HIV reservoirs and immune surveillance evasion cause the failure of structured treatment interruptions: a computational study

Continuous antiretroviral therapy is currently the most effective way to treat HIV infection. Unstructured interruptions are quite common due to side effects and toxicity, among others, and cannot be prevented. Several attempts to structure these interruptions failed due to an increased morbidity compared to continuous treatment. The cause of this failure is poorly understood and often attributed to drug resistance. Here we show that structured treatment interruptions would fail regardless of the emergence of drug resistance. Our computational model of the HIV infection dynamics in lymphoid tissue inside lymph nodes, demonstrates that HIV reservoirs and evasion from immune surveillance themselves are sufficient to cause the failure of structured interruptions. We validate our model with data from a clinical trial and show that it is possible to optimize the schedule of interruptions to perform as well as the continuous treatment in the absence of drug resistance. Our methodology enables studying the problem of treatment optimization without having impact on human beings. We anticipate that it is feasible to steer new clinical trials using computational models.     

Liver mtDNA content increases during development: a comparison of methods and the importance of age- and tissue-specific controls for the diagnosis of mtDNA depletion

BACKGROUND: The quantitative loss of mitochondrial DNA (mtDNA) known as mtDNA depletion, often gives rise to liver disease. The diagnosis of mtDNA depletion syndrome is frequently imprecise, both for technical reasons and because of the lack of established age-adjusted normal ranges. We aimed to refine quantitative methods for diagnosing the hepatic type of mtDNA depletion syndrome, firstly by establishing an age-matched reference range for mitochondrial to nuclear DNA ratio (henceforth "mtDNA content") and secondly by investigating mtDNA in fibroblasts. METHODS: By comparing realtime PCR with an established method for quantifying mtDNA content we established a reference range for young children using biopsy and post-mortem material from patients <15 years. In addition, we investigated the arrangement of mtDNA in nucleoids from fibroblasts using fluorescence microscopy. RESULTS: Both methods showed that the mtDNA content of liver increases rapidly over the perinatal period. In a patient whose liver mtDNA content fell, but remained within the reference range, early investigation and age-matched controls were essential, as we found a progressive increase in muscle mtDNA copy number, respiratory chain activity and muscle power with age. In three further patients, fluorescence microscopy of the fibroblasts proved diagnostic. In one case a movement disorder was an important pointer. CONCLUSIONS: These cases highlight the (i) need for comparing mtDNA copy number data generated from patients to DNA isolated from an age-matched normal range from the tissue of interest and (ii) the utility of mtDNA staining with PicoGreen as a method to detect aberrant nucleoid morphology in mtDNA depletion patient fibroblast lines when affected tissues are not available for measuring mtDNA copy number.     

First report of Garella musculana (Erschov, 1874) (Lepidoptera: Nolidae) in Italy with insights into its identity

The Asian walnut moth, Garella musculana (Erschov, 1874) (Lepidoptera: Nolidae), is a major pest of walnut. Native to Central Asia, it was found to be invasive in 2008 in Sevastopol (Crimea) and nowadays widespread in Turkey, Bulgaria, Romania and Russia. Here, we account for the finding of G. musculana in NE Italy (Veneto region) in 2021, where adults were found in a light lamp, representing the first record of the Asian walnut moth for this country and Western Europe. Adult specimens were identified morphologically on both external characters and genitalia features. G. musculana larvae and damage were also observed on a plantation of Juglans regia L. (Fagales: Juglandaceae) located in Veneto in October 2021. A COI-barcoding analysis was performed to attain a molecular characterization of our specimens and probate our morphological identification. However, because no sequence of G. musculana was present in major gene databases and the similarity of our sequences with those attributed to Garella ruficirra (Hampson, 1905) (Lepidoptera: Nolidae) made clear that these taxa deserved further scrutiny regarding their specific distinction. Some subtle differences in the male terminalia could be found between them and their vast geographic distributions, but the strong similarity in most features calls for further morphological and genetical insights on a broad set of samples to assess whether they represent two closely related, substantially parapatric species, or a unique, geographically varying entity. Solving this issue may turn out crucial in the identification and proper management of walnut moths of the genus Garella.     

Tripodal polyphosphine ligands in silver (I) coordination chemistry: Mononuclear cf. polynuclear complex dependence vis-a-vis counterion and ligand to metal ratio

1:2, 1:1, 3:2 and 6:2 AgX:L adducts (where L is a tridentate phosphine, in detail: 1,1,1-tris(diphenylphosphinomethyl)ethane (Me-triphos) and bis(2-diphenylphosphinoethyl)phenylphosphine (Ph-triphos), X = O₃SCF₃, O₃SCH₃, BF₄ or O₂CCF₃) have been synthesized and characterized by IR, NMR (¹H, ³¹P and ¹⁹F) and ESI MS spectroscopy. The stoichiometry of the complexes is strongly dependent on the ligand to metal ratio employed and also on the nature of the counterion. ³¹P NMR (solution) data also show the complexes existing in solution, in some cases, however, disproportionating to adducts of different nuclearity. Oligonuclear species have been detected through ESI MS spectroscopy that has been demonstrated as a powerful tool for the identification of the solution species. AgBF₄:Me-triphos (1:2) has been structurally characterized as [Ag(P,P′-Me-triphos)₂](BF₄) · H₂O · 7/2 MeOH, while Ag(O₃SCF₃): Ph-triphos: H₂O (6:2:4) is a spectacular two-dimensional polymer.     

Oligothiophene molecular beacons

Oligomers of thiophene are widely studied compounds for their electronic and optoelectronic properties. Despite their strong fluorescence, their use as markers for biomolecules, especially for oligonucleotides (ONs), is still largely unexplored. Here, we describe the synthesis of a series of ON molecular beacons employing different oligothiophenes as fluorescent probes and discuss their fluorescence emissions in comparative experiments with and without dabcyl as a quencher, in their hairpin and linear conformations, and as duplexes after hybridization with a complementary target.     

Direct resolution of ergot alkaloid enantiomers on a novel chiral silica-based stationary phase

A new covalently-bonded, silica-based stationary phase, using as the chiral selector the 1-(3-aminopropyl) derivative of (+)-(5R,8S,10R)-terguride, has been developed to resolve optically active isomers by HPLC. Good resolution of structurally related racemic ergot alkaloids were obtained using water-methanol mixtures as the eluent. Analysis of the influence of the type and concentration of the organic modifier, and the pH of the buffer in the mobile phase allowed the enantioseparation of these compounds to be optimized. Determination of the optical purity of a lisuride-containig drug is reported. © 1994 Wiley-Liss, Inc.     

Plasma N-glycome composition associates with chronic low back pain

Background

Low back pain (LBP) is the symptom of a group of syndromes with heterogeneous underlying mechanisms and molecular pathologies, making treatment selection and patient prognosis very challenging. Moreover, symptoms and prognosis of LBP are influenced by age, gender, occupation, habits, and psychological factors. LBP may be characterized by an underlying inflammatory process. Previous studies indicated a connection between inflammatory response and total plasma N-glycosylation. We wanted to identify potential changes in total plasma N-glycosylation pattern connected with chronic low back pain (CLBP), which could give an insight into the pathogenic mechanisms of the disease.

Changes in Cyclins and Cyclin-Dependent Kinases Induced by DNA Damaging Agents in a Human Ovarian Cancer Cell Line Expressing Mutated or Wild-Type P53

The expression of cyclins, cyclin-dependent kinases (cdk), and cdk inhibitors was evaluated in clones from a human ovarian cancer cell line transfected with a temperature-sensitive mutant of p53, after treatment with the anticancer agents doxorubicin (DX) and AMSA. The two drugs were selected on the basis of their activity in these clones, since AMSA is equally active in cells expressing mutated or wild-type (wt) p53, while DX was much less cytotoxic in cells expressing wt p53. In untreated cells, the expression of wt p53 induced an accumulation of cells in the G2 and perhaps also the G1 phase of the cell cycle. Concomitantly cyclin B1 and cdc2 increased. Cyclin E and particularly D1 levels were also raised by wt p53 expression. Treatment of mutated p53-expressing cells (SK23a cells kept at 37°C) with DX or, more so, with AMSA, resulted in a strong accumulation of cyclin B1 and cdc2, in accordance with their ability to block cells in G2 phase of the cell cycle. Wt p53-expressing cells (SK23a cells kept at 32°C) treated with the drugs showed an increase in p21 expression and consequently decreased kinase activity after immunoprecipitation with p21 antibodies. Cdc2-associated kinase activity was also reduced in these conditions. We could also observe a decrease in the percentage of cells in G1 and G2 phases and an accumulation of cells in S phase after both DX and AMSA. Cdk2, retinoblastoma, and p27 levels did not change significantly. Treatment with DX or AMSA caused similar effects, suggesting that p53-induced changes in cyclin, cdk, and cdk inhibitors after DNA damage are not responsible for the marked reduction in the cytotoxicity of DX we observed in wt p53-expressing cells.     

A nuclear export signal and phosphorylation regulate Dok1 subcellular localization and functions

Dok1 is believed to be a mainly cytoplasmic adaptor protein which down-regulates mitogen-activated protein kinase activation, inhibits cell proliferation and transformation, and promotes cell spreading and cell migration. Here we show that Dok1 shuttles between the nucleus and cytoplasm. Treatment of cells with leptomycin B (LMB), a specific inhibitor of the nuclear export signal (NES)-dependent receptor CRM1, causes nuclear accumulation of Dok1. We have identified a functional NES (348LLKAKLTDPKED359) that plays a major role in the cytoplasmic localization of Dok1. Src-induced tyrosine phosphorylation prevented the LMB-mediated nuclear accumulation of Dok1. Dok1 cytoplasmic localization is also dependent on IKKbeta. Serum starvation or maintaining cells in suspension favor Dok1 nuclear localization, while serum stimulation, exposure to growth factor, or cell adhesion to a substrate induce cytoplasmic localization. Functionally, nuclear NES-mutant Dok1 had impaired ability to inhibit cell proliferation and to promote cell spreading and cell motility. Taken together, our results provide the first evidence that Dok1 transits through the nucleus and is actively exported into the cytoplasm by the CRM1 nuclear export system. Nuclear export modulated by external stimuli and phosphorylation may be a mechanism by which Dok1 is maintained in the cytoplasm and membrane, thus regulating its signaling functions.     

Light induced transmembrane proton gradient in artificial lipid vesicles reconstituted with photosynthetic reaction centers

Photosynthetic reaction center (RC) is the minimal nanoscopic photoconverter in the photosynthetic membrane that catalyzes the conversion of solar light to energy readily usable for the metabolism of the living organisms. After electronic excitation the energy of light is converted into chemical potential by the generation of a charge separated state accompanied by intraprotein and ultimately transmembrane proton movements. We designed a system which fulfills the minimum structural and functional requirements to investigate the physico/chemical conditions of the processes: RCs were reconstituted in closed lipid vesicles made of selected lipids entrapping a pH sensitive indicator, and electron donors (cytochrome c? and K?[Fe(CN)?]) and acceptors (decylubiquinone) were added to sustain the photocycle. Thanks to the low proton permeability of our preparations, we could show the formation of a transmembrane proton gradient under illumination and low buffering conditions directly by measuring proton-related signals simultaneously inside and outside the vesicles. The effect of selected ionophores such as gramicidin, nigericin and valinomycin was used to gain more information on the transmembrane proton gradient driven by the RC photochemistry.