bluuebunny/crossref_metadata_2025_split huggingface dataset:
ScalaFlux: a scalable approach to quantify fluxes in metabolic subnetworks
Authors: Millard Pierre , Schmitt Uwe , Kiefer Patrick , Vorholt Julia A. , Heux Stéphanie , Portais Jean-Charles 
Published: August 2019

Abstract13C-metabolic flux analysis (13C-MFA) allows metabolic fluxes to be quantified in living organisms and is a major tool in biotechnology and systems biology. Current13C-MFA approaches model label propagation starting from the extracellular13C-labeled nutrient(s), which limits their applicability to the analysis of pathways close to this metabolic entry point. Here, we propose a new approach to quantify fluxes through any metabolic subnetwork of interest by modeling label propagation directly from the metabolic precursor(s) of this subnetwork. The flux calculations are thus purely based on information from within the subnetwork of interest, and no additional knowledge about the surrounding network (such as atom transitions in upstream reactions or the labeling of the extracellular nutrient) is required. This approach, termed ScalaFlux for SCALAble metabolic FLUX analysis, can be scaled up from individual reactions to pathways to sets of pathways. ScalaFlux has several benefits compared with current13C-MFA approaches: greater network coverage, lower data requirements, independence from cell physiology, robustness to gaps in data and network information, better computational efficiency, applicability to rich media, and enhanced flux identifiability. We validated ScalaFlux using a theoretical network and simulated data. We also used the approach to quantify fluxes through the prenyl pyrophosphate pathway ofSaccharomyces cerevisiaemutants engineered to produce phytoene, using a dataset for which fluxes could not be calculated using existing approaches. A broad range of metabolic systems can be targeted with minimal cost and effort, making ScalaFlux a valuable tool for the analysis of metabolic fluxes.Author SummaryMetabolism is a fundamental biochemical process that enables all organisms to operate and grow by converting nutrients into energy and ‘building blocks’. Metabolic flux analysis allows the quantification of metabolic fluxesin vivo, i.e. the actual rates of biochemical conversions in biological systems, and is increasingly used to probe metabolic activity in biology, biotechnology and medicine. Isotope labeling experiments coupled with mathematical models of large metabolic networks are the most commonly used approaches to quantify fluxes within cells. However, many biological questions only require flux information from a subset of reactions, not the full network. Here, we propose a new approach with three main advantages over existing methods: better scalability (fluxes can be measured through a single reaction, a metabolic pathway or a set of pathways of interest), better robustness to missing data and information gaps, and lower requirements in terms of measurements and computational resources. We validate our method both theoretically and experimentally. ScalaFlux can be used for high-throughput flux measurements in virtually any metabolic system and paves the way to the analysis of dynamic fluxome rearrangements.
A novel human monoclonal antibody specific to the A33 glycoprotein recognizes colorectal cancer and inhibits metastasis
Authors: Murer Patrizia , Plüss Louis , Neri Dario 
Published: August 2019

ABSTRACTColorectal cancer represents the second most common cause of cancer-related death. The human A33 transmembrane glycoprotein is a validated tumor-associated antigen, expressed in 95% of primary and metastatic colorectal cancers. Using phage display technology, we generated a human monoclonal antibody (termed A2) specific to A33 and we compared its epitope and performance to those of previously described clinical-stage anti-human A33 antibodies. All antibodies recognized a similar immunodominant epitope, located in the V-domain of A33, as revealed by SPOT-analysis. The A2 antibody homogenously stained samples of poorly, moderately and well-differentiated colon adenocarcinomas. All antibodies also exhibited an intense staining of healthy human colon sections. The A2 antibody, reformatted in murine IgG2a format, preferentially localized to A33-transfected CT26 murine colon adenocarcinomas in immunocompetent mice with a homogenous distribution within the tumor mass, while other antibodies exhibited a patchy uptake in neoplastic lesions. A2 efficiently induced killing of A33-expressing cells through antibody-dependent cell-mediated cytotoxicity in vitro and was able to inhibit the growth of A33-positive murine CT26 and C51 lung metastases in vivo. Anti-A33 antibodies may thus represent useful vehicles for the selective delivery of bioactive payloads to colorectal cancer, or may be used in IgG format in settings of minimal residual disease.
Expression and Purification of a Mammalian Protein: Cytosolic Domain of IRE1α from Insect Sf21 Cells
Authors: Oak Amrita , Jansen Grace , Chan Christina 
Published: August 2019

AbstractEukaryotic proteins can be expressed in different heterologous systems. However, mammalian proteins in general have specific post-translational processing requirements that may not be fulfilled by a regular bacterial expression system. In this study, we use an insect cell system to express a mammalian protein of interest. Spodoptera frugiperda (Sf21) cells were used in conjunction with a baculoviral expression system to produce the cytosolic domain (CD) of IRE1, an endoplasmic reticulum (ER) stress sensor protein. Inositol Requiring Enzyme 1 (IRE1) is a dual function kinase and endoribonuclease protein that cleaves X-box binding protein (XBP1) mRNA. We used the pFastBac plasmid to insert the coding sequence into a recombinant bacmid shuttle vector which was then used to infect Sf21 cells. The expressed protein was then purified with an MBPTrap column to obtain >85% pure protein.
HMGB1 mediates the development of tendinopathy due to mechanical overloading
Authors: Zhao Guangyi , Zhang Jianying , Nie Daibang , Zhou Yiqin , Li Feng , Onishi Kentaro , Wang James H-C. 
Published: August 2019

AbstractMechanical overloading is a major cause of tendinopathy, but the underlying pathogenesis of tendinopathy is unclear. Here we report that high mobility group box1 (HMGB1) is released to the tendon extracellular matrix and initiates an inflammatory cascade in response to mechanical overloading in a mouse model. Moreover, administration of glycyrrhizin (GL), a naturally occurring triterpene and a specific inhibitor of HMGB1, the tendon’s inflammatory reactions. Also, while prolonged mechanical overloading in the form of long-term intensive treadmill running induces Achilles tendinopathy in mice, administration of GL completely blocks the tendinopathy development. Additionally, mechanical overloading of tendon cells in vitro induces HMGB1 release to the extracellular milieu, thereby eliciting inflammatory and catabolic responses as marked by increased production of prostaglandin E2 (PGE2) and matrix metalloproteinase-3 (MMP-3) in tendon cells. Application of GL abolishes the cellular inflammatory/catabolic responses. Collectively, these findings point to HMGB1 as a key molecule that is responsible for the induction of tendinopathy due to mechanical overloading placed on the tendon.
Solution structure and assembly of β-amylase2 fromArabidopsis thaliana
Authors: Chandrasekharan Nithesh P. , Ravenburg Claire M. , Roy Ian R. , Monroe Jonathan D. , Berndsen Christopher E. 
Published: August 2019

AbstractStarch is a key energy storage molecule in plants that requires controlled synthesis and breakdown for effective plant growth. β-amylases (BAMs) hydrolyze starch into maltose to help meet the metabolic needs of the plant. In the model plant,Arabidopsis thaliana, there are nine BAMs which have apparently distinct functional and domain structures, although the functions of only a few of the BAMs are known and there are no 3-D structures of BAMs from this organism. Recently, AtBAM2 was proposed to form a tetramer based on chromatography and activity assays of mutants, however there was no direct observation of this tetramer. We collected small-angle X-ray scattering data on AtBAM2 and N-terminal mutants to describe the structure and assembly of the tetramer. Comparison of the scattering of the AtBAM2 tetramer to data collected using the sweet potato (Ipomoea batatas) BAM5, which is also reported to form a tetramer, showed there were differences in the overall assembly. Analysis of N-terminal truncations of AtBAM2 identified a loop sequence found only in BAM2 orthologs that appears to be critical for AtBAM2 tetramer assembly as well as activity.
The hunger games: sensing host arginine is essential for Leishmania parasite virulence
Authors: Goldman-Pinkovich Adele , Kannan Sriram , Nitzan-Koren Roni , Puri Madhu , Bar-Avraham Yael , McDonald Jacqueline A. , Sur Aakash , Zhang Wen-Wei , Matlashewski Greg , Madhubala Rentala , Michaeli Shulamit , Myler Peter J. , Zilberstein Dan 
Published: August 2019

AbstractArginine homeostasis in lysosomes is critical for growth and metabolism of mammalian cells. They employ a specific sensor (SLC38A9) that monitors intra-lysosome arginine sufficiency and subsequently up-regulates cellular mTORC1 activity. Lysosomes of macrophages (phagolysosomes) are the niche where the parasitic protozoan Leishmania resides and causes important human disease. Several years ago, we discovered that upon arginine starvation, cultured Leishmania parasites promptly activate a MAPK2-mediated Arginine Deprivation Response (ADR) pathway, resulting in up-regulation of the Leishmania arginine transporter (AAP3), as well as a small group of other transporters. Significantly, ADR is also activated during macrophage infection, implying that the intracellular parasite actively depletes arginine within the host phagolysosome, likely to prevent mTORC1 activation and enhance intracellular development. We hypothesize that ADR-mediated up-regulation of AAP3 activity is necessary to withstand the resultant arginine starvation. Both copies of the AAP3 genes are located (in tandem) on a tetrasomic chromosome (chr31), but only one (AAP3.2) is responsive to arginine deprivation. CRISPR/Cas9-mediated disruption of the AAP3 locus yielded mutants that retain a basal level of arginine transport (mediated by AAP3.1), but lack a functional copy of AAP3.2 and are therefore not responsive to arginine starvation. While these mutants grow normally in culture as promastigotes, they were impaired in their ability to develop inside THP1 macrophages grown under physiological concentrations of arginine (0.1 mM). However, flooding the macrophage growth medium with arginine (1.5 mM) restored parasite infectivity and intracellular growth to that of wild type. The results indicate that inside the host macrophage, Leishmania must overcome the arginine “Hunger Games” by up-regulating transport of arginine via the ADR. Furthermore, the AAP3.2 mutants were ~70-80% less virulent in Balb/C mice, showing, for the first time, that the ability to monitor and respond to changes in host metabolite levels is essential for pathogenesis.
Cut and paste – Efficient cotyledon micrografting for Arabidopsis thaliana seedlings
Authors: Bartusch Kai , Trenner Jana , Quint Marcel 
Published: August 2019

AbstractCotyledon micrografting represents a very useful tool for studying the central role of cotyledons during early plant development, especially their interplay with other plant organs with regard to long distance transport. While hypocotyl grafting methods are established, cotyledon grafting is still inefficient. By optimizing cotyledon micrografting, we aim for higher success rates and increased throughput in the model species Arabidopsis thaliana. We established a cut and paste cotyledon surgery procedure on a flat solid but moist surface which improved handling of small plant seedlings. Applying a specific cutting and joining pattern throughput was increased up to 40 seedlings per hour. The combination of short day conditions and low light intensities for germination and long day plus high light intensities and vertical plate positioning after grafting significantly increased ‘ligation’ efficiency. Together, we achieved up to 46 % grafting success in A. thaliana. Reconnection of vasculature was shown by successful transport of a vasculature-specific dye across the grafting site. On a whole plant level, plants with grafted cotyledons match plants with intact cotyledons in biomass production and rosette development. This cut and paste cotyledon-to-petiole grafting protocol simplifies the handling of plant seedlings in surgery, increases the number of grafted plants per hour and produces higher success rates for A. thaliana seedlings. The developed cotyledon micrografting method is also suitable for other plant species of comparable size.
Sugar availability suppresses the auxin-induced strigolactone pathway to promote bud outgrowth
Authors: Bertheloot Jessica , Barbier François , Boudon Frédéric , Perez-Garcia Maria Dolores , Péron Thomas , Citerne Sylvie , Dun Elizabeth , Beveridge Christine , Godin Christophe , Sakr Soulaiman 
Published: August 2019

SUMMARYApical dominance occurs when the growing shoot tip inhibits the outgrowth of axillary buds. Apically-derived auxin in the nodal stem indirectly inhibits bud outgrowth via cytokinins and strigolactones. Recently, sugar deprivation was found to contribute to this phenomenon.Using rose and pea, we investigated whether sugar availability interacts with auxin in bud outgrowth control, and the role of cytokinins and strigolactones, in vitro and in planta.We show that sucrose antagonizes auxin’s effect on bud outgrowth, in a dose-dependent and coupled manner. Sucrose also suppresses strigolactone-inhibition of outgrowth, and rms3 strigolactone-perception mutant is less affected by reducing sucrose supply; however, sucrose does not interfere with the regulation of cytokinin levels by auxin, and stimulates outgrowth even with optimal cytokinin supply. These observations were assembled into a computational model where sucrose represses bud response to strigolactones, largely independently of cytokinin levels. It quantitatively captures our observed dose-dependent sucrose-hormones effects on bud outgrowth, and allows us to express outgrowth response to various combinations of auxin and sucrose levels as a simple quantitative law.This study places sugars in the bud outgrowth regulatory network, and paves the way for better understanding of branching plasticity in response to environmental and genotypic factors.
CD47 suppresses phagocytosis by repositioning SIRPA and preventing integrin activation
Authors: Morrissey Meghan A. , Vale Ronald D. 
Published: August 2019

SummaryMacrophages must engulf dead cells, debris, and pathogens, while selecting against healthy cells to prevent autoimmunity. Healthy cells express CD47 on their surface, which activates the SIRPA receptor on macrophages to suppress engulfment. Cancer cells overexpress CD47 to evade clearance by the innate immune system, making the CD47-SIRPA signaling axis an appealing therapeutic target. However, the mechanism by which CD47-SIRPA inhibits engulfment remains poorly understood. Here, we dissect SIRPA signaling using a reconstituted target with varying concentrations of activating and inhibitor ligands. We find that SIRPA is excluded from the phagocytic synapse between the macrophage and its target unless CD47 is present. Artificially directing SIRPA to the kinase-rich synapse in the absence of CD47 activates SIRPA and suppresses engulfment, indicating that the localization of the receptor is critical for inhibitory signaling. CD47-SIRPA inhibits integrin activation in the macrophage, reducing macrophage-target contact and suppressing phagocytosis. Chemical activation of integrins can override this effect and drive engulfment of CD47-positive targets, including cancer cells. These results suggest new strategies for overcoming CD47-SIRPA inhibition of phagocytosis with potential applications in cancer immunotherapy.
Rod nuclear architecture determines contrast transmission of the retina and behavioral sensitivity in mice
Authors: Subramanian Kaushikaram , Weigert Martin , Borsch Oliver , Petzold Heike , Garcia Alfonso , Myers Eugene , Ader Marius , Solovei Irina , Kreysing Moritz 
Published: August 2019

AbstractRod photoreceptors of nocturnal mammals display a striking inversion of nuclear architecture, which has been proposed as an evolutionary adaptation to dark environments. However, the nature of visual benefits and underlying mechanisms remains unclear. It is widely assumed that improvements in nocturnal vision would depend on maximization of photon capture, at the expense of image detail. Here we show that retinal optical quality improves 2-fold during terminal development, which, confirmed by a mouse model, happens due to nuclear inversion.We further reveal that improved retinal contrast-transmission, rather than photon-budget or resolution, leads to enhanced contrast sensitivity under low light condition. Our findings therefore add functional significance to a prominent exception of nuclear organization and establish retinal contrast-transmission as a decisive determinant of mammalian visual perception.One Sentence SummaryOur study reveals that chromatin compaction in rod cells augments contrast sensitivity in mice.
Promoting access to health information
Authors: Senteio Charles R. 
Published: August 2019

PurposeDescribe the design of a health information and technology educational intervention that promotes health information sharing and technology use for older adult African Americans to support access to health information. The paper aims to discuss this issue.Design/methodology/approachThe study team developed a novel method to design the intervention. It drew upon three approaches: intergenerational technology transfer, participatory design and community-based participatory research.FindingsOlder adult African Americans (55+) with diabetes and young adults (18–54) connected to them via familial or naturally occurring social networks designed the intervention, which was conducted in the two study sites in Michigan, USA. In total, 29 participants helped design the intervention. Four themes emerged concerning factors that promote intergenerational information exchange in the context of technology and health. First, focus on one technology skill. Second, working together in small groups is preferred. Third, patience is essential. Last, physical capabilities (i.e., eyesight, operating on relatively small screens) and literacy levels should be considered.Originality/valueThis novel method of having participants from the sample population select the health information materials and technology exercises serves as a guide for implementing health information and education interventions aimed at technology use to support self-management for vulnerable patient populations.
Perspectives of teachers’ on the selection and the development of the school leaders in the United Arab Emirates
Authors: David Solomon Arulraj , Abukari Abdulai 
Published: August 2019

PurposeThe purpose of this paper is to examine teachers’ perspectives on school leaders’ selection and development strategies in order to propose/recommend strategies that are relevant to the context of the United Arab Emirates.Design/methodology/approachThe study gathered data through group discussion of school teachers who attended the module “leadership for school improvement” taught by the researchers. The teachers who participated in this study include local and expat teachers who are currently working in both public and private schools in the UAE. The reports of the group discussion were used as transcripts and thematic analysis was used to analyse the results.FindingsThe results indicate that there is a strong aspiration for setting better standards for the selection of the school leaders. There is great interest in engaging experts and instrumenting accredited continued professional development training on developing school leaders. The respondents emphasised on the required qualifications, experiences and knowledge, and the need for mentorship approach.Research limitations/implicationsThe key limitation of the study is the smaller sample size.Practical implicationsThe outcome of the study offers necessary insight to the decision makers on the selection and development of school leaders in the UAE.Social implicationsThe study insists that the social and cultural values of the UAE to be considered in the selection and development of school leaders in the UAE.Originality/valueThe study offers potential gap and scope for further research on school leadership in the UAE that could be further explored with many samples and cases for broader understanding.
Human resources management practices and organizational commitment in higher education
Authors: Aboramadan Mohammed , Albashiti Belal , Alharazin Hatem , Dahleez Khalid Abed 
Published: August 2019

PurposeThe purpose of this paper is to investigate the impact of human resource management (HRM) practices on organizational commitment in Palestinian universities, and to examine the mediating effect of work engagement as a black-box mechanism that defines HRM practices–organizational commitment relationship.Design/methodology/approachThe source of the data is from 237 employees (academics and administrative staff) from Palestinian universities. The authors used structural equation modeling to verify the hypotheses.FindingsThe results reveal that HRM practices have a significant impact on employee organizational commitment in higher education. In addition, work engagement showed a significant mediating effect between performance appraisal and organizational commitment on the one hand, and between rewards and compensation and organizational commitment on the other hand.Practical implicationsThe study suggests university managers to capitalize on HRM practices as vehicle to trigger positive work-related attitudes.Originality/valueThe study contributes to the literature by examining the impact of HRM practices on organizational commitment through the mediation role of work engagement in higher education of a non-western context. The study is one of the few studies that is conducted in the middle east.