Somatic mutation load of estrogen receptor-positive breast tumors predicts overall survival: an analysis of genome sequence data.

Breast cancer is one of the most commonly diagnosed cancers in women. While there are several effective therapies for breast cancer and important single gene prognostic/predictive markers, more than 40,000 women die from this disease every year. The increasing availability of large-scale genomic datasets provides opportunities for identifying factors that influence breast cancer survival in smaller, well-defined subsets. The purpose of this study was to investigate the genomic landscape of various breast cancer subtypes and its potential associations with clinical outcomes. We used statistical analysis of sequence data generated by the Cancer Genome Atlas initiative including somatic mutation load (SML) analysis, Kaplan-Meier survival curves, gene mutational frequency, and mutational enrichment evaluation to study the genomic landscape of breast cancer. We show that ER(+), but not ER(-), tumors with high SML associate with poor overall survival (HR = 2.02). Further, these high mutation load tumors are enriched for coincident mutations in both DNA damage repair and ER signature genes. While it is known that somatic mutations in specific genes affect breast cancer survival, this study is the first to identify that SML may constitute an important global signature for a subset of ER(+) tumors prone to high mortality. Moreover, although somatic mutations in individual DNA damage genes affect clinical outcome, our results indicate that coincident mutations in DNA damage response and signature ER genes may prove more informative for ER(+) breast cancer survival. Next generation sequencing may prove an essential tool for identifying pathways underlying poor outcomes and for tailoring therapeutic strategies

The effect of cryopreservation media on the quality of β-thalassemia mouse spermatozoa

Background: The mouse model of human diseases is commonly used for biomedical study, including β-thalassemia (β-thal), an inherited hemoglobin disorder. Maintaining the mice strain by natural mating systems is costly and seems impractical, especially during the COVID-19 pandemic. Sperm-freezing is a cost-effective solution for β-thal mouse colony management. Aim: To determine appropriate cryopreservation media for β-thal mouse spermatozoa to establish a β-thal mouse sperm bank. Methods: The epididymal spermatozoa of C57BL/6 wild-type (WT) and β-globin gene knockout thalassemia (BKO) mice were frozen in four freezing media: I) raffinose–skim milk–monothioglycerol (MTG), II) raffinose–skim milk– glutamine, III) raffinose–egg yolk–glycerol, and IV) egg yolk–TES–Tris. The sperm quality was assessed prior to and following freeze-thawing. Results: Compared with WT counterparts, the viable spermatozoa before freezing exhibiting elevated levels of oxidative stress were significantly greater in BKO (p = 0.01). After thawing, the membrane integrity of BKO spermatozoa preserved in I was significantly lower (p = 0.001). The sperm viability and membrane integrity of BKO males were also inferior when media III and IV were used (p = 0.008–0.027). The amount of oxidative stress in the spermatozoon of BKO mice was significantly greater when preserved in I, III, and IV (p = 0.002–0.044). Comparing freezing media, the motility and acrosome integrity of WT and BKO spermatozoa preserved in IV were significantly higher than those in other media (p < 0.001 to p = 0.01). Spermatozoa with the highest mitochondrial membrane potential were observed in I in both genotypes (p = 0.012 to p > 0.05). The viability, membrane integrity, and oxidative stress of post-thaw BKO spermatozoa did not significantly differ among freezing solutions. Conclusion: Irrespective of freezing media, spermatozoa of BKO males are rather more sensitive to cryopreservation than those of WT. Raffinose–skim milk–MTG/glutamine, raffinose–egg yolk–glycerol, and egg yolk–TES–Tris can all be used to preserve BKO mouse spermatozoa. However, with slightly better sperm characteristics, egg yolk–TES– Tris may be a diluent of choice for BKO mouse sperm cryopreservation. The addition of a reducing agent to thawing media is also strongly recommended to efficiently prevent oxidative stress and therefore improve frozen-thawed sperm survival

Immobilized lipase from potential lipolytic microbes for catalyzing biodiesel production using palm oil as feedstock

Biodiesel has been regarded as a biodegradable and non-polluting fuel. Enzymatic transesterification reaction for manufacturing biodiesel from vegetable oils with alcohol is an attractive approach. However, the cost of enzyme remains a barrier for its industrial implementation. The aim of this research was the screening of lipase-producing microorganisms and the studies of potential lipase-mediated biodiesel production using palm oil as substrate. A total of 360 strains of bacteria, yeasts and fungi were isolated and screened from the samples of oil-contaminated soil and waste water. Among all the screened microbes, the potential lipolytic bacterium,  Staphylococcus warneri, unicellular yeast, Candida rugosa and filamentous fungus, Fusarium solani were selected because of their high specific  activities. The lipase-producing conditions were subsequently optimized by using palm oil as an inducer and lipase activities were compared for both hydrolytic and synthetic catalysis. C. rugosa lipase, which exhibited the highest potential for catalyzing the biodiesel production, was further  purified and immobilized on various hydrophobic supports. The catalysis of transesterification between methanol and palm oil by the C. rugosa immobilized lipases revealed that immobilized lipase from C. rugosa on Sepabeads EC-OD was the most promising for further development as a biocatalyst for the application of enzyme-catalyzed biodiesel synthesis.Key words: Screening, lipases, immobilization, biodiesel

Effects of green tea extract treatment on erythropoiesis and iron parameters in iron-overloaded β-thalassemic mice

β-Thalassemia is characterized by ineffective erythropoiesis leading to chronic anemia. Thus, increased iron absorption from the duodenum and via blood transfusions is required to maintain normal blood hemoglobin (Hb) levels and iron chelators in the removal of excessive iron. Certain agents are also needed for the improvement of stress erythropoiesis and iron dysregulation. Green tea extract (GTE), which is rich in epigallocatechin-3-gallate (EGCG), is known to possess radical scavenging and iron-chelating activities. We aimed to assess the effects of green tea extract on erythroid regulators, iron mobilization and anti–lipid peroxidation in the liver, spleen, and kidneys of iron-loaded β-globin gene knockout thalassemic (BKO) mice. Our results indicate that treatments of green tea extract and/or deferiprone (DFP) diminished levels of plasma erythropoietin (EPO) and erythroferrone (ERFE), and consistently suppressed kidney Epo and spleen Erfe mRNA expressions (p <.05) in iron- loaded BKO mice when compared with untreated mice. Coincidently, the treatments decreased plasma ferritin (Ft) levels, iron content levels in the liver (p <.05), spleen (p <.05), and kidney tissues of iron–loaded BKO mice. Furthermore, lipid-peroxidation products in the tissues and plasma were also decreased when compared with untreated mice. This is the first evidence of the orchestral role of green tea extract abundant with epigallocatechin-3-gallate in improving ineffective erythropoiesis, iron dysregulation and oxidative stress in iron-overloaded β-thalassemic mice

Proteome level changes in the root of Brassica alboglabra induced by alachlor herbicide

Chinese kale (Brassica alboglabra) is a famous and extensively grown vegetable in Southeast Asia. Despite its nutritional values, pesticides are heavily applied to it. In this study, changes in protein expression due to alachlor treatment on B. alboglabra were investigated by using the 2-dimensional PAGE. Differential protein expressions were determined by using Image Master Software with volume (%) ≥2 fold as significant. Ten spots of interest have been identified by LC/MS/MS showing significant increases in differential protein expression between B. alboglabra roots treated with alachlor as compared to the untreated group which include HSC-cognate binding proteins, adenosylmethionine synthetase and beta-tubulin involved in defence mechanism in plants. Little is known about the function of other proteins identified which include knox-like proteins and hypothetical protein. Further investigations on plant proteomics would provide more information on the effects of different types of pesticides.Keywords: Brassica alboglabra, pesticides, proteomics, two-dimensional electrophoresisAfrican Journal of Biotechnology Vol. 12(20), pp. 2840-284

Proteomic Studies of Cholangiocarcinoma and Hepatocellular Carcinoma Cell Secretomes

Cholangiocarcinoma (CCA) and hepatocellular carcinoma (HCC) occur with relatively high incidence in Thailand. The secretome, proteins secreted from cancer cells, are potentially useful as biomarkers of the diseases. Proteomic analysis was performed on the secreted proteins of cholangiocarcinoma (HuCCA-1) and hepatocellular carcinoma (HCC-S102, HepG2, SK-Hep-1, and Alexander) cell lines. The secretomes of the five cancer cell lines were analyzed by SDS-PAGE combined with LC/MS/MS. Sixty-eight proteins were found to be expressed only in HuCCA-1. Examples include neutrophil gelatinase-associated lipocalin (lipocalin 2), laminin 5 beta 3, cathepsin D precursor, desmoplakin, annexin IV variant, and annexin A5. Immunoblotting was used to confirm the presence of lipocalin 2 in conditioned media and cell lysate of 5 cell lines. The results showed that lipocalin 2 was a secreted protein which is expressed only in the conditioned media of the cholangiocarcinoma cell line. Study of lipocalin 2 expression in different types of cancer and normal tissues from cholangiocarcinoma patients showed that lipocalin 2 was expressed only in the cancer tissues. We suggest that lipocalin 2 may be a potential biomarker for cholangiocarcinoma