Dynamic changes in B cell subpopulations in response to triple-negative breast cancer development

Despite presenting a worse prognosis and being associated with highly aggressive tumors, triple-negative breast cancer (TNBC) is characterized by the higher frequency of tumor-infiltrating lymphocytes, which have been implicated in better overall survival and response to therapy. Though recent studies have reported the capacity of B lymphocytes to recognize overly-expressed normal proteins, and tumor-associated antigens, how tumor development potentially modifies B cell response is yet to be elucidated. Our findings reveal distinct effects of 4T1 and E0771 murine tumor development on B cells in secondary lymphoid organs. Notably, we observe a significant expansion of total B cells and plasma cells in the tumor-draining lymph nodes (tDLNs) as early as 7 days after tumor challenge in both murine models, whereas changes in the spleen are less pronounced. Surprisingly, within the tumor microenvironment (TME) of both models, we detect distinct B cell subpopulations, but tumor development does not appear to cause major alterations in their frequency over time. Furthermore, our investigation into B cell regulatory phenotypes highlights that the B10 Breg phenotype remains unaffected in the evaluated tissues. Most importantly, we identified an increase in CD19 + LAG-3 + cells in tDLNs of both murine models. Interestingly, although CD19 + LAG-3 + cells represent a minor subset of total B cells (< 3%) in all evaluated tissues, most of these cells exhibit elevated expression of IgD, suggesting that LAG-3 may serve as an activation marker for B cells. Corroborating with these findings, we detected distinct cell cycle and proliferation genes alongside LAG-3 analyzing scRNA-Seq data from a cohort of TNBC patients. More importantly, our study suggests that the presence of LAG-3 B cells in breast tumors could be associated with a good prognosis, as patients with higher levels of LAG-3 B cell transcripts had a longer progression-free interval (PFI). This novel insight could pave the way for targeted therapies that harness the unique properties of LAG-3 + B cells, potentially offering new avenues for improving patient outcomes in TNBC. Further research is warranted to unravel the mechanistic pathways of these cells and to validate their prognostic value in larger, diverse patient cohorts.

From In-Person to the Online World: Insights Into Organizing Events in Bioinformatics

Bioinformatics is a fast-evolving research field, requiring effective educational initiatives to bring computational knowledge to Life Sciences. Since 2017, an organizing committee composed of graduate students and postdoctoral researchers from the Universidade Federal de Minas Gerais (Brazil) promotes a week-long event named Summer Course in Bioinformatics (CVBioinfo). This event aims to diffuse bioinformatic principles, news, and methods mainly focused on audiences of undergraduate students. Furthermore, as the advent of the COVID-19 global pandemic has precluded in-person events, we offered the event in online mode, using free video transmission platforms. Herein, we present and discuss the insights obtained from promoting the Online Workshop in Bioinformatics (WOB) organized in November 2020, comparing it to our experience in previous in-person editions of the same event.

Which came first, the transcriptional regulator or its target genes? An evolutionary perspective into the construction of eukaryotic regulons

Eukaryotic regulons are regulatory units formed by a set of genes under the control of the same transcription factor (TF). Despite the functional plasticity, TFs are highly conserved and recognize the same DNA sequences in different organisms. One of the main factors that confer regulatory specificity is the distribution of the binding sites of the TFs along the genome, allowing the configuration of different transcriptional regulatory networks (TRNs) from the same regulator. A similar scenario occurs between tissues of the same organism, where a TRN can be rewired by epigenetic factors, modulating the accessibility of the TF to its binding sites. In this article we discuss concepts that can help to formulate testable hypotheses about the construction of regulons, exploring the presence and absence of the elements that form a TRN throughout the evolution of an ancestral lineage. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.

Analysis of the microarray gene expression for breast cancer progression after the application modified logistic regression

Methods based around statistics and linear algebra have been increasingly used in attempts to address emerging questions in microarray literature. Microarray technology is a long-used tool in the global analysis of gene expression, allowing for the simultaneous investigation of hundreds or thousands of genes in a sample. It is characterized by a low sample size and a large feature number created a non-square matrix, and by the incomplete rank, that can generate countless more solution in classifiers. To avoid the problem of the 'curse of dimensionality' many authors have performed feature selection or reduced the size of data matrix. In this work, we introduce a new logistic regression-based model to classify breast cancer tumor samples based on microarray expression data, including all features of gene expression and without reducing the microarray data matrix. If the user still deems it necessary to perform feature reduction, it can be done after the application of the methodology, still maintaining a good classification. This methodology allowed the correct classification of breast cancer sample data sets from Gene Expression Omnibus (GEO) data series GSE65194, GSE20711, and GSE25055, which contain the microarray data of said breast cancer samples. Classification had a minimum performance of 80% (sensitivity and specificity), and explored all possible data combinations, including breast cancer subtypes. This methodology highlighted genes not yet studied in breast cancer, some of which have been observed in Gene Regulatory Networks (GRNs). In this work we examine the patterns and features of a GRN composed of transcription factors (TFs) in MCF-7 breast cancer cell lines, providing valuable information regarding breast cancer. In particular, some genes whose αi ∗ associated parameter values revealed extreme positive and negative values, and, as such, can be identified as breast cancer prediction genes. We indicate that the PKN2, MKL1, MED23, CUL5 and GLI genes demonstrate a tumor suppressor profile, and that the MTR, ITGA2B, TELO2, MRPL9, MTTL1, WIPI1, KLHL20, PI4KB, FOLR1 and SHC1 genes demonstrate an oncogenic profile. We propose that these may serve as potential breast cancer prediction genes, and should be prioritized for further clinical studies on breast cancer. This new model allows for the assignment of values to the αi ∗ parameters associated with gene expression. It was noted that some αi ∗ parameters are associated with genes previously described as breast cancer biomarkers, as well as other genes not yet studied in relation to this disease.

Molecular typing of Leptospira interrogans serovar Hardjo isolates from leptospirosis outbreaks in Brazilian livestock

Background

Leptospirosis is caused by pathogenic spirochetes of the genus Leptospira spp. This zoonotic disease is distributed globally and affects domestic animals, including cattle. Leptospira interrogans serogroup Sejroe serovar Hardjo and Leptospira borgpetersenii serogroup Sejroe serovar Hardjo remain important species associated with this reproductive disease in livestock production. Previous studies on Brazilian livestock have reported that L. interrogans serovar Hardjo is the most prevalent leptospiral agent in this country and is related to clinical signs of leptospirosis, which lead to economic losses in production. Here, we described the isolation of three clinical strains (Norma, Lagoa and Bolivia) obtained from leptospirosis outbreaks that occurred in Minas Gerais state in 1994 and 2008.

Results

Serological and molecular typing using housekeeping (secY and 16SrRNA) and rfb locus (ORF22 and ORF36) genes were applied for the identification and comparative analysis of Leptospira spp. Our results identified the three isolates as L. interrogans serogroup Sejroe serovar Hardjo and confirmed the occurrence of this bacterial strain in Brazilian livestock. Genetic analysis using ORF22 and ORF36 grouped the Leptospira into serogroup Sejroe and subtype Hardjoprajitno. Genetic approaches were also applied to compare distinct serovars of L. interrogans strains by verifying the copy numbers of the IS1500 and IS1533 insertion sequences (ISs). The IS1500 copy number varied among the analyzed L. interrogans strains.

Conclusion

This study provides evidence that L. interrogans serogroup Sejroe serovar Hardjo subtype Hardjoprajitno causes bovine leptospirosis in Brazilian production. The molecular results suggested that rfb locus (ORF22 and ORF36) could improve epidemiological studies by allowing the identification of Leptospira spp. at the serogroup level. Additionally, the IS1500 and IS1533 IS copy number analysis suggested distinct genomic features among closely related leptospiral strains.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-017-1081-9) contains supplementary material, which is available to authorized users.

Inositol 1, 4, 5-trisphosphate-dependent nuclear calcium signals regulate angiogenesis and cell motility in triple negative breast cancer

Increases in nuclear calcium concentration generate specific biological outcomes that differ from those resulting from increased cytoplasmic calcium. Nuclear calcium effects on tumor cell proliferation are widely appreciated; nevertheless, its involvement in other steps of tumor progression is not well understood. Therefore, we evaluated whether nuclear calcium is essential in other additional stages of tumor progression, including key steps associated with the formation of the primary tumor or with the metastatic cascade. We found that nuclear calcium buffering impaired 4T1 triple negative breast cancer growth not just by decreasing tumor cell proliferation, but also by enhancing tumor necrosis. Moreover, nuclear calcium regulates tumor angiogenesis through a mechanism that involves the upregulation of the anti-angiogenic C-X-C motif chemokine 10 (CXCL10-IP10). In addition, nuclear calcium buffering regulates breast tumor cell motility, culminating in less cell invasion, likely due to enhanced vinculin expression, a focal adhesion structural protein. Together, our results show that nuclear calcium is essential for triple breast cancer angiogenesis and cell migration and can be considered as a promising strategic target for triple negative breast cancer therapy.

Evolutionary hallmarks of the human proteome: chasing the age and coregulation of protein-coding genes

Background

The development of large-scale technologies for quantitative transcriptomics has enabled comprehensive analysis of the gene expression profiles in complete genomes. RNA-Seq allows the measurement of gene expression levels in a manner far more precise and global than previous methods. Studies using this technology are altering our view about the extent and complexity of the eukaryotic transcriptomes. In this respect, multiple efforts have been done to determine and analyse the gene expression patterns of human cell types in different conditions, either in normal or pathological states. However, until recently, little has been reported about the evolutionary marks present in human protein-coding genes, particularly from the combined perspective of gene expression and protein evolution.

Results

We present a combined analysis of human protein-coding gene expression profiling and time-scale ancestry mapping, that places the genes in taxonomy clades and reveals eight evolutionary major steps (“hallmarks”), that include clusters of functionally coherent proteins. The human expressed genes are analysed using a RNA-Seq dataset of 116 samples from 32 tissues. The evolutionary analysis of the human proteins is performed combining the information from: (i) a database of orthologous proteins (OMA), (ii) the taxonomy mapping of genes to lineage clades (from NCBI Taxonomy) and (iii) the evolution time-scale mapping provided by TimeTree (Timescale of Life). The human protein-coding genes are also placed in a relational context based in the construction of a robust gene coexpression network, that reveals tighter links between age-related protein-coding genes and finds functionally coherent gene modules.

Conclusions

Understanding the relational landscape of the human protein-coding genes is essential for interpreting the functional elements and modules of our active genome. Moreover, decoding the evolutionary history of the human genes can provide very valuable information to reveal or uncover their origin and function.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3062-y) contains supplementary material, which is available to authorized users.

Metazoan remaining genes for essential amino acid biosynthesis: sequence conservation and evolutionary analyses

Essential amino acids (EAA) consist of a group of nine amino acids that animals are unable to synthesize via de novo pathways. Recently, it has been found that most metazoans lack the same set of enzymes responsible for the de novo EAA biosynthesis. Here we investigate the sequence conservation and evolution of all the metazoan remaining genes for EAA pathways. Initially, the set of all 49 enzymes responsible for the EAA de novo biosynthesis in yeast was retrieved. These enzymes were used as BLAST queries to search for similar sequences in a database containing 10 complete metazoan genomes. Eight enzymes typically attributed to EAA pathways were found to be ubiquitous in metazoan genomes, suggesting a conserved functional role. In this study, we address the question of how these genes evolved after losing their pathway partners. To do this, we compared metazoan genes with their fungal and plant orthologs. Using phylogenetic analysis with maximum likelihood, we found that acetolactate synthase (ALS) and betaine-homocysteine S-methyltransferase (BHMT) diverged from the expected Tree of Life (ToL) relationships. High sequence conservation in the paraphyletic group Plant-Fungi was identified for these two genes using a newly developed Python algorithm. Selective pressure analysis of ALS and BHMT protein sequences showed higher non-synonymous mutation ratios in comparisons between metazoans/fungi and metazoans/plants, supporting the hypothesis that these two genes have undergone non-ToL evolution in animals.

Brazilian Microbiome Project: revealing the unexplored microbial diversity--challenges and prospects

The Brazilian Microbiome Project (BMP) aims to assemble a Brazilian Metagenomic Consortium/Database. At present, many metagenomic projects underway in Brazil are widely known. Our goal in this initiative is to co-ordinate and standardize these together with new projects to come. It is estimated that Brazil hosts approximately 20 % of the entire world's macroorganism biological diversity. It is 1 of the 17 countries that share nearly 70 % of the world's catalogued animal and plant species, and is recognized as one of the most megadiverse countries. At the end of 2012, Brazil has joined GBIF (Global Biodiversity Information Facility), as associated member, to improve the access to the Brazilian biodiversity data in a free and open way. This was an important step toward increasing international collaboration and clearly shows the commitment of the Brazilian government in directing national policies toward sustainable development. Despite its importance, the Brazilian microbial diversity is still considered to be largely unknown, and it is clear that to maintain ecosystem dynamics and to sustainably manage land use, it is crucial to understand the biological and functional diversity of the system. This is the first attempt to collect and collate information about Brazilian microbial genetic and functional diversity in a systematic and holistic manner. The success of the BMP depends on a massive collaborative effort of both the Brazilian and international scientific communities, and therefore, we invite all colleagues to participate in this project.

Changes in the intracellular concentrations of the adenosine phosphates and nicotinamide adenine dinucleotides ofSaccharomyces cerevisiae during batch fermentation

Significant changes in the intracellular concentrations of adenosine phosphates and nicotinamide adenine dinucleotides were observed during fermentation of grape must by three different strains ofSaccharomyces cerevisiae: S. cerevisiae var.cerevisiae, a typical fermentative yeast strain and two flor-veil-forming strains,S. cerevisiae var.bayanus andS. cerevisiae var.capensis. The intracellular concentration of ATP was always higher inS. cerevisiae var.cerevisiae than in the flor-veil-forming strains. NAD(+) and NADP(+) concentrations decreased at faster rates in the flor-veil-forming yeasts than in the other yeast but NADH concentration was the same in all yeasts for the first 10 days of fermentation. NADPH concentration was always lower inS. cerevisiae var.cerevisiae than in the other yeasts and this yeast also showed higher rates of growth and fermentation during the early stages of the fermentation and the presence of non-viable cells at the end of fermentation. In contrast, the flor-veil-forming strains maintained growth and fermentation capabilities for a relatively long time and viable cells were present throughout the entire fermentation process (31 days).

A Porous Media Model for Blood Flow within Reticulated Foam

A porous media model is developed for non-Newtonian blood flow through reticulated foam at Reynolds numbers ranging from 10-8 to 10. This empirical model effectively divides the pressure gradient versus flow speed curve into three regimes, in which either the non-Newtonian viscous forces, the Newtonian viscous forces, or the inertial fluid forces are most prevalent. When compared to simulation data of blood flow through two reticulated foam geometries, the model adequately captures the pressure gradient within all three regimes, especially that within the Newtonian regime where blood transitions from a power-law to a constant viscosity fluid.

Amino acids biosynthesis and nitrogen assimilation pathways: a great genomic deletion during eukaryotes evolution

Background

Besides being building blocks for proteins, amino acids are also key metabolic intermediates in living cells. Surprisingly a variety of organisms are incapable of synthesizing some of them, thus named Essential Amino Acids (EAAs). How certain ancestral organisms successfully competed for survival after losing key genes involved in amino acids anabolism remains an open question. Comparative genomics searches on current protein databases including sequences from both complete and incomplete genomes among diverse taxonomic groups help us to understand amino acids auxotrophy distribution.

Results

Here, we applied a methodology based on clustering of homologous genes to seed sequences from autotrophic organisms Saccharomyces cerevisiae (yeast) and Arabidopsis thaliana (plant). Thus we depict evidences of presence/absence of EAA biosynthetic and nitrogen assimilation enzymes at phyla level. Results show broad loss of the phenotype of EAAs biosynthesis in several groups of eukaryotes, followed by multiple secondary gene losses. A subsequent inability for nitrogen assimilation is observed in derived metazoans.

Conclusions

A Great Deletion model is proposed here as a broad phenomenon generating the phenotype of amino acids essentiality followed, in metazoans, by organic nitrogen dependency. This phenomenon is probably associated to a relaxed selective pressure conferred by heterotrophy and, taking advantage of available homologous clustering tools, a complete and updated picture of it is provided.

Improvement in the prediction of the translation initiation site through balancing methods, inclusion of acquired knowledge and addition of features to sequences of mRNA

BACKGROUND

The accurate prediction of the initiation of translation in sequences of mRNA is an important activity for genome annotation. However, obtaining an accurate prediction is not always a simple task and can be modeled as a problem of classification between positive sequences (protein codifiers) and negative sequences (non-codifiers). The problem is highly imbalanced because each molecule of mRNA has a unique translation initiation site and various others that are not initiators. Therefore, this study focuses on the problem from the perspective of balancing classes and we present an undersampling balancing method, M-clus, which is based on clustering. The method also adds features to sequences and improves the performance of the classifier through the inclusion of knowledge obtained by the model, called InAKnow.

RESULTS

Through this methodology, the measures of performance used (accuracy, sensitivity, specificity and adjusted accuracy) are greater than 93% for the Mus musculus and Rattus norvegicus organisms, and varied between 72.97% and 97.43% for the other organisms evaluated: Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Nasonia vitripennis. The precision increases significantly by 39% and 22.9% for Mus musculus and Rattus norvegicus, respectively, when the knowledge obtained by the model is included. For the other organisms, the precision increases by between 37.10% and 59.49%. The inclusion of certain features during training, for example, the presence of ATG in the upstream region of the Translation Initiation Site, improves the rate of sensitivity by approximately 7%. Using the M-Clus balancing method generates a significant increase in the rate of sensitivity from 51.39% to 91.55% (Mus musculus) and from 47.45% to 88.09% (Rattus norvegicus).

CONCLUSIONS

In order to solve the problem of TIS prediction, the results indicate that the methodology proposed in this work is adequate, particularly when using the concept of acquired knowledge which increased the accuracy in all databases evaluated.

Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains

Background

Corynebacterium pseudotuberculosis, a Gram-positive, facultative intracellular pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL mainly affects small ruminants, such as goats and sheep; it also causes infections in humans, though rarely. This species is distributed worldwide, but it has the most serious economic impact in Oceania, Africa and South America. Although C. pseudotuberculosis causes major health and productivity problems for livestock, little is known about the molecular basis of its pathogenicity.

Methodology and Findings

We characterized two C. pseudotuberculosis genomes (Cp1002, isolated from goats; and CpC231, isolated from sheep). Analysis of the predicted genomes showed high similarity in genomic architecture, gene content and genetic order. When C. pseudotuberculosis was compared with other Corynebacterium species, it became evident that this pathogenic species has lost numerous genes, resulting in one of the smallest genomes in the genus. Other differences that could be part of the adaptation to pathogenicity include a lower GC content, of about 52%, and a reduced gene repertoire. The C. pseudotuberculosis genome also includes seven putative pathogenicity islands, which contain several classical virulence factors, including genes for fimbrial subunits, adhesion factors, iron uptake and secreted toxins. Additionally, all of the virulence factors in the islands have characteristics that indicate horizontal transfer.

Conclusions

These particular genome characteristics of C. pseudotuberculosis, as well as its acquired virulence factors in pathogenicity islands, provide evidence of its lifestyle and of the pathogenicity pathways used by this pathogen in the infection process. All genomes cited in this study are available in the NCBI Genbank database (http://www.ncbi.nlm.nih.gov/genbank/) under accession numbers CP001809 and CP001829.

A procedure to recruit members to enlarge protein family databases--the building of UECOG (UniRef-Enriched COG Database) as a model

A procedure to recruit members to enlarge protein family databases is described here. The procedure makes use of UniRef50 clusters produced by UniProt. Current family entries are used to recruit additional members based on the UniRef50 clusters to which they belong. Only those additional UniRef50 members that are not fragments and whose length is within a restricted range relative to the original entry are recruited. The enriched dataset is then limited to contain only genomes from selected clades. We used the COG database - used for genome annotation and for studies of phylogenetics and gene evolution - as a model. To validate the method, a UniRef-Enriched COG0151 (UECOG) was tested with distinct procedures to compare recruited members with the recruiters: PSI-BLAST, secondary structure overlap (SOV), Seed Linkage, COGnitor, shared domain content, and neighbor-joining single-linkage, and observed that the former four agree in their validations. Presently, the UniRef50-based recruitment procedure enriches the COG database for Archaea, Bacteria and its subgroups Actinobacteria, Firmicutes, Proteobacteria, and other bacteria by 2.2-, 8.0-, 7.0-, 8.8-, 8.7-, and 4.2-fold, respectively, in terms of sequences, and also considerably increased the number of species.

An algorithm to infer similarity among cell types and organisms by examining the most expressed sequences

Following sequence alignment, clustering algorithms are among the most utilized techniques in gene expression data analysis. Clustering gene expression patterns allows researchers to determine which gene expression patterns are alike and most likely to participate in the same biological process being investigated. Gene expression data also allow the clustering of whole samples of data, which makes it possible to find which samples are similar and, consequently, which sampled biological conditions are alike. Here, a novel similarity measure calculation and the resulting rank-based clustering algorithm are presented. The clustering was applied in 418 gene expression samples from 13 data series spanning three model organisms: Homo sapiens, Mus musculus, and Arabidopsis thaliana. The initial results are striking: more than 91% of the samples were clustered as expected. The MESs (most expressed sequences) approach outperformed some of the most used clustering algorithms applied to this kind of data such as hierarchical clustering and K-means. The clustering performance suggests that the new similarity measure is an alternative to the traditional correlation/distance measures typically used in clustering algorithms.

[Forestier-Rotes-Querol's disease. Ossification of the anterior cervical longitudinal ligament as a cause of dysphagia]

Forestier's disease or diffuse idiophatic skeletal hyperostosis is a systemic reumathological abnormality of unknown etiology. It produces calcificationossification of the anterior longitudinal ligament. The low dorsal region is the most affected in the raquis. These patients are tipically asymptomatic or with few symptoms (minimal joint pain, spinal pain, stiffness). Dysphagia is the most common symptom when the disease affects the cervical spine; less frequent is dyspnea, both secondary to extrinsic compression of the esophagus and trachea. Neurological complaints are quite rare. In the 1970s Resnick described specific radiological criteria for the diagnosis of Forestier's disease that are still used today. It affects men more frequently than women (2:1); the peak occurrence is in patients in their 60s. We present two cases diagnosed by severe difficulty with deglution, a 84 years-old woman and a 54 years-old man; we operated on them for surgical decompression of the esophagus with resection of osteophytes C3-C4 and C5-C6 respectively through a conventional anterolateral neck approach. Relief of difficulty in swallowing was immediately ensued.

Sub-100 nm IR spectromicroscopy of living cells

We have performed IR spectromicroscopy of cells immersed in liquid water, with a lateral resolution better than 100 nm. Here, we use the motion of an atomic force microscope tip, probing the local transient deformation induced by an IR pulsed laser tuned at a sample absorbing wavelength. By Fourier analysis of the vibration of the cantilever tip, we can discriminate frequencies that are characteristic of the object, thus eliminating the influence of the water absorption. This opens the door of chemical imaging of living species in vivo, with spatial resolution of the order of the size of cell components.

Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases

Data integration has become an important task for biological database providers. The current model for data exchange among different sources simplifies the manner that distinct information is accessed by users. The evolution of data representation from HTML to XML enabled programs, instead of humans, to interact with biological databases. We present here SRS.php, a PHP library that can interact with the data integration Sequence Retrieval System (SRS). The library has been written using SOAP definitions, and permits the programmatic communication through webservices with the SRS. The interactions are possible by invoking the methods described in WSDL by exchanging XML messages. The current functions available in the library have been built to access specific data stored in any of the 90 different databases (such as UNIPROT, KEGG and GO) using the same query syntax format. The inclusion of the described functions in the source of scripts written in PHP enables them as webservice clients to the SRS server. The functions permit one to query the whole content of any SRS database, to list specific records in these databases, to get specific fields from the records, and to link any record among any pair of linked databases. The case study presented exemplifies the library usage to retrieve information regarding registries of a Plant Defense Mechanisms database. The Plant Defense Mechanisms database is currently being developed, and the proposal of SRS.php library usage is to enable the data acquisition for the further warehousing tasks related to its setup and maintenance.

Analysis of nano-chemical mapping performed by an AFM-based (“AFMIR”) acousto-optic technique

In this paper, we analyze in detail a new method of infrared micro-spectroscopy, which aims at performing "chemical mapping" of various objects with sub-wavelength lateral resolution by using the infrared vibrational signature characterizing different molecular species. Its principle consists in an atomic force microscope tip, probing the local transient deformation induced by an infrared pulsed laser tuned at a sample absorbing wavelength. The cantilever oscillates at resonant frequencies, which amplitudes can be correlated with local absorption. We show that the system acts as an amplifier of extremely small motions induced by optical absorption and that different frequencies provide different informations, leading to a full description of the sample deformation. We estimate also the influence of the light confinement in the sample and exemplify the accuracy of the method by mapping Escherichia coli bacteria at different cantilever frequencies.

Effects of sample re-sequencing and trimming on the quality and size of assembled consensus sequences

The production of nucleic acid sequences by automatic DNA sequencer machines is always associated with some base-calling errors. In order to produce a high-quality DNA sequence from a molecule of interest, researchers normally sequence the same sample many times. Considering base-calling errors as rare events, re-sequencing the same molecule and assembling the reads produced are frequently thought to be a good way to generate reliable sequences. However, a relevant question on this issue is: how many times the sample needs to be re-sequenced to minimize costs and achieve a high-fidelity sequence? We examined how both the number of re-sequenced reads and PHRED trimming parameters affect the accuracy and size of final consensus sequences. Hundreds of single-pool reaction pUC18 reads were generated and assembled into consensus sequences with CAP3 software. Using local alignment against the published pUC18 cloning vector sequence, the position and number of errors in the consensus were identified and stored in MySQL databases. Stringent PHRED trimming parameters proved to be efficient for the reduction of errors; however, this procedure also decreased consensus size. Moreover, re-sequencing did not have a clear effect on the removal of consensus errors, although it was able to slightly increase consensus.

Delayed intracerebral hemorrhage after ventriculoperitoneal shunt insertion. Case report and literature review

We present another case of delayed intracerebral hemorrhage after a ventriculoperitoneal (VP) shunting procedure. In this case, a right occipital intraparenchymal hematoma and associated intraventricular hemorrhage occurred six days after the operation for hydrocephalus secondary to subarachnoid hemorrhage in a 64 year old woman. It is a rare complication of VP shunting, with few cases reported previously in the literature. The presumed mechanism is the erosion of a cerebral blood vessel secondary to a close contact with the ventricular catheter; bleeding disorder, vascular malformation, head trauma or brain tumor were excluded in this patient.

Sex-biased gene flow in African Americans but not in American Caucasians

We have previously shown evidence of strong sex-biased genetic blending in the founding and ongoing history of the Brazilian population, with the African and Amerindian contribution being highest from maternal lineages (as measured by mitochondrial DNA) and the European contribution foremost from paternal lineages (estimated from Y-chromosome haplogroups). The same phenomenon has been observed in several other Latin American countries, suggesting that it might constitute a universal characteristic of the Iberian colonization of the Americas. However, it has also recently been detected in the Black population of the United States. We thus wondered if the same could be observed in American Caucasians. To answer that question, we retrieved 1387 hypervariable I Caucasian mitochondrial DNA sequences from the FBI population database and established their haplogroups and continental geographical sources. In sharp contrast with the situation of the Caucasian population of Latin American countries, only 3.1% of the American Caucasian sequences had African and/or Amerindian origin. To explain this discrepancy we propose that the finding of elevated genomic contributions from European males and Amerindian or African females depends not only on the occurrence of directional mating, but also on the "racial" categorization of the children born from these relations. In this respect, social practices in Latin America and in the United States diverge considerably; in the former socially significant "races" are normally designated according to physical appearance, while in the latter descent appears to be the most important factor.

Relationship between ethanol tolerance, H+ -ATPase activity and the lipid composition of the plasma membrane in different wine yeast strains

Ethanol tolerance, ATPase activity and the lipid composition of the plasma membrane to study potential relationship among them were examined in five different wine yeast strains. Yeast cells were subjected to ethanol stress (4% v/v). Principal component analysis of the results revealed that the wine yeasts studied can be distinguished in terms of ATPase activity and oleic acid (C18:1), and palmitoleic acid (C16:1), in plasma membrane. Multiple regression analysis was used to identify a potential influence of some components of the plasma membrane on ethanol tolerance and ATPase activity. Based on the results, the ergosterol, oleic acid and palmitoleic acid are highly correlated with ATPase activity and ethanol tolerance. Ethanol tolerance and the ATPase activity of the plasma membrane were correlated at the 96.64% level with the oleic acid and ergosterol in plasma membrane. The Saccharomyces cerevisiae var. capensis flor yeast strain, which exhibited the highest ergosterol concentration in plasma membrane when grown in the presence of 4% v/v ethanol, was found to be the most ethanol-tolerant.

A picture of gene sampling/expression in model organisms using ESTs and KOG proteins

The expressed sequence tag (EST) is an instrument of gene discovery. When available in large numbers, ESTs may be used to estimate gene expression. We analyzed gene expression by EST sampling, using the KOG database, which includes 24,154 proteins from Arabidopsis thaliana (Ath), 17,101 from Caenorhabditis elegans (Cel), 10,517 from Drosophila melanogaster (Dme), and 26,324 from Homo sapiens (Hsa), and 178,538 ESTs for Ath, 215,200 for Cel, 261,404 for Dme, and 1,941,556 for Hsa. BLAST similarity searches were performed to assign KOG annotation to all ESTs. We determined the amount of gene sampling or expression dedicated to each KOG functional category by each model organism. We found that the 25% most-expressed genes are frequently shared among these organisms. The KOG protein classification allowed the EST sampling calculation throughout the glycolysis pathway. We calculated the KOG cluster coverage and inferred that 50 to 80 K ESTs would efficiently cover 80-85% of the KOG database clusters in a transcriptome project. Since KOG is a database biased towards housekeeping genes, this is probably the number of ESTs needed to include the more commonly expressed genes in these organisms. We also examined a still unaddressed question: what is the minimum number of ESTs that should be produced in a transcriptome project?

Influence of pre-fermentative treatment on the fatty acid content of Saccharomyces cerevisiae (M(3)30-9) during alcoholic fermentation of grape must

The effect of skin maceration and must filtration on the growth and fermentative capacity of one strain of Saccharomyces cerevisiae was studied. Skin maceration increased the fatty acid concentration of the must, thus affecting the lipid composition of the yeast cell membranes. Sterile filtration resulted in a reduction of the fatty acid content of the must extracted during maceration, but increased the fatty acid content of the yeast membranes, thus increasing the fermentative capacity without affecting either growth or cell viability.

Local infrared microspectroscopy with subwavelength spatial resolution with an atomic force microscope tip used as a photothermal sensor

We describe a new method of infrared microspectroscopy. It is intended for performing chemical mapping of various objects with subwavelength lateral resolution by using the infrared vibrational signature characterizing different molecular species. We use the photothermal expansion effect, detected by an atomic force microscope tip, probing the local transient deformation induced by an infrared pulsed laser tuned at a sample absorbing wavelength. We show that this new tool opens the way for measuring and identifying spectroscopic contrasts not accessible by far-field or near-field optical methods and with a subwavelength lateral resolution.

Evaluation of window cohabitation of DNA sequencing errors and lowest PHRED quality values

When analyzing sequencing reads, it is important to distinguish between putative correct and wrong bases. An open question is how a PHRED quality value is capable of identifying the miscalled bases and if there is a quality cutoff that allows mapping of most errors. Considering the fact that a low quality value does not necessarily indicate a miscalled position, we decided to investigate if window-based analyses of quality values might better predict errors. There are many reasons to look for a perfect window in DNA sequences, such as when using SAGE technique, looking for BLAST seeding and clustering sequences. Thus, we set out to find a quality cutoff value that would distinguish non-perfect windows from perfect ones. We produced and compared 846 reads of pUC18 with the published pUC consensus, by local alignment. We then generated a database containing all mismatches, insertions and gaps in order to map real perfect windows. An investigation was made to find the potential to predict perfect windows when all bases in the window show quality values over a given cutoff. We conclude that, in window-based applications, a PHRED quality value cutoff of 7 masks most of the errors without masking real correct windows. We suggest that the putative wrong bases be indicated in lower case, increasing the information on the sequence databases without increasing the size the files.

Changes in gluconic acid, polyols and major volatile compounds in sherry wine during aging with submerged flor yeast cultures

The traditional biological process by which sherry wines are aged can be accelerated by using submerged Saccharomyces cerevisiae var. capensis (G1) strain cultures previously grown in glycerol. The used controlled shaking conditions raise the acetaldehyde, acetoin, and meso 2,3-butanediol contents in the wine, and increases the consumption of gluconic acid by flor yeast relative to traditional biological aging under flor yeast velum.

Detergent effect on cytochrome b559 electron paramagnetic resonance signals in the photosystem II reaction centre

The detergent effect on Cytochrome b559 from spinach photosystem II was studied by electron paramagnetic resonance (EPR) spectroscopy in D1-D2-Cyt b559 complex preparations. Various n-dodecyl-beta-D-maltoside concentrations from 0 to 0.2% (w/v) were used to stabilise the D1-D2-Cyt b559 complexes. Low spin heme EPR spectra were obtained but the g(z) feature positions changed depending on the detergent conditions Redox potentiometric titrations showed a unique redox potential cytochrome b559 form (E'm = + 123-150 mV) in all the D1-D2-Cyt b559 complex preparations indicating that detergent does not affect this property of the protein in those conditions. A similar effect on Cytochrome b559 EPR spectrum was observed in more intact photosystem II preparations independently of their aggregation state. This finding indicates that changes due to detergent could be a common phenomenon in photosystem II complexes. Results are discussed in terms of the environment each detergent provides to the protein.

Mining microorganism EST databases in the quest for new proteins

Microorganisms with large genomes are commonly the subjects of single-round partial sequencing of cDNA, generating expressed sequence tags (ESTs). Usually there is a great distance between gene discovery by EST projects and submission of amino acid sequences to public databases. We analyzed the relationship between available ESTs and protein sequences and used the sequences available in the secondary database, clusters of orthologous groups (COG), to investigate ESTs from eight microorganisms of medical and/or economic relevance, selecting for candidate ESTs that may be further pursued for protein characterization. The organisms chosen were Paracoccidioides brasiliensis, Dictyostelium discoideum, Fusarium graminearum, Plasmodium yoelii, Magnaporthe grisea, Emericella nidulans, Chlamydomonas reinhardtii and Eimeria tenella, which have more than 10,000 ESTs available in dbEST. A total of 77,114 protein sequences from COG were used, corresponding to 3,201 distinct genes. At least 212 of these were capable of identifying candidate ESTs for further studies (E. tenella). This number was extended to over 700 candidate ESTs (C. reinhardtii, F. graminearum). Remarkably, even the organism that presents the highest number of ESTs corresponding to known proteins, P. yoelii, showed a considerable number of candidate ESTs for protein characterization (477). For some organisms, such as P. brasiliensis, M. grisea and F. graminearum, bioinformatics has allowed for automatic annotation of up to about 20% of the ESTs that did not correspond to proteins already characterized in the organism. In conclusion, 4093 ESTs from these eight organisms that are homologous to COG genes were selected as candidates for protein characterization.

Inhibition of the TEF/TEAD transcription factor activity by nuclear calcium and distinct kinase pathways

Transcription enhancer factor (TEF/TEAD) is a family of four transcription factors that share a common TEA-DNA binding domain and are involved in similar cellular functions, such as cell differentiation and proliferation. All adult tissues express at least one of the four TEAD genes, so this family of transcription factors may be of widespread importance, yet little is known about their regulation. Here we examine the factors that regulate TEAD activity in CHO cells. RT-PCR indicated the presence of TEAD-1, TEAD-3, and both isoforms of TEAD-4, but not TEAD-2. Quantitative measurements showed that TEAD-4 is most abundant, followed by TEAD-3, then TEAD-1. We examined the relative effects of nuclear and cytosolic Ca(2+) on TEAD activity, since TEAD proteins are localized to the nucleus and since free Ca(2+) within the nucleus selectively regulates transcription in some systems. Chelation of nuclear but not cytosolic Ca(2+) increased TEAD activity two times above control. Inhibition of mitogen-activated protein kinase (MAPK) also increased TEAD activity, while cAMP decreased TEAD activity, and protein kinase C had no effect. Together, these results show that nuclear Ca(2+), MAPK, and cAMP each negatively regulate the activity of the TEAD transcription factor.

Gas phase infrared spectroscopy of selectively prepared ions

The first example of direct structural characterization of polyaromatic ions by coupling a Fourier transform ion cyclotron resonance mass spectrometer with an infrared free-electron laser is presented. Measurement of the IR spectra of selectively prepared ionic reactive intermediates is allowed by the association of the high peak power and wide tunability of the laser with the flexibility of the spectrometer, where several mass selection and ion reaction steps can be combined, as demonstrated in the case of iron cation complexes of hydrocarbons. The present experimental setup opens the way to understanding chemical reaction paths.

Effect of protein relaxation on electron transfer from the cytochrome subunit to the bacteriochlorophyll dimer in Rps. sulfoviridis reaction centers within mixed adiabatic/nonadiabatic model

The broad set of nonexponential electron transfer (ET) kinetics in reaction centers (RC) from Rhodopseudomonas sulfoviridis in temperature range 297-40 K are described within a mixed adiabatic/nonadiabatic model. The key point of the model is the combination of Sumi-Marcus and Rips-Jortner approaches which can be represented by the separate contributions of temperature-independent vibrational (v) and temperature-dependent diffusive (d) coordinates to the preexponential factor, to the free energy of reaction DeltaG=DeltaG(v)+DeltaG(d)(T) and to the reorganization energy lambda=lambda(v)+lambda(d)(T). The broad distribution of protein dielectric relaxation times along the diffusive coordinate is considered within the Davidson-Cole formalism.

Long polaron lifetime in InAs/GaAs self-assembled quantum dots

We have investigated the polaron dynamics in n-doped InAs/GaAs self-assembled quantum dots by pump-probe midinfrared spectroscopy. A long T1 polaron decay time is measured at both low temperature and room temperature, with values around 70 and 37 ps, respectively. The decay time decreases for energies closer to the optical phonon energy. The relaxation is explained by the strong coupling for the electron-phonon interaction and by the finite lifetime of the optical phonons. We show that, even for a large detuning of 19 meV from the LO photon energy in GaAs, the carrier relaxation remains phonon assisted.

Influence of skin maceration and oxygen on anaerobic fermentation of grape musts with high sugar content

Saccharomyces cerevisiae race cerevisiae was used to ferment grape musts in strictly anaerobic conditions, subjected to a prefermentative treatment of skin maceration and following a short aeration after 48 h of fermentation. Skin maceration caused an increase in the cellular phospholipid content which affected neither viability nor the fermentative capacity of the yeasts. The short aeration had no significant effect on the unsaturation index of the cellular fatty acids, although it did increase the ergosterol/phospholipid ratio. This was reflected by an increase in the growth rate, viability and fermentative capacity of the yeasts. Maceration did not increase the effect of aeration.

Factors determining the special redox properties of photosynthetic cytochrome b559

Factors controlling the redox properties of the two conventional forms of cytochrome b559, i.e. the unstable high-potential form and the stable low-potential form, have been further investigated using PSII-enriched membranes from pea and spinach chloroplasts. The redox potential of the stable form of cytochrome b559 is pH independent both above pH 7.5 (E'm approximately +110 mV) and below pH 6.0 (E'm approximately +203 mV), but it changes with a slope of 58 mV per pH unit between these two pH values. Thus, cytochrome b559 seems to have a single ionizing group influencing its redox potential, with a higher affinity for protons in the reduced form (pK(red) = 7.5) and a lower affinity in the oxidized form (pK(ox) = 6.0); consequently, one unprotonated low-potential form (LP) and one protonated intermediate-potential form (IP). The redox potential of the high-potential form (HP) is pH-independent between pH 5.0 and 8.0, but its relative content (compared to the total amount of protein) decreases progressively above pH 7.0. This conversion to the stable LP form is interpreted as corresponding to the loss of a proton by one ionizing group, the protonation of which is essential for maintaining the unstable HP state. According to chemical modification experiments with diethylpyrocarbonate, one of the two histidine ligands of the heme seems to be the ionizing group responsible for the existence of both the protonated IP and HP forms. It is proposed that the difference between the IP and HP forms is due to the formation of an additional hydrogen bond between the protonated histidine and the protein in the HP state that stabilizes a special hydrophobic heme environment responsible for its high redox potential.

[Leiomyosarcoma of the paranasal sinuses with intracranial involvement: report of a clinical case and review of the literature]

We describe a 53 year old man with a two months history of frontal headache and right visual loss, with complete right blindness at the moment of diagnosis. Neither nasal obstruction nor endocrine symptoms were found. Computerized Tomography showed a neoplasm involving both paranasal sinuses and sellar region, with bilateral orbital extension. The patient underwent a bifrontal craniotomy with apparent complete excision. Histopathologic examination proved smooth muscle cells sarcoma (leiomyosarcoma). Clinical evolution was unfavorable, with rapid local recurrence. The patient died of cerebellar metastasis 4 months after the initial diagnosis and treatment. Leiomyosarcoma of the sinonasal tract is an unusual tumor, and we have found only 63 cases previously reported. The most frequent clinical presentation is nasal obstruction. Surgery is the treatment of choice, as far as radiotherapy or chemotherapy do not appear to slow disease progression. No relationship has been found between the aggressiveness of leiomyosarcoma of the sinonasal tract and morphologic parameters; instead, prognosis is dependent on the distribution of disease at clinical onset. Leiomyosarcoma of the sinonasal tract may be regarded as a locally aggressive neoplasm with only limited metastatic potential.

Influence of aeration on the physiological activity of flor yeasts

The effect of periodic aeration on the physiological activity of a strain of Saccharomyces cerevisiae yeast during development of velum (flor) and biological aging of Sherry wine of the Fino type was investigated. L-Proline amino acid was the main nitrogen source for yeasts cells during the biological aging, and its exhaustion may be the cause of the production and consumption of other compounds that are involved in the aroma of wines. Aeration was found to increase adenylate energy charge, growth, and viability of the yeast cells. Also, it affected the intracellular redox equilibrium and the consumption and production of compounds including acetoin, acetaldehyde, higher alcohols, ethanol, glycerol, and acetic acid. Acetaldehyde reached its highest level after the second aeration, which coincided with the exhaustion of the nitrogen source in the medium. The enzyme activity of alcohol dehydrogenases I and II decreased immediately after each aeration, subsequently increasing once all of the dissolved oxygen in the wine had been consumed by yeast cells. Aldehyde dehydrogenase activity was detected only after the first aeration, and it may be related to the production and consumption of acetic acid in the wine.

Changes in nitrogen compounds in must and wine during fermentation and biological aging by flor yeasts

Urea, ammonium, and free amino acid contents were quantified in a must from Vitis vinifera cv. Pedro Ximenez grapes and in fermented wine and after a short aging of this wine by Saccharomyces cerevisiae race capensis yeast under variable oxygen availability conditions. The previous compounds were also determined in a wine in which the nitrogen source was depleted by the same race of flor yeast (old wine) and also following the addition of ammonium ion, L-glutamic acid, and L-proline. Under specific conditions such as low oxygen level and the absence of some nutrients, the yeasts release some amino acids including L-threonine, L-tryptophan, L-cysteine, and L-methionine to the medium. These amino acids must originate primarily in a de novo synthesis from ethanol that regenerates NAD(P)+. On the basis of these results, the yeasts may be able to use amino acids not only as nitrogen sources but also as redox agents to balance the oxidation-reduction potential under conditions of restricted oxygen, when electron transport along the respiratory chain may be hindered or limited.

Time domain investigation on vibrational dephasing and spectral diffusion in CO-doped solid N2

Infrared picosecond accumulated photon echo experiments have been performed for the first time, using the Orsay Free Electron Laser, on the v = 0-->v = 1 transition of CO in solid nitrogen. The vibrational dephasing time is found to be exceptionally long ( T2>/=120 ns) at low temperature. The analysis of the observed spectral diffusion leads one to assume different energy transfer mechanisms depending on the CO concentration.

Indigenous yeasts associated with two Vitis vinifera grape varieties cultured in southern Spain

The yeast microbiota present on the surface of grapes of two Vitis vinifera varieties, Pedro Ximénez and Tempranillo de Rioja, grown in the Montilla-Moriles region of southern Spain was identified. The changes between veraison and the physiological ripeness time during 3 years were monitored. Overall, the yeast microbiota isolated was of oxidative metabolism. Sporobolomyces roseus and Cryptococcus albidus species occurred at all physiological stages, in the two Vitis vinifera varieties, and the three seasons studied. On the other hand, Kloeckera apiculata was never detected and Saccharomyces cerevisiae was scarcely isolated, it was only present, testimonial, in Tempranillo de Rioja grapes during the 1992 vintage. The widest variety of yeast species was observed in the 1992 season, and in contrast, the lowest number of species in both varieties of Vitis was detected in the 1994 season.

Analysis of the gene expression profile of Schistosoma mansoni cercariae using the expressed sequence tag approach

ESTs constitute rapid and informative tools with which to study gene-expression profiles of the diverse stages of the schistosome life cycle. Following a comprehensive EST study of adult worms, analysis has now targeted the cercaria, the parasite larval form responsible for infection of the vertebrate host. Two Schistosoma mansoni cercarial cDNA libraries were examined and partial sequence obtained from 957 randomly selected clones. On the basis of database searches, 551 (57.6%) ESTs generated had no homologs in the public databases whilst 308 (32.2%) were putatively identified, totaling 859 informative ESTs. The remaining 98 (10.2%) were uninformative ESTs (ribosomal RNA and non-coding mitochondrial sequences). By clustering analysis we have identified 453 different genes. The most common sequences in both libraries represented Sm8 calcium binding protein (8% of ESTs), fructose-1,6-bisphosphate aldolase, glyceraldehyde-3-phosphate dehydrogenase, cytochrome oxidase subunit 1, ATP guanidine kinase and triose phosphate isomerase. One hundred and nineteen identified genes were sorted into 11 functional categories, with genes associated with energy metabolism being the most abundant (13%) and diverse. The diversity and abundance of genes associated with the transcription/translation machinery and with regulatory/signaling functions were also marked. A paramyosin transcript was identified, indicating that this gene is not exclusively expressed in adult worms and sporocysts (as had been suggested previously). The possible physiological relevance to cercariae of the presence of transcripts with homology to calcium binding proteins of the EF-hand superfamily, Gq-coupled rhodopsin photoreceptor, rod phosphodiesterase 8 subunit and peripheral-type benzodiazepine receptor is discussed.

Light-induced degradation of cytochrome b559 during photoinhibition of the photosystem II reaction center

The behaviour of cytochrome (cyt) b559 during acceptor- and donor-side photoinhibition has been investigated in oxygen-evolving and non-evolving photosystem II (PSII) membranes. Strong illumination at 20 degrees C under aerobiosis induced a strong decrease in the absorbance of the cyt b559 alpha-band in the two preparations. This absorbance decline was observed only in non-oxygen-evolving PSII samples when illumination was performed under aerobiosis but at 4 degrees C, or under anaerobiosis at 20 degrees C. These results suggest that acceptor-side photoinhibition induces the degradation of cyt b559 by a mechanism related to an enzymatic reaction mediated by singlet oxygen. Donor-side photoinhibition may induce, however, a non-enzymatic photocleavage of the protein.

Nucleoskeleton and initiation of DNA replication in metazoan cells

To determine whether or not initiation sites for DNA replication in mammalian cells are defined by association with nuclear structure, attachments between the nucleoskeleton and the hamster DHFR gene initiation zone were examined. Nucleoskeletons were prepared by encapsulating cells in agarose and then extracting them with a nonionic detergent in a physiological buffer. The fraction of DNA that remained following endonuclease digestion was resistant to salt, sensitive to Sarkosyl, and essentially unchanged by glutaraldehyde crosslinking. Although newly replicated DNA was preferentially attached to the nucleoskeleton, no specific sequence was preferentially attached within a 65 kb locus containing the DHFR gene, two origins of bi-directional replication and at least one nuclear matrix attachment region. Instead, the entire region went from preferentially unattached to preferentially attached as cells progressed from G1 to late S-phase. Thus, initiation sites in mammalian chromosomes are not defined by attachments to the nucleoskeleton. To further assess the relationship between the nucleoskeleton and DNA replication, plasmid DNA containing the DHFR initiation region was replicated in a Xenopus egg extract. All of the DNA associated with the nucleoskeleton prior to S-phase without preference for a particular sequence and was released upon mitosis. However, about half of this DNA was trapped rather than bound to the nucleoskeleton. Thus, attachments to the nucleoskeleton can form in the absence of either DNA replication or transcription, but if they are required for replication, they are not maintained once replication is completed.

Low-temperature electron transfer from cytochrome to the special pair in Rhodopseudomonas viridis: role of the L162 residue

Electron transfer from the tetraheme cytochrome c to the special pair of bacteriochlorophylls (P) has been studied by flash absorption spectroscopy in reaction centers isolated from seven strains of the photosynthetic purple bacterium Rhodopseudomonas viridis, where the residue L162, located between the proximal heme c-559 and P, is Y (wild type), F, W, G, M, T, or L. Measurements were performed between 294 K and 8 K, under redox conditions in which the two high-potential hemes of the cytochrome were chemically reduced. At room temperature, the kinetics of P+ reduction include two phases in all of the strains: a dominant very fast phase (VF), and a minor fast phase (F). The VF phase has the following t(1/2): 90 ns (M), 130 ns (W), 135 ns (F), 189 ns (Y; wild type), 200 ns (G), 390 ns (L), and 430 ns (T). These data show that electron transfer is fast whatever the nature of the amino acid at position L162. The amplitudes of both phases decrease suddenly around 200 K in Y, F, and W. The effect of temperature on the extent of fast phases is different in mutants G, M, L, and T, in which electron transfer from c-559 to P+ takes place at cryogenic temperatures in a substantial fraction of the reaction centers (T, 48%; G, 38%; L, 23%, at 40 K; and M, 28%, at 60 K), producing a stable charge separated state. In these nonaromatic mutants the rate of VF electron transfer from cytochrome to P+ is nearly temperature-independent between 294 K and 8 K, remaining very fast at very low temperatures (123 ns at 60 K for M; 251 ns at 40 K for L; 190 ns at 8 K for G, and 458 ns at 8 K for T). In all cases, a decrease in amplitudes of the fast phases is paralleled by an increase in very slow reduction of P+, presumably by back-reaction with Q(A)-. The significance of these results is discussed in relation to electron transfer theories and to freezing at low temperatures of cytochrome structural reorganization.

Update of the gene discovery program in Schistosoma mansoni with the expressed sequence tag approach

Continuing the Schistosoma mansoni Genome Project 363 new templates were sequenced generating 205 more ESTs corresponding to 91 genes. Seventy four of these genes (81%) had not previously been described in S. mansoni. Among the newly discovered genes there are several of significant biological interest such as synaptophysin, NIFs-like and rho-GDP dissociation inhibitor.

Evaluation of cDNA libraries from different developmental stages of Schistosoma mansoni for production of expressed sequence tags (ESTs)

A comparative study of the gene expression profile in different developmental stages of Schistosoma mansoni has been initiated based on the expressed sequence tag (EST) approach. A total of 1401 ESTs were generated from seven different cDNA libraries constructed from four distinct stages of the parasite life cycle. The libraries were first evaluated for their quality for a large-scale cDNA sequencing program. Most of them were shown to have less than 20% useless clones and more than 50% new genes. The redundancy of each library was also analyzed, showing that one adult worm cDNA library was composed of a small number of highly frequent genes. When comparing ESTs from distinct libraries, we could detect that most genes were present only in a single library, but others were expressed in more than one developmental stage and may represent housekeeping genes in the parasite. When considering only once the genes present in more than one library, a total of 466 unique genes were obtained, corresponding to 427 new S. mansoni genes. From the total of unique genes, 20.2% were identified based on homology with genes from other organisms, 8.3% matched S. mansoni characterized genes and 71.5% represent unknown genes.

Determination of the relative ploidy in different Saccharomyces cerevisiae strains used for fermentation and 'flor' film ageing of dry sherry-type wines

The full chromosomal karyotype of six enological Saccharomyces cerevisiae strains used for fermentation and biological ageing of sherry-type wines was studied. A genetic method based on the analysis of segregation frequencies of auxotrophic markers, among random spore progeny of hybrids, constructed between laboratory and industrial wine strains (Bakalinsky and Snow, 1990) was used. This method was combined with the analysis of strains by pulsed-field gel electrophoresis. The results obtained clearly indicate the presence of two, three or four copies of a chromosome in the industrial strains examined, and thus confirm that aneuploidy/polyploidy is not uncommon in these strains. In all strains examined, chromosome XIII polysomy is observed. This chromosome contains the ADH2 and ADH3 loci, that code for the ADHII and ADHIII isoenzymes of alcohol dehydrogenase, which are involved in ethanol oxidative utilization during biological ageing of wines. Tetrad analysis for the 'flor formation' character suggest two possibilities: this character is either regulated by at least a digenic system, or by only one gene present on a chromosome which is, at least, disomic.