bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synergetic engineering of central carbon and nitrogen metabolism for the production of N‐acetylglucosamine in Bacillus subtilis
Authors: Niu Tengfei , Lv Xueqin , Liu Zhenmin , Li Jianghua , Du Guocheng , Liu Long 
Published: October 2019

AbstractN‐acetylglucosamine (GlcNAc) is a nitrogen‐containing compound, which is widely used as a nutraceutical and pharmaceutical. In our previous work, we constructed a recombinant Bacillus subtilis strain for the biosynthesis of GlcNAc by engineering the central carbon metabolism. However, nitrogen is also required for the synthesis of GlcNAc. Hence, it is necessary to simultaneously coordinate the carbon and nitrogen metabolism to improve production of GlcNAc. In this work, we attempted to enhance GlcNAc production in B. subtilis by increasing supply of precursors N‐acetylglucosamine 6‐phosphate (GlcNAc6P) and glutamate. The expression of a key enzyme, GlcNAc6P N‐acetyltransferase (GNA1), was enhanced by engineering the promoter and ribosome binding site to enhance the production of GlcNAc6P. Next, we examined the effect of different nitrogen sources on GlcNAc synthesis. We observed that urea can promote nitrogen assimilation for GlcNAc synthesis. The glutamate synthesis was improved by deleting the two endogenous glutamate dehydrogenase genes (rocG and gudB) and by integrating one exogenous glutamate dehydrogenase gene (gdh). This strategy enhanced the intracellular glutamate and glutamine by 69.8% and 46.9%, respectively. The synergetic engineering of central carbon and nitrogen metabolisms increased the GlcNAc titer from 14.0 to 22.2 g/L in the shaker flask. Hence, our study demonstrated the importance of carbon and nitrogen metabolism coordination in the production of nitrogen‐containing compounds.
Genome‐wide association studies of structural birth defects: A review and commentary
Authors: Lupo Philip J. , Mitchell Laura E. , Jenkins Mary M. 
Published: October 2019

AbstractBackgroundWhile there is strong evidence that genetic risk factors play an important role in the etiologies of structural birth defects, compared to other diseases, there have been relatively few genome‐wide association studies (GWAS) of these conditions. We reviewed the current landscape of GWAS conducted for birth defects, noting novel insights, and future directions.MethodsThis article reviews the literature with regard to GWAS of structural birth defects. Key defects included in this review include oral clefts, congenital heart defects (CHDs), biliary atresia, pyloric stenosis, hypospadias, craniosynostosis, and clubfoot. Additionally, other issues related to GWAS are considered, including the assessment of polygenic risk scores and issues related to genetic ancestry, as well as utilizing genome‐wide single nucleotide polymorphism array data to evaluate gene–environment interactions and Mendelian randomization.ResultsFor some birth defects, including oral clefts and CHDs, several novel susceptibility loci have been identified and replicated through GWAS, including 8q24 for oral clefts, DGKK for hypospadias, and 4p16 for CHDs. Relatively common birth defects for which there are currently no published GWAS include neural tube defects, anotia/microtia, anophthalmia/microphthalmia, gastroschisis, and omphalocele.ConclusionsOverall, GWAS have been successful in identifying several novel susceptibility genes and genomic regions for structural birth defects. These findings have provided new insights into the etiologies of these phenotypes. However, GWAS have been underutilized for understanding the genetic etiologies of several birth defects.
A CRISPR–Cas9 system for multiple genome editing and pathway assembly in Candida tropicalis
Authors: Zhang Lihua , Zhang Haibing , Liu Yufei , Zhou Jingyu , Shen Wei , Liu Liming , Li Qi , Chen Xianzhong 
Published: October 2019

AbstractGenetic manipulation is among the most important tools for synthetic biology; however, modifying multiple genes is extremely time‐consuming and can sometimes be impossible when dealing with gene families. Here, we present a clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR‐associated protein 9 (Cas9) system for use in the diploid yeast Candida tropicalis that is vastly superior to traditional techniques. This system enables the rapid and reliable introduction of multiple genetic deletions or mutations, as well as a stable expression using an integrated CRISPR–Cas9 cassette or a transient CRISPR–Cas9 cassette, together with a short donor DNA. We further show that the system can be used to promote the in vivo assembly of multiple DNA fragments and their stable integration into a target locus (or loci) in C. tropicalis. Based on this system, we present a platform for the biosynthesis of β‐carotene and its derivatives. These results enable the practical application of C. tropicalis and the application of the system to other organisms.
Substrate stiffness affects the morphology and gene expression of epidermal neural crest stem cells in a short term culture
Authors: Pandamooz Sareh , Jafari Arman , Salehi Mohammad S. , Jurek Benjamin , Ahmadiani Abolhassan , Safari Anahid , Hassanajili Shadi , Borhani‐Haghighi Afshin , Dianatpour Mehdi , Niknejad Hassan , Azarpira Negar , Dargahi Leila 
Published: October 2019

AbstractAccording to the intrinsic plasticity of stem cells, controlling their fate is a critical issue in cell‐based therapies. Recently, a growing body of evidence has suggested that substrate stiffness can affect the fate decisions of various stem cells. Epidermal neural crest stem cells as one of the main neural crest cell derivatives hold great promise for cell therapies due to presenting a high level of plasticity. This study was conducted to define the influence of substrate stiffness on the lineage commitment of these cells. Here, four different polyacrylamide hydrogels with elastic modulus in the range of 0.7–30 kPa were synthesized and coated with collagen and stem cells were seeded on them for 24 hr. The obtained data showed that cells can attach faster to hydrogels compared with culture plate and cells on <1 kPa stiffness show more neuronal‐like morphology as they presented several branches and extended longer neurites over time. Moreover, the transcription of actin downregulated on all hydrogels, while the expression of Nestin, Tubulin, and PDGFR‐α increased on all of them and SOX‐10 and doublecortin gene expression were higher only on <1 kPa. Also, it was revealed that soft hydrogels can enhance the expression of glial cell line‐derived neurotrophic factor, neurotrophin‐3, and vascular endothelial growth factor in these stem cells. On the basis of the results, these cells can respond to the substrate stiffness in the short term culture and soft hydrogels can alter their morphology and gene expression. These findings suggested that employing proper substrate stiffness might result in cells with more natural profiles similar to the nervous system and superior usefulness in therapeutic applications.
Comparative genome‐scale analysis of Pichia pastoris variants informs selection of an optimal base strain
Authors: Brady Joseph R. , Whittaker Charles A. , Tan Melody C. , Kristensen D. Lee , Ma Duanduan , Dalvie Neil C. , Love Kerry Routenberg , Love J. Christopher 
Published: October 2019

AbstractKomagataella phaffii, also known as Pichia pastoris, is a common host for the production of biologics and enzymes, due to fast growth, high productivity, and advancements in host engineering. Several K. phaffii variants are commonly used as interchangeable base strains, which confounds efforts to improve this host. In this study, genomic and transcriptomic analyses of Y‐11430 (CBS7435), GS115, X‐33, and eight other variants enabled a comparative assessment of the relative fitness of these hosts for recombinant protein expression. Cell wall integrity explained the majority of the variation among strains, impacting transformation efficiency, growth, methanol metabolism, and secretion of heterologous proteins. Y‐11430 exhibited the highest activity of genes involved in methanol utilization, up to two‐fold higher transcription of heterologous genes, and robust growth. With a more permeable cell wall, X‐33 displayed a six‐fold higher transformation efficiency and up to 1.2‐fold higher titers than Y‐11430. X‐33 also shared nearly all mutations, and a defective variant of HIS4, with GS115, precluding robust growth. Transferring two beneficial mutations identified in X‐33 into Y‐11430 resulted in an optimized base strain that provided up to four‐fold higher transformation efficiency and three‐fold higher protein titers, while retaining robust growth. The approach employed here to assess unique banked variants in a species and then transfer key beneficial variants into a base strain should also facilitate rational assessment of a broad set of other recombinant hosts.
Physiological responses of Saccharomyces cerevisiae to industrially relevant conditions: Slow growth, low pH, and high CO2 levels
Authors: Hakkaart Xavier , Liu Yaya , Hulst Mandy , el Masoudi Anissa , Peuscher Eveline , Pronk Jack , van Gulik Walter , Daran‐Lapujade Pascale 
Published: October 2019

AbstractEngineered strains of Saccharomyces cerevisiae are used for industrial production of succinic acid. Optimal process conditions for dicarboxylic‐acid yield and recovery include slow growth, low pH, and high CO2. To quantify and understand how these process parameters affect yeast physiology, this study investigates individual and combined impacts of low pH (3.0) and high CO2 (50%) on slow‐growing chemostat and retentostat cultures of the reference strain S. cerevisiae CEN.PK113‐7D. Combined exposure to low pH and high CO2 led to increased maintenance‐energy requirements and death rates in aerobic, glucose‐limited cultures. Further experiments showed that these effects were predominantly caused by low pH. Growth under ammonium‐limited, energy‐excess conditions did not aggravate or ameliorate these adverse impacts. Despite the absence of a synergistic effect of low pH and high CO2 on physiology, high CO2 strongly affected genome‐wide transcriptional responses to low pH. Interference of high CO2 with low‐pH signaling is consistent with low‐pH and high‐CO2 signals being relayed via common (MAPK) signaling pathways, notably the cell wall integrity, high‐osmolarity glycerol, and calcineurin pathways. This study highlights the need to further increase robustness of cell factories to low pH for carboxylic‐acid production, even in organisms that are already applied at industrial scale.
Manipulation of micro‐ and nanoparticles in viscoelastic fluid flows within microfluid systems
Authors: Manshadi Mohammad K. D. , Mohammadi Mehdi , Monfared Leila Karami , Sanati‐Nezhad Amir 
Published: October 2019

AbstractManipulation of micro‐ and nanoparticles in complex biofluids is highly demanded in most biological and biomedical applications. A significant number of microfluidic platforms have been developed for inexpensive, rapid, accurate, and efficient particle manipulation. Due to the enormous potential of viscoelastic fluids (VEFs) for particle manipulation, various emerging microfluidic‐based VEFs techniques have been presented over the last decade. This review provides an intuitive understanding of VEF physics for particle separation in different microchannel geometries. Besides, active and passive VEF methods are critically reviewed, highlighting the potential and practical challenges of each technique for particle/cell focusing, sorting, and separation. The outcome of this study could enable recognizing deliverable VEF technology with the promising prospect in the manipulation of submicron biological samples (e.g., exosomes, DNA, and proteins).
Targeted capture of Chinese hamster ovary host cell proteins: Peptide ligand binding by proteomic analysis
Authors: Lavoie R. Ashton , di Fazio Alice , Williams Taufika Islam , Carbonell Ruben , Menegatti Stefano 
Published: October 2019

AbstractThe clearance of host cell proteins (HCPs) is of crucial importance in biomanufacturing, given their diversity in composition, structure, abundance, and occasional structural homology with the product. The current approach to HCP clearance in the manufacturing of monoclonal antibodies (mAbs) relies on product capture with Protein A followed by removal of residual HCPs in flow‐through mode using ion exchange or mixed‐mode chromatography. Recent studies have highlighted the presence of “problematic HCP” species, which are either difficult to remove (Group I), can degrade the mAb product (Group II), or trigger immunogenic reactions (Group III). To improve the clearance of these species, we developed a family of synthetic peptides that target HCPs and exhibit low binding to IgG product. In this study, these peptides were conjugated onto chromatographic resins and evaluated in terms of HCP clearance and mAb yield, using an industrial mAb‐producing CHO harvest as model supernatant. To gather detailed knowledge on the binding of individual HCPs, the unbound fractions were subjected to shotgun proteomic analysis by mass spectrometry. It was found that these peptide ligands exhibit superior HCP binding capability compared to those of the benchmark commercial resins commonly used in mAb purification. In addition, some peptide‐based resins resulted in much lower losses of product yield compared to these commercial supports. The proteomic analysis showed effective capture of many “problematic HCPs” by the peptide ligands, especially some that are weakly bound by commercial media. Collectively, these results indicate that these peptides show great promise toward the development of next‐generation adsorbents for safer and cost‐effective manufacturing of biologics.
Predicting return to work among patients with colorectal cancer
Authors: den Bakker C M , Anema J R , Huirne J A F , Twisk J , Bonjer H J , Schaafsma F G 
Published: October 2019

Abstract

Background
The increase in prevalence of colorectal cancer among young patients coupled with an older retirement age in developed countries means that more patients are being diagnosed with colorectal cancer while still at work. The aim of this study was to develop prediction models for return to work by 1 and 2 years after the start of sick leave.

Methods
This was a retrospective registry-based cohort study of data from a nationwide occupational health service in the Netherlands. Only employed patients with colonic or rectal cancer treated with curative intent were included. Two predictor variable models were developed using multivariable logistic regression with backward selection. Calibration, discrimination and explained variance were used to assess model performance, and internal validation by bootstrapping was performed.

Results
Median time to return to work for 317 included patients was 423 (95 per cent c.i. 379 to 467) days. Two-thirds of patients had returned to work by 2 years after the start of the sick leave. Presence of metastases, adjuvant treatment, stoma, emotional distress and postoperative complications were predictors of not returning to work in the 1-year model. In the 2-year model, presence of metastases, emotional distress, postoperative complications, company size and the trajectory of the return-to-work process were predictors.

Conclusion
Almost 70 per cent of patients with colorectal cancer in this population returned to work within 2 years after the start of sick leave. The models can be used to guide patients early in colorectal cancer treatment about the likelihood of returning to work, and to identify and modify barriers that could facilitate this.
Significance of the surgical hepatic resection margin in patients with a single hepatocellular carcinoma
Authors: Aoki T , Kubota K , Hasegawa K , Kubo S , Izumi N , Kokudo N , Sakamoto M , Shiina S , Takayama T , Nakashima O , Matsuyama Y , Murakami T , Kudo M 
Published: October 2019

Abstract

Background
The impact of a wide surgical margin on the outcome of patients with hepatocellular carcinoma (HCC) has not been evaluated in relation to the type of liver resection performed, anatomical or non-anatomical. The aim of this study was to evaluate the impact of surgical margin status on outcomes in patients undergoing anatomical or non-anatomical resection for solitary HCC.

Methods
Data from patients with solitary HCC who had undergone non-anatomical partial resection (Hr0 group) or anatomical resection of one Couinaud segment (HrS group) between 2000 and 2007 were extracted from a nationwide survey database in Japan. Overall and recurrence-free survival associated with the surgical margin status and width were evaluated in the two groups.

Results
A total of 4457 patients were included in the Hr0 group and 3507 in the HrS group. A microscopically positive surgical margin was associated with poor overall survival in both groups. A negative but 0-mm surgical margin was associated with poorer overall and recurrence-free survival than a wider margin only in the Hr0 group. In the HrS group, the width of the surgical margin was not associated with patient outcome.

Conclusion
Anatomical resection with a negative 0-mm surgical margin may be acceptable. Non-anatomical resection with a negative 0-mm margin was associated with a less favourable survival outcome.
Evaluation of Phytochemical Compositions and Biological Properties of Achillea gypsicola at Different Phenological Stages
Authors: Akif Açıkgöz Muhammed 
Published: October 2019

AbstractPhytochemicals, which are commonly found at different levels in many medicinal plants, are natural strong antioxidants used in traditional medicine. In this research, determination of differences of phytochemical compositions and biological properties were aimed as periodically (pre‐, full and post flowering) and daily (6 am, 1 pm and 8 pm) in Achillea gypsicola Hub.‐Mor. The volatile oils belonging to A. gypsicola were obtained by hydrodistillation and analyzed by gas chromatography‐flame ionization detection (GC‐FID) and gas chromatography‐mass spectrometry (GC/MS). The antimicrobial activities of the volatile oils were determined with disc diffusion method. The microdilution method was used to determine minimum inhibitory concentration (MIC). Total phenolic and flavonoid contents were determined by spectrophotometric methods and antioxidant capacities were evaluated by 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH) free radical, reducing power (RP) and metal chelating activity (MCA) assay. In addition, the phenolic acid and flavonoid compositions were evaluated by reversed phase‐high‐performance liquid chromatography (RP‐HPLC). This study presented a comprehensive report for the first time on evaluation of the phytochemical composition and the biological properties of A. gypsicola at different phenological stages. Thirty‐two compounds, containing the major component as camphor, 1,8‐cineole and borneol, were detected. Designated harvest time for the highest yield of volatile oils was found to be at full flowering stage‐1 pm. It has been observed that the volatile oil composition changes periodically and even daily. Also, in this research, menthol and menthone were found as the composition of volatile oil in Achillea species for the first time. Full flowering stage was found as the richest period in terms of phenolic acid and flavonoid compositions of A. gypsicola for the first time. The species examined in this research showed a high antioxidant and antimicrobial activity in comparison to other studies with Achillea species. The volatile oils exhibited high performances with range of inhibition zones (8.3–42.3 mm) and minimum inhibitory concentration values (2.25—144 μg/ml). Besides, a high correlation between antioxidant activity and phenolic content of A. gypsicola was found. These results suggest that A. gypsicola can be used as a safe source in the cosmetic, food and pharmaceutical industries.
Comparison of residual shunt rate and complications across 6 different closure devices for patent foramen ovale
Authors: Gevorgyan Fleming Rubine , Kumar Preetham , West Brian , Noureddin Nabil , Rusheen Joshua , Aboulhosn Jamil , Tobis Jonathan M. 
Published: October 2019

AbstractObjectivesTo compare residual shunt rate and complications associated with six different devices used for PFO closure.BackgroundTranscutaneous PFO closure is an effective treatment for preventing recurrent stroke in patients with a history of cryptogenic stroke. The rate of residual shunt is one metric by which the technical success of PFO closure can be measured.MethodsPatients who underwent PFO closure at a single center between February 2001 and July 2019 were retrospectively enrolled in the study. Right‐to‐left shunt at baseline and during follow‐up was assessed using transcranial Doppler (TCD) or transthoracic echocardiography (TTE). Periprocedural and device‐related complications, including atrial fibrillation, were also assessed.ResultsOf 467 PFO closures performed during this period, 320 patients received quantitative assessment of right‐to‐left shunting both before and after percutaneous closure. The highest effective closure was achieved with the Cardioform device (100%, n = 104), followed by the Amplatzer Cribriform (93%, n = 14), Helex (90%, n = 137), Amplatzer ASO (88%, n = 17), CardioSEAL (86%, n = 14), and Amplatzer PFO (85%, n = 33) devices. The most common significant adverse event was atrial fibrillation, which was more common with the Cardioform device (13%) than the Helex (4%) or the Amplatzer PFO (4%) devices.ConclusionsThe Gore Cardioform Septal Occluder provides more robust closure of a PFO when compared to other devices but its effectiveness is offset by the higher prevalence of transient atrial fibrillation.
The Single‐access for Hi‐risk PCI (SHiP) technique
Authors: Wollmuth Jason , Korngold Ethan , Croce Kevin , Pinto Duane S. 
Published: October 2019

AbstractCurrently, the Impella CP (Abiomed, Danvers, Massachusetts) percutaneous ventricular assist catheter requires implantation through a 14 French sheath. Additional arterial access is commonly obtained to perform therapeutic or diagnostic procedures. Multiple arterial access requires time and results in increased risk for vascular complications. Some patients may have limited arterial access. We describe the Single‐access for Hi‐risk PCI (SHiP) technique to allow for rapid and safer single access utilizing only the Impella access site. After the Impella catheter is placed in the standard fashion, a micropuncture needle is used to pierce the hemostasis valve of the Impella insertion sheath. After dilating the hemostasis valve and exchanging for a 0.035″ wire, up to a 7 French sheath can be inserted for PCI within the 14 French access sheath and alongside the 9 French portion of the Impella catheter. After PCI, the sheath is removed. We report on a case series of 17 patients using this technique. There were no instances of bleeding during the procedure or after removal of the PCI sheath, and no evidence of disruption of the Impella sheath.