Retroviral integration site selection

The stable insertion of a copy of their genome into the host cell genome is an essential step of the life cycle of retroviruses. The site of viral DNA integration, mediated by the viral-encoded integrase enzyme, has important consequences for both the virus and the host cell. The analysis of retroviral integration site distribution was facilitated by the availability of the human genome sequence, revealing the non-random feature of integration site selection and identifying different favored and disfavored genomic locations for individual retroviruses. This review will summarize the current knowledge about retroviral differences in their integration site preferences as well as the mechanisms involved in this process.     

Insertional oncogenesis by non-acute retroviruses: implications for gene therapy

Retroviruses cause cancers in a variety of animals and humans. Research on retroviruses has provided important insights into mechanisms of oncogenesis in humans, including the discovery of viral oncogenes and cellular proto-oncogenes. The subject of this review is the mechanisms by which retroviruses that do not carry oncogenes (non-acute retroviruses) cause cancers. The common theme is that these tumors result from insertional activation of cellular proto-oncogenes by integration of viral DNA. Early research on insertional activation of proto-oncogenes in virus-induced tumors is reviewed. Research on non-acute retroviruses has led to the discovery of new proto-oncogenes through searches for common insertion sites (CISs) in virus-induced tumors. Cooperation between different proto-oncogenes in development of tumors has been elucidated through the study of retrovirus-induced tumors, and retroviral infection of genetically susceptible mice (retroviral tagging) has been used to identify cellular proto-oncogenes active in specific oncogenic pathways. The pace of proto-oncogene discovery has been accelerated by technical advances including PCR cloning of viral integration sites, the availability of the mouse genome sequence, and high throughput DNA sequencing. Insertional activation has proven to be a significant risk in gene therapy trials to correct genetic defects with retroviral vectors. Studies on non-acute retroviral oncogenesis provide insight into the potential risks, and the mechanisms of oncogenesis.     

Consistent, persistent expression from modified retroviral vectors in murine hematopoietic stem cells

Retroviral vectors based on the Moloney murine leukemia virus (MoMuLV) have shown inconsistent levels and duration of expression as well as a propensity for the acquisition of de novo methylation in vivo. MoMuLV-based vectors are known to contain sequences that are capable of suppressing or preventing expression from the long terminal repeat. Previously, we constructed a series of modified retroviral vectors and showed that they function significantly better than MoMuLV-based vectors in vitro. To test the efficacy of the modified vectors in hematopoietic stem cells in vivo, we examined gene expression and proviral methylation in differentiated hematopoietic colonies formed in the spleens of mice after serial transplantation with transduced bone marrow (2°CFU-S). We found a significant increase in the frequency of expression with our modified vectors (>90% expression in vector DNA containing 2°CFU-S) over the frequency observed with the standard MoMuLV-based vector (28% expression in vector containing 2°CFU-S). Expression from the modified vectors was highly consistent, with expression in >50% of the vector-containing 2°CFU-S from all 20 transplant recipients analyzed, whereas expression from the standard MoMuLV-based vector was inconsistent, with expression in 0–10% of the vector containing 2°CFU-S from 8 recipients and expression in >50% of the vector-containing 2°CFU-S from 4 other recipients. In addition, we established that the modified vectors had a lower level of DNA methylation than the control vector. These findings represent significant advances in the development and evaluation of effective retroviral vectors for application in vivo.     

Site-specific recombination for the modification of transgenic strains of the Mediterranean fruit fly Ceratitis capitata

Insect transgenesis is mainly based on the random genomic integration of DNA fragments embedded into non-autonomous transposable elements. Once a random insertion into a specific location of the genome has been identified as particularly useful with respect to transgene expression, the ability to make the insertion homozygous, and lack of fitness costs, it may be advantageous to use that location for further modification. Here we describe an efficient method for the modification of previously inserted transgenes by the use of the site-specific integration system from phage phiC31 in a tephritid pest species, the Mediterranean fruit fly Ceratitis capitata. First, suitable transgenic strains with randomly integrated attP landing sites within transposon-based vectors were identified by molecular and functional characterization. Second, donor plasmids containing an attB site, with additional markers, and transposon ends were integrated into attP sites by phiC31 integrase-mediated recombination. Third, transposase-encoding ‘jumpstarter’ strains were created and mated to transgenic strains resulting in the postintegrational excision of transposon ends, which left stably integrated transgene insertions that could not be remobilized. This three-step integration and stabilization system will allow the combination of several transgene-encoded advantageous traits at evaluated genomic positions to generate optimized strains for pest control that minimize environmental concerns.     

Duration of antiretroviral therapy among people living with HIV and incidence of hypertension in Ghana

Understanding the differential rates of incident hypertension among People Living with HIV (PLWH) based of duration of exposure to combination antiretroviral therapy (cART) may provide insights into the pathogenesis of hypertension in this population. Utilizing the dataset of a prospective study conducted at a Ghanaian tertiary medical center, we evaluated factors associated with incident hypertension among PLWH previously naïve to cART before study enrollment (cART newly prescribed group, n = 221) versus PLWH established on cART for at least a year (cART established group, n = 212). New‐onset hypertension was diagnosed as clinic BP > 140/90 mmHg on two separate clinic visits over 12‐month follow‐up. Cox proportional hazards regression models were used to assess factors associated with incident hypertension. Mean age of new versus cART established was 41.1 ± 8.2 versus 45.1 ± 8.6 years (p < .001), with more women in the cART established group (68.3 vs. 82%, p = .0009). There were 105 (24.3%) episodes of incident hypertension over 328 person‐years follow‐up (PYFU), incidence rate of 320.1 (95% CI: 263.1‐385.9)/1000 PYFU, with higher rates in new versus cART established (476.6/1000 PYFU vs. 222.8/1000 PYFU, p = 0.0002). Overall, age by increasing decile (aHR 0.76; 95% CI: 0.59‐0.98), log HIV‐1 viral load (aHR 1.16; 1.04‐1.35), and use of tenofovir (aHR 1.66; 1.04‐2.64) were associated with incident hypertension. While CD4 counts, age, BMI, pre‐diabetes, and urban/peri‐urban residency were independently associated with hypertension in the cART established group; no independent predictors were identified among the cART newly prescribed group. Further studies to explore the potential mechanisms underlying incidence of hypertension in PLWH are warranted.     

Retroviral vectors: post entry events and genomic alterations

The curative potential of retroviral vectors for somatic gene therapy has been demonstrated impressively in several clinical trials leading to sustained long-term correction of the underlying genetic defect. Preclinical studies and clinical monitoring of gene modified hematopoietic stem and progenitor cells in patients have shown that biologically relevant vector induced side effects, ranging from in vitro immortalization to clonal dominance and oncogenesis in vivo, accompany therapeutic efficiency of integrating retroviral gene transfer systems. Most importantly, it has been demonstrated that the genotoxic potential is not identical among all retroviral vector systems designed for clinical application. Large scale viral integration site determination has uncovered significant differences in the target site selection of retrovirus subfamilies influencing the propensity for inducing genetic alterations in the host genome. In this review we will summarize recent insights gained on the mechanisms of insertional mutagenesis based on intrinsic target site selection of different retrovirus families. We will also discuss examples of side effects occurring in ongoing human gene therapy trials and future prospectives in the field.     

Acoustic measurement of the Deepwater Horizon Macondo well flow rate

On May 31, 2010, a direct acoustic measurement method was used to quantify fluid leakage rate from the Deepwater Horizon Macondo well prior to removal of its broken riser. This method utilized an acoustic imaging sonar and acoustic Doppler sonar operating onboard a remotely operated vehicle for noncontact measurement of flow cross-section and velocity from the well’s two leak sites. Over 2,500 sonar cross-sections and over 85,000 Doppler velocity measurements were recorded during the acquisition process. These data were then applied to turbulent jet and plume flow models to account for entrained water and calculate a combined hydrocarbon flow rate from the two leak sites at seafloor conditions. Based on the chemical composition of end-member samples collected from within the well, this bulk volumetric rate was then normalized to account for contributions from gases and condensates at initial leak source conditions. Results from this investigation indicate that on May 31, 2010, the well’s oil flow rate was approximately 0.10 ± 0.017 m³ s^-1 at seafloor conditions, or approximately 85 ± 15 kg s^-1 (7.4 ± 1.3 Gg d^-1), equivalent to approximately 57,000 ± 9,800 barrels of oil per day at surface conditions. End-member chemical composition indicates that this oil release rate was accompanied by approximately an additional 24 ± 4.2 kg s^-1 (2.1 ± 0.37 Gg d^-1) of natural gas (methane through pentanes), yielding a total hydrocarbon release rate of 110 ± 19 kg s^-1 (9.5 ± 1.6 Gg d^-1).     

Molecular keys of the tropism of integration of the cholera toxin phage

Cholera toxin is encoded in the genome of CTXφ, a lysogenic filamentous phage of Vibrio cholerae. CTXφ variants contribute to the genetic diversity of cholera epidemic strains. It has been shown that the El Tor variant of CTXφ hijacks XerC and XerD, two host-encoded tyrosine recombinases that normally function to resolve chromosome dimers, to integrate at dif1, the dimer resolution site of the larger of the two V. cholerae chromosomes. However, the exact mechanism of integration of CTXφ and the rules governing its integration remained puzzling, with phage variants integrated at either or both dimer resolution sites of the two V. cholerae chromosomes. We designed a genetic system to determine experimentally the tropism of integration of CTXφ and thus define rules of compatibility between phage variants and dimer resolution sites. We then showed in vitro how these rules are explained by the direct integration of the single-stranded phage genome into the double-stranded bacterial genome. Finally, we showed how the evolution of phage attachment and chromosome dimer resolution sites contributes to the generation of genetic diversity among cholera epidemic strains.     

An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain

A reversible structural unlocking reaction, in which the close-packed van der Waals interactions break cooperatively, has been found for the villin headpiece subdomain (HP35) using triplet-triplet-energy transfer to monitor conformational fluctuations from equilibrium. Unlocking is associated with an unfavorable enthalpy change (ΔH⁰ = 35 ± 4 kJ/mol) which is nearly compensated in free energy by the entropy change (ΔS⁰ = 112 ± 20 J·mol^-1·K^-1). The unlocking reaction has a time constant of about 1 μs at 5 °C and is enthalpy-limited with an activation energy of 32 ± 1 kJ/mol and a large Arrhenius preexponential factor of A = 7.5 × 10¹¹ s^-1. In the unlocked state a fast local conformational fluctuation with a time constant of 170 ns and a low activation barrier of 17 ± 1 kJ/mol leads to unfolding of the C-terminal helix and to its undocking from the core. On a much slower time scale, global unfolding occurs from the unlocked state. These results suggest that native protein structures are locked into conformations with low amplitude motions. Large scale motions and global unfolding require an initial structural unlocking step leading to a state with properties of a dry molten globule. The experiments additionally yielded information on the dynamics of loop formation between different positions in unfolded HP35. Comparison of the results with dynamics in unstructured model peptides indicates slightly decelerated kinetics of local loop formation in the C-terminal region which points at residual, nonrandom structure. Dynamics of long-range loop formation, in contrast, are not influenced by residual structure, which argues against unfolded state properties as molecular origin for ultrafast folding of HP35.     

The Lumbar Spine as a Dynamic Structure Depicted in Upright MRI

Spinal canal stenosis is a dynamic phenomenon that becomes apparent during spinal loading. Current diagnostic procedures have considerable short comings in diagnosing the disease to full extend, as they are performed in supine situation. Upright MRI imaging might overcome this diagnostic gap.This study investigated the lumbar neuroforamenal diameter, spinal canal diameter, vertebral body translation, and vertebral body angles in 3 different body positions using upright MRI imaging.Fifteen subjects were enrolled in this study. A dynamic MRI in 3 different body positions (at 0° supine, 80° upright, and 80° upright + hyperlordosis posture) was taken using a 0.25 T open-configuration scanner equipped with a rotatable examination bed allowing a true standing MRI.The mean diameter of the neuroforamen at L5/S1 in 0° position was 8.4 mm on the right and 8.8 mm on the left, in 80° position 7.3 mm on the right and 7.2 mm on the left, and in 80° position with hyperlordosis 6.6 mm (P < 0.05) on the right and 6.1 mm on the left (P < 0.001).The mean area of the neuroforamen at L5/S1 in 0° position was 103.5 mm² on the right and 105.0 mm² on the left, in 80° position 92.5 mm² on the right and 94.8 mm² on the left, and in 80° position with hyperlordosis 81.9 mm² on the right and 90.2 mm² on the left.The mean volume of the spinal canal at the L5/S1 level in 0° position was 9770 mm³, in 80° position 10600 mm³, and in 80° position with hyperlordosis 9414 mm³.The mean intervertebral translation at level L5/S1 was 8.3 mm in 0° position, 9.9 mm in 80° position, and 10.1 mm in the 80° position with hyperlordosis.The lordosis angle at level L5/S1 was 49.4° in 0° position, 55.8° in 80° position, and 64.7 mm in the 80° position with hyperlordosis.Spinal canal stenosis is subject to a dynamic process, that can be displayed in upright MRI imaging. The range of anomalies is clinically relevant and dynamic positioning of the patient during MRI can provide essential diagnostic information which are not attainable with other methods.     

Denatured states of low-complexity polypeptide sequences differ dramatically from those of foldable sequences

How the primary sequence of a protein encodes conformational preferences that operate early in folding to promote efficient formation of the correct native topology is still poorly understood. To address this issue, we have prepared a set of yeast iso-1-cytochrome c variants that contain polyalanine inserts ranging from 6 to 30 residues in length near the N terminus of the protein. We study the thermodynamics and kinetics of His-heme loop formation in the denatured state at 3 and 6 M guanidine-HCl concentration. We find that polyalanine closely approximates a random coil with excluded volume giving scaling exponents, ν₃, for equilibrium loop formation of 2.26 ± 0.13 and 1.97 ± 0.04 in 3 and 6 M guanidine-HCl, respectively. The rate of loop breakage initially decreases and then becomes independent of loop size as would be expected for a random coil. Comparison with previously reported data for denatured state His-heme loop formation for iso-1-cytochrome c and Rhodopseudomonas palustris cytochrome c′, shows that foldable sequences deviate significantly from random coil behavior and that the deviation is fold-dependent.     

Assignment of the Hydrogen Bonded Proton Resonances in (Escherichia coli) tRNAGlu by Sequential Melting

The 300 MHz nuclear magnetic resonance peaks from the hydrogen bonded protons in (Escherichia coli) tRNA^Glu in Mg⁺⁺ solutions have been measured at temperatures between 25° and 74°. Between 25° and 49° four resonances broaden, three of which are assigned to the hU arm and one to a G·C pair of the tertiary structure. By 64° these four resonances have disappeared and the nuclear magnetic resonance spectrum is fitted very well by a computer simulation based upon resonances from the acceptor, T-Ψ-C, and anticodon arms. At 66° the resonances from the T-Ψ-C arm are lost and at 74° only those from the anticodon are left. All 20 resonances expected from the cloverleaf model have been assigned by comparing the calculated positions of resonances in a particular arm with the stepwise loss of intensity with temperature. The root mean square error between calculated and observed positions is 0.17 ppm. Resonances at the end of helical regions which are sensitive to stacking beyond the helix allow us to conclude that the acceptor arm is stacked upon the T-Ψ-C in a regular helix and that G [unk]73 is stacked upon base pair [unk]1-72 but the hU and anticodon arms are not stacked in a regular helix upon the intervening base A [unk]27.     

Whole Genome Analysis of Human Rotaviruses Reveals Single Gene Reassortant Rotavirus Strains in Zambia

Rotarix^® vaccine was implemented nationwide in Zambia in 2013. In this study, four unusual strains collected in the post-vaccine period were subjected to whole genome sequencing and analysis. The four strains possessed atypical genotype constellations, with at least one reassortant genome segment within the constellation. One of the strains (UFS-NGS-MRC-DPRU4749) was genetically and phylogenetically distinct in the VP4 and VP1 gene segments. Pairwise analyses demonstrated several amino acid disparities in the VP4 antigenic sites of this strain compared to that of Rotarix^®. Although the impact of these amino acid disparities remains to be determined, this study adds to our understanding of the whole genomes of reassortant strains circulating in Zambia following Rotarix^® vaccine introduction.     

Reactive and nonreactive quenching of O(1D) by the potent greenhouse gases SO2F2, NF3, and SF5CF3

A laser flash photolysis–resonance fluorescence technique has been employed to measure rate coefficients and physical vs. reactive quenching branching ratios for O(¹D) deactivation by three potent greenhouse gases, SO₂F₂(k₁), NF₃(k₂), and SF₅CF₃(k₃). In excellent agreement with one published study, we find that k₁(T) = 9.0 × 10^-11 exp(+98/T) cm³ molecule^-1 s^-1 and that the reactive quenching rate coefficient is k_1b = (5.8 ± 2.3) × 10^-11 cm³ molecule^-1 s^-1 independent of temperature. We find that k₂(T) = 2.0 × 10^-11 exp(+52/T) cm³ molecule^-1 s^-1 with reaction proceeding almost entirely (∼99%) by reactive quenching. Reactive quenching of O(¹D) by NF₃ is more than a factor of two faster than reported in one published study, a result that will significantly lower the model-derived atmospheric lifetime and global warming potential of NF₃. Deactivation of O(¹D) by SF₅CF₃ is slow enough (k₃ < 2.0 × 10^-13 cm³ molecule^-1 s^-1 at 298 K) that reaction with O(¹D) is unimportant as an atmospheric removal mechanism for SF₅CF₃. The kinetics of O(¹D) reactions with SO₂ (k₄) and CS₂ (k₅) have also been investigated at 298 K. We find that k₄ = (2.2 ± 0.3) × 10^-10 and k₅ = (4.6 ± 0.6) × 10^-10 cm³ molecule^-1 s^-1; branching ratios for reactive quenching are 0.76 ± 0.12 and 0.94 ± 0.06 for the SO₂ and CS₂ reactions, respectively. All uncertainties reported above are estimates of accuracy (2σ) and rate coefficients k_i(T) (i = 1,2) calculated from the above Arrhenius expressions have estimated accuracies of ± 15% (2σ).     

From the Cover: Ecosystem responses in the southern Caribbean Sea to global climate change

Over the last few decades, rising greenhouse gas emissions have promoted poleward expansion of the large-scale atmospheric Hadley circulation that dominates the Tropics, thereby affecting behavior of the Intertropical Convergence Zone (ITCZ) and North Atlantic Oscillation (NAO). Expression of these changes in tropical marine ecosystems is poorly understood because of sparse observational datasets. We link contemporary ecological changes in the southern Caribbean Sea to global climate change indices. Monthly observations from the CARIACO Ocean Time-Series between 1996 and 2010 document significant decadal scale trends, including a net sea surface temperature (SST) rise of ∼1.0 ± 0.14 °C (±SE), intensified stratification, reduced delivery of upwelled nutrients to surface waters, and diminished phytoplankton bloom intensities evident as overall declines in chlorophyll a concentrations (ΔChla = −2.8 ± 0.5%⋅y⁻¹) and net primary production (ΔNPP = −1.5 ± 0.3%⋅y⁻¹). Additionally, phytoplankton taxon dominance shifted from diatoms, dinoflagellates, and coccolithophorids to smaller taxa after 2004, whereas mesozooplankton biomass increased and commercial landings of planktivorous sardines collapsed. Collectively, our results reveal an ecological state change in this planktonic system. The weakening trend in Trade Winds (−1.9 ± 0.3%⋅y⁻¹) and dependent local variables are largely explained by trends in two climatic indices, namely the northward migration of the Azores High pressure center (descending branch of Hadley cell) by 1.12 ± 0.42°N latitude and the northeasterly progression of the ITCZ Atlantic centroid (ascending branch of Hadley cell), the March position of which shifted by about 800 km between 1996 and 2009.