International Journal of Molecular Sciences

285 KiB

Open AccessArticle

Possible Role of −374T/A Polymorphism of RAGE Gene in Longevity

by Colomba Falcone, Sara Bozzini, Anna Colonna, Benedetta Matrone, Edoardo Maria Paganini, Rossana Falcone and Gabriele Pelissero

Int. J. Mol. Sci. 2013, 14(11), 23203-23211; https://doi.org/10.3390/ijms141123203 - 21 Nov 2013

Cited by 5 | Viewed by 5881

Abstract

Demographic and social changes in the last decades have resulted in improvements in health and longevity. The survival of elderly people has improved significantly and thus centenarians are becoming the fastest growing population group. Environmental, genetic, and accidental factors have influenced the human [...] Read more.

Demographic and social changes in the last decades have resulted in improvements in health and longevity. The survival of elderly people has improved significantly and thus centenarians are becoming the fastest growing population group. Environmental, genetic, and accidental factors have influenced the human life span. Researchers have gained substantial evidence that advanced glycation end products may play an important role in the processes of physiological aging. The aim of the present study was to investigate any differences in the frequencies of −374T/A polymorphism in subjects aged >90 years and in middle-aged individuals. We observed association between the A allele and genotype homozygous for this allele (AA) with a longer life expectancy in the male population. In particular, there was a prevalence of AA genotype and A allele in long-living subjects and a prevalence of the allele T in middle-aged subjects, indicating a possible protective role of the allele A to aging. In conclusion, our results support the hypothesis that longevity is the result of a good functioning of the immune system and a presumable hyper-expression of variants of anti-inflammatory genes of immunity. The differences in the genetic regulation of inflammatory processes may influence the presence of age-related disorders. Full article

(This article belongs to the Section Biochemistry)

1384 KiB

Open AccessArticle

Different Effects of Androgen on the Expression of Fut1, Fut2, Fut4 and Fut9 in Male Mouse Reproductive Tract

by Chun-Mei Wang, Shuang-Gang Hu, Yan-Fei Ru, Guang-Xin Yao, Wu-Bin Ma, Yi-Hua Gu, Chen Chu, Shou-Lin Wang, Zuo-Min Zhou, Qiang Liu, Yu-Chuan Zhou and Yong-Lian Zhang

Int. J. Mol. Sci. 2013, 14(11), 23188-23202; https://doi.org/10.3390/ijms141123188 - 21 Nov 2013

Cited by 6 | Viewed by 7630

Abstract

The α-(1,2) fucosyltransferases (Fut1 and Fut2) and α-(1,3) fucosyltransferases (Fut4, Fut9) are responsible for the synthesis of Lewis X (LeX) and Lewis Y (LeY) conjugated to glycoproteins. We recently reported that these fucosyltransferases were differentially expressed in the [...] Read more.

The α-(1,2) fucosyltransferases (Fut1 and Fut2) and α-(1,3) fucosyltransferases (Fut4, Fut9) are responsible for the synthesis of Lewis X (LeX) and Lewis Y (LeY) conjugated to glycoproteins. We recently reported that these fucosyltransferases were differentially expressed in the reproductive tract of male mouse. Here, we studied the effect of androgen on fucosyltransferase expression through the use of mouse castration models. We found that Fut1 mRNA and Fut4 mRNA were upregulated, while Fut2 mRNA and Fut9 mRNA were downregulated by androgen in the caput epididymis. However, in the vas deferens and prostate, only Fut4 mRNA and Fut2 mRNA were respectively upregulated following exposure to androgen. In the seminal vesicle, all fucosyltransferases, with the exception of Fut9, were upregulated. We identified the androgen receptor binding sites (ARBSs) of Fut2, Fut4 and Fut9 in the caput epididymis. Luciferase assay for these ARBSs is able to provide an indication as to why Fut4 and Fut9 are differently expressed and regulated by androgen, although they catalyze the same α-(1,3) fucose linkage. Our study showed that androgen could differentially regulate the expression of these fucosyltransferases and provided an insight into the characteristic distribution of each fucosyltransferase responsible for LeX/LeY biosynthesis in the male reproductive tract. Full article

(This article belongs to the Special Issue Glycosylation and Glycoproteins)

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Open AccessArticle

Systems Biology Approach to the Dissection of the Complexity of Regulatory Networks in the S. scrofa Cardiocirculatory System

by Paolo Martini, Gabriele Sales, Enrica Calura, Mattia Brugiolo, Gerolamo Lanfranchi, Chiara Romualdi and Stefano Cagnin

Int. J. Mol. Sci. 2013, 14(11), 23160-23187; https://doi.org/10.3390/ijms141123160 - 21 Nov 2013

Cited by 4 | Viewed by 8190

Abstract

Genome-wide experiments are routinely used to increase the understanding of the biological processes involved in the development and maintenance of a variety of pathologies. Although the technical feasibility of this type of experiment has improved in recent years, data analysis remains challenging. In [...] Read more.

Genome-wide experiments are routinely used to increase the understanding of the biological processes involved in the development and maintenance of a variety of pathologies. Although the technical feasibility of this type of experiment has improved in recent years, data analysis remains challenging. In this context, gene set analysis has emerged as a fundamental tool for the interpretation of the results. Here, we review strategies used in the gene set approach, and using datasets for the pig cardiocirculatory system as a case study, we demonstrate how the use of a combination of these strategies can enhance the interpretation of results. Gene set analyses are able to distinguish vessels from the heart and arteries from veins in a manner that is consistent with the different cellular composition of smooth muscle cells. By integrating microRNA elements in the regulatory circuits identified, we find that vessel specificity is maintained through specific miRNAs, such as miR-133a and miR-143, which show anti-correlated expression with their mRNA targets. Full article

(This article belongs to the Special Issue Regulation by non-coding RNAs 2013)

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206 KiB

Open AccessArticle

Tetra-Repeat Microsatellite Markers for the Masu Salmon (Oncorhynchus masou masou) and Its Application in Cross-Subspecies Amplification

by Shoichiro Yamamoto, Tadahide Kurokawa, Masashi Sekino, Motoshige Yasuike and Kenji Saitoh

Int. J. Mol. Sci. 2013, 14(11), 23153-23159; https://doi.org/10.3390/ijms141123153 - 21 Nov 2013

Cited by 4 | Viewed by 5662

Abstract

We developed tetranucleotide-repeat microsatellite markers for the masu salmon (Oncorhynchus masou) complex. 454 pyrosequencing was used to discover repeat motifs, and seven polymorphic microsatellite-primer sets were identified. The number of alleles detected at each locus ranged from four to 24 and [...] Read more.

We developed tetranucleotide-repeat microsatellite markers for the masu salmon (Oncorhynchus masou) complex. 454 pyrosequencing was used to discover repeat motifs, and seven polymorphic microsatellite-primer sets were identified. The number of alleles detected at each locus ranged from four to 24 and the expected heterozygosity varied from 0.57 to 0.92. Cross-subspecies amplification for O. m. masou, O. m. ishikawae and O. m. subsp. was successful. These microsatellites can be utilized in studies of genetic structure, genetic diversity, and intra- and inter-subspecific hybridization, making a contribution to conservation and management of the Oncorhynchus masou complex. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Detection of Lymph Node Metastases in Human Colorectal Cancer by Using 5-Aminolevulinic Acid-Induced Protoporphyrin IX Fluorescence with Spectral Unmixing

by Kenichi Harada, Yoshinori Harada, Masatomo Beika, Noriaki Koizumi, Koji Inoue, Yasutoshi Murayama, Yoshiaki Kuriu, Masayoshi Nakanishi, Takeo Minamikawa, Yoshihisa Yamaoka, Ping Dai, Akio Yanagisawa, Eigo Otsuji and Tetsuro Takamatsu

Int. J. Mol. Sci. 2013, 14(11), 23140-23152; https://doi.org/10.3390/ijms141123140 - 21 Nov 2013

Cited by 22 | Viewed by 7452

Abstract

Accurate evaluation of metastatic lymph nodes (LNs) is indispensable for adequate treatment of colorectal cancer (CRC) patients. Here, we demonstrate detection of metastases of human CRC in removed fresh LNs using 5-aminolevulinic acid (ALA)-induced protoporphyrin IX (PpIX) fluorescence. A spectral unmixing method was [...] Read more.

Accurate evaluation of metastatic lymph nodes (LNs) is indispensable for adequate treatment of colorectal cancer (CRC) patients. Here, we demonstrate detection of metastases of human CRC in removed fresh LNs using 5-aminolevulinic acid (ALA)-induced protoporphyrin IX (PpIX) fluorescence. A spectral unmixing method was employed to reduce the overlap of collagen autofluorescence on PpIX fluorescence. A total of 17 surgery patients with advanced CRC were included in this study. After 5-ALA at a dose of 15 mg/kg of body weight was applied orally 2 h prior to surgery, 87 LNs were subjected to spectral fluorescence imaging and histopathological diagnosis, and statistical analysis was performed. No apparent side effect was observed to be associated with 5-ALA administration. The spectral unmixing fluorescence intensity of PpIX in metastatic LNs was 10.2-fold greater than that in nonmetastaic LNs. The receiver-operating-characteristic (ROC) analysis showed that the area under the curve (AUC) was calculated as 0.95. Our results show the potential of 5-ALA-induced PpIX fluorescence processed by spectral unmixing for detecting metastases in excised fresh LNs from patients with CRC, suggesting that this rapid and feasible method is applicable to gross evaluation of resected LN samples in pathology laboratories. Full article

(This article belongs to the Special Issue Frontiers of Micro-Spectroscopy in Biological Applications)

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246 KiB

Open AccessArticle

GC and GC/MS Analysis of Essential Oil Composition of the Endemic Soqotraen Leucas virgata Balf.f. and Its Antimicrobial and Antioxidant Activities

by Ramzi A. Mothana, Mansour S. Al-Said, Mohammed A. Al-Yahya, Adnan J. Al-Rehaily and Jamal M. Khaled

Int. J. Mol. Sci. 2013, 14(11), 23129-23139; https://doi.org/10.3390/ijms141123129 - 21 Nov 2013

Cited by 45 | Viewed by 8255

Abstract

Leucas virgata Balf.f. (Lamiaceae) was collected from the Island Soqotra (Yemen) and its essential oil was obtained by hydrodistillation. The chemical composition of the oil was investigated by GC and GC-MS. Moreover, the essential oil was evaluated for its antimicrobial activity against two [...] Read more.

Leucas virgata Balf.f. (Lamiaceae) was collected from the Island Soqotra (Yemen) and its essential oil was obtained by hydrodistillation. The chemical composition of the oil was investigated by GC and GC-MS. Moreover, the essential oil was evaluated for its antimicrobial activity against two Gram-positive bacteria, two Gram-negative bacteria, and one yeast species by using broth micro-dilution assay for minimum inhibitory concentrations (MIC) and antioxidant activity by measuring the scavenging activity of the DPPH radical. The investigation led to the identification of 43 constituents, representing 93.9% of the total oil. The essential oil of L. virgata was characterized by a high content of oxygenated monoterpenes (50.8%). Camphor (20.5%) exo-fenchol (3.4%), fenchon (5.4%), and borneol (3.1%) were identified as the main components. Oxygenated sesquiterpenes were found as the second major group of compounds (21.0%). β-Eudesmol (6.1%) and caryophyllene oxide (5.1%) were the major compounds among oxygenated sesquiterpenes. The results of the antimicrobial assay showed that the oil exhibited a great antibacterial activity against the tested S. aureus, B. subtilis, and E. coli. No activity was found against P. aeruginosa and C. albicans. Moreover, the DPPH-radical scavenging assay exhibited only a moderate antioxidant activity (31%) for the oil at the highest concentration tested (1 mg/mL). Full article

(This article belongs to the Section Biochemistry)

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Open AccessReview

Oxidative Stress Mechanisms Underlying Parkinson’s Disease-Associated Neurodegeneration in C. elegans

by Sudipta Chakraborty, Julia Bornhorst, Thuy T. Nguyen and Michael Aschner

Int. J. Mol. Sci. 2013, 14(11), 23103-23128; https://doi.org/10.3390/ijms141123103 - 21 Nov 2013

Cited by 46 | Viewed by 11022

Abstract

Oxidative stress is thought to play a significant role in the development and progression of neurodegenerative diseases. Although it is currently considered a hallmark of such processes, the interweaving of a multitude of signaling cascades hinders complete understanding of the direct role of [...] Read more.

Oxidative stress is thought to play a significant role in the development and progression of neurodegenerative diseases. Although it is currently considered a hallmark of such processes, the interweaving of a multitude of signaling cascades hinders complete understanding of the direct role of oxidative stress in neurodegeneration. In addition to its extensive use as an aging model, some researchers have turned to the invertebrate model Caenorhabditis elegans (C. elegans) in order to further investigate molecular mediators that either exacerbate or protect against reactive oxygen species (ROS)-mediated neurodegeneration. Due to their fully characterized genome and short life cycle, rapid generation of C. elegans genetic models can be useful to study upstream markers of oxidative stress within interconnected signaling pathways. This report will focus on the roles of C. elegans homologs for the oxidative stress-associated transcription factor Nrf2, as well as the autosomal recessive, early-onset Parkinson’s disease (PD)-associated proteins Parkin, DJ-1, and PINK1, in neurodegenerative processes. Full article

(This article belongs to the Special Issue Molecular Research in Neurotoxicology)

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Open AccessReview

Let-7 in Cardiovascular Diseases, Heart Development and Cardiovascular Differentiation from Stem Cells

by Mei-Hua Bao, Xing Feng, Yi-Wen Zhang, Xiao-Ya Lou, Yu Cheng and Hong-Hao Zhou

Int. J. Mol. Sci. 2013, 14(11), 23086-23102; https://doi.org/10.3390/ijms141123086 - 21 Nov 2013

Cited by 166 | Viewed by 11601

Abstract

The let-7 family is the second microRNA found in C. elegans. Recent researches have found it is highly expressed in the cardiovascular system. Studies have revealed the aberrant expression of let-7 members in cardiovascular diseases, such as heart hypertrophy, cardiac fibrosis, dilated [...] Read more.

The let-7 family is the second microRNA found in C. elegans. Recent researches have found it is highly expressed in the cardiovascular system. Studies have revealed the aberrant expression of let-7 members in cardiovascular diseases, such as heart hypertrophy, cardiac fibrosis, dilated cardiomyopathy (DCM), myocardial infarction (MI), arrhythmia, angiogenesis, atherosclerosis, and hypertension. Let-7 also participates in cardiovascular differentiation of embryonic stem cells. TLR4, LOX-1, Bcl-xl and AGO1 are by now the identified target genes of let-7. The circulating let-7b is suspected to be the biomarker of acute MI and let-7i, the biomarker of DCM. Further studies are necessary for identifying the gene targets and signaling pathways of let-7 in cardiovascular diseases. Let-7 might be a potential therapeutic target for cardiovascular diseases. This review focuses on the research progresses regarding the roles of let-7 in cardiovascular development and diseases. Full article

(This article belongs to the Section Biochemistry)

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Open AccessReview

Nutraceuticals: Potential for Chondroprotection and Molecular Targeting of Osteoarthritis

by Daniel J. Leong, Marwa Choudhury, David M. Hirsh, John A. Hardin, Neil J. Cobelli and Hui B. Sun

Int. J. Mol. Sci. 2013, 14(11), 23063-23085; https://doi.org/10.3390/ijms141123063 - 21 Nov 2013

Cited by 61 | Viewed by 14413

Abstract

Osteoarthritis (OA) is a degenerative joint disease and a leading cause of adult disability. There is no cure for OA, and no effective treatments which arrest or slow its progression. Current pharmacologic treatments such as analgesics may improve pain relief but do not [...] Read more.

Osteoarthritis (OA) is a degenerative joint disease and a leading cause of adult disability. There is no cure for OA, and no effective treatments which arrest or slow its progression. Current pharmacologic treatments such as analgesics may improve pain relief but do not alter OA disease progression. Prolonged consumption of these drugs can result in severe adverse effects. Given the nature of OA, life-long treatment will likely be required to arrest or slow its progression. Consequently, there is an urgent need for OA disease-modifying therapies which also improve symptoms and are safe for clinical use over long periods of time. Nutraceuticals—food or food products that provide medical or health benefits, including the prevention and/or treatment of a disease—offer not only favorable safety profiles, but may exert disease- and symptom-modification effects in OA. Forty-seven percent of OA patients use alternative medications, including nutraceuticals. This review will overview the efficacy and mechanism of action of commonly used nutraceuticals, discuss recent experimental and clinical data on the effects of select nutraceuticals, such as phytoflavonoids, polyphenols, and bioflavonoids on OA, and highlight their known molecular actions and limitations of their current use. We will conclude with a proposed novel nutraceutical-based molecular targeting strategy for chondroprotection and OA treatment. Full article

(This article belongs to the Special Issue The Chondrocyte Phenotype in Cartilage Biology)

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Open AccessArticle

Oxidative Stress/Angiotensinogen/Renin-Angiotensin System Axis in Patients with Diabetic Nephropathy

by Masumi Kamiyama, Maki Urushihara, Takashi Morikawa, Yoshio Konishi, Masahito Imanishi, Akira Nishiyama and Hiroyuki Kobori

Int. J. Mol. Sci. 2013, 14(11), 23045-23062; https://doi.org/10.3390/ijms141123045 - 21 Nov 2013

Cited by 59 | Viewed by 7761

Abstract

Although recent studies have proven that renin-angiotensin system (RAS) blockades retard the progression of diabetic nephropathy, the detailed mechanisms of their reno-protective effects on the development of diabetic nephropathy remain uncertain. In rodent models, it has been reported that reactive oxygen species (ROS) [...] Read more.

Although recent studies have proven that renin-angiotensin system (RAS) blockades retard the progression of diabetic nephropathy, the detailed mechanisms of their reno-protective effects on the development of diabetic nephropathy remain uncertain. In rodent models, it has been reported that reactive oxygen species (ROS) are important for intrarenal angiotensinogen (AGT) augmentation in the progression of diabetic nephropathy. However, no direct evidence is available to demonstrate that AGT expression is enhanced in the kidneys of patients with diabetes. To examine whether the expression levels of ROS- and RAS-related factors in kidneys are increased with the progression of diabetic nephropathy, biopsied samples from 8 controls and 27 patients with type 2 diabetes were used. After the biopsy, these patients were diagnosed with minor glomerular abnormality or diabetes mellitus by clinical and pathological findings. The intensities of AGT, angiotensin II (Ang II), 4-hydroxy-2-nonenal (4-HNE), and heme oxygenase-1 (HO-1) were examined by fluorescence in situ hybridization and/or immunohistochemistry. Expression levels were greater in patients with diabetes than in control subjects. Moreover, the augmented intrarenal AGT mRNA expression paralleled renal dysfunction in patients with diabetes. These data suggest the importance of the activated oxidative stress/AGT/RAS axis in the pathogenesis of diabetic nephropathy. Full article

(This article belongs to the Special Issue Oxidative Stress and Ageing)

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Open AccessArticle

Nano-Nutrition of Chicken Embryos. The Effect of in Ovo Administration of Diamond Nanoparticles and l-Glutamine on Molecular Responses in Chicken Embryo Pectoral Muscles

by Marta Grodzik, Filip Sawosz, Ewa Sawosz, Anna Hotowy, Mateusz Wierzbicki, Marta Kutwin, Sławomir Jaworski and André Chwalibog

Int. J. Mol. Sci. 2013, 14(11), 23033-23044; https://doi.org/10.3390/ijms141123033 - 20 Nov 2013

Cited by 37 | Viewed by 7415

Abstract

It has been demonstrated that the content of certain amino acids in eggs is not sufficient to fully support embryonic development. One possibility to supply the embryo with extra nutrients and energy is in ovo administration of nutrients. Nanoparticles of diamond are highly [...] Read more.

It has been demonstrated that the content of certain amino acids in eggs is not sufficient to fully support embryonic development. One possibility to supply the embryo with extra nutrients and energy is in ovo administration of nutrients. Nanoparticles of diamond are highly biocompatible non-toxic carbonic structures, and we hypothesized that bio-complexes of diamond nanoparticles with l-glutamine may affect molecular responses in breast muscle. The objective of the investigation was to evaluate the effect of diamond nanoparticle (ND) and l-glutamine (Gln) on expression of growth and differentiation factors of chicken embryo pectoral muscles. ND, Gln, and Gln/ND solutions (50 mg/L) were injected into fertilized broiler chicken eggs at the beginning of embryogenesis. Muscle tissue was dissected at day 20 of incubation and analysed for gene expression of FGF2, VEGF-A, and MyoD1. ND and especially Gln/ND up-regulated expression of genes related to muscle cell proliferation (FGF2) and differentiation (MyoD1). Furthermore, the ratio between FGF2 and MyoD1 was highest in the Gln/ND group. At the end of embryogenesis, Gln/ND enhanced both proliferation and differentiation of pectoral muscle cells and differentiation dominated over proliferation. These preliminary results suggest that the bio-complex of glutamine and diamond nanoparticles may accelerate growth and maturation of muscle cells. Full article

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Open AccessReview

Pathogenesis of Chronic Cardiorenal Syndrome: Is There a Role for Oxidative Stress?

by Speranza Rubattu, Silvia Mennuni, Marco Testa, Mara Mennuni, Giorgia Pierelli, Beniamino Pagliaro, Erica Gabriele, Roberta Coluccia, Camillo Autore and Massimo Volpe

Int. J. Mol. Sci. 2013, 14(11), 23011-23032; https://doi.org/10.3390/ijms141123011 - 20 Nov 2013

Cited by 66 | Viewed by 13922

Abstract

Cardiorenal syndrome is a frequently encountered clinical condition when the dysfunction of either the heart or kidneys amplifies the failure progression of the other organ. Complex biochemical, hormonal and hemodynamic mechanisms underlie the development of cardiorenal syndrome. Both in vitro and experimental studies [...] Read more.

Cardiorenal syndrome is a frequently encountered clinical condition when the dysfunction of either the heart or kidneys amplifies the failure progression of the other organ. Complex biochemical, hormonal and hemodynamic mechanisms underlie the development of cardiorenal syndrome. Both in vitro and experimental studies have identified several dysregulated pathways in heart failure and in chronic kidney disease that lead to increased oxidative stress. A decrease in mitochondrial oxidative metabolism has been reported in cardiomyocytes during heart failure. This is balanced by a compensatory increase in glucose uptake and glycolysis with consequent decrease in myocardial ATP content. In the kidneys, both NADPH oxidase and mitochondrial metabolism are important sources of TGF-β1-induced cellular ROS. NOX-dependent oxidative activation of transcription factors such as NF-kB and c-jun leads to increased expression of renal target genes (phospholipaseA2, MCP-1 and CSF-1, COX-2), thus contributing to renal interstitial fibrosis and inflammation. In the present article, we postulate that, besides contributing to both cardiac and renal dysfunction, increased oxidative stress may also play a crucial role in cardiorenal syndrome development and progression. In particular, an imbalance between the renin-angiotensin-aldosterone system, the sympathetic nervous system, and inflammation may favour cardiorenal syndrome through an excessive oxidative stress production. This article also discusses novel therapeutic strategies for their potential use in the treatment of patients affected by cardiorenal syndrome. Full article

(This article belongs to the Special Issue Oxidative Stress in Cardiovascular Disease)

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Open AccessArticle

Alteration of Tight Junction Gene Expression by Calcium- and Vitamin D-Deficient Diet in the Duodenum of Calbindin-Null Mice

by Inho Hwang, Hyun Yang, Hong-Seok Kang, Changhwan Ahn, Eui-Ju Hong, Beum-Soo An and Eui-Bae Jeung

Int. J. Mol. Sci. 2013, 14(11), 22997-23010; https://doi.org/10.3390/ijms141122997 - 20 Nov 2013

Cited by 26 | Viewed by 7120

Abstract

Calcium absorption is regulated by both active (transcellular) and passive (paracellular) pathways. Although each pathway has been studied, correlations between the two pathways have not been well elucidated. In previous investigations, the critical transcellular proteins, calbindin-D_9k (CaBP-9k) and -D_28k (CaBP-28k), were [...] Read more.

Calcium absorption is regulated by both active (transcellular) and passive (paracellular) pathways. Although each pathway has been studied, correlations between the two pathways have not been well elucidated. In previous investigations, the critical transcellular proteins, calbindin-D_9k (CaBP-9k) and -D_28k (CaBP-28k), were shown to affect other transcellular pathways by buffering intracellular calcium concentrations. The rate of paracellular calcium transport in the duodenum is generally determined by the expression of tight junction genes. In the present study, the effect of dietary calcium and/or vitamin D supplementation on the expression of tight junction genes (occludin, ZO-1 and claudin 2, 10b, 12 and 15) in the duodenum of CaBP-9k- and/or -28k-deficient mice was examined. With a normal diet, the expression of most tight junction genes in the duodenum was significantly increased in CaBP-9k knockout (KO) mice compared to wild-type (WT) animals. With a calcium- and vitamin D-deficient diet, tight junction gene expression was significantly decreased in the duodenum of the CaBP-9k KO mice. These findings suggest that expression of paracellular tight junction genes is regulated by transcellular CaBP proteins, suggesting that active and passive calcium transport pathways may function cooperatively. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Differential Proteomic Analysis of Anthers between Cytoplasmic Male Sterile and Maintainer Lines in Capsicum annuum L.

by Zhiming Wu, Jiaowen Cheng, Cheng Qin, Zhiqun Hu, Caixia Yin and Kailin Hu

Int. J. Mol. Sci. 2013, 14(11), 22982-22996; https://doi.org/10.3390/ijms141122982 - 20 Nov 2013

Cited by 53 | Viewed by 8259

Abstract

Cytoplasmic male sterility (CMS), widely used in the production of hybrid seeds, is a maternally inherited trait resulting in a failure to produce functional pollen. In order to identify some specific proteins associated with CMS in pepper, two-dimensional gel electrophoresis (2-DE) was applied [...] Read more.

Cytoplasmic male sterility (CMS), widely used in the production of hybrid seeds, is a maternally inherited trait resulting in a failure to produce functional pollen. In order to identify some specific proteins associated with CMS in pepper, two-dimensional gel electrophoresis (2-DE) was applied to proteomic analysis of anthers/buds between a CMS line (designated NA3) and its maintainer (designated NB3) in Capsicum annuum L. Thirty-three spots showed more than 1.5-fold in either CMS or its maintainer. Based on mass spectrometry, 27 spots representing 23 distinct proteins in these 33 spots were identified. Proteins down-regulated in CMS anthers/buds includes ATP synthase D chain, formate dehydrogenase, alpha-mannosidas, RuBisCO large subunit-binding protein subunit beta, chloroplast manganese stabilizing protein-II, glutathione S-transferase, adenosine kinase isoform 1T-like protein, putative DNA repair protein RAD23-4, putative caffeoyl-CoA 3-O-methyltransferase, glutamine synthetase (GS), annexin Cap32, glutelin, allene oxide cyclase, etc. In CMS anthers/buds, polyphenol oxidase, ATP synthase subunit beta, and actin are up-regulated. It was predicted that male sterility in NA3 might be related to energy metabolism turbulence, excessive ethylene synthesis, and suffocation of starch synthesis. The present study lays a foundation for future investigations of gene functions associated with pollen development and cytoplasmic male sterility, and explores the molecular mechanism of CMS in pepper. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Nox Gene Expression and Cytochemical Localization of Hydrogen Peroxide in Polyporus umbellatus Sclerotial Formation

by Yong-Mei Xing, Juan Chen, Chao Song, Ying-Ying Liu, Shun-Xing Guo and Chun-Lan Wang

Int. J. Mol. Sci. 2013, 14(11), 22967-22981; https://doi.org/10.3390/ijms141122967 - 20 Nov 2013

Cited by 22 | Viewed by 6415

Abstract

The effect of temperature shift on Polyporus umbellatus sclerotial development was investigated. Micromorphology of the sclerotia was observed by using scanning electron microscopy (SEM). The cytochemical localization of H₂O₂ expressed as CeCl₃ deposition at the subcellular level was observed [...] Read more.

The effect of temperature shift on Polyporus umbellatus sclerotial development was investigated. Micromorphology of the sclerotia was observed by using scanning electron microscopy (SEM). The cytochemical localization of H₂O₂ expressed as CeCl₃ deposition at the subcellular level was observed by using transmission electron microscopy (TEM). Nox gene expression in sclerotia and mycelia was detected by quantitative real-time PCR (qRT-PCR) analysis. In addition, superoxide dismutase (SOD) and catalase (CAT) specific activities increased during sclerotial development and decreased after the antioxidant diphenyleneiodonium (DPI) was used. Results indicated that the temperature shift treatment induced P. umbellatus sclerotial formation. Compared with the mycelia, the Nox gene was respectively upregulated by 10.577-, 30.984- and 25.469-fold in the sclerotia of SI, SD and SM stages respectively. During the sclerotial formation, H₂O₂ accumulation was observed in the cell walls or around the organelle membranes of the mycelial cells. The antioxidant DPI decreased the generation of H₂O₂ in mycelial cells. The specific activity of SOD and CAT levels was decreased significantly by DPI. The activity of the two antioxidant enzymes in the mycelia increased much more during sclerotial formation (p < 0.05). Oxidative stress was closely associated with sclerotial development in P. umbellatus induced by temperature shift treatment. Full article

(This article belongs to the Section Biochemistry)

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Open AccessReview

Nonalcoholic Fatty Liver: A Possible New Target for Type 2 Diabetes Prevention and Treatment

by Barbara Fruci, Stefania Giuliano, Angela Mazza, Roberta Malaguarnera and Antonino Belfiore

Int. J. Mol. Sci. 2013, 14(11), 22933-22966; https://doi.org/10.3390/ijms141122933 - 20 Nov 2013

Cited by 89 | Viewed by 11380

Abstract

Non-alcoholic fatty liver disease (NAFLD) is the most common liver disorder worldwide. Several lines of evidence have indicated a pathogenic role of insulin resistance, and a strong association with type 2 diabetes (T2MD) and metabolic syndrome. Importantly, NAFLD appears to enhance the risk [...] Read more.

Non-alcoholic fatty liver disease (NAFLD) is the most common liver disorder worldwide. Several lines of evidence have indicated a pathogenic role of insulin resistance, and a strong association with type 2 diabetes (T2MD) and metabolic syndrome. Importantly, NAFLD appears to enhance the risk for T2MD, as well as worsen glycemic control and cardiovascular disease in diabetic patients. In turn, T2MD may promote NAFLD progression. The opportunity to take into account NAFLD in T2MD prevention and care has stimulated several clinical studies in which antidiabetic drugs, such as metformin, thiazolidinediones, GLP-1 analogues and DPP-4 inhibitors have been evaluated in NAFLD patients. In this review, we provide an overview of preclinical and clinical evidences on the possible efficacy of antidiabetic drugs in NAFLD treatment. Overall, available data suggest that metformin has beneficial effects on body weight reduction and metabolic parameters, with uncertain effects on liver histology, while pioglitazone may improve liver histology. Few data, mostly preclinical, are available on DPP4 inhibitors and GLP-1 analogues. The heterogeneity of these studies and the small number of patients do not allow for firm conclusions about treatment guidelines, and further randomized, controlled studies are needed. Full article

(This article belongs to the Special Issue Non-Alcoholic Fatty Liver Disease Research)

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Open AccessReview

New Insights into Functional Roles of the Polypyrimidine Tract-Binding Protein

by Maria Grazia Romanelli, Erica Diani and Patricia Marie-Jeanne Lievens

Int. J. Mol. Sci. 2013, 14(11), 22906-22932; https://doi.org/10.3390/ijms141122906 - 20 Nov 2013

Cited by 95 | Viewed by 15220

Abstract

Polypyrimidine Tract Binding Protein (PTB) is an intensely studied RNA binding protein involved in several post-transcriptional regulatory events of gene expression. Initially described as a pre-mRNA splicing regulator, PTB is now widely accepted as a multifunctional protein shuttling between nucleus and cytoplasm. Accordingly, [...] Read more.

Polypyrimidine Tract Binding Protein (PTB) is an intensely studied RNA binding protein involved in several post-transcriptional regulatory events of gene expression. Initially described as a pre-mRNA splicing regulator, PTB is now widely accepted as a multifunctional protein shuttling between nucleus and cytoplasm. Accordingly, PTB can interact with selected RNA targets, structural elements and proteins. There is increasing evidence that PTB and its paralog PTBP2 play a major role as repressors of alternatively spliced exons, whose transcription is tissue-regulated. In addition to alternative splicing, PTB is involved in almost all steps of mRNA metabolism, including polyadenylation, mRNA stability and initiation of protein translation. Furthermore, it is well established that PTB recruitment in internal ribosome entry site (IRES) activates the translation of picornaviral and cellular proteins. Detailed studies of the structural properties of PTB have contributed to our understanding of the mechanism of RNA binding by RNA Recognition Motif (RRM) domains. In the present review, we will describe the structural properties of PTB, its paralogs and co-factors, the role in post-transcriptional regulation and actions in cell differentiation and pathogenesis. Defining the multifunctional roles of PTB will contribute to the understanding of key regulatory events in gene expression. Full article

(This article belongs to the Special Issue Post-Transcriptional Gene Regulation by Ribonucleoprotein Complexes)

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Open AccessArticle

Molecular Cloning and Characterization of a P-Glycoprotein from the Diamondback Moth, Plutella xylostella (Lepidoptera: Plutellidae)

by Lixia Tian, Jiaqiang Yang, Wenjie Hou, Baoyun Xu, Wen Xie, Shaoli Wang, Youjun Zhang, Xuguo Zhou and Qingjun Wu

Int. J. Mol. Sci. 2013, 14(11), 22891-22905; https://doi.org/10.3390/ijms141122891 - 20 Nov 2013

Cited by 28 | Viewed by 7064

Abstract

Macrocyclic lactones such as abamectin and ivermectin constitute an important class of broad-spectrum insecticides. Widespread resistance to synthetic insecticides, including abamectin and ivermectin, poses a serious threat to the management of diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), a major pest of cruciferous [...] Read more.

Macrocyclic lactones such as abamectin and ivermectin constitute an important class of broad-spectrum insecticides. Widespread resistance to synthetic insecticides, including abamectin and ivermectin, poses a serious threat to the management of diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), a major pest of cruciferous plants worldwide. P-glycoprotein (Pgp), a member of the ABC transporter superfamily, plays a crucial role in the removal of amphiphilic xenobiotics, suggesting a mechanism for drug resistance in target organisms. In this study, PxPgp1, a putative Pgp gene from P. xylostella, was cloned and characterized. The open reading frame (ORF) of PxPgp1 consists of 3774 nucleotides, which encodes a 1257-amino acid peptide. The deduced PxPgp1 protein possesses structural characteristics of a typical Pgp, and clusters within the insect ABCB1. PxPgp1 was expressed throughout all developmental stages, and showed the highest expression level in adult males. PxPgp1 was highly expressed in midgut, malpighian tubules and testes. Elevated expression of PxPgp1 was observed in P. xylostella strains after they were exposed to the abamectin treatment. In addition, the constitutive expressions of PxPgp1 were significantly higher in laboratory-selected and field-collected resistant strains in comparison to their susceptible counterpart. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Hydration of AMP and ATP Molecules in Aqueous Solution and Solid Films

by Dzhigangir Faizullin, Nataliya Zakharchenko, Yuriy Zuev, Alexander Puzenko, Evgeniya Levy and Yuri Feldman

Int. J. Mol. Sci. 2013, 14(11), 22876-22890; https://doi.org/10.3390/ijms141122876 - 20 Nov 2013

Cited by 10 | Viewed by 6023

Abstract

Water enables life and plays a critical role in biology. Considered as a versatile and adaptive component of the cell, water engages a wide range of biomolecular interactions. An organism can exist and function only if its self-assembled molecular structures are hydrated. It [...] Read more.

Water enables life and plays a critical role in biology. Considered as a versatile and adaptive component of the cell, water engages a wide range of biomolecular interactions. An organism can exist and function only if its self-assembled molecular structures are hydrated. It was shown recently that switching of AMP/ATP binding to the insulin-independent glucose transporter Human Erythrocyte Glucose Transport Protein (GLUT1) may greatly influence the ratio of bulk and bound water during regulation of glucose uptake by red blood cells. In this paper, we present the results on the hydration properties of AMP/ATP obtained by means of dielectric spectroscopy in aqueous solution and for fully ionized forms in solid amorphous films with the help of gravimetric studies. Full article

(This article belongs to the Special Issue Frontiers of Micro-Spectroscopy in Biological Applications)

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Open AccessArticle

The Changes in mGluR2 and mGluR7 Expression in Rat Medial Vestibular Nucleus and Flocculus Following Unilateral Labyrinthectomy

by Wen Zhou, Liu-Qing Zhou, Su-Lin Zhang, Bo Liu, Yang-Ming Leng, Ren-Hong Zhou and Wei-Jia Kong

Int. J. Mol. Sci. 2013, 14(11), 22857-22875; https://doi.org/10.3390/ijms141122857 - 20 Nov 2013

Cited by 6 | Viewed by 6447

Abstract

It is known that the medial vestibular nucleus (MVN) and the cerebellar flocculus are the key areas, which contribute to the behavioral recovery (“vestibular compensation”) after unilateral labyrinthectomy (UL). In these areas, how the genetic activities of the metabotropic glutamate receptors mGluR2 and [...] Read more.

It is known that the medial vestibular nucleus (MVN) and the cerebellar flocculus are the key areas, which contribute to the behavioral recovery (“vestibular compensation”) after unilateral labyrinthectomy (UL). In these areas, how the genetic activities of the metabotropic glutamate receptors mGluR2 and mGluR7 performance after UL is unknown. With the means of quantitative real-time PCR, Western blotting, and immunohistochemistry, we analyzed the expression of mGluR2 and mGluR7 in the bilateral MVN and the flocculus of rats in different stages after UL (the 1st, 3rd, and 7th day). Our results show that in the MVN, the mRNA, and protein expressions of mGluR7 were ipsilaterally decreased at the 1st day following UL. However, in the MVN, no change was observed in the mRNA and protein expressions of mGluR2. On the other hand, the mRNA and protein expression of mGluR2 were enhanced in the ipsilateral flocculus at the 1st day following UL, while in the flocculus no change was shown in mGluR7 mRNA and protein expressions. Our results suggest that mGluR2 and mGluR7 may contribute to the early rebalancing of spontaneous resting activity in the MVN. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Identification of Novel Small Molecules as Inhibitors of Hepatitis C Virus by Structure-Based Virtual Screening

by Jing Li, Xian Liu, Shanshan Li, Yulan Wang, Nannan Zhou, Cheng Luo, Xiaomin Luo, Mingyue Zheng, Hualiang Jiang and Kaixian Chen

Int. J. Mol. Sci. 2013, 14(11), 22845-22856; https://doi.org/10.3390/ijms141122845 - 20 Nov 2013

Cited by 16 | Viewed by 8389

Abstract

Hepatitis C virus (HCV) NS3/NS4A serine protease is essential for viral replication, which is regarded as a promising drug target for developing direct-acting anti-HCV agents. In this study, sixteen novel compounds with cell-based HCV replicon activity ranging from 3.0 to 28.2 μM (IC [...] Read more.

Hepatitis C virus (HCV) NS3/NS4A serine protease is essential for viral replication, which is regarded as a promising drug target for developing direct-acting anti-HCV agents. In this study, sixteen novel compounds with cell-based HCV replicon activity ranging from 3.0 to 28.2 μM (IC₅₀) were successfully identified by means of structure-based virtual screening. Compound 5 and compound 11, with an IC₅₀ of 3.0 μM and 5.1 μM, respectively, are the two most potent molecules with low cytotoxicity. Full article

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

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2808 KiB

Open AccessArticle

Tuning Fluidic Resistance via Liquid Crystal Microfluidics

by Anupam Sengupta

Int. J. Mol. Sci. 2013, 14(11), 22826-22844; https://doi.org/10.3390/ijms141122826 - 19 Nov 2013

Cited by 21 | Viewed by 7815

Abstract

Flow of molecularly ordered fluids, like liquid crystals, is inherently coupled with the average local orientation of the molecules, or the director. The anisotropic coupling—typically absent in isotropic fluids—bestows unique functionalities to the flowing matrix. In this work, we harness this anisotropy to [...] Read more.

Flow of molecularly ordered fluids, like liquid crystals, is inherently coupled with the average local orientation of the molecules, or the director. The anisotropic coupling—typically absent in isotropic fluids—bestows unique functionalities to the flowing matrix. In this work, we harness this anisotropy to pattern different pathways to tunable fluidic resistance within microfluidic devices. We use a nematic liquid crystalline material flowing in microchannels to demonstrate passive and active modulation of the flow resistance. While appropriate surface anchoring conditions—which imprint distinct fluidic resistances within microchannels under similar hydrodynamic parameters—act as passive cues, an external field, e.g., temperature, is used to actively modulate the flow resistance in the microfluidic device. We apply this simple concept to fabricate basic fluidic circuits, which can be hierarchically extended to create complex resistance networks, without any additional design or morphological patterning of the microchannels. Full article

(This article belongs to the Special Issue Experimental and Theoretical Studies of Liquid Crystalline Materials: Where Do We Stand after 120 Years?)

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163 KiB

Open AccessArticle

Usefulness of Plasma YKL-40 in Management of Community-Acquired Pneumonia Severity in Patients

by Hsiang-Ling Wang, Pei-Ching Hsiao, Hsiu-Ting Tsai, Chao-Bin Yeh and Shun-Fa Yang

Int. J. Mol. Sci. 2013, 14(11), 22817-22825; https://doi.org/10.3390/ijms141122817 - 19 Nov 2013

Cited by 23 | Viewed by 5821

Abstract

Plasma YKL-40 level has been reported as playing a significant role in community-acquired pneumonia (CAP). However, the correlation between plasma level of YKL-40 and the severity of CAP has not been reported. This study identifies the relationship between plasma level changes of the [...] Read more.

Plasma YKL-40 level has been reported as playing a significant role in community-acquired pneumonia (CAP). However, the correlation between plasma level of YKL-40 and the severity of CAP has not been reported. This study identifies the relationship between plasma level changes of the YKL-40 gene in adult patients hospitalized with CAP. The ELISA was used to measure the plasma YKL-40 level from 61 adult CAP patients before and after antibiotic treatment and from 60 healthy controls. The plasma YKL-40 levels were significantly increased in patients with CAP compared to normal controls. Moreover, the plasma concentration of YKL-40 correlated with the severity of CAP based on the pneumonia severity index (PSI) score (r = 0.630, p < 0.001), the CURB-65 (confusion, uremia, respiratory rate, BP, age 65 years) score (r = 0.640, p < 0.001), the Acute Physiology And Chronic Health Evaluation II (APACHE II) score (r = 0.539, p < 0.001) and length of hospital stay (r = 0.321, p = 0.011), respectively. In conclusion, plasma YKL-40 may play a role in the diagnosis and clinical assessment of CAP severity, which could potentially guide the development of treatment strategies. Full article

(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)

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Open AccessReview

ADAR Enzyme and miRNA Story: A Nucleotide that Can Make the Difference

by Sara Tomaselli, Barbara Bonamassa, Anna Alisi, Valerio Nobili, Franco Locatelli and Angela Gallo

Int. J. Mol. Sci. 2013, 14(11), 22796-22816; https://doi.org/10.3390/ijms141122796 - 19 Nov 2013

Cited by 46 | Viewed by 13030

Abstract

Adenosine deaminase acting on RNA (ADAR) enzymes convert adenosine (A) to inosine (I) in double-stranded (ds) RNAs. Since Inosine is read as Guanosine, the biological consequence of ADAR enzyme activity is an A/G conversion within RNA molecules. A-to-I editing events can occur on [...] Read more.

Adenosine deaminase acting on RNA (ADAR) enzymes convert adenosine (A) to inosine (I) in double-stranded (ds) RNAs. Since Inosine is read as Guanosine, the biological consequence of ADAR enzyme activity is an A/G conversion within RNA molecules. A-to-I editing events can occur on both coding and non-coding RNAs, including microRNAs (miRNAs), which are small regulatory RNAs of ~20–23 nucleotides that regulate several cell processes by annealing to target mRNAs and inhibiting their translation. Both miRNA precursors and mature miRNAs undergo A-to-I RNA editing, affecting the miRNA maturation process and activity. ADARs can also edit 3' UTR of mRNAs, further increasing the interplay between mRNA targets and miRNAs. In this review, we provide a general overview of the ADAR enzymes and their mechanisms of action as well as miRNA processing and function. We then review the more recent findings about the impact of ADAR-mediated activity on the miRNA pathway in terms of biogenesis, target recognition, and gene expression regulation. Full article

(This article belongs to the Special Issue Regulation by non-coding RNAs 2013)

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Open AccessCommunication

Identification of Novel Pepper Genes Involved in Bax- or INF1-Mediated Cell Death Responses by High-Throughput Virus-Induced Gene Silencing

by Jeong Hee Lee, Young Cheol Kim, Doil Choi and Jeong Mee Park

Int. J. Mol. Sci. 2013, 14(11), 22782-22795; https://doi.org/10.3390/ijms141122782 - 19 Nov 2013

Cited by 8 | Viewed by 7701

Abstract

Hot pepper is one of the economically important crops in Asia. A large number of gene sequences, including expressed sequence tag (EST) and genomic sequences are publicly available. However, it is still a daunting task to determine gene function due to difficulties in [...] Read more.

Hot pepper is one of the economically important crops in Asia. A large number of gene sequences, including expressed sequence tag (EST) and genomic sequences are publicly available. However, it is still a daunting task to determine gene function due to difficulties in genetic modification of a pepper plants. Here, we show the application of the virus-induced gene silencing (VIGS) repression for the study of 459 pepper ESTs selected as non-host pathogen-induced cell death responsive genes from pepper microarray experiments in Nicotiana benthamiana. Developmental abnormalities in N. benthamiana plants are observed in the 32 (7%) pepper ESTs-silenced plants. Aberrant morphological phenotypes largely comprised of three groups: stunted, abnormal leaf, and dead. In addition, by employing the combination of VIGS and Agrobacterium-mediated transient assays, we identified novel pepper ESTs that involved in Bax or INF1-mediated cell death responses. Silencing of seven pepper ESTs homologs suppressed Bax or INF1-induced cell death, five of which suppressed both cell death responses in N. benthamiana. The genes represented by these five ESTs encode putative proteins with functions in endoplasmic reticulum (ER) stress and lipid signaling. The genes represented by the other two pepper ESTs showing only Bax-mediated cell death inhibition encode a CCCH-type zinc finger protein containing an ankyrin-repeat domain and a probable calcium-binding protein, CML30-like. Taken together, we effectively isolated novel pepper clones that are involved in hypersensitive response (HR)-like cell death using VIGS, and identified silenced clones that have different responses to Bax and INF1 exposure, indicating separate signaling pathways for Bax- and INF1-mediated cell death. Full article

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

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Open AccessReview

Opportunities for Live Cell FT-Infrared Imaging: Macromolecule Identification with 2D and 3D Localization

by Eric C. Mattson, Ebrahim Aboualizadeh, Marie E. Barabas, Cheryl L. Stucky and Carol J. Hirschmugl

Int. J. Mol. Sci. 2013, 14(11), 22753-22781; https://doi.org/10.3390/ijms141122753 - 19 Nov 2013

Cited by 26 | Viewed by 8431

Abstract

Infrared (IR) spectromicroscopy, or chemical imaging, is an evolving technique that is poised to make significant contributions in the fields of biology and medicine. Recent developments in sources, detectors, measurement techniques and speciman holders have now made diffraction-limited Fourier transform infrared (FTIR) imaging [...] Read more.

Infrared (IR) spectromicroscopy, or chemical imaging, is an evolving technique that is poised to make significant contributions in the fields of biology and medicine. Recent developments in sources, detectors, measurement techniques and speciman holders have now made diffraction-limited Fourier transform infrared (FTIR) imaging of cellular chemistry in living cells a reality. The availability of bright, broadband IR sources and large area, pixelated detectors facilitate live cell imaging, which requires rapid measurements using non-destructive probes. In this work, we review advances in the field of FTIR spectromicroscopy that have contributed to live-cell two and three-dimensional IR imaging, and discuss several key examples that highlight the utility of this technique for studying the structure and chemistry of living cells. Full article

(This article belongs to the Special Issue Frontiers of Micro-Spectroscopy in Biological Applications)

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Open AccessArticle

Small Molecule Binding, Docking, and Characterization of the Interaction between Pth1 and Peptidyl-tRNA

by Mary C. Hames, Hana McFeeters, W. Blake Holloway, Christopher B. Stanley, Volker S. Urban and Robert L. McFeeters

Int. J. Mol. Sci. 2013, 14(11), 22741-22752; https://doi.org/10.3390/ijms141122741 - 19 Nov 2013

Cited by 10 | Viewed by 9632

Abstract

Bacterial Pth1 is essential for viability. Pth1 cleaves the ester bond between the peptide and nucleotide of peptidyl-tRNA generated from aborted translation, expression of mini-genes, and short ORFs. We have determined the shape of the Pth1:peptidyl-tRNA complex using small angle neutron scattering. Binding [...] Read more.

Bacterial Pth1 is essential for viability. Pth1 cleaves the ester bond between the peptide and nucleotide of peptidyl-tRNA generated from aborted translation, expression of mini-genes, and short ORFs. We have determined the shape of the Pth1:peptidyl-tRNA complex using small angle neutron scattering. Binding of piperonylpiperazine, a small molecule constituent of a combinatorial synthetic library common to most compounds with inhibitory activity, was mapped to Pth1 via NMR spectroscopy. We also report computational docking results, modeling piperonylpiperazine binding based on chemical shift perturbation mapping. Overall these studies promote Pth1 as a novel antibiotic target, contribute to understanding how Pth1 interacts with its substrate, advance the current model for cleavage, and demonstrate feasibility of small molecule inhibition. Full article

(This article belongs to the Collection Computational, Structural and Spectroscopic Studies of Enzyme Mechanisms, Inhibition and Dynamics)

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Open AccessArticle

Genes Responsive to Low-Intensity Pulsed Ultrasound in MC3T3-E1 Preosteoblast Cells

by Yoshiaki Tabuchi, Yuuki Sugahara, Mika Ikegame, Nobuo Suzuki, Kei-ichiro Kitamura and Takashi Kondo

Int. J. Mol. Sci. 2013, 14(11), 22721-22740; https://doi.org/10.3390/ijms141122721 - 18 Nov 2013

Cited by 18 | Viewed by 7544

Abstract

Although low-intensity pulsed ultrasound (LIPUS) has been shown to enhance bone fracture healing, the underlying mechanism of LIPUS remains to be fully elucidated. Here, to better understand the molecular mechanism underlying cellular responses to LIPUS, we investigated gene expression profiles in mouse MC3T3-E1 [...] Read more.

Although low-intensity pulsed ultrasound (LIPUS) has been shown to enhance bone fracture healing, the underlying mechanism of LIPUS remains to be fully elucidated. Here, to better understand the molecular mechanism underlying cellular responses to LIPUS, we investigated gene expression profiles in mouse MC3T3-E1 preosteoblast cells exposed to LIPUS using high-density oligonucleotide microarrays and computational gene expression analysis tools. Although treatment of the cells with a single 20-min LIPUS (1.5 MHz, 30 mW/cm²) did not affect the cell growth or alkaline phosphatase activity, the treatment significantly increased the mRNA level of Bglap. Microarray analysis demonstrated that 38 genes were upregulated and 37 genes were downregulated by 1.5-fold or more in the cells at 24-h post-treatment. Ingenuity pathway analysis demonstrated that the gene network U (up) contained many upregulated genes that were mainly associated with bone morphology in the category of biological functions of skeletal and muscular system development and function. Moreover, the biological function of the gene network D (down), which contained downregulated genes, was associated with gene expression, the cell cycle and connective tissue development and function. These results should help to further clarify the molecular basis of the mechanisms of the LIPUS response in osteoblast cells. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Hsa-Let-7g miRNA Targets Caspase-3 and Inhibits the Apoptosis Induced by ox-LDL in Endothelial Cells

by Yefei Zhang, Naiyun Chen, Jihao Zhang and Yaling Tong

Int. J. Mol. Sci. 2013, 14(11), 22708-22720; https://doi.org/10.3390/ijms141122708 - 18 Nov 2013

Cited by 50 | Viewed by 7255

Abstract

It has been well confirmed ox-LDL plays key roles in the development of atherosclerosis via binding to LOX-1 and inducing apoptosis in vascular endothelial cells. Recent studies have shown ox-LDL can suppress microRNA has-let-7g, which in turn inhibits the ox-LDL induced apoptosis. However, [...] Read more.

It has been well confirmed ox-LDL plays key roles in the development of atherosclerosis via binding to LOX-1 and inducing apoptosis in vascular endothelial cells. Recent studies have shown ox-LDL can suppress microRNA has-let-7g, which in turn inhibits the ox-LDL induced apoptosis. However, details need to be uncovered. To determine the anti-atherosclerosis effect of microRNA has-let-7g, and to evaluate the possibility of CASP3 as an anti-atherosclerotic drug target by has-let-7g, the present study determined the role of hsa-let-7g miRNA in ox-LDL induced apoptosis in the vascular endothelial cells. We found that miRNA has-let-7g was suppressed during the ox-LDL-induced apoptosis in EAhy926 endothelial cells. In addition, overexpression of has-let-7g negatively regulated apoptosis in the endothelial cells by targeting caspase-3 expression. Therefore, miRNA let-7g may play important role in endothelial apoptosis and atherosclerosis. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Hyperoside Downregulates the Receptor for Advanced Glycation End Products (RAGE) and Promotes Proliferation in ECV304 Cells via the c-Jun N-Terminal Kinases (JNK) Pathway Following Stimulation by Advanced Glycation End-Products In Vitro

by Zhengyu Zhang, Mosha Silas Sethiel, Weizhi Shen, Sentai Liao and Yuxiao Zou

Int. J. Mol. Sci. 2013, 14(11), 22697-22707; https://doi.org/10.3390/ijms141122697 - 18 Nov 2013

Cited by 23 | Viewed by 6823

Abstract

Hyperoside is a major active constituent in many medicinal plants which are traditionally used in Chinese medicines for their neuroprotective, anti-inflammatory and antioxidative effects. The molecular mechanisms underlying these effects are unknown. In this study, quiescent ECV304 cells were treated in vitro with [...] Read more.

Hyperoside is a major active constituent in many medicinal plants which are traditionally used in Chinese medicines for their neuroprotective, anti-inflammatory and antioxidative effects. The molecular mechanisms underlying these effects are unknown. In this study, quiescent ECV304 cells were treated in vitro with advanced glycation end products (AGEs) in the presence or absence of hyperoside. The results demonstrated that AGEs induced c-Jun N-terminal kinases (JNK) activation and apoptosis in ECV304 cells. Hyperoside inhibited these effects and promoted ECV304 cell proliferation. Furthermore, hyperoside significantly inhibited RAGE expression in AGE-stimulated ECV304 cells, whereas knockdown of RAGE inhibited AGE-induced JNK activation. These results suggested that AGEs may promote JNK activation, leading to viability inhibition of ECV304 cells via the RAGE signaling pathway. These effects could be inhibited by hyperoside. Our findings suggest a novel role for hyperoside in the treatment and prevention of diabetes. Full article

(This article belongs to the Section Biochemistry)

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Int. J. Mol. Sci., Volume 14, Issue 11 (November 2013) – 116 articles , Pages 21202-23211

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