Alcohol and HIV decrease proteasome and immunoproteasome function in macrophages: implications for impaired immune function during disease

Proteasomes (proteinase complexes, PR) and immunoproteasomes (IPR) degrade damaged proteins and affect protein processing required for antigen presentation by mononuclear phagocytes. These critical immune processes are attenuated during progressive HIV-1 infection and are affected by alcohol abuse. To investigate the mechanisms underlying these functional changes, we measured PR and CYP2E1 activities [an ethanol (EtOH) metabolizing enzyme] and reactive oxygen species (ROS) in human monocyte-derived macrophages (MDM) following HIV-1 infection and EtOH treatment. We observed progressive declines of PR activity and PR/IPR contents in HIV-1-infected MDM. PR activity and IPR expression increased after IFN-gamma stimulation but reduced after HIV-1 infection. EtOH inhibited both IFN-gamma-induced PR and IPR. Paradoxically, EtOH attenuated PR catalytic activity in infected MDM and suppressed viral replication. Elevated ROS followed EtOH exposure and paralleled decreased PR activity. The latter was restored by anti-oxidant. The data support the notion that HIV-1 infection and EtOH may work in concert to affect immune function including antigen presentation and thereby affect disease progression.     

Genetics and pathophysiology of hyperinsulinism in infancy

Hyperinsulinism in infancy (HI) is a condition of neonates and early childhood. For many years the pathophysiology of this potentially lethal disorder was unknown. Advances in the genetics, histopathology and molecular physiology of this disease have now provided insights into the causes of beta-cell dysfunction and revealed levels of diversity far in excess of our previous knowledge. These include defects in ion channel subunit genes and mutations in several enzymes associated with beta-cell metabolism and anaplerosis. In most cases, beta-cell pathophysiology leads to an alteration in the function of ATP-sensitive K(+) channels. This can manifest as 'channelopathies' of K(ATP) channels through gene defects in ABCC8 and KCNJ11 (Ch.11p15); or as a result of 'metabolopathies' through defects in the genes encoding glucokinase (GCK, Ch.7p15-p13), glutamate dehydrogenase (GLUD1, Ch.10q23.3) and short-chain L-3-hydroxyacyl-CoA dehydrogenase (HADHSC, Ch.4q22-q26). This review focuses upon the relationship between the causes of HI and therapeutic options.     

Generation of pokeweed antiviral protein mutations in Saccharomyces cerevisiae: evidence that ribosome depurination is not sufficient for cytotoxicity

Pokeweed antiviral protein (PAP) is a ribosome-inactivating protein that depurinates the highly conserved α-sarcin/ricin loop in the large rRNA. Here, using site-directed mutagenesis and systematic deletion analysis from the 5′ and the 3′ ends of the PAP cDNA, we identified the amino acids important for ribosome depurination and cytotoxicity of PAP. Truncating the first 16 amino acids of PAP eliminated its cytotoxicity and the ability to depurinate ribosomes. Ribosome depurination gradually decreased upon the sequential deletion of C-terminal amino acids and was abolished when a stop codon was introduced at Glu-244. Cytotoxicity of the C-terminal deletion mutants was lost before their ability to depurinate ribosomes. Mutations in Tyr-123 at the active site affected cytotoxicity without altering the ribosome depurination ability. Total translation was not inhibited in yeast expressing the non-toxic Tyr-123 mutants, although ribosomes were depurinated. These mutants depurinated ribosomes only during their translation and could not depurinate ribosomes in trans in a translation-independent manner. A mutation in Leu-71 in the central domain affected cytotoxicity without altering the ability to depurinate ribosomes in trans and inhibit translation. These results demonstrate that the ability to depurinate ribosomes in trans in a catalytic manner is required for the inhibition of translation, but is not sufficient for cytotoxicity.     

Enhanced inflammation and attenuated tumor suppressor pathways are associated with oncogene‐induced lung tumors in aged mice

Aging is often accompanied by a dramatic increase in cancer susceptibility. To gain insights into how aging affects tumor susceptibility, we generated a conditional mouse model in which oncogenic Kras^G12D was activated specifically in lungs of young (3–5 months) and old (19–24 months) mice. Activation of Kras^G12D in old mice resulted in shorter survival and development of higher‐grade lung tumors. Six weeks after Kras^G12D activation, old lung tissues contained higher numbers of adenomas than their young tissue counterparts. Lung tumors in old mice displayed higher proliferation rates, as well as attenuated DNA damage and p53 tumor suppressor responses. Gene expression comparison of lung tumors from young and old mice revealed upregulation of extracellular matrix‐related genes in young tumors, indicative of a robust cancer‐associated fibroblast response. In old tumors, numerous inflammation‐related genes such as Ccl7, IL‐1β, Cxcr6, and IL‐15ra were consistently upregulated. Increased numbers of immune cells were localized around the periphery of lung adenomas from old mice. Our experiments indicate that more aggressive lung tumor formation in older Kras^G12D mice may be in part the result of subdued tumor suppressor and DNA damage responses, an enhanced inflammatory milieu, and a more accommodating tissue microenvironment.     

Intracellular Localization of N-Acylphosphatidylethanolamine Synthesis in Cotyledons of Cotton (Gossypium hirsutm L.) Seedlings

N-Acylphosphatidylethanolamine (NAPE) is synthesized from freefatty acids and phosphatidylethanolamine (PE) by a membrane-boundacyltransferase enzyme designated NAPE synthase. Here we reportthe subcellular location of NAPE synthase in cotyledons of germinatedcotton seedlings. Organelle marker enzyme assays and transmissionelectron microscopy were used to evaluate cellular fractionsseparated by differential centrifugation, sucrose-density gradientcentrifugation, and aqueous two-phase partitioning. NAPE synthasewas associated with fractions enriched in ER, Golgi and plasmamembranes. NAPE synthase was not located in mitochondria, plastids,peroxi-somes, or cytosol. Consistent with these observations,NAPE synthase also was localized in membranes of the secretorypathway in spinach leaves. Because PE is synthesized primarilyin the ER, these results suggest that JV-acyla-tion of PE maybe a lipid modification of the compartments of the secretorypathway providing a mechanism for supplying NAPE to the plasmamembrane. These data are particularly relevant given the recentfindings that NAPE biosynthesis is increased in elicitor-treatedplant cells [Chapman et al. (1995) Physiol. Plant. 95: 120]. (Received July 25, 1997; Accepted October 6, 1997)     

An ensemble micro neural network approach for elucidating interactions between zinc finger proteins and their target DNA

Background

The ability to engineer zinc finger proteins binding to a DNA sequence of choice is essential for targeted genome editing to be possible. Experimental techniques and molecular docking have been successful in predicting protein-DNA interactions, however, they are highly time and resource intensive. Here, we present a novel algorithm designed for high throughput prediction of optimal zinc finger protein for 9 bp DNA sequences of choice. In accordance with the principles of information theory, a subset identified by using K-means clustering was used as a representative for the space of all possible 9 bp DNA sequences. The modeling and simulation results assuming synergistic mode of binding obtained from this subset were used to train an ensemble micro neural network. Synergistic mode of binding is the closest to the DNA-protein binding seen in nature, and gives much higher quality predictions, while the time and resources increase exponentially in the trade off. Our algorithm is inspired from an ensemble machine learning approach, and incorporates the predictions made by 100 parallel neural networks, each with a different hidden layer architecture designed to pick up different features from the training dataset to predict optimal zinc finger proteins for any 9 bp target DNA.

Results

The model gave an accuracy of an average 83% sequence identity for the testing dataset. The BLAST e-value are well within the statistical confidence interval of E-05 for 100% of the testing samples. The geometric mean and median value for the BLAST e-values were found to be 1.70E-12 and 7.00E-12 respectively. For final validation of approach, we compared our predictions against optimal ZFPs reported in literature for a set of experimentally studied DNA sequences. The accuracy, as measured by the average string identity between our predictions and the optimal zinc finger protein reported in literature for a 9 bp DNA target was found to be as high as 81% for DNA targets with a consensus sequence GCNGNNGCN reported in literature. Moreover, the average string identity of our predictions for a catalogue of over 100 9 bp DNA for which the optimal zinc finger protein has been reported in literature was found to be 71%.

Conclusions

Validation with experimental data shows that our tool is capable of domain adaptation and thus scales well to datasets other than the training set with high accuracy. As synergistic binding comes the closest to the ideal mode of binding, our algorithm predicts biologically relevant results in sync with the experimental data present in the literature. While there have been disjointed attempts to approach this problem synergistically reported in literature, there is no work covering the whole sample space. Our algorithm allows designing zinc finger proteins for DNA targets of the user’s choice, opening up new frontiers in the field of targeted genome editing. This algorithm is also available as an easy to use web server, ZifNN, at http://web.iitd.ac.in/~sundar/ZifNN/.

     

Effects of Minocycline on Urine Albumin,Interleukin-6, and Osteoprotegerin in Patients with Diabetic Nephropathy: A Randomized Controlled Pilot Trial

Background

We tested minocycline as an anti-proteinuric adjunct to renin-angiotensin-aldosterone system inhibitors (RAASi) in diabetic nephropathy (DN) and measured urinary biomarkers to evaluate minocycline’s biological effects.

Methods

Design: Prospective, single center, randomized, placebo-controlled, intention-to-treat pilot trial. Inclusion. Type 2 diabetes/DN; Baseline creatinine clearance > 30 mL/min; proteinuria ≥ 1.0 g/day; Age ≥30 years; BP <150/95 mm Hg; intolerant of/at maximum RAASi dose. Protocol. 3-wk screening; Baseline randomization; Urine and blood measures at months 1, 2, 4, and Month 6 study completion. Urine interleukin-6 (IL-6) and osteoprotegerin were measured in a subset. Primary outcome. Natural log of urine protein/creatinine (ln U P:Cr) ratio at Month 6 vs Baseline.

Results

30 patients completed the study. The 15% decline in U P: Cr in minocycline patients (6 month P:Cr ÷ Baseline P:Cr, 0.85 vs. 0.92) was not significant (p = 0.27). Creatinine clearance did not differ in the 2 groups. Urine IL-6:Cr (p = 0.03) and osteoprotegerin/Cr (p = 0.046) decrements were significant. Minocycline modified the relationship between urine IL-6 and proteinuria, suggesting a protective biological effect.

Conclusions

Although the decline in U P:Cr in minocycline patients was not statistically significant, the significant differences in urine IL-6 and osteoprotegerin suggest that minocycline may confer cytoprotection in patients with DN, providing a rationale for further study.

Trial Registration

Clinicaltrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01779089","term_id":"NCT01779089"}}NCT01779089