Development of an indirect method of microalgal lipid quantification using a lysochrome dye, Nile red

Earlier studies showed that the lipophilic dye, Nile red (9-diethylamino 5H-benzo[α]phenoxazine-5-one) can be used to measure the lipid content of microalgae by cellular in vivo fluorescence. It was observed that a higher amount of lipid present in lipid droplets of microalgal cells would result in higher degree of emitted fluorescent light. In this present study, the feasibility of using Nile red, a fluorescent dye specific for intracellular lipid droplets, as an indirect method of lipid quantifications was investigated. Following cellular staining of different microalgal species with nile red, the in vivo fluorescence of the whole cell was visualized by fluorescence microscopy (excitation: 450 to 590 nm and emission: 520 nm). Intensity of the relative in vivo fluorescence was measured using a fluorescence spectrophotometer at excitation and emission wavelengths of 485 and 590 nm, respectively. Lipid content was determined gravimetrically and the fluorescence of the extract was measured using the microemulsion method at emission and excitation wavelengths of 540 and 617 nm. The equivalent oil content of the extracted lipid was correlated to the fluorescence of pure olive oil using the microemulsion method. Cellular in vivo fluorescence of stained cells (ex: 485 nm and em: 590 nm), fluorescence of extracted lipid (ex: 540 nm and em: 617 nm) and gravimetrically determined lipid were linearly correlated. This suggests that Nile red can serve as a vital stain which allows a relatively rapid method of determining the lipid content of microalgal samples and is as good as the gravimetric method used for lipid determination, eliminating the requirement for the toxic solvents and timeconsuming manipulations.Keywords: Nile red, microalgae, lipid, fluorescenc

The operation performance of an expanded bed contactor characterised by mechanical stirring

The performance of an expanded bed contactor (UpFront i.d. 20 mm) characterised by mechanical stirring flow distribution in the adsorption of intracellular proteins from concentrated unclarified yeast extract was investigated. High density pellicular adsorbent (UpFront steel-agarose; ρ = 2.65 g ml-1) derivatized with selective ligand chemistries (Cibacron Blue 3GA) was adopted in this study. The adsorption of glyceraldehyde 3-phosphate dehydrogenase (G3PDH) from bakers’ yeast was chosen as a demonstration of this approach. It was demonstrated that a high biomass throughput adsorption operation (25 % ww/v of yeast extract) was achieved in this contactor design

Overview of citric acid production from Aspergillus niger

Citric acid has high economic potential owing to its numerous applications. It is mostly produced by microbial fermentation using Aspergillus niger. In view of surges in demand and growing markets, there is always a need for the discovery and development of better production techniques and solutions to improve production yields and the efficiency of product recovery. To support the enormous scale of production, it is necessary and important for the production process to be environmentally friendly by utilizing readily available and inexpensive agro-industrial waste products, while maintaining high production yields. This article reviews the biochemistry of citric acid formation, choices of citric-acid producing microorganisms and raw materials, fermentation strategies, the effects of various fermentation conditions, citric acid recovery options and the numerous applications of citric acid, based on information drawn from the literature over the past 10 years

Optimization of recovery of esterase from Serratia marcescens using combination of the solvent impregnated resin and aqueous two-phase extraction techniques

The performance of tunable aqueous polymer phase impregnated resins (TAPPIR) which is the combination of the solvent impregnated resin principle and an aqueous two-phase system for the separation of esterase from Serratia marcescens was evaluated in this study. Different molecular weight of polyethylene glycol (PEG) (2000, 4000 and 6000) at concentration ranging from 5% to 20% (w/w) and potassium citrate were used to construct the aqueous phase in TAPPIR technology. Optimum composition of PEG and salt for esterase partitioning was determined using response surface methodology. The optimum condition for the purification of esterase was impregnation of 25% (w/w) of PEG 2000 into 4 mm porous glass beads and extraction of esterase using 15% (w/w) potassium citrate at pH 8 containing 12% (w/w) crude loading with the addition of 4% (w/w) NaCl. Esterase from S. marcescens was successfully purified by the TAPPIR technology up to 5.32 of purification factor with a yield of 75.98%

Functional Ginger Extracts from Supercritical Fluid Carbon Dioxide Extraction via In Vitro

Supercritical fluid carbon dioxide extraction technology was developed to gain the active components from a Taiwan native plant, Zingiber officinale (ginger). We studied the biological effects of ginger extracts via multiple assays and demonstrated the biofunctions in each platform. Investigations of ginger extracts indicated antioxidative properties in dose-dependant manners on radical scavenging activities, reducing powers and metal chelating powers. We found that ginger extracts processed moderate scavenging values, middle metal chelating levels, and slight ferric reducing powers. The antibacterial susceptibility of ginger extracts on Staphylococcus aureus, Streptococcus sobrinus, S. mutans, and Escherichia coli was determined with the broth microdilution method technique. The ginger extracts had operative antimicroorganism potentials against both Gram-positive and Gram-negative bacteria. We further discovered the strong inhibitions of ginger extracts on lethal carcinogenic melanoma through in vivo xenograft model. To sum up, the data confirmed the possible applications as medical cosmetology agents, pharmaceutical antibiotics, and food supplements

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field

Production and Recovery of Ectoine: A Review of Current State and Future Prospects

Ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) is a revolutionizing substance with vast applications in the cosmetic and food industries. Ectoine is often sourced from halobacteria. The increasing market demand for ectoine has urged the development of cost-effective and sustainable large-scale production of ectoine from microbial sources. This review describes the existing and potential microbial sources of ectoine and its derivatives, as well as microbial production and fermentation approaches for ectoine recovery. In addition, conventional methods and emerging technologies for enhanced production and recovery of ectoine from microbial fermentation with a focus on the aqueous biphasic system (ABS) are discussed. The ABS is a practically feasible approach for the integration of fermentation, cell disruption, bioconversion, and clarification of various biomolecules in a single-step operation. Nonetheless, the implementation of the ABS on an industrial-scale basis for the enhanced production and recovery of ectoine is yet to be exploited. Therefore, the feasibility of the ABS to integrate the production and direct recovery of ectoine from microbial sources is also highlighted in this review

Purification of lipase derived from Burkholderia pseudomallei with alcohol/salt-based aqueous two-phase systems

Alcohol/salt-based aqueous two-phase systems (ATPSs) were used to recover lipase derived from Burkholderia pseudomallei (B. pseudomallei). Nine biphasic systems, comprised of an alcohol-based top phase (ethanol, 2-propanol and 1-propanol) and a salt-based bottom phase (ammonium sulfate, potassium phosphate and sodium citrate), were evaluated for their effectiveness in lipase recovery. The stability of lipase in each of the solutions was tested, and phase diagrams were constructed for each system. The optimum partition efficiency for the purification of lipase was obtained in an ATPS of 16% (w/w) 2-propanol and 16% (w/w) phosphate in the presence of 4.5% (w/v) NaCl. The purified lipase had a purification factor of 13.5 and a yield of 99%