bluuebunny/crossref_metadata_2025 huggingface dataset:
Mannose metabolism in recombinant CHO cells and its effect on IgG glycosylation
Authors: Slade Peter G. , Caspary R. Guy , Nargund Shilpa , Huang Chung‐Jr
Published: January 2016

Understanding the causes of high‐mannose (HM) glycosylation of recombinant IgG in CHO cells would facilitate the production of therapeutics. CHO cells grown with mannose as the major carbon source demonstrated a dramatic increase in total HM glycosylation in recombinant IgG, with no effect on cell growth, viability, or titer. Quantitative metabolomics and 13C flux analysis were used to explore the mechanism for increased HM glycosylation and understand the metabolism of mannose in CHO cells. It was demonstrated that mannose was a good carbon source for CHO cell growth and IgG production, readily entering both glycolysis and the TCA Cycle. Previous mechanisms for increased HM glycosylation during antibody production have been attributed to changes in pH, osmolality, increased specific productivity, and nutrient limitation. The results from this study propose a novel mechanism where an increased carbon flux in the GDP‐mannose synthetic pathway increased the intracellular concentration of mannose‐containing metabolites. The abnormally high concentration of mannose and mannose–metabolites were shown to inhibit α‐mannosidase activity and it was proposed that this inhibition in the ER and Golgi caused the production of IgG with increased high‐mannose glycosylation. Biotechnol. Bioeng. 2016;113: 1468–1480. © 2016 Wiley Periodicals, Inc.
Fully automatized high‐throughput enzyme library screening using a robotic platform
Authors: Dörr Mark , Fibinger Michael P.C. , Last Daniel , Schmidt Sandy , Santos‐Aberturas Javier , Böttcher Dominique , Hummel Anke , Vickers Clare , Voss Moritz , Bornscheuer Uwe T.
Published: January 2016

A fully automatized robotic platform has been established to facilitate high‐throughput screening for protein engineering purposes. This platform enables proper monitoring and control of growth conditions in the microtiter plate format to ensure precise enzyme production for the interrogation of enzyme mutant libraries, protein stability tests and multiple assay screenings. The performance of this system has been exemplified for four enzyme classes important for biocatalysis such as Baeyer–Villiger monooxygenase, transaminase, dehalogenase and acylase in the high‐throughput screening of various mutant libraries. This allowed the identification of novel enzyme variants in a sophisticated and highly reliable manner. Furthermore, the detailed optimization protocols should enable other researchers to adapt and improve their methods. Biotechnol. Bioeng. 2016;113: 1421–1432. © 2016 Wiley Periodicals, Inc.
Identification of an important motif that controls the activity and specificity of sugar transporters
Authors: Wang Meng , Yu Chenzhao , Zhao Huimin
Published: January 2016

Efficient glucose–xylose co‐utilization is critical for economical biofuel production from lignocellulosic biomass. To enable glucose–xylose co‐utilization, a highly active xylose specific transporter without glucose inhibition is desirable. However, our understanding of the structure‐activity/specificity relationship of sugar transporters in general is limited, which hinders our ability to engineer xylose‐specific transporters. In this study, via homology modeling and analysis of hexose sugar transporter HXT14 mutants, we identified a highly conserved YYX(T/P) motif that plays an important role in controlling the activity and specificity of sugar transporters. We demonstrated that mutating the two tyrosine residues of the motif to phenylalanine, respectively, improved glucose transport capacity across several different sugar transporters. Furthermore, we illustrated that by engineering the fourth position in the YYX(T/P) motif, the sugar specificity of transporters was significantly altered or even reversed towards xylose. Finally, using the engineered sugar transporter, genuine glucose–xylose co‐fermentation was achieved. Biotechnol. Bioeng. 2016;113: 1460–1467. © 2016 Wiley Periodicals, Inc.
Combinatorial optimization of CO2 transport and fixation to improve succinate production by promoter engineering
Authors: Yu Jun‐Han , Zhu Li‐Wen , Xia Shi‐Tao , Li Hong‐Mei , Tang Ya‐Ling , Liang Xin‐Hua , Chen Tao , Tang Ya‐Jie
Published: January 2016

To balance the flux of an engineered metabolic pathway to achieve high yield of target product is a major challenge in metabolic engineering. In previous work, the collaborative regulation of CO2 transport and fixation was investigated with co‐overexpressing exogenous genes regulating both CO2 transport (sbtA and bicA) and PEP carboxylation (phosphoenolpyruvate (PEP) carboxylase (ppc) and carboxykinase (pck)) under trc promoter in Escherichia coli for succinate biosynthesis. For balancing metabolic flux to maximize succinate titer, a combinatorial optimization strategy to fine‐tuning CO2 transport and fixation process was implemented by promoter engineering in this study. Firstly, based on the energy matrix a synthetic promoter library containing 20 rationally designed promoters with strengths ranging from 0.8% to 100% compared with the widely used trc promoter was generated. Evaluations of rfp and cat reporter genes provided evidence that the synthetic promoters were stably and had certain applicability. Secondly, four designed promoters with different strengths were used for combinatorial assembly of single CO2 transport gene (sbtA or bicA) and single CO2 fixation gene (ppc or pck) expression. Three combinations, such as Tang1519 (P4‐bicA + pP19‐pck), Tang1522 (P4‐sbtA + P4‐ppc), Tang1523 (P4‐sbtA + P17‐ppc) with a more than 10% increase in succinate production were screened in bioreactor. Finally, based on the above results, co‐expression of the four transport and fixation genes were further investigated. Co‐expression of sbtA, bicA, and ppc with weak promoter P4 and pck with strong promoter P19 (AFP111/pT‐P4‐bicA‐P4‐sbtA + pACYC‐P19‐pck‐P4‐ppc) provided the best succinate production among all the combinations. The highest succinate production of 89.4 g/L was 37.5% higher than that obtained with empty vector control. This work significantly enhanced succinate production through combinatorial optimization of CO2 transport and fixation. The promoter engineering and combinatorial optimization strategies used herein represents a powerful approach to tailor‐making metabolic pathways for the production of other industrially important chemicals. Biotechnol. Bioeng. 2016;113: 1531–1541. © 2016 Wiley Periodicals, Inc.
Tunable osteogenic differentiation of hMPCs in tubular perfusion system bioreactor
Authors: Nguyen Bao‐Ngoc B. , Ko Henry , Fisher John P.
Published: January 2016

The use of bioreactors for bone tissue engineering has been widely investigated. While the benefits of shear stress on osteogenic differentiation are well known, the underlying effects of dynamic culture on subpopulations within a bioreactor are less evident. In this work, we explore the influence of applied flow in the tubular perfusion system (TPS) bioreactor on the osteogenic differentiation of human mesenchymal progenitor cells (hMPCs), specifically analyzing the effects of axial position along the growth chamber. TPS bioreactor experiments conducted with unidirectional flow demonstrated enhanced expression of osteogenic markers in cells cultured downstream from the inlet flow. We utilized computational fluid dynamic modeling to confirm uniform shear stress distribution on the surface of the scaffolds and along the length of the growth chamber. The concept of paracrine signaling between cell populations was validated with the use of alternating flow, which diminished the differences in osteogenic differentiation between cells cultured at the inlet and outlet of the growth chamber. After the addition of controlled release of bone morphogenic protein‐2 (BMP‐2) into the system, osteogenic differentiation among subpopulations along the growth chamber was augmented, yet remained homogenous. These results allow for greater understanding of axial bioreactor cultures, their microenvironment, and how well‐established parameters of osteogenic differentiation affect bone tissue development. With this work, we have demonstrated the capability of tuning osteogenic differentiation of hMPCs through the application of fluid flow and the addition of exogenous growth factors. Such precise control allows for the culture of distinct subpopulation within one dynamic system for the use of complex engineered tissue constructs. Biotechnol. Bioeng. 2016;113: 1805–1813. © 2016 Wiley Periodicals, Inc.
A droplet microfluidics platform for rapid microalgal growth and oil production analysis
Authors: Kim Hyun Soo , Guzman Adrian R. , Thapa Hem R. , Devarenne Timothy P. , Han Arum
Published: January 2016

Microalgae have emerged as a promising source for producing future renewable biofuels. Developing better microalgal strains with faster growth and higher oil production rates is one of the major routes towards economically viable microalgal biofuel production. In this work, we present a droplet microfluidics‐based microalgae analysis platform capable of measuring growth and oil content of various microalgal strains with single‐cell resolution in a high‐throughput manner. The platform allows for encapsulating a single microalgal cell into a water‐in‐oil emulsion droplet and tracking the growth and division of the encapsulated cell over time, followed by on‐chip oil quantification. The key feature of the developed platform is its capability to fluorescently stain microalgae within microdroplets for oil content quantification. The performance of the developed platform was characterized using the unicellular microalga Chlamydomonas reinhardtii and the colonial microalga Botryococcus braunii. The application of the platform in quantifying growth and oil accumulation was successfully confirmed using C. reinhardtii under different culture conditions, namely nitrogen‐replete and nitrogen‐limited conditions. These results demonstrate the capability of this platform as a rapid screening tool that can be applied to a wide range of microalgal strains for analyzing growth and oil accumulation characteristics relevant to biofuel strain selection and development. Biotechnol. Bioeng. 2016;113: 1691–1701. © 2016 Wiley Periodicals, Inc.
Synthetic and natural consensus design for engineering charge within an affibody targeting epidermal growth factor receptor
Authors: Case Brett A. , Hackel Benjamin J.
Published: January 2016

Protein ligand charge can impact physiological delivery with charge reduction often benefiting performance. Yet neutralizing mutations can be detrimental to protein function. Herein, three approaches are evaluated to introduce charged‐to‐neutral mutations of three cations and three anions within an affibody engineered to bind epidermal growth factor receptor. These approaches—combinatorial library sorting or consensus design, based on natural homologs or library‐sorted mutants—are used to identify mutations with favorable affinity, stability, and recombinant yield. Consensus design, based on 942 affibody homologs, yielded a mutant of modest function (Kd = 11 ±4 nM, Tm = 62°C, and yield = 4.0 ± 0.8 mg/L as compared to 5.3 ± 1.7 nM, 71°C, and 3.5 ± 0.3 mg/L for the parental affibody). Extension of consensus design to 10 additional mutants exhibited varied performance including a substantially improved mutant (Kd = 6.9 ± 1.4 nM, Tm = 71°C, and 12.7 ± 0.9 mg/L yield). Sorting a homolog‐based combinatorial library of 7 × 105 mutants generated a distribution of mutants with lower stability and yield, but did identify one strongly binding variant (Kd = 1.2 ± 0.3 nM, Tm = 69°C, and 6.0 ± 0.4 mg/L yield). Synthetic consensus design, based on the amino acid distribution in functional library mutants, yielded higher affinities (P = 0.05) with comparable stabilities and yields. The best of four analyzed clones had Kd = 1.7 ± 0.5 nM, Tm = 68°C, and 7.0 ± 0.5 mg/L yield. While all three approaches were effective in creating targeted affibodies with six charged‐to‐neutral mutations, synthetic consensus design proved to be the most robust. Synthetic consensus design provides a valuable tool for ligand engineering, particularly in the context of charge manipulation. Biotechnol. Bioeng. 2016;113: 1628–1638. © 2016 Wiley Periodicals, Inc.
Redistribution of connexin 43 during cell division
Authors: Vanderpuye Oluseyi A. , Bell Cheryl L. , Murray Sandra A.
Published: January 2016

Gap junction channels, once clustered into gap junction plaques, allow communication of essential metabolites between cells. Gap junction plaques have been reported to be lost from the cell surface during cell division. The mechanism involved in this loss of gap junction plaques during mitosis is unclear, but we hypothesize that an endoexocytotic mechanism that results in cytoplasmic double‐membraned annular gap junction vesicles is involved. In this study, gap junction plaque changes in dividing cells were examined in SW‐13 adrenocortical tumor cells. Endogenous gap junction protein, connexin 43 (Cx43), was detected with immunofluorescence, and live cell imaging was used to monitor green fluorescent protein‐tagged Cx43 (Cx43‐GFP). Mitotic stages were identified by Hoechst chromosomal staining. During interphase, large gap junction plaques were detected; however, the presence of these plaques decreased, whereas cytoplasmic puncta increased beginning with prophase. The cytoplasmic puncta were demonstrated with immunoelectron microscopy to be Cx43‐ positive annular gap junction vesicles. As gap junction plaques reformed at cleavage furrows between daughter cells, the number of annular gap junctions decreased during cytokinesis. The data are consistent with the mechanism of gap junction plaque loss during mitosis relying on an endoexocytotic process that results in annular gap junction vesicles formation. The rapid formation of gap junction plaques during cytokinesis points to the intriguing possibility of connexin recycling from annular gap junction vesicles to form gap junction plaques as mitosis is completed.
A new breakable stent for recoarctation in early infancy: Preliminary Clinical Experience
Authors: Grohmann Jochen , Sigler Matthias , Siepe Matthias , Stiller Brigitte
Published: January 2016

Objectives

Transcatheter treatment of aortic coarctation (CoA) via stent implantation has become an established treatment option depending on the patient's age and CoA type.

Background

The Osypka BabyStent® is a low‐profiled, balloon‐expandable cobalt‐chrome stent to treat aortic CoA in infants, which is breakable to permit unrestricted growth. We hereby evaluated our initial clinical experience to demonstrate the feasibility and efficacy of this new nonlicensed device, which we have occasionally implanted in critically ill patients or when redo‐surgery would entail an excessively high risk.

Methods

Retrospective single‐center analysis of all available data during and after treatment with a BabyStent implanted in infants with considerable re‐CoA or reobstruction of the aortic arch after former surgery. All interventions took place under fluoroscopy and conscious sedation with local anesthesia or general anesthesia.

Results

Five BabyStents were implanted in four infants with technical success in all of them—median age 10 weeks (range 5–21), median bodyweight 3.8 kg (range 2.7–4.5). Aortic diameters enlarged from median 2.25 mm (range 1.5–3.3) to median 5.3 mm (range 4.6–6.0). The follow‐up period lasting up to 26 months (median 8.5, range 2–26) was uneventful concerning stent‐related complications.

Conclusions

BabyStent® implantation for recoarctation was effective. However, our initial experience with the device is limited to short‐ and midterm follow‐up only. None of the stents was subsequently overdilated with the intention to break due to our patients’ limited somatic growth so far. A multicenter survey has been initiated to justify device approval. © 2016 Wiley Periodicals, Inc.
Complete resolution of non‐necrotizing lung granuloma and pyoderma gangrenosum after restorative proctocolectomy in a woman with severe ulcerative colitis and cytomegalovirus infection
Authors: Sartini Alessandro , Bianchini Marcello , Schepis Filippo , Marzi Luca , De Maria Nicola , Villa Erica
Published: January 2016

Key Clinical Message

Here, we report the unusual case of an ulcerative colitis female patient presenting together with cytomegalovirus infection, pyoderma gangrenosum and a noncaseating lung granuloma, both resistant to immunomodulatory drugs which dramatically obtained a clinical stable remission after restorative proctocolectomy.
The diffusion dynamics of choice: From durable goods markets to fashion first names
Authors: Coulmont Baptiste , Supervie Virginie , Breban Romulus
Published: January 2016

Goods, styles, ideologies are adopted by society through various mechanisms. In particular, adoption driven by innovation is extensively studied by marketing economics. Mathematical models are currently used to forecast sales of innovative goods. Inspired by the theory of diffusion processes developed for marketing economics, we propose a modelling framework for the mechanism of fashion, which we apply to first names. Analyses of French, Dutch, and US national databases validate our modelling approach for thousands of first names, covering, on average, more than 50% of the yearly incidence in each database. In these cases, it is thus possible to study how first names become popular and when they run out of fashion. Furthermore, we uncover a clear distinction between popularity and fashion: less popular names, typically not included in studies of fashion, may be driven by fashion, as well. © 2016 The Authors Complexity Published byWiley Periodicals, Inc. Complexity 21: 362–369, 2016
Age‐related and light‐induced plasticity in opsin gene expression and in primary and secondary visual centers of the nectar‐feeding ant Camponotus rufipes
Authors: Yilmaz Ayse , Lindenberg Annekathrin , Albert Stefan , Grübel Kornelia , Spaethe Johannes , Rössler Wolfgang , Groh Claudia
Published: January 2016

Camponotus rufipes workers are characterized by an age‐related polyethism. In the initial weeks of adult life, young workers perform tasks inside the nest before they switch to multimodal foraging tasks outside. We tested the hypothesis that this transition is accompanied by profound adaptations in the peripheral and central visual systems. Our results show that C. rufipes workers of all tested ages (between 1 and 42 days) express three genes encoding for ultraviolet (UV), blue (BL), and long‐wavelength (LW1) sensitive opsins in their retina, which are likely to provide the substrate for trichromatic color vision. Expression levels of all three opsin genes increased significantly within the first two weeks of adulthood and following light exposure. Interestingly, the volumes of all three optic neuropils (lamina, medulla, and lobula) showed corresponding volume increases. Tracing of connections to higher visual centers in the mushroom bodies (MBs) revealed only one optic pathway, the anterior superior optic tract, emerging from the medulla and sending segregated input to the MB‐calyx collar. The MB collar volumes and densities of synaptic complexes (microglomeruli, MGs) increased with age. Exposure to light for 4 days induced a decrease in MG densities followed by an increase after extended light exposure. This shows that plasticity in retinal opsin gene expression and structural neuroplasticity in primary and secondary visual centers comprise both “experience‐independent” and “experience‐dependent” elements. We conclude that both sources of plasticity in the visual system represent important components promoting optimal timing of the interior–forager transition and flexibility of age‐related division of labor. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 76: 1041–1057, 2016
Early postnatal maturation in vestibulospinal pathways involved in neck and forelimb motor control
Authors: Lambert François M. , Bras Hélène , Cardoit Laura , Vinay Laurent , Coulon Patrice , Glover Joel C.
Published: January 2016

To assess the organization and functional development of vestibulospinal inputs to cervical motoneurons (MNs), we have used electrophysiology (ventral root and electromyographic [EMG] recording), calcium imaging, trans‐synaptic rabies virus (RV) and conventional retrograde tracing and immunohistochemistry in the neonatal mouse. By stimulating the VIIIth nerve electrically while recording synaptically mediated calcium responses in MNs, we characterized the inputs from the three vestibulospinal tracts, the separate ipsilateral and contralateral medial vestibulospinal tracts (iMVST/cMVST) and the lateral vestibulospinal tract (LVST), to MNs in the medial and lateral motor columns (MMC and LMC) of cervical segments. We found that ipsilateral inputs from the iMVST and LVST were differentially distributed to the MMC and LMC in the different segments, and that all contralateral inputs to MMC and LMC MNs in each segment derive from the cMVST. Using trans‐synaptic RV retrograde tracing as well as pharmacological manipulation of VIIIth nerve‐elicited synaptic responses, we found that a substantial proportion of inputs to both neck and forelimb extensor MNs was mediated monosynaptically, but that polysynaptic inputs were also significant. By recording EMG responses evoked by natural stimulation of the vestibular apparatus, we found that vestibular‐mediated motor output to the neck and forelimb musculature became more robust during the first 10 postnatal days, concurrently with a decrease in the latency of MN discharge evoked by VIIIth nerve electrical stimulation. Together, these results provide insight into the complexity of vestibulospinal connectivity in the cervical spinal cord and a cogent demonstration of the functional maturation that vestibulospinal connections undergo postnatally. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 76: 1061–1077, 2016
Delays in GABAergic interneuron development and behavioral inhibition after prenatal stress
Authors: Lussier Stephanie J. , Stevens Hanna E.
Published: January 2016

Prenatal stress is associated with altered behavioral, cognitive, and psychiatric outcomes in offspring. Due to the importance of GABAergic systems in normal development and in psychiatric disorders, prenatal stress effects on these neurons have been investigated in animal models. Prenatal stress delays GABAergic progenitor migration, but the significance of these early developmental disruptions for the continued development of GABAergic cells in the juvenile brain is unclear. Here, we examined effects of prenatal stress on populations of GABAergic neurons in juvenile and adult medial frontal cortex (mFC) and hippocampus through stereological counting, gene expression, and relevant anxiety‐like and social behaviors. Postnatally, the total GABAergic cell number that peaks in adolescence showed altered trajectories in mFC and hippocampus. Parvalbumin neuron proportion in juvenile brain was altered by prenatal stress, but parvalbumin gene expression showed no differences. In adult brain, parvalbumin neuron proportions were altered by prenatal stress with opposite gene expression changes. Adult prenatally stressed offspring showed a lack of social preference on a three‐chambered task, increased anxiety‐like behavior on the elevated plus maze, and reduced center time in an open field. Despite a lack of significant group differences in adult total GABAergic cell populations, performance of these tasks was correlated with GABAergic populations in mFC and hippocampus. In conclusion, prenatal stress resulted in a delay in GABAergic cell number and maturation of the parvalbumin subtype. Influences of prenatal stress on GABAergic populations during developmentally dynamic periods and during adulthood may be relevant to the anxiety‐like behaviors that occur after prenatal stress. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 76: 1078–1091, 2016
Intraspecific variation in defense against a generalist lepidopteran herbivore in populations of Eruca sativa (Mill.)
Authors: Ogran Ariel , Landau Netanel , Hanin Nir , Levy Maggie , Gafni Yedidya , Barazani Oz
Published: January 2016

Populations of Eruca sativa (Brassicaceae) from desert and Mediterranean (Med) habitats in Israel differ in their defense against larvae of the generalist Spodoptera littoralis but not the specialist Pieris brassicae. Larvae of the generalist insect feeding on plants of the Med population gained significantly less weight than those feeding on the desert plants, and exogenous application of methyl jasmonate (MJ) on leaves of the Med plants significantly reduced the level of damage created by the generalist larvae. However, MJ treatment significantly induced resistance in plants of the desert population, whereas the generalist larvae caused similar damage to MJ‐induced and noninduced plants. Analyses of glucosinolates and expression of genes in their synthesis pathway indicated that defense in plants of the Med population against the generalist insect is governed by the accumulation of glucosinolates. In plants of the desert population, trypsin proteinase inhibitor activity was highly induced in response to herbivory by S. littoralis. Analysis of genes in the defense‐regulating signaling pathways suggested that in response to herbivory, differences between populations in the induced levels of jasmonic acid, ethylene, and salicylic acid mediate the differential defenses against the insect. In addition, expression analysis of myrosinase‐associated protein NSP2 suggested that in plants of the desert population, glucosinolates breakdown products were primarily directed to nitrile production. We suggest that proteinase inhibitors provide an effective defense in the desert plants, in which glucosinolate production is directed to the less toxic nitriles. The ecological role of nitrile production in preventing infestation by specialists is discussed.
Does measuring azimuthal variations in sap flux lead to more reliable stand transpiration estimates?
Authors: Komatsu Hikaru , Shinohara Yoshinori , Kume Tomonori , Tsuruta Kenji , Otsuki Kyoichi
Published: January 2016

Stand transpiration (E) estimated using the sap‐flux method includes uncertainty induced by variations in sap flux (F) within a tree (i.e. radial and azimuthal variations) and those between trees. Unlike radial variations, azimuthal variations are not particularly systematic (i.e. higher/lower F is not always recorded for a specific direction). Here, we present a theoretical framework to address the question on how to allocate a limited number of sensors to minimize uncertainty in E estimates. Specifically, we compare uncertainty in E estimates for two cases: (1) measuring F for two or more directions to cover azimuthal variations in F and (2) measuring F for one direction to cover between‐tree variations in F. The framework formulates the variation in the probability density function for E (σE) based on F recorded in m different azimuthal directions (e.g. north, east, south and west). This formula allows us to determine the m value that minimizes σE. This study applied the framework to F data recorded for a 55‐year‐old Cryptomeria japonica stand. σE for m = 1 was found to be less than the values for m = 2, 3 and 4. Our results suggest that measuring F for one azimuthal direction provides more reliable E estimates than measuring F for two or more azimuthal directions for this stand, given a limited number of sensors. Application of this framework to other datasets helps us decide how to allocate sensors most effectively. Copyright © 2016 John Wiley & Sons, Ltd.
Predicting Future Groundwater Resources of Coral Atoll Islands
Authors: Bailey Ryan T. , Barnes Kaitlyn , Wallace Corey D.
Published: January 2016

Fresh groundwater reserves on small coral islands are under continual threat of salinization and contamination because of droughts, storm‐surge overwash events, over‐extraction, island community urbanization, and sea level rise. Whereas storm‐surge overwash events can cause sudden groundwater salinization, long‐term changes in rainfall patterns and sea level elevation have the potential of rendering these islands uninhabitable in the coming decades. This study demonstrates the use of a tested freshwater lens thickness simulator to estimate the groundwater resources of a set of atoll islands in the coming decades. The method uses ranges of projected rates of annual rainfall and sea level rise (SLR) to provide a range of probable lens thickness for each island. Projected rainfall is provided by General Circulation Models that accurately replicate the historical rainfall patterns in the geographic region of the islands. Methodology is applied to 68 atoll islands in the Federated States of Micronesia. These islands have widths that range between 150 and 1000 m, and experience annual rainfall rates of between 2.8 and 4.8 m. Results indicate that under average conditions of SLR, beach slope, and rainfall, almost half of the island will experience a 20% decrease in lens thickness by the year 2050. For worst‐case scenarios (high SLR, low rainfall), average decrease in lens thickness is 55%, with almost half of the islands experiencing a decrease of greater than 75% and half of the islands having a lens thickness less than 1.0 m. Small islands (widths less than 400 m) are particularly vulnerable because of shoreline recession. Groundwater on islands in the western region is less vulnerable to SLR because of a projected increase in rainfall during the coming decades. Results indicate the vulnerability of small islands to changing climatic conditions, and can be used for water resources management and community planning. Methodology can be applied to any group of islands as a first approximation of the effect of future climate conditions on groundwater resources. Copyright © 2016 John Wiley & Sons, Ltd.
Effects of Parathyroid Hormone Administration on Bone Strength in Hypoparathyroidism
Authors: Rubin Mishaela R , Zwahlen Alexander , Dempster David W , Zhou Hua , Cusano Natalie E , Zhang Chengchen , Müller Ralph , Bilezikian John P
Published: January 2016

The microstructural skeletal phenotype of hypoparathyroidism (HypoPT), a disorder of inadequate parathyroid hormone secretion, is altered trabecular microarchitecture with increased trabecular bone volume and thickness. Using 2-D histomorphometric analysis, we previously found that 2 years of PTH(1-84) in HypoPT is associated with reduced trabecular thickness (Tb.Th) and an increase in trabecular number (Tb.N). We have now utilized direct 3-D microstructural analysis to determine the extent to which these changes may be related to bone strength. Iliac crest bone biopsies from HypoPT subjects (n = 58) were analyzed by microcomputed tomography (μCT) and by microfinite element (μFE) analysis. Biopsies were performed at baseline and at 1 or 2 years of recombinant human PTH(1-84) [rhPTH(1-84)]. In a subset of subjects (n = 13) at 3 months, we demonstrated a reduction in trabecular separation (Tb.Sp, 0.64 ± 0.1 to 0.56 ± 0.1 mm; p = 0.005) and in the variance of trabecular separation (Tb.SD, 0.19 ± 0.1 to 0.17 ± 0.1 mm; p = 0.01), along with an increase in bone volume/total volume (BV/TV, 26.76 ± 10.1 to 32.83 ± 13.5%; p = 0.02), bone surface/total volume (BS/TV, 3.85 ± 0.7 to 4.49 ± 1.0 mm2/mm3; p = 0.005), Tb.N (1.84 ± 0.5 versus 2.36 ± 1.3 mm−1; p = 0.02) and Young's modulus (649.38 ± 460.7 to 1044.81 ± 1090.5 N/mm2; p = 0.049). After 1 year of rhPTH(1-84), Force increased (144.08 ± 102.4 to 241.13 ± 189.1 N; p = 0.04) and Young's modulus tended to increase (662.15 ± 478.2 to 1050.80 ± 824.1 N/m2; p = 0.06). The 1-year change in cancellous mineralizing surface (MS/BS) predicted 1-year changes in μCT variables. The biopsies obtained after 2 years of rhPTH(1-84) showed no change from baseline. These data suggest that administration of rhPTH(1-84) in HypoPT is associated with transient changes in key parameters associated with bone strength. The results indicate that rhPTH(1-84) improves skeletal quality in HypoPT early in treatment. © 2016 American Society for Bone and Mineral Research.
Grasshopper Plague Control in the Alpine Rangelands of the Qilian Mountains, China. A Socio‐Economic and Biological Approach
Authors: Sun Tao , Liu Xiaoli , Sun Guojun , Long Ruijun , Liu Zhiyun
Published: January 2016

The probability and frequency of grasshopper plague outbreaks in the alpine rangelands of China have greatly increased since the middle of the last century, adversely affecting grassland ecosystems and the livelihood of herders. We propose that herders could use poultry to forage on grasshoppers to control plague. Here, we investigated the proximate (application in 2007) and persistence (continued effects across 2008–2011) effects of three different control agents (foraging chickens, a broad spectrum insecticide Beta‐Cypermethrin and an entomopathogenic fungus Metarhizium) on grasshopper population density. The comparative effectiveness of the three control agents was assessed by calculating grasshopper mortality and nymph:adult ratios. Subsequently, we examined the efficiency of chicken foraging activity at controlling grasshopper numbers under various levels of outbreaks. Finally, we used a cost–benefit analysis to assess the economic benefits of a traditional sheep rearing system versus a system that includes chicken rearing. In the first year, all three agents were initially effective at reducing grasshopper densities, but only chickens generated a persistence effect (lasting up to 5 years). Overall, chickens also provided the greatest economic benefits to herders than the other two control agents. Using foraging chickens to suppress grasshopper infestation in the alpine rangelands of China provides a novel approach toward mitigating outbreaks. Copyright © 2016 John Wiley & Sons, Ltd.
Synthesis and Evaluation of Surface and Biological Properties of Some Lactic Acid‐Based Anionic Surfactants
Authors: sathyam Reddy Yasa , Sujitha Pombala , Kumar Chityal Ganesh , Kanjilal Sanjit , Vijayalakshmi Penumarthy
Published: January 2016

In the present study, 11 lactic acid‐based anionic surfactants were synthesized and evaluated for their surface and biological activities. The synthesis involved the esterification of lactic acid with a range of fatty alcohols differing in chain length as well as in branching and unsaturation. The resultant ester was sulfonated by treatment with chlorosulfonic acid followed by salt formation with aqueous NaOH solution. The surface properties of all the synthesized surfactants were determined using surface tensiometry. Synthesized surfactants showed low critical micelle concentration (CMC) values and a decreasing trend with an increase in the alkyl chain length. Alkyl branching also led to a mild change in CMC values when compared with linear counterparts having the same number of carbon atoms, though such decreases or increases were observed to be dependent on the position and number of the branching. Some of the synthesized surfactants exhibited good antimicrobial and anti‐cancer activities against the tested microbial strains and cell lines.
Protected Designation of Origin Extra Virgin Olive Oils Assessment by Nuclear Magnetic Resonance and Multivariate Statistical Analysis: “Terra di Bari”, an Apulian (Southeast Italy) Case Study
Authors: Del Coco Laura , Mondelli Donato , Mezzapesa Giuseppe Natale , Miano Teodoro , De Pascali Sandra Angelica , Girelli Chiara Roberta , Fanizzi Francesco Paolo
Published: January 2016

We report a study on the chemical characterization of 102 monovarietal micro‐extracted and genetically characterized extra virgin olive oils (EVOOs) from Coratina, Ogliarola Barese and Cima di Mola cultivar, according to “Terra di Bari” (Apulia, southeast Italy) PDO requirement. Three additional geographical mentions, all belonging to the same Bari district (Bitonto, Castel del Monte and Murgia dei Trulli e delle Grotte), were studied and potential microclimate differences were evaluated. Our results indicate the possibility of distinguishing EVOOs from the same “Terra di Bari” PDO with respect to different cultivars and (to some extent) different subareas. In particular, two cultivars (Ogliarola Barese and Coratina), obtained from the same Bitonto area, and a single cultivar (Coratina), obtained from Bitonto and Castel del Monte subareas, were compared to investigate the micro‐area pedoclimatic effect. Finally, 1H NMR data were found significant for classification purposes of unknown EVOO samples, the results of which were included in the model space, as they were correctly predicted by the OPLS‐DA obtained by 1H NMR data. This work aims to classify commercial “Terra di Bari” PDO EVOOs by comparison of the declared cultivar and geographical origin with a reference dataset of genetically characterized micro‐extracted monovarietal oils. In conclusion, the effect of the pedoclimatic micro‐areas of origin on the Coratina cultivar, which is the main component of the “Terra di Bari” PDO, has been studied in order to improve the traceability of the raw material used to produce this valuable food.
Phospholipid Hydrolysis and Transphosphatidylation by Phospholipase D from Indian Mustard Seeds in Two‐Phase Systems
Authors: Khatoon Hafeeza , Mansfeld Johanna , Ulbrich‐Hofmann Renate
Published: January 2016

Phospholipase D (PLD), isolated from Indian mustard seeds and purified to homogeneity, has recently been identified as typical α‐type PLD with a high activity toward phosphatidylcholine (PC) in an aqueous mixed micellar system (Khatoon et al. 2014, Phytochemistry 117, 65–75). In light of biocatalytical application, we have now studied the enzyme in aqueous‐organic two‐phase systems and compared the results with the properties of the enzyme in aqueous mixed micellar systems. n‐Hexane containing 5–10 mol% of 1‐ or 2‐octanol proved to be optimal as an organic solvent in the two‐phase system, whereas anionic detergents such as sodium dodecyl sulfate or sodium deoxycholate were favorable components in the mixed micellar system. The optimum pH value (5.5–5.6) and the optimum Ca2+ ion concentration (70 mM) were independent of the reaction system. The head group selectivity in terms of activity toward different phospholipids (PC > phosphatidylethanolamine > phosphatidylglycerol) was similar in both types of reaction systems. Also, the KM values toward PC were on the same order of magnitude. In contrast, the Vmax value in the two‐phase system was 20‐fold lower than in the mixed micellar system. The enzyme was able to catalyze the substitution of choline in PC by ethanolamine, glycerol, and ethylene glycol with high efficiency. l‐Serine was exchanged for choline with low activity. Myo‐inositol was not an alcohol acceptor, but promoted the hydrolysis of PC.
Twin Pregnancy with Complete Hydatidiform Mole and Co-existent Live Fetus
Authors: Seo So Young , Cho Hyun Jin
Published: January 2016

A 14-week pregnant woman had a mixed echogenic mass of size 4x12 cm at placenta portion and normal fetus at ultrasound. The image of the mass was very similar to a huge subchorionic hematoma (SCH). The fetal chromosomes by amniocentesis were normal. The presumed diagnoses were huge SCH or twin pregnancy with complete hydatidiform mole and co-existent fetus (CHMCF). A male fetus weighing 760 g was delivered at 25 gestational weeks. The findings on the placental biopsy showed twin pregnancy with CHCMF. With ultrasound findings of this type, the possibility of a huge SCH and twin pregnancy with CHMCF should be considered.
Urinary Biomarkers of Brain Diseases
Authors: An Manxia , Gao Youhe
Published: January 2016

Biomarkers are the measurable changes associated with a physiological or pathophysiological process. Unlike blood, urine is not subject to homeostatic mechanisms. Therefore, greater fluctuations could occur in urine than in blood, better reflecting the changes in human body. The roadmap of urine biomarker era was proposed. Although urine analysis has been attempted for clinical diagnosis, and urine has been monitored during the progression of many diseases, particularly urinary system diseases, whether urine can reflect brain disease status remains uncertain. As some biomarkers of brain diseases can be detected in the body fluids such as cerebrospinal fluid and blood, there is a possibility that urine also contain biomarkers of brain diseases. This review summarizes the clues of brain diseases reflected in the urine proteome and metabolome.
Melphalan‐flufenamide is cytotoxic and potentiates treatment with chemotherapy and the Src inhibitor dasatinib in urothelial carcinoma
Authors: Viktorsson Kristina , Shah Carl-Henrik , Juntti Therese , Hååg Petra , Zielinska-Chomej Katarzyna , Sierakowiak Adam , Holmsten Karin , Tu Jessica , Spira Jack , Kanter Lena , Lewensohn Rolf , Ullén Anders
Published: January 2016

Background: Chemotherapy options in advanced urothelial carcinoma (UC) remain limited. Here we evaluated the peptide‐based alkylating agent melphalan‐flufenamide (mel‐flufen) for UC.

Methods: UC cell lines J82, RT4, TCCsup and 5637 were treated with mel‐flufen, alone or combined with cisplatin, gemcitabine, dasatinib or bestatin. Cell viability (MTT assay), intracellular drug accumulation (liquid chromatography) apoptosis induction (apoptotic cell nuclei morphology, western blot analysis of PARP‐1/caspase‐9 cleavage and Bak/Bax activation) were evaluated. Kinome alterations were characterized by PathScan array and phospho‐Src validated by western blotting. Aminopeptidase N (ANPEP) expression was evaluated in UC clinical specimens in relation to patient outcome.

Results: In J82, RT4, TCCsup and 5637 UC cells, mel‐flufen amplified the intracellular loading of melphalan in part via aminopeptidase N (ANPEP), resulting in increased cytotoxicity compared to melphalan alone. Mel‐flufen induced apoptosis seen as activation of Bak/Bax, cleavage of caspase‐9/PARP‐1 and induction of apoptotic cell nuclei morphology. Combining mel‐flufen with cisplatin or gemcitabine in J82 cells resulted in additive cytotoxic effects and for gemcitabine also increased apoptosis induction. Profiling of mel‐flufen‐induced kinome alterations in J82 cells revealed that mel‐flufen alone did not inhibit Src phosphorylation. Accordingly, the Src inhibitor dasatinib sensitized for mel‐flufen cytotoxicity. Immunohistochemical analysis of the putative mel‐flufen biomarker ANPEP demonstrated prominent expression levels in tumours from 82 of 83 cystectomy patients. Significantly longer median overall survival was found in patients with high ANPEP expression (P = 0.02).

Conclusion: Mel‐flufen alone or in combination with cisplatin, gemcitabine or Src inhibition holds promise as a novel treatment for UC.
Development and regeneration of salivary gland toward for clinical application
Authors: Sakai Takayoshi
Published: January 2016

Salivary gland hypofunction, also termed as xerostomia, is caused by radiation therapy for head and neck cancer or Sjögren's syndrome, leading to a detrimental impact on oral health and quality of life. This review describes current studies on salivary gland development and the translational approaches of basic science to treating patients with dysfunction and hypofunction of the salivary gland. Here, we review the most recent studies that have offered better insight into the mechanisms of salivary gland development and regeneration. Furthermore, we highlight proposed approaches with the aim of recovering salivary gland function using both gene‐ and cell‐based therapy. A thorough understanding of the mechanisms involved in salivary gland development is necessary in order to design effective therapies for regeneration and repair of damaged salivary glands.
ShapeCluster: Applying parametric regression to analyse time-series gene expression data
Authors: Law Philip , Buchanan-Wollaston Vicky , Mead Andrew
Published: January 2016

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High-throughput technologies have made it possible to perform genome-scale analyses to investigate a variety of research areas. From these analyses, vast amounts of data are generated. However, this data can be noisy, which could obscure the underlying signal. Here, a high-throughput regression analysis approach was developed, where a variety of linear and nonlinear parametric models were fitted to gene expression profiles from time course experiments. These models include the logistic, Gompertz, exponential, critical exponential, linear+exponential, Gaussian and linear functions. The fitted parameters from these models reflect aspects of the model shape, and thus allowed for the interpretation of gene expression profiles in terms of the underlying biology, such as the time of initial gene expression. This provides a potentially more mechanistic approach to studying the genetic responses to stimuli. Together with a cluster analysis, termed ShapeCluster, it was possible to group genes based on these aspects of the expression profiles. By investigating different combinations of parameters, this added flexibility to the analysis and allowed for the investigation of the data in multiple ways, including the identification of groups of genes that may be co-regulated, or participate in response to the biological stress in question. Clusters from these methods were assessed for significance through the use of over-represented annotation terms and motifs, and found to produce biologically relevant sets of genes. The ShapeCluster package is available fromhttps://sourceforge.net/projects/shapecluster/.
Genome-wide Prediction of DNase I Hypersensitivity Using Gene Expression
Authors: Zhou Weiqiang , Sherwood Ben , Ji Zhicheng , Du Fang , Bai Jiawei , Ji Hongkai
Published: January 2016

We evaluate the feasibility of using a biological sample’s transcriptome to predict its genome-wide regulatory element activities measured by DNase I hypersensitivity (DH). We develop BIRD, Big Data Regression for predicting DH, to handle this high-dimensional problem. Applying BIRD to the Encyclopedia of DNA Element (ENCODE) data, we found that gene expression to a large extent predicts DH, and information useful for prediction is contained in the whole transcriptome rather than limited to a regulatory element’s neighboring genes. We show that the predicted DH predicts transcription factor binding sites (TFBSs), prediction models trained using ENCODE data can be applied to gene expression samples in Gene Expression Omnibus (GEO) to predict regulome, and one can use predictions as pseudo-replicates to improve the analysis of high-throughput regulome profiling data. Besides improving our understanding of the regulome-transcriptome relationship, this study suggests that transcriptome-based prediction can provide a useful new approach for regulome mapping.
Global Prediction of Chromatin Accessibility Using RNA-seq from Small Number of Cells
Authors: Zhou Weiqiang , Ji Zhicheng , Ji Hongkai
Published: January 2016

Conventional high-throughput technologies for mapping regulatory element activities such as ChIP-seq, DNase-seq and FAIRE-seq cannot analyze samples with small number of cells. The recently developed ATAC-seq allows regulome mapping in small-cell-number samples, but its signal in single cell or samples with ≤500 cells remains discrete or noisy. Compared to these technologies, measuring transcriptome by RNA-seq in single-cell and small-cell-number samples is more mature. Here we show that one can globally predict chromatin accessibility and infer regulome using RNA-seq. Genome-wide chromatin accessibility predicted by RNA-seq from 30 cells is comparable with ATAC-seq from 500 cells. Predictions based on single-cell RNA-seq can more accurately reconstruct bulk chromatin accessibility than using single-cell ATAC-seq by pooling the same number of cells. Integrating ATAC-seq with predictions from RNA-seq increases power of both methods. Thus, transcriptome-based prediction can provide a new tool for decoding gene regulatory programs in small-cell-number samples.