Whole-exome sequencing capture kit biases yield false negative mutation calls in TCGA cohorts.

The Cancer Genome Atlas (TCGA) provides a genetic characterization of more than ten thousand tumors, enabling the discovery of novel driver mutations, molecular subtypes, and enticing drug targets across many histologies. Here we investigated why some mutations are common in particular cancer types but absent in others. As an example, we observed that the gene CCDC168 has no mutations in the stomach adenocarcinoma (STAD) cohort despite its common presence in other tumor types. Surprisingly, we found that the lack of called mutations was due to a systematic insufficiency in the number of sequencing reads in the STAD and other cohorts, as opposed to differential driver biology. Using strict filtering criteria, we found similar behavior in four other genes across TCGA cohorts, with each gene exhibiting systematic sequencing depth issues affecting the ability to call mutations. We identified the culprit as the choice of exome capture kit, as kit choice was highly associated with the set of genes that have insufficient reads to call a mutation. Overall, we found that thousands of samples across all cohorts are subject to some capture kit problems. For example, for the 6353 samples using the Broad Institute\u27s Custom capture kit there are undercalling biases for at least 4833 genes. False negative mutation calls at these genes may obscure biological similarities between tumor types and other important cancer driver effects in TCGA datasets

Differential Effects of Methoxy Group on the Interaction of Curcuminoids with Two Major Ligand Binding Sites of Human Serum Albumin

Curcuminoids are a group of compounds with a similar chemical backbone structure but containing different numbers of methoxy groups that have therapeutic potential due to their anti-inflammatory and anti-oxidant properties. They mainly bind to albumin in plasma. These findings influence their body disposition and biological activities. Spectroscopic analysis using site specific probes on human serum albumin (HSA) clearly indicated that curcumin (Cur), demethylcurcumin (Dmc) and bisdemethoxycurcumin (Bdmc) bind to both Site I (sub-site Ia and Ib) and Site II on HSA. At pH 7.4, the binding constants for Site I were relatively comparable between curcuminoids, while the binding constants for Site II at pH 7.4 were increased in order Cur , Dmc , Bdmc. Binding experiments using HSA mutants showed that Trp214 and Arg218 at Site I, and Tyr411 and Arg410 at Site II are involved in the binding of curcuminoids. The molecular docking of all curcuminoids to the Site I pocket showed that curcuminoids stacked with Phe211 and Trp214, and interacted with hydrophobic and aromatic amino acid residues. In contrast, each curcuminoid interacted with Site II in a different manner depending whether a methoxy group was present or absent. A detailed analysis of curcuminoids-albumin interactions would provide valuable information in terms of understanding the pharmacokinetics and the biological activities of this class of compounds

Factors Influencing Students’ Perceptions of Online Teamwork

The evolution of online teaching in higher education demands a change in the types of pedagogies used in those courses. An example of one of these important pedagogies includes online teamwork. Teamwork in this context is one in which the majority of the individual’s grade is dependent on the positive or negative group experiences. This study utilized the theoretical framework of social motivation and cohesion to identify the factors shaping students’ perceptions of teamwork in online college courses. In these courses, the pedagogical approach known as the Five Pillars of effective collaborative work was applied. An Online Teamwork Learning Survey was developed based on these principles and completed by 62 undergraduate students enrolled in semester-long online courses required in their early childhood education program of study. Using a comparison between pre–post surveys and regression analysis, the results showed that although the students’ perceptions of teamwork did not significantly change, the factors influencing their responses during the post-test doubled in number. The results showed that through carefully designed virtual teamwork activities, students learned that essential team characteristics such as promotive interaction, individual accountability, and positive interdependence are an integral part of effective collaboration and strong predictors of teamwork perception

A novel S-sulfhydrated human serum albumin preparation suppresses melanin synthesis

Products of ultraviolet (UV) irradiation such as reactive oxygen species (ROS) and nitric oxide (NO) stimulate melanin synthesis. Reactive sulfur species (RSS) have been shown to have strong ROS and NO scavenging effects. However, the instability and low retention of RSS limit their use as inhibitors of melanin synthesis. The free thiol at Cys34 on human serum albumin (HSA) is highly stable, has a long retention and possess a high reactivity for RSS. We report herein on the developm ent of an HSA based RSS delivery system. Sulfane sulfur derivatives released from sodium polysulfides (Na 2 S n ) react readily with HSA. An assay for estimating the elimination of sulfide from polysulfide showed that almost all of the sulfur released from Na 2 S n bound to HSA. The Na 2 S n -treated HSA was found to efficiently scavenge ROS and NO produced from chemical reagents. The Na 2 S n -treated HSA was also found to inhibit melanin synthesis in B16 melanoma cells and this inhibition was independent of the number of added sulfur atoms. In B16 melanoma cells, the Na 2 S n -treated HSA also inhibited the levels of ROS and NO induced by UV radiation. Finally, the Na 2 S n -treated HSA inhibited melanin synthesis from L-DOPA and mushroom tyrosinase and suppressed the extent of aggregation of melanin pigments. These data suggest that Na 2 S n -treated HSA inhibits tyrosinase activity for melanin synthesis via two pathways; by directly inhibiting ROS signaling and by scavenging NO. These findings indicate that Na 2 S n -treated HSA has potential to be an attractive and effective candidate for use as a skin whitening agent

The Therapeutic Effect of Human Serum Albumin Dimer-Doxorubicin Complex against Human Pancreatic Tumors

Human serum albumin (HSA) is a versatile drug carrier with active tumor targeting capacity for an antitumor drug delivery system. Nanoparticle albumin-bound (nab)-technology, such as nab-paclitaxel (Abraxane®), has attracted significant interest in drug delivery research. Recently, we demonstrated that HSA dimer (HSA-d) possesses a higher tumor distribution than HSA monomer (HSA-m). Therefore, HSA-d is more suitable as a drug carrier for antitumor therapy and can improve nab technology. This study investigated the efficacy of HSA-d-doxorubicin (HSA-d-DOX) as next-generation nab technology for tumor treatment. DOX conjugated to HSA-d via a tunable pH-sensitive linker for the controlled release of DOX. Lyophilization did not affect the particle size of HSA-d-DOX or the release of DOX. HSA-d-DOX showed significantly higher cytotoxicity than HSA-m-DOX in vitro. In the SUIzo Tumor-2 (SUIT2) human pancreatic tumor subcutaneous inoculation model, HSA-d-DOX could significantly inhibit tumor growth without causing serious side effects, as compared to the HSA binding DOX prodrug, which utilized endogenous HSA as a nano-drug delivery system (DDS) carrier. These results indicate that HSA-d could function as a natural solubilizer of insoluble drugs and an active targeting carrier in intractable tumors with low vascular permeability, such as pancreatic tumors. In conclusion, HSA-d can be an effective drug carrier for the antitumor drug delivery system against human pancreatic tumors

A novel S-sulfhydrated human serum albumin preparation suppresses melanin synthesis

Products of ultraviolet (UV) irradiation such as reactive oxygen species (ROS) and nitric oxide (NO) stimulate melanin synthesis. Reactive sulfur species (RSS) have been shown to have strong ROS and NO scavenging effects. However, the instability and low retention of RSS limit their use as inhibitors of melanin synthesis. The free thiol at Cys34 on human serum albumin (HSA) is highly stable, has a long retention and possess a high reactivity for RSS. We report herein on the development of an HSA based RSS delivery system. Sulfane sulfur derivatives released from sodium polysulfides (Na2Sn) react readily with HSA. An assay for estimating the elimination of sulfide from polysulfide showed that almost all of the sulfur released from Na2Sn bound to HSA. The Na2Sn-treated HSA was found to efficiently scavenge ROS and NO produced from chemical reagents. The Na2Sn-treated HSA was also found to inhibit melanin synthesis in B16 melanoma cells and this inhibition was independent of the number of added sulfur atoms. In B16 melanoma cells, the Na2Sn-treated HSA also inhibited the levels of ROS and NO induced by UV radiation. Finally, the Na2Sn-treated HSA inhibited melanin synthesis from L-DOPA and mushroom tyrosinase and suppressed the extent of aggregation of melanin pigments. These data suggest that Na2Sn-treated HSA inhibits tyrosinase activity for melanin synthesis via two pathways; by directly inhibiting ROS signaling and by scavenging NO. These findings indicate that Na2Sn-treated HSA has potential to be an attractive and effective candidate for use as a skin whitening agent

S-Nitrosated alpha-1-acid glycoprotein exhibits antibacterial activity against multidrug-resistant bacteria strains and synergistically enhances the effect of antibiotics

Alpha-1-acid glycoprotein (AGP) is a major acute-phase protein. Biosynthesis of AGP increases markedly during inflammation and infection, similar to nitric oxide (NO) biosynthesis. AGP variant A (AGP) contains a reduced cysteine (Cys149). Previously, we reported that S-nitrosated AGP (SNO-AGP) synthesized by reaction with a NO donor, possessed very strong broad-spectrum antimicrobial activity (IC50 = 10−9-10−6 M). In this study, using a cecal ligation and puncture animal model, we confirmed that AGP can be endogenously S-nitrosated during infection. Furthermore, we examined the antibacterial property of SNO-AGP against multidrug-resistant Klebsiella pneumoniae and Pseudomonas aeruginosa to investigate the involvement of SNO-AGP in the host defense system. Our results showed that SNO-AGP could inhibit multidrug efflux pump, AcrAB-TolC, a major contributor to bacterial multidrug resistance. In addition, SNO-AGP decreased biofilm formation and ATP level in bacteria, indicating that SNO-AGP can revert drug resistance. It was also noteworthy that SNO-AGP showed synergistic effects with the existing antibiotics (oxacillin, imipenem, norfloxacin, erythromycin, and tetracycline). In conclusion, SNO-AGP participated in the host defense system and has potential as a novel agent for single or combination antimicrobial therapy

Negative Quasi-Probability as a Resource for Quantum Computation

A central problem in quantum information is to determine the minimal physical resources that are required for quantum computational speedup and, in particular, for fault-tolerant quantum computation. We establish a remarkable connection between the potential for quantum speed-up and the onset of negative values in a distinguished quasi-probability representation, a discrete analog of the Wigner function for quantum systems of odd dimension. This connection allows us to resolve an open question on the existence of bound states for magic-state distillation: we prove that there exist mixed states outside the convex hull of stabilizer states that cannot be distilled to non-stabilizer target states using stabilizer operations. We also provide an efficient simulation protocol for Clifford circuits that extends to a large class of mixed states, including bound universal states.Comment: 15 pages v4: This is a major revision. In particular, we have added a new section detailing an explicit extension of the Gottesman-Knill simulation protocol to deal with positively represented states and measurement (even when these are non-stabilizer). This paper also includes significant elaboration on the two main results of the previous versio

Distribution of Polysulfide in Human Biological Fluids and Their Association with Amylase and Sperm Activities

Intracellular polysulfide could regulate the redox balance via its anti-oxidant activity. However, the existence of polysulfide in biological fluids still remains unknown. Recently, we developed a quantitative analytical method for polysulfide and discovered that polysulfide exists in plasma and responds to oxidative stress. In this study, we confirmed the presence of polysulfide in other biological fluids, such as semen and nasal discharge. The levels of polysulfide in these biological fluids from healthy volunteers (n = 9) with identical characteristics were compared. Additionally, the circadian rhythm of plasma polysulfide was also investigated. The polysulfide levels detected from nasal discharge and seminal fluid were approximately 400 and 600 μM, respectively. No correlation could be found between plasma polysulfide and the polysulfide levels of tear, saliva, and nasal discharge. On the other hand, seminal polysulfide was positively correlated with plasma polysulfide, and almost all polysulfide contained in semen was found in seminal fluid. Intriguingly, saliva and seminal polysulfide strongly correlated with salivary amylase and sperm activities, respectively. These results provide a foundation for scientific breakthroughs in various research areas like infertility and the digestive system process