bluuebunny/crossref_metadata_2025 huggingface dataset:
Platyspondylic lethal dysplasia torrance type with a heterozygous mutation in the triple helical domain of COL2A1 in two sibs from phenotypically normal parents
Authors: Okamoto Toshio , Nagaya Ken , Asai Hiroko , Tsuchida Etsushi , Nohara Fumikatsu , Hayashi Tokitsugi , Yamashita Akiko , Nishimura Gen , Azuma Hiroshi
Published: June 2012

Heterozygous COL2A1 mutations create a group of skeletal dysplasias collectively termed type II collagenopathies. Sporadic cases of type II collagenopathies are almost exclusively caused by de novo mutations. Very few cases with intrafamilial recurrence due to germinal mosaicism have been known. We report here on a family in which a severe form of skeletal dysplasia was recurrent in two sibs whose phenotype was most consistent with platyspondylic lethal skeletal dysplasia Torrance type (PLSD‐T). A COL2A1 analysis showed that the two sibs had a heterozygous mutation in the encoded triple helical region of COL2A1, c.3545G>A (p.Gly1182Asp) in exon 50. The parents did not consent to a molecular analysis; however, the presence of the same mutation in the two sibs is proof of germinal mosaicism in one of the parents. PLSD‐T has been shown to arise from a heterozygous dominant negative COL2A1 mutation in the encoded C‐propeptide region. However, our observation suggests that the phenotype is also caused by a COL2A1 mutation in the encoded C‐terminal triple helical region. © 2012 Wiley Periodicals, Inc.
The t‐U‐V‐J model in cuprates: Strengths of the interactions
Authors: Koinov Z.G.
Published: June 2012

The t‐U‐V‐J model fits together three major parts of the superconductivity puzzle of the cuprite compounds: (i) it describes the opening of a d‐wave pairing gap, (ii) it is consistent with the fact that the basic pairing mechanism arises from the antiferromagnetic exchange correlations, and (iii) it takes into account the charge fluctuations associated with double occupancy of a site which play an essential role in doped systems. The strengths of the interactions U, V and J in YBa2Cu3O6.7 and La2‐xSrxCuO4 (x = 0.16) samples are obtained by requiring quantitative consistency between the angle‐resolved photoemission spectroscopy (ARPES) measurements, the sharp collective mode at the antiferromagnetic wave vector QAF=(π,π), and the observed inelastic neutron scattering resonance (INSR) positions of the incommensurate peaks at wave vectors Qδ = ((1 ± δ)π,π) and Qδ = (π(1 ± δ)π).
Photoredoxkatalyse mit sichtbarem Licht
Authors: Xuan Jun , Xiao Wen‐Jing
Published: June 2012

Organische Umsetzungen, die durch sichtbares Licht ausgelöst werden, finden seit einigen Jahren immer größere Aufmerksamkeit. Insbesondere im Hinblick auf Kosten, Sicherheit, Verfügbarkeit und Umweltfreundlichkeit ist die Entwicklung solcher photokatalytischer Reaktionen zur effizienten Herstellung von Feinchemikalien höchst wünschenswert. In diesem Kurzaufsatz werden die jüngsten Fortschritte auf diesem sich schnell entwickelnden Forschungsgebiet erörtert.
Human Masseter Muscle Fibers From the Elderly Express Less Neonatal Myosin Than Those of Young Adults
Authors: Cvetko Erika , Karen PetŘ , JanÁček JiŘí , KubínovÁ Lucie , Plasencia Ana LÓpez , Eržen Ida
Published: June 2012

In contrast to limb muscles where neonatal myosin (MyHC‐neo) is present only shortly after birth, adult masseter muscles contain a substantial portion of MyHC‐neo, which is coexpressed with mature MyHC isoforms. Changes in the numerical and area proportion of muscle fibers containing MyHC‐neo in masseter muscle with aging could be expected, based on previously reported findings that (i) developmental MyHC‐containing muscle fibers exhibit lower shortening velocities compared to fibers with exclusively fast MyHC isoforms and (ii) transformation toward faster phenotype occurs in elderly compared to young masseter muscle. In this study, we detected MyHC isoforms in the anterior superficial part of the human masseter muscle in a sufficiently large sample of young, middle‐aged, and elderly subjects to reveal age‐related changes in the coexpression of MyHC‐neo with adult MyHC isoforms. MyHC isoforms were visualized with immunoperoxidase method and the results were presented by (i) the area proportion of fibers containing particular MyHC isoforms and (ii) the numerical proportion of fiber types defined by MyHC‐1, ‐2a, ‐2x, and ‐neonatal isoform expression from a successive transverse sections. We found a lower numerical and area proportion of fibers expressing MyHC‐neo as well as a lower area proportion of fibers containing MyHC‐1 in elderly than in young subjects. We conclude that the diminished expression of MyHC‐neo with age could point to a lower regeneration capacity of masseter muscle in the elderly. Anat Rec, 2012. © 2012 Wiley Periodicals, Inc.
Dye‐Sensitized TiO2 Nanotube Solar Cells: Rational Structural and Surface Engineering on TiO2 Nanotubes
Authors: Wang Jun , Lin Zhiqun
Published: June 2012

Owing to well‐defined structural parameters and enhanced electronic properties, highly ordered TiO2 nanotube arrays have been employed to substitute TiO2 nanoparticles for use in dye‐sensitized solar cells. To further improve the performance of dye‐sensitized TiO2 nanotube solar cells, efforts have been directed toward the optimization of TiO2 photoanodes, dyes, electrolytes, and counter electrodes. Herein, we highlight recent progress in rational structural and surface engineering on anodic TiO2 nanotube arrays and their effects on improving the power conversion efficiency of dye‐sensitized TiO2 nanotube solar cells.
Protein interaction affinity determination by quantitative FRET technology
Authors: Song Yang , Rodgers V.G.J. , Schultz Jerome S. , Liao Jiayu
Published: June 2012

The dissociation constant, Kd, is an important parameter for characterizing protein–protein interaction affinities. SUMOylation is one of the important protein post‐translational modifications and it involves a multi‐step enzymatic cascade reaction, resulting in peptide activation and substrate conjugation. Multiple covalent and non‐covalent protein–protein interactions are involved in this cascade. Techniques involving Förster resonance energy transfer (FRET) have been widely used in biological studies in vitro and in vivo, and they are very powerful tools for elucidating protein interactions in many regulatory cascades. In our previous studies, we reported the attempt to develop a new method for the determination of the Kd by FRET assay using the interaction of SUMO1 and its E2 ligase, Ubc9 as a test system. However, the generality and specifications of this new method have not been fully determined. Here we report a systematic approach for determining the dissociation constant (Kd) in the SUMOylation cascade and for further sensitivity and accuracy testing by the FRET technology. From a FRET donor to acceptor concentration ratio range of 4–40, the Kds of SUMO1 and Ubc9 consistently agree well with values from surface plasmon resonance and isothermal titration calorimetry. These results demonstrate the high sensitivity and accuracy of the FRET‐based Kd determination approach. This technology, therefore, can be used in general for protein–protein interaction dissociation constant determination. Biotechnol. Bioeng. 2012; 109: 2875–2883. © 2012 Wiley Periodicals, Inc.
Growth kinetics of microalgae in microfluidic static droplet arrays
Authors: Dewan Alim , Kim Jihye , McLean Rebecca H. , Vanapalli Siva A. , Karim Muhammad Nazmul
Published: June 2012

We investigated growth kinetics of microalgae, Chlorella vulgaris, in immobilized arrays of nanoliter‐scale microfluidic drops. These static drop arrays enabled simultaneous monitoring of growth of single as well as multiple cells encapsulated in individual droplets. To monitor the growth, individual drop volumes were kept nearly intact for more than a month by controlling the permeation of water in and out of the microfluidic device. The kinetic growth parameters were quantified by counting the increase in the number of cells in each drop over time. In addition to determining the kinetic parameters, the cell‐size distribution of the microalgae was correlated with different stages of the growth. The single‐cell growth kinetics of C. vulgaris showed significant heterogeneity. The specific growth rate ranged from 0.55 to 1.52 day−1 for different single cells grown in the same microfluidic device. In comparison, the specific growth rate in bulk‐scale experiment was 1.12 day−1. It was found that the average cell size changes significantly at different stages of the cell growth. The mean cell‐size increased from 5.99 ± 1.08 to 7.33 ± 1.3 µm from exponential to stationary growth phase. In particular, when multiple cells are grown in individual drops, we find that in the stationary growth phase, the cell size increases with the age of cell suggesting enhanced accumulation of fatty acids in older cells. Biotechnol. Bioeng. 2012; 109: 2987–2996. © 2012 Wiley Periodicals, Inc.
Characterization of the activity and stability of amylase from saliva and detergent: Laboratory practicals for studying the activity and stability of amylase from saliva and various commercial detergents
Authors: Valls Cristina , Rojas Cristina , Pujadas Gerard , Garcia‐Vallve Santi , Mulero Miquel
Published: June 2012

This article presents two integrated laboratory exercises intended to show students the role of α‐amylases (AAMYs) in saliva and detergents. These laboratory practicals are based on the determination of the enzymatic activity of amylase from saliva and different detergents using the Phadebas test (quantitative) and the Lugol test (qualitative) under different conditions (e.g. variations in temperature and alkalinity). This work also proposes the study of enzyme stability in the presence of several surfactants and oxidizing agents using the same technical approach. The proposed laboratory exercises promote the understanding of the physiological function of this enzyme and the biotechnological applications of AAMYs in the detergent industry. The exercises also promote the understanding that the enzymatic stability and performance are dependent on the organism of origin, and if necessary, these properties could be modified by genetic engineering. In addition, this article reinforces the development of laboratory skills, problem‐solving capabilities, and the ability to write a laboratory report. The exercises are proposed primarily as an undergraduate project for advanced students in the biochemical and biotechnological sciences. These laboratory practicals are complementary to the previously published BAMBED article (Biochemistry and Molecular Biology Education Vol. 39, No. 4, pp. 280–290, 2011) on detergent proteases.
Teaching the fluctuation test in silico by using mutate: A program to distinguish between the adaptive and spontaneous mutation hypotheses
Authors: Carvajal‐Rodríguez Antonio
Published: June 2012

Mutate is a program developed for teaching purposes to impart a virtual laboratory class for undergraduate students of Genetics in Biology. The program emulates the so‐called fluctuation test whose aim is to distinguish between spontaneous and adaptive mutation hypotheses in bacteria. The plan is to train students in certain key multidisciplinary aspects of current genetics such as sequence databases, DNA mutations, and hypothesis testing, while introducing the fluctuation test. This seminal experiment was originally performed studying Escherichia coli resistance to the infection by bacteriophage T1. The fluctuation test initiated the modern bacterial genetics that 25 years later ushered in the era of the recombinant DNA. Nowadays we know that some deletions in fhuA, the gene responsible for E. coli membrane receptor of T1, could cause the E. coli resistance to this phage. For the sake of simplicity, we will introduce the assumption that a single mutation generates the resistance to T1. During the practical, the students use the program to download some fhuA gene sequences, manually introduce some stop codon mutations, and design a fluctuation test to obtain data for distinguishing between preadaptative (spontaneous) and induced (adaptive) mutation hypotheses. The program can be launched from a browser or, if preferred, its executable file can be downloaded from http://webs.uvigo.es/acraaj/MutateWeb/Mutate.html. It requires the Java 5.0 (or higher) Runtime Environment (freely available at http://www.java.com).
Blended learning in biochemistry education: Analysis of medical students' perceptions
Authors: de Fátima Wardenski Rosilaine , de Espíndola Marina Bazzo , Struchiner Miriam , Giannella Taís Rabetti
Published: June 2012

The objective of this study was to analyze first‐year UFRJ medical students' perceptions about the implementation of a blended learning (BL) experience in their Biochemistry I course. During the first semester of 2009, three Biochemistry professors used the Constructore course management system to develop virtual learning environments (VLEs) for complementing course Modules I, II, and IV, using different resources and activities. Forty‐nine students (46%) took part in the study. Results show that, in general, students gave positive evaluations to their experiences with BL, indicating that the VLEs have not only motivated but also facilitated learning. Most of the students reported that access to resources in the three modules provided a more in‐depth approach to Biochemistry education and greater study autonomy. Students suggested that the VLEs could be better used for promoting greater communication among participants.
Development of the enzyme–substrate interactions concept inventory
Authors: Bretz Stacey Lowery , Linenberger Kimberly J.
Published: June 2012

Enzyme function is central to student understanding of multiple topics within the biochemistry curriculum. In particular, students must understand how enzymes and substrates interact with one another. This manuscript describes the development of a 15‐item Enzyme–Substrate Interactions Concept Inventory (ESICI) that measures student understanding of enzyme–substrate interactions. The validity and reliability of ESICI data were established through multiple methods. Results from the administration of the ESICI to biochemistry students across the United States (N = 707) are discussed in terms of instrument quality. The manuscript concludes with suggestions for how to use the ESICI for both teaching and biochemistry education research.
Moritz Heinrich Romberg (1795–1873): Early founder of neurology
Authors: Housman Brian , Bellary Sharath S. , Walters Andrew , Mirzayan Nadine , Shane Tubbs R. , Loukas Marios
Published: June 2012

Moritz Heinrich Romberg (1795–1873) began his pursuit of neurology in 1820 by translating into German Andrew Marshall's The Morbid Anatomy of the Brain. In 1830, Romberg was hired as Privatdozent of special pathology and therapy in the Charité, the University Hospital of Berlin. He quickly rose to director of the royal clinic in 1845, at which time he wrote Lehrbuch der Nervenkrankheiten des Menschen, a text generally regarded as the first formal treatise on nervous diseases. He identified the role of proprioception in tabes dorsalis, and became the first neurologist to describe the typical pupillary presentation found in patients with tertiary syphilis. Romberg is perhaps most famous for identifying “Romberg's sign,” the distinctive sensory ataxia observed in neuropathies of the dorsal columns. Clin. Anat. 27:147–149, 2014. © 2012 Wiley Periodicals, Inc
Cembranoid, Steroid, and Sesquiterpenoid Derivatives from the South China Sea Soft Coral Sinularia numerosa
Authors: Qin Mingli , Li Xiaoming , Wang Bingui
Published: June 2012

Two new cembranoids, namely, sinumerolides A and B (1 and 2), one new steroid, 7β‐hydroxygorgosterol (7), along with four known cembranoid derivatives (3–6), four known steroids (8–11), and four known africane sesquiterpenoids (12–15), were isolated and identified from the marine soft coral Sinularia numerosa that was collected from South China Sea waters. The structures of these metabolites were elucidated on the basis of extensive spectroscopic analysis and by comparison of their spectral data with those of literature reports. The isolated compounds were evaluated for the antimicrobial and cytotoxic activity.
Design, Synthesis and Biological Evaluation of 2‐(2‐Aryl‐morpholino‐4‐yl)ethyl Esters of Indomethacin as Potential Cyclooxygenase‐2 (COX‐2) Inhibitors
Authors: Shi Lei , Hu Aixi , Xu Jiangping , Jiang Yiping
Published: June 2012

A number of novel 2‐(2‐arylmorpholino‐4‐yl)ethyl 1‐(4‐chlorobenzoyl)‐5‐methoxy‐2‐methyl‐1H‐indol‐3‐acetate hydrochlorides were synthesized and tested for their cyclooxygenase (COX‐1 and COX‐2) inhibition properties in vitro. Many of these compounds exhibited moderate to good selective COX‐2 inhibition, and subtle structural changes in the substituents on the side chain of the ester moiety altered the inhibitory properties significantly. 2‐[2‐(4‐Butoxyphenyl)morpholino‐4‐yl]ethyl 1‐(4‐chlorobenzoyl)‐5‐methoxy‐2‐methyl‐1H‐indol‐3‐acetate hydrochloride (1f), showed good selective COX‐2 inhibitory activity (Selective index (SI) 182), which is comparative with celecoxib (SI 214), a COX‐2 inhibitor of diarylpyrazoles. While 2‐[2‐(2,4‐dichloro‐5‐fluorophenyl)morpholino‐4‐yl]ethyl 1‐(4‐chlorobenzoyl)‐5‐methoxy‐2‐methyl‐1H‐indol‐3‐acetate hydrochloride (1g), showed greater selective COX‐2 inhibitory activity (SI 358) than celecoxib. Both compounds were identified as compromising derivatives in this class to reduce the side effects generated by nonsteroidal anti‐inflammatory drugs (NSAIDs) indomethacin.
Homology in the development of triadic interaction and language
Authors: Moore Chris
Published: June 2012

Conceiving of development with reference to homology can help identify developmental continuity where surface form shows considerable variation across age. I argue that there is a homology of structure between the object‐centred, or triadic, interactions that emerge in infancy and later language. The structure of triadic interaction in infancy is first described as involving joint attention and joint engagement about a shared topic, and then a case is made that this structure is maintained through three levels of complexity in language—single word utterances, multiword utterances, and finally complex constructions. A focus on the homological relation between these social interactive structures may be useful in revealing developmental continuities where these may be obscured by quite different surface forms. © 2012 Wiley Periodicals, Inc. Dev Psychobiol 55: 59–66, 2013.
The concept of homology in the development of handedness
Authors: Michel George F.
Published: June 2012

The construct of homology in the development of behavior is examined using human handedness. Research on the development of hand‐use preferences in infants provides some evidence that it may be homologous with adult handedness. Nevertheless, I propose that the construct of homology may not be relevant to the study of human behavioral development. However, other constructs from developmental biology may prove useful in improving developmental psychological research. © 2012 Wiley Periodicals, Inc. Dev Psychobiol 55: 84–91, 2013.
Fatty acid profile, oxidative stability, and sensory properties of breast meat from turkeys fed diets with a different n‐6/n‐3 PUFA ratio
Authors: Jankowski Jan , Zdunczyk Zenon , Mikulski Dariusz , Juskiewicz Jerzy , Naczmanski Jakub , Pomianowski Janusz F. , Zdunczyk Przemysław
Published: June 2012

The objective of this study was to determine the effect of diets with a different n‐6/n‐3 PUFAs ratio (7.31, 4.43, and 0.99), resulting from the addition of different dietary oils: soybean, rapeseed, and linseed (diets S, R, and L, respectively), on the fatty acid (FA) profile, oxidative status, and sensory properties of turkey breast meat. After 15 wk of feeding, breast meat yield and chemical properties of the meat were similar in all groups. Raw breast meat of R turkeys had a significantly higher content of all‐trans‐retinol and α‐tocopherol, compared with S and L. The physicochemical properties of breast meat, including pH, color, drip loss, and cooking loss, did not differ significantly. Cooked meat samples differed significantly with respect to the concentrations of oleic acid, linoleic acid (S and R>L), and linolenic acid (S and R<L). Compared with S and R, breast meat of L turkeys was characterized by higher concentrations of total PUFAs (35.1 vs. 30.1 and 29.3%), a significantly lower n‐6/n‐3 PUFAs ratio (1.51 vs. 5.43 and 5.07%) and a higher thiobarbituric acid reactive substances content (TBARS; 31.9 vs. 26.4 and 26.7 nmol/g). After 4 months of deep‐freeze storage the n‐6/n‐3 PUFAs ratio did not deteriorate. It may be concluded that replacing soybean oil with linseed oil, but not with rapeseed oil, increased the proportion of PUFAs in the total FAs pool and improved the n‐6/n‐3 PUFAs ratio, yet it also adversely affected the sensory properties and oxidative stability of meat. Both raw and stored breast meat from L turkeys was susceptible to oxidative changes, as manifested by the significantly higher TBARS concentrations (17.07 and 81.06) compared with those of the S group (10.91 and 53.00 nmol/g, respectively).

Practical applications: Studies investigating the possibility of increasing the health benefits of poultry meat have been performed mostly on broilers, while the problem remains poorly researched in turkeys. Our findings show that linseed oil, in contrast to rapeseed oil, is a good source of PUFAs, in particular n‐3 PUFAs, that can be effectively transferred from feed to carcass lipids. However, desirable changes in the fatty acid profile are accompanied by increased susceptibility to lipid oxidation and deterioration of the sensory properties of meat. Thus, the linseed oil content of turkey diets should be reduced, or diets supplemented with linseed oil should be fed for shorter periods of time to alleviate the negative effects of linseed oil on the sensory attributes and oxidative status of meat.
Free sterols and steryl glycosides in sunflower seeds with high phytosterol contents
Authors: Aguirre Marta R. , Ruiz‐Méndez M. Victoria , Velasco Leonardo , Dobarganes M. Carmen
Published: June 2012

In this paper, the distribution of sterol compounds has been analyzed in 10 samples of new sunflower seeds with high contents of phytosterols. The sunflower seeds were first extracted with hexane and the residual oil was then extracted with a mixture of chloroform:methanol (2:1). In addition, the lipids from the defatted seeds and from the total seeds were analyzed after acid hydrolysis and subsequent extraction. The evaluation of the sterol compounds was performed by high temperature GC directly in the sylanized unsaponifiable matter using α‐cholestanol as internal standard. This procedure allows for the quantification of free sterols and steryl glycosides in the oils extracted by hexane and chloroform:methanol (2:1) while in defatted meal and total seeds, they are determined as free sterols. The main characteristics of the fractions extracted by hexane were a variable oil content (19.8–38.7%) with medium unsaponifiable matter (1.4–4.8%), The major sterol compounds in the oil extracted by hexane were free sterols (4034–8507 mg/kg) while steryl glycosides were in low concentrations (80–280 mg/kg). On the contrary, the fraction extracted by chloroform:methanol had low lipid content (2.2–6.7%) with a high unsaponifiable matter (12.6–28.2%). The major sterol compounds in this fraction were steryl glycosides (9711–22 514 mg/kg). Finally, a third of the total sterols remained in the meal after the extraction of edible oil by hexane.
Prediction of fatty acid composition of vegetable oils based on rheological measurements using nonlinear models
Authors: Yalcin Hasan , Toker Omer Said , Ozturk Ismet , Dogan Mahmut , Kisi Ozgur
Published: June 2012

The aim of this study was to model the fatty acid composition of vegetable oils by using the adaptive neuro fuzzy inference system (ANFIS) and artificial neural network (ANN) based on rheological measurements. For this aim, seven different refined vegetable oils (hazelnut, soybean, sunflower, olive, canola, corn, and cotton seed) were used. Olive oil had the highest viscosity value of 0.067 Pa s. Principal component analysis (PCA) was performed to determine the correlations among the fatty acids of the oils to reduce parameters which were modeled. PC1 composed of C18:0, C18:1, C18:2, and C20:0 as PC2 composed of C16:0, C18:3, and C22:0. After determination of the fatty acid composition and the rheological properties of the oils, ANN and ANFIS models were established. The inputs were selected as oil type, shear rate and shear stress and the outputs were C16:0 and C18:2. The root mean square error (RMSE), mean absolute error (MAE), and determination coefficient (R2) were used for testing the accuracy of the models. This comparison showed that ANFIS and ANN achieved a satisfactory prediction for fatty acid composition of the vegetable oils studied and ANFIS is better than ANN.

Practical applications: Determination of the fatty acid composition of vegetable oils is important for the assessment of the purity of the oils as well as the nutritional quality. The fatty acid composition of the oils affects their rheological characteristics. Rheological measurements are easier than chromatographic analysis. Therefore, we aimed to establish a model for prediction of the fatty acid composition of the oils based on their rheological behaviors.
Assessing a Spectroelectrochemical Sensor’s Performance for Detecting [Ru(bpy)3]2+ in Natural and Treated Water
Authors: Abu Eme A. , Bryan Samuel A. , Seliskar Carl J. , Heineman William R.
Published: June 2012

A spectroelectrochemical sensor that combines three modes of selectivity in a single device was evaluated in natural and treated water samples using tris‐(2,2′‐bipyridyl) ruthenium(II) dichloride hexahydrate, [Ru(bpy)3]2+, as a model analyte. The sensor was an optically transparent indium tin oxide (ITO) electrode coated with a thin film of partially sulfonated polystyrene‐block‐poly(ethylene‐ran‐butylene)‐block‐polystyrene (SSEBS). As the potential of the ITO electrode was cycled from +0.7 to +1.3 V, the analyte changed from the colored [Ru(bpy)3]2+ complex to colorless [Ru(bpy)3]3+ complex and the change in absorbance at 450 nm was used as the optical signal for quantification. Calibration curves were obtained for [Ru(bpy)3]2+ in natural well water, river water and treated tap water with detection limits of 108, 139 and 264 nM, respectively. A standard addition method was developed to determine an ‘unknown’ spike addition concentration of [Ru(bpy)3]2+ in well water. The spectroelectrochemical sensor determined the concentration of [Ru(bpy)3]2+ spiked into a sample of Hanford well water to be 0.39±0.03 µM versus the actual concentration of 0.40 µM.
Transcriptomic profiling reveals hepatic stem-like gene signatures and interplay of miR-200c and epithelial-mesenchymal transition in intrahepatic cholangiocarcinoma
Authors: Oishi Naoki , Kumar Mia R. , Roessler Stephanie , Ji Junfang , Forgues Marshonna , Budhu Anuradha , Zhao Xuelian , Andersen Jesper B. , Ye Qing-Hai , Jia Hu-Liang , Qin Lun-Xiu , Yamashita Taro , Woo Hyun Goo , Kim Yoon Jun , Kaneko Shuichi , Tang Zhao-You , Thorgeirsson Snorri S. , Wang Xin Wei
Published: June 2012

Intrahepatic cholangiocellular carcinoma (ICC) is the second most common type of primary liver cancer. However, its tumor heterogeneity and molecular characteristics are largely unknown. In this study, we conducted transcriptomic profiling of 23 ICC and combined hepatocellular cholangiocarcinoma tumor specimens from Asian patients using Affymetrix messenger RNA (mRNA) and NanoString microRNA microarrays to search for unique gene signatures linked to tumor subtypes and patient prognosis. We validated the signatures in an additional 68 ICC cases derived from Caucasian patients. We found that both mRNA and microRNA expression profiles could independently classify Asian ICC cases into two main subgroups, one of which shared gene expression signatures with previously identified hepatocellular carcinoma (HCC) with stem cell gene expression traits. ICC-specific gene signatures could predict survival in Asian HCC cases and independently in Caucasian ICC cases. Integrative analyses of the ICC-specific mRNA and microRNA expression profiles revealed that a common signaling pathway linking miR-200c signaling to epithelial-mesenchymal transition (EMT) was preferentially activated in ICC with stem cell gene expression traits. Inactivation of miR-200c resulted in an induction of EMT, whereas activation of miR-200c led to a reduction of EMT including a reduced cell migration and invasion in ICC cells. We also found that miR-200c and neural cell adhesion molecule 1 (NCAM1) expression were negatively correlated and their expression levels were predictive of survival in ICC samples. NCAM1, a known hepatic stem/progenitor cell marker, was experimentally demonstrated to be a direct target of miR-200c.

Conclusion:

Our results indicate that ICC and HCC share common stem-like molecular characteristics and poor prognosis. We suggest that the specific components of EMT may be exploited as critical biomarkers and clinically relevant therapeutic targets for an aggressive form of stem cell-like ICC.
Oncogenic activation of glypican-3 by c-Myc in human hepatocellular carcinoma
Authors: Li Li , Jin Ronghua , Zhang Xiaoli , Lv Fudong , Liu Lifeng , Liu Daojie , Liu Kai , Li Ning , Chen Dexi
Published: June 2012

Glypican-3 (GPC3) is a heparan sulfate proteoglycan that has an important role in cell growth and differentiation, and its function in tumorigenesis is tissue-dependent. In hepatocellular carcinoma (HCC), the overexpression of GPC3 has been demonstrated to be a reliable diagnostic indicator. However, the mechanisms that regulate the expression and function of GPC3 remain unclear. The oncoprotein c-Myc is a transcription factor that plays a significant role in more than 50% of human tumors. We report here that GPC3 is a transcriptional target of c-Myc and that the expression of c-Myc is also regulated by GPC3, thus forming a positive feedback signaling loop. We found that the overexpression of c-Myc could induce GPC3 promoter-dependent luciferase activity in luciferase reporter experiments. Furthermore, mutational analysis identified c-Myc-binding sites within the GPC3 promoter. The exogenous overexpression of c-Myc increased the endogenous messenger RNA (mRNA) and protein levels of GPC3. Chromatin immunoprecipitation experiments revealed the binding of c-Myc to the endogenous GPC3 promoter, indicating that c-Myc can directly transcriptionally activate GPC3. Interestingly, GPC3 can also elevate c-Myc expression. Overexpression of GPC3 increased c-Myc protein levels, whereas the knockdown of GPC3 reduced c-Myc expression levels. Lastly, the elevated levels of c-Myc correlate with the overexpression of GPC3 in human HCC samples. Conclusion: These data provide new mechanistic insight into the roles of GPC3 and of c-Myc in the development of HCC.
Learned integration of visual, vestibular, and motor cues in multiple brain regions computes head direction during visually guided navigation
Authors: Fortenberry Bret , Gorchetchnikov Anatoli , Grossberg Stephen
Published: June 2012

Effective navigation depends upon reliable estimates of head direction (HD). Visual, vestibular, and outflow motor signals combine for this purpose in a brain system that includes dorsal tegmental nucleus, lateral mammillary nuclei, anterior dorsal thalamic nucleus, and the postsubiculum. Learning is needed to combine such different cues to provide reliable estimates of HD. A neural model is developed to explain how these three types of signals combine adaptively within the above brain regions to generate a consistent and reliable HD estimate, in both light and darkness, which explains the following experimental facts. Each HD cell is tuned to a preferred head direction. The cell's firing rate is maximal at the preferred direction and decreases as the head turns from the preferred direction. The HD estimate is controlled by the vestibular system when visual cues are not available. A well‐established visual cue anchors the cell's preferred direction when the cue is in the animal's field of view. Distal visual cues are more effective than proximal cues for anchoring the preferred direction. The introduction of novel cues in either a novel or familiar environment can gain control over a cell's preferred direction within minutes. Turning out the lights or removing all familiar cues does not change the cell's firing activity, but it may accumulate a drift in the cell's preferred direction. The anticipated time interval (ATI) of the HD estimate is greater in early processing stages of the HD system than at later stages. The model contributes to an emerging unified neural model of how multiple processing stages in spatial navigation, including postsubiculum head direction cells, entorhinal grid cells, and hippocampal place cells, are calibrated through learning in response to multiple types of signals as an animal navigates in the world. © 2012 Wiley Periodicals, Inc.
Mothers' and Fathers' Internal State Language with Their Young Children: An Examination of Gender Differences During an Emotions Task
Authors: Roger Katherine M. , Rinaldi Christina M. , Howe Nina
Published: June 2012

The current study examined gender differences in mothers' and fathers' internal state language (ISL), children's use of ISL, and whether ISL was related to parents' ratings of the children's social skills. Fifty‐seven (28 boys, 29 girls) toddler/preschool children (M age = 32.5 months, SD = 5.38 months) were observed separately with their mothers and fathers in their homes while they discussed pictures of children's facial expressions of emotions. Parents completed a questionnaire concerning their child's social–emotional behaviours (i.e. BASC‐2). Parents used more ISL with sons compared with daughters, and sons used more ISL with mothers than with fathers. No overall differences were found between mothers' and fathers' ISL. Children's social skills as rated by mothers were predicted by mothers' ISL comments, whereas children's social skills as rated by fathers were predicted by children's age and fathers' ISL clarifications. Implications and limitations of the study are discussed. Copyright © 2012 John Wiley & Sons, Ltd.
Stable isotopes as indicators for seasonally dominant nitrogen cycling processes in a subarctic lake
Authors: Gu Binhe
Published: June 2012

Nitrogen stable isotopes (δ15N) of dissolved inorganic nitrogen (DIN = NH4+ and NO3–), dissolved organic nitrogen (DON), and particulate organic nitrogen (PON) were measured in Smith Lake, Alaska to assess their usefulness as proxies for the biological nitrogen cycling processes, nutrient concentration, and lake productivity. Large seasonal variations in δ15NH4+, δ15NO3– and δ15NPON occurred in response to different processes of nitrogen transformation that dominated a specific time period of the annual production cycle. In spring, 15N depletion in all three pools was closely related to the occurrences of a N2‐fixing cyanobacterial bloom (Anabaena flos‐aquae). In summer, δ15NPON increased as phytoplankton community shifted to use NH4+ and decreased as a brief N2‐fixing bloom (Aphanizomenon flos‐aquae) occurred in August. In early and mid‐winter, microbial nitrogen processes were dominated by nitrification that resulted in the largest isotope fractionation between NO3– and NH4+ in the annual cycle. This was followed by denitrification that led to the highest 15N enrichment in NO3–. A peak of NH4+ assimilation by phytoplankton along with the elevated δ15NPON and Chl a concentration occurred just before the ice break due to increased light penetration. The δ15NDON displayed little temporal and spatial variations. This suggests that the DON pool was not altered by biological transformations of nitrogen as the results of its large size and possibly refractory nature. There was a positive correlation between Chl a concentration and δ15NPON, and a negative correlation between NH4+ and δ15NPON, suggesting that δ15NPON is a useful proxy for nitrogen productivity and ammonium concentration. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Spatial Distribution of Macroinvertebrate Community along a Longitudinal Gradient in a Eutrophic Reservoir‐Bay during Different Impoundment Stages, China
Authors: Zhang Min , Cai Qinghua , Xu Yaoyang , Kong Linghui , Tan Lu , Wang Lan
Published: June 2012

The longitudinal patterns of the macroinvertebrate community in the Xiangxi Bay of the Three Gorges Reservoir (TGR) were investigated during the second (2nd) and third (3rd) impoundment stages (October 2006–July 2010), to test the effects of increased water level fluctuations (WLF) on the macroinvertebrates. By comparing to the former reports of the first (1st) impoundment stage (inter‐annual WLF 4 m), we found that oligochaetes dominated in three different stages in the Xiangxi Bay. However, the total abundance of macroinvertebrates showed a dramatical decline from the 1st to 2nd stage (inter‐annual WLF 11 m), but changed slightly from the 2nd to 3rd stage (inter‐annual WLF 30 m). This indicated that higher WLF in the 2nd stage had already greatly reduced the macroinvertebrates abundance, thereby the disturbance in the 3rd stage could only slightly affect the already reduced abundance. Three longitudinal zones (the mainstream zone, the lacustrine zone and the transitional zone) were found based on the macroinvertebrate density, biomass, and taxa richness, combined with the geographical location of each site. Significant differences in density and biomass of macroinvertebrate were found among different zones (P < 0.05), yet no significant difference was found in taxa richness (P > 0.05). Two‐way indicator species analysis showed that the community type in most sites varied in different seasons from the 2nd stage, exhibiting a dynamic zonation pattern, which differed with the stable pattern of the 1st stage. This seasonal feature was coupled to the seasonal changes of the WLF. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
‘Go with the flow ’: A review of methods and advancements in blood flow imaging
Authors: Daly Susan M. , Leahy Martin J.
Published: June 2012

Physics has delivered extraordinary developments in almost every facet of modern life. From the humble thermometer and stethoscope to X‐Ray, CT, MRI, ultrasound, PET and radiotherapy, our health has been transformed by these advances yielding both morphological and functional metrics. Recently high resolution label‐free imaging of the microcirculation at clinically relevant depths has become available in the research domain. In this paper, we present a comprehensive review on current imaging techniques, state‐of‐the‐art advancements and applications, and general perspectives on the prospects for these modalities in the clinical realm. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quiescence and attenuated DNA damage response promote survival of esophageal cancer stem cells
Authors: Chen Yulin , Li Dan , Wang Dapeng , Liu Xuefeng , Yin Ning , Song Yongmei , Lu Shih Hsin , Ju Zhenyu , Zhan Qimin
Published: June 2012

Accumulating evidence indicates cancer stem cells (CSCs) possess the capability to resist DNA‐damage induced cell death, whereas the mechanism is largely unknown. Here we show that cell cycle status and DNA damage response (DDR) in CSCs probably contribute to their survival in genotoxic insults. In this study, we isolated esophageal cancer stem cells (ECSCs) from esophageal cancer cell line EC9706 by side‐population (SP) phenotype through flow cytometry and found that ECSCs preferentially stay quiescent as compared to the non‐ECSCs and are more resistant to DNA damage agents. Further study revealed that ECSCs express a lower level of EGFR, phosphoralated Stat3, and c‐Myc, yet abnormally upregulated p27. More interestingly, different from non‐ECSCs, when suffering DNA damage agents, ECSCs showed attenuated DDR, as well as declined DNA repair potential. These data indicated ECSCs probably employed an impaired DDR to handle severe genomic insults. Conclusively, we infer that the damage‐resistance ability of ECSCs is likely attributed to their slow‐cycling status and avoidance of apoptosis or senescence triggered by an excessive DDR. J. Cell. Biochem. 113: 3643–3652, 2012. © 2012 Wiley Periodicals, Inc.
Chromosome dynamic changes in two cultured chinese human embryonic stem cell lines: Single nucleotide polymorphism, copy number variation and loss of heterozygosity
Authors: Chen Xue‐Mei , Kan Quan‐Cheng , Wang Fang , Kong Hui‐Juan , Zhang Yong‐Yong , Yu Wen‐Zhu , Sun Ying‐Pu
Published: June 2012

The quality and safety of human embryonic stem cells (hESCs) in clinical application depend on gene stability. Two Chinese hESC lines, Zh1 and Zh21, were incubated over a long period. We observed and compared the gene stability in the passage numbers 20, 17 for Zh1 cell line and passage numbers 27, 60, 68 for Zh21 cell line. Single nucleotide polymorphisis analysis indicated that hESCs in early passages had relative gene stability; and with the increase in passage number, gene instability became strong. We also found that there were copy number variations (CNVs) in both Zh21 and Zh1. We analyzed the CNVs of Chinese Han Beijing man (CHB; normal Chinese people) and found that the all CNV forms were the loss in Zh21, Zh1, and CHB. We also analyzed and compared the related pathways of the mutant genes. We propose three steps to ensure hESC safety. Firstly, besides the conventional methods such as pluripotent genes, chromosome G‐banding and teratoma, high‐resolution DNA chip analysis should also be adopted; secondly, chromosomal properties are monitored every 10 passages in less than passage 50 and every 5 passages in more than passage 50; thirdly, the related pathways of mutant genes should be observed because only the mutant genes with variations of their related pathways may affected cell functions. J. Cell. Biochem. 113: 3520–3527, 2012. © 2012 Wiley Periodicals, Inc.
Binding of piano‐stool Ru(II) complexes to DNA; QM/MM study
Authors: Futera Zdeněk , Platts James A. , Burda Jaroslav V.
Published: June 2012

Ru(II) “piano‐stool” complexes belong to group of biologically active metallocomplexes with promising anticancer activity. In this study, we investigate the reaction mechanism of [(η6‐benzene)Ru(II)(en)(H2O)]2+(en = ethylenediamine) complex binding to DNA by hybrid QM/MM computational techniques. The reaction when the Ru(II) complex is coordinated on N7‐guanine from major groove is explored. Two reaction pathways, direct binding to N7 position and two‐step mechanism passing through O6 position, are considered. It was found that the reaction is exothermic and the direct binding process is preferred kinetically. In analogy to cisplatin, we also explored the possibility of intrastrand cross‐link formation where the Ru(II) complex makes a bridge between two adjacent guanines. Two different pathways were found, leading to a final structure with released benzene ligand. This process is exothermic; however, one pathway is blocked by relatively high initial activation barrier. Geometries, energies, and electronic properties analyzed by atoms in molecules and natural population analysis methods are discussed. © 2012 Wiley Periodicals, Inc.
Dramatic Expansion and Developmental Expression Diversification of the Methuselah Gene Family During Recent Drosophila Evolution
Authors: PATEL MEGHNA V. , HALLAL DANA A. , JONES JEFFERY W. , BRONNER DENISE N. , ZEIN RAMI , CARAVAS JASON , HUSAIN ZAHABIYA , FRIEDRICH MARKUS , VANBERKUM* MARK F.A.
Published: June 2012

Functional studies of the methuselah/methuselah‐like (mth/mthl) gene family have focused on the founding member mth, but little is known regarding the developmental functions of this receptor or any of its paralogs. We undertook a comprehensive analysis of developmental expression and sequence divergence in the mth/mthl gene family. Using in situ hybridization techniques, we detect expression of six genes (mthl1, 5, 9, 11, 13, and 14) in the embryo during gastrulation and development of the gut, heart, and lymph glands. Four receptors (mthl3, 4, 6, and 8) are expressed in the larval central nervous system, imaginal discs, or both, and two receptors (mthl10 and mth) are expressed in both embryos and larvae. Phylogenetic analysis of all mth/mthl genes in five Drosophila species, mosquito and flour beetle structured the mth/mthl family into several subclades. mthl1, 5, and 14 are present in most species, each forming a separate clade. A newly identified Drosophila mthl gene (CG31720; herein mthl15) formed another ancient clade. The remaining Drosophila receptors, including mth, are members of a large “superclade” that diversified relatively recently during dipteran evolution, in many cases within the melanogaster subgroup. Comparing the expression patterns of the mth/mthl “superclade” paralogs to the embryonic expression of the singleton ortholog in Tribolium suggests both subfunctionalization and acquisition of novel functionalities. Taken together, our findings shed novel light on mth as a young member of an adaptively evolving developmental gene family. J. Exp. Zool. (Mol. Dev. Evol.) 318B:368‐387, 2012. © 2012 Wiley Periodicals, Inc.
Composition and Phylogenetic Analysis of Vitellogenin Coding Sequences in the Indonesian Coelacanth Latimeria menadoensis
Authors: CANAPA ADRIANA , OLMO ETTORE , FORCONI MARIKO , PALLAVICINI ALBERTO , MAKAPEDUA MONICA DAISY , BISCOTTI MARIA ASSUNTA , BARUCCA MARCO
Published: June 2012

The coelacanth Latimeria menadoensis, a living fossil, occupies a key phylogenetic position to explore the changes that have affected the genomes of the aquatic vertebrates that colonized dry land. This is the first study to isolate and analyze L. menadoensis mRNA. Three different vitellogenin transcripts were identified and their inferred amino acid sequences compared to those of other known vertebrates. The phylogenetic data suggest that the evolutionary history of this gene family in coelacanths was characterized by a different duplication event than those which occurred in teleosts, amniotes, and amphibia. Comparison of the three sequences highlighted differences in functional sites. Moreover, despite the presence of conserved sites compared with the other oviparous vertebrates, some sites were seen to have changed, others to be similar only to those of teleosts, and others still to resemble only to those of tetrapods. J. Exp. Zool. (Mol. Dev. Evol.) 318B:404‐416, 2012. © 2012 Wiley Periodicals, Inc.