bluuebunny/crossref_metadata_2025 huggingface dataset:
Assemblages of Plasmodium and Related Parasites in Birds with Different Migration Statuses
Authors: Huang Xi , Chen Zelin , Yang Guocheng , Xia Canwei , Luo Qiujin , Gao Xiang , Dong Lu
Published: September 2022

Migratory birds spend several months in their breeding grounds in sympatry with local resident birds and relatively shorter periods of time at stopover sites. During migration, parasites may be transmitted between migratory and resident birds. However, to what extent they share these parasites remains unclear. In this study, we compared the assemblages of haemosporidian parasites in migratory, resident, and passing birds, as well as the correlations between parasite assemblages and host phylogeny. Compared with passing birds, migratory birds were more likely to share parasites with resident birds. Shared lineages showed significantly higher prevalence rates than other lineages, indicating that common parasites are more likely to spill over from the current host to other birds. For shared lineages, the prevalence was significantly higher in resident birds than in migratory birds, suggesting that migratory birds pick up parasites at their breeding ground. Among the shared lineages, almost two-thirds presented no phylogenetic signal in their prevalence, indicating that parasite transmission among host species is weakly or not correlated with host phylogeny. Moreover, similarities between parasite assemblages are not correlated with either migration status or the phylogeny of hosts. Our results show that the prevalence, rather than host phylogeny, plays a central role in parasite transmission between migratory and resident birds in breeding grounds.
Development of the Connecting Piece in ODF1-Deficient Mouse Spermatids
Authors: Hoyer-Fender Sigrid
Published: September 2022

ODF1 is a major protein of the accessory fibres of the mammalian sperm tail. In addition, ODF1 is found in the connecting piece, a complex structure located at the posterior end of the nucleus that connects the sperm head and tail. The tight coupling of the sperm head and tail is critical for the progressive motility of the sperm to reach the oocyte for fertilisation. The depletion of ODF1 by homologous recombination in mice led to male infertility. Although sperm tails were present in the epididymis, no intact spermatozoa were found. Instead, the depletion of ODF1 resulted in sperm decapitation, suggesting that ODF1 is essential for the formation of the coupling apparatus and the tight linkage of the sperm head and tail. However, the development of the linkage complex in the absence of ODF1 has never been investigated. Here, I analysed the fine structure of the developing connecting piece by transmission electron microscopy. I show that the connecting piece develops as in wild-type spermatids. Structural abnormalities were not observed when ODF1 was absent. Thus, ODF1 is dispensable for the development of the connecting piece. However, the decapitation of ODF1-deficient spermatozoa indicates that the heads and tails of the spermatozoa are not linked, so that they separate when force is applied.
microRNAs Control Antiviral Immune Response, Cell Death and Chemotaxis Pathways in Human Neuronal Precursor Cells (NPCs) during Zika Virus Infection
Authors: Polonio Carolina M. , da Silva Patrick , Russo Fabiele B. , Hyppolito Brendo R. N. , Zanluqui Nagela G. , Benazzato Cecília , Beltrão-Braga Patrícia C. B. , Muxel Sandra M. , Peron Jean Pierre S.
Published: September 2022

Viral infections have always been a serious burden to public health, increasing morbidity and mortality rates worldwide. Zika virus (ZIKV) is a flavivirus transmitted by the Aedes aegypti vector and the causative agent of severe fetal neuropathogenesis and microcephaly. The virus crosses the placenta and reaches the fetal brain, mainly causing the death of neuronal precursor cells (NPCs), glial inflammation, and subsequent tissue damage. Genetic differences, mainly related to the antiviral immune response and cell death pathways greatly influence the susceptibility to infection. These components are modulated by many factors, including microRNAs (miRNAs). MiRNAs are small noncoding RNAs that regulate post-transcriptionally the overall gene expression, including genes for the neurodevelopment and the formation of neural circuits. In this context, we investigated the pathways and target genes of miRNAs modulated in NPCs infected with ZIKV. We observed downregulation of miR-302b, miR-302c and miR-194, whereas miR-30c was upregulated in ZIKV infected human NPCs in vitro. The analysis of a public dataset of ZIKV-infected human NPCs evidenced 262 upregulated and 3 downregulated genes, of which 142 were the target of the aforementioned miRNAs. Further, we confirmed a correlation between miRNA and target genes affecting pathways related to antiviral immune response, cell death and immune cells chemotaxis, all of which could contribute to the establishment of microcephaly and brain lesions. Here, we suggest that miRNAs target gene expression in infected NPCs, directly contributing to the pathogenesis of fetal microcephaly.
Cytogenetic and Molecular Marker Analyses of a Novel Wheat–Psathyrostachys huashanica 7Ns Disomic Addition Line with Powdery Mildew Resistance
Authors: Tan Binwen , Wang Miaomiao , Cai Li , Li Sanyue , Zhu Wei , Xu Lili , Wang Yi , Zeng Jian , Fan Xing , Sha Lina , Wu Dandan , Cheng Yiran , Zhang Haiqin , Chen Guoyue , Zhou Yonghong , Kang Houyang
Published: September 2022

Powdery mildew caused by Blumeria graminis f. sp. tritici is a devastating disease that reduces wheat yield and quality worldwide. The exploration and utilization of new resistance genes from wild wheat relatives is the most effective strategy against this disease. Psathyrostachys huashanica Keng f. ex P. C. Kuo (2n = 2x = 14, NsNs) is an important tertiary gene donor with multiple valuable traits for wheat genetic improvement, especially disease resistance. In this study, we developed and identified a new wheat—P. huashanica disomic addition line, 18-1-5—derived from a cross between P. huashanica and common wheat lines Chinese Spring and CSph2b. Sequential genomic and multicolor fluorescence in situ hybridization analyses revealed that 18-1-5 harbored 21 pairs of wheat chromosomes plus a pair of alien Ns chromosomes. Non-denaturing fluorescence in situ hybridization and molecular marker analyses further demonstrated that the alien chromosomes were derived from chromosome 7Ns of P. huashanica. The assessment of powdery mildew response revealed that line 18-1-5 was highly resistant at the adult stage to powdery mildew pathogens prevalent in China. The evaluation of agronomic traits indicated that 18-1-5 had a significantly reduced plant height and an increased kernel length compared with its wheat parents. Using genotyping-by-sequencing technology, we developed 118 PCR-based markers specifically for chromosome 7Ns of P. huashanica and found that 26 of these markers could be used to distinguish the genomes of P. huashanica and other wheat-related species. Line 18-1-5 can therefore serve as a promising bridging parent for wheat disease resistance breeding. These markers should be conducive for the rapid, precise detection of P. huashanica chromosomes and chromosomal segments carrying Pm resistance gene(s) during marker-assisted breeding and for the investigation of genetic differences and phylogenetic relationships among diverse Ns genomes and other closely related ones.
Erythrocyte-Derived Nanoparticles with Folate Functionalization for Near Infrared Pulsed Laser-Mediated Photo-Chemotherapy of Tumors
Authors: Mac Jenny T. , Vankayala Raviraj , Lee Chi-Hua , Anvari Bahman
Published: September 2022

Despite its common side effects and varying degrees of therapeutic success, chemotherapy remains the gold standard method for treatment of cancer. Towards developing a new therapeutic approach, we have engineered nanoparticles derived from erythrocytes that contain indocyanine green as a photo-activated agent that enables near infrared photothermal heating, and doxorubicin hydrochloride (DOX) as a chemotherapeutic drug. We hypothesize that milliseconds pulsed laser irradiation results in rapid heating and photo-triggered release of DOX, providing a dual photo-chemo therapeutic mechanism for tumor destruction. Additionally, the surface of the nanoparticles is functionalized with folate to target the folate receptor-α on tumor cells to further enhance the therapeutic efficacy. Using non-contract infrared radiometry and absorption spectroscopy, we have characterized the photothermal response and photostability of the nanoparticles to pulsed laser irradiation. Our in vitro studies show that these nanoparticles can mediate photo-chemo killing of SKOV3 ovarian cancer cells when activated by pulsed laser irradiation. We further demonstrate that this dual photo-chemo therapeutic approach is effective in reducing the volume of tumor implants in mice and elicits an apoptotic response. This treatment modality presents a promising approach in destruction of small tumor nodules.
Uba1: A Potential Ubiquitin-like Activator Protein of Urm1 in Toxoplasma gondii
Authors: Xiao Qianqian , Li Jinxuan , Chen Junpeng , Tan Qianqian , Chen Xiao , Li Hongmei , Zhao Xiaomin , Zhang Xiao
Published: September 2022

We had shown in our previous study that TgUrm1 (ubiquitin-related Modifier 1) was involved in the regulation of anti-oxidant stress in Toxoplasma gondii by conjugating with TgAhp1. It is generally believed that Urm1 binds to target proteins through a mechanism involving Uba (ubiquitin-like activator protein). Here, we identified the TgUrm1-exclusive ubiquitin-like activator-TgUba1, which was located in the cytoplasm of Toxoplasma. TgUba1 contained three domains, including the atrophin-1 domain (ANT1), the E1-like domain (AD), and the rhodanese homology domain (RHD). We explored the interaction of TgUba1 with TgUrm1, and the AD domain was essential for the interaction of the two proteins. The TgUba1 knockout and complementary mutants were obtained based on CRISPR/Cas9 gene editing technology. The knockout of TgUba1 attenuated parasite proliferation and virulence in mice, but not invasion and egress processes, revealing the pivotal role played by TgUba1 in T. gondii survival. Meanwhile, the conjugate band of TgUrm1 was significantly reduced under oxidative stress stimulation without TgUba1, indicating that TgUba1 enhanced the targeted conjugation ability of TgUrm1 in response to oxidative stress, especially under diamide (Dia) stimulation. Furthermore, eleven TgUba1-interacting proteins were identified by proximity-based protein labeling techniques, relating them to ubiquitin-like modifications, anti-oxidative stress and metabolic regulation processes. In conclusion, TgUba1 was essential for T. gondii survival and might be a potential ubiquitin-like activator protein for TgUrm1.
Histidine-Rich Glycoprotein Suppresses the S100A8/A9-Mediated Organotropic Metastasis of Melanoma Cells
Authors: Tomonobu Nahoko , Kinoshita Rie , Wake Hidenori , Inoue Yusuke , Ruma I Made Winarsa , Suzawa Ken , Gohara Yuma , Komalasari Ni Luh Gede Yoni , Jiang Fan , Murata Hitoshi , Yamamoto Ken-ichi , Sumardika I Wayan , Chen Youyi , Futami Junichiro , Yamauchi Akira , Kuribayashi Futoshi , Kondo Eisaku , Toyooka Shinichi , Nishibori Masahiro , Sakaguchi Masakiyo
Published: September 2022

The dissection of the complex multistep process of metastasis exposes vulnerabilities that could be exploited to prevent metastasis. To search for possible factors that favor metastatic outgrowth, we have been focusing on secretory S100A8/A9. A heterodimer complex of the S100A8 and S100A9 proteins, S100A8/A9 functions as a strong chemoattractant, growth factor, and immune suppressor, both promoting the cancer milieu at the cancer-onset site and cultivating remote, premetastatic cancer sites. We previously reported that melanoma cells show lung-tropic metastasis owing to the abundant expression of S100A8/A9 in the lung. In the present study, we addressed the question of why melanoma cells are not metastasized into the brain at significant levels in mice despite the marked induction of S100A8/A9 in the brain. We discovered the presence of plasma histidine-rich glycoprotein (HRG), a brain-metastasis suppression factor against S100A8/A9. Using S100A8/A9 as an affinity ligand, we searched for and purified the binding plasma proteins of S100A8/A9 and identified HRG as the major protein on mass spectrometric analysis. HRG prevents the binding of S100A8/A9 to the B16-BL6 melanoma cell surface via the formation of the S100A8/A9 complex. HRG also inhibited the S100A8/A9-induced migration and invasion of A375 melanoma cells. When we knocked down HRG in mice bearing skin melanoma, metastasis to both the brain and lungs was significantly enhanced. The clinical examination of plasma S100A8/A9 and HRG levels showed that lung cancer patients with brain metastasis had higher S100A8/A9 and lower HRG levels than nonmetastatic patients. These results suggest that the plasma protein HRG strongly protects the brain and lungs from the threat of melanoma metastasis.
Sugarcane Rhizosphere Bacteria Community Migration Correlates with Growth Stages and Soil Nutrient
Authors: Yuan Zhaonian , Liu Qiang , Pang Ziqin , Fallah Nyumah , Liu Yueming , Hu Chaohua , Lin Wenxiong
Published: September 2022

Plants and rhizosphere bacterial microbiota have intimate relationships. As neighbors of the plant root system, rhizosphere microorganisms have a crucial impact on plant growth and health. In this study, we sampled rhizosphere soil of sugarcane in May (seedling), July (tillering), September (elongation) and November (maturity), respectively. We employ 16S rRNA amplicon sequencing to investigate seasonal variations in rhizosphere bacteria community structure and abundance, as well as their association with soil edaphic factors. The results demonstrate that soil pH, total nitrogen (TN) and available nitrogen (AN) decrease substantially with time. Rhizosphere bacteria diversity (Shannon) and the total enriched OTUs are also significantly higher in July relative to other months. Bacteria OTUs and functional composition exhibit a strong and significant correlation with soil temperature (Tem), suggesting that Tem was the potential determinant controlling rhizosphere bacteria diversity, enriched OTUs as well as functional composition. Redundancy analysis (RDA) point toward soil total potassium (TK), pH, TN, Tem and AN as principal determinant altering shifting bacteria community structure. Variation partitioning analysis (VPA) analysis further validate that a substantial proportion of variation (70.79%) detected in the rhizosphere bacteria community structure was attributed to edaphic factors. Mfuzz analysis classified the bacterial genera into four distinct clusters, with cluster two exhibiting a distinct and dramatic increase in July, predominantly occupied by Allocatelliglobosispora. The stochastic forest model found the key characteristic bacterial populations that can distinguish the four key growth periods of sugarcane. It may help us to answer some pending questions about the interaction of rhizosphere microorganisms with plants in the future.
The Entero-Mammary Pathway and Perinatal Transmission of Gut Microbiota and SARS-CoV-2
Authors: Juárez-Castelán Carmen Josefina , Vélez-Ixta Juan Manuel , Corona-Cervantes Karina , Piña-Escobedo Alberto , Cruz-Narváez Yair , Hinojosa-Velasco Alejandro , Landero-Montes-de-Oca María Esther , Davila-Gonzalez Eduardo , González-del-Olmo Eduardo , Bastida-Gonzalez Fernando , Zárate-Segura Paola Berenice , García-Mena Jaime
Published: September 2022

COVID-19 is a severe respiratory disease threatening pregnant women, which increases the possibility of adverse pregnancy outcomes. Several recent studies have demonstrated the ability of SARS-CoV-2 to infect the mother enterocytes, disturbing the gut microbiota diversity. The aim of this study was to characterize the entero-mammary microbiota of women in the presence of the virus during delivery. Fifty mother–neonate pairs were included in a transversal descriptive work. The presence of SARS-CoV-2 RNA was detected in nasopharyngeal, mother rectal swabs (MRS) and neonate rectal swabs (NRS) collected from the pairs, and human colostrum (HC) samples collected from mothers. The microbiota diversity was characterized by high-throughput DNA sequencing of V3-16S rRNA gene libraries prepared from HC, MRS, and NRS. Data were analyzed with QIIME2 and R. Our results indicate that several bacterial taxa are highly abundant in MRS positive for SARS-CoV-2 RNA. These bacteria mostly belong to the Firmicutes phylum; for instance, the families Bifidobacteriaceae, Oscillospiraceae, and Microbacteriaceae have been previously associated with anti-inflammatory effects, which could explain the capability of women to overcome the infection. All samples, both positive and negative for SARS-CoV-2, featured a high abundance of the Firmicutes phylum. Further data analysis showed that nearly 20% of the bacterial diversity found in HC was also identified in MRS. Spearman correlation analysis highlighted that some genera of the Proteobacteria and Actinobacteria phyla were negatively correlated with MRS and NRS (p < 0.005). This study provides new insights into the gut microbiota of pregnant women and their potential association with a better outcome during SARS-CoV-2 infection.
Chondrocytes In Vitro Systems Allowing Study of OA
Authors: Bednarczyk Ewa
Published: September 2022

Osteoarthritis (OA) is an extremely complex disease, as it combines both biological-chemical and mechanical aspects, and it also involves the entire joint consisting of various types of tissues, including cartilage and bone. This paper describes the methods of conducting cell cultures aimed at searching for the mechanical causes of OA development, therapeutic solutions, and methods of preventing the disease. It presents the systems for the cultivation of cartilage cells depending on the level of their structural complexity, and taking into account the most common solutions aimed at recreating the most important factors contributing to the development of OA, that is mechanical loads. In-vitro systems used in tissue engineering to investigate the phenomena associated with OA were specified depending on the complexity and purposefulness of conducting cell cultures.
Glycyrrhizic Acid Derivatives Bearing Amino Acid Residues in the Carbohydrate Part as Dengue Virus E Protein Inhibitors: Synthesis and Antiviral Activity
Authors: Hour Mann-Jen , Chen Yeh , Lin Chen-Sheng , Baltina Lidia A. , Kan Ju-Ying , Tsai Yan-Ting , Kiu Yan-Tung , Lai Hsueh-Chou , Baltina Lia A. , Petrova Svetlana F. , Lin Cheng-Wen
Published: September 2022

Dengue virus (DENV) is one of the most geographically distributed mosquito-borne flaviviruses, like Japanese encephalitis virus (JEV), and Zika virus (ZIKV). In this study, a library of the known and novel Glycyrrhizic acid (GL) derivatives bearing amino acid residues or their methyl/ethyl esters in the carbohydrate part were synthesized and studied as DENV inhibitors in vitro using the cytopathic effect (CPE), viral infectivity and virus yield assays with DENV1 and DENV-2 in Vero E6 and A549 cells. Among the GL conjugates tested, compound hits GL-D-ValOMe 3, GL-TyrOMe 6, GL-PheOEt 11, and GL-LysOMe 21 were discovered to have better antiviral activity than GL, with IC50 values ranging from <0.1 to 5.98 μM on the in vitro infectivity of DENV1 and DENV2 in Vero E6 and A549 cells. Compound hits 3, 6, 11, and 21 had a concentration-dependent inhibition on the virus yield in Vero E6, in which GL-D-ValOMe 3 and GL-PheOEt 11 were the most active inhibitors of DENV2 yield. Meanwhile, the time-of-addition assay indicated that conjugates GL-D-ValOMe 3 and GL-PheOEt 11 exhibited a substantial decrease in the DENV2 attachment stage. Subsequently, chimeric single-round infectious particles (SRIPs) of DENV2 C-prM-E protein/JEV replicon and DENV2 prM-E/ZIKV replicon were utilized for the DENV envelope I protein-mediated attachment assay. GL conjugates 3 and 11 significantly reduced the attachment of chimeric DENV2 C-prM-E/JEV and DENV2 prM-E/ZIKV SRIPs onto Vero E6 cells in a concentration-dependent manner but did not impede the attachment of wild-type JEV CprME/JEV and ZIKV prM-E/ZIKV SRIPs, indicating the inhibition of Compounds 3 and 11 on DENV2 E-mediated attachment. Molecular docking data revealed that Compounds 3 and 11 have hydrophobic interactions within a hydrophobic pocket among the interfaces of Domains I, II, and the stem region of the DENV2 envelope (E) protein. These results displayed that Compounds 3 and 11 were the lead compounds targeting the DENV E protein. Altogether, our findings provide new insights into the structure–activity relationship of GL derivatives conjugated with amino acid residues and can be the new fundamental basis for the search and development of novel flavivirus inhibitors based on natural compounds.
Exploring the Expression of Pro-Inflammatory and Hypoxia-Related MicroRNA-20a, MicroRNA-30e, and MicroRNA-93 in Periodontitis and Gingival Mesenchymal Stem Cells under Hypoxia
Authors: Chaparro Alejandra , Lozano Mauricio , Gaedechens Dominique , López Carolina , Albers Daniela , Hernández Marcela , Pascual Andrés , Nart José , Irarrazabal Carlos E.
Published: September 2022

Hypoxia associated with inflammation are common hallmarks observed in several diseases, and it plays a major role in the expression of non-coding RNAs, including microRNAs (miRNAs). In addition, the miRNA target genes for hypoxia-inducible factor-1α (HIF-1α) and nuclear factor of activated T cells-5 (NFAT5) modulate the adaptation to hypoxia. The objective of the present study was to explore hypoxia-related miRNA target genes for HIF-1α and NFAT5, as well as miRNA-20a, miRNA-30e, and miRNA-93 expression in periodontitis versus healthy gingival tissues and gingival mesenchymal stem cells (GMSCs) cultured under hypoxic conditions. Thus, a case-control study was conducted, including healthy and periodontitis subjects. Clinical data and gingival tissue biopsies were collected to analyze the expression of miRNA-20a, miRNA-30e, miRNA-93, HIF-1α, and NFAT5 by qRT-PCR. Subsequently, GMSCs were isolated and cultured under hypoxic conditions (1% O2) to explore the expression of the HIF-1α, NFAT5, and miRNAs. The results showed a significant upregulation of miRNA-20a (p = 0.028), miRNA-30e (p = 0.035), and miRNA-93 (p = 0.026) in periodontitis tissues compared to healthy gingival biopsies. NFAT5 mRNA was downregulated in periodontitis tissues (p = 0.037), but HIF-1α was not affected (p = 0.60). Interestingly, hypoxic GMSCs upregulated the expression of miRNA-20a and HIF-1α, but they downregulated miRNA-93e. In addition, NFAT5 mRNA expression was not affected in hypoxic GMSCs. In conclusion, in periodontitis patients, the expression of miRNA-20a, miRNA-30e, and miRNA-93 increased, but a decreased expression of NFAT5 mRNA was detected. In addition, GMSCs under hypoxic conditions upregulate the HIF-1α and increase miRNA-20a (p = 0.049) expression. This study explores the role of inflammatory and hypoxia-related miRNAs and their target genes in periodontitis and GMSCs. It is crucial to determine the potential therapeutic target of these miRNAs and hypoxia during the periodontal immune–inflammatory response, which should be analyzed in greater depth in future studies.
Phagocytosis-Regulators-Based Signature to Predict the Prognosis and Chemotherapy Resistance for Breast Cancer Patients
Authors: Feng Juan , Ren Jun , Li Xiuqi , Zhang Xue , Yang Qingfeng , Wu Zankai , Cui Le , Liao Lingxia , Gong Yiping , Cao Dedong
Published: September 2022

Phagocytosis is crucial in tumor surveillance and immune function. The association between phagocytosis and the outcomes of breast cancer patients has not been well-determined. In this study, data were downloaded from the cancer genome atlas (TCGA) and gene expression omnibus (GEO) databases to investigate the role of phagocytosis in breast cancer. Data from the TCGA and GEO databases were used to investigate the prognostic role of phagocytosis in breast cancer. Then, we performed pathway enrichment analysis, copy number variation (CNV) and single-nucleotide variant (SNV) analyses, immune infiltration analysis, calculation of tumor purity, stromal score, and immune score, and consistent clustering. We also constructed a phagocytosis-regulators-based signature system to examine its association in survival and drug response. The genomic and expression differences in the phagocytosis regulators in breast cancer were systematically analyzed, explaining the widespread dysregulation of phagocytosis regulators. Using the investigated association of phagocytosis regulators with the prognosis and tumor immune environment, we constructed a prognostic model based on phagocytosis regulators. We discovered that patients with high risk scores had a poor prognosis and were negatively associated with immune functions. The model had preferential predictive performance and significantly consistent drug-resistance prediction results. Our findings suggest that the phagocytosis-factors-based scoring system can be used as a novel prognostic factor, serving as a powerful reference tool for predicting prognosis and developing methods against drug resistance.
Indications of Peripheral Pain, Dermal Hypersensitivity, and Neurogenic Inflammation in Patients with Lipedema
Authors: Chakraborty Adri , Crescenzi Rachelle , Usman Timaj A. , Reyna Andrea J. , Garza Maria E. , Al-Ghadban Sara , Herbst Karen L. , Donahue Paula M. C. , Rutkowski Joseph M.
Published: September 2022

Lipedema is a disease with abnormally increased adipose tissue deposition and distribution. Pain sensations have been described in the clinical evaluation of lipedema, but its etiology remains poorly understood. We hypothesized that pain sensitivity measurements and ex vivo quantitation of neuronal cell body distribution in the skin would be lipedema stage-dependent, and could, thus, serve to objectively characterize neuropathic pain in lipedema. The pain was assessed by questionnaire and peripheral cutaneous mechanical sensitization (von-Frey) in lipedema (n = 27) and control (n = 23) consenting female volunteers. Dermal biopsies from (n = 11) Stages 1–3 lipedema and control (n = 10) participants were characterized for neuronal cell body and nociceptive neuropeptide calcitonin gene-related peptide (CGRP) and nerve growth factor (NGF) distribution. Stage 2 or 3 lipedema participants responded positively to von Frey sensitization in the calf and thigh, and Stage 3 participants also responded in the arm. Lipedema abdominal skin displayed reduced Tuj-1+ neuronal cell body density, compared to healthy controls, while CGRP and NGF was significantly elevated in Stage 3 lipedema tissues. Together, dermal neuronal cell body loss is consistent with hyper-sensitization in patients with lipedema. Further study of neuropathic pain in lipedema may elucidate underlying disease mechanisms and inform lipedema clinical management and treatment impact.
Cell-Based and Selected Cell-Free Therapies for Myocardial Infarction: How Do They Compare to the Current Treatment Options?
Authors: Csöbönyeiová Mária , Beerová Nikoleta , Klein Martin , Debreová-Čeháková Michaela , Danišovič Ľuboš
Published: September 2022

Because of cardiomyocyte death or dysfunction frequently caused by myocardial infarction (MI), heart failure is a leading cause of morbidity and mortality in modern society. Paradoxically, only limited and non-curative therapies for heart failure or MI are currently available. As a result, over the past two decades research has focused on developing cell-based approaches promoting the regeneration of infarcted tissue. Cell-based therapies for myocardial regeneration include powerful candidates, such as multipotent stem cells (mesenchymal stem cells (MSCs), bone-marrow-derived stem cells, endothelial progenitor cells, and hematopoietic stem cells) and induced pluripotent stem cells (iPSCs). These possess unique properties, such as potency to differentiate into desired cell types, proliferation capacity, and patient specificity. Preclinical and clinical studies have demonstrated modest improvement in the myocardial regeneration and reduced infarcted areas upon transplantation of pluripotent or multipotent stem cells. Another cell population that need to be considered as a potential source for cardiac regeneration are telocytes found in different organs, including the heart. Their therapeutic effect has been studied in various heart pathologies, such as MI, arrhythmias, or atrial amyloidosis. The most recent cell-free therapeutic tool relies on the cardioprotective effect of complex cargo carried by small membrane-bound vesicles—exosomes—released from stem cells via exocytosis. The MSC/iPSC-derived exosomes could be considered a novel exosome-based therapy for cardiovascular diseases thanks to their unique content. There are also other cell-free approaches, e.g., gene therapy, or acellular cardiac patches. Therefore, our review provides the most recent insights into the novel strategies for myocardial repair based on the regenerative potential of different cell types and cell-free approaches.
Cheminformatics-Based Discovery of Potential Chemical Probe Inhibitors of Omicron Spike Protein
Authors: Khan Salman Ali , Khan Alamgir , Zia Komal , Shawish Ihab , Barakat Assem , Ul-Haq Zaheer
Published: September 2022

During the past two decades, the world has witnessed the emergence of various SARS-CoV-2 variants with distinct mutational profiles influencing the global health, economy, and clinical aspects of the COVID-19 pandemic. These variants or mutants have raised major concerns regarding the protection provided by neutralizing monoclonal antibodies and vaccination, rates of virus transmission, and/or the risk of reinfection. The newly emerged Omicron, a genetically distinct lineage of SARS-CoV-2, continues its spread in the face of rising vaccine-induced immunity while maintaining its replication fitness. Efforts have been made to improve the therapeutic interventions and the FDA has issued Emergency Use Authorization for a few monoclonal antibodies and drug treatments for COVID-19. However, the current situation of rapidly spreading Omicron and its lineages demands the need for effective therapeutic interventions to reduce the COVID-19 pandemic. Several experimental studies have indicated that the FDA-approved monoclonal antibodies are less effective than antiviral drugs against the Omicron variant. Thus, in this study, we aim to identify antiviral compounds against the Spike protein of Omicron, which binds to the human angiotensin-converting enzyme 2 (ACE2) receptor and facilitates virus invasion. Initially, docking-based virtual screening of the in-house database was performed to extract the potential hit compounds against the Spike protein. The obtained hits were optimized by DFT calculations to determine the electronic properties and molecular reactivity of the compounds. Further, MD simulation studies were carried out to evaluate the dynamics of protein–ligand interactions at an atomistic level in a time-dependent manner. Collectively, five compounds (AKS-01, AKS-02, AKS-03, AKS-04, and AKS-05) with diverse scaffolds were identified as potential hits against the Spike protein of Omicron. Our study paves the way for further in vitro and in vivo studies.
Functional Characterization of the N-Terminal Disordered Region of the piggyBac Transposase
Authors: Wachtl Gerda , Schád Éva , Huszár Krisztina , Palazzo Antonio , Ivics Zoltán , Tantos Ágnes , Orbán Tamás I.
Published: September 2022

The piggyBac DNA transposon is an active element initially isolated from the cabbage looper moth, but members of this superfamily are also present in most eukaryotic evolutionary lineages. The functionally important regions of the transposase are well described. There is an RNase H-like fold containing the DDD motif responsible for the catalytic DNA cleavage and joining reactions and a C-terminal cysteine-rich domain important for interaction with the transposon DNA. However, the protein also contains a ~100 amino acid long N-terminal disordered region (NTDR) whose function is currently unknown. Here we show that deletion of the NTDR significantly impairs piggyBac transposition, although the extent of decrease is strongly cell-type specific. Moreover, replacing the NTDR with scrambled but similarly disordered sequences did not rescue transposase activity, indicating the importance of sequence conservation. Cell-based transposon excision and integration assays reveal that the excision step is more severely affected by NTDR deletion. Finally, bioinformatic analyses indicated that the NTDR is specific for the piggyBac superfamily and is also present in domesticated, transposase-derived proteins incapable of catalyzing transposition. Our results indicate an essential role of the NTDR in the “fine-tuning” of transposition and its significance in the functions of piggyBac-originated co-opted genes.
Hemodynamics and Tissue Optical Properties in Bimodal Infarctions Induced by Middle Cerebral Artery Occlusion
Authors: Wu Chun-Wei , Chen Jia-Jin , Lin Chou-Ching K. , Chen Chien-An , Wu Chun-Ie , Hwang Ing-Shiou , Hsieh Tsung-Hsun , Lin Bor-Shing , Peng Chih-Wei
Published: September 2022

Various infarct sizes induced by middle cerebral artery occlusion (MCAO) generate inconsistent outcomes for stroke preclinical study. Monitoring cerebral hemodynamics may help to verify the outcome of MCAO. The aim of this study was to investigate the changes in brain tissue optical properties by frequency-domain near-infrared spectroscopy (FD-NIRS), and establish the relationship between cerebral hemodynamics and infarct variation in MCAO model. The rats were undergone transient MCAO using intraluminal filament. The optical properties and hemodynamics were measured by placing the FD-NIRS probes on the scalp of the head before, during, and at various time-courses after MCAO. Bimodal infarction severities were observed after the same 90-min MCAO condition. Significant decreases in concentrations of oxygenated hemoglobin ([HbO]) and total hemoglobin ([HbT]), tissue oxygenation saturation (StO2), absorption coefficient (μa) at 830 nm, and reduced scattering coefficient (μs’) at both 690 and 830 nm were detected during the occlusion in the severe infarction but not the mild one. Of note, the significant increases in [HbO], [HbT], StO2, and μa at both 690 and 830 nm were found on day 3; and increases in μs’ at both 690 and 830 nm were found on day 2 and day 3 after MCAO, respectively. The interhemispheric correlation coefficient (IHCC) was computed from low-frequency hemodynamic oscillation of both hemispheres. Lower IHCCs standing for interhemispheric desynchronizations were found in both mild and severe infarction during occlusion, and only in severe infarction after reperfusion. Our finding supports that sequential FD-NIRS parameters may associated with the severity of the infarction in MCAO model, and the consequent pathologies such as vascular dysfunction and brain edema. Further study is required to validate the potential use of FD-NIRS as a monitor for MCAO verification.
High-Precision Automatic Identification of Fentanyl-Related Drugs by Terahertz Spectroscopy with Molecular Dynamics Simulation and Spectral Similarity Mapping
Authors: Qu Fangfang , Lin Lei , Nie Pengcheng , Xia Zhengyan
Published: September 2022

Fentanyl is a potent opioid analgesic with high bioavailability. It is the leading cause of drug addiction and overdose death. To better control the abuse of fentanyl and its derivatives, it is crucial to develop rapid and sensitive detection methods. However, fentanyl-related substrates undergo similar molecular structures resulting in similar properties, which are difficult to be identified by conventional spectroscopic methods. In this work, a method for the automatic identification of 8 fentanyl-related substances with similar spectral characteristics was developed using terahertz (THz) spectroscopy coupled with density functional theory (DFT) and spectral similarity mapping (SSM). To characterize the THz fingerprints of these fentanyl-related samples more accurately, the method of baseline estimation and denoising with sparsity was performed before revealing the unique molecular dynamics of each substance by DFT. The SSM method was proposed to identify these fentanyl analogs based on weighted spectral cosine–cross similarity and fingerprint discrete Fréchet distance, generating a matching list by stepwise searching the entire spectral database. The top matched list returned the identification results of the target fentanyl analogs with accuracies of 94.48~99.33%. Results from this work provide algorithms’ increased reliability, which serves as an artificial intelligence-based tool for high-precision fentanyl analysis in real-world samples.
Comparative Analysis of Peniophora lycii and Trametes hirsuta Exoproteomes Demonstrates “Shades of Gray” in the Concept of White-Rotting Fungi
Authors: Shabaev Alexander V. , Moiseenko Konstantin V. , Glazunova Olga A. , Savinova Olga S. , Fedorova Tatyana V.
Published: September 2022

White-rot basidiomycete fungi are a unique group of organisms that evolved an unprecedented arsenal of extracellular enzymes for an efficient degradation of all components of wood such as cellulose, hemicelluloses and lignin. The exoproteomes of white-rot fungi represent a natural enzymatic toolbox for white biotechnology. Currently, only exoproteomes of a narrow taxonomic group of white-rot fungi—fungi belonging to the Polyporales order—are extensively studied. In this article, two white-rot fungi, Peniophora lycii LE-BIN 2142 from the Russulales order and Trametes hirsuta LE-BIN 072 from the Polyporales order, were compared and contrasted in terms of their enzymatic machinery used for degradation of different types of wood substrates—alder, birch and pine sawdust. Our findings suggested that the studied fungi use extremely different enzymatic systems for the degradation of carbohydrates and lignin. While T. hirsuta LE-BIN 072 behaved as a typical white-rot fungus, P. lycii LE-BIN 2142 demonstrated substantial peculiarities. Instead of using cellulolytic and hemicellulolytic hydrolytic enzymes, P. lycii LE-BIN 2142 primarily relies on oxidative polysaccharide-degrading enzymes such as LPMO and GMC oxidoreductase. Moreover, exoproteomes of P. lycii LE-BIN 2142 completely lacked ligninolytic peroxidases, a well-known marker of white-rot fungi, but instead contained several laccase isozymes and previously uncharacterized FAD-binding domain-containing proteins.
Towards Molecular Understanding of the Functional Role of UbiJ-UbiK2 Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies
Authors: Launay Romain , Teppa Elin , Martins Carla , Abby Sophie S. , Pierrel Fabien , André Isabelle , Esque Jérémy
Published: September 2022

Ubiquinone (UQ) is a polyisoprenoid lipid found in the membranes of bacteria and eukaryotes. UQ has important roles, notably in respiratory metabolisms which sustain cellular bioenergetics. Most steps of UQ biosynthesis take place in the cytosol of E. coli within a multiprotein complex called the Ubi metabolon, that contains five enzymes and two accessory proteins, UbiJ and UbiK. The SCP2 domain of UbiJ was proposed to bind the hydrophobic polyisoprenoid tail of UQ biosynthetic intermediates in the Ubi metabolon. How the newly synthesised UQ might be released in the membrane is currently unknown. In this paper, we focused on better understanding the role of the UbiJ-UbiK2 heterotrimer forming part of the metabolon. Given the difficulties to gain functional insights using biophysical techniques, we applied a multiscale molecular modelling approach to study the UbiJ-UbiK2 heterotrimer. Our data show that UbiJ-UbiK2 interacts closely with the membrane and suggests possible pathways to enable the release of UQ into the membrane. This study highlights the UbiJ-UbiK2 complex as the likely interface between the membrane and the enzymes of the Ubi metabolon and supports that the heterotrimer is key to the biosynthesis of UQ8 and its release into the membrane of E. coli.
Micro- and Nanoplastics’ Effects on Protein Folding and Amyloidosis
Authors: Windheim Joseph , Colombo Laura , Battajni Nora C. , Russo Luca , Cagnotto Alfredo , Diomede Luisa , Bigini Paolo , Vismara Elena , Fiumara Ferdinando , Gabbrielli Silvia , Gautieri Alfonso , Mazzuoli-Weber Gemma , Salmona Mario , Colnaghi Luca
Published: September 2022

A significant portion of the world’s plastic is not properly disposed of and, through various processes, is degraded into microscopic particles termed micro- and nanoplastics. Marine and terrestrial faunae, including humans, inevitably get in contact and may inhale and ingest these microscopic plastics which can deposit throughout the body, potentially altering cellular and molecular functions in the nervous and other systems. For instance, at the cellular level, studies in animal models have shown that plastic particles can cross the blood–brain barrier and interact with neurons, and thus affect cognition. At the molecular level, plastics may specifically influence the folding of proteins, induce the formation of aberrant amyloid proteins, and therefore potentially trigger the development of systemic and local amyloidosis. In this review, we discuss the general issue of plastic micro- and nanoparticle generation, with a focus on their effects on protein folding, misfolding, and their possible clinical implications.
Isoquinoline Alkaloids from Coptis chinensis Franch: Focus on Coptisine as a Potential Therapeutic Candidate against Gastric Cancer Cells
Authors: Nakonieczna Sylwia , Grabarska Aneta , Gawel Kinga , Wróblewska-Łuczka Paula , Czerwonka Arkadiusz , Stepulak Andrzej , Kukula-Koch Wirginia
Published: September 2022

Gastric cancer (GC) has high incidence rates and constitutes a common cause of cancer mortality. Despite advances in treatment, GC remains a challenge in cancer therapy which is why novel treatment strategies are needed. The interest in natural compounds has increased significantly in recent years because of their numerous biological activities, including anti-cancer action. The isolation of the bioactive compounds from Coptis chinensis Franch was carried out with the Centrifugal Partition Chromatography (CPC) technique, using a biphasic solvent system composed of chloroform (CHCl3)—methanol (MeOH)—water (H2O) (4:3:3, v/v) with an addition of hydrochloric acid and trietylamine. The identity of the isolated alkaloids was confirmed using a high resolution HPLC-MS chromatograph. The phytochemical constituents of Coptis chinensis such as berberine, jatrorrhizine, palmatine and coptisine significantly inhibited the viability and growth of gastric cancer cell lines ACC-201 and NCI-N87 in a dose-dependent manner, with coptisine showing the highest efficacy as revealed using MTT and BrdU assays, respectively. Flow cytometry analysis confirmed the coptisine-induced population of gastric cancer cells in sub-G1 phase and apoptosis. The combination of coptisine with cisplatin at the fixed-ratio of 1:1 exerted synergistic and additive interactions in ACC-201 and NCI-N87, respectively, as determined by means of isobolographic analysis. In in vivo assay, coptisine was safe for developing zebrafish at the dose equivalent to the highest dose active in vitro, but higher doses (greater than 10 times) caused morphological abnormalities in larvae. Our findings provide a theoretical foundation to further studies on more detailed mechanisms of the bioactive compounds from Coptis chinensis Franch anti-cancer action that inhibit GC cell survival in in vitro settings.
The Role of Bradykinin Receptors in Hereditary Angioedema Due to C1-Inhibitor Deficiency
Authors: Dyga Wojciech , Obtulowicz Aleksander , Mikolajczyk Tomasz , Bogdali Anna , Dubiela Pawel , Obtulowicz Krystyna
Published: September 2022

Background: Hereditary angioedema (HAE) is a rare, genetic disease caused by the decreased level or function of the C1 inhibitor. The primary mediator of symptoms in HAE is bradykinin acting through its two receptors, namely receptors 1 (BR1) and 2 (BR2). Although BR2 is well characterized, the role of BR1 remains unclear. Objective: To study the role of bradykinin receptors 1 (BR1) in the etiopathogenesis of HAE. Methods: A total of 70 individuals, 40 patients with HAE, and 30 healthy subjects were recruited to the study. HAE was diagnosed in accordance with the international guideline. The level of bradykinin receptors was determined in populations of CD3+, CD4+, CD8+, and CD14++CD16−, CD14++CD16+ monocytes. In addition, the level of disease activity-specific markers was measured. Results: There were statistically significant differences in the subpopulation of lymphocytes and monocytes between patients with HAE compared to healthy subjects. The level of BR1 and BR2 on PBMCs was comparable in healthy subjects and HAE patients during remission with significant overexpression of both receptors, triggered by HAE attack. Moreover, a significant increase in TNF-alpha and IL-1 plasma levels was observed among HAE patients. Conclusions: BR1 expression may play an important role in the pathomechanism of HAE.
Bioactive Composite for Orbital Floor Repair and Regeneration
Authors: AL-Hamoudi Fahad , Rehman Hamza U. , Almoshawah Yasir A. , Talari Abdullah C. S. , Chaudhry Aqif A. , Reilly Gwendolen C. , Rehman Ihtesham U.
Published: September 2022

In the maxillofacial area, specifically the orbital floor, injuries can cause bone deformities in the head and face that are difficult to repair or regenerate. Treatment methodologies include use of polymers, metal, ceramics on their own and in combinations mainly for repair purposes, but little attention has been paid to identify suitable materials for orbital floor regeneration. Polyurethane (PU) and hydroxyapatite (HA) micro- or nano- sized with different percentages (25%, 40% & 60%) were used to fabricate bioactive tissue engineering (TE) scaffolds using solvent casting and particulate leaching methods. Mechanical and physical characterisation of TE scaffolds was investigated by tensile tests and SEM respectively. Chemical and structural properties of PU and PU/HA scaffolds were evaluated by infrared (IR) spectroscopy and Surface properties of the bioactive scaffold were analysed using attenuated total reflectance (ATR) sampling accessory coupled with IR. Cell viability, collagen formed, VEGF protein amount and vascularisation of bioactive TE scaffold were studied. IR characterisation confirmed the integration of HA in composite scaffolds, while ATR confirmed the significant amount of HA present at the top surface of the scaffold, which was a primary objective. The SEM images confirmed the pores’ interconnectivity. Increasing the content of HA up to 40% led to an improvement in mechanical properties, and the incorporation of nano-HA was more promising than that of micro-HA. Cell viability assays (using MG63) confirmed biocompatibility and CAM assays confirmed vascularization, demonstrating that HA enhances vascularization. These properties make the resulting biomaterials very useful for orbital floor repair and regeneration.