bluuebunny/crossref_metadata_2025_split huggingface dataset:
HECTAR: A method to predict subcellular targeting in heterokonts
Authors: Gschloessl Bernhard , Guermeur Yann , Cock J Mark 
Published: September 2008

Abstract

Background
The heterokonts are a particularly interesting group of eukaryotic organisms; they include many key species of planktonic and coastal algae and several important pathogens. To understand the biology of these organisms, it is necessary to be able to predict the subcellular localisation of their proteins but this is not straightforward, particularly in photosynthetic heterokonts which possess a complex chloroplast, acquired as the result of a secondary endosymbiosis. This is because the bipartite target peptides that deliver proteins to these chloroplasts can be easily confused with the signal peptides of secreted proteins, causing currently available algorithms to make erroneous predictions. HECTAR, a subcellular targeting prediction method which takes into account the specific properties of heterokont proteins, has been developed to address this problem.

Results
HECTAR is a statistical prediction method designed to assign proteins to five different categories of subcellular targeting: Signal peptides, type II signal anchors, chloroplast transit peptides, mitochondrion transit peptides and proteins which do not possess any N-terminal target peptide. The recognition rate of HECTAR is 96.3%, with Matthews correlation coefficients ranging from 0.67 to 0.95. The method is based on a hierarchical architecture which implements the divide and conquer approach to identify the different possible target peptides one at a time. At each node of the hierarchy, the most relevant outputs of various existing subcellular prediction methods are combined by a Support Vector Machine.

Conclusion
The HECTAR method is able to predict the subcellular localisation of heterokont proteins with high accuracy. It also efficiently predicts the subcellular localisation of proteins from cryptophytes, a group that is phylogenetically close to the heterokonts. A variant of HECTAR, called HECTAR
SEC
, can be used to identify signal peptide and type II signal anchor sequences in proteins from any eukaryotic organism. Both HECTAR and HECTAR
SEC
are available as a web application at the following address: http://www.sb-roscoff.fr/hectar/.
Distinct roles of Shh and Fgf signaling in regulating cell proliferation during zebrafish pectoral fin development
Authors: Prykhozhij Sergey V , Neumann Carl J 
Published: September 2008

Abstract
Background
Cell proliferation in multicellular organisms must be coordinated with pattern formation. The major signaling pathways directing pattern formation in the vertebrate limb are well characterized, and we have therefore chosen this organ to examine the interaction between proliferation and patterning. Two important signals for limb development are members of the Hedgehog (Hh) and Fibroblast Growth Factor (Fgf) families of secreted signaling proteins. Sonic hedgehog (Shh) directs pattern formation along the anterior/posterior axis of the limb, whereas several Fgfs in combination direct pattern formation along the proximal/distal axis of the limb.

Results
We used the genetic and pharmacological amenability of the zebrafish model system to dissect the relative importance of Shh and Fgf signaling in regulating proliferation during development of the pectoral fin buds. In zebrafish mutants disrupting the shh gene, proliferation in the pectoral fin buds is initially normal, but later is strongly reduced. Correlating with this reduction, Fgf signaling is normal at early stages, but is later lost in shh mutants. Furthermore, pharmacological inhibition of Hh signaling for short periods has little effect on either Fgf signaling, or on expression of G1- and S-phase cell-cycle genes, whereas long periods of inhibition lead to the downregulation of both. In contrast, even short periods of pharmacological inhibition of Fgf signaling lead to strong disruption of proliferation in the fin buds, without affecting Shh signaling. To directly test the ability of Fgf signaling to regulate proliferation in the absence of Shh signaling, we implanted beads soaked with Fgf protein into shh mutant fin buds. We find that Fgf-soaked beads rescue proliferation in the pectoral find buds of shh mutants, indicating that Fgf signaling is sufficient to direct proliferation in zebrafish fin buds in the absence of Shh.

Conclusion
Previous studies have shown that both Shh and Fgf signaling are crucial for outgrowth of the vertebrate limb. The results presented here show that the role of Shh in this process is indirect, and is mediated by its effect on Fgf signaling. By contrast, the activity of the Fgf pathway affects proliferation directly and independently of its effect on Shh. These results show that Fgf signaling is of primary importance in directing outgrowth of the limb bud, and clarify the role of the Shh-Fgf feedback loop in regulating proliferation.
Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication
Authors: Tingaud-Sequeira Angèle , Chauvigné François , Fabra Mercedes , Lozano Juanjo , Raldúa Demetrio , Cerdà Joan 
Published: September 2008

Abstract

Background
Teleost radiation in the oceans required specific physiological adaptations in eggs and early embryos to survive in the hyper-osmotic seawater. Investigating the evolution of aquaporins (AQPs) in these vertebrates should help to elucidate how mechanisms for water homeostasis evolved. The marine teleost gilthead sea bream (Sparus aurata) has a mammalian aquaporin-1 (AQP1)-related channel, termed AQP1o, with a specialized physiological role in mediating egg hydration. However, teleosts have an additional AQP isoform structurally more similar to AQP1, though its relationship with AQP1o is unclear.

Results
By using phylogenetic and genomic analyses we show here that teleosts, unlike tetrapods, have two closely linked AQP1 paralogous genes, termed aqp1a and aqp1b (formerly AQP1o). In marine teleosts that produce hydrated eggs, aqp1b is highly expressed in the ovary, whereas in freshwater species that produce non-hydrated eggs, aqp1b has a completely different expression pattern or is not found in the genome. Both Aqp1a and Aqp1b are functional water-selective channels when expressed in Xenopus laevis oocytes. However, expression of chimeric and mutated proteins in oocytes revealed that the sea bream Aqp1b C-terminus, unlike that of Aqp1a, contains specific residues involved in the control of Aqp1b intracellular trafficking through phosphorylation-independent and -dependent mechanisms.

Conclusion
We propose that 1) Aqp1a and Aqp1b are encoded by distinct genes that probably originated specifically in the teleost lineage by duplication of a common ancestor soon after divergence from tetrapods, 2) Aqp1b possibly represents a neofunctionalized AQP adapted to oocytes of marine and catadromous teleosts, thereby contributing to a water reservoir in eggs and early embryos that increases their survival in the ocean, and 3) Aqp1b independently acquired regulatory domains in the cytoplasmatic C-terminal tail for the specific control of Aqp1b expression in the plasma membrane.
Identification of transcripts involved in meiosis and follicle formation during ovine ovary development
Authors: Baillet Adrienne , Mandon-Pépin Béatrice , Cabau Cédric , Poumerol Elodie , Pailhoux Eric , Cotinot Corinne 
Published: September 2008

AbstractBackgroundThe key steps in germ cell survival during ovarian development are the entry into meiosis of oogonies and the formation of primordial follicles, which then determine the reproductive lifespan of the ovary. In sheep, these steps occur during fetal life, between 55 and 80 days of gestation, respectively. The aim of this study was to identify differentially expressed ovarian genes during prophase I meiosis and early folliculogenesis in sheep.ResultsIn order to elucidate the molecular events associated with early ovarian differentiation, we generated two ovary stage-specific subtracted cDNA libraries using SSH. Large-scale sequencing of these SSH libraries identified 6,080 ESTs representing 2,535 contigs. Clustering and assembly of these ESTs resulted in a total of 2,101 unique sequences depicted in 1,305 singleton (62.11%) and 796 contigs (37.9%) ESTs (clusters). BLASTX evaluation indicated that 99% of the ESTs were homologous to various known genes/proteins in a broad range of organisms, especially ovine, bovine and human species. The remaining 1% which exhibited any homology to known gene sequences was considered as novel. Detailed study of the expression patterns of some of these genes using RT-PCR revealed new promising candidates for ovary differentiation genes in sheep.ConclusionWe showed that the SSH approach was relevant to determining new mammalian genes which might be involved in oogenesis and early follicle development, and enabled the discovery of new potential oocyte and granulosa cell markers for future studies. These genes may have significant implications regarding our understanding of ovarian function in molecular terms, and for the development of innovative strategies to both promote and control fertility.
Staphylococcus epidermidis: A differential trait of the fecal microbiota of breast-fed infants
Authors: Jiménez Esther , Delgado Susana , Maldonado Antonio , Arroyo Rebeca , Albújar Mar , García Natalia , Jariod Manel , Fernández Leonides , Gómez Adolfo , Rodríguez Juan M 
Published: September 2008

AbstractBackgroundBreast milk is an important source of staphylococci and other bacterial groups to the infant gut. The objective of this work was to analyse the bacterial diversity in feces of breast-fed infants and to compare it with that of formula-fed ones. A total of 23 women and their respective infants (16 breast-fed and 7 formula-fed) participated in the study. The 16 women and their infants provided a sample of breast milk and feces, respectively, at days 7, 14, and 35. The samples were plated onto different culture media. Staphylococcal and enterococcal isolates were submitted to genetic profiling and to a characterization scheme, including detection of potential virulence traits and sensitivity to antibiotics.ResultsThe feeding practice had a significant effect on bacterial counts. A total of 1,210 isolates (489 from milk, 531 from breast-fed and 190 from formula-fed infants) were identified.Staphylococcus epidermidiswas the predominant species in milk and feces of breast-fed infants while it was less prevalent in those of formula fed-infants.Enterococcus faecaliswas the second predominant bacterial species among the fecal samples provided by the breast-fed infants but it was also present in all the samples from the formula-fed ones. The biofilm-relatedicaDgene and themecAgene were only detected in a low number of theS. epidermidisstrains. Several enterococcal isolates were also characterized and none of them contained thecylAor thevanABDEGantibiotic-resistance genes. All were sensitive to vancomycin.ConclusionThe presence ofS. epidermidisis a differential trait of the fecal microbiota of breast-fed infants. Globally, the staphyloccal isolates obtained from milk and feces of breast-fed infants contain a low number of virulence determinants and are sensitive to most of the antibiotics tested.
Overlapping functions of the starch synthases SSII and SSIII in amylopectin biosynthesis in Arabidopsis
Authors: Zhang Xiaoli , Szydlowski Nicolas , Delvallé David , D'Hulst Christophe , James Martha G , Myers Alan M 
Published: September 2008

AbstractBackgroundThe biochemical mechanisms that determine the molecular architecture of amylopectin are central in plant biology because they allow long-term storage of reduced carbon. Amylopectin structure imparts the ability to form semi-crystalline starch granules, which in turn provides its glucose storage function. The enzymatic steps of amylopectin biosynthesis resemble those of the soluble polymer glycogen, however, the reasons for amylopectin's architectural distinctions are not clearly understood. The multiplicity of starch biosynthetic enzymes conserved in plants likely is involved. For example, amylopectin chain elongation in plants involves five conserved classes of starch synthase (SS), whereas glycogen biosynthesis typically requires only one class of glycogen synthase.ResultsNull mutations were characterized inAtSS2, which codes for SSII, and mutant lines were compared to lines lacking SSIII and to anAtss2,Atss3double mutant. Loss of SSII did not affect growth rate or starch quantity, but caused increased amylose/amylopectin ratio, increased total amylose, and deficiency in amylopectin chains with degree of polymerization (DP) 12 to DP28. In contrast, loss of both SSII and SSIII caused slower plant growth and dramatically reduced starch content. Extreme deficiency in DP12 to DP28 chains occurred in the double mutant, far more severe than the summed changes in SSII- or SSIII-deficient plants lacking only one of the two enzymes.ConclusionSSII and SSIII have partially redundant functions in determination of amylopectin structure, and these roles cannot be substituted by any other conserved SS, specifically SSI, GBSSI, or SSIV. Even though SSIII is not required for the normal abundance of glucan chains of DP12 to DP18, the enzyme clearly is capable of functioning in production such chains. The role of SSIII in producing these chains cannot be detected simply by analysis of an individual mutation. Competition between different SSs for binding to substrate could in part explain the specific distribution of glucan chains within amylopectin.
A large waterborne outbreak of campylobacteriosis in Norway: The need to focus on distribution system safety
Authors: Jakopanec Irena , Borgen Katrine , Vold Line , Lund Helge , Forseth Tore , Hannula Raisa , Nygård Karin 
Published: September 2008

Abstract

Background
On 7 May 2007 the medical officer in Røros (population 5600) reported 15 patients with gastroenteritis. Three days later he estimated hundreds being ill. Untreated tap water from a groundwater source was suspected as the vehicle and chlorination was started 11 May. Campylobacter was isolated from patients' stool samples. We conducted an investigation to identify the source and describe the extent of the outbreak.

Methods
We undertook a retrospective cohort study among a random sample of customers of Røros and neighbouring Holtålen waterworks. Holtålen, which has a different water source, was used as a control city. We conducted telephone interviews to gather data on illness from all household members. One randomly selected household member was asked about detailed exposure history. The regional hospital laboratory tested patients' stools for enteropathogens. Campylobacter isolates were typed by AFLP for genetic similarity at the Norwegian Institute of Public Health. Local authorities conducted the environmental investigation.

Results
We identified 105 cases among 340 individuals from Røros and Holtålen (Attack Rate = 31%). Tap water consumption was the only exposure associated with illness. Among randomly selected household members from Røros, a dose-response relationship was observed in daily consumed glasses of tap water (χ2 for trend = 8.1, p = 0.004). Campylobacter with identical AFLP was isolated from 25 out of 26 submitted stool samples. No pathogens were detected in water samples. We identified several events that might have caused pressure fall and influx of contaminated water into the water distribution system. On two occasions, pressure fall was noticed and parts of the distribution system were outdated.

Conclusion
The investigation confirmed a waterborne outbreak of campylobacteriosis in Røros. Although no single event was identified as the cause of contamination, this outbreak illustrates the vulnerability of water distribution systems. Good quality source water alone is not enough to ensure water safety. For a better risk management, more focus should be put on the distribution system security. Waterworks personnel should monitor the pressure regularly; reduce the leakage by upgrading the distribution network and use chlorination when conducting maintenance work.
A haplotype variation affecting the mitochondrial transportation of hMYH protein could be a risk factor for colorectal cancer in Chinese
Authors: Chen Huimei , Xu Lizhi , Qi Qiufeng , Yao Yanweng , Zhu Ming , Wang Yaping 
Published: September 2008

Abstract

Background
The human MutY homolog (hMYH), a DNA glycolsylase involved in the excision repair of oxidative DNA damage, is currently studied in colorectal cancer (CRC). We previously demonstrated a haplotype variant c.53C>T/c.74G>A of hMYH (T/A) increasing the risk for gastric cancer in Chinese. However, most investigations on correlation between hMYH and CRC are conducted in Western countries and the underlying mechanism has been poorly understood.

Methods
To determine whether the haplotype T/A variant of hMYH was related to colorectal carcinogenesis, we performed a case-control study in 138 colorectal cancer (CRC) patients and 343 healthy controls in a Chinese population. Furthermore, the C/G for wild-type, C/A or T/G for single base variant and T/A for haplotype variant hMYH cDNAs with a flag epitope tag were cloned into pcDNA3.1+ vector and transfected into cos-7 cell line. Their subcellular localizations were determined by immunofluorescence assay.

Results
It was found that the frequency of haplotype variant allele was statistically higher in CRC patients than that in controls (P = 0.02, odds ratio = 5.06, 95% confidence interval = 1.26 – 20.4). Similarly, significant difference of heterozygote frequency was indicated between the two groups (P = 0.019), while no homozygote was found. In addition, immunofluorescence analysis showed that hMYH protein with haplotype T/A variation presented in both nucleus and mitochondria, in contrast to the wild-type protein only converging in mitochondria. However, neither of the single missense mutations alone changed the protein subcelluar localization.

Conclusion
Although preliminarily, these results suggest that: the haplotype variant allele of hMYH leads to a missense protein, which partly affects the protein mitochondrial transportation and results as nuclear localization. This observation might be responsible for the increased susceptibility to cancers, including CRC, in Chinese.
Longitudinal population-based studies of affective disorders: Where to from here?
Authors: Beard John R , Galea Sandro , Vlahov David 
Published: September 2008

Abstract

Background
Longitudinal, population-based, research is important if we are to better characterize the lifetime patterns and determinants of affective disorders. While studies of this type are becoming increasingly prevalent, there has been little discussion about the limitations of the methods commonly used.

Methods
Discussion paper including a brief review of key prospective population-based studies as the basis for a critical appraisal of current approaches.

Results
We identified a number of common methodological weaknesses that restrict the potential of longitudinal research to characterize the diversity, prognosis, and determinants of affective disorders over time. Most studies using comprehensive diagnostic instruments have either been of relatively brief duration, or have suffered from long periods between waves. Most etiologic research has focused on first onset diagnoses, although these may be relatively uncommon after early adulthood and the burden of mental disorders falls more heavily on individuals with recurring disorders. Analysis has tended to be based on changes in diagnostic status rather than anges in symptom levels, limiting study power. Diagnoses have generally been treated as homogeneous entities and few studies have explored whether diagnostic subtypes such as atypical depression vary in their etiology or prognosis. Little research has considered whether there are distinct trajectories of symptoms over time and most has focused on individual disorders such as depression, rather than considering the relationship over time between symptoms of different affective disorders. There has also been limited longitudinal research on factors in the physical or social environment that may influence the onset, recurrence or chronicity of symptoms.

Conclusion
Many important, and in some respects quite basic, questions remain about the trajectory of depression and anxiety disorders over the life course and the factors that influence their incidence, recurrence and prognosis. Innovative approaches that consider symptoms of all affective disorders, and how these change over time, has the potential to greatly increase our understanding of the heterogeneity of these important conditions and of the individual and environmental characteristics that influence their life course.
Using longitudinal research to define sub classes of affective disorders may also be of great benefit for studies seeking to define the genetic determinants of susceptibility to these conditions.
Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias
Authors: van der Walt Eric , Martin Darren P , Varsani Arvind , Polston Jane E , Rybicki Edward P 
Published: September 2008

Abstract

Background
Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families Geminiviridae, Parvoviridae and Anellovirus may be evolving at rates of ~10-4 substitutions per site per year (subs/site/year). These evolution rates are similar to those of RNA viruses and are surprisingly high given that ssDNA virus replication involves host DNA polymerases with fidelities approximately 10 000 times greater than those of error-prone viral RNA polymerases. Although high ssDNA virus evolution rates were first suggested in evolution experiments involving the geminivirus maize streak virus (MSV), the evolution rate of this virus has never been accurately measured. Also, questions regarding both the mechanistic basis and adaptive value of high geminivirus mutation rates remain unanswered.

Results
We determined the short-term evolution rate of MSV using full genome analysis of virus populations initiated from cloned genomes. Three wild type viruses and three defective artificial chimaeric viruses were maintained in planta for up to five years and displayed evolution rates of between 7.4 × 10-4 and 7.9 × 10-4 subs/site/year.

Conclusion
These MSV evolution rates are within the ranges observed for other ssDNA viruses and RNA viruses. Although no obvious evidence of positive selection was detected, the uneven distribution of mutations within the defective virus genomes suggests that some of the changes may have been adaptive. We also observed inter-strand nucleotide substitution imbalances that are consistent with a recent proposal that high mutation rates in geminiviruses (and possibly ssDNA viruses in general) may be due to mutagenic processes acting specifically on ssDNA molecules.
Tetany caused by chronic diarrhea in a child with celiac disease: A case report
Authors: Hurtado-Valenzuela Jaime Gabriel , Sotelo-Cruz Norberto , López-Cervantes Guillermo , de la Barca Ana María Calderón 
Published: September 2008

Abstract
There is no awareness about celiac disease (CD) in Mexico. A 2.9 year old mestizo boy was admitted to a Mexican hospital with muscle cramps and fine tremors. He suffered chronic diarrhea, abdominal distention, hypotrophic limbs, stunting and wasting, and presented hypocalcemia, anemia and high titers of serological markers. Diagnosis of CD was confirmed by a duodenal biopsy. After replacement of calcium and a gluten-free diet, the symptoms resolved within 6 weeks. After 2-months, serum analyses, anthropometric data as well as antibodies titers were normal after 4 years. CD screening tests are needed in chronic diarrhea for any ethnicity patients.