P-370 The vaginal microbiome in the first trimester of pregnancy is different in spontaneous versus IVF gestation

Study question

Are there differences in the vaginal microbiome of pregnant women who had a spontaneous pregnancy compared to those who required IVF?

Summary answer

The composition of the vaginal microbiome at 12 week's gestation is different in women who achieve the pregnancy spontaneously or by IVF.

What is known already

The vaginal microbiome plays an important role in women's reproductive health, finding associations between different microbiome patterns and the presence of infertility and embryo implantation failure in IVF. Additionally, recent studies show a correlation between obstetrics and perinatal outcomes and the composition of vaginal microbiota in pregnant women, as well as an increased risk of obstetrics complications in pregnant women after IVF.

Study design, size, duration

Observational, prospective and multicentre study. A total of 64 women were enrolled between January 2020 and June 2021. Spontaneous pregnancies n = 30; and IVF pregnancies n = 34.

Participants/materials, setting, methods

Vaginal swabs were obtained by speculum exam at 12 weeks of gestation in two public hospitals and a fertility private clinic in Spain, to evaluate the differences in vaginal microbiome between both cohorts. The microbiome composition was analyzed by sequencing the V3-V4 region of the 16S rRNA on the Illumina MiSeq platform.

Main results and the role of chance

There were no significant differences in socio-demographic characteristics between groups, except for an expected higher maternal age in the IVF cohort.

Lactobacillus was the most prevalent genus in both groups. When we compared the beta diversity of vaginal microbial by cohort a significant difference was obtained (p = 0.001).

Gardenella, Neisseria, Prevotella and Staphyloccocus were significantly enriched in the IVF group (p = 0.01).

A further evaluation of the four most abundant Lactobacillus species showed that Lactobacillus iners was dominant in IVF pregnancies (15.2%) compared to spontaneous (9.8%) (p = 0.002). On the other hand, Lactobacillus  gasseri showed a lower abundance in vaginal microbiome from women belonged to IVF (9.2%) vs spontaneous pregnant group (13.8%) (p = 0.005).

These findings allowed us to create a model to identify a microbial signature. This model is able to discriminate between IVF and spontaneous pregnancies.

Limitations, reasons for caution

The main limitation of our study is the small sample size. Larger studies are needed to corroborate our findings and their relationship with important aspects such as obstetric and perinatal complications.

Wider implications of the findings

The microbiome composition is different between both cohorts. The microbiome found in our IVF cohort has been also associated with obstetric complications as preterm delivery in previous studies. This suggest that the microbiome composition could be a plausible etiology for a higher risk of adverse pregnancy outcomes in IVF patients.

Trial registration number

Not applicable

Color of extra virgin olive oils enriched with carotenoids from microalgae: influence of ultraviolet exposure and heating

A carotenoid-rich extract containing 2.5 mg/mL of lutein and 3.3 mg/mL of β-carotene from the microalga Scenedesmus almeriensis was added to ten extra virgin olive oils from four Spanish cultivars with differing degrees of ripeness, obtaining carotenoid enriched oils with lutein and β-carotene concentrations of 0.082 and 0.11 mg/mL, respectively. Extra virgin olive oils enriched with carotenoids from microalgae were studied by analyzing the effect on color of three different treatments: ultraviolet exposure, microwave heating and immersion bath heating. The methodology was designed to simulate, in controlled laboratory conditions, the effects of household treatments. Spectrophotometric color measurements were then performed to monitor color changes in the enriched and non-enriched extra virgin olive oil samples. Enriched oils are much more chromatic, darker and redder than natural oils. After 55 days UV irradiation, 40 min microwave heating, and 72 hours thermostatic heating, the average color differences for natural/enriched extra virgin olive oils were 98/117, 15/9 and 57/28 CIELAB units, respectively. In general, increasing temperature and ultraviolet exposure produced higher CIELAB color differences in the non-enriched samples. The addition of microalga extracts to extra virgin olive oils was found to induce some color stability and may constitute a future way of increasing the daily intake of beneficial bioactive compounds such as carotenoids.

Identification of vaginal microbiome associated with IVF pregnancy

The factors that cause a preterm birth (PTB) are not completely understood up to date. Moreover, PTB is more common in pregnancies achieved by in-vitro fertilization (IVF) than in spontaneous pregnancies. Our aim was to compare the composition of vaginal microbiome at 12 weeks of gestation between women who conceived naturally or through IVF in order to study whether IVF PTB-risk could be related to vaginal microbiome composition. We performed an observational, prospective and multicentre study among two public hospitals and a fertility private clinic in Spain. Vaginal swabs from 64 pregnant women at 12 weeks of gestation were collected to analyse the microbiome composition by sequencing the V3-V4 region of the 16S rRNA. Our results showed that the vaginal microbiome signature at 12 weeks of pregnancy was different from women who conceived naturally or through IVF. The beta diversity and the genus composition were different between both cohorts. Gardnerella, Neisseria, Prevotella, and Staphylococcus genus were enriched genus in the vaginal microbiome from the IVF group, allowing us to create a balance model to predict both cohorts. Moreover, at species level the L. iners abundance was higher and L. gasseri was lower in the IVF group. As a conclusion, our findings were consistent with a proposed framework in which IVF pregnancy are related to risk for preterm birth (PTB) suggesting vaginal microbiome could be the reason to the relation between IVF pregnancy and risk for PTB.

The role of seagrass meadows in the coastal trapping of litter

The accelerated discard and mismanagement of human-made products are resulting in the continued input of litter into the oceans. Models and field observations show how floating litter can accumulate in remote areas throughout the global ocean, but far less is known about the non-floating litter fraction. Seagrass meadows play an important role in the sediment and natural-debris dynamics, and likely also in the storage and processing of non-floating litter. In this work, non-floating litter was studied across six Posidonia oceanica meadows. Litter accumulated mainly around the landside edge of the meadow. The outer margin of the edge predominantly trapped macro-litter, whilst microplastics accumulated mainly along the inner margin. On average, macro-litter concentrations increased 3-fold after heavy rainfall. Retention of non-floating litter by coastal meadows facilitates the recurrent landward-seaward conveyance of the easily-transportable litter (mainly plastic items) and its fragmentation before it is buried or transferred to deeper areas.

Distribution and abundance of microplastics in coastal sediments depends on grain size and distance from sources

Microplastic deposition in marine sediments is a geographically widespread problem. This study examines microplastics in intertidal and subtidal sediments at 87 locations in habitats designated as Special Areas of Conservation (SACs) and Special Protection Areas (SPAs) on the coastline of Ireland. Established methodological approaches including, organic matter digestion, density separation, particle extraction and polymer identification were applied. Microplastic abundance was closely related with distance from known sources and concentrations were greater in intertidal as opposed to subtidal sediments. Colourless, polyethylene fibres and polypropylene fragments were the most abundant MP recorded and finer grained sediments were shown to entrap more MPs than coarser sediments. The results demonstrate that an understanding of potential sources of pollution, sediment type and hydrodynamic conditions are very important in terms of MP abundance and distribution in marine sediments and also in terms of effective waste management strategies and policy aimed at reducing the global plastics problem.

PCNA Deubiquitylases Control DNA Damage Bypass at Replication Forks

DNA damage tolerance plays a key role in protecting cell viability through translesion synthesis and template switching-mediated bypass of genotoxic polymerase-blocking base lesions. Both tolerance pathways critically rely on ubiquitylation of the proliferating-cell nuclear antigen (PCNA) on lysine 164 and have been proposed to operate uncoupled from replication. We report that Ubp10 and Ubp12 ubiquitin proteases differentially cooperate in PCNA deubiquitylation, owing to distinct activities on PCNA-linked ubiquitin chains. Ubp10 and Ubp12 associate with replication forks in a fashion determined by Ubp10 dependency on lagging-strand PCNA residence, and they downregulate translesion polymerase recruitment and template switch events engaging nascent strands. These findings reveal PCNA^K164 deubiquitylation as a key mechanism for the modulation of lesion bypass during replication, which might set a framework for establishing strand-differential pathway choices. We propose that damage tolerance is tempered at replication forks to limit the extension of bypass events and sustain chromosome replication rates.

Analysis of Cohesin Association to Newly Replicated DNA Through Nascent Strand Binding Assay (NSBA)

Replication forks engage chromatin-bound cohesin complexes during chromosome replication. Interfacing between cohesin and replication forks influences both cohesion establishment and fork functionality. However, the mechanisms mediating this process are scarcely understood. Here we describe the nascent strand binding assay (NSBA) methodology, developed in budding yeast to discriminate the association of cohesin to either parental unreplicated or nascent DNA in the environment of replication forks. NSBA quantitatively estimates the association of a protein of interest to newly replicated DNA. For this, nascent strands are in vivo labeled with the thymine analogue bromodeoxyuridine and chromatin is immunoprecipitated to isolate a fraction enriched in DNA associated to the target protein. The abundance of nascent DNA is then assessed through BrdU immunoprecipitation followed by quantitative PCR, allowing for the parallel analysis of diverse genomic regions. While originally employed to characterize the association of cohesin to nascent sister chromatids, NSBA can be applied to study other factors dynamically associating to nascent DNA.

Strength limits in mesoscaled 3Y-TZP ceramics for micro-surgical instruments

Micro-surgical instruments are a new application for mesoscale ceramics formed using the lost mold-rapid infiltration forming (LM-RIF) process. Instrument strength and reliability are the foremost concerns for this sensitive application. It is hypothesized that increasing grain size can improve the damage tolerance of the parts associated with the transformation toughening in the 3Y-TZP material, while retaining high strength. In this work, mesoscale bend bars (314 × 22 × 18 µm) of 3Y-TZP fabricated using the LM-RIF process were heat treated at 1400 °C for 1 h, 8 h, or 16 h, respectively, to obtain samples with different grain sizes. Strength tests were performed under three-point bending and results were evaluated using Weibull statistics. Fractographic and confocal Raman spectroscopic analyses were carried out to interpret the data. Experimental findings showed that the characteristic strength decreased with increasing grain size contrary to the damage tolerance hypothesis. An Orowan-Petch model was recalled to correlate the strength with the flaw size to grain size ratio. At fine grain sizes the strength was controlled by the flaws introduced by the LM-RIF process, whereas at large grain sizes the strength become more grain size controlled. Although larger-grained samples did have a higher propensity to transform, and thus increase toughening, exaggerated grain growth in some of the specimens tested caused an additional flaw population which led to an overall lower strength. Finally, based on the experimental observations and fracture mechanics considerations, we believe that an upper bound of ∼2.5 GPa exists for the strength of mesoscale as-fabricated 3Y-TZP ceramic parts.

Cohesin dynamic association to chromatin and interfacing with replication forks in genome integrity maintenance

Proliferating cells need to accurately duplicate and pass their genetic material on to daughter cells. Problems during replication and partition challenge the structural and numerical integrity of chromosomes. Diverse mechanisms, as the DNA replication checkpoint, survey the correct progression of replication and couple it with other cell cycle events to preserve genome integrity. The structural maintenance of chromosomes (SMC) cohesin complex primarily contributes to chromosome duplication by mediating the tethering of newly replicated sister chromatids, thus assisting their equal segregation in mitosis. In addition, cohesin exerts important functions in genome organization, gene expression and DNA repair. These are determined by cohesin's ability to bring together different DNA segments and, hence, by the fashion and dynamics of its interaction with chromatin. It recently emerged that cohesin contributes to the protection of stalled replication forks through a mechanism requiring its timely mobilization from unreplicated DNA and relocation to nascent strands. This mechanism relies on DNA replication checkpoint-dependent cohesin ubiquitylation and promotes nascent sister chromatid entrapment, likely contributing to preserve stalled replisome-fork architectural integrity. Here we review how cohesin dynamic association to chromatin is controlled through post-translational modifications to dictate its functions during chromosome duplication. We also discuss recent insights on the mechanism that mediates interfacing of replisome components with chromatin-bound cohesin and its contribution to the establishment of sister chromatid cohesion and the protection of stalled replication forks.

Replisome-Cohesin Interfacing: A Molecular Perspective

Cohesion is established in S-phase through the action of key replisome factors as replication forks engage cohesin molecules. By holding sister chromatids together, cohesion critically assists both an equal segregation of the duplicated genetic material and an efficient repair of DNA breaks. Nonetheless, the molecular events leading the entrapment of nascent chromatids by cohesin during replication are only beginning to be understood. The authors describe here the essential structural features of the cohesin complex in connection to its ability to associate DNA molecules and review the current knowledge on the architectural-functional organization of the eukaryotic replisome, significantly advanced by recent biochemical and structural studies. In light of this novel insight, the authors discuss the mechanisms proposed to assist interfacing of replisomes with chromatin-bound cohesin complexes and elaborate on models for nascent chromatids entrapment by cohesin in the environment of the replication fork.

Cohesin Ubiquitylation and Mobilization Facilitate Stalled Replication Fork Dynamics

Replication fork integrity is challenged in conditions of stress and protected by the Mec1/ATR checkpoint to preserve genome stability. Still poorly understood in fork protection is the role played by the structural maintenance of chromosomes (SMC) cohesin complex. We uncovered a role for the Rsp5Bul2 ubiquitin ligase in promoting survival to replication stress by preserving stalled fork integrity. Rsp5Bul2 physically interacts with cohesin and the Mec1 kinase, thus promoting checkpoint-dependent cohesin ubiquitylation and cohesin-mediated fork protection. Ubiquitylation mediated by Rsp5Bul2 promotes cohesin mobilization from chromatin neighboring stalled forks, likely by stimulating the Cdc48/p97 ubiquitin-selective segregase, and its timely association to nascent chromatids. This Rsp5Bul2 fork protection mechanism requires the Wpl1 cohesin mobilizer as well as the function of the Eco1 acetyltransferase securing sister chromatid entrapment. Our data indicate that ubiquitylation facilitates cohesin dynamic interfacing with replication forks within a mechanism preserving stalled-fork functional architecture.

PP2A Controls Genome Integrity by Integrating Nutrient-Sensing and Metabolic Pathways with the DNA Damage Response

Mec1^ATR mediates the DNA damage response (DDR), integrating chromosomal signals and mechanical stimuli. We show that the PP2A phosphatases, ceramide-activated enzymes, couple cell metabolism with the DDR. Using genomic screens, metabolic analysis, and genetic and pharmacological studies, we found that PP2A attenuates the DDR and that three metabolic circuits influence the DDR by modulating PP2A activity. Irc21, a putative cytochrome b5 reductase that promotes the condensation reaction generating dihydroceramides (DHCs), and Ppm1, a PP2A methyltransferase, counteract the DDR by activating PP2A; conversely, the nutrient-sensing TORC1-Tap42 axis sustains DDR activation by inhibiting PP2A. Loss-of-function mutations in IRC21, PPM1, and PP2A and hyperactive tap42 alleles rescue mec1 mutants. Ceramides synergize with rapamycin, a TORC1 inhibitor, in counteracting the DDR. Hence, PP2A integrates nutrient-sensing and metabolic pathways to attenuate the Mec1^ATR response. Our observations imply that metabolic changes affect genome integrity and may help with exploiting therapeutic options and repositioning known drugs.

The Multiple Roles of Ubiquitylation in Regulating Challenged DNA Replication

DNA replication is essential for the propagation of life and the development of complex organisms. However, replication is a risky process as it can lead to mutations and chromosomal alterations. Conditions challenging DNA synthesis by replicative polymerases or DNA helix unwinding, generally termed as replication stress, can halt replication fork progression. Stalled replication forks are unstable, and mechanisms exist to protect their integrity, which promote an efficient restart of DNA synthesis and counteract fork collapse characterized by the accumulation of DNA lesions and mutagenic events. DNA replication is a highly regulated process, and several mechanisms control replication timing and integrity both during unperturbed cell cycles and in response to replication stress. Work over the last two decades has revealed that key steps of DNA replication are controlled by conjugation of the small peptide ubiquitin. While ubiquitylation was traditionally linked to protein degradation, the complexity and flexibility of the ubiquitin system in regulating protein function have recently emerged. Here we review the multiple roles exerted by ubiquitin-conjugating enzymes and ubiquitin-specific proteases, as well as readers of ubiquitin chains, in the control of eukaryotic DNA replication and replication-coupled DNA damage tolerance and repair.

Nucleolytic processing of aberrant replication intermediates by an Exo1-Dna2-Sae2 axis counteracts fork collapse-driven chromosome instability

Problems during DNA replication underlie genomic instability and drive malignant transformation. The DNA damage checkpoint stabilizes stalled replication forks thus counteracting aberrant fork transitions, DNA breaks and chromosomal rearrangements. We analyzed fork processing in checkpoint deficient cells by coupling psoralen crosslinking with replication intermediate two-dimensional gel analysis. This revealed a novel role for Exo1 nuclease in resecting reversed replication fork structures and counteracting the accumulation of aberrant intermediates resembling fork cleavage products. Genetic analyses demonstrated a functional interplay of Exo1 with Mus81, Dna2 and Sae2 nucleases in promoting cell survival following replication stress, suggestive of concerted nucleolytic processing of stalled forks. While Mus81 and other Structure Specific Endonucleases do not contribute to obvious collapsed fork transitions, Dna2 promotes reversed fork resection likely by facilitating Exo1 access to nascent strands. Instead, Sae2 cooperates with Exo1 in counteracting putative fork cleavage events linked to double strand breaks formation and increased gross chromosomal rearrangement rates. Our data indicate that in checkpoint deficient cells diverse nuclease activities interface to eliminate aberrant replication intermediates and prevent chromosome instability.

[Takotsubo cardiomyopathy in the context of Staphylococcus aureus sepsis]

Takotsubo cardiomyopathy consists of a transient dysfunction of the left ventricle. It is characterised by an impaired left ventricular segmentary contractility, without significant coronary lesions in the coronary angiography. It usually occurs after an episode of physical or emotional stress. We present the case of a 70 year-old woman, who, in the postoperative period of an ankle osteosynthesis, developed a Takotsubo cardiomyopathy in the context of a sepsis caused by Staphylococcus aureus. She presented with acute lung oedema and a clinical picture of low cardiac output. The echocardiogram showed left ventricular medioapical akinesia. Coronary angiography was normal. She was treated with supportive measures with good progress. At 33 days from onset she was able to be discharged from hospital to home with normal systolic function on echocardiography.

DNA bending facilitates the error-free DNA damage tolerance pathway and upholds genome integrity

DNA replication is sensitive to damage in the template. To bypass lesions and complete replication, cells activate recombination-mediated (error-free) and translesion synthesis-mediated (error-prone) DNA damage tolerance pathways. Crucial for error-free DNA damage tolerance is template switching, which depends on the formation and resolution of damage-bypass intermediates consisting of sister chromatid junctions. Here we show that a chromatin architectural pathway involving the high mobility group box protein Hmo1 channels replication-associated lesions into the error-free DNA damage tolerance pathway mediated by Rad5 and PCNA polyubiquitylation, while preventing mutagenic bypass and toxic recombination. In the process of template switching, Hmo1 also promotes sister chromatid junction formation predominantly during replication. Its C-terminal tail, implicated in chromatin bending, facilitates the formation of catenations/hemicatenations and mediates the roles of Hmo1 in DNA damage tolerance pathway choice and sister chromatid junction formation. Together, the results suggest that replication-associated topological changes involving the molecular DNA bender, Hmo1, set the stage for dedicated repair reactions that limit errors during replication and impact on genome stability.

The DNA damage checkpoint response to replication stress: A Game of Forks

Conditions challenging replication fork progression, collectively referred to as replication stress, represent a major source of genomic instability and are associated to cancer onset. The replication checkpoint, a specialized branch of the DNA damage checkpoint, monitors fork problems, and triggers a cellular response aimed at preserving genome integrity. Here, we review the mechanisms by which the replication checkpoint monitors and responds to replication stress, focusing on the checkpoint-mediated pathways contributing to protect replication fork integrity. We discuss how cells achieve checkpoint signaling inactivation once replication stress is overcome and how a failure to timely revert checkpoint-mediated changes in cellular physiology might impact on replication dynamics and genome integrity. We also highlight the checkpoint function as an anti-cancer barrier preventing cells malignant transformation following oncogene-induced replication stress.

Senataxin associates with replication forks to protect fork integrity across RNA-polymerase-II-transcribed genes

Transcription hinders replication fork progression and stability. The ATR checkpoint and specialized DNA helicases assist DNA synthesis across transcription units to protect genome integrity. Combining genomic and genetic approaches together with the analysis of replication intermediates, we searched for factors coordinating replication with transcription. We show that the Sen1/Senataxin DNA/RNA helicase associates with forks, promoting their progression across RNA polymerase II (RNAPII)-transcribed genes. sen1 mutants accumulate aberrant DNA structures and DNA-RNA hybrids while forks clash head-on with RNAPII transcription units. These replication defects correlate with hyperrecombination and checkpoint activation in sen1 mutants. The Sen1 function at the forks is separable from its role in RNA processing. Our data, besides unmasking a key role for Senataxin in coordinating replication with transcription, provide a framework for understanding the pathological mechanisms caused by Senataxin deficiencies and leading to the severe neurodegenerative diseases ataxia with oculomotor apraxia type 2 and amyotrophic lateral sclerosis 4.

Cnn1 inhibits the interactions between the KMN complexes of the yeast kinetochore

Kinetochores attach the replicated chromosomes to the mitotic spindle and orchestrate their transmission to the daughter cells. Kinetochore-spindle binding and chromosome segregation are mediated by the multi-copy KNL1(Spc105), MIS12(Mtw1) and NDC80(Ndc80) complexes that form the so-called KMN network. KMN-spindle attachment is regulated by the Aurora B(Ipl1) and MPS1(Mps1) kinases. It is unclear whether other mechanisms exist that support KMN activity during the cell cycle. Using budding yeast, we show that kinetochore protein Cnn1 localizes to the base of the Ndc80 complex and promotes a functionally competent configuration of the KMN network. Cnn1 regulates KMN activity in a spatiotemporal manner by inhibiting the interaction between its complexes. Cnn1 activity peaks in anaphase and is driven by the Cdc28, Mps1 and Ipl1 kinases.

The replication checkpoint protects fork stability by releasing transcribed genes from nuclear pores

Transcription hinders replication fork progression and stability, and the Mec1/ATR checkpoint protects fork integrity. Examining checkpoint-dependent mechanisms controlling fork stability, we find that fork reversal and dormant origin firing due to checkpoint defects are rescued in checkpoint mutants lacking THO, TREX-2, or inner-basket nucleoporins. Gene gating tethers transcribed genes to the nuclear periphery and is counteracted by checkpoint kinases through phosphorylation of nucleoporins such as Mlp1. Checkpoint mutants fail to detach transcribed genes from nuclear pores, thus generating topological impediments for incoming forks. Releasing this topological complexity by introducing a double-strand break between a fork and a transcribed unit prevents fork collapse. Mlp1 mutants mimicking constitutive checkpoint-dependent phosphorylation also alleviate checkpoint defects. We propose that the checkpoint assists fork progression and stability at transcribed genes by phosphorylating key nucleoporins and counteracting gene gating, thus neutralizing the topological tension generated at nuclear pore gated genes.

Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles

THO/TREX is a conserved nuclear complex that functions in mRNP biogenesis and prevents transcription-associated recombination. Whether or not it has a ubiquitous role in the genome is unknown. Chromatin immunoprecipitation (ChIP)-chip studies reveal that the Hpr1 component of THO and the Sub2 RNA-dependent ATPase have genome-wide distributions at active ORFs in yeast. In contrast to RNA polymerase II, evenly distributed from promoter to termination regions, THO and Sub2 are absent at promoters and distributed in a gradual 5' → 3' gradient. This is accompanied by a genome-wide impact of THO-Sub2 deletions on expression of highly expressed, long and high G+C-content genes. Importantly, ChIP-chips reveal an over-recruitment of Rrm3 in active genes in THO mutants that is reduced by RNaseH1 overexpression. Our work establishes a genome-wide function for THO-Sub2 in transcription elongation and mRNP biogenesis that function to prevent the accumulation of transcription-mediated replication obstacles, including R-loops.

Whisking in air: encoding of kinematics by VPM neurons in awake rats

Rodent whisking behavior generates two types of neural signals: one produced by whisker contact with objects; the other by movements in air. While kinematic signals generated by contact reliably activate neurons at all levels of the trigeminal neuraxis, the extent to which the kinematics of whisking in air are reliably encoded at each level remains unclear. Previously, we showed that the responses of trigeminal ganglion (TG) neurons in awake, head-fixed rats are correlated with whisking kinematic parameters, but that individual neurons may differ substantially in the reliability of their kinematic encoding. Here, we extend that analysis to neurons in the ventral posterior medial (VPM) nucleus. Three possible coding strategies were examined: (1) firing rate across an entire movement; (2) the probability of individual spikes as a function of the instantaneous movement trajectory; and (3) the coherence between spikes and whisking. While VPM neurons were clearly responsive to variations in whisker kinematics during whisking in air, the encoding of whisker kinematics by VPM neurons was less consistent than that of TG neurons. Furthermore, we found that, in VPM as in TG, movement direction is an important determinant of unit responsiveness during whisking in air.

Replication termination at eukaryotic chromosomes is mediated by Top2 and occurs at genomic loci containing pausing elements

Chromosome replication initiates at multiple replicons and terminates when forks converge. In E. coli, the Tus-TER complex mediates polar fork converging at the terminator region, and aberrant termination events challenge chromosome integrity and segregation. Since in eukaryotes, termination is less characterized, we used budding yeast to identify the factors assisting fork fusion at replicating chromosomes. Using genomic and mechanistic studies, we have identified and characterized 71 chromosomal termination regions (TERs). TERs contain fork pausing elements that influence fork progression and merging. The Rrm3 DNA helicase assists fork progression across TERs, counteracting the accumulation of X-shaped structures. The Top2 DNA topoisomerase associates at TERs in S phase, and G2/M facilitates fork fusion and prevents DNA breaks and genome rearrangements at TERs. We propose that in eukaryotes, replication fork barriers, Rrm3, and Top2 coordinate replication fork progression and fusion at TERs, thus counteracting abnormal genomic transitions.

One whisker whisking: unit recording during conditioned whisking in rats

Understanding of the functional neurobiology of the rodent whisker system would be advanced by neurobehavioral studies in awake, behaving animals that combine unit recording from structures at various levels of the system with quantitative characterization of the kinematics and temporal organization of whisking. Such studies require the solution of a number of methodological problems. These include: chronic recording procedures ensuring unit isolation, stability and maximum yield, monitoring and display of unit activity and whisker movements within the same (ms) timeframe and behavioral paradigms which bring whisking movement parameters under the control of the experimenter rather than the rat. Here we describe a head-fixed rodent preparation which makes possible chronic recording of unit activity in the awake, whisking rat, combined with real-time, high resolution monitoring of whisker and pad movements in two dimensions and under behavioral control. While the head-fixed "whisking" preparation has some inherent limitations, it may be used to address a number of important neurobehavioral problems. We suggest that it should contribute significantly to understanding the functional neurobiology of the whisker system.

Topography of whisking II: Interaction of whisker and pad

The peripheral effector system mediating rodent whisking produces protraction/retraction movements of the whiskers and translation movements of the collagenous mystacial pad. To examine the interaction of these movements during whisking in air we used high-resolution, optoelectronic methods for two-dimensional monitoring of whisker and pad movements in head-fixed rats. Under these testing conditions (1) whisker movements on the same side of the face are synchronous and of similar amplitude; (2) pad movements exhibit the characteristic 'exploratory' rhythm (6-12 Hz) of whisking but their movements often have a low frequency (1-2 Hz) component; (3) Pad movements occur in both antero-posterior and dorso-ventral planes but there are considerable variations in the amplitude and topography of movement parameters in the two planes. We conclude that (a) both whisker and pad receive input from a common central rhythm generator; (b) differences in whisker and pad amplitude and topography probably reflect differences in the biomechanical properties of the structures receiving that input; (c) pad movements make a significant contribution to the kinematics of whisking behavior and (d) the two-dimensional nature of pad translation movements significantly increases the rat's flexible control of its mobile sensor.

Use of contraceptive methods and risk of unwanted pregnancy in Spanish women aged 40–50 years: results of a survey conducted in Spain

A survey intended to ascertain the rate of use and type of contraceptive methods applied by Spanish women aged 40 to 50 years, and to determine the proportion of women in this group at risk of an unwanted pregnancy, was designed and validated. To achieve representative national results for the study population, it was estimated that a sample size of 2000 women was required. Women were selected using probabilistic, stratified random sampling. The survey questionnaire was prepared by the research group with the collaboration of experts in the conduct of population studies of this type. Participants were interviewed face to face by qualified and trained staff from a specialised company external to the research group. Overall, 1039 women (52%) resorted to some contraceptive method, of which (male or female) sterilisation was the most common. We estimate that in Spain there are 840,000 women (31.8%) aged 40 to 50 years at risk of unwanted pregnancy.

Ambient air levels of volatile organic compounds (VOC) and nitrogen dioxide (NO2) in a medium size city in Northern Spain

Ambient concentrations of volatile organic compounds (VOC) and nitrogen dioxide (NO2) were measured by means of passive sampling at 40 sampling points in a medium-size city in Northern Spain, from June 2006 to June 2007. VOC and NO2 samplers were analysed by thermal desorption followed by gas chromatography/mass-selective detector and by visible spectrophotometry, respectively. Mean concentrations of benzene, toluene, ethylbenzene, xylenes, propylbenzene, trimethylbenzenes, and NO(2) were 2.84, 13.26, 2.15, 6.01, 0.59, 1.32 and 23.17 microg m(-3) respectively, and found to be highly correlated. Their spatial distribution showed high differences in small distances and pointed to traffic as the main emission source of these compounds. The lowest levels of VOC and NO2 occurred during summer, owing to the increase in solar radiation and to lower traffic densities. Mean concentrations of benzene and NO2 exceeded the European limits at some of the monitored points.

ChIP-on-chip analysis of DNA topoisomerases

Here we describe an adapted ChIP-on-chip protocol for the analysis of DNA topoisomerase chromosomal binding in Saccharomyces cerevisiae cells. The ChIP-on-chip technique is based on the immunoprecipitation of crosslinked chromatin (ChIP, chromatin immunoprecipitation), followed by DNA amplification and hybridization to high-density oligonucleotide arrays (Chip). Comparison of the signal intensities of immunoprecipitated and control fractions provides a measurement of the protein-DNA association along entire genomes. ChIP-on-chip analysis of DNA topoisomerase binding to chromosomal DNA opens a window to the understanding of the in vivo contribution of these enzymes to the different DNA transactions taking place concomitantly within the context of the highly organized eukaryotic genome. Chromosomal binding profiles obtained from synchronized cells allow scoring the temporal and spatial restriction of these enzymes at different cell cycle stages. By using this approach, novel aspects of DNA topoisomerase function in chromosome metabolism might be unmasked.

Whisking in air: encoding of kinematics by trigeminal ganglion neurons in awake rats

Active sensing requires the brain to distinguish signals produced by external inputs from those generated by the animal's own movements. Because the rodent whisker musculature lacks proprioceptors, we asked whether trigeminal ganglion neurons encode the kinematics of the rat's own whisker movements in air. By examining the role of kinematics, we have extended previous findings showing that many neurons that respond during such movements do not do so consistently. Nevertheless, the majority ( approximately 70%) of trigeminal ganglion neurons display significant correlations between firing rate and a kinematic parameter, and a subset, approximately 30%, represent kinematics with high reliability. Preferential firing to movement direction was observed but was strongly modulated by movement amplitude and speed. However, in contrast to the precise time-locking that occurs in response to active whisker contacts, whisker movements in air generate temporally dispersed responses that are not time-locked to the onset of either protractions or retractions.

Cohesion by topology: sister chromatids interlocked by DNA

Sister chromatid cohesion is coupled with chromosome replication and influences chromosome segregation and intra-S repair. Specialized proteins, the cohesins, together with other pathways contribute to tether sister chromatids. In this issue of Genes & Development, Wang and colleagues (pp. 2426-2433 demonstrate that TopoIV, a type II DNA topoisomerase, modulates cohesion in Escherichia coli, by removing interlocked DNA junctions between sister chromatids. They propose that DNA precatenanes, arising during replication fork progression, hold sister chromatids together.

Exposure to volatile organic compounds (VOC) in public buses of Pamplona, Northern Spain

This study examines the exposure level of passengers and drivers to VOC in public buses in a medium-size metropolitan area (Northern Spain). In-vehicle monitoring was performed on different routes, on peak and non-peak hours, during January and February 2007. A total of 112 air samples were collected onto adsorbent tubes and analysed by thermal desorption (TD) and gas chromatography/mass selective detector (GC/MSD) technique. Statistical differences were found among route to route concentrations, with those routes with major prevalence in the commercial area of the city displaying higher values; differences between peak and non-peak hours were also observed. A decrease in VOC concentrations was also registered during the weekend. BTEX ratios were estimated and found to be related to traffic emissions and similar for all the surveyed routes. Correlations confirmed traffic as the main emission source for BTEX and trimethylbenzene, their concentrations being highly associated to changes in meteorological conditions.

Top1- and Top2-mediated topological transitions at replication forks ensure fork progression and stability and prevent DNA damage checkpoint activation

DNA topoisomerases solve topological problems during chromosome metabolism. We investigated where and when Top1 and Top2 are recruited on replicating chromosomes and how their inactivation affects fork integrity and DNA damage checkpoint activation. We show that, in the context of replicating chromatin, Top1 and Top2 act within a 600-base-pair (bp) region spanning the moving forks. Top2 exhibits additional S-phase clusters at specific intergenic loci, mostly containing promoters. TOP1 ablation does not affect fork progression and stability and does not cause activation of the Rad53 checkpoint kinase. top2 mutants accumulate sister chromatid junctions in S phase without affecting fork progression and activate Rad53 at the M-G1 transition. top1 top2 double mutants exhibit fork block and processing and phosphorylation of Rad53 and gamma H2A in S phase. The exonuclease Exo1 influences fork processing and DNA damage checkpoint activation in top1 top2 mutants. Our data are consistent with a coordinated action of Top1 and Top2 in counteracting the accumulation of torsional stress and sister chromatid entanglement at replication forks, thus preventing the diffusion of topological changes along large chromosomal regions. A failure in resolving fork-related topological constrains during S phase may therefore result in abnormal chromosome transitions, DNA damage checkpoint activation, and chromosome breakage during segregation.

Contraceptive practices and trends in Spain: 1997-2003

OBJECTIVE

To know the contraceptive use and trends in the Spanish female population.

STUDY DESIGN

Since 1997, we have conducted a survey every 2 years on the use of contraceptive methods among a representative sample of Spanish women of childbearing potential (15-49 years).

RESULTS

In the period 1997-2003, the percentage of use of contraceptive methods in Spain rose from 55.6% to 71.2%. The most commonly used method was the condom (21% in 1997, 21.9% in 1999, 29.5% in 2001 and 35.7% in 2003), followed by the contraceptive pill (14.2%, 16.5%, 19.2% and 18.3%, respectively). Male or female sterilization remained stable with percentages of use of 5-7%. IUDs are used by about 5% of women.

CONCLUSIONS

The use of contraceptive methods among Spanish women of childbearing potential generally fits quite well the patterns found in other developed countries, and we observed a trend towards increased use of effective methods.

Contraception in the Spanish press: an analysis of the 1997-2002 period

OBJECTIVE

Based on the hypothesis that the media represent an important source of information about contraceptive methods and sexuality, this paper reviews the news items about contraception published by four important Spanish newspapers and four women's magazines.

MATERIALS AND METHODS

All news items appearing from January 1, 1997 to December 31, 2002 in the following publications: El País, El Mundo, ABC, La Vanguardia, Mía, Clara, Ragazza, and Epoca were collected during the first 6 months of 2003. Results Seven hundred and ten news items about contraception were identified during the period analysed, of which 117 (16.5%) had a negative character.

CONCLUSIONS

Over 80% of news items appearing in the Spanish press in the 1997-2002 period give a positive information about contraceptive methods.

Spatial and temporal trends of volatile organic compounds (VOC) in a rural area of northern Spain

Ambient concentrations of volatile organic compounds (VOCs) were measured at 40 rural sampling points in Navarre (northern Spain). Air samples were collected by means of sorbent passive sampling and analyzed by thermal desorption (TD) and gas chromatography/mass-selective detector (GC/MSD). A total of 140 VOCs were identified during the study, which was carried out between May to October 2004 for a total of a 10 biweekly sampling campaigns. Concentrations of benzene, toluene, ethylbenzene, m/p-xylenes, o-xylene (BTEX) and 1,3,5-trimethylbenzene were determined in order to investigate their temporal and spatial distributions. Geostatistical analysis pointed to traffic as the main emission source of these compounds. Supporting this idea, BTEX and nitrogen oxides concentrations were found to be highly significantly correlated (r = 0.495, P = 0.001), whereas a strong negative correlation between BTEX and ozone was also observed (r = -0.355, P = 0.025). The concentrations for the BTEX group were similar to the values that have been previously reported for other rural areas.

A novel E2 box-GATA element modulates Cdc6 transcription during human cells polyploidization

Cdc6 is a key regulator of the strict alternation of S and M phases during the mitotic cell cycle. In mammalian and plant cells that physiologically become polyploid, cdc6 is transcriptionally and post-translationally regulated. We have recently reported that Cdc6 levels are maintained in megakaryoblastic HEL cells, but severely downregulated by ectopic expression of transcriptional repressor Drosophila melanogaster escargot. Here, we show that cdc6 promoter activity is upregulated during megakaryocytic differentiation of HEL endoreplicating cells, and that Escargot interferes with such activation. Transactivation experiments showed that a 1.7 kb region located at 2800 upstream cdc6 transcription initiation site behaved as a potent enhancer in endoreplicating cells only. This activity was mainly dependent on a novel cis-regulatory element composed by an E2 box overlapping a GATA motif. Ectopic Escargot could bind this regulatory element in vitro and endogenous GATA-1 and E2A formed specific complexes in megakaryoblastic cells as well as in primary megakaryocytes. Chromatin Immunoprecipitation analysis revealed that both transcription factors were occupying the E2 box/GATA site in vivo. Altogether, these data suggest that cdc6 expression could be actively maintained during megakaryocytic differentiation through transcriptional mechanisms involving specific cis- and trans-regulatory elements.