bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative transcriptome analysis identifies CARM1 and DNMT3A as genes associated with osteoporosis
Authors: Panach Layla , Pertusa Clara , Martínez-Rojas Beatriz , Acebrón Álvaro , Mifsut Damián , Tarín Juan J. , Cano Antonio , García-Pérez Miguel Ángel
Published: October 2020

To identify new candidate genes in osteoporosis, mainly involved in epigenetic mechanisms, we compared whole gene-expression in osteoblasts (OBs) obtained from women undergoing hip replacement surgery due to fragility fracture and severe osteoarthritis. Then, we analyzed the association of several SNPs with BMD in 1028 women. Microarray analysis yielded 2542 differentially expressed transcripts belonging to 1798 annotated genes, of which 45.6% (819) were overexpressed, and 54.4% (979) underexpressed (fold-change between − 7.45 and 4.0). Among the most represented pathways indicated by transcriptome analysis were chondrocyte development, positive regulation of bone mineralization, BMP signaling pathway, skeletal system development and Wnt signaling pathway. In the translational stage we genotyped 4 SNPs in DOT1L, HEY2, CARM1 and DNMT3A genes. Raw data analyzed against inheritance patterns showed a statistically significant association between a SNP of DNMT3A and femoral neck-(FN) sBMD and primarily a SNP of CARM1 was correlated with both FN and lumbar spine-(LS) sBMD. Most of these associations remained statistically significant after adjusting for confounders. In analysis with anthropometric and clinical variables, the SNP of CARM1 unexpectedly revealed a close association with BMI (p = 0.000082), insulin (p = 0.000085), and HOMA-IR (p = 0.000078). In conclusion, SNPs of the DNMT3A and CARM1 genes are associated with BMD, in the latter case probably owing to a strong correlation with obesity and fasting insulin levels.
NemaLife chip: a micropillar-based microfluidic culture device optimized for aging studies in crawling C. elegans
Authors: Rahman Mizanur , Edwards Hunter , Birze Nikolajs , Gabrilska Rebecca , Rumbaugh Kendra P. , Blawzdziewicz Jerzy , Szewczyk Nathaniel J. , Driscoll Monica , Vanapalli Siva A.
Published: October 2020

In this study, we report a microfluidic device for the whole-life culture of the nematode Caenorhabditis elegans that allows the scoring of animal survival and health measures. This device referred to as the NemaLife chip features: (1) an optimized micropillar arena in which animals can crawl, (2) sieve channels that separate progeny and prevent the loss of adults from the arena during culture maintenance, and (3) ports that allow rapid accessibility for feeding the adult-only population and introducing reagents as needed. The pillar arena geometry was optimized to accommodate the growing body size during culture and emulate the body gait and locomotion of animals reared on agar. Likewise, feeding protocols were optimized to recapitulate longevity outcomes typical of standard plate growth. Key benefits of the NemaLife Chip include eliminating the need to perform repeated manual transfers of adults during survival assays, negating the need for progeny-blocking chemical interventions, and avoiding the swim-induced stress across lifespan in animals reared in liquid. We also show that the culture of animals in pillar-less microfluidic chambers reduces lifespan and introduces physiological stress by increasing the occurrence of age-related vulval integrity disorder. We validated our pillar-based device with longevity analyses of classical aging mutants (daf-2, age-1, eat-2, and daf-16) and animals subjected to RNAi knockdown of age-related genes (age-1 and daf-16). We also showed that healthspan measures such as pharyngeal pumping and tap-induced stimulated reversals can be scored across the lifespan in the NemaLife chip. Overall, the capacity to generate reliable lifespan and physiological data underscores the potential of the NemaLife chip to accelerate healthspan and lifespan investigations in C. elegans.
Sclerostin antibody stimulates periodontal regeneration in large alveolar bone defects
Authors: Yao Yao , Kauffmann Frederic , Maekawa Shogo , Sarment Lea V. , Sugai James V. , Schmiedeler Caroline A. , Doherty Edward J. , Holdsworth Gill , Kostenuik Paul J. , Giannobile William V.
Published: October 2020

Destruction of the alveolar bone in the jaws can occur due to periodontitis, trauma or following tumor resection. Common reconstructive therapy can include the use of bone grafts with limited predictability and efficacy. Romosozumab, approved by the FDA in 2019, is a humanized sclerostin-neutralizing antibody (Scl-Ab) indicated in postmenopausal women with osteoporosis at high risk for fracture. Preclinical models show that Scl-Ab administration preserves bone volume during periodontal disease, repairs bone defects surrounding dental implants, and reverses alveolar bone loss following extraction socket remodeling. To date, there are no studies evaluating Scl-Ab to repair osseous defects around teeth or to identify the efficacy of locally-delivered Scl-Ab for targeted drug delivery. In this investigation, the use of systemically-delivered versus low dose locally-delivered Scl-Ab via poly(lactic-co-glycolic) acid (PLGA) microspheres (MSs) was compared at experimentally-created alveolar bone defects in rats. Systemic Scl-Ab administration improved bone regeneration and tended to increase cementogenesis measured by histology and microcomputed tomography, while Scl-Ab delivered by MSs did not result in enhancements in bone or cemental repair compared to MSs alone or control. In conclusion, systemic administration of Scl-Ab promotes bone and cemental regeneration while local, low dose delivery did not heal periodontal osseous defects in this study.
A study of associations between CUBN, HNF1A, and LIPC gene polymorphisms and coronary artery disease
Authors: Park Han Sung , Kim In Jai , Kim Eun Gyo , Ryu Chang Soo , Lee Jeong Yong , Ko Eun Ju , Park Hyeon Woo , Sung Jung Hoon , Kim Nam Keun
Published: October 2020

The aim of this study was to identify novel genetic markers related to coronary artery disease (CAD) using a whole-exome sequencing (WES) approach and determine any associations between the selected gene polymorphisms and CAD prevalence. CUBN, HNF1A and LIPC gene polymorphisms related to CAD susceptibility were identified using WES screening. Possible associations between the five gene polymorphisms and CAD susceptibility were examined in 452 CAD patients and 421 control subjects. Multivariate logistic regression analyses indicated that the CUBN rs2291521GA and HNF1A rs55783344CT genotypes were associated with CAD (GG vs. GA; adjusted odds ratio [AOR] = 1.530; 95% confidence interval [CI] 1.113–2.103; P = 0.002 and CC vs. CT; AOR = 1.512; 95% CI 1.119–2.045; P = 0.007, respectively). The CUBN rs2291521GA and HNF1A rs55783344CT genotype combinations exhibited a stronger association with CAD risk (AOR = 2.622; 95% CI 1.518–4.526; P = 0.001). Gene-environment combinatorial analyses indicated that the CUBN rs2291521GA, HNF1A rs55783344CT, and LIPC rs17269397AA genotype combination and several clinical factors (fasting blood sugar (FBS), high-density lipoprotein (HDL), and low-density lipoprotein (LDL) levels) were associated with increased CAD risk. The CUBN rs2291521GA, HNF1A rs55783344CT, and LIPC rs17269397AA genotypes in conjunction with abnormally elevated cholesterol levels increase the risk of developing CAD. This exploratory study suggests that polymorphisms in the CUBN, HNF1A, and LIPC genes can be useful biomarkers for CAD diagnosis and treatment.
Microbiological and host-derived biomarker evaluation following non-surgical periodontal therapy with short-term administration of systemic antimicrobials: secondary outcomes of an RCT
Authors: Cosgarea Raluca , Eick S. , Jepsen S. , Arweiler N. B. , Juncar R. , Tristiu R. , Salvi G. E. , Heumann C. , Sculean A.
Published: October 2020

Nonsurgical periodontal therapy with adjunctive use of systemic antimicrobials (for 7–14 days) showed improved clinical, microbiological and immunological results over the mechanical protocol alone. Considering the increasing risk for antimicrobial resistance with longer antibiotic regimes, it is important to establish the optimal antibiotic protocol with a maximum antimicrobial benefit and minimum risk for adverse effects. The aim of the study was to evaluate the microbiological and inflammatory outcomes 12-months after a 3-/7-day systemic antibiotic protocol [amoxicillin (AMX) + metronidazole (MET)] adjunctive to subgingival debridement in severe periodontitis compared to mechanical treatment alone. From the initially treated 102 patients, 75 subjects (Placebo group: n = 26; 3-day AMX + MET group: n = 24; 7-day AMX + MET group: n = 25) completed the 12-month examination. Clinical parameters, eight periodontal pathogens and inflammatory markers were determined at baseline and 3-, 6-, 12-months after therapy using real-time PCR and ELISA respectively. After 6 months, several periodontopathogens were significantly more reduced in the two antibiotic groups compared to placebo (p < 0.05). After 1 year, both antibiotic protocols showed significant reductions and detection of the keystone pathogen P. gingivalis compared to placebo. Antibiotic protocols, smoking, disease severity, baseline-BOP, -CAL and -IL-1β, as well as detection of T. denticola at 12-months significantly influenced the residual number of deep sites. The present data indicate that the systemic use of both short and longer antibiotic protocols (AMX + MET) adjunctive to nonsurgical periodontal therapy lead to higher microbiological improvements compared to subgingival debridement alone. The two investigated antibiotic protocols led to comparable microbiological and inflammatory results.
Metformin enhances protection in guinea pigs chronically infected with Mycobacterium tuberculosis
Authors: Frenkel Jessica D. Haugen , Ackart David F. , Todd Alexandra K. , DiLisio James E. , Hoffman Siana , Tanner Samantha , Kiran Dilara , Murray Megan , Chicco Adam , Obregón-Henao Andrés , Podell Brendan K. , Basaraba Randall J.
Published: October 2020

Tuberculosis (TB) is a chronic inflammatory disease that is often associated with alterations in systemic and cellular metabolism that resolves following successful antimicrobial drug treatment. We hypothesized that altered systemic glucose metabolism as a consequence of Mycobacterium tuberculosis (Mtb) infection, contributes to TB pathogenesis, and when normalized with anti-glycemic drugs would improve clinical outcomes. To test this hypothesis, guinea pigs were treated daily with the anti-diabetic drug metformin starting 4 weeks prior or concurrent with aerosol exposure to the H37Rv strain of Mtb. In the chronic stages of infection, Mtb infected metformin-treated animals had restored systemic insulin sensitivity but remained glucose intolerant as determined by oral glucose tolerance testing. Despite persistent glucose intolerance, metformin-treated guinea pigs had a 2.8-fold reduction in lung lesion burden and a 0.7 log decrease in CFUs. An alternative hypothesis that metformin treatment improved clinical disease by having a direct effect on immune cell energy metabolism was tested using extracellular flux analysis and flow cytometry. The proinflammatory immune response to Mtb infection in untreated guinea pigs was associated with a marked increase in energy metabolism (glycolysis and mitochondrial respiration) of peripheral blood mononuclear cells (PBMCs), which was normalized in metformin-treated guinea pigs. Moreover, both CD4+ and CD8+ T lymphocytes from Mtb infected, metformin treated animals maintained a more normal mitochondrial membrane potential while those isolated from untreated animals had persistent mitochondrial hyperpolarization. These data suggest that metformin promotes natural host resistance to Mtb infection by maintaining immune cell metabolic homeostasis and function during the chronic stages of active TB disease.
Protein-N-myristoylation-dependent phosphorylation of serine 13 of tyrosine kinase Lyn by casein kinase 1γ at the Golgi during intracellular protein traffic
Authors: Kinoshita-Kikuta Emiko , Utsumi Toshihiko , Miyazaki Aya , Tokumoto Chiharu , Doi Kyosuke , Harada Haruna , Kinoshita Eiji , Koike Tohru
Published: October 2020

Protein N-myristoylation of Src-family kinases (SFKs) is a critical co-translational modification to anchor the enzymes in the plasma membrane. Phosphorylation of SFKs is also an essential modification for regulating their enzymatic activities. In this study, we used Phos-tag SDS-PAGE to investigate N-myristoylation-dependent phosphorylation of SFKs and their non-N-myristoylated G2A mutants. The serine-13 residue of Lyn (Lyn-S13) was shown to be N-myristoylation-dependently phosphorylated. Although there have been more than 40 reports of mass spectrometric studies on phosphorylation at Lyn-S13, the kinase responsible remained unclear. We succeeded in identifying casein kinase 1γ (CK1γ) as the kinase responsible for phosphorylation of Lyn-S13. In HEK293 cells co-expressing Lyn and CK1γ, the phosphorylation level of Lyn-S13 increased significantly. CK1γ is unique among the CK1 family (α, γ, δ, and ε) in carrying an S-palmitoylation site for membrane binding. Co-expression with the non-S-palmitoylated CK1γ mutant, which localized in the cytosol, gave no increase in the phosphorylation level at Lyn-S13. In HEK293 cells expressing the non-S-palmitoylated Lyn-C3A mutant, on the other hand, the Lyn-C3A mutant was phosphorylated at Lyn-S13, and the mutant remained at the Golgi. These results showed that S-palmitoylated CK1γ can phosphorylate S13 of N-myristoylated Lyn at the Golgi during intracellular protein traffic.
The influence of PI3K inhibition on the radiotherapy response of head and neck cancer cells
Authors: Glorieux Mary , Dok Rüveyda , Nuyts Sandra
Published: October 2020

Radiotherapy has a central role in the treatment of head and neck squamous cell carcinoma (HNSCC). Activation of the PI3K/AKT/mTOR pathway can decrease the efficiency of radiotherapy via the promotion of cell survival and DNA repair. Here, the influence of PI3K pathway inhibition on radiotherapy response was investigated. Two PI3K inhibitors were investigated and both BKM120 and GDC0980 effectively inhibited cellular and clonogenic growth in 6 HNSCC cells, both HPV-positive as well as HPV-negative. Despite targeted inhibition of the pathway and slight increase in DNA damage, PI3K inhibition did not show significant radiosensitization. Currently only one clinical trial is assessing the effectiveness of combining BKM120 with RT in HNSCC (NCT02113878) of which the results are eagerly awaited.
New insecticide screening platforms indicate that Mitochondrial Complex I inhibitors are susceptible to cross-resistance by mosquito P450s that metabolise pyrethroids
Authors: Lees Rosemary S. , Ismail Hanafy M. , Logan Rhiannon A. E. , Malone David , Davies Rachel , Anthousi Amalia , Adolfi Adriana , Lycett Gareth J. , Paine Mark J. I.
Published: October 2020

Fenazaquin, pyridaben, tolfenpyrad and fenpyroximate are Complex I inhibitors offering a new mode of action for insecticidal malaria vector control. However, extended exposure to pyrethroid based products such as long-lasting insecticidal nets (LLINs) has created mosquito populations that are largely pyrethroid-resistant, often with elevated levels of P450s that can metabolise and neutralise diverse substrates. To assess cross-resistance liabilities of the Complex I inhibitors, we profiled their susceptibility to metabolism by P450s associated with pyrethroid resistance in Anopheles gambiae (CYPs 6M2, 6P3, 6P4, 6P5, 9J5, 9K1, 6Z2) and An. funestus (CYP6P9a). All compounds were highly susceptible. Transgenic An. gambiae overexpressing CYP6M2 or CYP6P3 showed reduced mortality when exposed to fenpyroximate and tolfenpyrad. Mortality from fenpyroximate was also reduced in pyrethroid-resistant strains of An. gambiae (VK7 2014 and Tiassalé 13) and An. funestus (FUMOZ-R). P450 inhibitor piperonyl butoxide (PBO) significantly enhanced the efficacy of fenpyroximate and tolfenpyrad, fully restoring mortality in fenpyroximate-exposed FUMOZ-R. Overall, results suggest that in vivo and in vitro assays are a useful guide in the development of new vector control products, and that the Complex I inhibitors tested are susceptible to metabolic cross-resistance and may lack efficacy in controlling pyrethroid resistant mosquitoes.
Exploring celiac disease candidate pathways by global gene expression profiling and gene network cluster analysis
Authors: Banaganapalli Babajan , Mansour Haifa , Mohammed Arif , Alharthi Arwa Mastoor , Aljuaid Nada Mohammed , Nasser Khalidah Khalid , Ahmad Aftab , Saadah Omar I. , Al-Aama Jumana Yousuf , Elango Ramu , Shaik Noor Ahmad
Published: October 2020

Celiac disease (CeD) is a gastrointestinal autoimmune disorder, whose specific molecular basis is not yet fully interpreted. Therefore, in this study, we compared the global gene expression profile of duodenum tissues from CeD patients, both at the time of disease diagnosis and after two years of the gluten-free diet. A series of advanced systems biology approaches like differential gene expression, protein–protein interactions, gene network-cluster analysis were deployed to annotate the candidate pathways relevant to CeD pathogenesis. The duodenum tissues from CeD patients revealed the differential expression of 106 up- and 193 down-regulated genes. The pathway enrichment of differentially expressed genes (DEGs) highlights the involvement of biological pathways related to loss of cell division regulation (cell cycle, p53 signalling pathway), immune system processes (NOD-like receptor signalling pathway, Th1, and Th2 cell differentiation, IL-17 signalling pathway) and impaired metabolism and absorption (mineral and vitamin absorptions and drug metabolism) in celiac disease. The molecular dysfunctions of these 3 biological events tend to increase the number of intraepithelial lymphocytes (IELs) and villous atrophy of the duodenal mucosa promoting the development of CeD. For the first time, this study highlights the involvement of aberrant cell division, immune system, absorption, and metabolism pathways in CeD pathophysiology and presents potential novel therapeutic opportunities.
Evidence of motor injury due to damaged corticospinal tract following acute hemorrhage in the basal ganglia region
Authors: Li Jing , Wei Xue Hu , Liu Yong Kang , Chen Ling Shan , Zhu Zheng Qiu , Hou Si Yuan , Fang Xiao Kun , Wang Zhong Qiu
Published: October 2020

The integrity of the corticospinal tract (CST) is significantly affected following basal ganglia haemorrhage. We aimed to assess the local features of CST and to effectively predict motor function by diffusion characteristics of CST in patients with motor injury following acute haemorrhage in the acute basal ganglia region. We recruited 37 patients with paresis of the lateral limbs caused by acute basal ganglia haemorrhage. Based on the automated fiber quantification method to track CST, assessed the character of each CST segment between the affected and contralateral sides, and correlated these with the Fugl–Meyer (FM) and Barthel Index (BI) scores at 6 months after onset. The fractional anisotropy (FA) values of the injured side of CST showed a significantly lower FA than the contralateral side along the tract profiles (p < 0.05, corrections for multiple comparisons). The FA values of each site at the internal capsule, closed corona radiata were positively correlated with the FM and BI score at 6 months after onset (p < 0.001, respectively). Our findings assessed the character of CST vividly in detail and dementated the primary sites of CST can predict the long-term outcome of motor function. This study may facilitate future clinical and cognitive studies of acute haemorrhage.
Lifelong smoking trajectories of Northern Finns are characterized by sociodemographic and lifestyle differences in a 46-year follow-up
Authors: Oura Petteri , Rissanen Ina , Junno Juho-Antti , Harju Terttu , Paananen Markus
Published: October 2020

Smoking remains among the leading causes of mortality worldwide. Obtaining a comprehensive understanding of a population’s smoking behaviour is essential for tobacco control. Here, we aim to characterize lifelong smoking patterns and explore underlying sociodemographic and lifestyle factors in a population-based birth cohort population followed up for 46 years. Our analysis is based on 5797 individuals from the Northern Finland Birth Cohort 1966 who self-reported their tobacco smoking behaviour at the ages of 14, 31 and 46. Data on sex, education, employment, body mass index, physical activity, alcohol consumption, and substance addiction were also collected at the follow-ups. We profile each individual’s annual smoking history from the age of 5 to 47, and conduct a latent class trajectory analysis on the data. We then characterize the identified smoking trajectory classes in terms of the background variables, and compare the heaviest smokers with other classes in order to reveal specific predictors of non-smoking and discontinued smoking. Six smoking trajectories are identified in our sample: never-smokers (class size 41.0%), youth smokers (12.6%), young adult quitters (10.8%), late adult quitters (10.5%), late starters (4.3%), and lifetime smokers (20.7%). Smoking is generally associated with male sex, lower socioeconomic status and unhealthier lifestyle. Multivariable between-class comparisons identify unemployment (odds ratio [OR] 1.28–1.45) and physical inactivity (OR 1.20–1.52) as significant predictors of lifetime smoking relative to any other class. Female sex increases the odds of never-smoking and youth smoking (OR 1.29–1.33), and male sex increases the odds of adult quitting (OR 1.30–1.41), relative to lifetime smoking. We expect future initiatives to benefit from our data by exploiting the identified predictors as direct targets of intervention, or as a means of identifying individuals who may benefit from such interventions.
Elevated adipose tissue associated IL-2 expression in obesity correlates with metabolic inflammation and insulin resistance
Authors: Kochumon Shihab , Al Madhoun Ashraf , Al-Rashed Fatema , Thomas Reeby , Sindhu Sardar , Al-Ozairi Ebaa , Al-Mulla Fahd , Ahmad Rasheed
Published: October 2020

Adipose tissue (AT) associated cytokines are involved in the development of chronic low-grade inflammation in obese individuals. IL-2, a pleiotropic cytokine, contributes to immune alterations during inflammation. However, the interaction between AT-IL-2 and other inflammatory biomolecules in obesity remains elusive. We investigated whether AT-IL-2 expression was associated with markers of inflammation and insulin resistance in overweight/obese individuals. Subcutaneous fat tissues were collected from 56 individuals (lean/overweight/obese) for RNA extraction. IL-2 and inflammatory mediators were quantified by qRT-PCR and immunohistochemistry. CRP was measured by ELISA. AT-IL-2 expression was higher in obese compared with lean individuals (P < 0.021) and correlated with BMI. IL-2 correlated with interleukins IL-8 and IL-12A (r = 0.333–0.481; p = 0.0001–0.029); as well as with chemokines and their receptors including CCL5, CCL19, CCR2 and CCR5 (r = 0.538–0.677; p < 0.0001). Moreover, IL-2 correlated with toll-like receptors (TLR2, TLR8, TLR10), interferon regulatory factor 5 (IRF5) and cluster of differentiation CD11c (r = 0.282–0.357; p < 0.039). Notably, IL-2 was associated positively with fasting blood glucose (FBG), HbA1c, TGL and CRP (r ≥ 0.423;P ≤ 0.007). In multiple regression analysis, IL-2 is an independent predictor of IL-8, IL-12A, TLR10, TGL and HbA1c. Overall, our data demonstrate that increased expression of the AT-IL-2, in obesity, may represent a novel biomarker for progression of metabolic inflammation and insulin-resistance.
Endometriosis and chronic pelvic pain have similar impact on women, but time to diagnosis is decreasing: an Australian survey
Authors: Armour Mike , Sinclair Justin , Ng Cecilia H. M. , Hyman Mikayla S. , Lawson Kenny , Smith Caroline A. , Abbott Jason
Published: October 2020

Chronic pelvic pain (CPP) affects a significant number of women worldwide. Internationally, people with endometriosis report significant negative impact across many areas of their life. We aimed to use an online survey using the EndoCost tool to determine if there was any difference in the impact of CPP in those with vs. those without a confirmed diagnosis of endometriosis, and if there was any change in diagnostic delay since the introduction of clinical guidelines in 2005. 409 responses were received; 340 with a diagnosis of endometriosis and 69 with no diagnosis. People with CPP, regardless of diagnosis, reported moderate to severe dysmenorrhea and non-cyclical pelvic pain. Dyspareunia was also common. Significant negative impact was reported for social, academic, and sexual/romantic relationships in both cohorts. In the endometriosis cohort there was a mean diagnostic delay of eight years, however there was a reduction in both the diagnostic delay (p < 0.001) and number of doctors seen before diagnosis (p < 0.001) in those presenting more recently. Both endometriosis and CPP have significant negative impact. Whilst there is a decrease in the time to diagnosis, there is an urgent need for improved treatment options and support for women with the disease once the diagnosis is made.
The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes
Authors: Tan Wei , Gao Han , Jiang Weiling , Zhang Huanyu , Yu Xiaolei , Liu Erwei , Tian Xiaoxuan
Published: October 2020

Chloroplast genomes have been widely considered an informative and valuable resource for molecular marker development and phylogenetic reconstruction in plant species. This study evaluated the complete chloroplast genomes of the traditional Chinese medicine Gleditsia sinensis and G. japonica, an adulterant of the former. The complete chloroplast genomes of G. sinensis and G. japonica were found to be of sizes 163,175 bp and 162,391 bp, respectively. A total of 111 genes were identified in each chloroplast genome, including 77 coding sequences, 30 tRNA, and 4 rRNA genes. Comparative analysis demonstrated that the chloroplast genomes of these two species were highly conserved in genome size, GC contents, and gene organization. Additionally, nucleotide diversity analysis of the two chloroplast genomes revealed that the two short regions of ycf1b were highly diverse, and could be treated as mini-barcode candidate regions. The mini-barcode of primers ZJ818F-1038R was proven to precisely discriminate between these two species and reflect their biomass ratio accurately. Overall, the findings of our study will shed light on the genetic evolution and guide species identification of G. sinensis and G. japonica.
Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis
Authors: Walker Sidney P. , Barrett Maurice , Hogan Glenn , Flores Bueso Yensi , Claesson Marcus J. , Tangney Mark
Published: October 2020

The targeted sequencing of the 16S rRNA gene is one of the most frequently employed techniques in the field of microbial ecology, with the bacterial communities of a wide variety of niches in the human body have been characterised in this way. This is performed by targeting one or more hypervariable (V) regions within the 16S rRNA gene in order to produce an amplicon suitable in size for next generation sequencing. To date, all technical research has focused on the ability of different V regions to accurately resolve the composition of bacterial communities. We present here an underreported artefact associated with 16S rRNA gene sequencing, namely the off-target amplification of human DNA. By analysing 16S rRNA gene sequencing data from a selection of human sites we highlighted samples susceptible to this off-target amplification when using the popular primer pair targeting the V3–V4 region of the gene. The most severely affected sample type identified (breast tumour samples) were then re-analysed using the V1–V2 primer set, showing considerable reduction in off target amplification. Our data indicate that human biopsy samples should preferably be amplified using primers targeting the V1–V2 region. It is shown here that these primers result in on average 80% less human genome aligning reads, allowing for more statistically significant analysis of the bacterial communities residing in these samples.
Evidence of cortical thickness reduction and disconnection in high myopia
Authors: Wu Ya-Jun , Wu Na , Huang Xin , Rao Jie , Yan Li , Shi Ling , Huang Hui , Li Si-Yu , Zhou Fu-Qing , Wu Xiao-Rong
Published: October 2020

High myopia (HM) is associated with impaired long-distance vision. accumulating evidences reported that abnormal visual experience leads to dysfunction in brain activity in HM even corrected. However, whether the long-term of abnormal visual experience lead to neuroanatomical changes remain unknown, the aim at this study is to investigate the alternation of cortical surface thickness in HM patients. 82 patients with HM (HM groups), 57 healthy controls (HC groups) were recruited. All participants underwent high-resolution T1 and resting-state functional magnetic resonance imaging (MRI) scans. The cortical thickness analysis was preformed to investigate the neuroanatomical changes in HM patients using computational anatomy toolbox (CAT 12) toolbox. Compare with HCs, HM patients showed decreased the cortical surface thickness in the left middle occipital gyrus (MOG), left inferior parietal lobule (IPL), right inferior temporal gyrus (ITG), right precuneus, right primary visual area 1 (V1), right superior temporal gyrus (STG), right superior parietal lobule (SPL), right occipital pole, and right the primary motor cortex (M1), and increased to the parietal operculum (OP4) (P < 0.01, FWE-corrected), the mean cortical thickness of right orbitofrontal cortex (OFC), right dorsolateral prefrontal cortex (DLPFC) and right subcallosal cortex showed negatively correlation between clinical variables (axis length (ALM), the average macular thickness (AMT), keratometer (KER) 1, KER2, the mean KER, the mean macular fovea thickness (MFK), the refractive diopter) in HM patients. Our result mainly provided an evidence of cortical thickness reduction and disconnection in visual center and visual processing area, and cortical thickness increase in left multimodal integration region in HM patients. This may provide important significance of the study of the neural mechanism of HM.
Fokker–Planck dynamics of the El Niño-Southern Oscillation
Authors: An Soon-Il , Kim Soong-Ki , Timmermann Axel
Published: October 2020

The asymmetric nature of the El Niño-Southern Oscillation (ENSO) is explored by using a probabilistic model (PROM) for ENSO. Based on a Fokker–Planck Equation (FPE), PROM describes the dynamics of a nonlinear stochastic ENSO recharge oscillator model for eastern equatorial Pacific temperature anomalies and equatorial Pacific basin-averaged thermocline depth changes. Eigen analyses of PROM provide new insights into the stationary and oscillatory solutions of the stochastic dynamical system. The first probabilistic eigenmode represents a stationary mode, which exhibits the asymmetric features of ENSO, in case deterministic nonlinearities or multiplicative noises are included. The second mode is linked to the oscillatory nature of ENSO and represents a cyclic asymmetric probability distribution, which emerges from the key dynamical processes. Other eigenmodes are associated with the temporal evolution of higher order statistical moments of the ENSO system. The model solutions demonstrate that the deterministic nonlinearity plays a stronger role in establishing the observed asymmetry of ENSO as compared to the multiplicative stochastic part.
Utilizing conductivity of seawater for bioelectric measurement of fish
Authors: Saiki Tsunemasa , Takizawa Yukako , Miyahara Kazutaka , Arima Masakazu
Published: October 2020

To manage health conditions of farmed fish and other living creatures, a simple method to measure bioelectric signals of the creatures in seawater is expected. A novel method to measure bioelectric signals by utilizing the conductivity of seawater surrounding the entire body of a fish is proposed. As for the proposed method, a needle-type internal electrode is inserted into the fish’s muscle at a certain measurement point, and an external electrode is sunk in seawater. The internal electrode is isolated from the seawater by virtue of being inserted in the fish. Bioelectric signals generated between the external and internal electrodes are then measured. By sharing the external electrode with the internal electrode, it is possible to measure bioelectric signals with half the number of bioelectrodes used by conventional methods. To demonstrate the practicality of the proposed method, two internal electrodes were inserted into different parts (above the gills and near the tail) of three fish (Parajulis poecilepterus, ca. 20 cm fork length) kept in a tank. The proposed method obtained reliable bioelectric signals corresponding to electrocardiograms (ECGs) and electromyograms (EMGs) from each part of the individual fish.
Polystyrene adsorbents: rapid and efficient surrogate for dialysis in membrane protein purification
Authors: Palanirajan Santosh Kumar , Govindasamy Punitha , Gummadi Sathyanarayana N.
Published: October 2020

Membrane protein purification is a laborious, expensive, and protracted process involving detergents for its extraction. Purifying functionally active form of membrane protein in sufficient quantity is a major bottleneck in establishing its structure and understanding the functional mechanism. Although overexpression of the membrane proteins has been achieved by recombinant DNA technology, a majority of the protein remains insoluble as inclusion bodies, which is extracted by detergents. Detergent removal is essential for retaining protein structure, function, and subsequent purification techniques. In this study, we have proposed a new approach for detergent removal from the solubilized extract of a recombinant membrane protein: human phospholipid scramblase 3 (hPLSCR3). N-lauryl sarcosine (NLS) has been established as an effective detergent to extract the functionally active recombinant 6X-his- hPLSCR3 from the inclusion bodies. NLS removal before affinity-based purification is essential as the detergent interferes with the matrix binding. Detergent removal by adsorption onto hydrophobic polystyrene beads has been methodically studied and established that the current approach was 10 times faster than the conventional dialysis method. The study established the potency of polystyrene-based beads as a convenient, efficient, and alternate tool to dialysis in detergent removal without significantly altering the structure and function of the membrane protein.
Publisher Correction: Architectured ZnO–Cu particles for facile manufacturing of integrated Li-ion electrodes
Authors: Bargardi Fabio L. , Billaud Juliette , Villevieille Claire , Bouville Florian , Studart André R.
Published: October 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
FUBP1 and FUBP2 enforce distinct epigenetic setpoints for MYC expression in primary single murine cells
Authors: Zheng Ying , Dubois Wendy , Benham Craig , Batchelor Eric , Levens David
Published: October 2020

Physiologically, MYC levels must be precisely set to faithfully amplify the transcriptome, but in cancer MYC is quantitatively misregulated. Here, we study the variation of MYC amongst single primary cells (B-cells and murine embryonic fibroblasts, MEFs) for the repercussions of variable cellular MYC-levels and setpoints. Because FUBPs have been proposed to be molecular “cruise controls” that constrain MYC expression, their role in determining basal or activated MYC-levels was also examined. Growing cells remember low and high-MYC setpoints through multiple cell divisions and are limited by the same expression ceiling even after modest MYC-activation. High MYC MEFs are enriched for mRNAs regulating inflammation and immunity. After strong stimulation, many cells break through the ceiling and intensify MYC expression. Lacking FUBPs, unstimulated MEFs express levels otherwise attained only with stimulation and sponsor MYC chromatin changes, revealed by chromatin marks. Thus, the FUBPs enforce epigenetic setpoints that restrict MYC expression.
Over-activation of a nonessential bacterial protease DegP as an antibiotic strategy
Authors: Cho Hyunjin , Choi Yuri , Min Kyungjin , Son Jung Bae , Park Hyojin , Lee Hyung Ho , Kim Seokhee
Published: October 2020

Rising antibiotic resistance urgently begs for novel targets and strategies for antibiotic discovery. Here, we report that over-activation of the periplasmic DegP protease, a member of the highly conserved HtrA family, can be a viable strategy for antibiotic development. We demonstrate that tripodal peptidyl compounds that mimic DegP-activating lipoprotein variants allosterically activate DegP and inhibit the growth of an Escherichia coli strain with a permeable outer membrane in a DegP-dependent fashion. Interestingly, these compounds inhibit bacterial growth at a temperature at which DegP is not essential for cell viability, mainly by over-proteolysis of newly synthesized proteins. Co-crystal structures show that the peptidyl arms of the compounds bind to the substrate-binding sites of DegP. Overall, our results represent an intriguing example of killing bacteria by activating a non-essential enzyme, and thus expand the scope of antibiotic targets beyond the traditional essential proteins or pathways.
Unbiased description of magnetic polarons in a Mott insulator
Authors: Blomquist Emil , Carlström Johan
Published: October 2020

Polarons are among the most elementary quasiparticles of interacting quantum matter, consisting of a charge carrier dressed by an excited background. In Mott insulators, they take the form of a dopant surrounded by a distorted spin-background. Despite the fundamental importance of polarons for the electronic structure of strongly correlated systems, access to their internal structure was only recently realized in experiments, while controllable theoretical results are still lacking due to the sign problem. Here we report unbiased high-precision data obtained from worm-algorithm Monte Carlo that reveal the real-space structure of a polaron in the t-J model deep inside the region where the sign problem becomes significant. These results are directly comparable to recent quantum gas microscopy experiments, but give access to significantly lower temperatures.
Correction: Melittin-encapsulating peptide hydrogels for enhanced delivery of impermeable anticancer peptides
Authors: Feng Jue-Ping , Zhu Ru , Jiang Fagang , Xie Jie , Gao Chang , Li Min , Jin Honglin , Fu Dehao
Published: October 2020

Correction for ‘Melittin-encapsulating peptide hydrogels for enhanced delivery of impermeable anticancer peptides’ by Jue-Ping Feng et al., Biomater. Sci., 2020, 8, 4559–4569, DOI: 10.1039/C9BM02080B.
Hypervalent iodine reagent-mediated reactions involving rearrangement processes
Authors: Zhang Beibei , Li Xiaoxian , Guo Boying , Du Yunfei
Published: October 2020

We summarize the developments of hypervalent iodine reagents-mediated reactions involving [1,2]-migration, Hofmann rearrangement, Beckmann rearrangement, ring contraction/expansion, [3,3]-sigmatropic/iodonium-Claisen rearrangement and some miscellaneous rearrangements.
Correction: Electrochemically shape-controlled synthesis of great stellated dodecahedral Au nanocrystals with high-index facets for nitrogen reduction to ammonia
Authors: Jiang Yu-Chen , Mao Yu-Jie , Zou Jin , Wang Hong-Hui , Liu Feng , Wei Yong-Sheng , Sheng Tian , Zhao Xin-Sheng , Wei Lu
Published: October 2020

Correction for ‘Electrochemically shape-controlled synthesis of great stellated dodecahedral Au nanocrystals with high-index facets for nitrogen reduction to ammonia’ by Yu-Chen Jiang et al., Chem. Commun., 2020, DOI: 10.1039/d0cc04326e.
Correction: An ionic liquid-modified RGO/polyaniline composite for high-performance flexible all-solid-state supercapacitors
Authors: Dong Chang , Zhang Xiaoling , Yu Yijia , Huang Liyan , Li Jun , Wu Ying , Liu Zhengping
Published: October 2020

Correction for ‘An ionic liquid-modified RGO/polyaniline composite for high-performance flexible all-solid-state supercapacitors’ by Chang Dong et al., Chem. Commun., 2020, DOI: 10.1039/d0cc04691d.
The synthesis of cyclometalated platinum(ii) complexes with benzoaryl-pyridines as C^N ligands for investigating their photophysical, electrochemical and electroluminescent properties
Authors: Wang Dezhi , Chen Xi , Yang Hua , Zhong Daokun , Liu Boao , Yang Xiaolong , Yue Ling , Zhou Guijiang , Ma Miaofeng , Wu Zhaoxin
Published: October 2020

(C^N)Pt(acac)-type complexes with benzo[b]furan, benzo[b]thiophene, benzo[b]selenophene, and benzo[b]tellurophene moieties were synthesized, and their optoelectronic properties were studied.
Pt nanoparticles on Ti3C2Tx-based MXenes as efficient catalysts for the selective hydrogenation of nitroaromatic compounds to amines
Authors: Chen Qian , Jiang Weidong , Fan Guangyin
Published: October 2020

Pt/Ti3C2Tx-D-AB synthesized using ammonia borane as a reducing agent showed excellent performance for the selective hydrogenation of p-CNB to p-CAN.
Fe–N4 engineering of S and N co-doped hierarchical porous carbon-based electrocatalysts for enhanced oxygen reduction in Zn–air batteries
Authors: Gao Jingxia , Liu Sa , Zhu Ping , Zhao Xinsheng , Wang Guoxiang
Published: October 2020

A highly active yet stable electrocatalyst was prepared by in situ formed template-assisting method.
Matcha green tea prevents obesity-induced hypothalamic inflammation via suppressing the JAK2/STAT3 signaling pathway
Authors: Zhou Jihong , Lin Haiyu , Xu Ping , Yao Liyun , Xie Qingyi , Mao Limin , Wang Yuefei
Published: October 2020

Matcha green tea effectively alleviates high fat-induced microglial overactivation and hypothalamic inflammation through the JAK2/STAT3 signaling pathway.
Iron-induced peroxidation of trilinolein nano-emulsions under model gastric conditions and its inhibition by dietary phenolic antioxidants
Authors: Vallier Marie-José , Le Bourvellec Carine , Dangles Olivier
Published: October 2020

An early mechanism for the health benefits of dietary plant phenols is their antioxidant activity during the initial phase of gastric digestion.
Chloride-free hydrolytic sol–gel synthesis of Nb–P–Si oxides: an approach to solid acid materials
Authors: Clayden Nigel J. , Imparato Claudio , Avolio Roberto , Ferraro Giarita , Errico Maria E. , Vergara Alessandro , Busca Guido , Gervasini Antonella , Aronne Antonio , Silvestri Brigida
Published: October 2020

A straightforward and sustainable synthesis of Nb–P–Si acid solid materials was developed through a hydrolytic one-step sol–gel route avoiding organic solvents, foreign catalysts or additives starting from cheap and available precursors.
Functionalized gold nanoparticles: promising and efficient diagnostic and therapeutic tools for HIV/AIDS
Authors: Gulati Shikha , Singh Parinita , Diwan Anchita , Mongia Ayush , Kumar Sanjay
Published: October 2020

This graphical abstract demonstrates different shapes of gold nanoparticles that can be functionalized and employed for targeting HIV. Various methods that are used for its detection and treatment are depicted.
Shell isolated nanoparticle enhanced Raman spectroscopy for renewable energy electrocatalysis
Authors: Kuruvinashetti Kiran , Zhang Yuxuan , Li Junnan , Kornienko Nikolay
Published: October 2020

This review covers the use of shell isolated nanoparticle enhanced Raman spectroscopy (SHINERS) to investigate heterogeneous electrocatalytic processes.
One-pot synthesis of N,S-doped pearl chain tube-loaded Ni3S2 composite materials for high-performance lithium–air batteries
Authors: An Bohan , Li Jiacheng , Wu Xiaochao , Li Wanqing , Li Yongliang , Sun Lingna , Mi Hongwei , Zhang Qianling , He Chuanxin , Ren Xiangzhong
Published: October 2020

To improve the high reversibility of lithium–air batteries, an air electrode needs to have excellent electrochemical performance and spatial structure.
Total synthesis of the actinoallolides and a designed photoaffinity probe for target identification
Authors: Anketell Matthew J. , Sharrock Theodore M. , Paterson Ian
Published: October 2020

A convergent synthesis of the actinoallolides with late-stage diversification provides access to a photoaffinity probe to identify the target of these potent anti-trypanosomal natural products.
Element table of TM-substituted polyoxotungstates for direct electrocatalytic reduction of nitric oxide to ammonia: a DFT guideline for experiments
Authors: Lang Zhongling , Miao Jun , Tan Huaqiao , Su Zhongmin , Li Yangguang , Zheng Zhiping
Published: October 2020

We screened out NiII, CoII, CuII, PdII, PtII, and AgI substituted heteropolytungstates as promising electrocatalysts for nitric oxide to ammonia with high activity and high selectivity.
Analysis of yield stability of strawberry varieties and hybrids
Authors: Lapshin Vadim , Yakovenko Valentina , Shcheglov Sergey
Published: October 2020

The profitability of strawberry cultivation is largely determined by the capacity and quality of the yield, depended on the features of the variety genotype. The aim of this work was to estimate the yield stability of varieties and hybrids by the methods of multivariate statistical analysis and identify the best genotypes. To solve this problem, we have used the two-factor analysis of variance and hierarchical cluster analysis according to the Ward’s method as well as the integral estimate of the differences between the values of yield. The results of the studies have shown that the genotype of the variety (hybrid) are makes a decisive factor of influence for variability of the yield structure signs from 17,1% (number of inflorescences) to 32,2% (number of berries). The «genotype × environment» interaction is comparable with the genotype influence, the share of influence of the year conditions of the year is insignificant. Cluster analysis according to complex of economic valuable signs allows us to identify the eight forms that the most adapted to the conditions of the Krasnodar Territory as 13-1-15, Florence, Roxana, 18-1-15, Asia, Onda, Kemia, Nelli from which the Roxana, Florence, 18-1-15, 13-1-15 have a high and steadily rising biological yield.