Computer-assisted coloring and illuminating based on a region-tree structure

Arginine transportation mechanism through cationic amino acid transporter 1: insights from molecular dynamics studies

Metabolic and signaling mechanisms in mammalian cells are facilitated by the transportation of L-arginine (Arg) across the plasma membrane through cationic amino acid transporter (CAT) proteins. Due to a lack of argininosuccinate synthase (ASS) activity in various tumor cells such as acute myeloid leukemia, acute lymphocytic leukemia, and chronic lymphocytic leukemia, these tumor entities are arginine-auxotrophic and therefore depend on the uptake of the amino acid arginine. Cationic amino acid transporter-1 (CAT-1) is the leading arginine importer expressed in the aforementioned tumor entities. Hence, in the present study, to investigate the transportation mechanism of arginine in CAT-1, we performed molecular dynamics (MD) simulation methods on the modeled human CAT-1. The MM-PBSA approach was conducted to determine the critical residues interacting with arginine within the corresponding binding site of CAT-1. In addition, we found out that the water molecules have the leading role in forming the transportation channel within CAT-1. The conductive structure of CAT-1 was formed only when the water molecules were continuously distributed across the channel. Steered molecular dynamics (SMD) simulation approach showed various energy barriers against arginine transportation through CAT-1, especially while crossing the bottlenecks of the related channel. These findings at the molecular level might shed light on identifying the crucial amino acids in the binding of arginine to eukaryotic CATs and also provide fundamental insights into the arginine transportation mechanisms through CAT-1. Understanding the transportation mechanism of arginine is essential to developing CAT-1 blockers, which can be potential medications for some types of cancers.Communicated by Ramaswamy H. Sarma.

Bioinformatic analyses to uncover genes involved in trehalose metabolism in the polyploid sugarcane

Trehalose-6-phosphate (T6P) is an intermediate of trehalose biosynthesis that plays an essential role in plant metabolism and development. Here, we comprehensively analyzed sequences from enzymes of trehalose metabolism in sugarcane, one of the main crops used for bioenergy production. We identified protein domains, phylogeny, and in silico expression levels for all classes of enzymes. However, post-translational modifications and residues involved in catalysis and substrate binding were analyzed only in trehalose-6-phosphate synthase (TPS) sequences. We retrieved 71 putative full-length TPS, 93 trehalose-6-phosphate phosphatase (TPP), and 3 trehalase (TRE) of sugarcane, showing all their conserved domains, respectively. Putative TPS (Classes I and II) and TPP sugarcane sequences were categorized into well-known groups reported in the literature. We measured the expression levels of the sequences from one sugarcane leaf transcriptomic dataset. Furthermore, TPS Class I has specific N-glycosylation sites inserted in conserved motifs and carries catalytic and binding residues in its TPS domain. Some of these residues are mutated in TPS Class II members, which implies loss of enzyme activity. Our approach retrieved many homo(eo)logous sequences for genes involved in trehalose metabolism, paving the way to discover the role of T6P signaling in sugarcane.

Fast Fluorine-18 labeling and preclinical evaluation of novel Mucin1 and its Folate hybrid peptide conjugate for targeting breast carcinoma

Background

There is a need to develop new and more potent radiofluorinated peptide and their hybrid conjugates for multiple-receptors targeting properties that overexpress on many cancers.

Methods

We have synthesized MUC1-[¹⁸F] SFB and MUC1-FA-[¹⁸F] SFB hybrid conjugates using a convenient and one-step nucleophilic displacement reaction. In vitro cell binding and in vivo evaluation in animals were performed to determine the potential of these radiolabeled compounds.

Results

Radiochemical yields for MUC1-[¹⁸F] SFB and MUC1-FA-[¹⁸F] SFB conjugates were greater than 70% in less than 30 min synthesis time. Radiochemical purities were greater than 97% without HPLC purification, which makes these approaches amenable to automation. In vitro studies on MCF7 breast cancer cells showed that the significant amounts of the radiofluorinated conjugates were associated with cell fractions and held good affinity and specificity for MCF7 cells. In vivo characterization in Balb/c mice revealed rapid blood clearance with excretion predominantly by urinary as well as hepatobiliary systems for MUC1-[18F] SFB and MUC1-FA-[18F] SFB, respectively.

Biodistribution in SCID mice bearing MCF7 xenografts, demonstrated excellent tumor uptake (12% ID/g) and favorable kinetics for MUC1-FA-[¹⁸F] SFB over MUC1-[¹⁸F]SFB. The tumor uptake was blocked by the excess co-injection of cold peptides suggesting the receptor-mediated process.

Conclusion

Initial PET/CT imaging of SCID mice with MCF7 xenografts, confirmed these observations. These results demonstrate that MUC1-FA-[¹⁸F] SFB may be a useful PET imaging probe for breast cancer detection and monitoring tumor response to the treatment.

The strong competitive role of 2n pollen in several polyploidy hybridizations in Rosa hybrida

BACKGROUND

2n pollen play a strong competitive role in hybridization and breeding of multiploids in Rosa hybrida. The ploidy inheritable characteristic of 'Orange Fire' × 'Old Blush' were analyzed.

RESULT

The results of the cytological observations indicated that 2n pollen developed from the defeated cytoplasmic division or nuclear division in the meiosis metaphase II of PMC (pollen mother cell) in 'Old Blush'. The natural generation rate of the 2n pollen in 'Old Blush' (2x) was about 1.39 in percentage of all male gametes, whereas the tetraploids in the F1 offspring possessed a high rate, i.e., 44.00%. The temporal and spatial characteristics of 'Old Blush' pollen germination on the stigma and growth in pistil of 'Orange Fire' and 'DEE' were observed, and the results suggested that the germination rate of 2n pollen on the stigma was not superior to that of 1n pollen, but that the proportion of 2n pollen increased to 30.90 and 37.20%, respectively, while it traversed the stigma and entered into style. The callose plug in the 2n pollen tube was significantly thinner than that of 1n pollen tube. And each trait involved in our experiment probably is very important for F1 morphological phenotypes.

CONCLUSION

We conclude that 2n pollen are involved in hybridization and have a competitive advantage while it traversed the stigma and entered into style. The callose plug in the 2n pollen tube was may have strongly influenced the competitive process in R. hybrida.

Metabolic Engineered Biocatalyst: A Solution for PLA Based Problems

Polylactic acid (PLA) is a biodegradable thermoplastic polyester. In 2010, PLA became the second highest consumed bioplastic in the world due to its wide application. Conventionally, PLA is produced by direct condensation of lactic acid monomer and ring opening polymerization of lactide, resulting in lower molecular weight and lesser strength of polymer. Furthermore, conventional methods of PLA production require a catalyst which makes it inappropriate for biomedical applications. Newer method utilizes metabolic engineering of microorganism for direct production of PLA through fermentation which produces good quality and high molecular weight and yield as compared to conventional methods. PLA is used as decomposing packaging material, sheet casting, medical implants in the form of screw, plate, and rod pin, etc. The main focus of the review is to highlight the synthesis of PLA by various polymerization methods that mainly include metabolic engineering fermentation as well as salient biomedical applications of PLA.

Effective adoptive immunotherapy of triple-negative breast cancer by folate receptor-alpha redirected CAR T cells is influenced by surface antigen expression level

BACKGROUND

The poor prognosis and the limited efficacy of targeted therapy in patients with triple-negative breast cancer (TNBC) have raised the need for alternative therapies. Recent studies have demonstrated that folate receptor-alpha (FRα) may represent an ideal tumor-associated marker for immunotherapy for TNBC.

METHODS

The aim of the present study was to apply a chimeric antigen receptor (CAR) approach for the targeting of FRα expressed on TNBC cells and evaluate the antitumor activity of CAR-engineered T cells in vitro and in vivo.

RESULTS

We found that human T cells expressing a FRα-specific CAR were potent and specific killers of TNBC cells that express moderate levels of FRα in vitro and significantly inhibited tumor outgrowth following infusion into immunodeficient mice bearing an MDA-MB-231 tumor xenograft. However, the antitumor activity of the FRα CAR T cells was modest when compared to the same CAR T cells applied in an ovarian tumor xenograft model where FRα expression is more abundant. Notably, FRα CAR T cells induced superior tumor regression in vivo against MDA-MB-231 that was engineered for overexpression of FRα.

CONCLUSIONS

Taken together, our results show that FRα CAR T cells can mediate antitumor activity against established TNBC tumor, particularly when FRα is expressed at higher levels. These results have significant implications for the pre-selection of patients with high antigen expression levels when utilizing CAR-based adoptive T cell therapies of cancer in future clinical trials.

Chronic Traumatic Encephalopathy and Movement Disorders: Update

Association of repetitive brain trauma with progressive neurological deterioration has been described since the 1920s. Punch drunk syndrome and dementia pugilistica (DP) were introduced first to explain symptoms in boxers, and more recently, chronic traumatic encephalopathy (CTE) has been used to describe a neurodegenerative disease in athletes and military personal with a history of multiple concussions. Although there are many similarities between DP and CTE, a number of key differences are apparent especially when comparing movement impairments. The aim of this review is to compare clinical and pathological aspects of DP and CTE with a focus on disorders of movement.

Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package

As the use of RNA-seq has popularized, there is an increasing consciousness of the importance of experimental design, bias removal, accurate quantification and control of false positives for proper data analysis. We introduce the NOISeq R-package for quality control and analysis of count data. We show how the available diagnostic tools can be used to monitor quality issues, make pre-processing decisions and improve analysis. We demonstrate that the non-parametric NOISeqBIO efficiently controls false discoveries in experiments with biological replication and outperforms state-of-the-art methods. NOISeq is a comprehensive resource that meets current needs for robust data-aware analysis of RNA-seq differential expression.

Mixotrophic cultivation of microalgae for biodiesel production: status and prospects

Biodiesel from microalgae provides a promising alternative for biofuel production. Microalgae can be produced under three major cultivation modes, namely photoautotrophic cultivation, heterotrophic cultivation, and mixotrophic cultivation. Potentials and practices of biodiesel production from microalgae have been demonstrated mostly focusing on photoautotrophic cultivation; mixotrophic cultivation of microalgae for biodiesel production has rarely been reviewed. This paper summarizes the mechanisms and virtues of mixotrophic microalgae cultivation through comparison with other major cultivation modes. Influencing factors of microalgal biodiesel production under mixotrophic cultivation are presented, development of combining microalgal biodiesel production with wastewater treatment is especially reviewed, and bottlenecks and strategies for future commercial production are also identified.

Plasma total homocysteine level in association with folate, pyridoxine, and cobalamin status among Iranian primary breast cancer patients

Recently the elevated plasma total homocysteine (tHcy) concentration has been concerned as the secondary feature of tumoral proliferation and enhances the likelihood of thrombogenesis in cancer patients. The objective of this study was to determine the associations between folate, cobalamin, and pyridoxine with fasting plasma tHcy concentration in breast cancer (BC) patients. The intake levels of nutrients were assessed using a validated food frequency questionnaire in 141 newly diagnosed BC patients. The plasma tHcy and pyridoxal-5-phosphate were measured using high performance liquid chromatography with fluorescence detector. Plasma tHcy levels were observed to be significantly higher among BC participants with Stage III where the plasma concentrations of folate was also comparatively less (P < 0.05) than other stages. Dietary pyridoxine was even being consumed less at this stage (P < 0.05). The plasma, dietary, and residual variables of folate were inversely correlated with plasma tHcy concentration (P < 0.05). Dietary cobalamin was also associated negatively with tHcy (P < 0.05). The odds ratio of comparing the highest tertile of plasma cobalamin (>394 pmol/l) and folate (>11.4 ng/ml) vs. the lowest categories were associated with reduced odds of high tHcy occurrence with 0.20 (95% confidence interval: 0.04-0.98) and 0.14 (95% confidence interval: 0.03-0.64), respectively. In conclusion, nutrition-related methyl-group insufficiency could lead to imbalance in tHcy metabolism, as a possible cancer marker.

A new lipid-rich microalga Scenedesmus sp. strain R-16 isolated using Nile red staining: effects of carbon and nitrogen sources and initial pH on the biomass and lipid production

BACKGROUND

Biodiesel production from oleaginous microalgae shows great potential as a promising alternative to conventional fossil fuels. Currently, most research focus on algal biomass production with autotrophic cultivation, but this cultivation strategy induces low biomass concentration and it is difficult to be used in large-scale algal biomass production. By contrast, heterotrophic algae allows higher growth rate and can accumulate higher lipid. However, the fast-growing and lipid-rich microalgae that can be cultivated in heterotrophic system for the industrial application of biodiesel production are still few. Traditional solvent extraction and gravimetric determination to detect the microalgal total lipid content is time-consuming and laborious, which has become a major limiting factor for selecting large number of algae specimens. Thus, it is critical to develop a rapid and efficient procedure for the screening of lipid-rich microalgae.

RESULTS

A novel green microalga Scenedesmus sp. strain R-16 with high total lipid content was selected using the Nile red staining from eighty-eight isolates. Various carbon sources (fructose, glucose and acetate) and nitrogen sources (nitrate, urea, peptone and yeast extract) can be utilized for microalgal growth and lipid production, and the optimal carbon and nitrogen sources were glucose (10 g L-1) and nitrate (0.6 g L-1), respectively. Compared to autotrophic situation, the strain R-16 can grow well heterotrophically without light and the accumulated total lipid content and biomass reached 43.4% and 3.46 g L-1, respectively. In addition, nitrogen deficiency led to an accumulation of lipid and the total lipid content was as high as 52.6%, and it was worth noting that strain R-16 exhibited strong tolerance to high glucose (up to 100 g L-1) and a wide range of pH (4.0-11.0).

CONCLUSIONS

The newly developed ultrasonic-assisted Nile red method proved to be an efficient isolation procedure and was successfully used in the selection of oleaginous microalgae. The isolated novel green microalgal strain R-16 was rich in lipid and can live in varied and contrasting conditions. The algae appeared to have great potential for application in microalgae-based biodiesel production.