bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of functionally significant single nucleotide polymorphisms inPTENtumor suppressor gene: Anin silicoapproach
Authors: Khan Imran , Ansari Irfan A. , Singh Pratichi , Dass J Febin Prabhu
Published: January 2016

The phosphatase and tensin homolog (PTEN) gene plays a crucial role in signal transduction by negatively regulating the PI3K signaling pathway. It is the most frequent mutated gene in many human‐related cancers. Considering its critical role, a functional analysis of missense mutations ofPTENgene was undertaken in this study. Thirty five nonsynonymous single nucleotide polymorphisms (nsSNPs) within the coding region of thePTENgene were selected for ourin silicoinvestigation, and five nsSNPs (G129E, C124R, D252G, H61D, and R130G) were found to be deleterious based on combinatorial predictions of different computational tools. Moreover, molecular dynamics (MD) simulation was performed to investigate the conformational variation between native and all the five mutantPTENproteins having predicted deleterious nsSNPs. The results of MD simulation of all mutant models illustrated variation in structural attributes such as root‐mean‐square deviation, root‐mean‐square fluctuation, radius of gyration, and total energy; which depicts the structural stability ofPTENprotein. Furthermore, mutantPTENprotein structures also showed a significant variation in the solvent accessible surface area and hydrogen bond frequencies from the nativePTENstructure. In conclusion, results of this study have established the deleterious effect of the all the five predicted nsSNPs on thePTENprotein structure. Thus, results of the current study can pave a new platform to sort out nsSNPs that can be undertaken for the confirmation of their phenotype and their correlation with diseased status in case of control studies.
Conformational studies on peptides having dipropylglycine (Dpg) or 1‐aminocycloheptanecarboxylic acid (Ac7c) within the sequence of l‐leucine (Leu) residues
Authors: Oba Makoto , Nonaka Hikaru , Doi Mitsunobu , Tanaka Masakazu
Published: January 2016

A conformational analysis of peptides having dipropylglycine (Dpg) or 1‐aminocycloheptanecarboxylic acid (Ac7c) within l‐leucine (Leu) residues was conducted in solution and in a crystal state. Dpg and Ac7c had similar structures with acyclic and cyclic side chains, respectively. FTIR, 1H NMR, and CD spectra measurements revealed that the preferred conformations of Dpg‐ and Ac7c‐containing l‐Leu peptides in solution were similar; both had a right‐handed (P) 310‐helix. The Dpg‐containing octapeptide adopted a right‐handed (P) α‐helix in the crystal state. Dpg and Ac7c homopeptides had planar and helical structures as their preferred conformations, respectively; however, Dpg‐ and Ac7c‐containing l‐Leu peptides adopted similar structures in solution. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 210–218, 2016.
Incorporating modeling and simulations in undergraduate biophysical chemistry course to promote understanding of structure‐dynamics‐function relationships in proteins
Authors: Hati Sanchita , Bhattacharyya Sudeep
Published: January 2016

A project‐based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure‐function of biomolecules is integrated with the discovery‐guided laboratory study of these molecules using computer modeling and simulations. In particular, modern computational tools are employed to elucidate the relationship between structure, dynamics, and function in proteins. Computer‐based laboratory protocols that we introduced in three modules allow students to visualize the secondary, super‐secondary, and tertiary structures of proteins, analyze non‐covalent interactions in protein–ligand complexes, develop three‐dimensional structural models (homology model) for new protein sequences and evaluate their structural qualities, and study proteins' intrinsic dynamics to understand their functions. In the fourth module, students are assigned to an authentic research problem, where they apply their laboratory skills (acquired in modules 1–3) to answer conceptual biophysical questions. Through this process, students gain in‐depth understanding of protein dynamics—the missing link between structure and function. Additionally, the requirement of term papers sharpens students' writing and communication skills. Finally, these projects result in new findings that are communicated in peer‐reviewed journals. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:140–159, 2016.
γ‐Secretase inhibitor reverts the Notch signaling attenuation of osteogenic differentiation in aged bone marrow mesenchymal stem cells
Authors: Tang Zhaolong , Wei Junjun , Yu Yunbo , Zhang Jiankang , Liu Lei , Tang Wei , Long Jie , Zheng Xiaohui , Jing Wei
Published: January 2016

The age‐related changes in cell viability and osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) play pivotal roles in the fracture healing process, especially in geriatric individuals. This study was designed to explore the age‐related changes in murine BMSCs and the regulation of osteogenic differentiation in aged BMSCs in vitro. Notch signaling pathway took part in the regulation of osteogensis, while the relationship between Notch and the osteogenic differentiation in aged BMSCs has not been reported yet. BMSCs harvested from the bone marrow of young, adult, and aged C57BL/6 mice were cultured in osteogenic and adipogenic differentiation media. Histochemical staining results indicated that the osteogenic ability of BMSCs gradually decreased with aging, whereas the adipogenic ability increased. Cell activity assays showed that the proliferative and migrated capacity did not decline with aging significantly. According to real‐time PCR and Western blotting results, the aged cells exhibited higher Notch signaling expression level than the younger ones did. After the aged BMSCs being treated with γ‐secretase inhibitor, however, Notch activity was changed and the aging‐imparied osteogenic ability reverted to a normal level. This study demonstrated that the decreased bone formation capacity in aged BMSCs had relationship with the transdifferentiation between osteogenesis and adipogenesis, which would be regulated by Notch signaling pathway and the attenuated osteogenesis in aged BMSCs could be promoted when the inhibition of Notch pathway.
miR‐483‐3p plays an oncogenic role in esophageal squamous cell carcinoma by targeting tumor suppressor EI24
Authors: Ma Jiaojiao , Hong Liu , Xu Guanghui , Hao Junfeng , Wang Rui , Guo Hao , Liu Jinqiang , Zhang Yujie , Nie Yongzhan , Fan Daiming
Published: January 2016

microRNAs (miRNAs), through negatively regulating their target genes, influence the development and progression of many cancers. Previously, we found miR‐483 was overexpressed in esophageal squamous cell carcinoma (ESCC) tissues, and its overexpression was negatively correlated with the prognosis and positively correlated with multidrug resistance of ESCC, but whether it could affect the biological role of proliferation and migration in ESCC cell lines is unknown. In the present study, we found miR‐483‐3p was overexpressed in ESCC cell lines as compared with the normal esophageal squamous epithelial cell line. Functional experiments in vitro showed that miR‐483‐3p could promote the proliferation, migration, transformation of cell cycle from G1 phase to G2 phase of ESCC cells and could inhibit cells' sensitivity to chemotherapy drugs. Nude mouse tumorigenicity assay indicated that miR‐483‐3p could promote the growth of ESCC cells in vivo. Western blot assay showed that ectopic expression of miR‐483‐3p in ESCC cells could downregulate the protein level of etoposide induced 2.4 (EI24), which is a tumor suppressor and has not been reported in ESCC. Luciferase reporter assay demonstrated that EI24 was a direct target of miR‐483‐3p. Collectively, our study demonstrated that miR‐483‐3p could promote ESCC progression at least in part through directly targeting EI24, supplying a potential strategy for miRNA‐based ESCC therapy.
Identification of microRNAs regulating Hlxb9 gene expression during the induction of insulin‐producing cells
Authors: Mu Changzheng , Wang Tao , Wang Xiaomei , Tian He , Liu Yong
Published: January 2016

Bone marrow mesenchymal stem cells (bMSCs) with the capacity of self‐ renewal and multilineage differentiation are promising sources for cell replacement therapy in diabetes. Here, we developed an effective method with activin A, conophylline, and nicotinamide to induce mouse bMSCs to differentiate into insulin‐producing cells (IPCs). The homeobox gene Hlxb9 (encoding HB9) is prominently expressed in adult human pancreas, which can also play a key role during the induction of IPCs. To find the microRNAs (miRNAs) regulating Hlxb9 gene expression, we respectively used miRanda and TargetScan to predict and got the intersection, miR‐200a and miR‐141, further identified by the Dual‐Luciferase assay. The results illustrated miR‐200a and miR‐141 could inhibit the expression of Hlxb9 by binding to its mRNA 3′UTR. Furthermore, the expression of miR‐200a and miR‐141 was almost reciprocal to that of Hlxb9. Overexpression of miR‐200a and miR‐141 downregulated the expression of pancreatic progenitor cell markers Hlxb9 and Pdx1. Therefore, miR‐200a and miR‐141 may directly or indirectly regulate the expression of pancreatic islet transcription factors to control the differentiation of IPCs.
Results of coil closure of patent ductus arteriosus using a tapered tip catheter for enhanced control
Authors: Devanagondi Rajiv , Latson Larry , Bradley‐Skelton Sharon , Prieto Lourdes
Published: January 2016

Objectives

This article describes the efficacy and embolization rates of coil delivery via modified vertebral catheter (MVC) for patent ductus arteriosus (PDA) closure.

Background

Various techniques have been devised to enhance coil control and prevent embolization during PDA closure. Since 1995, they have delivered coils via tapered vertebral catheters for improved coil control.

Methods

Catheterization reports, angiograms, and echocardiograms were reviewed for patients with PDA occlusion via MVC from 2001 to 2014. Residual shunting was determined by angiography and echocardiogram within 24 hr post‐procedure. Procedural success was defined as ≤ trivial angiographic and echocardiographic shunt, and no aortic nor LPA obstruction, after final coil delivery.

Results

About 125 coil occlusions were attempted in 103 patients. Minimal PDA diameter was 2 (0.6–6) mm. Four coils were removed with a snare/bioptome due to aortic/LPA obstruction following release. Seven were malpositioned while still held by the MVC of which three embolized while attempting withdrawal. Five embolized after full release from the MVC. The embolization rate was 6.4%. Embolizations were more likely in PDAs ≥ 2.5 mm (P < 0.05). Ultimately, 98/103 PDAs were occluded using the MVC. No patient had greater trivial residual shunt or aortic/LPA obstruction for an overall success rate of 95%. For PDAs < 2.5 mm the success rate was 97%.

Conclusions

Coil delivery via MVC was safe and effective for small PDAs. While fully controlled release and retrieval devices are now available for PDA closure with lower embolization rates, coil occlusion by MVC should still be considered for small PDAs, especially in resource limited regions. © 2016 Wiley Periodicals, Inc.
Cortical hierarchy governs rat claustrocortical circuit organization
Authors: White Michael G. , Cody Patrick A. , Bubser Michael , Wang Hui‐Dong , Deutch Ariel Y. , Mathur Brian N.
Published: January 2016

The claustrum is a telencephalic gray matter structure with various proposed functions, including sensory integration and attentional allocation. Underlying these concepts is the reciprocal connectivity of the claustrum with most, if not all, areas of the cortex. What remains to be elucidated to inform functional hypotheses further is whether a pattern exists in the strength of connectivity between a given cortical area and the claustrum. To this end, we performed a series of retrograde neuronal tract tracer injections into rat cortical areas along the cortical processing hierarchy, from primary sensory and motor to frontal cortices. We observed that the number of claustrocortical projections increased as a function of processing hierarchy; claustrum neurons projecting to primary sensory cortices were scant and restricted in distribution across the claustrum, whereas neurons projecting to the cingulate cortex were densely packed and more evenly distributed throughout the claustrum. This connectivity pattern suggests that the claustrum may preferentially subserve executive functions orchestrated by the cingulate cortex. J. Comp. Neurol. 525:1347–1362, 2017. © 2016 Wiley Periodicals, Inc.
Active immunization against vasoactive intestinal polypeptide decreases neuronal recruitment and inhibits reproduction in zebra finches
Authors: Vistoropsky Yulia , Heiblum Rachel , Smorodinsky Nechama‐Ina , Barnea Anat
Published: January 2016

Neurogenesis and neuronal recruitment occur in adult brains of many vertebrates, and the hypothesis is that these phenomena contribute to the brain plasticity that enables organisms to adjust to environmental changes. In mammals, vasoactive intestinal polypeptide (VIP) is known to have many neuroprotective properties, but in the avian brain, although widely distributed, its role in neuronal recruitment is not yet understood. In the present study we actively immunized adult zebra finches against VIP conjugated to KLH and compared neuronal recruitment in their brains, with brains of control birds, which were immunized against KLH. We looked at two forebrain regions: the nidopallium caudale (NC), which plays a role in vocal communication, and the hippocampus (HC), which is involved in the processing of spatial information. Our data demonstrate that active immunization against VIP reduces neuronal recruitment, inhibits reproduction, and induces molting, with no change in plasma prolactin levels. Thus, our observations suggest that VIP has a direct positive role in neuronal recruitment and reproduction in birds. J. Comp. Neurol. 524:2516–2528, 2016. © 2016 Wiley Periodicals, Inc.
Enzymatic degradation of fungal pigmentation from wall painting’s isolates
Authors: Marco A. , Moreira P. R. , Pintado M. , Vieira E.
Published: January 2016

Enzymatic discolouration of extracellular pigments produced in liquid media by a selected fungal isolate from Portuguese mural paintings was attempted both in solution and on solid support. A promising versatile peroxidase from Bjerkandera adusta was tested and presented interesting discolouration ability, although smaller than the values obtained with the use of hydrogen peroxide alone. © 2015 Wiley Periodicals, Inc. Col Res Appl, 41, 299–301, 2016
Color names, stimulus color, and their subjective links
Authors: Albertazzi Liliana , Da Pos Osvaldo
Published: January 2016

The aim of the research reported by this study was on the one hand to identify what colors were associated with particular words in relation to a specific language (Italian), by portraying them in color stimuli on the screen of a monitor; and on the other hand to verify whether some words of that language denoted colors that were either particularly well defined or confused with others. In an experiment using special software, the subjects were asked to produce colors directly, instead of choosing among a number of colors presented on the screen. The results showed that (i) it is possible to identify the color‐stimuli to which the terms of a language refer; that (ii) the “best” colors Giallo (Yellow), Rosso (Red), Blu (Blue), and Verde (Green) which the subjects were requested to produce were very similar to the corresponding unique hues; that (iii) among the mixed hues there were perceptually intermediate colors, that is, ones exactly midway between two consecutive unique colors: Arancione (Orange) and Viola (bluish Purple); that (iv) Turquoise and Lime were clearly positioned in the mental space of color of the participants; and that (v) for Italian speakers some hues coincide: Azzurro (Azure) and Celeste (Cerulean); Arancione (Orange), RossoGiallo (RedYellow) and Carota (Carrot); Lime and GialloVerde (YellowGreen), so that their color terms can be considered synonyms. Our most interesting finding, however, is that for Italian speakers these four mixed colors with their specific names (Lime, Turchese (Turquoise), Viola (bluish Purple) and Arancione (Orange) fall perceptually in the middle of each of the four quadrants formed in the hue circle by the four unique hues. The resulting circle is therefore characterized by eight colors of which four are unique and four are intermediate mixed. It would be advisable to repeat the study cross‐culturally to test for possible similarities and differences in color meanings with speakers of different languages. © 2016 Wiley Periodicals, Inc. Col Res Appl, 42, 89–101, 2017
Cytological findings of odontogenic myxofibroma: A diagnostic dilemma
Authors: Khare Akriti , Joshi Deepti , Majumdar Kaushik , Gupta Vikas , Goel Garima , Kapoor Neelkamal
Published: January 2016

Odontogenic myxofibroma represents a rare slow‐growing benign neoplasm, which usually occurs in the second and third decades of life and rarely in children or adults over 50 years of age. Myxomas in general represent from 2.3% to 17.7% of all odontogenic tumors, and myxofibromas represent a small number of all myxomas. Limited evidence is present in literature regarding the cytological diagnosis of odontogenic myxoma/myxofibroma. We hereby report the cytomorphological features of a histologically confirmed case of odontogenic myxofibroma and the pitfalls of the cytological diagnosis. A painless jaw swelling in a young boy was aspirated. Scanty mucoid material was obtained. Cytology Smears were moderately cellular and showed a population comprising predominantly of singly scattered plump to fusiform cells with bipolar cytoplasmic processes showing mild to moderate atypia embedded within dense myxoid matrix and another population of cells arranged in clusters. Case was interpreted as low grade mesenchymal tumor. Subsequent biopsy confirmed it as odontogenic myxofibroma arising in a odontogenic keratocyst. Precise interpretation of intraosseous jaw lesions FNAC may not always be possible, but an attempt should be made to broadly classify the lesion as an inflammatory lesion, cystic lesion, giant cell lesion, fibro‐osseous lesion or as an odontogenic tumor. If dual population of odontogenic epithelium and mesenchymal cells embedded in myxoid matrix are identified in such aspirates, a possibility of myxoid odontogenic tumor may be suggested. Triple correlation of cytological, clinical and radiological findings can guide the surgeon for taking appropriate therapeutic decisions. Diagn. Cytopathol. 2016;44:329–333. © 2016 Wiley Periodicals, Inc.
An analysis of human papillomavirus testing and endocervical component on pap tests: A pilot study using the Roche Cobas® assay
Authors: Pierce Kirsten J. , Currens Heather S. , Tafe Laura J. , Tsongalis Gregory J. , Padmanabhan Vijayalakshmi
Published: January 2016

Introduction

HPV is known to have a predilection for infecting the transformation zone (TZ). Endocervical cells (EC) on a Pap test (PT) indicate that the cervical TZ has been sampled. Earlier repeat testing of women lacking EC is of little value in further detecting disease, thus a sample without EC is not necessarily inadequate. Both HPV testing and PT can be performed using a single sample; however, few studies have investigated the relationship between HPV results and TZ sampling.

Materials and Methods

Specimens were collected following the ThinPrep® liquid‐based PT protocol. The Roche Cobas® HPV test was performed on post‐aliquot samples. Data was collected retrospectively on 500 patients: 250 consecutive cases of EC− and 250 of EC+ on PT. To maintain uniformity, we included only cases diagnosed as negative (NILM). We compared HPV test results within each category. As a positive control, five consecutive cases each of LSIL and HSIL were also reviewed.

Results

Of NILM cases, 11 of 250 EC+ cases and 14 of 250 EC− cases were positive for hrHPV. HPV 16 was present in 5 of 11 EC + cases and in 1 of 14 EC− cases. Of LSIL cases, 1 of 5 EC+ cases was positive for hrHPV, and 2 of 5 EC− cases were positive for hrHPV. Of HSIL cases, 5 of 5 EC+ cases were hrHPV+. In the time period studied, only one case of EC− HSIL was found, which was positive for hrHPV.

Discussion

Although our study did not prove a significant correlation between HPV testing results and EC on PT, more EC+ PTs were positive for HPV16 compared to EC− PTs. The absence of EC on PT does not appear to warrant re‐testing for HPV infection, though larger studies are required to determine the significance of low HPV 16 in PT without EC. Diagn. Cytopathol. 2016;44:280–282. © 2016 Wiley Periodicals, Inc.
Recent advances on separation and characterization of human milk oligosaccharides
Authors: Mantovani Veronica , Galeotti Fabio , Maccari Francesca , Volpi Nicola
Published: January 2016

Free human milk oligosaccharides (HMOs) are unique due to their highly complex nature and important emerging biological and protective functions during early life such as prebiotic activity, pathogen deflection, and epithelial and immune cell modulation. Moreover, four genetically determined heterogeneous HMO secretory groups are known to be based on their structure and composition. Over the years, several analytical techniques have been applied to characterize and quantitate HMOs, including nuclear magnetic resonance spectroscopy, high‐performance liquid chromatography (HPLC), high pH anion‐exchange chromatography, off‐line and on‐line mass spectrometry (MS), and capillary electrophoresis (CE). Even if these techniques have proven to be efficient and simple, most glycans have no significant UV absorption and derivatization with fluorophore groups prior to separation usually results in higher sensitivity and an improved chromatographic/electrophoretic profile. Consequently, the analysis by HPLC/CE of derivatized milk oligosaccharides with different chromophoric active tags has been developed. However, UV or fluorescence detection does not provide specific structural information and this is a key point in particular related to the highly complex nature of the milk glycan mixtures. As a consequence, for a specific determination of complex mixtures of oligomers, analytical separation is usually required with evaluation by means of MS, which has been successfully applied to HMOs, resulting in efficient compositional analysis and profiling in various milk samples. This review aims to give an overview of the current state‐of‐the‐art techniques used in HMO analysis.
The influence of reduced light intensity on the response of benthic diatoms to herbicide exposure
Authors: Wood Rebecca J. , Mitrovic Simon M. , Lim Richard P. , Kefford Ben J.
Published: January 2016

Herbicide pollution events in aquatic ecosystems often coincide with increased turbidity and reduced light intensity. It is therefore important to determine whether reduced light intensity can influence herbicide toxicity, especially to primary producers such as benthic diatoms. Benthic diatoms collected from 4 rivers were exposed to herbicides in 48 h rapid toxicity tests under high light (100 µmol m−2 s−1) and low light (20 µmol m−2 s−1) intensities. The effects of 2 herbicides (atrazine and glyphosate) were assessed on 26 freshwater benthic diatom taxa. There was no significant interaction of light and herbicide effects at the community level or on the majority (22 of 26) of benthic diatom taxa. This indicates that low light levels will likely have only a minor influence on the response of benthic diatoms to herbicides. Environ Toxicol Chem 2016;35:2252–2260. © 2016 SETAC
Mixture toxicity and interactions of copper, nickel, cadmium, and zinc to barley at low effect levels: Something from nothing?
Authors: Versieren Liske , Evers Steffie , De Schamphelaere Karel , Blust Ronny , Smolders Erik
Published: January 2016

Metal contamination is mostly a mixture of different metals, and these multicomponent mixtures can produce significant mixture effects. The present study was set up to investigate the toxicity of multiple metal mixtures of Cu, Ni, Cd, and Zn to plants at metal doses individually causing low-level phytotoxic effects. Barley (Hordeum vulgare L.) root elongation toxicity tests were performed in resin-buffered nutrient solutions to control metal speciation. Treatments included single-metal concentrations and binary, ternary, and quaternary mixtures. Mixtures of different metals at free ion concentrations, each causing <10% inhibition of root elongation, yielded significant mixture effects, with inhibition reaching up to 50%. The independent action (IA) model predicted mixture toxicity statistically better than the concentration addition (CA) model, but some synergisms relative to the IA model were observed. These synergisms relative to IA were most pronounced in quaternary mixtures and when the dose–response curves had steep slopes. Generally, antagonistic interactions relative to the CA model were observed. Increasing solution Zn concentrations shifted metal interactions (CA based) from additive or slightly synergistic at background Zn concentrations to antagonistic at higher Zn concentrations, suggesting a protective effect of Zn. Overall, the present study shows that the CA model can be used as a conservative model to predict metal mixture toxicity to barley. Environ Toxicol Chem 2016;35:2483–2492. © 2016 SETAC
Degradation and transformation of 17α-trenbolone in aerobic water–sediment systems
Authors: Robinson Joseph A. , Ma Qingli , Staveley Jane P. , Smolenski Walter J. , Ericson Jon
Published: January 2016

Synovex® ONE is an extended-release implant containing the active ingredients estradiol benzoate and trenbolone acetate for use in beef steers and heifers. Trenbolone acetate is rapidly hydrolyzed in cattle to form 17β-trenbolone and its isomer, 17α-trenbolone, which are further transformed to a secondary metabolite, trendione. As part of the environmental assessment for the use of Synovex ONE, data were generated to characterize the fate of 17α-trenbolone, which is the principal metabolite found in cattle excreta, in the environment. A study was conducted to determine the degradation and transformation of [14C]-17α-trenbolone in 2 representative water–sediment systems under aerobic conditions. The same transformation products, 17β-trenbolone and trendione, were formed, principally in the sediment phase, in both systems. From the production of these transformation products, the 50% disappearance time (DT50) values of 17β-trenbolone and trendione were determined, along with the DT50 values of the parent compound and the total drug (17α-trenbolone + 17β-trenbolone + trendione). The DT50 values for the total system (aqueous and sediment phase) and for the total residues (17α-trenbolone + 17β-trenbolone + trendione) in the 2 systems were 34.7 d and 53.3 d, respectively. Environ Toxicol Chem 2017;36:630–635. © 2016 SETAC
Sensitivity of six subantarctic marine invertebrates to common metal contaminants
Authors: Holan Jessica R. , King Catherine K. , Davis Andrew R.
Published: January 2016

A long history of anthropogenic activities in the relatively pristine subantarctic has resulted in areas of accumulated waste and contaminants. Sensitivities to metals of subantarctic and Antarctic species may contrast with related species from temperate and tropical areas because of the unique characteristics of polar biota. In addition, response to contaminants may be delayed, and hence longer exposure periods may be required in toxicity tests with polar species. In the present study, the sensitivity of 6 common subantarctic marine invertebrates to copper, zinc, and cadmium contaminants was determined. Large variations in sensitivities, both between species and between metals within species, were found. The bivalve Gaimardia trapesina and the copepod Harpacticus sp. were the most sensitive to copper, with 7-d median lethal concentration (LC50) values for both species ranging between 28 μg/L and 62 μg/L, whereas the copepod Tigriopus angulatus was the most tolerant of copper (7-d Cu LC50 1560 μg/L). Sensitivity to zinc varied by approximately 1 order of magnitude between species (7-d LC50: 329–3057 μg/L). Sensitivity to cadmium also varied considerably between species, with 7-d LC50 values ranging from 1612 μg/L to >4383 μg/L. The present study is the first to report the sensitivity of subantarctic marine invertebrate to metals, and contributes significantly to the understanding of latitudinal gradients in the sensitivity of biota to metals. Although sensitivity is highly variable between species, in a global comparison of copepod data, it appears that species from higher latitudes may be more sensitive to copper. Environ Toxicol Chem 2016;35:2245–2251. © 2016 SETAC
Evaluation of different fermentation processes for use by small cocoa growers in mexico
Authors: Hernández‐ Hernández C. , López‐Andrade Procopio Alejandro , Ramírez‐Guillermo Miguel A. , Guerra Ramírez Diana , Caballero Pérez Juan F.
Published: January 2016

The aim of this research was to evaluate four different cacao (Theobroma cacao L.) fermentation conditions and their effect on fermented bean quality, in order to be able to recommend the most suitable condition to producers in the municipality of Huimanguillo, Tabasco, Mexico. Fermentations were carried out in square wooden boxes with capacity for 1000, 300, and 100 kg of fresh beans, as well as a rotary drum with capacity for 500 kg thereof. The fermentation process was carried out for 7 days, and the response variables measured were mass temperature, total soluble solids (TSS), pH, and acidity. The TSS were totally depleted after 2 days, during which time the yeasts transformed them into ethanol at temperatures of 25–35°C. The most notable temperature increase in the four treatments was 49°C on the third day, corresponding to a decrease in pH from 6.31 ± 0.40 to 4.76 ± 0.03 and an increase in acidity from 0.38 ± 0.04 to 1.17 ± 0.25 g kg−1, due to the formation of organic acids. There were no significant differences among the four treatments (Tukey α = 0.05). The cut test showed that fermentation in 300‐ and 100‐kg boxes and in the 500‐kg rotary drum produced the same effect on fermentation quality, but the 1000‐kg boxes exhibited lower quality (Tukey α = 0.05).
Differential alterations of resting‐state functional connectivity in generalized anxiety disorder and panic disorder
Authors: Cui Huiru , Zhang Jie , Liu Yicen , Li Qingwei , Li Hui , Zhang Lanlan , Hu Qiang , Cheng Wei , Luo Qiang , Li Jianqi , Li Wei , Wang Jijun , Feng Jianfeng , Li Chunbo , Northoff Georg
Published: January 2016

Generalized anxiety disorder (GAD) and panic disorder (PD) are most common anxiety disorders with high lifetime prevalence while the pathophysiology and disease‐specific alterations still remain largely unclear. Few studies have taken a whole‐brain perspective in the functional connectivity (FC) analysis of these two disorders in resting state. It limits the ability to identify regionally and psychopathologically specific network abnormalities with their subsequent use as diagnostic marker and novel treatment strategy. The whole brain FC using a novel FC metric was compared, that is, scaled correlation, which they demonstrated to be a reliable FC statistics, but have higher statistical power in two‐sample t‐test of whole brain FC analysis. About 21 GAD and 18 PD patients were compared with 22 matched control subjects during resting‐state, respectively. It was found that GAD patients demonstrated increased FC between hippocampus/parahippocampus and fusiform gyrus among the most significantly changed FC, while PD was mainly associated with greater FC between somatosensory cortex and thalamus. Besides such regional specificity, it was observed that psychopathological specificity in that the disrupted FC pattern in PD and GAD correlated with their respective symptom severity. The findings suggested that the increased FC between hippocampus/parahippocampus and fusiform gyrus in GAD were mainly associated with a fear generalization related neural circuit, while the greater FC between somatosensory cortex and thalamus in PD were more likely linked to interoceptive processing. Due to the observed regional and psychopathological specificity, their findings bear important clinical implications for the potential treatment strategy. Hum Brain Mapp 37:1459‐1473, 2016. © 2016 Wiley Periodicals, Inc.
Altered short‐term plasticity within the working memory neural network: Is it neuroticism or is it depression?
Authors: Bianchi Renzo , Laurent Eric
Published: January 2016

In the present article, we discuss (1) the importance of assessing and statistically considering both clinical and subclinical forms of depression when examining the relationship between neuroticism and short‐term plasticity within the working memory neural network, and (2) the hypothesis of an antagonism between neuroticism and conscientiousness in personality research. We suggest that (1) neuroticism and depression should be examined in a relational manner, and (2) neuroticism and conscientiousness should not be antagonized. Hum Brain Mapp 37:1512‐1513, 2016. © 2016 Wiley Periodicals, Inc.
The plastic cellular states of liver cells: Are EpCAM and Lgr5 fit for purpose?
Authors: Huch Meritxell , Dollé Laurent
Published: January 2016

Adult liver cells have been considered restricted regarding their fate and lineage potential. That is, hepatocytes have been thought able only to generate hepatocytes and duct cells, only duct cells. While this may be the case for the majority of scenarios in a state of quiescence or homeostasis, evidence suggests that liver cells are capable of interconverting between cellular states of distinct phenotypic traits. This interconversion or plasticity had been suggested by classical studies using cellular markers, but recently lineage tracing approaches have proven that cells are highly plastic and retain an extraordinary ability to respond differently to normal tissue homeostasis, to tissue repair, or when challenged to expand ex vivo or to differentiate upon transplantation. Stemness, as “self‐renewal and multipotency,” seems not to be limited to a particular cell type but rather to a cellular state in which cells exhibit a high degree of plasticity and can move back and forth in different phenotypic states. For instance, upon damage cells can dedifferentiate to acquire stem cell potential that allows them to self‐renew, repopulate a damaged tissue, and then undergo differentiation. In this review, we will discuss the evidence on cellular plasticity in the liver, focusing our attention on two markers, epithelial cell adhesion molecule and leucine‐rich repeat‐containing G protein‐coupled receptor 5, which identify cells with stem cell potential. (Hepatology 2016;64:652‐662)
Lithological control of land subsidence induced by groundwater withdrawal in new urban AREAS (Granada Basin, SE Spain). Multiband DInSAR monitoring
Authors: Notti Davide , Mateos Rosa María , Monserrat Oriol , Devanthéry Nùria , Peinado Tomás , Roldán Francisco Javier , Fernández‐Chacón Francisca , Galve Jorge Pedro , Lamas Francisco , Azañón Jose Miguel
Published: January 2016

Ground subsidence in the southeastern border of the Granada Basin (SE Spain) has been studied using remote sensing techniques. Over the last decades, the region has experienced a huge urban expansion, which has caused a substantial increase in water supply requirements. Water needs are exclusively met by groundwater by means of numerous pumping wells, which exploit a confined detrital aquifer of alluvial fan deposits with a heterogeneous facies distribution. A general piezometric level decline (up to 50 m) has been recorded in the aquifer during the past 30 years that has induced the generation of a subsiding area with oval shape oriented WNW‐ESE just where the new urban areas and pumping wells are located. Subsidence has been monitored by exploiting synthetic aperture radar (SAR) images from ENVISAT (2003–2009) and Cosmo‐SkyMed (2011–2014). A new approach, which combines A‐DInSAR and small‐area persistent scatterer interferometry (PSI) analysis, has been applied obtaining a good accuracy regarding temporal and spatial dimension of the subsidence. ENVISAT data (2003–2009) reveal subsidence rates up to 10–15 mm/year, and Cosmo‐SkyMed (2011–2014) values slightly lower; up to 10 mm/year. Temporal variations in the subsidence velocity are in accordance with the rainfall pattern and piezometric fluctuations in the aquifer. The sector with highest rates of subsidence does not correspond to the area with more intense groundwater exploitation but to the area with greater presence of clays in the confining layer of the aquifer. There is a clear lithological control in the spatial distribution of the ground subsidence. This work integrates detailed geological and hydrogeological data with differential SAR interferometry monitoring with the aim to better understand subsidence processes in detrital aquifers with small‐scale heterogeneity. Copyright © 2016 John Wiley & Sons, Ltd.
Aberrant splicing of the DMP1‐ARF‐MDM2‐p53 pathway in cancer
Authors: Inoue Kazushi , Fry Elizabeth A.
Published: January 2016

Alternative splicing (AS) of mRNA precursors is a ubiquitous mechanism for generating numerous transcripts with different activities from one genomic locus in mammalian cells. The gene products from a single locus can thus have similar, dominant‐negative or even opposing functions. Aberrant AS has been found in cancer to express proteins that promote cell growth, local invasion and metastasis. This review will focus on the aberrant splicing of tumor suppressor/oncogenes that belong to the DMP1‐ARF‐MDM2‐p53 pathway. Our recent study shows that the DMP1 locus generates both tumor‐suppressive DMP1α (p53‐dependent) and oncogenic DMP1β (p53‐independent) splice variants, and the DMP1β/α ratio increases with neoplastic transformation of breast epithelial cells. This process is associated with high DMP1β protein expression and shorter survival of breast cancer (BC) patients. Accumulating pieces of evidence show that ARF is frequently inactivated by aberrant splicing in human cancers, demonstrating its involvement in human malignancies. Splice variants from the MDM2 locus promote cell growth in culture and accelerate tumorigenesis in vivo. Human cancers expressing these splice variants are associated with advanced stage/metastasis, and thus have negative clinical impacts. Although they lack most of the p53‐binding domain, their activities are mostly dependent on p53 since they bind to wild‐type MDM2. The p53 locus produces splice isoforms that have either favorable (β/γ at the C‐terminus) or negative impact (Δ40, Δ133 at the N‐terminus) on patients' survival. As the oncogenic AS products from these loci are expressed only in cancer cells, they may eventually become targets for molecular therapies.
Winner of the Young Investigator Award of the Society for Biomaterials (USA) for 2016, 10th World Biomaterials Congress, May 17–22, 2016, Montreal QC, Canada: Aligned microribbon‐like hydrogels for guiding three‐dimensional smooth muscle tissue regeneration
Authors: Lee Soah , Tong Xinming , Han Li‐Hsin , Behn Anthony , Yang Fan
Published: January 2016

Smooth muscle tissue is characterized by aligned structures, which is critical for its contractile functions. Smooth muscle injury is common and can be caused by various diseases and degenerative processes, and there remains a strong need to develop effective therapies for smooth muscle tissue regeneration with restored structures. To guide cell alignment, previously cells were cultured on 2D nano/microgrooved substrates, but such method is limited to fabricating 2D aligned cell sheets only. Alternatively, aligned electrospun nanofiber has been employed as 3D scaffold for cell alignment, but cells can only be seeded post fabrication, and nanoporosity of electrospun fiber meshes often leads to poor cell distribution. To overcome these limitations, we report aligned gelatin‐based microribbons (µRBs) as macroporous hydrogels for guiding smooth muscle alignment in 3D. We developed aligned µRB‐like hydrogels using wet spinning, which allows easy fabrication of tissue‐scale (cm) macroporous matrices with alignment cues and supports direct cell encapsulation. The macroporosity within µRB‐based hydrogels facilitated cell proliferation, new matrix deposition, and nutrient diffusion. In aligned µRB scaffold, smooth muscle cells showed high viability, rapid adhesion, and alignment following µRB direction. Aligned µRB scaffolds supported retention of smooth muscle contractile phenotype, and accelerated uniaxial deposition of new matrix (collagen I/IV) along the µRB. In contrast, cells encapsulated in conventional gelatin hydrogels remained round with matrix deposition limited to pericellular regions only. We envision such aligned µRB scaffold can be broadly applicable in growing other anisotropic tissues including tendon, nerves and blood vessel. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1064–1071, 2016.
Immunomodulatory effects of amniotic membrane matrix incorporated into collagen scaffolds
Authors: Hortensius Rebecca A. , Ebens Jill H. , Harley Brendan A. C.
Published: January 2016

Adult tendon wound repair is characterized by the formation of disorganized collagen matrix which leads to decreases in mechanical properties and scar formation. Studies have linked this scar formation to the inflammatory phase of wound healing. Instructive biomaterials designed for tendon regeneration are often designed to provide both structural and cellular support. In order to facilitate regeneration, success may be found by tempering the body's inflammatory response. This work combines collagen‐glycosaminoglycan scaffolds, previously developed for tissue regeneration, with matrix materials (hyaluronic acid and amniotic membrane) that have been shown to promote healing and decreased scar formation in skin studies. The results presented show that scaffolds containing amniotic membrane matrix have significantly increased mechanical properties and that tendon cells within these scaffolds have increased metabolic activity even when the media is supplemented with the pro‐inflammatory cytokine interleukin‐1 beta. Collagen scaffolds containing hyaluronic acid or amniotic membrane also temper the expression of genes associated with the inflammatory response in normal tendon healing (TNF‐α, COLI, MMP‐3). These results suggest that alterations to scaffold composition, to include matrix known to decrease scar formation in vivo, can modify the inflammatory response in tenocytes. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1332–1342, 2016.
Biological functionality of extracellular matrix‐ornamented three‐dimensional printed hydroxyapatite scaffolds
Authors: Kumar A. , Nune K. C. , Misra R. D. K.
Published: January 2016

Three‐dimensional (3D) printing is considered an ideally suitable method to fabricate patient specific implantable devices. The approach enabled to produce a porous scaffold with tailored physical, mechanical, and biological properties because of the flexibility to tune the scaffold architecture. The objective of the study described was to elucidate the determining role of cell‐laid extracellular matrix (ECM) in impacting biological response. In this regard, to mimic the natural ECM environment or the attributes of the native tissue, a natural ECM analogue surface was produced on the 3D printed and sintered hydroxyapatite (HA) scaffold surface by the mineralized ECM of the osteoblast. This involved the growth of osteoblast on 3D printed scaffolds, followed by differentiation to deposit the mineralized ECM on the biomaterial surface. The cells were removed from the mineralized matrix using freeze–thaw cycles to obtain a decellularized extracellular matrix (dECM) on the biomaterial surface. Subsequently, seeding of osteoblast on dECM‐ornamented HA scaffolds led to 3D growth with enhanced expression of prominent proteins, actin and vinculin. Based on preliminary observations of present study, it was underscored that HA scaffolds‐ornamented with dECM provided an optimized microenvironment conducive to the growth of 3D structural tissue and favorably promoted biological functionality because of the availability of an environment that promoted cell–cell and cell–scaffold interaction. The primary advantage of dECM is that it enabled constructive remodeling and promoted the formation of tissue in lieu of less functional tissue. The study opens‐up a new path for printing of 3D structures suitable to treat segmental bone defects. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1343–1351, 2016.
Proteomic and peptidomic profiling of Brazilian artisanal ‘Coalho’ cheese
Authors: Silva Roberto A , Bezerra Vilma S , Pimentel Maria do Carmo B , Porto Ana Lúcia F , Cavalcanti Maria Taciana H , Filho José Luiz L
Published: January 2016

BACKGROUND

Artisanal ‘Coalho’ cheese is a product typically popular in the Brazilian north‐eastern region. Production of this cheese represents about 9.2% of the internal crude product of Pernambuco State. Several peptides are generated from hydrolysis of αS1‐, αS2‐, β‐, and κ‐caseins during manufacture of this cheese. The commercial importance of Brazilian artisanal ‘Coalho’ cheese justifies the examination of both the protein and peptide profiles of cheeses from six cities of the semi‐arid region of Pernambuco State, Brazil.

RESULTS

SDS‐PAGE of the aqueous extracts of ‘Coalho’ cheeses (WSP) showed bands of lactoferrin, β‐lactoglobulin, β‐lactoglobulin (dimer), α‐lactoalbumin, bovine serum albumin, α‐casein, β‐casein, κ‐casein and para‐κ‐casein. A total of 57 to 72 peptides were confirmed by mass spectra in the different samples of ‘Coalho’ cheese which 32 known peptides (11 from αS1‐casein, three from αS2‐casein, 15 from β‐casein and three from κ‐casein), comprising seven caseinphosphopeptides. Among the unidentified peptides, three showed high intensity peaks in all ‘Coalho’ cheeses studied (with molecular weights of 1597, 1725/1726, 2778/2779 Da).

CONCLUSION

The proteomic studies revealed peptides that may represent molecular markers or fingerprints for investigating the quality control and regional characterisation of these ‘Coalho’ cheeses. © 2016 Society of Chemical Industry
Chromatographic fractionation and molecular mass characterization of Cercidium praecox (Brea) gum
Authors: Castel Virginia , Zivanovic Svetlana , Jurat‐Fuentes Juan L , Santiago Liliana G , Rubiolo Amelia C , Carrara Carlos R , Harte Federico M
Published: January 2016

BACKGROUND

Brea gum (BG) is an exudate from the Cercidium praecox tree that grows in semi‐arid regions of Argentina. Some previous studies on BG have shown physicochemical characteristics and functional features similar to those of gum arabic. However, there is a need to elucidate the molecular structure of BG to understand the functionality. In this sense, BG was fractionated using hydrophobic interaction chromatography and the obtained fractions were analyzed by size exclusion chromatography.

RESULTS

Analysis of the fractions showed that the bulk of the gum (approx. 84% of the polysaccharides) was a polysaccharide of 2.79 × 103 kDa. The second major fraction (approx. 16% of the polysaccharides) was a polysaccharide–protein complex with a molecular mass of 1.92 × 105 kDa. A third fraction consisted of protein species with a wide range of molecular weights. The molecular weight distribution of the protein fraction was analyzed by size exclusion chromatography. Comparison of the elution profiles of the exudates in native and reducing conditions revealed that some of the proteins were forming aggregates through disulfide bridges in native conditions. Further analysis of the protein fraction by SDS‐PAGE showed proteins with molecular weight ranging from 6.5 to 66 kDa.

CONCLUSIONS

The findings showed that BG consists of several fractions with heterogeneous chemical composition and polydisperse molecular weight distributions. © 2016 Society of Chemical Industry