Full-length genomic sequence of hepatitis B virus genotype C2 isolated from a native Brazilian patient

The hepatitis B virus (HBV) is among the leading causes of chronic hepatitis, cirrhosis and hepatocellular carcinoma. In Brazil, genotype A is the most frequent, followed by genotypes D and F. Genotypes B and C are found in Brazil exclusively among Asian patients and their descendants. The aim of this study was to sequence the entire HBV genome of a Caucasian patient infected with HBV/C2 and to infer the origin of the virus based on sequencing analysis. The sequence of this Brazilian isolate was grouped with four other sequences described in China. The sequence of this patient is the first complete genome of HBV/C2 reported in Brazil.

Características morfológicas da pars de C2 de humanos

OBJETIVO: avaliar a morfometria da pars da segunda vértebra cervical, verificar as variações existentes e predizer sua segurança para a colocação de parafusos por meio de uma abordagem cervical posterior. MÉTODOS: 58 vértebras foram obtidas para estudo anatômico (116 pars de C2) e foram medidas a altura e largura da pars, além do comprimento eixo-pedículo, largura e comprimento do pedículo, angulação sagital e medial. Todas as medidas foram separadas quanto aos seus lados direito e esquerdo; foi realizado o cálculo da média, variação, desvio padrão e a médica foi comparada com os estudos prévios. RESULTADOS: a largura média da pars de C2 foi de 9,5 mm; a altura, 9,5 mm; não houve diferença significativa entre os lados esquerdo e direito. O comprimento médio do pedículo foi de 10,5 mm; a medida média encontrada para o comprimento eixo-pedículo foi de 24,9 mm; a largura do pedículo foi de 2,8 mm. A angulação sagital encontrada foi de 19,6º e a horizontal foi de 28,5º. CONCLUSÕES: este estudo demonstra a viabilidade para a colocação de parafuso na pars de C2 em uma população caucasiana, destacando-se, porém, a grande variabilidade anatômica encontrada nas referidas medidas.

Near full-length genome analysis of low prevalent human immunodeficiency virus type 1 subclade F1 in Sao Paulo, Brazil

Background: The genetic diversity of the human immunodeficiency virus type 1 (HIV-1) is critical to lay the groundwork for the design of successful drugs or vaccine. In this study we aimed to characterize and define the molecular prevalence of HIV-1 subclade F1 currently circulating in Sao Paulo, Brazil. Methods: A total of 36 samples were selected from 888 adult patients residing in Sao Paulo who had previously been diagnosed in two independent studies in our laboratory as being infected with subclade F1 based on pol subgenomic fragment sequencing. Proviral DNA was amplified from the purified genomic DNA of all 36 blood samples by 5 fragments overlapping PCR followed by direct sequencing. Sequence data were obtained from the 5 fragments of pure subclade F1 and phylogenetic trees were constructed and compared with previously published sequences. Subclades F1 that exhibited mosaic structure with other subtypes were omitted from any further analysis Results: Our methods of fragment amplification and sequencing confirmed that only 5 sequences inferred from pol region as subclade F1 also holds true for the genome as a whole and, thus, estimated the true prevalence at 0.56%. The results also showed a single phylogenetic cluster of the Brazilian subclade F1 along with non-Brazilian South American isolates in both subgenomic and the full-length genomes analysis with an overall intrasubtype nucleotide divergence of 6.9%. The nucleotide differences within the South American and Central African F1 strains, in the C2-C3 env, were 8.5% and 12.3%, respectively. Conclusion: All together, our findings showed a surprisingly low prevalence rate of subclade F1 in Brazil and suggest that these isolates originated in Central Africa and subsequently introduced to South America.

Length variation in HIV-1 gp120 as the product of DNA misalignment mechanism

Background: To determine whether misalignment structures such as duplications, repeats, and palindromes are associated to insertions/deletions (indels) in gp120, indicating that indels are indeed frameshift mutations generated by DNA misalignment mechanism. Methods: Cloning and sequencing of a fragment of HIV-1 gp120 spanning C2-C4 derived from plasma RNA in 12 patients with early chronic disease and naïve to antiretroviral therapy. Results: Indels in V4 involved always insertion and deletion of duplicated nucleotide segments, and AAT repeats, and were associated to the presence of palindromic sequences. No duplications were detected in V3 and C3. Palindromic sequences occurred with similar frequencies in V3, C3 and V4; the frequency of palindromes in individual genes was found to be significantly higher in structural (gp120, p ≤ 3.00E-7) and significantly lower in regulatory (Tat, p ≤ 9.00E-7) genes, as compared to the average frequency calculated over the full genome. Discussion: Indels in V4 are associated to misalignment structures (i.e. duplications repeat and palindromes) indicating DNA misalignment as the mechanism underlying length variation in V4. The finding that indels in V4 are caused by DNA misalignment has some very important implications: 1) indels in V4 are likely to occur in proviral DNA (and not in RNA), after integration of HIV into the host genome; 2) they are likely to occur as progressive modifications of the early founder virus during chronic infection, as more and more cells get infected; 3) frameshift mutations involving any number of base pairs are likely to occur evenly across gp120; however, only those mutants carrying a functional gp120 (indels as multiples of three base pairs) will be able to perpetuate the virus cycle and to keep spreading through the population.

Hepatitis B virus subgenotype C2- and B2-associated mutation patterns may be responsible for liver cirrhosis and hepatocellular carcinoma, respectively

The objective of this study was to examine hepatitis B virus (HBV) subgenotypes and mutations in enhancer II, basal core promoter, and precore regions of HBV in relation to risks of liver cirrhosis (LC) and hepatocellular carcinoma (HCC) in Southeast China. A case-control study was performed, including chronic hepatitis B (CHB; n=125), LC (n=120), and HCC (n=136). HBV was genotyped by multiplex polymerase chain reaction and subgenotyped by restriction fragment length polymorphism. HBV mutations were measured by DNA sequencing. HBV genotype C (68.2%) predominated and genotype B (30.2%) was the second most common. Of these, C2 (67.5%) was the most prevalent subgenotype, and B2 (30.2%) ranked second. Thirteen mutations with a frequency >5% were detected. Seven mutation patterns (C1653T, G1719T, G1730C, T1753C, A1762T, G1764A, and G1799C) were associated with C2, and four patterns (C1810T, A1846T, G1862T, and G1896A) were associated with B2. Six patterns (C1653T, G1730C, T1753C, A1762T, G1764A, and G1799C) were obviously associated with LC, and 10 patterns (C1653T, G1730C, T1753C, A1762T, G1764A, G1799C, C1810T, A1846T, G1862T, and G1896A) were significantly associated with HCC compared with CHB. Four patterns (C1810T, A1846T, G1862T, and G1896A) were significantly associated with HCC compared with LC. Multivariate regression analyses showed that HBV subgenotype C2 and C2-associated mutation patterns (C1653T, T1753C, A1762T, and G1764A) were independent risk factors for LC when CHB was the control, and that B2-associated mutation patterns (C1810T, A1846T, G1862T, and G1896A) were independent risk factors for HCC when LC was the control.

Impact of the length of vitamin D deficiency on cardiac remodeling.

This study was aimed to evaluate the influence of vitamin D (VD) deficiency on cardiac metabolism, morphology, and function. Thus, we investigated the relationship of these changes with the length of the nutrient restriction. Male weanling Wistar rats were allocated into 4 groups: C2 (n=24), animals were fed an AIN-93G diet with 1000 IU VD/kg of chow and were kept under fluorescent light for 2 months; D2 (n=22), animals were fed a VD-deficient AIN-93G diet and were kept under incandescent light for 2 months; C4 (n=21) animals were kept in the same conditions of C2 for 4 months; and D4 (n=23) animals were kept in the same conditions of D2 for 4 months. Biochemical analyses showed lower β-hydroxyacyl coenzyme-A dehydrogenase activity and higher lactate dehydrogenase activity in VD-deficient animals. Furthermore, VD deficiency was related to increased cytokines release, oxidative stress, apoptosis, and fibrosis. Echocardiographic data showed left ventricular hypertrophy and lower fractional shortening and ejection fraction in VD-deficient animals. Difference became evident in the lactate dehydrogenase activity, left ventricular weight, right ventricle weight, and left ventricular mass after 4 months of VD deficiency. Our data indicate that VD deficiency is associated with energetic metabolic changes, cardiac inflammation, oxidative stress, fibrosis and apoptosis, cardiac hypertrophy, left chambers alterations, and systolic dysfunction. Furthermore, length of the restriction influenced these cardiac changes.

TOMOGRAPHIC ANALYSIS FOR C2 SCREW PLACEMENT IN RHEUMATOID ARTHRITIS PATIENTS

Objective: A morphological analysis of the bone structure of 02 in patients with rheumatoid arthritis in order to enhance the security of the stabilization procedures for this vertebra. Methods: We retrospectively analyzed 20 CT scans of the cervical spine performed in patients with rheumatoid arthritis; the following parameters were measured: spinolaminar angle, thickness and length of C2 lamina. Results: The mean values are: 5.92mm and 5.87mm for thickness of right and left laminae retrospectively, 27.75mm for right lamina length and 27.94mm for left lamina length, and 44.7 degrees for spinolaminar angle. Conclusion: The values obtained are consistent with studies in normal subjects published by other groups, with no apparent need for change in the screw placement technique. Level of Evidence IV, Case Series.

Self-Assembly of Poly(4-vynil-N-alkylpyridinium) Bromide onto Silica: Effect of Side-Chain Length on Structural Aspects at a Molecular Level

Self-assembly of poly(4-vynil-N-alkyl)pyridinium bromide with alkyl side chains of 2, 5, 7, 10, or 16 carbons from ethanolic solutions onto flat silica surfaces was studied by means of ellipsometry, atomic force microscopy (AFM), contact angle measurements, and sum-frequency generation (SFG) vibrational spectroscopy in the CH3 and CH2 stretch region. Ab initio quantum-chemical calculations on the N-alkylpyridinium side-group with restricted Hartree-Fock (RHF) method and 6-311G (d,p) basis set were C one to estimate the charge distribution along the pyridinium ring and the alkyl side-chain. SFG results showed that longer side chains promote the disorientation of the alkyl groups at the surface, corroborating with the contact angle values. AFM images revealed film homogeneity, regardless the alkyl side group. However, after 24 h contact with water, ringlike structures appeared on the film surfaces, when the polycation alkyl side chain had 7 or less carbons, and as the alkyl chain increased to 10 or 16 carbons, the films dewetted because the hydrophobic interactions prevailed over the electrostatic interactions between the pyridinium charged groups and the negatively charged SiO2 surface. Under acid conditions (HCl 0.1 mol.L-1), the film mean thickness values decreased up to 50% of original values when the alkyl side chains were ethyl or pentyl groups due to ion-pair disruption, but for longer groups they remained unchanged. Quantum-chemical optimization and Mulliken electron population showed that (i) from C2 to C15 the positive charge at the headgroup (HG) decreased 0.025, while the charge at combined HG + alpha-CH2 increased 0.037; and (ii) for C6 or longer, the alkyl side group presents a tilt in the geometry, moving away from the plane. Such effects summed up over the whole polymer chain give support to suggest that when the side chains are longer than 7 carbons, the hydrophobic interaction decreases film stability and increases acid resistance.

Mesozooplankton biomass data from Disko Bay, West Greenland, 2008

The study site was located in the Disko Bay off Qeqertarsuaq, western Greenland. Due to land-connected sea ice coverage during winter, 2 sampling sites were combined. At the first site in winter (21 February to 23 March 2008), sampling was conducted through a hole in the ice at ca. 65 to 160 m depth approximately 0.5 nautical mile (n mile) south of Qeqertarsuaq (69° 14' N, 53° 29' W). In spring and summer (9 April to 18 July), sampling was done at a monitoring station 1 n mile south from Qeqertarsuaq (69° 14' N, 53° 23' W) at 300 m depth. Sampling was carried out between 10:00 and 17:00 h. During sampling from the ice, mesozooplankton was collected using a modified WP-2 net (45 µm) equipped with a closing mechanism (Hydrobios). Samples were collected in 3 depth strata (0-50, 50-100, and 100-150 m). During ship-based sampling, mesozooplankton was collected with a multinet (50 µm) equipped with a flow meter (Multinet, Hydrobios type midi), and 2 additional depth strata (150-200m and 200-250 m) were included. In addition to the seasonal study one diurnal investigation with sampling every 6 h was conducted from 29 April at 12:00 h to 30 April 30 at 12:00 h. Samples were immediately preserved in buffered formalin (5% final concentration) for later analyses. Biomass values of the different copepod species were calculated based on measurements of prosome length, and length/weight relationships. Two regressions for Calanus spp. were established for biomass calculations: one applicable prior to and during the phytoplankton bloom until 4 May, and another from 9 May onwards.

Abundance of mesozooplankton in the north-eastern Black Sea during SESRU02 cruise in September 2008

The SESRU_02_mesozooplankton dataset contains data collected in September 2008 at 15 stations located between 37°E and 39.5°E and between 42.4°N and 44.5°N in the north-eastern Black Sea. Samples were collected with a Juday net. Juday net: Vertical tows of a closing Juday net, with mouth area 0.1 m**2, mesh size 180 µm. Samples were taken from different layers. Towing speed: 1m/s. Samples were preserved by a 4% formaldehyde sea water buffered solution. Sampling volume was estimated by multiplying the mouth area with the wire length. Integrated samples were taken from the lower boundary of the oxic zone to the surface, stratified samples were taken according to CTD-profiles: samples were taken from the following depth strata: 1) the upper mixed layer (UML); 2) the layer of high temperature gradients (from the upper boundary of thermocline to the depth of 8 deg C temperature); 3) cold Intermediate layer (CIL) - the layer with the T< 8 deg C; 4) from the depth of sigma theta = 15.8 (oxycline) to the lower boundary of CIL; 5) from the depth of sigma theta = 16.2 to the depth of sigma theta = 15.8. Samples were analysed for zooplankton species and stage composition and abundance. The entire sample or an aliquot (1/2 to ¼) was analyzed under the binocular microscope. Mesozooplankton species and stages were identified and enumerated; meroplankton were identified and enumerated at higher taxonomic level. Taxonomic identification was done at Shirshov Institute of Oceanology using the relevant taxonomic literature (Rose, 1933, Brodsky, 1950 and Internet resources).

Abundance of mesozooplankton in the north-eastern Black Sea during SESRU01 cruise in April 2008

The SESRU01_mesozooplankton dataset contains data collected in April 2008 at 19 stations located between 37°E and 39.5°E and between 42.4°N and 44.5°N in the north-eastern Black Sea. Samples were collected with a Juday net (mesh size 180 ?m, mouth area 0.1 m**2). Integrated samples were taken from the lower boundary of the oxic zone to the surface, stratified samples were taken according to CTD-profiles: samples were taken from the following depth strata: 1) the upper mixed layer (UML); 2) the layer of high temperature gradients (from the upper boundary of thermocline to the depth of 8 deg C temperature); 3) cold Intermediate layer (CIL) - the layer with the T< 8 deg C; 4) from the depth of sigma theta = 15.8 (oxycline) to the lower boundary of CIL; 5) from the depth of sigma theta = 16.2 to the depth of sigma theta = 15.8. Samples were analysed for zooplankton species and stage composition and abundance. Juday net: Vertical tows of a closing Juday net, with mouth area 0.1 m**2, mesh size 180µm. Samples were taken from different layers. Towing speed: 1m/s. Samples were preserved by a 4% formaldehyde sea water buffered solution. Sampling volume was estimated by multiplying the mouth area by the wire length. The entire sample or an aliquot (1/2 to1/4) was analyzed under the binocular microscope. Mesozooplankton species and stages were identified and enumerated; meroplankton were identified and enumerated at higher taxonomic level. Taxonomic identification was done at Shirshov Institute of Oceanology using the relevant taxonomic literature (Rose, 1933, Brodsky, 1950, and Internet resources).

Mesozooplankton abundance data from Disko Bay, West Greenland, 2008

The study site was located in the Disko Bay off Qeqertarsuaq, western Greenland. Due to land-connected sea ice coverage during winter, 2 sampling sites were combined. At the first site in winter (21 February to 23 March 2008), sampling was conducted through a hole in the ice at ca. 65 to 160 m depth approximately 0.5 nautical mile (n mile) south of Qeqertarsuaq (69° 14' N, 53° 29' W). In spring and summer (9 April to 18 July), sampling was done at a monitoring station 1 n mile south from Qeqertarsuaq (69° 14' N, 53° 23' W) at 300 m depth. Sampling was carried out between 10:00 and 17:00 h. During sampling from the ice, mesozooplankton was collected using a modified WP-2 net (45 µm) equipped with a closing mechanism (Hydrobios). Samples were collected in 3 depth strata (0-50, 50-100, and 100-150 m). During ship-based sampling, mesozooplankton was collected with a multinet (50 µm) equipped with a flow meter (Multinet, Hydrobios type midi), and 2 additional depth strata (150-200m and 200-250 m) were included. In addition to the seasonal study one diurnal investigation with sampling every 6 h was conducted from 29 April at 12:00 h to 30 April 30 at 12:00 h. Samples were immediately preserved in buffered formalin (5% final concentration) for later analyses. Biomass values of the different copepod species were calculated based on measurements of prosome length, and length/weight relationships. Two regressions for Calanus spp. were established for biomass calculations: one applicable prior to and during the phytoplankton bloom until 4 May, and another from 9 May onwards.

Photoelastic Analysis Of Fixed Partial Prosthesis Crown Height And Implant Length On Distribution Of Stress In Two Dental Implant Systems.

The aim of this study was to evaluate by photoelastic analysis stress distribution on short and long implants of two dental implant systems with 2-unit implant-supported fixed partial prostheses of 8 mm and 13 mm heights. Sixteen photoelastic models were divided into 4 groups: I: long implant (5 × 11 mm) (Neodent), II: long implant (5 × 11 mm) (Bicon), III: short implant (5 × 6 mm) (Neodent), and IV: short implants (5 × 6 mm) (Bicon). The models were positioned in a circular polariscope associated with a cell load and static axial (0.5 Kgf) and nonaxial load (15°, 0.5 Kgf) were applied to each group for both prosthetic crown heights. Three-way ANOVA was used to compare the factors implant length, crown height, and implant system (α = 0.05). The results showed that implant length was a statistically significant factor for both axial and nonaxial loading. The 13 mm prosthetic crown did not result in statistically significant differences in stress distribution between the implant systems and implant lengths studied, regardless of load type (P > 0.05). It can be concluded that short implants showed higher stress levels than long implants. Implant system and length was not relevant factors when prosthetic crown height were increased.

Influence of the length of remaining root canal filling and post space preparation on the coronal leakage of Enterococcus faecalis

This study evaluated the sealing ability of different lengths of remaining root canal filling and post space preparation against coronal leakage of Enterococcus faecalis. Forty-one roots of maxillary incisors were biomechanically prepared, maintaining standardized canal diameter at the middle and coronal thirds. The roots were autoclaved and all subsequent steps were undertaken in a laminar flow chamber. The canals of 33 roots were obturated with AH Plus sealer and gutta-percha. The root canal fillings were reduced to 3 predetermined lengths (n=11): G1=6 mm, G2=4 mm and G3=2 mm. The remaining roots served as positive and negative controls. Bacterial leakage test apparatuses were fabricated with the roots attached to Eppendorf tubes keeping 2 mm of apex submerged in BHI in glass flasks. The specimens received an E. faecalis inoculum of 1 x 107 cfu/mL every 3 days and were observed for bacterial leakage daily during 60 days. Data were submitted to ANOVA, Tukey's test and Fisher's test. At 60 days, G1 (6 mm) and G2 (4 mm) presented statistically similar results (p>0.05) (54.4% of specimens with bacterial leakage) and both groups differed significantly (p<0.01) from G3 (2 mm), which presented 100% of specimens with E. faecalis leakage. It may be concluded that the shortest endodontic obturation remnant leaked considerably more than the other lengths, although none of the tested conditions avoids coronal leakage of E. faecalis.

A FIRST CONSTRAINT ON THE THICK DISK SCALE LENGTH: DIFFERENTIAL RADIAL ABUNDANCES IN K GIANTS AT GALACTOCENTRIC RADII 4, 8, AND 12 kpc

Based on high-resolution spectra obtained with the MIKE spectrograph on the Magellan telescopes, we present detailed elemental abundances for 20 red giant stars in the outer Galactic disk, located at Galactocentric distances between 9 and 13 kpc. The outer disk sample is complemented with samples of red giants from the inner Galactic disk and the solar neighborhood, analyzed using identical methods. For Galactocentric distances beyond 10 kpc, we only find chemical patterns associated with the local thin disk, even for stars far above the Galactic plane. Our results show that the relative densities of the thick and thin disks are dramatically different from the solar neighborhood, and we therefore suggest that the radial scale length of the thick disk is much shorter than that of the thin disk. We make a first estimate of the thick disk scale length of L(thick) = 2.0 kpc, assuming L(thin) = 3.8 kpc for the thin disk. We suggest that radial migration may explain the lack of radial age, metallicity, and abundance gradients in the thick disk, possibly also explaining the link between the thick disk and the metal-poor bulge.