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Joonhoon Kim et al.
Frontiers in bioengineering and biotechnology, 8, 612832-612832 (2021-02-16)
An oleaginous yeast Rhodosporidium toruloides is a promising host for converting lignocellulosic biomass to bioproducts and biofuels. In this work, we performed multi-omics analysis of lignocellulosic carbon utilization in R. toruloides and reconstructed the genome-scale metabolic network of R. toruloides.
Van T Luu et al.
Bio-protocol, 10(17), e3739-e3739 (2021-03-05)
Genetic transformation is crucial for both investigating gene functions and for engineering of crops to introduce new traits. Rice (Oryza sativa L.) is an important model in plant research, since it is the staple food for more than half of
Imène Mensi et al.
Bio-protocol, 7(2), e2111-e2111 (2017-01-20)
Sugarcane (interspecific hybrids of Saccharum species) is an economically important crop that provides 70% of raw table sugar production worldwide and contributes, in some countries, to bioethanol and electricity production. Leaf scald, caused by the bacterial plant pathogen Xanthomonas albilineans
Roshali T de Silva et al.
Microbiology (Reading, England), 167(2) (2021-01-19)
Some microbes display pleomorphism, showing variable cell shapes in a single culture, whereas others differentiate to adapt to changed environmental conditions. The pleomorphic archaeon Haloferax volcanii commonly forms discoid-shaped ('plate') cells in culture, but may also be present as rods
Monica Viladomiu et al.
Cell host & microbe, 29(4), 607-619 (2021-02-05)
Adherent-invasive E. coli (AIEC) are enriched in the intestinal microbiota of patients with Crohn's disease (CD) and promote intestinal inflammation. Yet, how AIEC metabolism of nutrients impacts intestinal homeostasis is poorly defined. Here, we show that AIEC encoding the large subunit
Zsigmond Benko et al.
Current HIV research, 17(6), 429-440 (2019-11-30)
HIV-1 protease inhibitor (PI) is one of the most potent classes of drugs in combinational antiretroviral therapies (cART). When a PI is used in combination with other anti- HIV drugs, cART can often suppress HIV-1 below detection thus prolonging the
Cinzia Fino et al.
MicrobiologyOpen, 9(8), e1064-e1064 (2020-06-20)
Antibiotic-tolerant persisters are often implicated in treatment failure of chronic and relapsing bacterial infections, but the underlying molecular mechanisms have remained elusive. Controversies revolve around the relative contribution of specific genetic switches called toxin-antitoxin (TA) modules and global modulation of
Sándor Gonda et al.
Phytochemistry, 106, 44-54 (2014-08-02)
Tissue cultures of a medicinal plant, Plantago lanceolata L. were screened for phenylethanoid glycosides (PGs) and other natural products (NPs) with LC-ESI-MS(3). The effects of N source concentration and NH4(+)/NO3(-) ratio were evaluated in a full-factorial (FF) experiment. N concentrations
Lisa M Røst et al.
Metabolites, 10(2) (2020-02-26)
Absolute quantification of intracellular metabolite pools is a prerequisite for modeling and in-depth biological interpretation of metabolomics data. It is the final step of an elaborate metabolomics workflow, with challenges associated with all steps-from sampling to quantifying the physicochemically diverse
Ziyi Yin et al.
Autophagy, 16(5), 900-916 (2019-07-18)
Cells are faced with various stresses during their growth and development, and autophagy is a degradative process in which cells can break down their own components to recycle macromolecules and provide energy under these stresses. For pathogenic fungi that utilize
K Maráková et al.
Die Pharmazie, 69(9), 663-668 (2014-10-03)
The advanced hyphenated method based on capillary electrophoresis (CE) on-line combined with electrospray ionization (ESI) and tandem mass spectrometry (MS/MS, here triple quadrupole, QqQ) was developed and applied in pharmaceutical analysis in this work. Under the optimized CE separation (background
Gabriel L Fiorin et al.
Bio-protocol, 10(8), e3588-e3588 (2021-03-05)
Plants recognize a wide variety of microbial molecules to detect and respond to potential invaders. Recognition of Microbe-Associated Molecular Patterns (MAMPs) by cell surface receptors initiate a cascade of biochemical responses that include, among others, ion fluxes across the plasma
Vishnupriya Pradeep et al.
International journal of molecular sciences, 16(9), 20674-20684 (2015-09-26)
A single Brachionus rotifer can consume thousands of algae cells per hour causing an algae pond to crash within days of infection. Thus, there is a great need to reduce rotifers in order for algal biofuel production to become reality.
Petia Kovatcheva-Datchary et al.
Cell reports, 26(13), 3772-3783 (2019-03-28)
The gut microbiota can modulate human metabolism through interactions with macronutrients. However, microbiota-diet-host interactions are difficult to study because bacteria interact in complex food webs in concert with the host, and many of the bacteria are not yet characterized. To
Kangming Tian et al.
Biotechnology and bioengineering, 113(1), 182-188 (2015-07-15)
Efficient production of D-lactate by engineered Escherichia coli entails balancing cell growth and product synthesis. To develop a metabolic switch to implement a desirable transition from cell growth to product fermentation, a thiamine auxotroph B0013-080A was constructed in a highly
Kaori Taguchi et al.
Journal of chromatography. A, 1362, 270-277 (2014-09-10)
Chromatography techniques usually use a single state in the mobile phase, such as liquid, gas, or supercritical fluid. Chromatographers manage one of these techniques for their purpose but are sometimes required to use multiple methods, or even worse, multiple techniques
Nicholas Fowler et al.
Toxicon : official journal of the International Society on Toxinology, 101, 85-91 (2015-05-20)
One of the most widely studied organisms responsible for Harmful Algal Blooms (HABs) is the marine dinoflagellate Karenia brevis. This organism produces neurotoxic compounds known as brevetoxins. A related dinoflagellate, Karenia papilionacea, has been reported to occasionally co-bloom with K.
Joseph E Kerschner et al.
Archives of otolaryngology--head & neck surgery, 135(1), 33-39 (2009-01-21)
To investigate genetic differences in middle ear mucosa (MEM) with nontypeable Haemophilus influenzae (NTHi) infection. Genetic upregulation and downregulation occurs in MEM during otitis media (OM) pathogenesis. A comprehensive assessment of these genetic differences using the techniques of complementary DNA
Katherine R Heal et al.
Rapid communications in mass spectrometry : RCM, 28(22), 2398-2404 (2014-10-11)
Vitamin B(12) is an essential nutrient for more than half of surveyed marine algae species, but methods for directly measuring this important cofactor in seawater are limited. Current mass spectrometry methods do not quantify all forms of B(12), potentially missing
N Milne et al.
FEMS yeast research, 20(2) (2019-09-27)
We present a teaching protocol suitable for demonstrating the use of EasyClone and CRISPR/Cas9 for metabolic engineering of industrially relevant yeasts Saccharomyces cerevisiae and Yarrowia lipolytica, using β-carotene production as a case study. The protocol details all steps required to
Fei Du et al.
STAR protocols, 2(1), 100301-100301 (2021-02-09)
Cortical microtubules (CMTs) play pivotal roles during plant cell growth and division. The organization of CMTs undergoes important changes during different cellular and developmental processes. Here, we describe two methods for the visualization of CMT organization in plant cells using
Gabriel B Akanni et al.
Journal of the science of food and agriculture, 95(5), 1094-1102 (2014-11-06)
The cladodes of Opuntia ficus-indica (prickly pear cactus) have a low protein content; for use as a balanced feed, supplementation with other protein sources is therefore desirable. We investigated protein enrichment by cultivation of the yeasts Candida utilis and Kluyveromyces
Lindsey C Vedder et al.
Alcoholism, clinical and experimental research, 39(11), 2143-2153 (2015-10-01)
Many alcoholics display moderate to severe cognitive dysfunction accompanied by brain pathology. A factor confounded with prolonged heavy alcohol consumption is poor nutrition, and many alcoholics are thiamine deficient. Thus, thiamine deficiency (TD) has emerged as a key factor underlying
Ashish K Singh et al.
Alcoholism, clinical and experimental research, 38(7), 2127-2137 (2014-06-17)
Chronic ethanol (EtOH) consumption is associated with oxidative tissue damage, decrease in antioxidant enzyme activities, and increase in hepatic and plasma lipids. This study investigates the effect of modified probiotic Escherichia coli Nissle 1917 (EcN) secreting pyrroloquinoline quinone (PQQ) against
Andreas Keymer et al.
Bio-protocol, 8(7), e2786-e2786 (2018-04-05)
Lipid transfer from host plants to arbuscular mycorrhiza fungi was hypothesized for several years because sequenced arbuscular mycorrhiza fungal genomes lack genes encoding cytosolic fatty acid synthase ( Wewer et al., 2014 ; Rich et al., 2017 ). It was
Irene Delgado-Blanca et al.
Analytical and bioanalytical chemistry, 407(2), 521-528 (2014-11-06)
A new approach for the implementation of liquid-liquid extraction in a sequential injection manifold is presented. The manifold consists of two syringe pumps and one multi-position valve. The use of a 30 % MeOH/H2O (v/v) solution as the carrier, with isobutanol
Paul O Sheridan et al.
Bio-protocol, 10(7), e3575-e3575 (2021-03-05)
Roseburia and Eubacterium species of the human gut microbiota play an important role in the maintaince of human health, partly by producing butyrate, the main energy source of our colonic epithelial cells. However, our knowledge of the biochemistry and physiology
Francesca Froldi et al.
The EMBO journal, 38(7) (2019-02-26)
Rewired metabolism of glutamine in cancer has been well documented, but less is known about other amino acids such as histidine. Here, we use Drosophila cancer models to show that decreasing the concentration of histidine in the diet strongly inhibits
Miranda Hart et al.
Mycorrhiza, 25(5), 359-376 (2014-11-14)
Arbuscular mycorrhizal (AM) fungi can affect many different micronutrients and macronutrients in plants and also influence host volatile compound synthesis. Their effect on the edible portions of plants is less clear. Two separate studies were performed to investigate whether inoculation
Qiang Zhang et al.
Drug metabolism and disposition: the biological fate of chemicals, 42(10), 1656-1662 (2014-07-27)
The clinical development of fedratinib, a Janus kinase (JAK2) inhibitor, was terminated after reports of Wernicke's encephalopathy in myelofibrosis patients. Since Wernicke's encephalopathy is induced by thiamine deficiency, investigations were conducted to probe possible mechanisms through which fedratinib may lead
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