Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Weighted mean depth of zooplankton measured during various cruises to the Baltic Sea

The Baltic Sea is the largest brackish water area of the world. On the basis of the data from 16 cruises, we show the seasonal and vertical distribution patterns of the appendicularians Fritillaria borealis, Oikopleura dioica and the cyclopoid copepod Oithona similis, in the highly stratified Bornholm Basin. These species live at least temporarily below the permanent halocline and use different life strategies to cope with the brackish environment. The cold-water species F. borealis is abundant in the upper layers of the water column before the thermocline develops. With the formation of the thermocline abundance decreases and the specimens outlast higher temperatures below the halocline. Distribution and strategy suggest that F. borealis might be a glacial relict species in the Baltic Sea. Although Oikopleura dioica is only abundant during summer, O. similis is present all year round. Both species have in common that their vertical distribution is restricted to the waters below the halocline, most likely due to their requirements of higher salinities. We argue that the observed strategies are determined by ecophysiological constraints and life history traits. These species share an omnivorous feeding behaviour and the capability to utilise a spectra of small particles as food. As phytoplankton concentration is negligible below the halocline, we suggest that these species feed on organic material and heterotrophic organisms that accumulate in the density gradient of the halocline. Therefore, the deep haline waters in the Baltic Sea represent a habitat providing shelter from predation and food supply for adapted species that allows them to gather sufficient resources and to maintain populations.

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.

Abundance and biomass of mesozooplankton in the Levantine Basin during the Bilim 2 cruise in April 2008

The Sesame dataset contains mesozooplankton data collected during April 2008 in the Levantine Basin (between 33.20 and 36.50 N latitude and between 30.99 and 31.008 E longitude). Mesozooplankton samples were collected by using a WP-2 closing net with 200 µm mesh size during day hours (07:00-18:00). Samples were taken from 0-50, 50-100, 100-200 m layers at 5 stations in Levantine Basin The dataset includes samples analyzed for mesozooplankton species composition, abundance and total mesozooplankton biomass. Sampling volume was estimated by multiplying the mouth area with the wire length. Sampling biomass was measured by weighing filters and then determined by sampling volume. The samples were sieved sequentially through meshes of 500 and 200 micron to separate the mesozooplankton into size fractions. The entire sample (1/2) or an aliquot of the taxon-specific mesozooplankton abundance and the total abundance of the mesozooplankton were was analyzed under the binocular microscope. Minimum 500 individuals of mesozooplankton were identified and numerated at higher taxonomic level. Taxonomic identification was done at the METU- Institute of Marine Sciences by Alexandra Gubanova,Tuba Terbiyik using the relevant taxonomic literatures. Mesozooplankton abundance and biomass were estimated by Zahit Uysal and Yesim Ak.