Bioenergetic adaptation in response to autophagy regulators during rotenone exposure

Parkinson's disease is the second most common neurodegenerative disorder with both mitochondrial dysfunction and insufficient autophagy playing a key role in its pathogenesis. Among the risk factors, exposure to the environmental neurotoxin rotenone increases the probability of developing Parkinson's disease. We previously reported that in differentiated SH‐SY5Y cells, rotenone‐induced cell death is directly related to inhibition of mitochondrial function. How rotenone at nM concentrations inhibits mitochondrial function, and whether it can engage the autophagy pathway necessary to remove damaged proteins and organelles, is unknown. We tested the hypothesis that autophagy plays a protective role against rotenone toxicity in primary neurons. We found that rotenone (10–100 nM) immediately inhibited cellular bioenergetics. Concentrations that decreased mitochondrial function at 2 h, caused cell death at 24 h with an LD50 of 10 nM. Overall, autophagic flux was decreased by 10 nM rotenone at both 2 and 24 h, but surprisingly mitophagy, or autophagy of the mitochondria, was increased at 24 h, suggesting that a mitochondrial‐specific lysosomal degradation pathway may be activated. Up‐regulation of autophagy by rapamycin protected against cell death while inhibition of autophagy by 3‐methyladenine exacerbated cell death. Interestingly, while 3‐methyladenine exacerbated the rotenone‐dependent effects on bioenergetics, rapamycin did not prevent rotenone‐induced mitochondrial dysfunction, but caused reprogramming of mitochondrial substrate usage associated with both complex I and complex II activities. Taken together, these data demonstrate that autophagy can play a protective role in primary neuron survival in response to rotenone; moreover, surviving neurons exhibit bioenergetic adaptations to this metabolic stressor. Exposure to the neurotoxin rotenone is a risk factor for Parkinson's disease. We tested the hypothesis that autophagy is protective against rotenone toxicity in primary neurons. Exposure to nanomolar concentrations of rotenone caused immediate mitochondrial dysfunction, associated with a suppression of macroautophagy. However, mitophagy occurred that was independent of LC3II accumulation, and the surviving neurons exhibited adaptations to their cellular bioenergetic profiles. Cotreatment with the autophagy enhancer rapamycin was protective, whereas further inhibition of autophagy with 3‐methyladenine (3‐MA) exacerbated cell death, resulting in additional bioenergetic adaptations in the surviving neurons.

     

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

The sensitivity of massively-parallel sequencing has confirmed that most cancers are oligoclonal, with subpopulations of neoplastic cells harboring distinct mutations. A fine resolution view of this clonal architecture provides insight into tumor heterogeneity, evolution, and treatment response, all of which may have clinical implications. Single tumor analysis already contributes to understanding these phenomena. However, cryptic subclones are frequently revealed by additional patient samples (e.g., collected at relapse or following treatment), indicating that accurately characterizing a tumor requires analyzing multiple samples from the same patient. To address this need, we present SciClone, a computational method that identifies the number and genetic composition of subclones by analyzing the variant allele frequencies of somatic mutations. We use it to detect subclones in acute myeloid leukemia and breast cancer samples that, though present at disease onset, are not evident from a single primary tumor sample. By doing so, we can track tumor evolution and identify the spatial origins of cells resisting therapy.     

Combined MTOR and autophagy inhibition: Phase I trial of hydroxychloroquine and temsirolimus in patients with advanced solid tumors and melanoma

The combination of temsirolimus (TEM), an MTOR inhibitor, and hydroxychloroquine (HCQ), an autophagy inhibitor, augments cell death in preclinical models. This phase 1 dose-escalation study evaluated the maximum tolerated dose (MTD), safety, preliminary activity, pharmacokinetics, and pharmacodynamics of HCQ in combination with TEM in cancer patients. In the dose escalation portion, 27 patients with advanced solid malignancies were enrolled, followed by a cohort expansion at the top dose level in 12 patients with metastatic melanoma. The combination of HCQ and TEM was well tolerated, and grade 3 or 4 toxicity was limited to anorexia (7%), fatigue (7%), and nausea (7%). An MTD was not reached for HCQ, and the recommended phase II dose was HCQ 600 mg twice daily in combination with TEM 25 mg weekly. Other common grade 1 or 2 toxicities included fatigue, anorexia, nausea, stomatitis, rash, and weight loss. No responses were observed; however, 14/21 (67%) patients in the dose escalation and 14/19 (74%) patients with melanoma achieved stable disease. The median progression-free survival in 13 melanoma patients treated with HCQ 1200mg/d in combination with TEM was 3.5 mo. Novel 18-fluorodeoxyglucose positron emission tomography (FDG-PET) measurements predicted clinical outcome and provided further evidence that the addition of HCQ to TEM produced metabolic stress on tumors in patients that experienced clinical benefit. Pharmacodynamic evidence of autophagy inhibition was evident in serial PBMC and tumor biopsies only in patients treated with 1200 mg daily HCQ. This study indicates that TEM and HCQ is safe and tolerable, modulates autophagy in patients, and has significant antitumor activity. Further studies combining MTOR and autophagy inhibitors in cancer patients are warranted.     

Optimization of the multiple enzymatic activities of the hepatitis C virus NS3 protein

The hepatitis C virus (HCV) nonstructural protein 3 (NS3) is known to possess multiple enzymatic activities. In addition to its well-characterized protease activity, HCV NS3 also has ATP hydrolase (ATPase) and nucleic acid unwinding (helicase) activities. We systematically studied the effect of common reagents on all three enzymatic activities with a view to improving assay sensitivity for compound screening and profiling. Inclusion of the detergent lauryl dimethylamine oxide (LDAO) improves protease and helicase activities significantly, allowing robust assays at much lower NS3 concentrations. These conditions enable a particularly sensitive protease assay that uses picomolar concentrations of NS3.     

Endogenous polyamine profiles in different tissues of <Emphasis Type="Italic">Coffea</Emphasis> sp., and their levels during the ontogeny of fruits

Polyamines are essential compounds for growth and development in plants. An attempt has been made to find out the endogenous polyamine profiles in various parts and during the ontogeny of fruit formation of two commercially important Coffea species viz., arabica and canephora. Putrescine (Put), spermine (Spm) and spermidine (Spd) are the predominant polyamines during the ontogeny of fruit and their level increased with the advancement of fruit development. However, in the initial stages of flower and fruit development Spm levels were found to be decreased. Elevated levels of major polyamines Put, Spd, and Spm were observed in zygotic embryos than in somatic embryos. Along with this cadavarine (Cad) and other biogenic amines viz., tyramine (Tyr) and tryptamine (Try) were also found during the ontogeny of fruit in C. canephora. In this study the enodogenous polyamine profiles in coffee tissues and beans have been addressed.     

Investigating the efficiency of the single backcrossing breeding strategy through computer simulation

A strategy combining single backcrossing with selected bulk breeding has been successfully used in wheat improvement at CIMMYT to introgress rust resistant genes from donor parents to elite adapted cultivars. In this research, the efficiency of this breeding strategy was compared to other crossing and selection strategies through computer simulation. Results indicated this breeding strategy has advantages in retaining or improving the adaptation of the recurrent parents, and at the same time transferring most of the desired donor genes in a wide range of scenarios. Two rounds of backcrossing have advantages when the adaptation of donor parents is much poorer than that of the adapted parents, but the advantage of three rounds of backcrossing over two rounds is minimal. We recommend using the single backcrossing breeding strategy (SBBS) when three conditions are met: (1) multiple genes govern the phenotypic traits to be transferred from donor parents to adapted parents, (2) the donor parents have some favorable genes that may contribute to the improvement of adaptation in the recipient parents, and (3) conventional phenotypic selection is being applied, or individual genotypes cannot be precisely identified. We envisage that all three conditions commonly exist in modern breeding programs, and therefore believe that SBBS could be applied widely. However, we do not exclude the use of repeated backcrossing if the transferred genes can be precisely identified by closely linked molecular markers, and the donor parents have extremely poor adaptation.     

Techniques for in utero,longitudinal MRI of fetal brain development in baboons at 3 T

Magnetic Resonance Imaging (MRI) is a promising tool for the noninvasive, longitudinal study of developing primate brains. We developed a protocol to scan pregnant baboons serially at 3 T for up to 3 h per session. This protocol includes procedures for animal preparation, anesthesia, MRI scanning, and post-scan animal care. We applied this protocol to scan 5 baboons multiple times across the latter 70% of gestation—from as early as 56 days post-conceptional age to as late as 185 days (term ～180 days). We successfully acquired high-resolution anatomical images and maps of relaxation times (T₁ and T₂) of the fetal brains at multiple time points across gestation. These images and maps demonstrated the convergence of gray and white matter contrast near term, and furthermore demonstrated that the convergence of contrast is a consequence of the continuous change in relaxation times during fetal brain development. We estimated the rates of decrease of T₁ and T₂ in white matter and gray matter, respectively. In addition, we measured the volumes of fetal brain at different gestational ages and calculated the growth rates of whole brain (0.91 ± 0.08 cm³/day) and cortical gray matter (0.40 ± 0.04 cm³/day). We also measured the mean diffusivity in white matter and deep gray matter using diffusion tensor imaging. In conclusion, in utero MRI of fetal baboon brains greatly enhances the use of nonhuman primate models to study fetal brain development longitudinally.     

Decoding the rice genome

Rice cultivation is one of the most important agricultural activities on earth, with nearly 90% of it being produced in Asia. It belongs to the family of crops that includes wheat, maize and barley, and it supplies more than 50% of calories consumed by the world population. Its immense economic value and a relatively small genome size makes it a focal point for scientific investigations, so much so that four whole genome sequence drafts with varying qualities have been generated by both public and privately funded ventures. The availability of a complete and high-quality map-based sequence has provided the opportunity to study genome organization and evolution. Most importantly, the order and identity of 37,544 genes of rice have been unraveled. The sequence provides the required ingredients for functional genomics and molecular breeding programs aimed at unraveling intricate cellular processes and improving rice productivity.     

Peroxisome proliferator-activated receptor-α selective ligand reduces adiposity, improves insulin sensitivity and inhibits atherosclerosis in LDL receptor-deficient mice

Fenofibrate, a selective ¹PPAR-α activator, is prescribed to treat human dyslipidemia. The aim of this study was to delineate the mechanism of fenofibrate-mediated reductions in adiposity, improvements in insulin sensitivity, and lowering of triglycerides (TG) and free fatty acids (FFA) and to investigate if these favorable changes are related to the inhibition of lipid deposition in the aorta. To test this hypothesis we used male LDLr deficient mice that exhibit the clinical features of metabolic syndrome X when fed a high fat high cholesterol (HF) diet. LDLr deficient mice fed HF diet and simultaneously treated with fenofibrate (100 mg/kg body weight) prevented development of obesity, lowered serum triglycerides and cholesterol, improved insulin sensitivity, and prevented accumulation of lipids in the aorta. Lowering of circulating lipids occurred via down-regulation of lipogenic genes, including fatty acid synthase, acetyl CoA carboxylase and diacyl glycerol acyl transferase-2, concomitant with decreased liver TG and cholesterol, and TG output rate. Fenofibrate also suppressed liver apoCIII mRNA levels and markedly increased lipoprotein lipase mRNA levels, known to enhance serum TG catabolism. In addition, fenofibrate profoundly reduced epididymal fat and mesenteric fat mass to the levels seen in lean mice. The reductions in body weight were associated with elevation of hepatic uncoupling protein 2 (UCP2) mRNA, a concomitant increase in the ketone body formation, and improved insulin sensitivity associated with tumor necrosis factor-α reductions and phosphoenol pyruvate carboxykinase down-regulation. These results demonstrate that fenofibrate improves lipid abnormalities partly via inhibition of TG production and partly via clearance of TG-rich apoB particles by elevating LPL and reduced apoCIII. The prevention of obesity development occurred via energy expenditure. Fenofibrate-mediated hypolipidemic effects together with improved insulin sensitivity and loss of adiposity led to the reductions in the aortic lipid deposition by inhibiting early stages of atherosclerosis possibly via vascular cell adhesion molecule-1 (VCAM-1) modulation. These results suggest that potent PPAR-α activators may be useful in the treatment of syndrome X. (Mol Cell Biochem xxx: 1–16, 2005)     

Development of methods for extraction and in vitro quantification of estrogenic and androgenic activity of wastewater samples

Chemicals released into the environment by anthropogenic activities have been linked to estrogenic or androgenic effects in exposed wildlife, and there is a need to develop and validate rapid and cost-effective methods to quantify the total estrogenic and androgenic activity of environmental water samples. In this study, estrogen receptors (ER) were isolated from sheep (Ovis aries) uteri and rainbow trout (Oncorhynchus mykiss) livers and androgen receptors (AR) were isolated from rainbow trout brains. The isolated receptors were used in competitive receptor binding assays to test the affinity of known estrogenic and androgenic chemicals for the receptor binding site, and results were compared with literature values for the rat uterine ER binding assay and the E-Screen. The relative binding affinities of the tested compounds to ER from different species were similar, and binding to the ER was a more responsive endpoint than the cellular effect measured in the E-Screen. Using the sheep ER binding assay in combination with solid-phase extraction, the estrogenic activity in a raw sewage sample from a municipal treatment plant in Brisbane (Queensland, Australia) was measured at 51-73 ng/L estradiol equivalents (EEq).