TASK DEFINITION: In this task, you are given a passage which has a question and the context. You have to generate an answer to the question based on the information present in the context.
PROBLEM: Context: Pandemic strains of HIV-1 (group M) encode a total of nine structural (gag, pol, env), regulatory (rev, tat) and accessory (vif, vpr, vpu, nef) genes. However, some subtype A and C viruses exhibit an unusual gene arrangement in which the first exon of rev (rev1) and the vpu gene are placed in the same open reading frame. Although this rev1-vpu gene fusion is present in a considerable fraction of HIV-1 strains, its functional significance is unknown.', 'Examining infectious molecular clones (IMCs) of HIV-1 that encode the rev1-vpu polymorphism, we show that a fusion protein is expressed in infected cells. Due to the splicing pattern of viral mRNA, however, these same IMCs also express a regular Vpu protein, which is produced at much higher levels. To investigate the function of the fusion gene, we characterized isogenic IMC pairs differing only in their ability to express a Rev1-Vpu protein. Analysis in transfected HEK293T and infected CD4+ T cells showed that all of these viruses were equally active in known Vpu functions, such as down-modulation of CD4 or counteraction of tetherin. Furthermore, the polymorphism did not affect Vpu-mediated inhibition of NF-B activation or Rev-dependent nuclear export of incompletely spliced viral mRNAs. There was also no evidence for enhanced replication of Rev1-Vpu expressing viruses in primary PBMCs or ex vivo infected human lymphoid tissues. Finally, the frequency of HIV-1 quasispecies members that encoded a rev1-vpu fusion gene did not change in HIV-1 infected individuals over time.\Question: Does a Naturally Occurring rev1-vpu Fusion Gene Confer a Fitness Advantage to HIV-1?

SOLUTION: Expression of a rev1-vpu fusion gene does not affect regular Rev and Vpu functions or alter HIV-1 replication in primary target cells. Since there is no evidence for increased replication fitness of rev1-vpu encoding viruses, this polymorphism likely emerged in the context of other mutations within and/or outside the rev1-vpu intergenic region, and may have a neutral phenotype.

PROBLEM: Context: Nonviral vectors based on polyethylenimine (PEI) usually contain an excess of PEI that is not complexed to DNA. Since unbound PEI contributes to cellular and systemic toxicity, purification of polyplexes from unbound PEI is desirable.', 'Size exclusion chromatography (SEC) was used to purify PEI polyplexes of free PEI. Transfection properties of purified polyplexes and the effect of free PEI on gene delivery were studied in vitro and in vivo after systemic application into mice.', 'SEC did not change the size and zeta-potential of polyplexes. Independent of the amount of PEI used for complex formation, purified PEI polyplexes had the same final PEI nitrogen/DNA phosphate ratio of 2.5. Notably, purified PEI polyplexes demonstrated low cellular and systemic toxicity. High transfection efficiency was achieved with purified polyplexes at high DNA concentrations (8-15 microg/ml). At low DNA concentrations (2-4 microg/ml) gene transfer with purified particles was less efficient than with polyplexes containing free PEI both in vitro and in vivo. Mechanistic studies showed that free PEI partly blocked cellular association of DNA complexes but was essential for the following intracellular gene delivery. Adding free PEI to cells treated with purified particles with a delay of up to 4 h resulted in significantly enhanced transfection efficiency compared with non-purified particles or purified particles without free PEI.\Question: Does purification of polyethylenimine polyplexes highlight the role of free polycations in gene transfer?

SOLUTION: This study presents an efficient method to remove free PEI from PEI polyplexes by SEC. Our results from transfection experiments demonstrate that free PEI substantially contributes to efficient gene expression but also mediates toxic effects in a dose-dependent manner. Purified polyplexes without free PEI have to be applied at increased concentrations to achieve high transfection levels, but exhibit a greatly improved toxicity profile.

PROBLEM: Context: Itaconate is an analog of phosphoenolpyruvate, which is an inhibitor of fructose-6-phosphate 2-kinase (F6P2Kinase), an enzyme that synthesizes fructose 2,6-bisphosphate (F26BP). Carbohydrates ingested are preferentially used for glycogen synthesis in the liver and muscles, and excess carbohydrates are metabolized by glycolysis in the liver and used for fatty acid synthesis. We hypothesized that itaconate is incorporated into liver cells and suppresses fat synthesis by inhibiting liver glycolysis at the step of phosphofructokinase, which is activated by F26BP.', 'Rats were allowed to eat ad libitum for 3 wk or, in separate experiments, to limit food intake by pair feeding. One group was given drinking water (control group) and the other group was given a 10 g/L itaconate solution (itaconate group). We measured body weight gain, visceral fat accumulation, and F6P2Kinase activity.', 'Body weight gain in the itaconate group was lower than that in the control group (P < 0.05). In the dietary-controlled rats, there was no difference in body weight increase between groups, but visceral fat content (P < 0.01), plasma free fatty acid, and triacylglycerol levels (P < 0.05) were lower in the itaconate group than in the control group. Further, itaconate decreased the F26BP level (P < 0.05) in vivo and partly inhibited rat liver-type F6P2Kinase in vitro.\Question: Does itaconate reduce visceral fat by inhibiting fructose 2,6-bisphosphate synthesis in rat liver?

SOLUTION:
These results indicate that itaconate, which is a decarboxylate and resembles phosphoenolpyruvate, is incorporated into liver cells and suppresses glycolysis by decreasing the level of F26BP, resulting in decreased visceral fat.