International Journal of Molecular Sciences

5 pages, 520 KiB

Open AccessEditorial

Highlight: Mitochondrial Mechanisms in Septic Cardiomyopathy

by International Journal of Molecular Sciences Editorial Office

Int. J. Mol. Sci. 2015, 16(8), 20095-20099; https://doi.org/10.3390/ijms160820095 - 25 Aug 2015

Viewed by 3802

The paper “Mitochondrial Mechanisms in Septic Cardiomyopathy” [1], published in the current issue offers an excellent overview for readers of the International Journal of Molecular Sciences.[...] Full article

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13 pages, 856 KiB

Open AccessArticle

A Futile Redox Cycle Involving Neuroglobin Observed at Physiological Temperature

by Anyang Liu and Thomas Brittain

Int. J. Mol. Sci. 2015, 16(8), 20082-20094; https://doi.org/10.3390/ijms160820082 - 24 Aug 2015

Cited by 6 | Viewed by 4701

Abstract

Previous studies identifying the potential anti-apoptotic role of neuroglobin raise the question as to how cells might employ neuroglobin to avoid the apoptotic impact of acute hypoxia whilst also avoiding chronic enhancement of tumour formation. We show that under likely physiological conditions neuroglobin [...] Read more.

Previous studies identifying the potential anti-apoptotic role of neuroglobin raise the question as to how cells might employ neuroglobin to avoid the apoptotic impact of acute hypoxia whilst also avoiding chronic enhancement of tumour formation. We show that under likely physiological conditions neuroglobin can take part in a futile redox cycle. Determination of the rate constants for each of the steps in the cycle allows us to mathematically model the steady state concentration of the active anti-apoptotic ferrous form of neuroglobin under various conditions. Under likely normal physiological conditions neuroglobin is shown to be present in the ferrous state at approximately 30% of its total cellular concentration. Under hypoxic conditions this rapidly rises to approximately 80%. Temporal analysis of this model indicates that the transition from low concentrations to high concentration of ferrous neuroglobin occurs on the seconds time scale. These findings indicate a potential control model for the anti-apoptotic activity of neuroglobin, under likely physiological conditions, whereby, in normoxic conditions, the anti-apoptotic activity of neuroglobin is maintained at a low level, whilst immediately a transition occurs to a hypoxic situation, as might arise during stroke, the anti-apoptotic activity is drastically increased. In this way the cell avoids unwanted increased oncogenic potential under normal conditions, but the rapid activation of neuroglobin provides anti-apoptotic protection in times of acute hypoxia. Full article

(This article belongs to the Section Biochemistry)

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15 pages, 718 KiB

Open AccessArticle

Variants of MicroRNA Genes: Gender-Specific Associations with Multiple Sclerosis Risk and Severity

by Ivan Kiselev, Vitalina Bashinskaya, Olga Kulakova, Natalia Baulina, Ekaterina Popova, Alexey Boyko and Olga Favorova

Int. J. Mol. Sci. 2015, 16(8), 20067-20081; https://doi.org/10.3390/ijms160820067 - 24 Aug 2015

Cited by 35 | Viewed by 7219

Abstract

Multiple sclerosis (MS) is an autoimmune neuro-inflammatory disease arising from complex interactions of genetic, epigenetic, and environmental factors. Variations in genes of some microRNAs—key post-transcriptional regulators of many genes—can influence microRNAs expression/function and contribute to MS via expression changes of protein-coding target mRNA [...] Read more.

Multiple sclerosis (MS) is an autoimmune neuro-inflammatory disease arising from complex interactions of genetic, epigenetic, and environmental factors. Variations in genes of some microRNAs—key post-transcriptional regulators of many genes—can influence microRNAs expression/function and contribute to MS via expression changes of protein-coding target mRNA genes. We performed an association study of polymorphous variants of MIR146A rs2910164, MIR196A2 rs11614913, MIR499A rs3746444 MIR223 rs1044165 and their combinations with MS risk and severity. 561 unrelated patients with bout-onset MS and 441 healthy volunteers were enrolled in the study. We observed associations of MS risk with allele MIR223*T and combination (MIR223*T + MIR146A*G/G) carriage in the entire groups and in women at Bonferroni-corrected significance level (p_corr < 0.05). Besides, MIR146A*G/G association with MS was observed in women with nominal significance (p_f = 0.025). No MS associations were found in men. A more severe MS course (MSSS value > 3.5) was associated with the carriage of MIR499A*C/T and, less reliably, of MIR499A*C (p_corr = 0.006 and p_corr = 0.024, respectively) and with the carriage of combinations (MIR499A*C/T + MIR196A2*C) and (MIR499A*C + MIR196A2*C) (p_corr = 0.00078 and p_corr = 0.0059, respectively). These associations also showed gender specificity, as they were not significant in men and substantially reinforced in women. The strongest association with MS severity was observed in women for combination (MIR499A*C/T + MIR196A2*C): p_corr = 4.43 × 10⁻⁶ and OR = 3.23 (CI: 1.99–5.26). Full article

(This article belongs to the Special Issue Advances in Multiple Sclerosis)

17 pages, 2393 KiB

Open AccessArticle

Development of a New Monomer for the Synthesis of Intrinsic Antimicrobial Polymers with Enhanced Material Properties

by Florian Brodkorb, Björn Fischer, Katrin Kalbfleisch, Oliver Robers, Carina Braun, Sophia Dohlen, Judith Kreyenschmidt, Reinhard Lorenz and Martin Kreyenschmidt

Int. J. Mol. Sci. 2015, 16(8), 20050-20066; https://doi.org/10.3390/ijms160820050 - 24 Aug 2015

Cited by 5 | Viewed by 7415

Abstract

The use of biocidal compounds in polymers is steadily increasing because it is one solution to the need for safety and hygiene. It is possible to incorporate an antimicrobial moiety to a polymer. These polymers are referred to as intrinsic antimicrobial. The biocidal [...] Read more.

The use of biocidal compounds in polymers is steadily increasing because it is one solution to the need for safety and hygiene. It is possible to incorporate an antimicrobial moiety to a polymer. These polymers are referred to as intrinsic antimicrobial. The biocidal action results from contact of the polymer to the microorganisms, with no release of active molecules. This is particularly important in critical fields like food technology, medicine and ventilation technology, where migration or leaching is crucial and undesirable. The isomers N-(1,1-dimethylethyl)-4-ethenyl-benzenamine and N-(1,1-dimethyl-ethyl)-3-ethenyl-benzenamine (TBAMS) are novel (Co-)Monomers for intrinsic anti-microbial polymers. The secondary amines were prepared and polymerized to the corresponding water insoluble polymer. The antimicrobial activity was analyzed by the test method JIS Z 2801:2000. Investigations revealed a high antimicrobial activity against Staphylococcus aureus and Escherichia coli with a reduction level of >4.5 log₁₀ units. Furthermore, scanning electron microscopy (SEM) of E. coli. in contact with the polymer indicates a bactericidal action which is caused by disruption of the bacteria cell membranes, leading to lysis of the cells. Full article

(This article belongs to the Special Issue Antimicrobial Polymers 2016)

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17 pages, 1978 KiB

Open AccessArticle

Extraction of Peptidoglycan from L. paracasei subp. Paracasei X12 and Its Preliminary Mechanisms of Inducing Immunogenic Cell Death in HT-29 Cells

by Pei-Jun Tian, Bao-Long Li, Yu-Juan Shan, Jin-Na Zhang, Jing-Yu Chen, Min Yu and Lan-Wei Zhang

Int. J. Mol. Sci. 2015, 16(8), 20033-20049; https://doi.org/10.3390/ijms160820033 - 24 Aug 2015

Cited by 36 | Viewed by 7867

Abstract

L. paracasei subp. paracasei X12 was previously isolated from a Chinese traditional fermented cheese with anticancer activities and probiotic potential. Herein, the integral peptidoglycan (X12-PG) was extracted by a modified trichloroacetic acid (TCA) method. X12-PG contained the four representative amino acids Asp, Glu, [...] Read more.

L. paracasei subp. paracasei X12 was previously isolated from a Chinese traditional fermented cheese with anticancer activities and probiotic potential. Herein, the integral peptidoglycan (X12-PG) was extracted by a modified trichloroacetic acid (TCA) method. X12-PG contained the four representative amino acids Asp, Glu, Ala and Lys, and displayed the similar lysozyme sensitivity, UV-visible scanning spectrum and molecular weight as the peptidoglycan standard. X12-PG could induce the production of apoptotic bodies observed by transmission electron microscopy (TEM). X12-PG could significantly induced the translocation of calreticulin (CRT) and the release of high mobility group box 1 protein (HMGB1), the two notable hallmarks of immunogenic cell death (ICD), with the endoplastic reticulum (ER) damaged and subsequently intracellular [Ca²⁺] elevated. Our findings implied that X12-PG could induce the ICD of HT-29 cells through targeting at the ER. The present results may enlighten the prospect of probiotics in the prevention of colon cancer. Full article

(This article belongs to the Section Biochemistry)

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13 pages, 2571 KiB

Open AccessArticle

Over-Expression of Porcine Myostatin Missense Mutant Leads to A Gender Difference in Skeletal Muscle Growth between Transgenic Male and Female Mice

by Dezun Ma, Pengfei Gao, Lili Qian, Qingqing Wang, Chunbo Cai, Shengwang Jiang, Gaojun Xiao and Wentao Cui

Int. J. Mol. Sci. 2015, 16(8), 20020-20032; https://doi.org/10.3390/ijms160820020 - 24 Aug 2015

Cited by 8 | Viewed by 7072

Abstract

Myostatin, a transforming growth factor-β family member, is a negative regulator of skeletal muscle development and growth. Piedmontese cattle breeds have a missense mutation, which results in a cysteine to tyrosine substitution in the mature myostatin protein (C313Y). This loss-of-function mutation in myostatin [...] Read more.

Myostatin, a transforming growth factor-β family member, is a negative regulator of skeletal muscle development and growth. Piedmontese cattle breeds have a missense mutation, which results in a cysteine to tyrosine substitution in the mature myostatin protein (C313Y). This loss-of-function mutation in myostatin results in a double-muscled phenotype in cattle. Myostatin propeptide is an inhibitor of myostatin activity and is considered a potential agent to stimulate muscle growth in livestock. In this study, we generated transgenic mice overexpressing porcine myostatin missense mutant (pmMS), C313Y, and wild-type porcine myostatin propeptide (ppMS), respectively, to examine their effects on muscle growth in mice. Enhanced muscle growth was observed in both pmMS and ppMS transgenic female mice and also in ppMS transgenic male mice. However, there was no enhanced muscle growth observed in pmMS transgenic male mice. To explore why there is such a big difference in muscle growth between pmMS and ppMS transgenic male mice, the expression level of androgen receptor (AR) mutant AR45 was measured by Western blot. Results indicated that AR45 expression significantly increased in pmMS transgenic male mice while it decreased dramatically in ppMS transgenic male mice. Our data demonstrate that both pmMS and ppMS act as myostatin inhibitors in the regulation of muscle growth, but the effect of pmMS in male mice is reversed by an increased AR45 expression. These results provide useful insight and basic theory to future studies on improving pork quality by genetically manipulating myostatin expression or by regulating myostatin activity. Full article

(This article belongs to the Section Biochemistry)

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19 pages, 2938 KiB

Open AccessArticle

Exploiting Size-Dependent Drag and Magnetic Forces for Size-Specific Separation of Magnetic Nanoparticles

by Hunter B. Rogers, Tareq Anani, Young Suk Choi, Ronald J. Beyers and Allan E. David

Int. J. Mol. Sci. 2015, 16(8), 20001-20019; https://doi.org/10.3390/ijms160820001 - 21 Aug 2015

Cited by 12 | Viewed by 6723

Abstract

Realizing the full potential of magnetic nanoparticles (MNPs) in nanomedicinerequires the optimization of their physical and chemical properties. Elucidation of the effectsof these properties on clinical diagnostic or therapeutic properties, however, requires thesynthesis or purification of homogenous samples, which has proved to be [...] Read more.

Realizing the full potential of magnetic nanoparticles (MNPs) in nanomedicinerequires the optimization of their physical and chemical properties. Elucidation of the effectsof these properties on clinical diagnostic or therapeutic properties, however, requires thesynthesis or purification of homogenous samples, which has proved to be difficult. Whileinitial simulations indicated that size-selective separation could be achieved by flowingmagnetic nanoparticles through a magnetic field, subsequent in vitro experiments wereunable to reproduce the predicted results. Magnetic field-flow fractionation, however, wasfound to be an effective method for the separation of polydisperse suspensions of iron oxidenanoparticles with diameters greater than 20 nm. While similar methods have been used toseparate magnetic nanoparticles before, no previous work has been done with magneticnanoparticles between 20 and 200 nm. Both transmission electron microscopy (TEM) anddynamic light scattering (DLS) analysis were used to confirm the size of the MNPs. Furtherdevelopment of this work could lead to MNPs with the narrow size distributions necessary fortheir in vitro and in vivo optimization. Full article

(This article belongs to the Special Issue Magnetic Nanoparticles 2015)

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12 pages, 669 KiB

Open AccessReview

Docosahexaenoic Acid Levels in Blood and Metabolic Syndrome in Obese Children: Is There a Link?

by Carlotta Lassandro, Giuseppe Banderali, Giovanni Radaelli, Elisa Borghi, Francesca Moretti and Elvira Verduci

Int. J. Mol. Sci. 2015, 16(8), 19989-20000; https://doi.org/10.3390/ijms160819989 - 21 Aug 2015

Cited by 8 | Viewed by 6284

Abstract

Prevalence of metabolic syndrome is increasing in the pediatric population. Considering the different existing criteria to define metabolic syndrome, the use of the International Diabetes Federation (IDF) criteria has been suggested in children. Docosahexaenoic acid (DHA) has been associated with beneficial effects on [...] Read more.

Prevalence of metabolic syndrome is increasing in the pediatric population. Considering the different existing criteria to define metabolic syndrome, the use of the International Diabetes Federation (IDF) criteria has been suggested in children. Docosahexaenoic acid (DHA) has been associated with beneficial effects on health. The evidence about the relationship of DHA status in blood and components of the metabolic syndrome is unclear. This review discusses the possible association between DHA content in plasma and erythrocytes and components of the metabolic syndrome included in the IDF criteria (obesity, alteration of glucose metabolism, blood lipid profile, and blood pressure) and non-alcoholic fatty liver disease in obese children. The current evidence is inconsistent and no definitive conclusion can be drawn in the pediatric population. Well-designed longitudinal and powered trials need to clarify the possible association between blood DHA status and metabolic syndrome. Full article

(This article belongs to the Special Issue Omega-3 Fatty Acids in Health and Diseases)

11 pages, 899 KiB

Open AccessArticle

Atherosclerotic Calcification Detection: A Comparative Study of Carotid Ultrasound and Cone Beam CT

by Fisnik Jashari, Pranvera Ibrahimi, Elias Johansson, Jan Ahlqvist, Conny Arnerlöv, Maria Garoff, Eva Levring Jäghagen, Per Wester and Michael Y. Henein

Int. J. Mol. Sci. 2015, 16(8), 19978-19988; https://doi.org/10.3390/ijms160819978 - 21 Aug 2015

Cited by 21 | Viewed by 6890

Abstract

Background and Aim: Arterial calcification is often detected on ultrasound examination but its diagnostic accuracy is not well validated. The aim of this study was to determine the accuracy of carotid ultrasound B mode findings in detecting atherosclerotic calcification quantified by cone beam [...] Read more.

Background and Aim: Arterial calcification is often detected on ultrasound examination but its diagnostic accuracy is not well validated. The aim of this study was to determine the accuracy of carotid ultrasound B mode findings in detecting atherosclerotic calcification quantified by cone beam computed tomography (CBCT). Methods: We analyzed 94 carotid arteries, from 88 patients (mean age 70 ± 7 years, 33% females), who underwent pre-endarterectomy ultrasound examination. Plaques with high echogenic nodules and posterior shadowing were considered calcified. After surgery, the excised plaques were examined using CBCT, from which the calcification volume (mm3) was calculated. In cases with multiple calcifications the largest calcification nodule volume was used to represent the plaque. Carotid artery calcification by the two imaging techniques was compared using conventional correlations. Results: Carotid ultrasound was highly accurate in detecting the presence of calcification; with a sensitivity of 88.2%. Based on the quartile ranges of calcification volumes measured by CBCT we have divided plaque calcification into four groups: <8; 8–35; 36–70 and >70 mm3. Calcification volumes ≥8 were accurately detectable by ultrasound with a sensitivity of 96%. Of the 21 plaques with <8 mm3 calcification volume; only 13 were detected by ultrasound; resulting in a sensitivity of 62%. There was no difference in the volume of calcification between symptomatic and asymptomatic patients. Conclusion: Carotid ultrasound is highly accurate in detecting the presence of calcified atherosclerotic lesions of volume ≥8 mm3; but less accurate in detecting smaller volume calcified plaques. Further development of ultrasound techniques should allow better detection of early arterial calcification. Full article

(This article belongs to the Special Issue Atherosclerosis and Vascular Imaging)

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18 pages, 1119 KiB

Open AccessArticle

Inhibition of NF-κB in Tumor Cells Exacerbates Immune Cell Activation Following Photodynamic Therapy

by Mans Broekgaarden, Milan Kos, Freek A. Jurg, Adriaan A. Van Beek, Thomas M. Van Gulik and Michal Heger

Int. J. Mol. Sci. 2015, 16(8), 19960-19977; https://doi.org/10.3390/ijms160819960 - 21 Aug 2015

Cited by 21 | Viewed by 7706

Abstract

Although photodynamic therapy (PDT) yields very good outcomes in numerous types of superficial solid cancers, some tumors respond suboptimally to PDT. Novel treatment strategies are therefore needed to enhance the efficacy in these therapy-resistant tumors. One of these strategies is to combine PDT [...] Read more.

Although photodynamic therapy (PDT) yields very good outcomes in numerous types of superficial solid cancers, some tumors respond suboptimally to PDT. Novel treatment strategies are therefore needed to enhance the efficacy in these therapy-resistant tumors. One of these strategies is to combine PDT with inhibitors of PDT-induced survival pathways. In this respect, the transcription factor nuclear factor κB (NF-κB) has been identified as a potential pharmacological target, albeit inhibition of NF-κB may concurrently dampen the subsequent anti-tumor immune response required for complete tumor eradication and abscopal effects. In contrast to these postulations, this study demonstrated that siRNA knockdown of NF-κB in murine breast carcinoma (EMT-6) cells increased survival signaling in these cells and exacerbated the inflammatory response in murine RAW 264.7 macrophages. These results suggest a pro-death and immunosuppressive role of NF-κB in PDT-treated cells that concurs with a hyperstimulated immune response in innate immune cells. Full article

(This article belongs to the Special Issue Advances in Photodynamic Therapy)

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24 pages, 5926 KiB

Open AccessReview

Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy

by Samuel Paul Jarvis

Int. J. Mol. Sci. 2015, 16(8), 19936-19959; https://doi.org/10.3390/ijms160819936 - 21 Aug 2015

Cited by 37 | Viewed by 13129

Abstract

A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated [...] Read more.

A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H2 molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions. Full article

(This article belongs to the Special Issue Supramolecular Interactions)

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16 pages, 21991 KiB

Open AccessArticle

Selection and Characterization of Single Chain Antibody Fragments Specific for Hsp90 as a Potential Cancer Targeting Molecule

by Edyta Petters, Aleksandra Sokolowska-Wedzina and Jacek Otlewski

Int. J. Mol. Sci. 2015, 16(8), 19920-19935; https://doi.org/10.3390/ijms160819920 - 21 Aug 2015

Cited by 4 | Viewed by 7233

Abstract

Heat shock proteins play an essential role in facilitating malignant transformation and they have been recognized as important factors in human cancers. One of the key elements of the molecular chaperones machinery is Hsp90 and it has recently become a target for anticancer [...] Read more.

Heat shock proteins play an essential role in facilitating malignant transformation and they have been recognized as important factors in human cancers. One of the key elements of the molecular chaperones machinery is Hsp90 and it has recently become a target for anticancer therapeutic approaches. The potential and importance of Hsp90-directed agents becomes apparent when one realizes that disruption of Hsp90 function may influence over 200 oncogenic client proteins. Here, we described the selection and characterization of Hsp90-specific antibody fragments from commercially available Tomlinson I and J phage display libraries. The affinities of Hsp90-binding scFv variants were measured using SPR method. Then, based on the best clone selected, we performed the affinity maturation procedure and obtained valuable Hsp90-specific clones. The selected binders were expressed and applied for immunostaining, ELISA and SPR analysis using model cancer cell lines. All performed experiments confirmed the ability of selected antibodies to interact with the Hsp90. Therefore, the presented Hsp90-specific scFv, might be a starting point for the development of a novel antibody-based strategy targeting cancer. Full article

(This article belongs to the Special Issue Advances in Molecular Oncology)

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34 pages, 1310 KiB

Open AccessReview

Regulatory Roles of Non-Coding RNAs in Colorectal Cancer

by Jun Wang, Yong-Xi Song, Bin Ma, Jia-Jun Wang, Jing-Xu Sun, Xiao-Wan Chen, Jun-Hua Zhao, Yu-Chong Yang and Zhen-Ning Wang

Int. J. Mol. Sci. 2015, 16(8), 19886-19919; https://doi.org/10.3390/ijms160819886 - 21 Aug 2015

Cited by 69 | Viewed by 9381

Abstract

Non-coding RNAs (ncRNAs) have recently gained attention because of their involvement in different biological processes. An increasing number of studies have demonstrated that mutations or abnormal expression of ncRNAs are closely associated with various diseases including cancer. The present review is a comprehensive [...] Read more.

Non-coding RNAs (ncRNAs) have recently gained attention because of their involvement in different biological processes. An increasing number of studies have demonstrated that mutations or abnormal expression of ncRNAs are closely associated with various diseases including cancer. The present review is a comprehensive examination of the aberrant regulation of ncRNAs in colorectal cancer (CRC) and a summary of the current findings on ncRNAs, including long ncRNAs, microRNAs, small interfering RNAs, small nucleolar RNAs, small nuclear RNAs, Piwi-interacting RNAs, and circular RNAs. These ncRNAs might become novel biomarkers and targets as well as potential therapeutic tools for the treatment of CRC in the near future and this review may provide important clues for further research on CRC and for the selection of effective therapeutic targets. Full article

(This article belongs to the Collection Regulation by Non-coding RNAs)

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18 pages, 503 KiB

Open AccessArticle

Accurate Ab Initio and Template-Based Prediction of Short Intrinsically-Disordered Regions by Bidirectional Recurrent Neural Networks Trained on Large-Scale Datasets

by Viola Volpato, Badr Alshomrani and Gianluca Pollastri

Int. J. Mol. Sci. 2015, 16(8), 19868-19885; https://doi.org/10.3390/ijms160819868 - 21 Aug 2015

Cited by 1 | Viewed by 5959

Abstract

Intrinsically-disordered regions lack a well-defined 3D structure, but play key roles in determining the function of many proteins. Although predictors of disorder have been shown to achieve relatively high rates of correct classification of these segments, improvements over the the years have been [...] Read more.

Intrinsically-disordered regions lack a well-defined 3D structure, but play key roles in determining the function of many proteins. Although predictors of disorder have been shown to achieve relatively high rates of correct classification of these segments, improvements over the the years have been slow, and accurate methods are needed that are capable of accommodating the ever-increasing amount of structurally-determined protein sequences to try to boost predictive performances. In this paper, we propose a predictor for short disordered regions based on bidirectional recurrent neural networks and tested by rigorous five-fold cross-validation on a large, non-redundant dataset collected from MobiDB, a new comprehensive source of protein disorder annotations. The system exploits sequence and structural information in the forms of frequency profiles, predicted secondary structure and solvent accessibility and direct disorder annotations from homologous protein structures (templates) deposited in the Protein Data Bank. The contributions of sequence, structure and homology information result in large improvements in predictive accuracy. Additionally, the large scale of the training set leads to low false positive rates, making our systems a robust and efficient way to address high-throughput disorder prediction. Full article

(This article belongs to the Special Issue In-Silico Prediction and Characterization of Intrinsic Disorder in Proteins)

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17 pages, 2257 KiB

Open AccessArticle

Curcumol Inhibits Growth and Induces Apoptosis of Colorectal Cancer LoVo Cell Line via IGF-1R and p38 MAPK Pathway

by Juan Wang, Fengxiang Huang, Zhun Bai, Bixia Chi, Jiacai Wu and Xu Chen

Int. J. Mol. Sci. 2015, 16(8), 19851-19867; https://doi.org/10.3390/ijms160819851 - 20 Aug 2015

Cited by 69 | Viewed by 9959

Abstract

Curcumol, isolated from the traditional medical plant Rhizoma Curcumae, is the bioactive component of Zedoary oil, whose potential anti-tumor effect has attracted considerable attention in recent years. Though many researchers have reported curcumol and its bioactivity, the potential molecular mechanism for its [...] Read more.

Curcumol, isolated from the traditional medical plant Rhizoma Curcumae, is the bioactive component of Zedoary oil, whose potential anti-tumor effect has attracted considerable attention in recent years. Though many researchers have reported curcumol and its bioactivity, the potential molecular mechanism for its anti-cancer effect in colorectal cancer LoVo cells still remains unclear. In the present study, we found that curcumol showed growth inhibition and induced apoptosis of LoVo cells in a dose- and time-dependent manner. The occurrence of its proliferation inhibition and apoptosis came with suppression of IGF-1R expression, and then increased the phosphorylation of p38 mitogen activated protein kinase (MAPK), which might result in a cascade response by inhibiting the CREB survival pathway and finally triggered Bax/Bcl-2 and poly(ADP-ribose) polymerase 1 (PARP-1) apoptosis signals. Moreover, curcumol inhibited colorectal cancer in xenograft models of nude mice. Immunohistochemical and Western blot analysis revealed that curcumol could decrease the expression of ki-67, Bcl-2 as well as CREB1, and increase the expression of Bax and the phosphorylation of p38, which were consistent with our in vitro study. Overall, our in vitro and in vivo data confirmed the anti-cancer activity of curcumol, which was related to a significant inhibition of IGF-1R and activation of p38 MAPKs, indicating that curcumol may be a potential anti-tumor agent for colorectal carcinoma therapy. Full article

(This article belongs to the Collection Programmed Cell Death and Apoptosis)

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15 pages, 1319 KiB

Open AccessReview

Mitochondrial Transcription Factor A and Mitochondrial Genome as Molecular Targets for Cisplatin-Based Cancer Chemotherapy

by Kimitoshi Kohno, Ke-Yong Wang, Mayu Takahashi, Tomoko Kurita, Yoichiro Yoshida, Masakazu Hirakawa, Yoshikazu Harada, Akihiro Kuma, Hiroto Izumi and Shinji Matsumoto

Int. J. Mol. Sci. 2015, 16(8), 19836-19850; https://doi.org/10.3390/ijms160819836 - 20 Aug 2015

Cited by 29 | Viewed by 10248

Abstract

Mitochondria are important cellular organelles that function as control centers of the energy supply for highly proliferative cancer cells and regulate apoptosis after cancer chemotherapy. Cisplatin is one of the most important chemotherapeutic agents and a key drug in therapeutic regimens for a [...] Read more.

Mitochondria are important cellular organelles that function as control centers of the energy supply for highly proliferative cancer cells and regulate apoptosis after cancer chemotherapy. Cisplatin is one of the most important chemotherapeutic agents and a key drug in therapeutic regimens for a broad range of solid tumors. Cisplatin may directly interact with mitochondria, which can induce apoptosis. The direct interactions between cisplatin and mitochondria may account for our understanding of the clinical activity of cisplatin and development of resistance. However, the basis for the roles of mitochondria under treatment with chemotherapy is poorly understood. In this review, we present novel aspects regarding the unique characteristics of the mitochondrial genome in relation to the use of platinum-based chemotherapy and describe our recent work demonstrating the importance of the mitochondrial transcription factor A (mtTFA) expression in cancer cells. Full article

(This article belongs to the Special Issue Mitochondrial Dysfunction in Ageing and Diseases)

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24 pages, 2835 KiB

Open AccessArticle

In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae

by Atsushi Kurotani and Tetsuya Sakurai

Int. J. Mol. Sci. 2015, 16(8), 19812-19835; https://doi.org/10.3390/ijms160819812 - 20 Aug 2015

Cited by 21 | Viewed by 6674

Abstract

Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae [...] Read more.

Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups. Full article

(This article belongs to the Special Issue In-Silico Prediction and Characterization of Intrinsic Disorder in Proteins)

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16 pages, 705 KiB

Open AccessArticle

Effect of Factor XIII-A G185T Polymorphism on Visual Prognosis after Photodynamic Therapy for Neovascular Macular Degeneration

by Francesco Parmeggiani, Ciro Costagliola, Francesco Semeraro, Mario R Romano, Michele Rinaldi, Carla Enrica Gallenga, Maria Luisa Serino, Carlo Incorvaia, Sergio D’Angelo, Katia De Nadai, Roberto Dell’Omo, Andrea Russo, Donato Gemmati and Paolo Perri

Int. J. Mol. Sci. 2015, 16(8), 19796-19811; https://doi.org/10.3390/ijms160819796 - 20 Aug 2015

Cited by 7 | Viewed by 5853

Abstract

Macular degenerations represent leading causes of central blindness or low vision in developed countries. Most of these severe visual disabilities are due to age-related macular degeneration (AMD) and pathologic myopia (PM), both of which are frequently complicated by subfoveal choroidal neovascularization (CNV). Photodynamic [...] Read more.

Macular degenerations represent leading causes of central blindness or low vision in developed countries. Most of these severe visual disabilities are due to age-related macular degeneration (AMD) and pathologic myopia (PM), both of which are frequently complicated by subfoveal choroidal neovascularization (CNV). Photodynamic therapy with verteporfin (PDT-V) is still employed for CNV treatment in selected cases or in combined regimen. In Caucasian patients, the common polymorphism G185T of factor XIII-A gene (FXIII-A-G185T; rs5985) has been described as predictor of poor angiographic CNV responsiveness to PDT-V. Nevertheless, the prognostic implications of this pharmacogenetic determinant on long-term visual outcome after a PDT-V regimen have not been evaluated. We retrospectively selected Caucasian patients presenting with treatment-naive CNV and receiving standardized PDT-V protocol for two years. The study population included patients affected by subfoveal CNV secondary to AMD or PM. We assessed the correlations between the polymorphic allele T of FXIII-A-G185T and: (1) total number of photodynamic treatments; and (2) change in visual acuity from baseline to the end of the follow-up period. Considering a total study population of 412 patients with neovascular AMD or PM, the carriers of 185 T-allele of FXIII-A (GT or TT genotype) received a higher number of photodynamic treatments than patients without it (GG wild-type genotype) (p < 0.01; mean number of PDT-V: 5.51 vs. 3.76, respectively). Moreover, patients with 185 T-allele of FXIII-A had a more marked worsening of visual acuity at 24 months than those with the GG-185 wild genotype (p < 0.01; mean difference in logMAR visual acuity: 0.22 vs. 0.08, respectively). The present findings show that the G185T polymorphism of the FXIII-A gene is associated with significant differences in the long-term therapeutic outcomes of patients treated with standardized PDT-V protocol. The comprehensive appraisal of both anti-thrombophilic effects due to FXIII-A G185T variant and photo-thrombotic action of PDT-V toward CNV provides several clues about the rationale of this intriguing pharmacogenetic correlation. Further investigations are warranted to outline the appropriate paradigm for guiding PDT-V utilization in the course of the combined therapeutic protocol for neovascular macular degeneration. Full article

(This article belongs to the Special Issue Pharmacogenetics and Personalized Medicine)

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16 pages, 5788 KiB

Open AccessArticle

Endoplasmic Reticulum Stress Cooperates in Zearalenone-Induced Cell Death of RAW 264.7 Macrophages

by Fenglei Chen, Qian Li, Zhe Zhang, Pengfei Lin, Lanjie Lei, Aihua Wang and Yaping Jin

Int. J. Mol. Sci. 2015, 16(8), 19780-19795; https://doi.org/10.3390/ijms160819780 - 20 Aug 2015

Cited by 50 | Viewed by 9977

Abstract

Zearalenone (ZEA) is a fungal mycotoxin that causes cell apoptosis and necrosis. However, little is known about the molecular mechanisms of ZEA toxicity. The objective of this study was to explore the effects of ZEA on the proliferation and apoptosis of RAW 264.7 [...] Read more.

Zearalenone (ZEA) is a fungal mycotoxin that causes cell apoptosis and necrosis. However, little is known about the molecular mechanisms of ZEA toxicity. The objective of this study was to explore the effects of ZEA on the proliferation and apoptosis of RAW 264.7 macrophages and to uncover the signaling pathway underlying the cytotoxicity of ZEA in RAW 264.7 macrophages. This study demonstrates that the endoplasmic reticulum (ER) stress pathway cooperated in ZEA-induced cell death of the RAW 264.7 macrophages. Our results show that ZEA treatment reduced the viability of RAW 264.7 macrophages in a dose- and time-dependent manner as shown by the 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide assay (MTT) and flow cytometry assay. Western blots analysis revealed that ZEA increased the expression of glucose-regulated protein 78 (GRP78) and CCAAT/enhancer binding protein homologous protein (CHOP), two ER stress-related marker genes. Furthermore, treating the cells with the ER stress inhibitors 4-phenylbutyrate (4-PBA) or knocking down CHOP, using lentivirus encoded short hairpin interfering RNAs (shRNAs), significantly diminished the ZEA-induced increases in GRP78 and CHOP, and cell death. In summary, our results suggest that ZEA induces the apoptosis and necrosis of RAW 264.7 macrophages in a dose- and time-dependent manner via the ER stress pathway in which the activation of CHOP plays a critical role. Full article

(This article belongs to the Special Issue Modulators of Endoplasmic Reticulum Stress)

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11 pages, 842 KiB

Open AccessArticle

Magnetic Nanoparticle Arrays Self-Assembled on Perpendicular Magnetic Recording Media

by Abdul Rahman Mohtasebzadeh, Longfei Ye and Thomas M. Crawford

Int. J. Mol. Sci. 2015, 16(8), 19769-19779; https://doi.org/10.3390/ijms160819769 - 20 Aug 2015

Cited by 16 | Viewed by 6122

Abstract

We study magnetic-field directed self-assembly of magnetic nanoparticles onto templates recorded on perpendicular magnetic recording media, and quantify feature width and height as a function of assembly time. Feature widths are determined from Scanning Electron Microscope (SEM) images, while heights are obtained with [...] Read more.

We study magnetic-field directed self-assembly of magnetic nanoparticles onto templates recorded on perpendicular magnetic recording media, and quantify feature width and height as a function of assembly time. Feature widths are determined from Scanning Electron Microscope (SEM) images, while heights are obtained with Atomic Force Microscopy (AFM). For short assembly times, widths were ~150 nm, while heights were ~14 nm, a single nanoparticle on average with a 10:1 aspect ratio. For long assembly times, widths approach 550 nm, while the average height grows to 3 nanoparticles, ~35 nm; a 16:1 aspect ratio. We perform magnetometry on these self-assembled structures and observe the slope of the magnetic moment vs. field curve increases with time. This increase suggests magnetic nanoparticle interactions evolve from nanoparticle–nanoparticle interactions to cluster–cluster interactions as opposed to feature–feature interactions. We suggest the aspect ratio increase occurs because the magnetic field gradients are strongest near the transitions between recorded regions in perpendicular media. If these gradients can be optimized for assembly, strong potential exists for using perpendicular recording templates to assemble complex heterogeneous materials. Full article

(This article belongs to the Special Issue Magnetic Nanoparticles 2015)

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17 pages, 4989 KiB

Open AccessArticle

Polymer/Iron Oxide Nanoparticle Composites—A Straight Forward and Scalable Synthesis Approach

by Jens Sommertune, Abhilash Sugunan, Anwar Ahniyaz, Rebecca Stjernberg Bejhed, Anna Sarwe, Christer Johansson, Christoph Balceris, Frank Ludwig, Oliver Posth and Andrea Fornara

Int. J. Mol. Sci. 2015, 16(8), 19752-19768; https://doi.org/10.3390/ijms160819752 - 20 Aug 2015

Cited by 24 | Viewed by 8224

Abstract

Magnetic nanoparticle systems can be divided into single-core nanoparticles (with only one magnetic core per particle) and magnetic multi-core nanoparticles (with several magnetic cores per particle). Here, we report multi-core nanoparticle synthesis based on a controlled precipitation process within a well-defined oil in [...] Read more.

Magnetic nanoparticle systems can be divided into single-core nanoparticles (with only one magnetic core per particle) and magnetic multi-core nanoparticles (with several magnetic cores per particle). Here, we report multi-core nanoparticle synthesis based on a controlled precipitation process within a well-defined oil in water emulsion to trap the superparamagnetic iron oxide nanoparticles (SPION) in a range of polymer matrices of choice, such as poly(styrene), poly(lactid acid), poly(methyl methacrylate), and poly(caprolactone). Multi-core particles were obtained within the Z-average size range of 130 to 340 nm. With the aim to combine the fast room temperature magnetic relaxation of small individual cores with high magnetization of the ensemble of SPIONs, we used small (<10 nm) core nanoparticles. The performed synthesis is highly flexible with respect to the choice of polymer and SPION loading and gives rise to multi-core particles with interesting magnetic properties and magnetic resonance imaging (MRI) contrast efficacy. Full article

(This article belongs to the Special Issue Magnetic Nanoparticles 2015)

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24 pages, 5799 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analyses of Aquaporin Gene Family during Development and Abiotic Stress in Banana

by Wei Hu, Xiaowan Hou, Chao Huang, Yan Yan, Weiwei Tie, Zehong Ding, Yunxie Wei, Juhua Liu, Hongxia Miao, Zhiwei Lu, Meiying Li, Biyu Xu and Zhiqiang Jin

Int. J. Mol. Sci. 2015, 16(8), 19728-19751; https://doi.org/10.3390/ijms160819728 - 20 Aug 2015

Cited by 70 | Viewed by 10106

Abstract

Aquaporins (AQPs) function to selectively control the flow of water and other small molecules through biological membranes, playing crucial roles in various biological processes. However, little information is available on the AQP gene family in bananas. In this study, we identified 47 banana [...] Read more.

Aquaporins (AQPs) function to selectively control the flow of water and other small molecules through biological membranes, playing crucial roles in various biological processes. However, little information is available on the AQP gene family in bananas. In this study, we identified 47 banana AQP genes based on the banana genome sequence. Evolutionary analysis of AQPs from banana, Arabidopsis, poplar, and rice indicated that banana AQPs (MaAQPs) were clustered into four subfamilies. Conserved motif analysis showed that all banana AQPs contained the typical AQP-like or major intrinsic protein (MIP) domain. Gene structure analysis suggested the majority of MaAQPs had two to four introns with a highly specific number and length for each subfamily. Expression analysis of MaAQP genes during fruit development and postharvest ripening showed that some MaAQP genes exhibited high expression levels during these stages, indicating the involvement of MaAQP genes in banana fruit development and ripening. Additionally, some MaAQP genes showed strong induction after stress treatment and therefore, may represent potential candidates for improving banana resistance to abiotic stress. Taken together, this study identified some excellent tissue-specific, fruit development- and ripening-dependent, and abiotic stress-responsive candidate MaAQP genes, which could lay a solid foundation for genetic improvement of banana cultivars. Full article

(This article belongs to the Special Issue Plant Molecular Biology)

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15 pages, 790 KiB

Open AccessArticle

Inhibitory Effects of Amorphigenin on the Mitochondrial Complex I of Culex pipiens pallens Coquillett (Diptera: Culicidae)

by Mingshan Ji, Yaping Liang, Zumin Gu and Xiuwei Li

Int. J. Mol. Sci. 2015, 16(8), 19713-19727; https://doi.org/10.3390/ijms160819713 - 20 Aug 2015

Cited by 6 | Viewed by 5373

Abstract

Previous studies in our laboratory found that the extract from seeds of Amorpha fruticosa in the Leguminosae family had lethal effects against mosquito larvae, and an insecticidal compound amorphigenin was isolated. In this study, the inhibitory effects of amorphigenin against the mitochondrial complex [...] Read more.

Previous studies in our laboratory found that the extract from seeds of Amorpha fruticosa in the Leguminosae family had lethal effects against mosquito larvae, and an insecticidal compound amorphigenin was isolated. In this study, the inhibitory effects of amorphigenin against the mitochondrial complex I of Culex pipiens pallens (Diptera: Culicidae) were investigated and compared with that of rotenone. The results showed that amorphigenin and rotenone can decrease the mitochondrial complex I activity both in vivo and in vitro as the in vivo IC₅₀ values (the inhibitor concentrations leading to 50% of the enzyme activity lost) were determined to be 2.4329 and 2.5232 μmol/L, respectively, while the in vitro IC₅₀ values were 2.8592 and 3.1375 μmol/L, respectively. Both amorphigenin and rotenone were shown to be reversible and mixed-I type inhibitors of the mitochondrial complex I of Cx. pipiens pallens, indicating that amorphigenin and rotenone inhibited the enzyme activity not only by binding with the free enzyme but also with the enzyme-substrate complex, and the values of K_I and K_IS for amorphigenin were determined to be 20.58 and 87.55 μM, respectively, while the values for rotenone were 14.04 and 69.23 μM, respectively. Full article

(This article belongs to the Section Biochemistry)

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15 pages, 391 KiB

Open AccessReview

Hepatocellular Carcinoma in Patients with a Sustained Response to Anti-Hepatitis C Therapy

by Roberta D'Ambrosio, Cristina Della Corte and Massimo Colombo

Int. J. Mol. Sci. 2015, 16(8), 19698-19712; https://doi.org/10.3390/ijms160819698 - 19 Aug 2015

Cited by 54 | Viewed by 6496

Abstract

Hepatocellular carcinoma (HCC) is a common, life-threatening complication of longstanding infection with the hepatitis C virus (HCV), likely a consequence of the direct oncogenic activity of the virus cooperating with liver cell inflammation in transforming the liver into a mitogenic and mutagenic environment. [...] Read more.

Hepatocellular carcinoma (HCC) is a common, life-threatening complication of longstanding infection with the hepatitis C virus (HCV), likely a consequence of the direct oncogenic activity of the virus cooperating with liver cell inflammation in transforming the liver into a mitogenic and mutagenic environment. The achievement of a sustained virological response (SVR) to interferon-based therapies has been shown to benefit the course of hepatitis C in terms of reduced rates of liver-related complications and mortality from all causes. Interestingly, while achievement of an SVR is associated with a negligible risk of developing clinical decompensation over the years, the risk of HCC is not fully abrogated following HCV clearance, but it remains the dominant complication in all SVR populations. The factors accounting for such a residual risk of HCC in SVR patients are not fully understood, yet the persistence of the subverted architecture of the liver, diabetes and alcohol abuse are likely culprits. In the end, the risk of developing an HCC in SVR patients is attenuated by 75% compared to non-responders or untreated patients, whereas responders who develop an HCC may be stratified in different categories of HCC risk by a score based on the same demographic and liver disease-based variables, such as those that predict liver cancer in viremic patients. All in all, this prevents full understanding of those factors that drive HCC risk once HCV has been eradicated. Here, we critically review current understanding of HCC in SVR patients focusing on factors that predict residual risk of HCC among these patients and providing a glimpse of the expected benefits of new anti-HCV regimens based on direct antiviral agents. Full article

(This article belongs to the Special Issue Viral Hepatitis Research)

27 pages, 3636 KiB

Open AccessReview

Spatial Regulation of Root Growth: Placing the Plant TOR Pathway in a Developmental Perspective

by Adam Barrada, Marie-Hélène Montané, Christophe Robaglia and Benoît Menand

Int. J. Mol. Sci. 2015, 16(8), 19671-19697; https://doi.org/10.3390/ijms160819671 - 19 Aug 2015

Cited by 44 | Viewed by 13965

Abstract

Plant cells contain specialized structures, such as a cell wall and a large vacuole, which play a major role in cell growth. Roots follow an organized pattern of development, making them the organs of choice for studying the spatio-temporal regulation of cell proliferation [...] Read more.

Plant cells contain specialized structures, such as a cell wall and a large vacuole, which play a major role in cell growth. Roots follow an organized pattern of development, making them the organs of choice for studying the spatio-temporal regulation of cell proliferation and growth in plants. During root growth, cells originate from the initials surrounding the quiescent center, proliferate in the division zone of the meristem, and then increase in length in the elongation zone, reaching their final size and differentiation stage in the mature zone. Phytohormones, especially auxins and cytokinins, control the dynamic balance between cell division and differentiation and therefore organ size. Plant growth is also regulated by metabolites and nutrients, such as the sugars produced by photosynthesis or nitrate assimilated from the soil. Recent literature has shown that the conserved eukaryotic TOR (target of rapamycin) kinase pathway plays an important role in orchestrating plant growth. We will summarize how the regulation of cell proliferation and cell expansion by phytohormones are at the heart of root growth and then discuss recent data indicating that the TOR pathway integrates hormonal and nutritive signals to orchestrate root growth. Full article

(This article belongs to the Special Issue Molecular Machinery of Cell Growth Regulation)

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14 pages, 1011 KiB

Open AccessReview

The Incremental Induction of Neuroprotective Properties by Multiple Therapeutic Strategies for Primary and Secondary Neural Injury

by Seunghoon Lee, Sookyoung Park, Jinyoung Won, Sang-Rae Lee, Kyu-Tae Chang and Yonggeun Hong

Int. J. Mol. Sci. 2015, 16(8), 19657-19670; https://doi.org/10.3390/ijms160819657 - 19 Aug 2015

Cited by 15 | Viewed by 6218

Abstract

Neural diseases including injury by endogenous factors, traumatic brain injury, and degenerative neural injury are eventually due to reactive oxygen species (ROS). Thus ROS generation in neural tissues is a hallmark feature of numerous forms of neural diseases. Neural degeneration and the neural [...] Read more.

Neural diseases including injury by endogenous factors, traumatic brain injury, and degenerative neural injury are eventually due to reactive oxygen species (ROS). Thus ROS generation in neural tissues is a hallmark feature of numerous forms of neural diseases. Neural degeneration and the neural damage process is complex, involving a vast array of tissue structure, transcriptional/translational, electrochemical, metabolic, and functional events within the intact neighbors surrounding injured neural tissues. During aging, multiple changes involving physical, chemical, and biochemical processes occur from the molecular to the morphological levels in neural tissues. Among many recommended therapeutic candidates, melatonin also plays a role in protecting the nervous system from anti-inflammation and efficiently safeguards neuronal cells via antioxidants and other endogenous/exogenous beneficial factors. Therefore, given the wide range of mechanisms responsible for neuronal damage, multi-action drugs or therapies for the treatment of neural injury that make use of two or more agents and target several pathways may have greater efficacy in promoting functional recovery than a single therapy alone. Full article

(This article belongs to the Special Issue Neurological Injuries’ Monitoring, Tracking and Treatment)

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12 pages, 1050 KiB

Open AccessArticle

Engineering of Self-Assembled Fibronectin Matrix Protein and Its Effects on Mesenchymal Stem Cells

by Ye-Rang Yun, Le B. Hang Pham, Yie-Ri Yoo, Sujin Lee, Hae-Won Kim and Jun-Hyeog Jang

Int. J. Mol. Sci. 2015, 16(8), 19645-19656; https://doi.org/10.3390/ijms160819645 - 19 Aug 2015

Cited by 10 | Viewed by 6091

Abstract

Fibronectin (FN) contributes to cell adhesion, proliferation, and differentiation in various cell types. To enhance the activity of fibronectin at the sites of focal adhesion, we engineered a novel recombinant fibronectin (FNIII10) fragment connected to the peptide amphiphile sequence (PA), LLLLLLCCCGGDS. In this [...] Read more.

Fibronectin (FN) contributes to cell adhesion, proliferation, and differentiation in various cell types. To enhance the activity of fibronectin at the sites of focal adhesion, we engineered a novel recombinant fibronectin (FNIII10) fragment connected to the peptide amphiphile sequence (PA), LLLLLLCCCGGDS. In this study, the effects of FNIII10-PA on rat mesenchymal stem cells (rMSCs) were compared with those of FNIII10. FNIII10-PA showed the prominent protein adhesion activity. In addition, FNIII10-PA showed a significantly higher effect on adhesion, proliferation, and differentiation of rMSCs than FNIII10. Taken together, the FNIII10-containing self-assembled sequence enhanced rMSCs adhesion, proliferation, and differentiation. Full article

(This article belongs to the Special Issue Protein Engineering)

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14 pages, 2711 KiB

Open AccessReview

Structural Features of the ATP-Binding Cassette (ABC) Transporter ABCA3

by Alessandro Paolini, Antonella Baldassarre, Ilaria Del Gaudio and Andrea Masotti

Int. J. Mol. Sci. 2015, 16(8), 19631-19644; https://doi.org/10.3390/ijms160819631 - 19 Aug 2015

Cited by 26 | Viewed by 11496

Abstract

In this review we reported and discussed the structural features of the ATP-Binding Cassette (ABC) transporter ABCA3 and how the use of bioinformatics tools could help researchers to obtain a reliable structural model of this important transporter. In fact, a model of ABCA3 [...] Read more.

In this review we reported and discussed the structural features of the ATP-Binding Cassette (ABC) transporter ABCA3 and how the use of bioinformatics tools could help researchers to obtain a reliable structural model of this important transporter. In fact, a model of ABCA3 is still lacking and no crystallographic structures (of the transporter or of its orthologues) are available. With the advent of next generation sequencing, many disease-causing mutations have been discovered and many more will be found in the future. In the last few years, ABCA3 mutations have been reported to have important pediatric implications. Thus, clinicians need a reliable structure to locate relevant mutations of this transporter and make genotype/phenotype correlations of patients affected by ABCA3-related diseases. In conclusion, we strongly believe that the model preliminarily generated by these novel bioinformatics tools could be the starting point to obtain more refined models of the ABCA3 transporter. Full article

(This article belongs to the Special Issue Proteins and Protein-Ligand Interactions)

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19 pages, 5080 KiB

Open AccessArticle

Preliminary Evidence on the Diagnostic and Molecular Role of Circulating Soluble EGFR in Non-Small Cell Lung Cancer

by Filippo Lococo, Massimiliano Paci, Cristian Rapicetta, Teresa Rossi, Valentina Sancisi, Luca Braglia, Silvio Cavuto, Alessandra Bisagni, Italia Bongarzone, Douglas M. Noonan, Adriana Albini and Sally Maramotti

Int. J. Mol. Sci. 2015, 16(8), 19612-19630; https://doi.org/10.3390/ijms160819612 - 19 Aug 2015

Cited by 21 | Viewed by 7036

Abstract

Assessment of biological diagnostic factors providing clinically-relevant information to guide physician decision-making are still needed for diseases with poor outcomes, such as non-small cell lung cancer (NSCLC). Epidermal growth factor receptor (EGFR) is a promising molecule in the clinical management of NSCLC. While [...] Read more.

Assessment of biological diagnostic factors providing clinically-relevant information to guide physician decision-making are still needed for diseases with poor outcomes, such as non-small cell lung cancer (NSCLC). Epidermal growth factor receptor (EGFR) is a promising molecule in the clinical management of NSCLC. While the EGFR transmembrane form has been extensively investigated in large clinical trials, the soluble, circulating EGFR isoform (sEGFR), which may have a potential clinical use, has rarely been considered. This study investigates the use of sEGFR as a potential diagnostic biomarker for NSCLC and also characterizes the biological function of sEGFR to clarify the molecular mechanisms involved in the course of action of this protein. Plasma sEGFR levels from a heterogeneous cohort of 37 non-advanced NSCLC patients and 54 healthy subjects were analyzed by using an enzyme-linked immunosorbent assay. The biological function of sEGFR was analyzed in vitro using NSCLC cell lines, investigating effects on cell proliferation and migration. We found that plasma sEGFR was significantly decreased in the NSCLC patient group as compared to the control group (median value: 48.6 vs. 55.6 ng/mL respectively; p = 0.0002). Moreover, we demonstrated that sEGFR inhibits growth and migration of NSCLC cells in vitro through molecular mechanisms that included perturbation of EGF/EGFR cell signaling and holoreceptor internalization. These data show that sEGFR is a potential circulating biomarker with a physiological protective role, providing a first approach to the functional role of the soluble isoform of EGFR. However, the impact of these data on daily clinical practice needs to be further investigated in larger prospective studies. Full article

(This article belongs to the Special Issue Molecular Classification of Human Cancer: Diagnosis and Treatment)

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10 pages, 455 KiB

Open AccessReview

Genetic Polymorphisms of Glutathione-Related Enzymes (GSTM1, GSTT1, and GSTP1) and Schizophrenia Risk: A Meta-Analysis

by Su Kang Kim, Sang Wook Kang, Joo-Ho Chung, Hae Jeong Park, Kyu Bong Cho and Min-Su Park

Int. J. Mol. Sci. 2015, 16(8), 19602-19611; https://doi.org/10.3390/ijms160819602 - 19 Aug 2015

Cited by 27 | Viewed by 6233

Abstract

The association between polymorphisms of glutathione-related enzyme (GST) genes and the risk of schizophrenia has been investigated in many published studies. However, their results were inconclusive. Therefore, we performed a meta-analysis to explore the association between the GSTM1, GSTT1, and GSTP1 [...] Read more.

The association between polymorphisms of glutathione-related enzyme (GST) genes and the risk of schizophrenia has been investigated in many published studies. However, their results were inconclusive. Therefore, we performed a meta-analysis to explore the association between the GSTM1, GSTT1, and GSTP1 polymorphisms and the risk of schizophrenia. Twelve case-control studies were included in this meta-analysis. The odds ratio (OR) and 95% confidence interval (95% CI) were used to investigate the strength of the association. Our meta-analysis results revealed that GSTM1, GSTT1, and GSTP1 polymorphisms were not related to risk of schizophrenia (p > 0.05 in each model). Further analyses based on ethnicity, GSTM polymorphism showed weak association with schizophrenia in East Asian population (OR = 1.314, 95% CI = 1.025–1.684, p = 0.031). In conclusion, our meta-analysis indicated the GSTM1 polymorphism may be the only genetic risk factor for schizophrenia in East Asian population. However, more meta-analysis with a larger sample size were needed to provide more precise evidence. Full article

(This article belongs to the Special Issue Mechanisms of Neurodegeneration)

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Int. J. Mol. Sci., Volume 16, Issue 8 (August 2015) – 181 articles , Pages 16710-20099

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