Vol. 21 (2016)

Cellular and Molecular Biology Letters goes open access with BioMed Central

Aleksander F. Sikorski

It is my great pleasure to announce the launch of a new alliance between our journal, Cellular and Molecular Biology Letters (CMBL), and an international publisher, BioMed Central (part of Springer Nature). This event opens the 21st year of publication of our journal and changes the model of publication to an open system. Therefore, I would like to take this occasion to thank my colleagues, Professors Jan Szopa and Arkadiusz Kozubek* and Ms Małgorzata Nietubyć for a wonderful 20 years of a lasting and common effort to publish the journal. I remember, in particular, the pioneering years, when we started the journal without financial support and with rather weak institutional help when conditions were very challenging. Without their help, support and contribution throughout this formative period, this venture would not have been possible.

I would like to thank all of our authors and readers who supported our initiative since its start in 1996. Of great importance was the tireless effort of the reviewers in taking care of the standards of the publications. Their contribution has been invaluable. The contributions of the first Editorial Board Members who helped us a lot through their advice, in particular our colleagues, Professors Stanisław Przestalski, Tadeusz Chojnacki and Włodzimierz Korohoda, have been greatly appreciated.

Our journal is published by the University of Wrocław, in collaboration with the Polish Society for Cell Biology, along with more than 15 years of lasting support from the Polish Ministry of Scientific Research and Higher Education. I would like to take this occasion to express our gratitude to these institutions.

Of course, the greatest support that we received was from all of our contributors who submitted work of such a standard that we were able to enter world-wide databases, in particular, the ISI Web of Science, so quickly. The quality of the contributions is reflected in the recently published Impact Factor for the journal, which is 1.753 for the past year, along with a five-year Impact Factor of 1.681.

CMBL is a forum for researchers, covering the broad areas of cell and molecular biology, including: the cell cycle and its regulation, cell differentiation, cell traffic and signaling, stem cells, gene expression regulation, cellular membranes, cytoskeleton and molecular biotechnology, not excluding other aspects of studies such as cellular proteomics, genomics and advanced imaging technologies. Research, review, short report and mini-review articles are all welcome.

Although our journal has developed well and to the point that it now has a small, but stable, circle of authors and readers, we have considered now for quite some time on how to get into an open access model of publication. Now, through establishing the collaboration with BioMed Central, the world-famous open access publisher, we gain this opportunity. Therefore, we hope that, with this new arrangement, the journal will continue to grow in its readership as well as upon its impact within the scientific community that it is trying to reach. Fortunately, the open access journals have become a standard vehicle of publication of the newest achievements of the research in cell and molecular biology. Both the Editorial Team and I, believe that the choice we have made are vital for the future of the journal and that we will be successful in achieving our goal. However, we still need the support of all of you, both our authors and our readers, in this.

With this move towards open access comes also a change in the way that the journal will charge for its services, with the introduction of a single flat-fee as an article processing charge (APC) for successful manuscripts. This is an inevitable part of the process of open access publishing, where the costs associated with an open access format are covered by the APC. We believe that, overall, this charge structure represents a cost-effective publishing route, especially when the wider reach of the open access format will bring manuscripts to the attention of a much larger audience, with a corresponding increase in weighting in the impact factor. On behalf of the Editorial team, I promise that our priority is the quality of research presented by the manuscripts it publishes, its novelty, technical advance and importance in learning molecular mechanisms underlying normal and pathological cell biology. All manuscripts will be treated equally, honestly peer-reviewed and published as soon as they will be accepted. So, we invite you all, as authors, to publish with us.

We trust that our authors will be satisfied with the publication service they receive from our Editorial Office and BioMed Central. It is my strong belief that this alliance will secure the stable progress of the journal and help it make a greater impact in the field of the molecular biology of the cell. I also hope very much that it will continue to provide a friendly vehicle for the publication of important and significant achievements in global research towards progress in learning about how cells function.

Editor-in-Chief, Cellular and Molecular Biology Letters

*Sadly, passed away on May 20, 2016

DOI: 10.1186/s11658-016-0003-3 Volume 21 (2016)
Authors Somayeh Arabzadeh1, Ghamartaj Hossein1,*, Zahra Salehi-Dulabi1 and Amir Hassan Zarnani2,3
Abstract Background: Wnt5A, which is a member of the non-transforming Wnt protein family, is implicated in inflammatory processes. It is also highly expressed by ovarian cancer cells. ROR2, which is a member of the Ror-family of receptor tyrosine kinases, acts as a receptor or co-receptor for Wnt5A. The Wnt5A–ROR2 signaling pathway plays essential roles in the migration and invasion of several types of tumor cell and influences their cell polarity. We investigated the modulation of Wnt5A–ROR2 by inflammatory mediators and its involvement in the migration of the human ovarian cancer cell line SKOV-3.
Methods: SKOV-3 cells were treated with LPS (lipopolysaccharide), LTA (lipoteichoic acid) and recombinant human IL-6 alone or in combination with STAT3 inhibitor (S1155S31-201) or NF-κB inhibitor (BAY11-7082) for 4, 8, 12, 24 and 48 h. The Wnt5A and ROR2 expression levels were determined at the gene and protein levels. Cells were transfected with specific siRNA against Wnt5A in the absence or presence of human anti-ROR2 antibody and cell migration was assessed using transwells.
Results: There was a strong downregulation of Wnt5A expression in the presence of STAT3 or NF-κB inhibitors. Cell stimulation with LTA or IL-6 for 8 h led to significantly increased levels of Wnt5A (5- and 3-fold higher, respectively). LPS, LTA or IL-6 treatment significantly increased ROR2 expression (2-fold after 48 h). LPS- or LTA-induced Wnt5A or ROR2 expression was abrogated in the presence of STAT3 inhibitor (p < 0.001). IL-6-induced Wnt5A expression was abrogated by both STAT3 and NF-κB inhibitors (p < 0.001). Although not significant, IL-6-induced ROR2 expression showed a modest decrease when STAT3 inhibitor was used. Moreover, cell migration was decreased by 80% in siRNA Wnt5A-transfected cells in the presence of anti-human ROR2 antibody (p < 0.001).
Conclusions: This study revealed for the first time that inflammatory mediators modulate Wnt5A and ROR2 through NF-κB and STAT3 transcription factors and this may play a role in ovarian cancer cell migration. The results described here provide new insight into the role of the Wnt5A–ROR2 complex in ovarian cancer progression in relation to inflammation.
Keywords Ovarian cancer, Inflammation, Wnt5A, ROR2, NF-κB/STAT3 signaling pathways, Migration
Address and Contact Information 1Department of Animal Physiology, Developmental Biology Laboratory, School of Biology, College of Science, University of Tehran, Tehran, Iran.
2 Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.
3 Immunology Research Center, Iran University of Medical Sciences, Tehran, Iran.
* Corresponding author: ghossein@khayam.ut.ac.ir
Read full article at BMC

DOI: 10.1186/s11658-016-0004-2 Volume 21 (2016)
Authors Ranran Kong1, Yuefeng Ma1, Jie Feng2, Shaomin Li1, Wei Zhang1, Jiantao Jiang1, Jin Zhang1, Zhe Qiao1, Xiaoping Yang1 and Bin Zhou1,*
Abstract Background: miR-126 is a key regulator of oncogenic processes. It is functionally linked to cellular proliferation, survival and migration. Vascular endothelial growth factor A (VEGF-A), which is regarded as a tumorgenesis activator, could directly target miR-126 in several tumors. However, the mechanism in esophageal cancer remains unclear.
Methods and results: In this study, the expression of miR-126 and VEGF-A were assessed in esophageal cancer tissues and esophageal cancer cell lines. We found that miR-126 has significantly lower expression in esophageal cancer tissues and esophageal cancer cell lines than in healthy tissues, while the expression of VEGF-A is high. Luciferase reporter assays were performed to investigate the relationship between VEGF-A and miR-126. We confirmed that VEGF-A is a target for miR-126. Furthermore, the proliferation of esophageal cancer cells with miR-126 overexpression and miR-126 knockdown was monitored using the MTT assay. The results showed that miR-126 could inhibit esophageal cancer cell proliferation in vitro. The effect of miR-126 was also detected in BALB/c nude mice with transplanted esophageal cancer cells. In vivo study showed that tumor growth was significantly suppressed by miR-126 overexpression.
Conclusions:We believe that restoring miR-126 levels may be a promising therapeutic approach in cases of esophageal cancer.
Keywords miR-126; Esophageal cancer; VEGF-A; Tumorgenesis; Cell proliferation;Lentivirus package; MTT assay; Xenograft model
Address and Contact Information 1Department of Thoracic Surgery, The Second Affiliated Hospital of Xi’an Jiaotong University, 710004, Xi’an, Shaanxi, China
2Department of Nephrology, The First Affiliated Hospital, Xi’an Jiaotong University, 710061, Xi’an, Shaanxi, China
* Corresponding author: zhoubineryuan@163.com
Read full article at BMC

DOI: 10.1186/s11658-016-0005-1 Volume 21 (2016)
Authors Fatemeh Keyfi2,4, Mohammad Reza Abbaszadegan3,4, Arndt Rolfs5,6, Slobodanka Orolicki7, Morteza Moghaddassian3 and Abdolreza Varasteh1,4
Abstract Background: Adenosylcobalamin (vitamin B12) is a coenzyme required for the activity of methylmalonyl-CoA mutase. Defects in this enzyme are a cause of methylmalonic acidemia (MMA). Methylmalonic acidemia, cblA type, is an inborn error of vitamin B12 metabolism that occurs due to mutations in the MMAA gene. MMAA encodes the enzyme which is involved in translocation of cobalamin into the mitochondria.
Methods: One family with two MMA-affected children, one unaffected child, and their parents were studied. The two affected children were diagnosed by urine organic acid analysis using gas chromatography-mass spectrometry. MMAA was analyzed by PCR and sequencing of its coding region.
Results: A homozygous deletion in exon 4 of MMAA, c.674delA, was found in both affected children. This deletion causes a nucleotide frame shift resulting in a change from asparagine to methionine at amino acid 225 (p.N225M) and a truncated protein which loses the ArgK conserved domain site. mRNA expression analysis of MMAA confirmed these results.
Conclusion: We demonstrate that the deletion in exon 4 of the MMAA gene (c.674 delA) is a pathogenic allele via a nucleotide frame shift resulting in a stop codon and termination of protein synthesis 38 nucleotides (12 amino acids) downstream of the deletion.
Keywords Mutation analysis, MMAA gene, Biochemical analysis, Methylmalonic acidemia, Vitamin B12, Novel deletion, Cobalamin, Structural analysis
Address and Contact Information 1Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
2Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
3Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
4Pardis Clinical and Genetic Laboratory, Mashhad, Iran
5Director of the Albrecht Kossel Institute for Neuroregeneration, University of Rostock,Rostock, Germany
6Chief Medical Director, Centogene AG, Rostock, Germany
7Clinical and medical scientist, Centogene AG, Rostock, Germany
* Corresponding author: varasteha@mums.ac.ir
Read full article at BMC

DOI: 10.1186/s11658-016-0006-0 Volume 21 (2016)
Authors Hideyuki Ishiguro* Takehiro Wakasugi, Yukio Terashita, Hiroki Takahashi, Nobuhiro Sakamoto, Tatsuya Tanaka, Koji Mizoguchi, Hiroyuki Sagawa, Tomotaka Okubo and Hiromitsu Takeyama
Abstract The prognosis for patients with esophageal cancer remains poor. Therefore, the identification of novel target molecules for the treatment of esophageal cancer is necessary. Here, we investigated the clinicopathological significance of transcription factor 4/transcription factor 7-like 2 (TCF4/TCF7L2) in resectable esophageal squamous cell carcinoma (ESCC), because TCF4/TCF7L2 expression has not been studied in esophageal cancer previously.
This study included 79 patients with esophageal cancer who underwent surgery between 1998 and 2005. The expression of the TCF4/TCF7L2 protein in the nucleus of esophageal cancer cells was analyzed using immunohistochemistry. We examined the correlation between TCF4/TCF7L2 expression, clinicopathological factors, and prognosis in patients with ESCC.
TCF4/TCF7L2 was expressed in 57 % (45/79) of patients. TCF4/TCF7L2 expression was correlated with T factor (T1 vs. T2-4, p = 0.001), stage (I vs. II-IV, p =0.0058), Ly factor (p =0.038), and V factor (p =0.038) and did not correlate with age, gender or N factor. Furthermore, patients who were positive for TCF4/TCF7L2 had a significantly lower survival rate than those who were negative for TCF4/TCF7L2 (log-rank test, p = 0.0040). TCF4/TCF7L2 expression significantly affected the survival of patients with ESCC. Positive expression of TCF4/TCF7L2 was correlated with a poor prognosis after a curative operation in patients with ESCC.
Keywords Esophageal cancer, Immunohistochemistry, Prognosis, TCF4/TCF7L2, Wnt signal, Surgery, Clinicopathological factor
Address and Contact Information Department of Gastroenterological Surgery, Nagoya City University Graduate School of Medical Science, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan.
* Corresponding author: h-ishi@med.nagoya-cu.ac.jp
Read full article at BMC

DOI: 10.1186/s11658-016-0007-z Volume 21 (2016)
Authors Fatemeh Saberi1, Mehdi Kamali2, Ali Najafi1, Alavieh Yazdanparast3 and Mehrdad Moosazadeh Moghaddam3,*
Abstract Naturally occurring antisense RNAs are small, diffusible, untranslated transcripts that pair to target RNAs at specific regions of complementarity to control their biological function by regulating gene expression at the post-transcriptional level. This review focuses on known cases of antisense RNA control in prokaryotes and provides an overview of some natural RNA-based mechanisms that bacteria use to modulate gene expression, such as mRNA sensors, riboswitches and antisense RNAs. We also highlight recent advances in RNA-based technology. The review shows that studies on both natural and synthetic systems are reciprocally beneficial.
Keywords Bacteria, Natural antisense, Cis-asRNA, Trans-asRNA, Regulation, Riboswitch, Hfq protein, RNA engineering, RNA silencing, RNA thermosensors
Address and Contact Information 1Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
2Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
3Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
* Corresponding author: mm.genetics@gmail.com, abrch@bmsu.ac.ir
Read full article at BMC

DOI: 10.1186/s11658-016-0008-y Volume 21 (2016)
Authors Mahmudul Hasan1, Mainul Hasan2, Jaime A. Teixeira da Silva3 and Xuexian Li1,*
Abstract Phosphorus is a poorly bioavailable macronutrient that is essential for crop growth and yield. Overuse of phosphorus fertilizers results in low phosphorus use efficiency (PUE), has serious environmental consequences and accelerates the depletion of phosphorus mineral reserves. It has become extremely challenging to improve PUE while preserving global food supplies and maintaining environmental sustainability. Molecular and genetic analyses have revealed the primary mechanisms of phosphorus uptake and utilization and their relationships to phosphorus transporters, regulators, root architecture, metabolic adaptations, quantitative trait loci, hormonal signaling and microRNA. The ability to improve PUE requires a transition from this knowledge of molecular mechanisms and plant architecture to practical strategies. These could include: i) the use of arbuscular mycorrhizal fungal symbioses for efficient phosphorus mining and uptake; ii) intercropping with suitable crop species to achieve phosphorus activation and mobilization in the soil; and iii) tissue-specific overexpression of homologous genes with advantageous agronomic properties for higher PUE along with breeding for phosphorus-efficient varieties and introgression of key quantitative trait loci. More effort is required to further dissect the mechanisms controlling phosphorus uptake and utilization within plants and provide new insight into the means to efficiently improve PUE.
Keywords Phosphorus uptake, Phosphorus transporter, Phosphorus use efficiency, Quantitative trait loci, Hormonal signaling, MicroRNA, Arbuscular mycorrhizal fungal symbiosis, Intercropping, Gene overexpression
Address and Contact Information 1The Key Laboratory of Plant-Soil Interactions, MOE, Center for Resources, Environment and Food Security, Department of Plant Nutrition, China Agricultural University, Beijing, 100193, China
2Faculty of Agriculture, Patuakhali Science and Technology University, Dumki, Patuakhali, Bangladesh
3P. O. Box 7, Miki cho post office, Ikenobe 3011-2, Kagawa-Ken, 761-0799, Japan
* Corresponding author: E-mail: steve@cau.edu.cn
Read full article at BMC

DOI: 10.1186/s11658-016-0009-x Volume 21 (2016)
Authors Wei Wei Zhang1,2, Xiao Feng Sun1, Hui Li Tong1, Ya Hui Wang1, Shu Feng Li1, Yun Qin Yan1,* and Guang Peng Li3
Abstract Background: The differentiation of skeletal muscle-derived satellite cells (MDSCs) is important in controlling muscle growth, improving livestock muscle quality, and healing of muscle-related disease. MicroRNAs (miRNAs) are a class of gene expression regulatory factors, which play critical roles in the regulation of muscle cell differentiation. This study aimed to compare the expression profile of miRNAs in MDSC differentiation, and to investigate the miRNAs which are involved in MDSC differentiation.
Method: Total RNA was extracted from MDSCs at three different stages of differentiation (MDSC-P, MDSC-D1 and MDSC-D3, representing 0, 1 and 3 days after differentiation, respectively), and used to construct small RNA libraries for RNA sequencing (RNA-seq).
Results: The results showed that in total 617 miRNAs, including 53 novel miRNA candidates, were identified. There were 9 up-expressed, 165 down-expressed, and 15 up-expressed, 145 down-expressed in MDSC-D1 and MDSC-D3, respectively, compared to those in MDSC-P. Also, 17 up-expressed, 55 down-expressed miRNAs were observed in MDSC-D3 compared to those in MDSC-D1. All known miRNAs belong to 237 miRNA gene families. Furthermore, we observed some sequence variants and base edits of the miRNAs. GO and KEGG pathway analysis showed that the majority of target genes regulated by miRNAs were involved in cellular metabolism, pathways in cancer, actin cytoskeleton regulation and the MAPK signaling pathway. Regarding the 53 novel miRNAs, there were 7 up-expressed, 31 down-expressed, and 8 up-expressed, 26 down-expressed in MDSC-D1 and MDSC-D3, respectively, compared to those in MDSC-P. The expression levels of 12 selected miRNA genes detected by RT-qPCR were consistent with those generated by deep sequencing.
Conclusions: This study confirmed the authenticity of 564 known miRNAs and identified 53 novel miRNAs which were involved in MDSC differentiation. The identification of novel miRNAs has significantly expanded the repertoire of bovine miRNAs and could contribute to advances in understanding muscle development in cattle.
Keywords Bovine, Skeletal muscle-derived satellite cells, Deep sequencing, miRNA, Differentiation, Proliferation, Differentially expressed miRNA, Target prediction, Gene Ontology, KEGG analysis
Address and Contact Information 1The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China, 2 College of Life Sciences and Agriculture & Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China, 3 The Key Laboratory of Mammal Reproductive Biology and Biotechnology Ministry of Education, Inner Mongolia University, Hohhot 010021, China
* Corresponding author: yanyunqin@sohu.com, 2205682371@qq.com
Read full article at BMC

DOI: 10.1186/s11658-016-0002-4 Volume 21 (2016)
Authors Zahra Sepehri1, Zohre Kiani2,3* , Ali Akbar Nasiri4 and Farhad Kohan5
Abstract Innate immunity plays a crucial role in the pathogenesis of type 2 diabetes and related complications. Since the toll-like receptors (TLRs) are central to innate immunity, it appears that they are important participants in the development and pathogenesis of the disease. Previous investigations demonstrated that TLR2 homodimers and TLR2 heterodimers with TLR1 or TLR6 activate innate immunity upon recognition of damage-associated molecular patterns (DAMPs). Several DAMPs are released during type 2 diabetes, so it may be hypothesized that TLR2 is significantly involved in its progression. Here, we review recent data on the important roles and status of TLR2 in type 2 diabetes and related complications.
Keywords Type 2 diabetes, TLR2, Complication, Innate immunity, DAMP, PAMP, MYD88, Activator protein 1, NF-kB, Leucine-rich repeats
Address and Contact Information 1 Department of Internal Medicine, Zabol University of Medical Sciences, Zabol, Iran.
2 Zabol Medicinal Plant Research Center, Zabol University of Medical Sciences, Zabol, Iran.
3 Department of Medicine, Kerman University of Medical Sciences, Kerman, Iran.
4 Department of Internal Anesthesiology, Zabol University of Medical Sciences, Zabol, Iran.
5 General Physician, Zabol University of Medical Sciences, Zabol, Iran.
* Corresponding author: zsepehri271@gmail.com
Read full article at BMC

DOI 10.1186/s11658-016-0013-1 Volume 21 (2016)
Authors Jitrada Phetfong1†, Tanwarat Sanvoranart1†, Kuneerat Nartprayut1, Natakarn Nimsanor1, Kanokwan Seenprachawong1, Virapong Prachayasittikul2 and Aungkura Supokawej1*
Abstract Osteoporosis, or bone loss, is a progressive, systemic skeletal disease that affects millions of people worldwide. Osteoporosis is generally age related, and it is underdiagnosed because it remains asymptomatic for several years until the development of fractures that confine daily life activities, particularly in elderly people. Most patients with osteoporotic fractures become bedridden and are in a life-threatening state. The consequences of fracture can be devastating, leading to substantial morbidity and mortality of the patients. The normal physiologic process of bone remodeling involves a balance between bone resorption and bone formation during early adulthood. In osteoporosis, this process becomes imbalanced, resulting in gradual losses of bone mass and density due to enhanced bone resorption and/or inadequate bone formation. Several growth factors underlying age-related osteoporosis and their signaling pathways have been identified, such as osteoprotegerin (OPG)/receptor activator of nuclear factor B (RANK)/RANK ligand (RANKL), bone morphogenetic protein (BMP), wingless-type MMTV integration site family (Wnt) proteins and signaling through parathyroid hormone receptors. In addition, the pathogenesis of osteoporosis has been connected to genetics. The current treatment of osteoporosis predominantly consists of antiresorptive and anabolic agents; however, the serious adverse effects of using these drugs are of concern. Cell-based replacement therapy via the use of mesenchymal stem cells (MSCs) may become one of the strategies for osteoporosis treatment in the future.
Keywords Osteoporosis, Cell therapy, Mesenchymal stem cells, MSCs, Stem cells
Address and Contact Information 1 Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Phuttamonthon, Salaya, Nakhon Pathom 73170, Thailand.
2 Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Phuttamonthon, Salaya, Nakhon Pathom 73170, Thailand.
* Corresponding author: aungkura.jer@mahidol.ac.th
Equal contributors
Read full article at BMC

DOI 10.1186/s11658-016-0016-y Volume 21 (2016)
Authors Ewelina Aleksander-Konert1, Piotr Paduszyński1*, Alicja Zajdel1, Zofia Dzierżewicz1,2 and Adam Wilczok1
Abstract Background: In this study, we evaluated the usefulness of two commercially available hyaluronic acid-based hydrogels, HyStem and HyStem-C, for the cultivation of Wharton’s jelly mesenchymal stem cells (WJ-MSCs) and their differentiation towards chondrocytes.
Methods: The WJ-MSCs were isolated from umbilical cord Wharton’s jelly using the explant method and their immunophenotype was evaluated via flow cytometry analysis. According to the criteria established by the International Society for Cellular Therapy, they were true MSCs. We assessed the ability of the WJ-MSCs and chondrocytes to grow in three-dimensional hydrogels and their metabolic activity. Chondrogenesis of WJ-MSCs in the hydrogels was determined using alcian blue and safranin O staining and real-time PCR evaluation of gene expression in the extracellular matrixes: collagen type I, II, III and aggrecan.
Results: Chondrocytes and WJ-MSCs cultured in the HyStem and HyStem-C hydrogels adopted spherical shapes, which are characteristic for encapsulated cells. The average viability of the WJ-MSCs and chondrocytes in the HyStem hydrogels was approximately 67 % when compared with the viability in 2D culture. Alcian blue and safranin O staining revealed intensive production of proteoglycans by the cells in the HyStem hydrogels. Increased expression of collagen type II and aggrecan in the WJ-MSCs cultured in the HyStem hydrogel in the presence of chondrogenic medium showed that under these conditions, the cells have a high capacity to differentiate towards chondrocytes. The relatively high viability of WJ-MSCs and chondrocytes in both HyStem hydrogels suggests the possibility of their use for chondrogenesis.
Conlusions: The results indicate that WJ-MSCs have some degree of chondrogenic potential in HyStem and HyStem-C hydrogels, showing promise for the engineering of damaged articular cartilage.
Keywords WJ-MSCs, Hydrogels, Chondrogenesis, Chondrocytes, HyStem, HyStem-C
Address and Contact Information 1Department of Biopharmacy, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, ul. Jednosci 8, 41-200 Sosnowiec, Poland.
2 Department of Health Care, Silesian Medical College, ul. Mickiewicza 29, 40-085 Katowice, Poland.
* Corresponding author: paduszyn@o2.pl; ppaduszynski@sum.edu.pl
Read full article at BMC

DOI 10.1186/s11658-016-0015-z Volume 21 (2016)
Authors Morena Gabriele1, Laura Pucci1*, Margherita La Marca1, Daniela Lucchesi3, Clara Maria Della Croce1, Vincenzo Longo1 and Valter Lubrano2
Abstract This study focused on an extract from fermented flour from the Lady Joy variety of the common bean Phaseolus vulgaris. The extract, Lady Joy lysate (Lys LJ), is enriched in antioxidant compounds during the fermentation. We assessed it for its protective effect on endothelial cells treated with oxidized-LDL (ox-LDL). The oxidative stress was determined by measuring the contents of thiobarbituric acid-reactive substances and reactive oxygen metabolites. ICAM-1, ET-1 and IL-6 concentrations were assessed using ELISA. LOX-1 and CHOP expression were analyzed using both quantitative RT-PCR and ELISA or western blotting. Ox-LDL treatment induced significant oxidative stress, which was strongly reduced by pre-treatment with the extract. The ox-LDL exposure significantly enhanced ICAM-1, IL-6 and ET-1 levels over basal levels. Lys LJ pre-treatment exerted an inhibitory effect on ox-LDL-induced endothelial activation with ICAM-1 levels comparable to those for the untreated cells. IL-6 and ET-1 production, although reduced, was still significantly higher than for the control. Both LOX-1 and CHOP expression were upregulated after ox-LDL exposure, but this effect was significantly decreased after Lys LJ pre-treatment. Lys LJ alone did not alter the ICAM-1, IL-6 and ET-1 concentrations or CHOP expression, but it did significantly lower the LOX-1 protein level. Our data suggest that Lys LJ is an effective antioxidant that is able to inhibit the oxidation process, but that it is only marginally active against inflammation and ET-1 production in HMEC-1 exposed to ox-LDL.
Keywords : Fermented Phaseolus vulgaris L, HMEC-1, Oxidative stress, Ox-LDL, ER stress, CHOP, LOX-1, ICAM-1, IL-6, ET-1
Address and Contact Information 1National Research Council (CNR), Institute of Biology and Agricultural Biotechnology (IBBA), Pisa Unit, Research Area of Pisa, Via Moruzzi 1, 56124 Pisa, Italy.
2Fondazione CNR/Regione Toscana G. Monasterio, Via Moruzzi 1, 56124 Pisa, Italy.
3Department of Clinical and Experimental Medicine, Section of Metabolic Diseases, University of Pisa, Via Paradisa 2, 56124 Pisa, Italy.
* Corresponding author: lauric16@yahoo.it
Read full article at BMC

DOI 10.1186/s11658-016-0011-3 Volume 21 (2016)
Authors Miha Bartolić, Andrej Vovk and Dušan Šuput*
Abstract Background: Hepatic encephalopathy (HE) is a complex disorder associated with increased ammonia levels in the brain. Although astrocytes are believed to be the principal cells affected in hyperammonemia (HA), endothelial cells (ECs) may also play an important role by contributing to the vasogenic effect of HA. Methods: Following acute application and removal of NH4CL on astrocytes and endothelial cells, we analyzed pH changes, using fluorescence imaging with BCECF/ AM, and changes in intracellular Ca2+ concentration ([Ca2+]i), employing fluorescence imaging with Fura-2/AM. Using confocal microscopy, changes in cell volume were observed accompanied by changes of [Ca2+]iin astrocytes and ECs. Results: Exposure of astrocytes and ECs to 1 – 20 mM NH4CL resulted in rapid concentration-dependent alkalinization of cytoplasm followed by slow recovery. Removal of the NH4CL led to rapid concentration-dependent acidification, again followed by slow recovery. Following the application of NH4CL, a transient, concentration-dependent rise in [Ca2+]iin astrocytes was observed. This was due to the release of Ca2+ from intracellular stores, since the response was abolished by emptying intracellular stores with thapsigargin and ATP, and was still present in the Ca2+ -free bathing solution. The removal of NH4CL also led to a transient concentration-dependent rise in [Ca2+]ithat resulted from Ca2+ release from cytoplasmic proteins, since removing Ca2+ from the bathing solution and emptying intracellular Ca2+ stores did not eliminate the rise. Similar results were obtained from experiments on ECs. Following acute application and removal of NH4CL no significant changes in astrocyte volume were detected; however, an increase of EC volume was observed after the administration of NH4CL, and EC shrinkage was demonstrated after the acute removal of NH4CL. Conclusions: This study reveals new data which may give a more complete insight into the mechanism of development and treatment of HE.
Keywords Hepatic encephalopathy, Hyperammonemia, Ammonia, Astrocytes, Endothelial cells, Volume, Calcium, pH
Address and Contact Information Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
* Corresponding author: dusan.suput@mf.uni-lj.si
Read full article at BMC

DOI 10.1186/s11658-016-0014-0 Volume 21 (2016)
Authors Andrzej Kowalski
Abstract Histone H1.0 belongs to the class of linker histones (H1), although it is substantially distinct from other histone H1 family members. The differences can be observed in the chromosomal location and organization of the histone H1.0 encoding gene, as well as in the length and composition of its amino acid chain. Whereas somatic (H1.1–H1.5) histone H1 variants are synthesized in the cell cycle S-phase, histone H1.0 is synthesized throughout the cell cycle. By replacing somatic H1 variants during cell maturation, histone H1.0 is gradually deposited in low dividing cells and achieves the highest level of expression in the terminally differentiated cells. Compared to other differentiation-specific H1 histone (H5) characteristic for unique tissue and organisms, the distribution of histone H1.0 remains non-specific. Classic investigations emphasize that histone H1.0 is engaged in the organization of nuclear chromatin accounting for formation and maintenance of its nucleosomal and higher-order structure, and thus influences gene expression. However, the recent data confirmed histone H1.0 peculiar localization in the nucleolus and unexpectedly revealed its potential for regulation of nucleolar, RNA-dependent, activity via interaction with other proteins. According to such findings, histone H1.0 participates in the formation of gene-coded information through its control at both transcriptional and translational levels. In order to reappraise the biological significance of histone H1.0, both aspects of its activity are presented in this review.
Keywords Chromatin, Histone H1.0, Histone H1 subtypes, Intrinsic protein disorder, Nucleus, Nucleolus, Protein-protein interaction
Address and Contact Information Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, Świętokrzyska 15, 25-406 Kielce, Poland
* Corresponding author: a.kowalski@ujk.edu.pl
Read full article at BMC

DOI 10.1186/s11658-016-0012-2 Volume 21 (2016)
Authors Piotr Paduszyński1*, Ewelina Aleksander-Konert1, Alicja Zajdel1, Adam Wilczok1, Katarzyna Jelonek2, Andrzej Witek3 and Zofia Dzierżewicz1,4
Abstract Background: In cartilage tissue regeneration, it is important to develop biodegradable scaffolds that provide a structural and logistic template for three-dimensional cultures of chondrocytes. In this study, we evaluated changes in expression of cartilaginous genes during in vitro chondrogenic differentiation of WJ-MSCs on PLGA scaffolds.
Methods: The biocompatibility of the PLGA material was investigated using WJ-MSCs by direct and indirect contact methods according to the ISO 10993–5 standard. PLGA scaffolds were fabricated by the solvent casting/salt-leaching technique. We analyzed expression of chondrogenic genes of WJ-MSCs after a 21-day culture.
Results: The results showed the biocompatibility of PLGA and confirmed the usefulness of PLGA as material for fabrication of 3D scaffolds that can be applied for WJ-MSC culture. The in vitro penetration and colonization of the scaffolds by WJ-MSCs were assessed by confocal microscopy. The increase in cell number demonstrated that scaffolds made of PLGA copolymers enabled WJ-MSC proliferation. The obtained data showed that as a result of chondrogenesis of WJ-MSCs on the PLGA scaffold the expression of the key markers collagen type II and aggrecan was increased.
Conclusions: The observed changes in transcriptional activity of cartilaginous genes suggest that the PLGA scaffolds may be applied for WJ-MSC differentiation. This primary study suggests that chondrogenic capacity of WJ-MSCs cultured on the PLGA scaffolds can be useful for cell therapy of cartilage.
Keywords Mesenchymal stem cells, Wharton’s Jelly, Umbilical cord, Biodegradable scaffold, PLGA, Chondrogenesis, Chondrocytes, Gene expression
Address and Contact Information 1Department of Biopharmacy, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland.
2Centre of Polymer and Carbon Materials, Polish Academy of Sciences, Zabrze, Poland.
3Department of Gynecology and Obstetrics, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland.
4Department of Health Care, Silesian Medical College, Katowice, Poland
* Corresponding author: ppaduszynski@sum.edu.pl; paduszyn@o2.pl
Read full article at BMC

DOI 10.1186/s11658-016-0017-x Volume 21 (2016)
Authors Leszek Kalinowski1*, Anna Janaszak-Jasiecka2, Anna Siekierzycka1, Sylwia Bartoszewska3, Marcin Woźniak1, Dawid Lejnowski2, James F. Collawn4 and Rafal Bartoszewski2*
Abstract Understanding the cellular pathways that regulate endothelial nitric oxide (eNOS, NOS3) expression and consequently nitric oxide (NO) bioavailability during hypoxia is a necessary aspect in the development of novel treatments for cardiovascular disorders. eNOS expression and eNOS-dependent NO cellular signaling during hypoxia promote an equilibrium of transcriptional and posttranscriptional molecular mechanisms that belong to both proapoptotic and survival pathways. Furthermore, NO bioavailability results not only from eNOS levels, but also relies on the presence of eNOS substrate and cofactors, the phosphorylation status of eNOS, and the presence of reactive oxygen species (ROS) that can inactivate eNOS. Since both NOS3 levels and these signaling pathways can also be a subject of posttranscriptional modulation by microRNAs (miRNAs), this class of short noncoding RNAs contribute another level of regulation for NO bioavailability. As miRNA antagomirs or specific target protectors could be used in therapeutic approaches to regulate NO levels, either by changing NOS3 mRNA stability or through factors governing eNOS activity, it is critical to understand their role in governing eNOS activity during hypoxa. In contrast to a large number of miRNAs reported to the change eNOS expression during hypoxia, only a few miRNAs modulate eNOS activity. Furthermore, impaired miRNA biogenesis leads to NOS3 mRNA stabilization under hypoxia. Here we discuss the recent studies that define miRNAs’ role in maintaining endothelial NO bioavailability emphasizing those miRNAs that directly modulate NOS3 expression or eNOS activity.
Keywords eNOS, ER stress, Hypoxia, miRNA, Nitric oxide, NO bioavailability, NOS3, sONE
Address and Contact Information 1Department of Medical Laboratory Diagnostics and Central Bank of Frozen Tissues & Genetic Specimens, Medical University of Gdansk, Debinki 7, 80-211 Gdansk, Poland.
2Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland.
3Department of Inorganic Chemistry, Medical University of Gdansk, Gdansk, Poland.
4Department of Cell Biology, Developmental, and Integrative, University of Alabama at Birmingham, Birmingham, USA.
* Corresponding author: lekal@gumed.edu.pl; rafalbar@gumed.edu.pl
Read full article at BMC

DOI 10.1186/s11658-016-0021-1 Volume 21 (2016)
Authors Yun-lin Shen, Hua-jie Liu, Lei Sun, Xiao-ling Niu, Xin-yu Kuang, Ping Wang, Sheng Hao and Wen-yan Huang*
Abstract Background: The aim of this study was to evaluate the influence of RGC-32 (response gene to complement 32) on cell cycle progression in renal tubular epithelial cell injury.
Methods: NRK-52E cells with overexpressed or silenced RGC-32 were constructed via transient transfection with RGC-32 expression plasmid and RGC-32 siRNA plasmid, and the cell cycle distribution was determined. The expression levels of fibrosis factors, including smooth muscle action (α-SMA), fibronectin (FN) and E-cadherin, were assessed in cells with silenced RGC-32.
Results: The cells were injured via TNF-α treatment, and the injury was detectable by the enhanced expression of neutrophil gelatinase-associated lipocalin (NGAL). RGC-32 expression also increased significantly. The number of cells at G2/M phase increased dramatically in RGC-32 silenced cells, indicating that RGC-32 silencing induced G2/M arrest. In addition, after treatment with TNF-α, the NRK-52E cells with silenced RGC-32 showed significantly increased expression of α-SMA and FN, but decreased expression of E-cadherin.
Conclusions: The results of this study suggest that RGC-32 probably has an important impact on the repair process of renal tubular epithelial cells in vitro by regulating the G2/M phase checkpoint, cell fibrosis and cell adhesion. However, the exact mechanism needs to be further elucidated.
Keywords Response gene to complement 32, Cell cycle, G2/M phase, Tumor necrosis factor-alpha, Tubulointerstitial fibrosis, Tubular epithelial cell repair
Address and Contact Information Department of Nephrology and Rheumatology, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
* Corresponding author: huangwenyan@sjtu.edu.cn
Read full article at BMC

DOI 10.1186/s11658-016-0020-2 Volume 21 (2016)
Authors Lixia Qin1,2, Jifeng Guo2, Qian Zheng1 and Hainan Zhang1*
Abstract Bcl2-associated athanogene 2 (BAG2) shares a similar molecular structure and function with other BAG family members. Functioning as a co-chaperone, it interacts with the ATPase domain of the heat shock protein 70 (dHsp70) through its BAG domain. It also interacts with many other molecules and regulates various cellular functions. An increasing number of studies have indicated that BAG2 is involved in the pathogenesis of various diseases, including cancers and neurodegenerative diseases. This paper is a comprehensive review of the structure, functions, and protein interactions of BAG2. We also discuss its roles in diseases, including cancer, Alzheimer’s disease, Parkinson’s disease and spinocerebellar ataxia type-3. Further research on BAG2 could lead to an understanding of the pathogenesis of these disorders or even to novel therapeutic approaches.
Keywords BAG2, Molecular chaperones, Carcinoma, Alzheimer’s disease, Parkinson’s disease, Spinocerebellar ataxia type-3
Address and Contact Information 1Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China.
2Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.
* Corresponding author: yyzhn@sina.com
Read full article at BMC

DOI 10.1186/s11658-016-0019-8 Volume 21 (2016)
Authors Wenqing Ma1, Yu Wang2, Xiaomeng Yao1,3, Zijian Xu1, Liguo An1 and Miao Yin1*
Abstract Background: As a key subunit of the exocyst complex, Exo70 has highly conserved sequence and is widely found in yeast, mammals, and plants. In yeast, Exo70 mediates the process of exocytosis and promotes anchoring and integration of vesicles with the plasma membrane. In mammalian cells, Exo70 is involved in maintaining cell morphology, cell migration, cell connection, mRNA splicing, and other physiological processes, as well as participating in exocytosis. However, Exo70’s function in mammalian cells has yet to be fully recognized. In this paper, the expression of Exo70 and its role in cell migration were studied in a rat vascular smooth muscle cell line A7r5.
Methods: Immunofluorescent analysis the expression of Exo70, α-actin, and tubulin in A7r5 cells showed a co-localization of Exo70 and α-actin, we treated the cells with cytochalasin B to depolymerize α-actin, in order to further confirm the co- localization of Exo70 and α-actin. We analyzed Exo70 co-localization with actin at the edge of migrating cells by wound-healing assay to establish whether Exo70 might play a role in cell migration. Next, we analyzed the migration and invasion ability of A7r5 cells before and after RNAi silencing through the wound healing assay and transwell assay.
Results: The mechanism of interaction between Exo70 and cytoskeleton can be clarified by the immunoprecipitation techniques and wound-healing assay. The results showed that Exo70 and α-actin were co-localized at the leading edge of migrating cells. The ability of A7r5 to undergo cell migration was decreased when Exo70 expression was silenced by RNAi. Reducing Exo70 expression in RNAi treated A7r5 cells significantly lowered the invasion and migration ability of these cells compared to the normal cells. These results indicate that Exo70 participates in the process of A7r5 cell migration.
Conclusions: This research is importance for the study on the pathological process of vascular intimal hyperplasia, since it provides a new research direction for the treatment of cardiovascular diseases such as atherosclerosis and restenosis after balloon angioplasty.
Keywords Exo70, Exocyst, Vascular smooth muscle cell, Cell migration, RNAi, Wound-healing assay, Immunohistochemistry, Transwell assay
Address and Contact Information 1Key Laboratory of Animal Resistant Biology of Shandong, College of Life Science, Shandong Normal University, Jinan 250014, People’s Republic of China.
2Shandong Provincial Hospital affiliated to Shandong University, Jinan 250014, People’s Republic of China.
3No.10 High School of Zibo, Zibo 255000, People’s Republic of China.
* Corresponding author: yinmiao@sdnu.edu.cn
Read full article at BMC

DOI 10.1186/s11658-016-0022-0 Volume 21 (2016)
Authors Jiachun Sun1†, Junqiang Yan2†, Xiaozhi Yuan1, Ruina Yang1, Tanyou Dan1, Xinshuai Wang1, Guoqiang Kong1 and Shegan Gao1*
Abstract Long non-coding RNAs (lncRNAs) play critical and complicated roles in the regulation of various biological processes, including chromatin modification, transcription and post-transcriptional processing. Interestingly, some lncRNAs serve as miRNA “sponges” that inhibit interaction with miRNA targets in post-transcriptional regulation. We constructed a putative competing endogenous RNA (ceRNA) network by integrating lncRNA, miRNA and mRNA expression based on high-throughput RNA sequencing and microarray data to enable a comparison of the SHEE and SHEEC cell lines. Using Targetscan and miRanda bioinformatics algorithms and miRTarbase microRNA-target interactions database, we established that 51 miRNAs sharing 13,623 MREs with 2260 genes and 82 lncRNAs were involved in this ceRNA network. Through a biological function analysis, the ceRNA network appeared to be primarily involved in cell proliferation, apoptosis, the cell cycle, invasion and metastasis. Functional pathway analyses demonstrated that the ceRNA network potentially modulated multiple signaling pathways, such as the MAPK, Ras, HIF-1, Rap1, and PI3K/Akt signaling pathways. These results might provide new clues to better understand the regulation of the ceRNA network in cancer.
Keywords SHEE, SHEEC, miRNA, lncRNA, ceRNA
Address and Contact Information 1Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China.
2Department of Neurology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People’s Republic of China.
* Corresponding author: zlk13837970300@126.com; zlk037964811906@163.com
† Equal contributors
Read full article at BMC

DOI 10.1186/s11658-016-0018-9 Volume 21 (2016)
Authors Susana Novoa-Herran1, Adriana Umaña-Perez1, Francesc Canals2 and Myriam Sanchez-Gomez1*
Abstract Background: How nutrition and growth factor restriction due to serum depletion affect trophoblast function remains poorly understood. We performed a proteomic differential study of the effects of serum depletion on a first trimester human immortalized trophoblast cell line.
Methods: The viability of HTR-8/SVneo trophoblast cells in culture with 0, 0.5 and 10 % fetal bovine serum (FBS) were assayed via MTT at 24, 48 and 64 h. A comparative proteomic analysis of the cells grown with those FBS levels for 24 h was performed using two-dimensional electrophoresis (2DE), followed by mass spectrometry for protein spot identification, and a database search and bioinformatics analysis of the expressed proteins. Differential spots were identified using the Kolmogorov-Smirnov test (n=3, significance level 0.10, D>0.642) and/or ANOVA (n= 3, p< 0.05).
Results: The results showed that low serum doses or serum depletion differentially affect cell growth and protein expression. Differential expression was seen in 25 % of the protein spots grown with 0.5 % FBS and in 84 % of those grown with 0 % FBS, using 10 % serum as the physiological control. In 0.5 % FBS, this difference was related with biological processes typically affected by the serum, such as cell cycle, regulation of apoptosis and proliferation. In addition to these changes, in the serum- depleted proteome we observed downregulation of keratin 8, and upregulation of vimentin, the glycolytic enzymes enolase and pyruvate kinase (PKM2) and tumor progression-related inosine-5’-monophosphate dehydrogenase 2 (IMPDH2) enzyme. The proteins regulated by total serum depletion, but not affected by growth in 0.5 % serum, are members of the glycolytic and nucleotide metabolic pathways and the epithelial-to-mesenchymal transition (EMT), suggesting an adaptive switch characteristic of malignant cells.
Conclusions: This comparative proteomic analysis and the identified proteins are the first evidence of a protein expression response to serum depletion in a trophoblast cell model. Our results show that serum depletion induces specific changes in protein expression concordant with main cell metabolic adaptations and EMT, resembling the progression to a malignant phenotype
Keywords Cancer, Metabolism, Proteomics, Placenta, Cell culture, Serum, Vimentin, MTT, Trophoblast, Western blot
Address and Contact Information 1Departamento de Química, Grupo de Investigación en Hormonas (Hormone Research Laboratory), Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Cra 30 45-03 Ed 451 Of 464, AA 111321 Bogotá, Colombia.
2Laboratory of Proteomics, Vall d’Hebron Institute of Oncology (VHIO), Centre Cellex, C Natzaret 115-117, 08035 Barcelona, Spain.
* Corresponding author: mysanchezd@unal.edu.co
Read full article at BMC

DOI 10.1186/s11658-016-0025-x Volume 21 (2016)
Authors Rafal Bartoszewski1*†, Jaroslaw Króliczewski2†, Arkadiusz Piotrowski1, Anna Janaszak Jasiecka1, Sylwia Bartoszewska3, Briana Vecchio-Pagan4, Lianwu Fu6,8, Aleksandra Sobolewska1, Sadis Matalon5,6,8, Garry R. Cutting4, Steven M. Rowe6,7,8 and James F. Collawn6,8†
Abstract Synonymous or silent mutations are often overlooked in genetic analyses for disease- causing mutations unless they are directly associated with potential splicing defects. More recent studies, however, indicate that some synonymous single polynucleotide polymorphisms (sSNPs) are associated with changes in protein expression, and in some cases, protein folding and function. The impact of codon usage and mRNA structural changes on protein translation rates and how they can affect protein structure and function is just beginning to be appreciated. Examples are given here that demonstrate how synonymous mutations alter the translational kinetics and protein folding and/or function. The mechanism for how this occurs is based on a model in which codon usage modulates the translational rate by introducing pauses caused by nonoptimal or rare codons or by introducing changes in the mRNA structure, and this in turn influences co-translational folding. Two examples of this include the multidrug resistance protein (p-glycoprotein) and the cystic fibrosis transmembrane conductance regulator gene (CFTR). CFTR is also used here as a model to illustrate how synonymous mutations can be examined using in silico predictive methods to identify which sSNPs have the potential to change protein structure. The methodology described here can be used to help identify “non-silent” synonymous mutations in other genes.
Keywords Synonymous mutations, Single nucleotide polymorphism (SNP), Codon usage, mRNA folding, Translation rate, in silico predictions, CFTR
Address and Contact Information 1Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland.
2Laboratory of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland.
3Department of Inorganic Chemistry, Medical University of Gdansk, Gdansk, Poland.
4Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA.
5Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, USA.
6Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA.
7Departments of Medicine and Pediatrics, University of Alabama at Birmingham, Birmingham, USA.
8Gregory Fleming James Cystic Fibrosis Center, University of Alabama at Birmingham, Birmingham, USA.
* Corresponding author: rafalbar@gumed.edu.pl
† Equal contributors
Read full article at BMC

DOI 10.1186/s11658-016-0023-z Volume 21 (2016)
Authors Enze Jin1†, Seongho Han2†, Mina Son3 and Sung-Whan Kim3,4*
Abstract Cordyceps belongs to a genus of acormycete fungi and is known to exhibit various pharmacological effects. The aim of this study was to investigate the effect of Cordyceps species on the proliferation of vascular smooth muscle cells (VSMC) and their underlying molecular mechanism. A cell proliferation assay showed that Cordyceps bassiana ethanol extract (CBEE) significantly inhibited VSMC proliferation. In addition, neointimal formation was significantly reduced by treatment with CBEE in the carotid artery of balloon-injured rats. We also investigated the effects of CBEE on the extracellular signal-regulated kinase (ERK) signal pathway. Western blot analysis revealed increased ERK 1/2 phosphorylation in VSMCs treated with CBEE. Pretreatment with U0126 completely abrogated CBEE-induced ERK 1/2 phosphorylation. In conclusion, CBEE exhibited anti-proliferative properties that affected VSMCs through the ERK1/2 MAPK signaling pathway. Our data may elucidate the inhibitory mechanism of this natural product.
Keywords Cordyceps, ERK pathway, Inhibitory, MAPK, Mechanism, Natural product, Neointimal formation, Proliferation, Smooth muscle cells, Vascular
Address and Contact Information 1Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China.
2Department of Family Medicine, College of Medicine, Dong-A University, Busan, Republic of Korea.
3Department of Medicine, College of Medicine, Catholic Kwandong University, Gangneung, Republic of Korea.
4International St. Mary’s Hospital, 25, Simgok-ro 100beon-gil, Seo-gu, Incheon 404-190, Republic of Korea.
* Corresponding author: swkim@cku.ac.kr
† Equal contributors
Read full article at BMC

DOI 10.1186/s11658-016-0026-9 Volume 21 (2016)
Authors Xin Li, Shanshan Zou, Zhen Li, Gaotai Cai, Bohong Chen, Ping Wang and Wenqi Dong*
Abstract Cytoglobin (CYGB), a member of the globin family, is thought to protect cells from reactive oxygen and nitrogen species and deal with hypoxic conditions and oxidative stress. However, its molecular mechanisms of action are not clearly understood. Through immunoprecipitation combined with a two-dimensional electrophoresis–mass spectrometry assay, we identified a CYGB interactor: aldo-keto reductase family 7 member A2 (AKR7A2). The interaction was further confirmed using yeast two-hybrid and co-immunoprecipitation assays. Our results show that AKR7A2 physically interacts with CYGB.
Keywords CYGB, AKR7A2, Protein-protein interactions, Yeast two-hybrid assay, Co-immunoprecipitation, 2-DE, Oxidative stress
Address and Contact Information Department of Biopharmaceutics, School of Laboratory Medicine and Biotechnology, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou 510515, China
* Corresponding author: dongwq63@263.net
Read full article at BMC

DOI 10.1186/s11658-016-0027-8 Volume 21 (2016)
Authors Edyta Wrobel1* , Joanna Leszczynska1 and Edyta Brzoska2
Abstract Background: The primary human bone-derived cell culture technique is used as a model to study human osteogenesis. Compared to cell line cultures, primary osteoprogenitor and osteoblast cultures provide more complex information about osteogenesis, bone remodeling and regeneration than cell line cultures.
Methods: In this study, we isolated human bone-derived cells (HBDCs) and promoted their differentiation into osteoblasts. The following parameters were evaluated: cell number and viability, total protein expression, alkaline phosphatase activity, collagenous matrix production and osteogenic genes expression, i.e., gene coding for type I collagen and alkaline phosphatase.
Results: It was proved the results show that HBDCs intensively proliferate during the first 7 days of culture followed by differentiation accompanied by an increase in alkaline phosphatase activity. Moreover, it was observed that during the differentiation of HBDCs, the expression of integrin β1 increased.
Conclusions: The process was also accompanied by changes in cell shape and rearrangement of the actin cytoskeleton and focal contacts containing FAK and the integrin β1 subunit. We suggest that the β1 integrin subunit may be a suitable new target in studies of the differentiation of primary human osteoblasts in culture. Keywords: Human bone-derived cells, Integrins, Osteoblast differentiation, Osteogenesis in vitro, Osteogenic markers, Primary osteoblasts.
Keywords Human bone-derived cells, Integrins, Osteoblast differentiation, Osteogenesis in vitro, Osteogenic markers, Primary osteoblasts
Address and Contact Information 1Department of Biophysics and Human Physiology, Faculty of Health Sciences, Medical University of Warsaw, ul.Chalubinskiego 5, 02-004, Warsaw, Poland.
2 Department of Cytology, Institute of Zoology, Faculty of Biology, University of Warsaw, ul. Miecznikowa 1, 02-096, Warsaw, Poland.
* Corresponding author: edyta.wrobel@wum.edu.pl
Read full article at BMC

DOI 10.1186/s11658-016-0029-6 Volume 21 (2016)
Authors Yawen Xu *, Binshen Chen ,, Shaobo Zheng, Yong Wen, Abai Xu, Kai Xu, Bingkun Li and Chunxiao Liu
Abstract Immunoglobulin G (IgG) has been implicated in the progression of various cancers. This study explored the role of IgG in the proliferation, apoptosis, cell cycle and in vitro invasive properties of LNCaP prostate cancer cells. We used IGHG1 small interfering RNA to silence IgG1 expression in LNCaP cells. The efficacy of IgG1 gene knockdown was confirmed using qPCR and western blotting. The colony formation, proliferation, migration and invasion abilities of LNCaP cells after transfection were assessed using colony-forming, flow cytometry and transwell assays. The expressions of PCNA and caspase-3 proteins in LNCaP cells after transfection were detected with immunofluorescence staining and western blotting. IgG1 silencing significantly decreased the colony formation, survival, cell cycle progression, migration and invasion of LNCaP cells (p < 0.05). IgG1 silencing also reduced the amount of the proliferation marker PCNA and induced formation of the apoptotic marker caspase-3 (p < 0.05). Our results show that IgG1 produced by LNCaP cells confers advantages for tumor cell survival, proliferation, migration and invasion, suggesting that IgG1 is a potential target for prostate cancer treatment.
Keywords LNCaP cells, Prostate cancer, RNA interference, Immunoglobulin G, Proliferation, Apoptosis, Migration, Invasion, Cell cycle, Caspase-3
Address and Contact Information Department of Urology, Zhujiang Hospital, Southern Medical University, No. 253, Industrial Road, Guangzhou, Guangdong, China
* Corresponding author: mouse72@foxmail.com
Equal contributors
Read full article at BMC

DOI 10.1186/s11658-016-0028-7 Volume 21 (2016)
Authors Megan Finch-Edmondson1,2* and Marius Sudol1,2*
Abstract Mechanobiology has shifted our understanding of fundamental cellular and physiological functions. Changes to the stiffness of the extracellular matrix, cell rigidity, or shape of the cell environment were considered in the past to be a consequence of aging or pathological processes. We now understand that these factors can actually be causative biological mediators of cell growth to control organ size. Mechanical cues are known to trigger a relatively fast translocation of specific transcriptional co-factors such as MRTFs, YAP and TAZ from the cytoplasm to the cell nucleus to initiate discrete transcriptional programs. The focus of this review is the molecular mechanisms by which biophysical stimuli that induce changes in cytoplasmic actin dynamics are communicated within cells to elicit gene-specific transcription via nuclear localisation or activation of specialized transcription factors, namely MRTFs and the Hippo pathway effectors YAP and TAZ. We propose here that MRTFs, YAP and TAZ closely collaborate as mechano-effectors.
Keywords Mechanotransduction, Actin, Myocardin, MRTF, YAP, TAZ, β-catenin, Epithelial- mesenchymal transition
Address and Contact Information 1Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411 Singapore, Singapore.
2Department of Physiology, National University of Singapore, Yong Loo Lin School of Medicine, 2 Medical Drive, 117597 Singapore, Singapore.
* Corresponding author: mbimlf@nus.edu.sg; phsms@nus.edu.sg
Read full article at BMC

DOI 10.1186/s11658-016-0031-z Volume 21 (2016)
Authors Wei Jing Liu1,2†, Lin Ye1†, Wei Fang Huang1, Lin Jie Guo1, Zi Gan Xu1, Hong Luan Wu1, Chen Yang1 and Hua Feng Liu1*
Abstract The ubiquitin–proteasome system (UPS) and autophagy are two distinct and interacting proteolytic systems. They play critical roles in cell survival under normal conditions and during stress. An increasing body of evidence indicates that ubiquitinated cargoes are important markers of degradation. p62, a classical receptor of autophagy, is a multifunctional protein located throughout the cell and involved in many signal transduction pathways, including the Keap1–Nrf2 pathway. It is involved in the proteasomal degradation of ubiquitinated proteins. When the cellular p62 level is manipulated, the quantity and location pattern of ubiquitinated proteins change with a considerable impact on cell survival. Altered p62 levels can even lead to some diseases. The proteotoxic stress imposed by proteasome inhibition can activate autophagy through p62 phosphorylation. A deficiency in autophagy may compromise the ubiquitin–proteasome system, since overabundant p62 delays delivery of the proteasomal substrate to the proteasome despite proteasomal catalytic activity being unchanged. In addition, p62 and the proteasome can modulate the activity of HDAC6 deacetylase, thus influencing the autophagic degradation.
Keywords p62, Autophagy, Ubiquitin–proteasome system (UPS), Ubiquitinated protein, Aggresome, Proteostasis, p62 phosphorylation, Keap1–Nrf2 pathway, Histone deacetylase 6 (HDAC6), Mechanistic target of rapamycin complex 1 (mTORC1)
Address and Contact Information 1The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001, China.
2Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing 100700, China.
* Corresponding author: hf-liu@263.net
Equal contributors
Read full article at BMC