter gene expression levels significantly (as previously reported) but also affects the control of their expression fluctuations and profoundly remodel the transcriptional networks.

Targeted metagenomics is the solution of choice to reveal differential microbial profiles (defined by richness, diversity and composition) as part of case-control studies. It is well documented that each data processing step may have the potential to introduce bias in the results. However, selecting a bioinformatics pipeline to analyze high-throughput sequencing data from A to Z remains one of the critical considerations in a case-control microbiota study design. Consequently, the aim of this study was to assess whether the same biological conclusions regarding human gut microbiota composition and diversity could be reached using different bioinformatics pipelines. In this work, we considered four pipelines (mothur, QIIME, kraken and CLARK) with different versions and databases, and examined their impact on the outcome of metagenetic analysis of Ion Torrent 16S sequencing data. We re-analyzed a case-control study evaluating the impact of the colonization of the intestinal protozoa Blastocystis sp. on the human gut microbial profile. Although most pipelines reported the same trends in this case-control study, we demonstrated how the use of different pipelines affects the biological conclusions that can be drawn. Targeted metagenomics must therefore rather be considered as a profiling tool to obtain a broad sense of the variations of the microbiota, rather than an accurate identification tool.

Type 1 diabetes (T1D) results from the progressive loss of pancreatic beta cells as a result of autoimmune destruction. We recently reported that during the natural history of T1D in humans and the female nonobese diabetic (NOD) mouse model, beta cells acquire a senescence-associated secretory phenotype (SASP) that is a major driver of disease onset and progression, but the mechanisms that activate SASP in beta cells were not explored. Here, we show that the SASP in islet cells is transcriptionally controlled by Bromodomain ExtraTerminal (BET) proteins, including Bromodomain containing protein 4 (BRD4). A chromatin analysis of key beta cell SASP genes in NOD islets revealed binding of BRD4 at active regulatory regions. BET protein inhibition in NOD islets diminished not only the transcriptional activation and secretion of SASP factors, but also the non-cell autonomous activity. BET protein inhibition also decreased the extent of SASP induction in human islets exposed to DNA damage. The BET protein inhibitor iBET-762 prevented diabetes in NOD mice and also attenuated SASP in islet cells in vivo. Taken together, our findings support a crucial role for BET proteins in the activation of the SASP transcriptional program in islet cells. These studies suggest avenues for preventing T1D by transcriptional inhibition of SASP.

Calcific tendonitis is a frequent cause of chronic shoulder pain. Its cause is currently poorly known. The objectives of this study were to better characterize the cells and mechanisms involved in depositing apatite crystals in human tendons. Histologic sections of cadaveric calcified tendons were analyzed, and human calcific deposits from patients undergoing lavage of their calcification were obtained to perform infrared spectroscopy and mass spectrometry-based proteomic characterizations. In vitro, the mineralization ability of human rotator cuff cells from osteoarthritis donors was assessed by alizarin red or Von Kossa staining. Calcifications were amorphous areas surrounded by a fibrocartilaginous metaplasia containing hypertrophic chondrocyte-like cells that expressed tissue non-specific alkaline phosphatase (TNAP) and ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1), which are two key enzymes of the mineralization process. Calcific deposits were composed of apatite crystals associated with proteins involved in bone and cartilage development and endochondral bone growth. In vitro, tenocyte-like cells extracted from the rotator cuff were able to mineralize in osteogenic cultures, and expressed TNAP, type X COLLAGEN, and MMP13, which are hypertrophic chondrocytes markers. The use of a TNAP inhibitor significantly prevented mineral deposits. We provide evidence that tenocytes have a propensity to differentiate into hypertrophic chondrocyte-like cells to produce TNAP-dependent calcium deposits. We believe that these results may pave the way to identifying regulating factors that might represent valuable targets in calcific tendonitis.

The use of iron-based nanomaterials for environmental remediation processes has recently received considerable attention. Here, we employed core-shell magnetite-humic acids nanoparticles as a heterogeneous photosensitizer and iron source in photo-Fenton reaction for the degradation of the psychiatric drug carbamazepine (CBZ). CBZ showed low photodegradation rates in the presence of the magnetic nanoparticles, whereas the addition of hydrogen peroxide at pH = 3 to the system drastically increased the abatement of the contaminant. The measured Fe2+ and Fe3+ profiles point to the generation of Fe3+ at the surface of the nanoparticles, indicating a heterogeneous oxidation of the contaminant mediated by hydroxyl radicals. Products with a higher transformation degree were observed in the photo-Fenton procedure and support the attack of the HO• radical on the CBZ molecule. Promising results encourage the use of the nanoparticles as efficient iron sources with enhanced magnet-sensitive properties, suitable for applications in photo-Fenton treatments for the purification of wastewater.

Therapy of acute myeloid leukemia (AML) is unsatisfactory. Histone deacetylase inhibitors (HDACi) are active against leukemic cells in vitro and in vivo. Clinical data suggest further testing of such epigenetic drugs and to identify mechanisms and markers for their efficacy. Primary and permanent AML cells were screened for viability, replication stress/DNA damage, and regrowth capacities after single exposures to the clinically used pan-HDACi panobinostat (LBH589), the class I HDACi entinostat/romidepsin (MS-275/FK228), the HDAC3 inhibitor RGFP966, the HDAC6 inhibitor marbostat-100, the non-steroidal anti-inflammatory drug (NSAID) indomethacin, and the replication stress inducer hydroxyurea (HU). Immunoblotting was used to test if HDACi modulate the leukemia-associated transcription factors β-catenin, Wilms tumor (WT1), and myelocytomatosis oncogene (MYC). RNAi was used to delineate how these factors interact. We show that LBH589, MS-275, FK228, RGFP966, and HU induce apoptosis, replication stress/DNA damage, and apoptotic fragmentation of β-catenin. Indomethacin destabilizes β-catenin and potentiates anti-proliferative effects of HDACi. HDACi attenuate WT1 and MYC caspase-dependently and -independently. Genetic experiments reveal a cross-regulation between MYC and WT1 and a regulation of β-catenin by WT1. In conclusion, reduced levels of β-catenin, MYC, and WT1 are molecular markers for the efficacy of HDACi. HDAC3 inhibition induces apoptosis and disrupts tumor-associated protein expression.

The functional hemizygosity could be caused by the MAE of a given gene and it can be one of the sources to affect the phenotypic variation in cattle. We aimed to identify MAE genes across the transcriptome in Korean cattle (Hanwoo). For three Hanwoo family trios, the transcriptome data of 17 tissues were generated in three offspring. Sixty-two MAE genes had a monoallelic expression in at least one tissue. Comparing genotypes among each family trio, the preferred alleles of 18 genes were identified (maternal expression, n = 9; paternal expression, n = 9). The MAE genes are involved in gene regulation, metabolic processes, and immune responses, and in particular, six genes encode transcription factors (FOXD2, FOXM1, HTATSF1, SCRT1, NKX6-2, and UBN1) with tissue-specific expression. In this study, we report genome-wide MAE genes in seventeen tissues of adult cattle. These results could help to elucidate epigenetic effects on phenotypic variation in Hanwoo.

In this work, we present a novel synthetic route to diblock copolymers based on styrene and 3-vinylpyridine monomers. Surfactant-free water-based reversible addition-fragmentation chain transfer (RAFT) emulsion polymerization of styrene in the presence of the macroRAFT agent poly(3-vinylpyridine) (P3VP) is used to synthesize diblock copolymers with molecular weights of around 60 kDa. The proposed mechanism for the poly(3-vinylpyridine)-block-poly(styrene) (P3VP-b-PS) synthesis is the polymerization-induced self-assembly (PISA) which involves the in situ formation of well-defined micellar nanoscale objects consisting of a PS core and a stabilizing P3VP macroRAFT agent corona. The presented approach shows a well-controlled RAFT polymerization, allowing for the synthesis of diblock copolymers with high monomer conversion. The obtained diblock copolymers display microphase-separated structures according to their composition.

An accurate equivalent method of metal joint interface is of great significance to optimize the dynamic performance of the whole machine. Therefore, it is necessary to establish an accurate equivalent method of joint interface. The virtual material method is a precise equivalent method of joint interface. The traditional virtual material method is based on the M-B fractal contact theory. By modeling the contact mechanics of the joint interface, the physical properties of the virtual material are obtained separately, such as elastic modulus, Poisson's ratio and density. In this paper, Persson contact theory is used to establish the interface contact mechanics model to find the physical properties of virtual materials. The virtual material methods constructed by two theories are respectively applied to the modal simulation to obtain the natural frequencies of the joint interface. By comparing the natural frequencies obtained by modal experiment and modal simulation, it is found that the natural frequencies obtained by the virtual material method based on Persson contact theory are closer to the results obtained by the modal experiment, and the error is within 5%. The error of the natural frequencies obtained by the virtual material method based on the M-B fractal contact theory is within 10%. Therefore, the Persson contact theory can establish a more accurate equivalent method of metal's joint interface.

Although reactive astrocytes constitute a major component of the cellular environment in glioblastoma, their function and crosstalk to other components of the environment is still poorly understood. Gene expression analysis of purified astrocytes from both the tumor core and non-infiltrated cortex reveals a tumor-related up-regulation of Chitinase 3-like 1 (CHI3L1), a cytokine which is related to inflammation, extracellular tissue remodeling, and fibrosis. Further, we established and validated a co-culture model to investigate the impact of reactive astrocytes within the tumor microenvironment. Here we show that reactive astrocytes promote a subtype-shift of glioblastoma towards the mesenchymal phenotype, driving mitogen-activated protein kinases (MAPK) signaling as well as increased proliferation and migration. In addition, we demonstrate that MAPK signaling is directly caused by a CHI3L1-IL13RA2 co-binding, which leads to increased downstream MAPK and AKT signaling. This novel microenvironmental crosstalk highlights the crucial role of non-neoplastic cells in malignant brain tumors and opens up new perspectives for targeted therapies in glioblastoma.

The history of dog domestication is still under debate, but it is doubtless the process of an ancient partnership between dogs (Canis familiaris) and humans. Although data on ancient DNA for dog diversity are still incomplete, it is clear that several regional dog populations had formed in Eurasia up to the Holocene. During the Neolithic Revolution and the transition from hunter-gatherer to farmer societies, followed by civilization changes in the Antiquity period, the dog population structure also changed. This process was due to replacement with newly formed dog populations. In this study, we present for the first time mitochondrial data of ancient dog remains from the Early Neolithic (8000 years before present (BP)) to Late Antiquity (up to 3th century AD) from southeastern Europe (the Balkans). A total of 16 samples were analyzed, using the mitochondrial D-loop region (HVR1). The results show the presence of A (70%) and B (25%) clades throughout the Early and Late Neolithic Period. In order to clarify the position of our results within the ancient dog population in Eneolithic Eurasia, we performed phylogenetic analysis with the available genetic data sets. This data showed a similarity of the ancient Bulgarian dogs to Italian (A, B, and C clades) and Iberian (clades A and C) dogs' populations. A clear border can be seen between southern European genetic dog structure, on the one hand, and on the other hand, central-western (clade C), eastern (clade D) and northern Europe (clades A and C). This corresponds to genetic data for European humans during the same period, without admixture between dog populations. Also, our data have shown the presence of clade B in ancient Eurasia. This is not unexpected, as the B haplogroup is widely distributed in extant Balkan dogs and wolves. The presence of this clade both in dogs and in wolves on the Balkans may be explained with hybridization events before the Neolithic period. The spreading of this clade across Europe, together with the A clade, is related to the possible dissemination of newly formed dog breeds from Ancient Greece, Thrace, and the Roman Empire.

Hyperglycemia and hyperinsulinemia activate the proliferative potential of hepatic stellate cells (HSCs) and promote hepatic fibrosis. Dipeptidyl peptidase-4 (DPP-4) inhibitors, antidiabetic agents, reportedly inhibit the HSC proliferation. Additionally, Takeda G protein-coupled receptor 5 (TGR5) agonists induce the systemic release of glucagon-like peptides from intestinal L cells, which maintains glycemic homeostasis. This study assessed the combined effect of TGR5 agonist and DPP-4 inhibitor on diabetes-based liver fibrosis development. Male diabetic rats received intraperitoneal injection of porcine serum (PS) to induce liver fibrosis, and they were orally administered the following agents: oleanolic acid (OA) as a TGR5 agonist, anagliptin (ANA) as a DPP-4 inhibitor, and a combination of both agents. Treatment with OA or ANA significantly improved glycemic status and attenuated intrahepatic steatosis and lipid peroxidation in diabetic rats. PS-induced liver fibrosis development was also drastically suppressed by treatment with either agent, and the combination of both reciprocally enhanced the antifibrotic effect. Fecal microbiome demonstrated that both agents inhibited the increase in the Firmicutes/Bacteroidetes ratio, an indicator of dysbiosis related to metabolic syndromes. Furthermore, ANA directly inhibited in vitro HSC proliferative and profibrogenic activities. Collectively, TGR5 agonist and DPP-4 inhibitor appears to be a novel strategy against liver fibrosis under diabetic conditions.

Canine B-cell lymphoma (CBL) is an incurable, spontaneous lymphoid malignancy constituting an accurate animal model for testing novel therapeutic strategies in human medicine. Resources of available species-specific therapeutic monoclonal antibodies (mAbs) targeting CBL are scarce. The aim of the present study was to evaluate the therapeutic potential of mAb B5, specific for the dog leukocyte antigen DR (DLA-DR) and its antibody-drug conjugate with methotrexate (B5-MTX). B5 induced caspase-dependent apoptosis of DLA-DR-expressing canine B cell lymphoma/CLBL1 and CLB70 leukemia lines, but not the GL-1 line not expressing DLA-DR. The cytotoxicity of B5-MTX to sensitive cells was further potentiated by a payload of MTX, but without any substantial off-target effects. The infusion of B5 and B5-MTX in a murine model of disseminated, advanced canine lymphoma, mediated >80% and >90% improvement in survival, respectively, and was well tolerated by the animals. Interestingly, the concentrations of soluble DLA-DR (sDLA-DR) antigens present in the blood serum of tumor-bearing mice were found proportional to the tumor burden. On this basis, sDLA-DR levels were evaluated as a potential biomarker using samples from canine lymphoma patients. In summary, the action of B5 and B5-MTX holds promise for further development as an alternative/complementary option for the diagnosis and treatment of canine lymphoma.

A part-based strategy has been applied to visual tracking with demonstrated success in recent years. Different from most existing part-based methods that only employ one type of tracking representation model, in this paper, we propose an effective complementary tracker based on structural patch response fusion under correlation filter and color histogram models. The proposed method includes two component trackers with complementary merits to adaptively handle illumination variation and deformation. To identify and take full advantage of reliable patches, we present an adaptive hedge algorithm to hedge the responses of patches into a more credible one in each component tracker. In addition, we design different loss metrics of tracked patches in two components to be applied in the proposed hedge algorithm. Finally, we selectively combine the two component trackers at the response maps level with different merging factors according to the confidence of each component tracker. Extensive experimental evaluations on OTB2013, OTB2015, and VOT2016 datasets show outstanding performance of the proposed algorithm contrasted with some state-of-the-art trackers.

The mitochondrial DNA (mtDNA), which is present in almost all eukaryotic organisms, is a useful marker for phylogenetic studies due to its relative high conservation and its inheritance manner. In Leishmania and other trypanosomatids, the mtDNA (also referred to as kinetoplast DNA or kDNA) is composed of thousands of minicircles and a few maxicircles, catenated together into a complex network. Maxicircles are functionally similar to other eukaryotic mtDNAs, whereas minicircles are involved in RNA editing of some maxicircle-encoded transcripts. Next-generation sequencing (NGS) is increasingly used for assembling nuclear genomes and, currently, a large number of genomic sequences are available. However, most of the time, the mitochondrial genome is ignored in the genome assembly processes. The aim of this study was to develop a pipeline to assemble Leishmania minicircles and maxicircle DNA molecules, exploiting the raw data generated in the NGS projects. As a result, the maxicircle molecules and the plethora of minicircle classes for Leishmania major, Leishmania infantum and Leishmania braziliensis have been characterized. We have observed that whereas the heterogeneity of minicircle sequences existing in a single cell hampers their use for Leishmania typing and classification, maxicircles emerge as an extremely robust genetic marker for taxonomic studies within the clade of kinetoplastids.

An innovative moderate-intensity resistive exercise-training (RT) program was tested in thirty-five sarcopenic elders (SAR). The subjects were randomized into two groups: SAR training (SAR-RT), n = 20, 73.0 ± 5.5 years, or SAR non-training (SAR-NT), n = 15, 71.7 ± 3.4 years. The training consisted of 12-week progressive RT, thrice/week, at 60% one-repetition maximum (1RM), 3 sets, 14-16 repetitions for both upper and lower limbs. The pre and post intervention measurements included: the skeletal muscle index (SMI%); strength (1RM); stair-climbing power (SCP); muscle thickness (MT) of vastus lateralis (VL) and elbow flexors (EF), VL pennation angle (PA), rectus femoris (RF) anatomical cross-sectional area (ACSA); reactive oxygen species (ROS), total antioxidant capacity (TAC), protein carbonyls (PC), thiobarbituric acid-reactive substances (TBARS), 8-isoprostane (8-iso-PGF2-α), 8-OH-2-deoxyguanosine (8-OH-dG), as markers of oxidative stress/damage (OxS). In SAR-RT, SCP increased by 7.7% (P < 0.01), MT increased by 5.5% for VL, 10.4% for EF and PA increased by 13.4% for VL (P < 0.001 for all). The RF ACSA increased by 14.5% (P < 0.001). 1RM significantly increased by at least 67% for all muscles tested. Notably muscle strength (1RM) positively correlated (P < 0.001) with TAC and negatively with PC (P < 0.001). In conclusion, moderate intensity RT is an effective strategy to increase muscle mass and strength in SAR, while minimizing OxS.

Aphis gossypii Glover (Hemiptera: Aphididae) is a serious polyphagous agricultural pest worldwide. In the present study, we used eight microsatellite markers to investigate the genetic structure and diversity of A. gossypii populations in Korea. Samples were collected from 37 locations in Korea (18 populations in 2016, 14 populations in 2017, and five populations in 2018) from pepper plants. A. gossypii had low to moderate genetic diversity, and expected heterozygosity (HE) ranged from 0.354 to 0.719. A Mantel test of isolation by distance indicated no relationship between genetic structure and geographic distance among all populations (r2 = 0.0004, p = 0.370), suggesting high gene flow among populations in Korea. Populations of A. gossypii in Korea were divided into two distinct genetic clusters (ΔK = 2). In 2016 and 2017, the genetic clusters changed into opposite genetic structures within one year mostly in northwest and southeast parts of Korea. Possible relevance of study results was discussed. Chemical control, cyclical parthenogenesis, and immigrants from the exterior might have resulted in this low genetic diversity and opposite genetic clusters.

Human infections with Brucella melitensis are occasionally reported in Sweden, despite the fact that the national flocks of sheep and goats are officially free from brucellosis. The aim of our study was to analyze 103 isolates of B. melitensis collected from patients in Sweden between 1994 and 2016 and determine their putative geographic origin using whole genome sequencing (WGS)-based tools. The majority of the strains were assigned to East Mediterranean and African lineages. Both in silico Multiple Loci VNTR (Variable Number of Tandem Repeats) Analysis (MLVA) and core genome Multilocus Sequence Typing (cgMLST) analyses identified countries of the Middle East as the most probable source of origin of the majority of the strains. Isolates collected from patients with travel history to Iraq or Syria were often associated with genotypes from Turkey, as the cgMLST profiles from these countries clustered together. Sixty strains were located within a distance of 20 core genes to related genotypes from the publicly available database, and for eighteen isolates, the closest genotype was different by more than 50 loci. Our study showed that WGS based tools are effective in tracing back the geographic origin of infection of patients with unknown travel status, provided that public sequences from the location of the source are available.

Corynespora leaf spot caused by Corynespora cassiicola is one of the major diseases in cucumber (Cucumis sativus L.). However, the resistance mechanisms and signals of cucumber to C. cassiicola are unclear. Here, we report that the mildew resistance locus O (MLO) genes, CsMLO1 and CsMLO2, are both negative modulators of the cucumber defense response to C. cassiicola. Subcellular localization analysis showed that CsMLO1 and CsMLO2 are localized in the plasma membrane. Expression analysis indicated that the transcript levels of CsMLO1 and CsMLO2 are linked to the defense response to C. cassiicola. Transient overexpression of either CsMLO1 or CsMLO2 in cucumber cotyledons reduced resistance to C. cassiicola, whereas silencing of either CsMLO1 or CsMLO2 enhanced resistance to C. cassiicola. The relationships of pathogenesis-related proteins, reactive oxygen species (ROS)-associated genes, and abscisic acid (ABA)-related genes to the overexpression and silencing of CsMLO1/CsMLO2 in non-infested cucumber plants were investigated. The results indicated that CsMLO1 mediated resistance against C. cassiicola by regulating the expression of pathogenesis-related proteins and ROS-associated genes, as well as through ABA signaling pathway-associated genes. The CsMLO2-mediated resistance against C. cassiicola primarily involves regulation of the expression of pathogenesis-related proteins. Our findings will guide strategies to enhance the resistance of cucumber to corynespora leaf spot.