Recent Submissions

  • Genomic insights into recent species divergence in Nicotiana benthamiana and natural variation in Rdr1 gene controlling viral susceptibility.

    Cauz-Santos, Luiz A.; Dodsworth, Steven; Samuel, Rosabelle; Christenhusz, Maarten J.M.; Patel, Denise; Shittu, Taiwo Adewale; Jakob, Aljaž; Paun, Ovidiu; Chase, Mark W.; ; et al. (Wiley, 2022-05-10)
    One of the most commonly encountered and frequently cited laboratory organisms worldwide is classified taxonomically as Nicotiana benthamiana (Solanaceae), an accession of which, typically referred to as LAB, is renowned for its unique susceptibility to a wide range of plant viruses and hence capacity to be transformed using a variety of methods. This susceptibility is the result of an insertion and consequent loss of function in the RNA dependent RNA polymerase 1 (Rdr1) gene. However, the origin and age of LAB and evolution of N. benthamiana across its wide distribution in Australia remains relatively underexplored. Here, we have used multispecies coalescent methods on genome-wide single nuclear polymorphisms (SNPs) to assess species limits, phylogenetic relationships and divergence times within N. benthamiana. Our results show that the previous taxonomic concept of this species in fact comprises five geographically, morphologically and genetically distinct species, one of which includes LAB. We provide clear evidence that LAB is closely related to accessions collected further north in the Northern Territory; this species split much earlier, c. 1.1 million years ago, from their common ancestor than the other four in this clade and is morphologically the most distinctive. We also found that the Rdr1 gene insertion is variable among accessions from the northern portions of the Northern Territory. Furthermore, this long-isolated species typically grows in sheltered sites in subtropical/tropical monsoon areas of northern Australia, contradicting the previously advanced hypothesis that this species is an extremophile that has traded viral resistance for precocious development.
  • ER stress in COVID-19 and Parkinson's Disease: in vitro and in silico evidences

    Chaudhry, Zahara Latif; Gamal, Mahmoud; Ferhati, Ingrid; Warda, Mohamad; Ahmed, Bushra Y.; ; University of Bedfordshire; Cairo University (MDPI, 2022-04-16)
    The outbreak of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) signifies a serious worldwide concern to public health. Both transcriptome and proteome of SARS-CoV-2-infected cells synergize the progression of infection in host, which may exacerbate symptoms and/or progression of other chronic diseases such as Parkinson's disease (PD). Oxidative stress is a well-known cause of endoplasmic reticulum (ER) stress observed in both SARS-CoV-2 and PD. In the current study, we aimed to explore the influence of PKR-like ER kinase (PERK) stress pathway under SARS-CoV-2-mediated infection and in human cell model of PD. Furthermore, we investigated whether they are interconnected and if the ER stress inhibitors could inhibit cell death and provide cellular protection. To achieve this aim, we have incorporated in silico analysis obtained from gene set enrichment analysis (GSEA), a literature review and laboratory data. The neurotoxin, 6-hydroxy dopamine (6OHDA), was used to mimic the biochemical and neuropathological characteristics of PD by inducing oxidative stress in dopamine-containing neurons differentiated from ReNVM cell line (dDCNs). Furthermore, we explored if ER stress influences activation of caspases-2, -4 and -8 in SARS-CoV-2 and in stressed dDCNs. Our laboratory data using Western blot, immunocytochemistry and 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide (MTT) analyses indicated that 6OHDA-induced toxicity triggered activation of caspases-2, -4 and -8 in dDCNs. Under SARS-CoV-2 infection of different cell types, GSEA revealed cell-specific sensitivities to oxidative and ER stresses. Cardiomyocytes and type II alveolar epithelial-like cells were more vulnerable to oxidative stress than neural cells. On the other side, only cardiomyocytes activated the unfolded protein response, however, the PERK pathway was operative in both cardiomyocytes and neural cells. In addition, caspase-4 activation by a SARS-CoV-2 was observed via in silico analyses. These results demonstrate that the ER stress pathway under oxidative stress in SARS-CoV-2 and PD are interconnected using diverse pathways. Furthermore, our results using the ER stress inhibitor and caspase specific inhibitors provided cellular protection suggesting that the use of specific inhibitors can provide effective therapeutic approaches for the treatment of COVID-19 and PD.
  • Regulation of cell cycle and differentiation markers by pathogenic, non-pathogenic and opportunistic skin bacteria

    Younis, Sidra; Deeba, Farah; Fatima Saeed, Rida; Mothana, Ramzi A.; Ullah, Riaz; Faheem, Muhammad; Javed, Qamar; Blumenberg, Miroslav; National University of Medical Sciences, Pakistan; Quaid-e-Azam University; et al. (Elsevier B.V., 2021-11-02)
    Skin is the first line of defense against the physical, chemical and the biological environment. It is an ideal organ for studying molecular responses to biological infections through a variety of skin cells that specialize in immune responses. Comparative analysis of skin response to pathogenic, non-pathogenic, and commensal bacteria would help in the identification of disease specific pathways for drug targets. In this study, we investigated human breast reduction skin responses to Cutibacterium acnes (C. acnes), Staphylococcus aureus (S. aureus), Staphylococcus epidermidis (S. epidermidis), and TLR1/2 agonist using Affymetrix microarray chips. The Pam3CSK4 solution and bacterial cultures were prepared and inoculated in steel rings, that were placed on the acetone treated epidermis in a petri dish. After 24 h incubation, 8 mm punch biopsies were taken from the center of the ring, and RNA was extracted. The genome-wide expression was then analyzed using Affymetrix HG-133A gene chip microarray. We found that the C. acnes and S. aureus boosted the production of extracellular matrix components and attenuated the expression of differentiation markers. The above responses were mediated through the TLR2 pathway. Skin also responded to S. aureus and C. acnes by inducing the genes of the cell cycle machinery; this response was not TLR2-dependent. S. aureus induced, whereas C. acnes suppressed the genes associated with apoptosis; this was also not TLR2-dependent. Moreover, S. epidermis apparently did not lead to changes in gene expression. We conclude that the breast reduction skin is a very useful model to study the global gene expression in response to bacterial treatments.
  • Effects and mechanism of Ganoderma lucidum polysaccharides in the treatment of diabetic nephropathy in streptozotocin-induced diabetic rats

    Hu, Yu; Wang, Shu-Xiang; Wu, Fu-Yu; Wu, Ke-Jia; Shi, Rui-Ping; Qin, Li-Hong; Lu, Chun-Feng; Wang, Shu-Qiu; Wang, Fang-Fang; Zhou, Shaobo; et al. (Hindawi, 2022-03-08)
    Ganoderma lucidum polysaccharides (GLP) have renal protection effect but there was no study on the diabetic nephropathy. This study was designed to investigate its effect and mechanism using a diabetic rat model induced by streptozotocin (50 mg/kg, i.p.). The diabetic rats were treated with GLP (300 mg/kg/day) for 10 weeks. The blood glucose, glycated hemoglobin, body weight, and the levels of blood creatinine, urea nitrogen, and urine protein were assessed. And renal pathologies were assessed by the tissue sections stained with hematoxylin-eosin, Masson’s trichome, and periodic acid-Schiff. The expression of phosphorylated phosphoinositide 3 kinase (p-PI3K), phosphorylated protein kinase B (p-Akt), and phosphorylated mammalian target of rapamycin (p-mTOR), the autophagy proteins beclin-1, LC3-II, LC3-I, and P62; the apoptosis-related proteins caspase-3 and caspase-9; and the inflammation markers IL-6, IL-1β, and TNF-ɑ were assessed. Results showed that GLP alleviated the impairment of renal function by reducing urinary protein excretion and the blood creatinine level and ameliorated diabetic nephropathy. The expression of p-PI3K, p-Akt, and p-mTOR in the diabetic kidney were significantly reduced in the GLP treatment group compared to the without treatment group. GLP treatment activated the autophagy indicators of beclin-1 and the ratio of LC3-II/LC3-I but reduced p62 and also inhibited the expression of caspase-3, caspase-9 and IL-6, IL-1β, and TNF-ɑ. In conclusion, the effect of GLP amelioration diabetic nephropathy may be via the PI3k/Akt/mTOR signaling pathway by inhibition of the apoptosis and inflammation and activation of the autophagy process.
  • Study on the association of dietary fatty acids intake and serum lipid profiles with cognition in aging subjects with type 2 diabetes mellitus

    Li, Pengfei; Gao, Yanyan; Ma, Xiaojun; Zhou, Shaobo; Guo, Yujie; Xu, Jingjing; Wang, Xixiang; Van Halm-Lutterodt, Nicholas; Yuan, Linhong; Capital Medical University, Beijing; et al. (Frontiers, 2022-03-31)
    Background: The correlation between dietary fatty acid (FA) intake and serum lipid profile levels with cognition in the aged population has been reported by previous studies. However, the association of dietary FA intake and serum lipid profile levels with cognition in subjects with type 2 diabetes mellitus (T2DM) is seldom reported. Objective: A cross-sectional study was conducted to explore the correlation between dietary FA intake and serum lipid profiles with cognition in the aged Chinese population with T2DM. Methods: A total of 1,526 aged Chinese subjects were recruited from communities. Fasting blood samples were collected for parameter measurement. The food frequency questionnaire (FFQ) method was applied for a dietary survey. Cognition was assessed using the Montreal Cognitive Assessment (MoCA) test. Dietary FA intake and serum lipid levels were compared between subjects with T2DM and control subjects. A logistic regression analysis was carried out for analyzing the association of FA intake and serum lipid levels with the risk of mild cognitive impairment (MCI) in subjects with T2DM and control subjects. Results: There was a significant difference in the serum lipid level between the T2DM group and the control group. Results of the logistic regression analysis demonstrated the potential associations of serum total cholesterol (TC), low-density lipoprotein cholesterol (LDL-c), and dietary n-3 polyunsaturated fatty acids (PUFAs) intake with the risk of MCI in subjects with T2DM, but the associations were not observed in control subjects. Conclusion: The T2DM phenotype might affect the relationship between dietary FA intake, circulating lipids, and cognitive performance. Large prospective cohort studies are needed to uncover the underlying mechanism of how dietary FA intake and serum lipid levels affect cognition in aged subjects with T2DM.
  • Prospective association of dietary soy and fibre intake with puberty timing: a cohort study among Chinese children

    Xiong, Jingyuan; Xu, Yujie; Liu, Xueting; Wang, Xiaoyu; Shan, Shufang; Crabbe, M. James C.; Zhao, Li; Fang, He; Cheng, Guo; ; et al. (BMC, 2022-04-04)
    Background: Dietary phytoestrogens have been suggested to influence puberty timing, a critical stage for wellbeing in adulthood. We hypothesized that childhood soy intake might prospectively influence puberty timing and that dietary fibre and the key isoflavone metabolite equol might play roles. Methods: Cox proportional hazard regression models were performed in 4781 children (2152 girls and 2629 boys) aged 6–8 years old from the Chinese Adolescent Cohort Study for whom a food frequency questionnaire at baseline and information about potential confounders were available. Anthropometry and pubertal status including age at Tanner stage 2 for breast development (B2) or age at the initiation of gonadal growth (G2), and age at menarche (M) or voice break (VB) were assessed annually. Equol excretion was determined by urine samples from 1311 participants. Results: Among girls and boys, higher soy intake was associated with later puberty timing (hazard ratio (HR)-B2: 0.88 (95% CI, 0.80–0.96), p=0.02; HR-M, 0.87 (0.77–0.94), p=0.01; HR-G2, 0.91 (0.82–0.98), p=0.013; HR-VB, 0.90 (0.82–0.9), p=0.02), independent of prepubertal body fatness and fibre intake. These associations were more pronounced among children with a high urinary equol level (pfor-interaction ≤ 0.04) or with a high cereal fibre intake (pfor-interaction ≤ 0.06). Intake of dietary fibre or its subtype was not prospectively associated with puberty onset after adjusting for dietary soy intake (p≥0.06). Conclusion: Higher childhood soy intake is prospectively associated with later puberty timing in both Chinese girls and boys, independent of prepubertal body fatness, and the association is particularly pronounced among individuals with a higher urinary equol level.
  • Spatial-temporal distribution, cancer risk, and disease burden attributed to the dietary dioxins exposure of Chinese residents

    Zheng, Weiwei; Zhao, Huijuan; Crabbe, M. James C.; Qu, Weidong; Fudan University; Oxford University; University of Bedfordshire (Elsevier, 2022-03-26)
    This study analyzed the characteristics of dioxins represented by polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) as well as dioxin-like polychlorinated biphenyls (dl-PCBs) in food from China. The spatial-temporal distribution characteristics of dioxins dietary intake, cancer risk, and disease burden were evaluated among the Chinese population. In the temporal dimension, descending trends in animal-origin-food were found both in dietary intake PCDD/Fs and dl-PCBs, with the reverse for plant-origin-food. The probability assessments of dietary intakes showed that after 2007, the exposure level of PCDD/Fs through diets of urban and rural residents in China was significantly lower than that before 2007 (p < 0.05). The spatial distribution results showed that the southern coastal regions were high exposure regions of dietary intakes of PCDD/Fs and dl-PCBs. Cancer risk and disease burden of dietary dioxins showed downward trends after 2007 both under an average exposure scenario and an extreme exposure scenario. After 2007, the disease burden resulting from exposure to dl-PCBs became higher and approached the median of values reported by the WHO, while the disease burden resulting from exposure to PCDD/Fs approached the lower level of 95% CI reported by the WHO. The results indicate that accompanying the National Implementation Plan and a series of subsequent scientific guidance documents launched for reducing dioxins pollution in 2007, the health benefits and the health risks caused by dl-PCBs should be given further attention and evaluation in future studies.
  • Effects of Tricholoma matsutake (Agaricomycetes) extracts on promoting proliferation of HaCaT cells and accelerating mice wound healing

    Zhu, Wenyu; Chen, Yujuan; Qu, Kaige; Lai, Chunyan; Lu, Zhengcheng; Yang, Fan; Ju, Tuoyu; Wang, Zuobin; ; Changchun University of Science and Technology; et al. (Begell House, 2021-01-01)
    Tricholoma matsutake is popular in Asian countries because of its edibility and medicinal use. T. matsutake is a precious natural medicinal fungus, and it is widely used in food and biological products. This study aimed to explore the mechanism of T. matsutake on promoting proliferation of human immortalized keratinocyte (HaCaT) cells and accelerating wound healing in mice. The MTT assay was used to test the effects of three different T. matsutake extracts (0, 62.5, 125, 250, 500, and 1000 μg/mL) on HaCaT cell viability. HaCaT cells were treated with the three T. matsutake extracts (100, 500 μg/mL) and morphological and biophysical properties were detected by atomic force microscopy with JPK data processing. Western blot analysis detected Notch signaling pathways of HaCaT cells treated with 50% ethanol extract of T. matsutake (50%T) for 24 h (100, 500 and 1000 μg/mL). Mouse wounds were treated with 50%T for 15 days. Wound healing effects were observed on the back skin of mice at different times. The quality of wound healing was estimated by histological staining (hematoxylin and eosin and Masson's trichrome). All data were counted by GraphPad Prism 5 software. The increased concentration of T. matsutake remarkably promoted HaCaT cell proliferation. The Young's modulus of HaCaT cells showed the biggest increase from 1.73 ± 0.13 kPa (0 μg/mL) to 4.57 ± 0.16 kPa (500 μg/mL) in the 50%T group. The Notch1/Jagged1 pathways were upregulated with an increase in concentration (0, 100, 500, and 1000 μg/mL). Moreover, compared with the negative and positive control groups, T. matsutake promoted wound healing in mice by epidermal regeneration, subepidermal tissue formation, and collagen deposition. The results showed that T. matsutake promotes not only proliferation of HaCaT cells but also wound healing in mice.
  • Multi-level analysis and identification of tumor mutational burden genes across cancer types

    Wang, Shuangkuai; Tong, Yuantao; Zong, Hui; Xu, Xuewen; Crabbe, M. James C.; Wang, Ying; Zhang, Xiaoyen; Tongji University; Oxford University; Second Military Medical University; et al. (MDPI, 2022-02-17)
    Tumor mutational burden (TMB) is considered a potential biomarker for predicting the response and effect of immune checkpoint inhibitors (ICIs). However, there are still inconsistent standards of gene panels using next-generation sequencing and poor correlation between the TMB genes, immune cell infiltrating, and prognosis. We applied text-mining technology to construct specific TMB-associated gene panels cross various cancer types. As a case exploration, Pearson’s correlation between TMB genes and immune cell infiltrating was further analyzed in colorectal cancer. We then performed LASSO Cox regression to construct a prognosis predictive model and calculated the risk score of each sample for receiver operating characteristic (ROC) analysis. The results showed that the assessment of TMB gene panels performed well with fewer than 500 genes, highly mutated genes, and the inclusion of synonymous mutations and immune regulatory and drug-target genes. Moreover, the analysis of TMB differentially expressed genes (DEGs) suggested that JAKMIP1 was strongly correlated with the gene expression level of CD8+ T cell markers in colorectal cancer. Additionally, the prognosis predictive model based on 19 TMB DEGs reached AUCs of 0.836, 0.818, and 0.787 in 1-, 3-, and 5-year OS models, respectively (C-index: 0.810). In summary, the gene panel performed well and TMB DEGs showed great potential value in immune cell infiltration and in predicting survival.
  • Optimized degradation and inhibition of α-glucosidase activity by gracilaria lemaneiformis polysaccharide and its production in vitro

    Long, Xiaoshan; Hu, Xiao; Zhou, Shaobo; Xiang, Huan; Chen, Shengjun; Li, Laihao; Liu, Shucheng; Yang, Xianqing; Chinese Academy of Fishery Sciences; Jiangsu Ocean University; et al. (MDPI, 2021-12-22)
    Gracilaria lemaneiformis polysaccharide (GLP) exhibits good physiological activities, and it is more beneficial as it is degraded. After its degradation by hydrogen peroxide combined with vitamin C (H2 O2-Vc) and optimized by Box–Behnken Design (BBD), a new product of GLP-HV will be generated. While using GLP as control, two products of GLP-H (H2 O2-treated) and GLP-V (Vc-treated) were also produced. These products chemical characteristics (total sugar content, molecular weight, monosaccharide composition, UV spectrum, morphological structure, and hypolipidemic activity in vitro) were assessed. The results showed that the optimal conditions for H2 O2-Vc degradation were as follows: H2 O2-Vc concentration was 18.7 mM, reaction time was 0.5 h, and reaction temperature was 56◦ C. The total sugar content of GLP and its degradation products (GLP-HV, GLP-H and GLP-V) were more than 97%, and their monosaccharides are mainly glucose and galactose. The SEM analysis demonstrated that H2 O2-Vc made the structure loose and broken. Moreover, GLP, GLP-HV, GLP-H, and GLP-V had significantly inhibition effect on α-glucosidase, and their IC50 value were 3.957, 0.265, 1.651, and 1.923 mg/mL, respectively. GLP-HV had the best inhibition effect on α-glucosidase in a dose-dependent manner, which was the mixed type of competitive and non-competitive. It had a certain quenching effect on fluorescence of α-glucosidase, which may be dynamic quenching.
  • AU-rich element RNA binding proteins: at the crossroads of post-transcriptional regulation and genome integrity

    Sidali, Ahmed; Teotia, Varsha; Solaiman, Nadeen Shaikh; Bashir, Nahida; Kanagaraj, Radhakrishnan; Murphy, John J.; Surendranath, Kalpana; University of Westminster; University of Bedfordshire (MDPI, 2021-12-22)
    Genome integrity must be tightly preserved to ensure cellular survival and to deter the genesis of disease. Endogenous and exogenous stressors that impose threats to genomic stability through DNA damage are counteracted by a tightly regulated DNA damage response (DDR). RNA binding proteins (RBPs) are emerging as regulators and mediators of diverse biological processes. Specifically, RBPs that bind to adenine uridine (AU)-rich elements (AREs) in the 3′ untranslated region (UTR) of mRNAs (AU-RBPs) have emerged as key players in regulating the DDR and preserving genome integrity. Here we review eight established AU-RBPs (AUF1, HuR, KHSRP, TIA-1, TIAR, ZFP36, ZFP36L1, ZFP36L2) and their ability to maintain genome integrity through various interactions. We have reviewed canonical roles of AU-RBPs in regulating the fate of mRNA transcripts encoding DDR genes at multiple post-transcriptional levels. We have also attempted to shed light on non-canonical roles of AU-RBPs exploring their post-translational modifications (PTMs) and sub-cellular localization in response to genotoxic stresses by various factors involved in DDR and genome maintenance. Dysfunctional AU-RBPs have been increasingly found to be associated with many human cancers. Further understanding of the roles of AU-RBPS in maintaining genomic integrity may uncover novel therapeutic strategies for cancer. View Full-Text
  • Single enrichment systems possibly underestimate both exposures and biological effects of organic pollutants from drinking water

    Yang, Lan; Zhou, Ying; Chen, Li; Chen, Hanyi; Liu, Wenhao; Zheng, Weiwei; Andersen, Melvin E.; Zhang, Yubing; Hu, Yi; Crabbe, M. James C.; et al. (Elsevier, 2022-01-03)
    Comprehensive enrichment of contaminants in drinking water is an essential step for accurately determining exposure levels of contaminants and testing their biological effects. Traditional methods using a single absorbent for enriching contaminants in water might not be adequate for complicated matrices with different physical-chemical profiles . To examine this hypothesis, we used an integrated enrichment system that had three sequential stages-XAD-2 resin, poly (styrene–divinylbenzene) and activated charcoal to capture organic pollutants and disinfection by-products (DBPs) from drinking water in Shanghai. Un-adsorbed Organic Compounds in Eluates (UOCEs) named UOCEs-A, -B, and-C following each adsorption stage were determined by gas chromatography-mass spectromet ry to evaluate adsorption efficiency of the enrichment system . Meanwhile, biological effects such as cytotoxicity, effects on reactive oxygen species (ROS) generation and glutathione (GSH) depletion were determined in human LO2 cells to identify potential adverse effects on exposure to low dose contaminants. We found that poly-styrene–divinylbenzene (PS-DVB) and activated charcoal (AC) could still partly collect UOCEs-A and-B that the upper adsorption column incompletely captured, and that potential carcinogens like 2- naphthamine were present in all eluates. UOCEs-A at (1-4000), UOCEs-B at (1000-4000), and UOCEs-C at (2400-4000) folds of the actual concentrations had significant cytotoxicity to LO2 cells. Additionally, ROS and GSH change in cells treated with UOCEs indicated the potential for long-term effects of exposure to some mixtures of contaminants such as DBPs at low doses . These results suggested that an enriching system with a single adsorbent would underestimate the exposure level of pollutants and the biological effects of organic pollutants from drinking water. Effective methods for pollutants’ enrichment and capture of drinking water should be given priority in future studies on accurate evaluation of biological effects exposed to mixed pollutants via drinking water.
  • Solubility study of acetylsalicylic acid in ethanol + water mixtures: measurement, mathematical modeling, and stability discussion

    Nokhodchi, Ali; Ghafourian, Taravat; Nashed, Nour; Asare-Addo, Kofi; Behboudi, Elmira; Sefid-Sefidehkhan, Yasaman; Zarghampour, Aynaz; Rahimpour, Elaheh; Jouyban, Abolghasem; (Springer Science and Business Media Deutschland GmbH, 2021-12-28)
    Solubility determination of poorly water-soluble drugs is pivotal for formulation scientists when they want to develop a liquid formulation. Performing such a test with different ratios of cosolvents with water is time-consuming and costly. The scarcity of solubility data for poorly water-soluble drugs increases the importance of developing correlation and prediction equations for these mixtures. Therefore, the aim of the current research is to determine the solubility of acetylsalicylic acid in binary mixtures of ethanol+water at 25 and 37°C. Acetylsalicylic acid is non-stable in aqueous solutions and readily hydrolyze to salicylic acid. So, the solubility of acetylsalicylic acid is measured in ethanolic mixtures by HPLC to follow the concentration of produced salicylic acid as well. Moreover, the solubility of acetylsalicylic acid is modeled using different cosolvency equations. The measured solubility data were also predicted using PC-SAFT EOS model. DSC results ruled out any changes in the polymorphic form of acetylsalicylic acid after the solubility test, whereas XRPD results showed some changes in crystallinity of the precipitated acetylsalicylic acid after the solubility test. Fitting the solubility data to the different cosolvency models showed that the mean relative deviation percentage for the Jouyban-Acree model was less than 10.0% showing that this equation is able to obtain accurate solubility data for acetylsalicylic acid in mixtures of ethanol and water. Also, the predicted data with an average mean relative deviation percentage (MRD%) of less than 29.65% show the capability of the PC-SAFT model for predicting solubility data. A brief comparison of the solubilities of structurally related solutes to acetylsalicylic acid was also provided.
  • Proteins and disease | Structural insight and functional diversity of mammalian fatty acid binding proteins in health and disease

    McDermott, Lindsay C.; Storch, Judith; University of Bedfordshire; Rutgers University (Elsevier, 2021-08-02)
    The mammalian Fatty Acid-Binding Protein (FABP) family consists of 9 members, each displaying a β barrel capped by 2 short α-helices. The FABPs exhibit distinct and overlapping tissue expression patterns and bind long chain fatty acids with high affinity. The FABPs use interactions with membranes and proteins to transport fatty acids to sites of utilization, and each FABP displays distinct tissue specific functions. Recently several FABPs have been shown to bind additional lipid ligands, notably endocannabinoids, and to exert systemic functions remote from their tissues of origin. Some FABPs are dysregulated in cancer and inflammatory diseases, offering potential as drug targets and biomarkers.
  • Dynamic changes of DNA methylation during wild strawberry (Fragaria nilgerrensis) tissue culture

    Cao, Qiang; Feng, Yuxi; Dai, Xiongwei; Huang, Lin; Li, Jiamin; Tao, Pang; Crabbe, M. James C.; Zhang, Ti-Cao; Qiao, Qin; Yunnan University; et al. (Frontiers, 2021-11-30)
    Tissue culture is an important tool for asexual propagation and genetic transformation of strawberry plants. In plant tissue culture, variation of DNA methylation is a potential source of phenotypic variation in regenerated plants. However, the genome wide dynamic methylation patterns of strawberry tissue culture remain unclear. In this study, we used whole-genome bisulfite sequencing (WGBS) to study genomic DNA methylation changes of a wild strawberry Fragaria nilgerrensis at six stages: from explants of shoot tips to outplanting and acclimation. Global methylation levels showed that CG sites exhibited the highest methylation level in all stages with an average of 49.5%, followed by CHG (33.2%) and CHH (12.4%). Although CHH accounted for the lowest proportion of total cytosine methylation, it showed the most obvious methylation change and the most of these changes occurred in the transposable element regions. The overall methylation levels alternately decreased and increased during the entire tissue culture process and the distribution of DNA methylation was non-uniform among different genetic regions. Furthermore, much more differentially methylated regions (DMRs) were detected in dedifferentiation and redifferentiation stages and most of them were transposable elements, suggesting these processes involved activating or silencing of amounts of transposons. The functional enrichment of the DMR-related genes indicated that genes involved in hormone metabolic processes, plant development and the stress response changed methylation throughout the tissue culture process. Finally, the quantitative real-time PCR (qRT-PCR) was conducted to examine the association of methylation and gene expression of a set of different methylated genes. Our findings give deeper insight into the epigenetic regulation of gene expression during the plant tissue cultures process, which will be useful in the efficient control of somaclonal variations and in crop improvement.
  • Identification of diverse lipid-binding modes in the groove of zinc α2 glycoprotein reveals its functional versatility

    Zahid, Henna; Lau, Andy M.; Kelly, Sharon M.; Karu, Kersti; Gor, Jayesh; Perkins, Stephen J.; McDermott, Lindsay C. (Wiley, 2021-11-24)
    ZAG is a multifunctional glycoprotein with a class I MHC-like protein fold and an α1-α2 lipid-binding groove. The intrinsic ZAG ligand is unknown. Our previous studies showed that ZAG binds the dansylated C11 fatty acid, DAUDA, differently to the boron dipyrromethane C16 fatty acid, C16-BODIPY. Here, the molecular basis for this difference was elucidated. Multi-wavelength analytical ultracentrifugation confirmed that DAUDA and C16-BODIPY individually bind to ZAG and compete for the same binding site. Molecular docking of lipid-binding in the structurally related CD1-proteins predicted nine conserved ligand contact residues in ZAG. Twelve mutants were accordingly created by alanine scanning site directed mutagenesis for characterisation. Mutation of Y12 caused ZAG to misfold. Mutation of K147, R157 and A158 abrogated C16-BODIPY but not DAUDA binding. L69 and T169 increased the fluorescence emission intensity of C16-BODIPY but not of DAUDA compared to wild-type ZAG and showed that C16-BODIPY binds close to T169 and L69. Distance measurements of the crystal structure revealed K147 forms a salt bridge with D83. A range of bioactive bulky lipids including phospholipids and sphingolipids displaced DAUDA from the ZAG binding site but unexpectedly did not displace C16-BODIPY. We conclude that the ZAG α1-α2 groove contains separate but overlapping sites for DAUDA and C16-BODIPY and is involved in binding to a bulkier and wider repertoire of lipids than previously reported. This work suggested that the in vivo activity of ZAG may be dictated by its lipid ligand.
  • Association of TNF-α polymorphisms (-857, -863 and -1031), TNF-α serum level and lipid profile with acne vulgaris

    Younis, Sidra; Shamim, Sana; Nisar, Kanwal; Deeba, Farah; Mehmood, Sabba; Mumtaz, Sara; Blumenberg, Miroslav; Javed, Qamar; ; National University of Medical Sciences, Pakistan; et al. (Elsevier, 2021-07-17)
    Background Acne is an inflammatory condition principally affected by genetic and dietary factors. Investigation into functional polymorphisms of TNF-α gene and their association with acne vulgaris will be helpful in exploring genetic influence on skin immune mediated inflammatory events. In the present study, we analyzed association of TNF-α gene polymorphisms, its expression levels and lipid profiles in a large cohort of acne patients and controls. Methods We used PCR-RFLP to study association of TNF-α polymorphisms at −857C/T, −863C/A and −1031 T/C sites with acne vulgaris. Lipid profiles were measured using enzymatic end-point method. The serum levels of TNF-α and apolipoprotein a were measured using ELISA. NIH, LDlink was used to investigate patterns of linkage disequilibrium across south Asian reference genome (Punjabi from Lahore Pakistan). Results We found that TNF-α −863 polymorphism is strongly associated with acne in overall population as well as in gender and severity based groups of acne patients. Polymorphisms at −863 and −1031 position were in linkage disequilibrium. Importantly, TNF-α serum level was significantly increased in acne patients with severe disease symptoms. Furthermore, levels of total cholesterol (TC) and triglycerides (TG) were significantly increased, whereas high density lipoprotein cholesterol (HDL-C) level was significantly decreased in acne patients. The levels of apolipoprotein a varied widely in studied populations and no significant difference was found in the analyzed groups. Conclusion In conclusion, we found that TNF-α expression increases in acne patients affected by TNF-α polymorphisms, and that the lipid profile is specifically disrupted in acne patients.
  • Nance-Horan Syndrome-like 1 protein negatively regulates Scar/WAVE-Arp2/3 activity and inhibits lamellipodia stability and cell migration

    Law, Ah-Lai; Jalal, Shamsinar; Pallett, Tommy; Mosis, Fuad; Guni, Ahmad; Brayford, Simon; Yolland, Lawrence; Marcotti, Stefania; Levitt, James A.; Poland, Simon P.; et al. (Nature Research, 2021-09-28)
    Cell migration is important for development and its aberrant regulation contributes to many diseases. The Scar/WAVE complex is essential for Arp2/3 mediated lamellipodia formation during mesenchymal cell migration and several coinciding signals activate it. However, so far, no direct negative regulators are known. Here we identify Nance-Horan Syndrome-like 1 protein (NHSL1) as a direct binding partner of the Scar/WAVE complex, which co-localise at protruding lamellipodia. This interaction is mediated by the Abi SH3 domain and two binding sites in NHSL1. Furthermore, active Rac binds to NHSL1 at two regions that mediate leading edge targeting of NHSL1. Surprisingly, NHSL1 inhibits cell migration through its interaction with the Scar/WAVE complex. Mechanistically, NHSL1 may reduce cell migration efficiency by impeding Arp2/3 activity, as measured in cells using a Arp2/3 FRET-FLIM biosensor, resulting in reduced F-actin density of lamellipodia, and consequently impairing the stability of lamellipodia protrusions.
  • Purification and identification of novel xanthine oxidase inhibitory peptides derived from round scad (Decapterus maruadsi) protein hydrolysates

    Hu, Xiao; Zhou, Ya; Zhou, Shaobo; Chen, Shengjun; Wu, Yanyan; Li, Laihao; Yang, Xianqing; Chinese Academy of Fishery Sciences; Jiangsu Ocean University; Shanghai Ocean University; et al. (MDPI, 2021-09-24)
    The objective of the present study was to investigate the xanthine oxidase (XO) inhibitory effects of peptides purified and identified from round scad (Decapterus maruadsi) hydrolysates (RSHs). In this study, RSHs were obtained by using three proteases (neutrase, protamex and alcalase). Among them, the RSHs of 6-h hydrolysis by neutrase displayed the strongest XO inhibitory activity and had an abundance of small peptides (<500 Da). Four novel peptides were purified by immobilized metal affinity chromatography and identified by nano-high-performance liquid chromatography mass/mass spectrometry. Their amino acid sequences were KGFP (447.53 Da), FPSV (448.51 Da), FPFP (506.59 Da) and WPDGR (629.66 Da), respectively. Then the peptides were synthesized to evaluate their XO inhibitory activity. The results indicated that the peptides of both FPSV (5 mM) and FPFP (5 mM) exhibited higher XO inhibitory activity (22.61 +- 1.81% and 20.09 +- 2.41% respectively). Fluorescence spectra assay demonstrated that the fluorescence quenching mechanism of XO by these inhibitors (FPSV and FPFP) was a static quenching procedure. The study of inhibition kinetics suggested that the inhibition of both FPSV and FPFP was reversible, and the type of their inhibition was a mixed one. Molecular docking revealed the importance of π-π stacking between Phe residue (contained in peptides) and Phe914 (contained in the XO) in the XO inhibitory activity of the peptides.
  • ABL1 and Cofilin1 promote T-cell acute lymphoblastic leukemia cell migration

    Luo, Jixian; Zheng, Huiguang; Wang, Sen; Li, Dingyun; Ma, Wenli; Wang, Lan; Crabbe, M. James C. (Oxford University Press, 2021-09-11)
    The fusion gene of ABL1 is closely related to tumor proliferation, invasion, and migration. It has been reported recently that ABL1 itself is required for T-cell acute lymphoblastic leukemia (T-ALL) cell migration induced by CXCL12. Further experiments revealed that ABL1 inhibitor Nilotinib inhibited leukemia cell migration induced by CXCL12, indicating the possible application of Nilotinib in T-ALL leukemia treatment. However, the interacting proteins of ABL1 and the specific mechanisms of their involvement in this process need further investigation. In the present study, ABL1 interacting proteins were characterized and their roles in the process of leukemia cell migration induced by CXCL12 were investigated. Co-immunoprecipitation in combination with mass spectrometry analysis identified 333 proteins that interact with ABL1, including Cofilin1. Gene ontology analysis revealed that many of them were enriched in the intracellular organelle or cytoplasm, including nucleic acid binding components, transfectors, or co-transfectors. Kyoto Encyclopedia of Genes and Genomes analysis showed that the top three enriched pathways were translation, glycan biosynthesis, and metabolism, together with human diseases. ABL1 and Cofilin1 were in the same complex. Cofilin1 binds the SH3 domain of ABL1 directly; however, ABL1 is not required for the phosphorylation of Cofilin1. Molecular docking analysis shows that ABL1 interacts with Cofilin1 mainly through hydrogen bonds and ionic interaction between amino acid residues. The mobility of leukemic cells was significantly decreased by Cofilin1 siRNA. These results demonstrate that Cofilin1 is a novel ABL1 binding partner. Furthermore, Cofilin1 participates in the migration of leukemia cells induced by CXCL12. These data indicate that ABL1 and Cofilin1 are possible targets for T-ALL treatment.

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