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https://www.readbyqxmd.com/read/28817312/disulfide-mapping-planner-software-tool
#1
Andreas M Kist, Angelika Lampert, Andrias O O'Reilly
Disulfide bridges are side-chain-mediated covalent bonds between cysteines that stabilize many protein structures. Disulfide mapping experiments to resolve these linkages typically involve proteolytic cleavage of the protein of interest followed by mass spectroscopy to identify fragments corresponding to linked peptides. Here we report the sequence-based "DIMPL" web tool to facilitate the planning and analysis steps of experimental mapping studies. The software tests permutations of user-selected proteases to determine an optimal peptic digest that produces cleavage between cysteine residues, thus separating each to an individual peptide fragment...
August 17, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28817121/meganuclease-assisted-generation-of-stable-transgenics-in-the-sea-anemone-nematostella-vectensis
#2
Eduard Renfer, Ulrich Technau
The sea anemone Nematostella vectensis is a model system used by a rapidly growing research community for comparative genomics, developmental biology and ecology. Here, we describe a microinjection procedure for creating stable transgenic lines in Nematostella based on meganuclease (I-SceI)-assisted integration of a transgenic cassette into the genome. The procedure describes the preparation of the reagents, microinjection of the transgenesis vector and the husbandry of transgenic animals. The microinjection setup differs from those of previously published protocols by the use of a holding capillary mounted on an inverted fluorescence microscope...
September 2017: Nature Protocols
https://www.readbyqxmd.com/read/28816852/assessing-nutrition-delivery-in-icus-a-difficult-problem-to-digest
#3
Stephanie Wappel, Elizabeth A Parker, Monica Serra, Avelino C Verceles
No abstract text is available yet for this article.
September 2017: Critical Care Medicine
https://www.readbyqxmd.com/read/28816740/the-value-of-direct-immunofluorescence-on-proteinase-digested-formalin-fixed-paraffin-embedded-skin-biopsies
#4
Aida Valencia-Guerrero, April Deng, Karen Dresser, Gail Bouliane, Kristine M Cornejo
Direct immunofluorescence (DIF) on frozen tissue (DIF-F) is the method of choice for the identification of immune deposits present in skin and other tissues. DIF can also be performed on formalin-fixed paraffin-embedded tissue (DIF-P) after antigen retrieval with proteases and has proven to be of value in renal pathology. However, its utility in skin biopsies has not been fully examined. In this study, we performed DIF-P on 60 skin biopsies that comprised of bullous pemphigoid (n = 18), pemphigoid gestationis (n = 1), pemphigus (n = 7), linear IgA disease (n = 7), vasculitis (n = 20), lupus erythematosus (n = 3), and dermatitis herpetiformis (n = 4) cases...
August 9, 2017: American Journal of Dermatopathology
https://www.readbyqxmd.com/read/28816555/chemical-utilization-of-albizia-lebbeck-leaves-for-developing-protein-concentrates-as-a-dietary-supplement
#5
Lutful Haque Khan, V K Varshney
In search of nonconventional sources of protein to combat widespread malnutrition, the possibility of developing a protein concentrate as an alternative dietary supplement from abundantly available yet poorly valorized leaves of Albizia lebbeck (siris) was examined. A process for recovery of leaf protein concentrate (LPC) from these leaves was optimized and applied for isolation of LPCs from lower, middle, and upper canopies of the tree. The optimized conditions (leaves to water 1:9, coagulation at pH 4.0 using 1 N citric acid at 90°C for 11 minutes) afforded LPCs containing protein 37...
August 17, 2017: Journal of Dietary Supplements
https://www.readbyqxmd.com/read/28816507/arthroscopic-harvest-of-adipose-derived-mesenchymal-stem-cells-from-the-infrapatellar-fat-pad
#6
Jason L Dragoo, Wenteh Chang
BACKGROUND: The successful isolation of adipose-derived mesenchymal stem cells (ADSCs) from the arthroscopically harvested infrapatellar fat pad (IFP) would provide orthopaedic surgeons with an autologous solution for regenerative procedures. PURPOSE: To demonstrate the quantity and viability of the mesenchymal stem cell population arthroscopically harvested from the IFP as well as the surrounding synovium. STUDY DESIGN: Descriptive laboratory study...
August 1, 2017: American Journal of Sports Medicine
https://www.readbyqxmd.com/read/28815506/preparing-fosmid-mate-paired-libraries-using-cre-loxp-recombination
#7
Ze Peng, Jeff L Froula, Jan-Fang Cheng
Fosmid end sequencing has been widely utilized in genome sequence assemblies and genome structural variation studies. We have developed a new approach to construct fosmid paired-end libraries that is suitable for Illumina sequencing platform. This approach employs a newly modified fosmid vector (pFosClip) which contains two loxP sites with identical orientation and two inverse Illumina adaptor priming sites flanking the cloning site. DNA prepared from the fosmid library constructed with pFosClip can be treated with the Cre recombinase to remove most of the vector DNA, leaving only 107 bp of the vector sequence with insert DNA...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28815293/the-novel-preventive-effect-of-daikenchuto-tj-100-a-japanese-herbal-drug-against-neonatal-necrotizing-enterocolitis-in-rats
#8
Shin Shinyama, Tatsuru Kaji, Motoi Mukai, Kazuhiko Nakame, Hiroshi Matsufuji, Hideo Takamatsu, Satoshi Ieiri
PURPOSE: Necrotizing enterocolitis (NEC) is a devastating gastrointestinal disease of premature infants. Daikenchuto, a Japanese herbal drug, has several effects on the digestive system, so we investigated its preventive effects in a rat model of NEC. METHODS: NEC was induced in newborn rats via asphyxia (100% N2 for 90 s; every 4 h) + LPS (4 mg/kg/day [administered orally on days 0 and 1]). The effects of Daikenchuto were evaluated in four groups (control: 0 g/kg/day, I: 0...
August 16, 2017: Pediatric Surgery International
https://www.readbyqxmd.com/read/28815245/-experimental-study-on-osteogenesis-of-acellular-porcine-pericardium-in-guided-bone-regeneration
#9
Jun-Zhao Gao, Xue-Jian Zhang, Jia-Li Hou, Yue Deng, Yun-Peng Li
PURPOSE: To observe the retention time and effect of acellular porcine pericardium (APP) in bone regeneration for rabbit femoral bone defects. METHODS: APP was prepared as follows: fresh porcine pericardium was chosen, high and low osmotic NaCl solution were used to soak the specimen alternately, trypsin+EDTA were used for digest, and then immersed with TritonX-100, cross-linked by using glutaraldehyde. 24 New Zealand rabbits were selected, and the area of bone defect was created 8 mm×8 mm×5 mm in size on bilateral distal femur...
April 2017: Shanghai Kou Qiang Yi Xue, Shanghai Journal of Stomatology
https://www.readbyqxmd.com/read/28815060/defective-expression-of-atg4d-abrogates-autophagy-and-promotes-growth-in-human-uterine-fibroids
#10
Abdeljabar El Andaloussi, Samar Habib, Gizem Soylemes, Archana Laknaur, Heba Elhusseini, Ayman Al-Hendy, Nahed Ismail
Uterine fibroids (UF) are the most common pelvic tumors in women of reproductive-age and they usually cause heavy menstrual bleeding, pain and infertility. Autophagy is a collection of processes that enables the cells to digest and recycle their cytoplasmic contents, such as toxic protein aggregates, defunct or disused organelles and invading microorganisms. Dysregulation in autophagy process were described in neoplasms; however, the contribution of autophagy to the pathogenesis of UF remains unknown. In this study, we demonstrate that autophagy is deregulated in human UF as evidenced by significant accumulation of autophagosome in human UF cells compared to normal myometrium cells...
2017: Cell Death Discovery
https://www.readbyqxmd.com/read/28814970/prevalence-and-characteristics-of-epstein-barr-virus-associated-gastric-carcinomas-in-portugal
#11
Célia Nogueira, Marta Mota, Rui Gradiz, Maria Augusta Cipriano, Francisco Caramelo, Hugo Cruz, Ana Alarcão, Francisco Castro E Sousa, Fernando Oliveira, Fernando Martinho, João Moura Pereira, Paulo Figueiredo, Maximino Leitão
BACKGROUND: Gastric cancer (GC) is one of the most common malignant tumors of the digestive tract and is the third leading cause of cancer death worldwide. Epstein-Barr virus (EBV) has been associated with approximately 10% of the total cases of gastric carcinomas. No previous study has analyzed the prevalence of EBV infection in gastric cancer of the Portuguese population. METHODS: In the present study, we have analyzed 82 gastric carcinoma cases and 33 healthy individuals (control group) from Coimbra region for the presence of EBV by polymerase chain reaction (PCR) and by in situ hybridization (ISH) for EBV-encoded small RNAs (EBERs)...
2017: Infectious Agents and Cancer
https://www.readbyqxmd.com/read/28814641/ceramide-activation-of-rhoa-rho-kinase-impairs-actin-polymerization-during-aggregated-ldl-catabolism
#12
Rajesh K Singh, Abigail S Haka, Alexandria Brumfield, Inna Grosheva, Priya Bhardwaj, Harvey F Chin, Yuquan Xiong, Timothy Hla, Frederick R Maxfield
Macrophages use an extracellular, hydrolytic compartment formed by local actin polymerization to digest aggregated LDL (agLDL). Catabolism of agLDL promotes foam cell formation and creates an environment rich in LDL catabolites including cholesterol and ceramide. Increased ceramide levels are present in lesional LDL, but the effect of ceramide on macrophage pro-atherogenic processes remains unknown. Here, we show that macrophages accumulate ceramide in atherosclerotic lesions. Using macrophages from Sphingosine Kinase 2 knockout (SK2KO) mice to mimic ceramide rich conditions of atherosclerotic lesions, we show that SK2KO macrophages display impaired actin polymerization and foam cell formation in response to contact with agLDL...
August 16, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/28814614/role-of-inactivity-in-chronic-diseases-evolutionary-insight-and-pathophysiological-mechanisms
#13
REVIEW
Frank W Booth, Christian K Roberts, John P Thyfault, Gregory N Ruegsegger, Ryan G Toedebusch
This review proposes that physical inactivity could be considered a behavior selected by evolution for resting, and also selected to be reinforcing in life-threatening situations in which exercise would be dangerous. Underlying the notion are human twin studies and animal selective breeding studies, both of which provide indirect evidence for the existence of genes for physical inactivity. Approximately 86% of the 325 million in the United States (U.S.) population achieve less than the U.S. Government and World Health Organization guidelines for daily physical activity for health...
October 1, 2017: Physiological Reviews
https://www.readbyqxmd.com/read/28814218/diagnosis-and-management-of-pancreatic-exocrine-insufficiency
#14
Mehrdad Nikfarjam, Jeremy S Wilson, Ross C Smith
In 2015, the Australasian Pancreatic Club (APC) published the Australasian guidelines for the management of pancreatic exocrine insufficiency (http://pancreas.org.au/2016/01/pancreatic-exocrine-insufficiency-guidelines). Pancreatic exocrine insufficiency (PEI) occurs when normal digestion cannot be sustained due to insufficient pancreatic digestive enzyme activity. This may be related to a breakdown, at any point, in the pancreatic digestive chain: pancreatic stimulation; synthesis, release or transportation of pancreatic enzymes; or synchronisation of secretions to mix with ingested food...
August 21, 2017: Medical Journal of Australia
https://www.readbyqxmd.com/read/28814092/flow-cytometric-examination-of-apoptotic-effect-on-brain-tissue-in-postnatal-period-created-by-intrauterine-oxcarbazepine-and-gabapentin-exposure
#15
Z Erisgin, Y Tekelioglu
OBJECTIVE: For epileptics, pregnancy contains the balance between no seizure period and antiepileptic use having the least teratogenicity risk. The purpose is to analyse with flow cytometry the apoptotic effects on postnatal brain tissue caused by prenatal use of second generation antiepileptics oxcarbazepine (OXC) and gabapentin (GBP) having different effect mechanisms. METHOD: 30 (n = 5 each group) Wistar albino male rats (45-days-old) are used. First 3 groups are exposed to OXC (100 mg/kg/day), GBP (50 mg/kg/day), and saline, respectively on the 1st-5th prenatal days (preimplantation-implantation period) while the second 3 groups are exposed to the same substances on the 6th-15th prenatal days (organogenesis), respectively...
2017: Bratislavské Lekárske Listy
https://www.readbyqxmd.com/read/28813510/construction-of-novel-pjrd215-derived-plasmids-using-chloramphenicol-acetyltransferase-cat-gene-as-a-selection-marker-for-acidithiobacillus-caldus
#16
Rui Wang, Chunmao Lin, Jianqiang Lin, Xin Pang, Xiangmei Liu, Chengjia Zhang, Jianqun Lin, Linxu Chen
BACKGROUND: Acidithiobacillus caldus, a Gram-negative, chemolithotrophic sulfur-oxidizing bacterium, is widely applied in bioleaching. The absence of an ideal selection marker has become a major obstacle to achieve high efficiency of the gene transfer system for A. caldus. Plasmid pJRD215, widely used in Acidithiobacillus spp., has severe drawbacks in molecular manipulations and potential biosafety issues due to its mobility. Therefore, finding a new selection marker and constructing new plasmids have become an urgent and fundamental work for A...
2017: PloS One
https://www.readbyqxmd.com/read/28812980/application-of-an-in-vitro-digestion-model-for-210po-bioaccessibility-assessment-in-seafood
#17
Carla Roselli, Donatella Desideri, Laura Feduzi, Lucia Ugolini, Maria Assunta Meli
This study aims to investigate the bioaccessibility of 210Po in seafood and the impact of food preparation on this radionuclide. Polonium bioaccessibility is the fraction of 210Po mobilized from food matrices into digestive extractants when applying an in vitro digestion model. The degree of bioaccessibility of 210Po in food has important implications for estimating ingestion doses from this radionuclide. The simulation of gastrointestinal digestion was divided into three stages through the use of synthetic saliva, gastric and bile-pancreas solutions...
August 16, 2017: Journal of Radiological Protection: Official Journal of the Society for Radiological Protection
https://www.readbyqxmd.com/read/28812732/genome-of-the-pitcher-plant-cephalotus-reveals-genetic-changes-associated-with-carnivory
#18
Kenji Fukushima, Xiaodong Fang, David Alvarez-Ponce, Huimin Cai, Lorenzo Carretero-Paulet, Cui Chen, Tien-Hao Chang, Kimberly M Farr, Tomomichi Fujita, Yuji Hiwatashi, Yoshikazu Hoshi, Takamasa Imai, Masahiro Kasahara, Pablo Librado, Likai Mao, Hitoshi Mori, Tomoaki Nishiyama, Masafumi Nozawa, Gergő Pálfalvi, Stephen T Pollard, Julio Rozas, Alejandro Sánchez-Gracia, David Sankoff, Tomoko F Shibata, Shuji Shigenobu, Naomi Sumikawa, Taketoshi Uzawa, Meiying Xie, Chunfang Zheng, David D Pollock, Victor A Albert, Shuaicheng Li, Mitsuyasu Hasebe
Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient absorption...
February 6, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812344/in-vitro-bile-acid-binding-capacities-of-red-leaf-lettuce-and-cruciferous-vegetables
#19
Isabelle Yang, Guddadarangavvanahal Jayaprakasha, Bhimanagouda S Patil
In the present study, we tested the bile acid binding capacity of red leaf lettuce, red cabbage, red kale, green kale, and Brussels sprouts in vitro digestion process by simulating mouth, gastric, and intestinal digestion using six bile acids at physiological pH. Green and red kale exhibited significantly higher (86.5±2.9 and 89.7±0.9%) bile acid binding capacity compared with the other samples. Further, three different compositions of bile acids were tested to understand the effect on different health conditions...
August 16, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28812268/oxytocin-and-human-evolution
#20
C Sue Carter
A small, but powerful neuropeptide, oxytocin coordinates processes that are central to both human reproduction and human evolution. Also embedded in the evolution of the human nervous system are unique pathways necessary for modern human sociality and cognition. Oxytocin is necessary for facilitating the birth process, especially in light of anatomical restrictions imposed by upright human locomotion, which depends on a fixed pelvis. Oxytocin, by facilitating birth, allowed the development of a large cortex and a protective bony cranium...
August 16, 2017: Current Topics in Behavioral Neurosciences
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