bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved Genetic Map Identified Major QTLs for Drought Tolerance- and Iron Deficiency Tolerance-Related Traits in Groundnut
Authors: Pandey Manish K. , Gangurde Sunil S. , Sharma Vinay , Pattanashetti Santosh K. , Naidu Gopalakrishna K. , Faye Issa , Hamidou Falalou , Desmae Haile , Kane Ndjido Ardo , Yuan Mei , Vadez Vincent , Nigam Shyam N. , Varshney Rajeev K.
Published: December 2020

A deep understanding of the genetic control of drought tolerance and iron deficiency tolerance is essential to hasten the process of developing improved varieties with higher tolerance through genomics-assisted breeding. In this context, an improved genetic map with 1205 loci was developed spanning 2598.3 cM with an average 2.2 cM distance between loci in the recombinant inbred line (TAG 24 × ICGV 86031) population using high-density 58K single nucleotide polymorphism (SNP) “Axiom_Arachis” array. Quantitative trait locus (QTL) analysis was performed using extensive phenotyping data generated for 20 drought tolerance- and two iron deficiency tolerance-related traits from eight seasons (2004–2015) at two locations in India, one in Niger, and one in Senegal. The genome-wide QTL discovery analysis identified 19 major main-effect QTLs with 10.0–33.9% phenotypic variation explained (PVE) for drought tolerance- and iron deficiency tolerance- related traits. Major main-effect QTLs were detected for haulm weight (20.1% PVE), SCMR (soil plant analytical development (SPAD) chlorophyll meter reading, 22.4% PVE), and visual chlorosis rate (33.9% PVE). Several important candidate genes encoding glycosyl hydrolases; malate dehydrogenases; microtubule-associated proteins; and transcription factors such as MADS-box, basic helix-loop-helix (bHLH), NAM, ATAF, and CUC (NAC), and myeloblastosis (MYB) were identified underlying these QTL regions. The putative function of these genes indicated their possible involvement in plant growth, development of seed and pod, and photosynthesis under drought or iron deficiency conditions in groundnut. These genomic regions and candidate genes, after validation, may be useful to develop molecular markers for deploying genomics-assisted breeding for enhancing groundnut yield under drought stress and iron-deficient soil conditions.
Production of Recombinant Monoclonal Antibodies in the Egg White of Gene-Targeted Transgenic Chickens
Authors: Mukae Takehiro , Okumura Sho , Watanobe Takuma , Yoshii Kyoko , Tagami Takahiro , Oishi Isao
Published: December 2020

Increased commercial demand for monoclonal antibodies (mAbs) has resulted in the urgent need to establish efficient production systems. We previously developed a transgenic chicken bioreactor system that effectively produced human cytokines in egg whites using genome-edited transgenic chickens. Here, we describe the application of this system to mAb production. The genes encoding the heavy and light chains of humanized anti-HER2 mAb, linked by a 2A peptide sequence, were integrated into the chicken ovalbumin gene locus using a CRISPR/Cas9 protocol. The knock-in hens produced a fully assembled humanized mAb in their eggs. The mAb expression level in the egg white was 1.4–1.9 mg/mL, as determined by ELISA. Furthermore, the antigen binding affinity of the anti-HER2 mAb obtained was estimated to be equal to that of the therapeutic anti-HER2 mAb (trastuzumab). In addition, antigen-specific binding by the egg white mAb was demonstrated by immunofluorescence against HER2-positive and -negative cells. These results indicate that the chicken bioreactor system can efficiently produce mAbs with antigen binding capacity and can serve as an alternative production system for commercial mAbs.
Identification of microRNA-Associated-ceRNA Networks Regulating Crop Milk Production in Pigeon (Columba livia)
Authors: Ge Pingzhuang , Ma Hui , Li Yunlei , Ni Aixin , Isa Adamu Mani , Wang Panlin , Bian Shixiong , Shi Lei , Zong Yunhe , Wang Yuanmei , Jiang Linlin , Hagos Hailai , Yuan Jingwei , Sun Yanyan , Chen Jilan
Published: December 2020

Pigeon belongs to altrices. Squab cannot forage independently. Nutrition can only be obtained from crop milk secreted by male and female pigeon. miRNA could regulate many biological events. However, the roles of miRNA and ceRNA in regulating crop milk production are still unknown. In this study, we investigated the miRNAs expression profile of female pigeon crop, explored the potential key genes, and found the regulatory mechanisms of crop milk production. A total of 71 miRNAs were identified differentially expressed significantly. Meanwhile, miR-20b-5p, miR-146b-5p, miR-21-5p, and miR-26b-5p were found to be the key miRNAs regulating lactation. Target genes of these miRNAs participated mainly in cell development; protein and lipid synthesis; and ion signaling processes, such as cell-cell adhesion, epithelial cell morphogenesis, calcium signaling pathway, protein digestion, and absorption. In the ceRNA network, miR-193-5p was located in the central position, and miR-193-5p/CREBRF/LOC110355588, miR-460b-5p/GRHL2/MSTRG.132954, and miR-193-5p/PIK3CD/LOC110355588 regulatory axes were believed to affect lactation. Collectively, our findings enriched the miRNA expression profile of pigeon and provided novel insights into the microRNA-associated-ceRNA networks regulating crop milk production in pigeon.
Strong Correlation between the Case Fatality Rate of COVID-19 and the rs6598045 Single Nucleotide Polymorphism (SNP) of the Interferon-Induced Transmembrane Protein 3 (IFITM3) Gene at the Population-Level
Authors: Kim Yong-Chan , Jeong Byung-Hoon
Published: December 2020

Coronavirus disease 2019 (COVID-19) is a fatal pandemic disease that is caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of 13 December, 2020, over 70,000,000 cases and 1,500,000 deaths have been reported over a period of several months; however, the mechanism underlying the pathogenesis of COVID-19 has not been elucidated. To identify the novel risk genetic biomarker for COVID-19, we evaluated the correlation between the case fatality rate of COVID-19 and the genetic polymorphisms of several potential COVID-19-related genes, including interferon-induced transmembrane protein 3 (IFITM3), the angiotensin I converting enzyme 2 (ACE2) gene, transmembrane protease, serine 2 (TMPRSS2), interleukin 6 (IL6), leucine zipper transcription factor-like protein 1 (LZTFL1), and the ABO genes, in various ethnic groups. We obtained the number of COVID-19 cases and deaths from the World Health Organization (WHO) COVID-19 dashboard and calculated the case fatality rate of each ethnic group. In addition, we obtained the allele distribution of the polymorphisms of the IFITM3, ACE2, TMPRSS2, IL6, LZTFL1, and ABO genes from the 1000 Genomes Project and performed Log-linear regression analysis using SAS version 9.4. We found different COVID-19 case fatality rates in each ethnic group. Notably, we identified a strong correlation between the case fatality rate of COVID-19 and the allele frequency of the rs6598045 single nucleotide polymorphism (SNP) of the IFITM3 gene. To the best of our knowledge, this report is the first to describe a strong correlation between the COVID-19 case fatality rate and the rs6598045 SNP of the IFITM3 gene at the population-level.
Geomatics—An Open Access Journal
Authors: El-Sheimy Naser
Published: December 2020

Geomatics is an information technology discipline which integrates the tasks of gathering, storing, processing, modeling, analyzing, and delivering spatially referenced or location information [...]
Change in Physical Activity, Sleep Quality, and Psychosocial Variables during COVID-19 Lockdown: Evidence from the Lothian Birth Cohort 1936
Authors: Okely Judith A. , Corley Janie , Welstead Miles , Taylor Adele M. , Page Danielle , Skarabela Barbora , Redmond Paul , Cox Simon R. , Russ Tom C.
Published: December 2020

(1) Objectives: The COVID-19 pandemic has disproportionately affected the lives of older people. In this study, we examine changes in physical activity, sleep quality, and psychosocial variables among older people during COVID-19 lockdown. We build on cross-sectional studies on this topic by assessing change longitudinally. We also examined whether participant characteristics including demographic, cognitive, personality, and health variables were related to more positive or negative changes during lockdown. (2) Methods: 137 older participants (mean age 84 years) from the Lothian Birth Cohort 1936 study were included in the analysis. They completed the same questionnaires assessing physical activity, sleep quality, mental wellbeing, social support, loneliness, neighbourhood cohesion, and memory problems before (mostly 2 years earlier) and again during national lockdown. (3) Results: On average, levels of physical activity were reduced (those doing minimal physical activity increased from 10% to 19%) and perceived social support increased during lockdown (effect size drm = 0.178). More positive change in the psychosocial and behavioural outcome variables during lockdown was associated with personality traits (greater intellect, emotional stability, and extraversion) and having a higher general cognitive ability. Participants with a history of cardiovascular disease, more symptoms of anxiety, or who lived alone were more likely to experience negative changes in the outcome variables during lockdown. (4) Discussion: These results provide further insight into the experiences of older people during the COVID-19 pandemic and could help to identify those at greatest risk of negative psychosocial or behavioural changes during this time.
A Two-Year Longitudinal Study of the Association between Oral Frailty and Deteriorating Nutritional Status among Community-Dwelling Older Adults
Authors: Iwasaki Masanori , Motokawa Keiko , Watanabe Yutaka , Shirobe Maki , Inagaki Hiroki , Edahiro Ayako , Ohara Yuki , Hirano Hirohiko , Shinkai Shoji , Awata Shuichi
Published: December 2020

Background: Limited longitudinal studies exist to evaluate whether poor oral health and functions affect the incidence of deteriorating nutritional status. We investigated if there were longitudinal associations between oral frailty, defined as accumulated deficits in oral health, and deteriorating nutritional status among community-dwelling older adults. Methods: The study population consisted of 191 men and 275 women (mean age, 76.4 years) from the Takashimadaira Study. Multifaced oral health assessment was performed at baseline, and oral frailty was defined as having ≥3 of the following six components: fewer teeth, low masticatory performance, low articulatory oral motor skill, low tongue pressure, and difficulties in chewing and swallowing. Nutritional status assessment was performed at baseline and two-year follow-up using the Mini Nutritional Assessment®-Short Form (MNA®-SF). Deteriorating nutritional status was defined as a decline in the nutritional status categories based on the MNA®-SF score during the study period. The association between oral frailty and deteriorating nutritional status was assessed using logistic regression analyses. Results: Oral frailty was observed in 67 (14.4%) participants at baseline. During the study, 58 (12.4%) participants exhibited deteriorating nutritional status. After adjusting for potential confounders, oral frailty was significantly associated with deteriorating nutritional status (adjusted odds ratio, 2.24; 95% confidence interval, 1.08–4.63). Conclusion: Community-dwelling older adults with oral frailty had an increased risk of deteriorating nutritional status.
Rapid and Accurate Species-Specific PCR for the Identification of Lethal Chironex Box Jellyfish in Thailand
Authors: Sathirapongsasuti Nuankanya , Khonchom Kasetsin , Poonsawat Thunyaporn , Pransilpa Mitila , Ongsara Supaporn , Detsri Usawadee , Bungbai Suwimon , Lawanangkoon Sam-ang , Pattanaporkrattana Worawut , Trakulsrichai Satariya
Published: December 2020

Box jellyfish are extremely potent venom-producing marine organisms. While they have been found worldwide, the highest health burden has been anticipated to be the tropical Indo-Pacific of Southeast Asia (SEA). At least 12 Cubozoan species have now been documented in Thai waters, and many of them inflict acutely lethal strings, especially those under the order Chirodropida. Our previous study has successfully differentiated species of box jellyfish using DNA sequencing to support the morphological study. In this study, we specifically designed polymerase chain reaction (PCR) primers for the 16S ribosomal RNA (rRNA) gene and the mitochondrial DNA cytochrome oxidase subunit I (COI) gene of lethal Thai Chironex species. The SYBR green-based real-time PCR panel was performed for rapid species identification. The sensitivity and specificity of the panel were determined by testing samples of different species. Moreover, we applied the panel to the tentacle sample from a real patient, which helped confirm the animal-of-cause of envenomation. Our results show a success for species identification of box jellyfish using 16S rRNA and COI PCR panel, which revealed congruence between molecular and morphological identification. Furthermore, the panel worked very well with the unknown samples and jellyfish tissue from the real envenomation case. The results demonstrated that molecular panels were able to identify three species of Chironex box jellyfish both rapidly and accurately, and can be performed without having a complete specimen or morphological study.
COVID-19-Related Fear and Anxiety: Spiritual-Religious Coping in Healthcare Workers in Portugal
Authors: Prazeres Filipe , Passos Lígia , Simões José Augusto , Simões Pedro , Martins Carlos , Teixeira Andreia
Published: December 2020

The COVID-19 pandemic has negatively affected the mental health of the general population, and for healthcare workers (HCWs) it has been no different. Religiosity and spirituality are known coping strategies for mental illnesses, especially in stressful times. This study aimed to describe the role of spiritual-religious coping regarding fear and anxiety in relation to COVID-19 in HCWs in Portugal. A cross-sectional quantitative online survey was performed. Socio-demographic and health data were collected as well as the Duke University Religion Index, Spirituality Scale, Fear of COVID-19 Scale, and Coronavirus Anxiety Scale. Two hundred and twenty-two HCWs participated in the study, 74.3% were female and 81.1% were physicians. The median age was 37 years (Q1, Q3: 31, 51.3). Religiosity was neither a significant factor for coronavirus-related anxiety nor it was for fear of COVID-19. Participants with higher levels in the hope/optimism dimension of the Spirituality Scale showed less coronavirus-related anxiety. Female HCWs, non-physicians, and the ones with a previous history of anxiety presented higher levels of fear and/or anxiety related to COVID-19. HCWs’ levels of distress should be identified and reduced, so their work is not impaired.
Frequency of Intimate Partner Violence among an Urban Emergency Department Sample: A Multilevel Analysis
Authors: Cunradi Carol B. , Ponicki William R. , Caetano Raul , Alter Harrison J.
Published: December 2020

Intimate partner violence (IPV) is a pervasive public health problem. Within the U.S., urban emergency department (ED) patients have elevated prevalence of IPV, substance use, and other social problems compared to those in the general household population. Using a social-ecological framework, this cross-sectional study analyzes the extent to which individual, household, and neighborhood factors are associated with the frequency of IPV among a socially disadvantaged sample of urban ED patients. Confidential survey interviews were conducted with 1037 married/partnered study participants (46% male; 50% Hispanic; 29% African American) at a public safety-net hospital. Gender-stratified multilevel Tobit regression models were estimated for frequency of past-year physical IPV (perpetration and victimization) and frequency of severe IPV. Approximately 23% of participants reported IPV. Among men and women, impulsivity, adverse childhood experiences, substance use, and their spouse/partner’s hazardous drinking were associated with IPV frequency. Additionally, household food insufficiency, being fired or laid off from their job, perceived neighborhood disorder, and neighborhood demographic characteristics were associated with IPV frequency among women. Similar patterns were observed in models of severe IPV frequency. IPV prevention strategies implemented in urban ED settings should address the individual, household, and neighborhood risk factors that are linked with partner aggression among socially disadvantaged couples.
Mind–Body Physical Activity Interventions and Stress-Related Physiological Markers in Educational Settings: A Systematic Review and Meta-Analysis
Authors: Strehli Ildiko , Burns Ryan D. , Bai Yang , Ziegenfuss Donna H. , Block Martin E. , Brusseau Timothy A.
Published: December 2020

Mind–Body Physical Activity (MBPA) in educational settings is one possible preventive strategy for ameliorating stress-related physiological health parameters. The objectives of this study were to conduct a systematic review of the literature with meta-analyses on the effects of MBPA on stress-related physiological health markers in primary, secondary, and higher education students. In accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, the search for peer-reviewed articles published in English was conducted in PubMed, EBSCOhost, PsychInfo, Scopus, and Cochrane Library databases. Criteria for inclusion consisted of empirical studies targeting the student population (primary, secondary, higher education), studies examining the effectiveness of an MBPA intervention, studies including a control or comparison group (pre-test/post-test studies excluded), studies targeting physiological marker outcomes such as heart rate, blood glucose, cortisol, and blood pressure, and finally, studies examining interventions implemented within educational settings. Twenty-six interventions were eligible for the review and quantitative synthesis, which comprised a total of 1625 participants, with 783 students serving within the control/comparison group. There were statistically significant and large pooled effects for MBPA effectiveness for lowering heart rate (Hedges’ g = −1.71, 95% Confidence Interval (CI): −2.43, −0.98), cortisol (Hedges’ g = −1.32, 95% CI: −2.50, −0.16), and systolic and diastolic blood pressure (Hedges’ g = −1.04, 95% CI: −1.53, −0.58). These effects tended to be stronger in older students compared to younger students. Most analyses were characterized as having high heterogeneity and only 10 of the 26 studies were characterized as good quality (38.4%). MBPA interventions may have a positive impact on specific physiological health markers in students, especially in students within higher education. However, higher-quality research is needed in this area.
Protocol for a Trial Assessing the Impacts of School-Based WaSH Interventions on Children’s Health Literacy, Handwashing, and Nutrition Status in Low- and Middle-Income Countries
Authors: Sangalang Stephanie O. , Medina Shelley Anne J. , Ottong Zheina J. , Lemence Allen Lemuel G. , Totanes Donrey , Valencia John Cedrick , Singson Patricia Andrea A. , Olaguera Mikaela , Prado Nelissa O. , Ocaña Roezel Mari Z. , Canja Rovin James F. , Benolirao Alfem John T. , Mariano Shyrill Mae F. , Gavieres Jergil Gyle , Aquino Clarisse P. , Latag Edison C. , Anglo Maria Vianca Jasmin C. , Borgemeister Christian , Kistemann Thomas
Published: December 2020

Diarrhea, soil-transmitted helminth infection and malnutrition are leading causes of child mortality in low- and middle-income countries (LMICs). To reduce the prevalence of these diseases, effective interventions for adequate water, sanitation, and hygiene (WaSH) should be implemented. This paper describes the design of a cluster-randomized controlled trial that will compare the efficacy of four school-based WaSH interventions for improving children’s health literacy, handwashing, and nutrition. Interventions consisted of (1) WaSH policy reinforcement; (2) low-, medium-, or high-volume health education; (3) hygiene supplies; and (4) WaSH facilities (e.g., toilets, urinals, handwashing basins) improvements. We randomly allocated school clusters from the intervention arm to one of four groups to compare with schools from the control arm. Primary outcomes were: children’s health literacy, physical growth, nutrition status, and handwashing prevalence. Secondary outcomes were: children’s self-reported health status and history of extreme hunger, satisfaction with WaSH facilities, and school restrooms’ WaSH adequacy. We will measure differences in pre- and post-intervention outcomes and compare these differences between control and intervention arms. This research protocol can be a blueprint for future school-based WaSH intervention studies to be conducted in LMICs. Study protocols were approved by the ethics committees of the University of Bonn, Germany, and the University of the Philippines Manila. This trial was retroactively registered, ID number: DRKS00021623.
Supply and Demand-Related Decisive Factors in the Utilization of Non-Medical Community Healthcare Services among Elderly Chinese
Authors: Yu Zhao , Wang Lijian , Ariyo Tolulope
Published: December 2020

There is little research on the utilization of non-medical community healthcare services among the elderly, compared with that of medical community healthcare services. From the perspective of both supply and demand, based on the survey data from Shaanxi province, this study examined supply-related factors (including service supply, service quality, service charge and service accessibility) and demand-related factors (including service need, individual financial status, family care support and knowledge of service) affecting the utilization of non-medical community healthcare services among the elderly in China by using Poisson regression. The findings show that service supply, service quality, service need and knowledge of service are positively associated with the utilization of non-medical community healthcare services among elderly Chinese, but the other factors identified in previous studies are not significant predictors for the utilization of the services among the elderly in the context of China. To our knowledge, this is the first study to examine both supply-related factors and demand-related factors affecting the utilization of non-medical community healthcare services among elderly Chinese.
The Effect of Perioral Scan and Artificial Skin Markers on the Accuracy of Virtual Dentofacial Integration: Stereophotogrammetry Versus Smartphone Three-Dimensional Face-Scanning
Authors: Mai Hang-Nga , Lee Du-Hyeong
Published: December 2020

This study evaluated the effects of different matching methods on the accuracy of dentofacial integration in stereophotogrammetry and smartphone face-scanning systems. The integration was done (N = 30) with different matching areas (n = 10), including teeth image only (TO), perioral area without markers (PN) and with markers (PM). The positional accuracy of the integrated models was assessed by measuring the midline linear deviations and incisal line canting between the experimental groups and laser scanner-based reference standards. Kruskal–Wallis and Mann–Whitney U tests were used for statistical analyses (α = 0.05). The PM method exhibited the smallest linear deviations in both systems; while the highest deviations were found in the TO in stereophotogrammetry; and in PN in smartphone. For the incisal line canting; the canting degree was the lowest in the PM method; followed by that in the TO and the PN in both systems. Although stereophotogrammetry generally exhibited higher accuracy than the smartphone; the two systems demonstrated no significant difference when the perioral areas were used for matching. The use of perioral scans with markers enables accurate dentofacial image integration; however; cautions should be given on the accuracy of the perioral image obtained without the use of markers.
Anticancer and Immunomodulatory Benefits of Taro (Colocasia esculenta) Corms, an Underexploited Tuber Crop
Authors: Ribeiro Pereira Patrícia , Bertozzi de Aquino Mattos Érika , Nitzsche Teixeira Fernandes Corrêa Anna Carolina , Afonso Vericimo Mauricio , Margaret Flosi Paschoalin Vania
Published: December 2020

Taro corms contain valuable bioactive molecules effective against cancer and cancer-related risk factors, such as carcinogens and biological agents, several pathophysiological conditions, including oxidative stress and inflammation, while controlling metabolic dysfunctions and boosting the immunological response. Such broad effects are achieved by the taro health-influencing compounds displaying antitumoral, antimutagenic, immunomodulatory, anti-inflammatory, antioxidant, anti-hyperglycemic, and anti-hyperlipidemic activities. Taro bioactivities are attributed to the combination of tarin, taro-4-I polysaccharide, taro polysaccharides 1 and 2 (TPS-1 and TPS-2), A-1/B-2 α-amylase inhibitors, monogalactosyldiacylglycerols (MGDGs), digalactosyldiacylglycerols (DGDGs), polyphenols, and nonphenolic antioxidants. Most of these compounds have been purified and successfully challenged in vitro and in vivo, proving their involvement in the aforementioned activities. Although these health-promoting effects have been recognized since ancient times, as well as other valuable features of taro for food profit, such as hypo-allergenicity, gluten-free, and carbohydrates with medium-glycemic index, taro crop remains underexploited. The popularization of taro intake should be considered a dietary intervention strategy to be applied to improve the overall health status of the organism and as supportive therapy to manage tumorigenesis.
Influence of ClearT and ClearT2 Agitation Conditions in the Fluorescence Imaging of 3D Spheroids
Authors: Silva Daniel N. , Costa Elisabete C. , Rodrigues Carolina F. , de Melo-Diogo Duarte , Correia Ilídio J. , Moreira André F.
Published: December 2020

3D tumor spheroids have arisen in the last years as potent tools for the in vitro screening of novel anticancer therapeutics. Nevertheless, to increase the reproducibility and predictability of the data originated from the spheroids it is still necessary to develop or optimize the techniques used for spheroids’ physical and biomolecular characterization. Fluorescence microscopy, such as confocal laser scanning microscopy (CLSM), is a tool commonly used by researchers to characterize spheroids structure and the antitumoral effect of novel therapeutics. However, its application in spheroids’ analysis is hindered by the limited light penetration in thick samples. For this purpose, optical clearing solutions have been explored to increase the spheroids’ transparency by reducing the light scattering. In this study, the influence of agitation conditions (i.e., static, horizontal agitation, and rotatory agitation) on the ClearT and ClearT2 methods’ clearing efficacy and tumor spheroids’ imaging by CLSM was characterized. The obtained results demonstrate that the ClearT method results in the improved imaging of the spheroids interior, whereas the ClearT2 resulted in an increased propidium iodide mean fluorescence intensity as well as a higher signal depth in the Z-axis. Additionally, for both methods, the best clearing results were obtained for the spheroids treated under the rotatory agitation. In general, this work provides new insights on the ClearT and ClearT2 clearing methodologies and their utilization for improving the reproducibility of the data obtained through the CLSM, such as the analysis of the cell death in response to therapeutics administration.
Spatio-Temporal Bone Remodeling after Hematopoietic Stem Cell Transplantation
Authors: Schwarz Constanze S. , Bucher Christian H. , Schlundt Claudia , Mertlitz Sarah , Riesner Katarina , Kalupa Martina , Verlaat Lydia , Schmidt-Bleek Oskar , Sass Radost A. , Schmidt-Bleek Katharina , Duda Georg N. , Penack Olaf , Na Il-Kang
Published: December 2020

The interaction of hematopoietic cells and the bone microenvironment to maintain bone homeostasis is increasingly appreciated. We hypothesized that the transfer of allogeneic T lymphocytes has extensive effects on bone biology and investigated trabecular and cortical bone structures, the osteoblast reconstitution, and the bone vasculature in experimental hematopoietic stem cell transplantations (HSCT). Allogeneic or syngeneic hematopoietic stem cells (HSC) and allogeneic T lymphocytes were isolated and transferred in a murine model. After 20, 40, and 60 days, bone structures were visualized using microCT and histology. Immune cells were monitored using flow cytometry and bone vessels, bone cells and immune cells were fluorescently stained and visualized. Remodeling of the bone substance, the bone vasculature and bone cell subsets were found to occur as early as day +20 after allogeneic HSCT (including allogeneic T lymphocytes) but not after syngeneic HSCT. We discovered that allogeneic HSCT (including allogeneic T lymphocytes) results in a transient increase of trabecular bone number and bone vessel density. This was paralleled by a cortical thinning as well as disruptive osteoblast lining and loss of B lymphocytes. In summary, our data demonstrate that the adoptive transfer of allogeneic HSCs and allogeneic T lymphocytes can induce profound structural and spatial changes of bone tissue homeostasis as well as bone marrow cell composition, underlining the importance of the adaptive immune system for maintaining a balanced bone biology.
The Role of Hypoxia-Inducible Factor Post-Translational Modifications in Regulating Its Localisation, Stability, and Activity
Authors: Albanese Adam , Daly Leonard A. , Mennerich Daniela , Kietzmann Thomas , Sée Violaine
Published: December 2020

The hypoxia signalling pathway enables adaptation of cells to decreased oxygen availability. When oxygen becomes limiting, the central transcription factors of the pathway, hypoxia-inducible factors (HIFs), are stabilised and activated to induce the expression of hypoxia-regulated genes, thereby maintaining cellular homeostasis. Whilst hydroxylation has been thoroughly described as the major and canonical modification of the HIF-α subunits, regulating both HIF stability and activity, a range of other post-translational modifications decorating the entire protein play also a crucial role in altering HIF localisation, stability, and activity. These modifications, their conservation throughout evolution, and their effects on HIF-dependent signalling are discussed in this review.
Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling
Authors: Dokainish Hisham M. , Sugita Yuji
Published: December 2020

Conformational transitions in multidomain proteins are essential for biological functions. The Apo conformations are typically open and flexible, while the Holo states form more compact conformations stabilized by protein-ligand interactions. Unfortunately, the atomically detailed mechanisms for such open-closed conformational changes are difficult to be accessed experimentally as well as computationally. To simulate the transitions using atomistic molecular dynamics (MD) simulations, efficient conformational sampling algorithms are required. In this work, we propose a new approach based on generalized replica-exchange with solute tempering (gREST) for exploring the open-closed conformational changes in multidomain proteins. Wherein, selected surface charged residues in a target protein are defined as the solute region in gREST simulation and the solute temperatures are different in replicas and exchanged between them to enhance the domain motions. This approach is called gREST selected surface charged residues (gREST_SSCR) and is applied to the Apo and Holo states of ribose binding protein (RBP) in solution. The conformational spaces sampled with gREST_SSCR are much wider than those with the conventional MD, sampling open-closed conformational changes while maintaining RBP domains’ stability. The free-energy landscapes of RBP in the Apo and Holo states are drawn along with twist and hinge angles of the two moving domains. The inter-domain salt-bridges that are not observed in the experimental structures are also important in the intermediate states during the conformational changes.
Adult Renal Stem/Progenitor Cells Can Modulate T Regulatory Cells and Double Negative T Cells
Authors: Curci Claudia , Picerno Angela , Chaoul Nada , Stasi Alessandra , De Palma Giuseppe , Franzin Rossana , Pontrelli Paola , Castellano Giuseppe , Pertosa Giovanni B. , Macchia Luigi , Di Lorenzo Vito Francesco , Sabbà Carlo , Gallone Anna , Gesualdo Loreto , Sallustio Fabio
Published: December 2020

Adult Renal Stem/Progenitor Cells (ARPCs) have been recently identified in the human kidney and several studies show their active role in kidney repair processes during acute or chronic injury. However, little is known about their immunomodulatory properties and their capacity to regulate specific T cell subpopulations. We co-cultured ARPCs activated by triggering Toll-Like Receptor 2 (TLR2) with human peripheral blood mononuclear cells for 5 days and 15 days and studied their immunomodulatory capacity on T cell subpopulations. We found that activated-ARPCs were able to decrease T cell proliferation but did not affect CD8+ and CD4+ T cells. Instead, Tregs and CD3+ CD4- CD8- double-negative (DN) T cells decreased after 5 days and increased after 15 days of co-culture. In addition, we found that PAI1, MCP1, GM-CSF, and CXCL1 were significantly expressed by TLR2-activated ARPCs alone and were up-regulated in T cells co-cultured with activated ARPCs. The exogenous cocktail of cytokines was able to reproduce the immunomodulatory effects of the co-culture with activated ARPCs. These data showed that ARPCs can regulate immune response by inducing Tregs and DN T cells cell modulation, which are involved in the balance between immune tolerance and autoimmunity.
The Proteomic Landscape of Resting and Activated CD4+ T Cells Reveal Insights into Cell Differentiation and Function
Authors: Subbannayya Yashwanth , Haug Markus , Pinto Sneha M. , Mohanty Varshasnata , Meås Hany Zakaria , Flo Trude Helen , Prasad T.S. Keshava , Kandasamy Richard K.
Published: December 2020

CD4+ T cells (T helper cells) are cytokine-producing adaptive immune cells that activate or regulate the responses of various immune cells. The activation and functional status of CD4+ T cells is important for adequate responses to pathogen infections but has also been associated with auto-immune disorders and survival in several cancers. In the current study, we carried out a label-free high-resolution FTMS-based proteomic profiling of resting and T cell receptor-activated (72 h) primary human CD4+ T cells from peripheral blood of healthy donors as well as SUP-T1 cells. We identified 5237 proteins, of which significant alterations in the levels of 1119 proteins were observed between resting and activated CD4+ T cells. In addition to identifying several known T-cell activation-related processes altered expression of several stimulatory/inhibitory immune checkpoint markers between resting and activated CD4+ T cells were observed. Network analysis further revealed several known and novel regulatory hubs of CD4+ T cell activation, including IFNG, IRF1, FOXP3, AURKA, and RIOK2. Comparison of primary CD4+ T cell proteomic profiles with human lymphoblastic cell lines revealed a substantial overlap, while comparison with mouse CD+ T cell data suggested interspecies proteomic differences. The current dataset will serve as a valuable resource to the scientific community to compare and analyze the CD4+ proteome.
Novel Approach to Tooth Chemistry: Quantification of Human Enamel Apatite in Context for New Biomaterials and Nanomaterials Development
Authors: Kuczumow Andrzej , Chałas Renata , Nowak Jakub , Smułek Wojciech , Jarzębski Maciej
Published: December 2020

A series of linear profiles of the elements of the enamel in human molar teeth were made with the use of an electron microprobe and a Raman microscope. It is postulated that the enamel can be treated as the superposition of variable “overbuilt” enamel on the stable “core” enamel at the macro-, micro- and nanoscale level. The excessive values characterize the “overbuilt enamel”. All the profiles of excessive parameters along the enamel thickness from the enamel surface to the dentin enamel junction (DEJ) can be approximated very precisely with the use of exponential functions, where Ca, P, Cl and F spatial profiles are decaying while Mg, Na, K and CO32− ones are growing distributions. The “overbuilt” apatite formed on the boundary with DEJ, enriched in Na, Mg, OH and carbonates, reacts continuously with Ca, Cl and F, passing into an acid-resistant form of the “overbuilt” enamel. The apparent phases arriving in boundary regions of the “overbuilt enamel” were proposed. Microdiffraction measurements reveal relative variation of energy levels during enamel transformations. Our investigations are the milestones for a further new class of biomaterial and nanomaterial development for biomedical applications.
Modeling Intestinal Epithelial Response to Interferon-γ in Induced Pluripotent Stem Cell-Derived Human Intestinal Organoids
Authors: Workman Michael J. , Troisi Elissa , Targan Stephan R. , Svendsen Clive N. , Barrett Robert J.
Published: December 2020

Human intestinal organoids (HIOs) are increasingly being used to model intestinal responses to various stimuli, yet few studies have confirmed the fidelity of this modeling system. Given that the interferon-gamma (IFN-γ) response has been well characterized in various other cell types, our goal was to characterize the response to IFN-γ in HIOs derived from induced pluripotent stem cells (iPSCs). To achieve this, iPSCs were directed to form HIOs and subsequently treated with IFN-γ. Our results demonstrate that IFN-γ phosphorylates STAT1 but has little effect on the expression or localization of tight and adherens junction proteins in HIOs. However, transcriptomic profiling by microarray revealed numerous upregulated genes such as IDO1, GBP1, CXCL9, CXCL10 and CXCL11, which have previously been shown to be upregulated in other cell types in response to IFN-γ. Notably, “Response to Interferon Gamma” was determined to be one of the most significantly upregulated gene sets in IFN-γ-treated HIOs using gene set enrichment analysis. Interestingly, similar genes and pathways were upregulated in publicly available datasets contrasting the gene expression of in vivo biopsy tissue from patients with IBD against healthy controls. These data confirm that the iPSC-derived HIO modeling system represents an appropriate platform to evaluate the effects of various stimuli and specific environmental factors responsible for the alterations in the intestinal epithelium seen in various gastrointestinal conditions such as inflammatory bowel disease.
Exploring Yeast as a Study Model of Pantothenate Kinase-Associated Neurodegeneration and for the Identification of Therapeutic Compounds
Authors: Ceccatelli Berti Camilla , Gilea Alexandru Ionut , De Gregorio Marco Armando , Goffrini Paola
Published: December 2020

Mutations in the pantothenate kinase 2 gene (PANK2) are the cause of pantothenate kinase-associated neurodegeneration (PKAN), the most common form of neurodegeneration with brain iron accumulation. Although different disease models have been created to investigate the pathogenic mechanism of PKAN, the cascade of molecular events resulting from CoA synthesis impairment is not completely understood. Moreover, for PKAN disease, only symptomatic treatments are available. Despite the lack of a neural system, Saccharomyces cerevisiae has been successfully used to decipher molecular mechanisms of many human disorders including neurodegenerative diseases as well as iron-related disorders. To gain insights into the molecular basis of PKAN, a yeast model of this disease was developed: a yeast strain with the unique gene encoding pantothenate kinase CAB1 deleted, and expressing a pathological variant of this enzyme. A detailed functional characterization demonstrated that this model recapitulates the main phenotypes associated with human disease: mitochondrial dysfunction, altered lipid metabolism, iron overload, and oxidative damage suggesting that the yeast model could represent a tool to provide information on pathophysiology of PKAN. Taking advantage of the impaired oxidative growth of this mutant strain, a screening for molecules able to rescue this phenotype was performed. Two molecules in particular were able to restore the multiple defects associated with PKAN deficiency and the rescue was not allele-specific. Furthermore, the construction and characterization of a set of mutant alleles, allowing a quick evaluation of the biochemical consequences of pantothenate kinase (PANK) protein variants could be a tool to predict genotype/phenotype correlation.
Immune Modulation by Inhibitors of the HO System
Authors: Fernández-Fierro Ayleen , Funes Samanta C. , Rios Mariana , Covián Camila , González Jorge , Kalergis Alexis M.
Published: December 2020

The heme oxygenase (HO) system involves three isoforms of this enzyme, HO-1, HO-2, and HO-3. The three of them display the same catalytic activity, oxidating the heme group to produce biliverdin, ferrous iron, and carbon monoxide (CO). HO-1 is the isoform most widely studied in proinflammatory diseases because treatments that overexpress this enzyme promote the generation of anti-inflammatory products. However, neonatal jaundice (hyperbilirubinemia) derived from HO overexpression led to the development of inhibitors, such as those based on metaloproto- and meso-porphyrins inhibitors with competitive activity. Further, non-competitive inhibitors have also been identified, such as synthetic and natural imidazole-dioxolane-based, small synthetic molecules, inhibitors of the enzyme regulation pathway, and genetic engineering using iRNA or CRISPR cas9. Despite most of the applications of the HO inhibitors being related to metabolic diseases, the beneficial effects of these molecules in immune-mediated diseases have also emerged. Different medical implications, including cancer, Alzheimer´s disease, and infections, are discussed in this article and as to how the selective inhibition of HO isoforms may contribute to the treatment of these ailments.
The Influence of New Silicate Cement Mineral Trioxide Aggregate (MTA Repair HP) on Metalloproteinase MMP-2 and MMP-9 Expression in Cultured THP-1 Macrophages
Authors: Barczak Katarzyna , Palczewska-Komsa Mirona , Lipski Mariusz , Chlubek Dariusz , Buczkowska-Radlińska Jadwiga , Baranowska-Bosiacka Irena
Published: December 2020

The aim of the present study was to investigate the new silicate cement mineral trioxide aggregate (MTA Repair HP) with respect to its effect on the inflammation process involving the tooth and periodontal tissues. The composition of MTA Repair HP was supplemented with plasticizer agents which can have a negative effect on the modulation of tooth inflammation. The silicate-based material in question is widely used in regeneration of the pulp-dentin complex, treatment of perforations of various locations in the tooth, as well as in surgical treatment of the complications of periapical tissue. The improved bioceramic restorative cement can affect the expression of metalloproteinases MMP-2 and MMP-9 in monocytes/macrophages involved in modulation of inflammation and regenerative processes of the tooth and periodontal tissues. The novel aspect of the present study lies in the application of the model of THP-1 monocyte/macrophage and applying the biomaterial in direct contact with the cells. Hence, it provides a representation of clinical conditions with respect to regenerative pulp and periodontal treatment with the use of MTA Repair HP. A lack of macrophage activation (as measured with flow cytometry) was found. Moreover, the study identified a lack of expression stimulation of the studied metalloproteinases (with the use of Western blotting and fluorescent microscopy). Similarly, no increase in MMP-2 and MMP-9 concentration was found (measured by ELISA method) in vitro when incubated with MTA Repair HP. Based on the results it can be concluded that new MTA Repair HP does not increase the inflammatory response in monocytes/macrophages associated with the activity of the described enzymes. It can also be speculated that they do not affect the process of dentin regeneration in which MMP-2 and MMP-9 play significant roles.
Dimethyl Fumarate Promotes the Survival of Retinal Ganglion Cells after Optic Nerve Injury, Possibly through the Nrf2/HO-1 Pathway
Authors: Mori Sotaro , Kurimoto Takuji , Maeda Hidetaka , Nakamura Makoto
Published: December 2020

This study aimed to verify whether dimethyl fumarate (DMF) promotes the survival of retinal ganglion cells (RGCs) after optic nerve crush (ONC) accompanied by activation of the NF-E2-related factor 2 (Nrf2)/heme oxygenase-1 (HO-1) pathway. We examined changes in the densities of tubulin β3 (TUBB3)-positive RGCs and the amplitudes of the positive scotopic threshold response (pSTR), reflecting the functional activity of RGCs, recorded on an electroretinogram, with daily administration of DMF, on day 7 after ONC. Furthermore, immunohistochemical and immunoblotting analyses were performed to study the activation of the Nrf2/HO-1 pathway using retinas treated with daily administration of DMF. Daily administration of DMF increasedthe density of TUBB3-positive RGCs in a dose-dependent fashion and significantly increased the amplitude of the pSTR. Immunohistochemical analysis showed that DMF administration increased the immunoreactivity for Nrf2 and HO-1, a potent antioxidant enzyme, in RGCs immunolabeled with RNA-binding protein with multiple splicing (RBPMS). Immunoblotting analysis revealed an increase in the nuclear expression of Nrf2 and marked upregulation of HO-1 after DMF administration. These results suggest that DMF has survival-promoting effects in RGC after ONC, possibly via the Nrf2/HO-1 pathway.
Curcumin Prevents Cerebellar Hypoplasia and Restores the Behavior in Hyperbilirubinemic Gunn Rat by a Pleiotropic Effect on the Molecular Effectors of Brain Damage
Authors: Gazzin Silvia , Dal Ben Matteo , Montrone Michele , Jayanti Sri , Lorenzon Andrea , Bramante Alessandra , Bottin Cristina , Moretti Rita , Tiribelli Claudio
Published: December 2020

Bilirubin toxicity to the central nervous system (CNS) is responsible for severe and permanent neurologic damage, resulting in hearing loss, cognitive, and movement impairment. Timely and effective management of severe neonatal hyperbilirubinemia by phototherapy or exchange transfusion is crucial for avoiding permanent neurological consequences, but these therapies are not always possible, particularly in low-income countries. To explore alternative options, we investigated a pharmaceutical approach focused on protecting the CNS from pigment toxicity, independently from serum bilirubin level. To this goal, we tested the ability of curcumin, a nutraceutical already used with relevant results in animal models as well as in clinics in other diseases, in the Gunn rat, the spontaneous model of neonatal hyperbilirubinemia. Curcumin treatment fully abolished the landmark cerebellar hypoplasia of Gunn rat, restoring the histological features, and reverting the behavioral abnormalities present in the hyperbilirubinemic rat. The protection was mediated by a multi-target action on the main bilirubin-induced pathological mechanism ongoing CNS damage (inflammation, redox imbalance, and glutamate neurotoxicity). If confirmed by independent studies, the result suggests the potential of curcumin as an alternative/complementary approach to bilirubin-induced brain damage in the clinical scenario.