Optical fiber immunosensors based on surface plasmon resonance for the detection of Escherichia coli.

Every year, millions of people suffer some form of illness associated with the consumption of contaminated food. Escherichia coli (E. coli), found in the intestines of humans and other animals, is commonly associated with various diseases, due to the existence of pathogenic strains. Strict monitoring of food products for human consumption is essential to ensure public health, but traditional cell culture-based methods are associated with long waiting times and high costs. New approaches must be developed to achieve cheap, fast, and on-site monitoring. Thus, in this work, we developed optical fiber sensors based on surface plasmon resonance. Gold and cysteamine-coated fibers were functionalized with anti-E. coli antibody and tested using E. coli suspensions with concentrations ranging from 1 cell/mL to 105 cells/mL. An average logarithmic sensitivity of 0.21 ± 0.01 nm/log(cells/mL) was obtained for three independent assays. An additional assay revealed that including molybdenum disulfide resulted in an increase of approximately 50% in sensitivity. Specificity and selectivity were also evaluated, and the sensors were used to analyze contaminated water samples, which verified their promising applicability in the aquaculture field.

Proteomic analysis reveals stage-specific reprogramed metabolism for the primary breast cancer cell lines MGSO-3 and MACL-1.

Breast cancer is the most prevalent cancer in women worldwide. Its molecular subtypes are based on the presence/absence of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). MACL-1 and MGSO-3 are cell lines derived from primary tumor sites of patients diagnosed with luminal A subtype carcinoma (ER+/PR+/HER2-) and ductal carcinoma in situ (ER-/PR-/HER2+), respectively. However, these cell lines lost the expression of these markers over cell culturing, and both have triple-negative phenotypes (ER-/PR-/HER2-), which has the poorest prognosis. Here, we sought to study the proteome signature of MGSO-3 and MACL-1, comparing them with the epithelial cell line MCF-10A and the well-established metastatic-derived breast cancer cell line MDA-MB-231. Our results showed that proteins associated with the tricarboxylic acid cycle (TCA) and oxidative phosphorylation (OXPHOS) were upregulated in MGSO-3 and MACL-1 cells. These cell lines also showed upregulation of pro-apoptotic proteins when compared with MDA-MB-231. The molecular differences highlighted in this study may clarify the molecular basis behind cancer cells functioning and may reveal novel signatures across the breast cancer cell models.

A 3D printable adapter for solid-state fluorescence measurements: the case of an immobilized enzymatic bioreceptor for organophosphate pesticides detection.

The widespread use of pesticides in the last decades and their accumulation into the environment gave rise to major environmental and human health concerns. To address this topic, the scientific community pointed out the need to develop methodologies to detect and measure the presence of pesticides in different matrices. Biosensors have been recently explored as fast, easy, and sensitive methods for direct organophosphate pesticides monitoring. Thus, the present work aimed at designing and testing a 3D printed adapter useful on different equipment, and a membrane support to immobilize the esterase-2 from Alicyclobacillus acidocaldarius (EST2) bioreceptor. The latter is labelled with the IAEDANS, a bright fluorescent probe. EST2 was selected since it shows a high specificity toward paraoxon. Our results showed good stability and replicability, with an increasing linear fluorescent intensity recorded from 15 to 150 pmol of labelled EST2. Linearity of data was also observed when using the immobilized labelled EST2 to detect increasing amounts of paraoxon, with a limit of detection (LOD) of 0.09 pmol. This LOD value reveals the high sensitivity of our membrane support when mounted on the 3D adapter, comparable to modern methods using robotic workstations. Notably, the use of an independent support significantly simplified the manipulation of the membrane during experimental procedures and enabled it to match the specificities of different systems. In sum, this work emphasizes the advantages of using 3D printed accessories adapted to respond to the newest research needs.

A FRET Approach to Detect Paraoxon among Organophosphate Pesticides Using a Fluorescent Biosensor.

The development of faster, sensitive and real-time methods for detecting organophosphate (OP) pesticides is of utmost priority in the in situ monitoring of these widespread compounds. Research on enzyme-based biosensors is increasing, and a promising candidate as a bioreceptor is the thermostable enzyme esterase-2 from Alicyclobacillus acidocaldarius (EST2), with a lipase-like Ser-His-Asp catalytic triad with a high affinity for OPs. This study aimed to evaluate the applicability of Förster resonance energy transfer (FRET) as a sensitive and reliable method to quantify OPs at environmentally relevant concentrations. For this purpose, the previously developed IAEDANS-labelled EST2-S35C mutant was used, in which tryptophan and IAEDANS fluorophores are the donor and the acceptor, respectively. Fluorometric measurements showed linearity with increased EST2-S35C concentrations. No significant interference was observed in the FRET measurements due to changes in the pH of the medium or the addition of other organic components (glucose, ascorbic acid or yeast extract). Fluorescence quenching due to the presence of paraoxon was observed at concentrations as low as 2 nM, which are considered harmful for the ecosystem. These results pave the way for further experiments encompassing more complex matrices.

Photodynamic Inactivation of Microorganisms Using Semisynthetic Chlorophyll a Derivatives as Photosensitizers.

In this study, we describe the semisynthesis of cost-effective photosensitizers (PSs) derived from chlorophyll a containing different substituents and using previously described methods from the literature. We compared their structures when used in photodynamic inactivation (PDI) against Staphylococcus aureus, Escherichia coli, and Candida albicans under different conditions. The PSs containing carboxylic acids and butyl groups were highly effective against S. aureus and C. albicans following our PDI protocol. Overall, our results indicate that these nature-inspired PSs are a promising alternative to selectively inactivate microorganisms using PDI.

Comparing Two- and Three-dimensional Antral Follicle Count in Patients with Endometriosis.

Background: The purpose of the study was to compare three-dimensional (3D) ultrasound semiautomatic antral follicle count (AFC) with two-dimensional (2D) ultrasound real-time AFC to evaluate patients with deep endometriosis and/or endometrioma submitted to ovarian stimulation (OS). Methods: This was a retrospective cohort study assessing all women with documented diagnosis of deep endometriosis who underwent OS for assisted reproduction treatment. The primary outcome was the difference between AFC by semiautomatic 3D follicle count using 3D volume datasets and 2D ultrasound count with the number of oocytes retrieved at the end of the cycle. The 3D ultrasound AFC was obtained using sonography-based automated volume count (SonoAVC), and the 2D ultrasound AFC data was collected from the electronic medical record. Results: Total of 36 women had deep endometriosis documented by magnetic resonance imaging, laparoscopy, or ultrasonography and 3D ovarian volume datasets stored from their first exam. The differences between the 2D and 3D AFC and the number of oocytes retrieved at the end of the stimulation were compared, showing no significant statistical difference between both methods (P = 0.59). Correlations were similar using both methods when compared to the number of oocytes retrieved (2D [r = 0.83, confidence interval (CI) = 0.68-0.9, P < 0.001]); (3D [r = 0.81, CI = 0.46-0.83, P < 0.001]). Conclusion: 3D semiautomatic AFC can be used to access the ovarian reserve in patients with endometriosis.

Comprehensive analysis of the isomiRome in the vegetative organs of the conifer Pinus pinaster under contrasting water availability.

An increasing number of microRNAs (miRNAs) and miRNA-related sequences produced during miRNA biogenesis, comprising the isomiRome, have been recently highlighted in different species as critical mediators of environmental stress responses. Conifers have some of the largest known genomes but an extensive characterization of the isomiRome from any conifer species has been lacking. We provide here a comprehensive overview of the Pinus pinaster isomiRome expressed in roots, stem and needles under well-watered and drought conditions. From the 13,441 unique small RNA sequences identified, 2,980 were annotated as canonical miRNAs or miRNA* and the remaining were classified as isomiRNA or miRNA-like sequences. A survey of their expression patterns highlighted roots as the most responsive organ under drought, where specific sequences of which a 24-nt novel miRNA stood out, were strongly down-regulated. Given the putative roles of the miRNA-targeted transcripts validated specifically in root tissues, some of the miRNAs, conserved and novel, are shortlisted as potential regulators of drought response. These results provide a valuable resource for comparative studies between gymnosperms and angiosperms. Furthermore, it evidences high transferability of the isomiRome between pine species being a useful basis for further molecular regulation and physiological studies, and especially those focused on adaptation to drought conditions.

Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos.

BACKGROUND: There are clear differences in embryo development between angiosperm and gymnosperm species. Most of the current knowledge on gene expression and regulation during plant embryo development has derived from studies on angiosperms species, in particular from the model plant Arabidopsis thaliana. The few published studies on transcript profiling of conifer embryogenesis show the existence of many putative embryo-specific transcripts without an assigned function. In order to extend the knowledge on the transcriptomic expression during conifer embryogenesis, we sequenced the transcriptome of zygotic embryos for several developmental stages that cover most of Pinus pinaster (maritime pine) embryogenesis. RESULTS: Total RNA samples collected from five zygotic embryo developmental stages were sequenced with Illumina technology. A de novo transcriptome was assembled as no genome sequence is yet published for Pinus pinaster. The transcriptome of reference for the period of zygotic embryogenesis in maritime pine contains 67,429 transcripts, which likely encode 58,527 proteins. The annotation shows a significant percentage, 31%, of predicted proteins exclusively present in pine embryogenesis. Functional categories and enrichment analysis of the differentially expressed transcripts evidenced carbohydrate transport and metabolism over-representation in early embryo stages, as highlighted by the identification of many putative glycoside hydrolases, possibly associated with cell wall modification, and carbohydrate transport transcripts. Moreover, the predominance of chromatin remodelling events was detected in early to middle embryogenesis, associated with an active synthesis of histones and their post-translational modifiers related to increased transcription, as well as silencing of transposons. CONCLUSIONS: Our results extend the understanding of gene expression and regulation during zygotic embryogenesis in conifers and are a valuable resource to support further improvements in somatic embryogenesis for vegetative propagation of conifer species. Specific transcripts associated with carbohydrate metabolism, monosaccharide transport and epigenetic regulation seem to play an important role in pine early embryogenesis and may be a source of reliable molecular markers for early embryogenesis.

Invasive Species Mediate Insecticide Effects on Community and Ecosystem Functioning.

Anthropogenic activities increase pesticide contamination and biological invasions in freshwater ecosystems. Understanding their combined effects on community structure and on ecosystem functioning presents challenges for an improved ecological risk assessment. This study focuses on an artificial stream mesocosms experiment testing for direct and indirect effects of insecticide (chlorantraniliprole - CAP) exposure on the structure of a benthic macroinvertebrate freshwater community and on ecosystem functioning (leaf decomposition, primary production). To understand how predator identity and resource quality alter the community responses to chemical stress, the mediating effects of an invasive predator species (crayfish Procambarus clarkii) and detritus quality (tested by using leaves of the invasive Eucalyptus globulus) on insecticide toxicity were also investigated. Low concentrations of CAP reduced the abundance of shredders and grazers, decreasing leaf decomposition and increasing primary production. Replacement of autochthonous predators and leaf litter by invasive species decreased macroinvertebrate survival, reduced leaf decomposition, and enhanced primary production. Structural equation modeling (SEM) highlighted that CAP toxicity to macroinvertebrates was mediated by the presence of crayfish or eucalypt leaf litter which are now common in many Mediterranean freshwaters. In summary, our results demonstrate that the presence of these two invasive species alters the effects of insecticide exposure on benthic freshwater communities. The approach used here also allowed for a mechanistic evaluation of indirect effects of these stressors and of their interaction on ecosystem functional endpoint, emphasizing the value of incorporating biotic stressors in ecotoxicological experiments.

Combined effects of insecticide exposure and predation risk on freshwater detritivores.

Insecticides usually present in low concentrations in streams are known to impair behaviour and development of non-target freshwater invertebrates. Moreover, there is growing awareness that the presence of natural stressors, such as predation risk may magnify the negative effects of pesticides. This is because perception of predation risk can by itself lead to changes on behaviour and physiology of prey species. To evaluate the potential combined effects of both stressors on freshwater detritivores we studied the behavioural and developmental responses of Chironomus riparius to chlorantraniliprole (CAP) exposure under predation risk. Also, we tested whether the presence of a shredder species would alter collector responses under stress. Trials were conducted using a simplified trophic chain: Alnus glutinosa leaves as food resource, the shredder Sericostoma vittatum and the collector C. riparius. CAP toxicity was thus tested under two conditions, presence/absence of the dragonfly predator Cordulegaster boltonii. CAP exposure decreased leaf decomposition. Despite the lack of significance for interactive effects, predation risk marginally modified shredder effect on leaf decomposition, decreasing this ecosystem process. Shredders presence increased leaf decomposition, but impaired chironomids performance, suggesting interspecific competition rather than facilitation. C. riparius growth rate was decreased independently by CAP exposure, presence of predator and shredder species. A marginal interaction between CAP and predation risk was observed regarding chironomids development. To better understand the effects of chemical pollution to natural freshwater populations, natural stressors and species interactions must be taken into consideration, since both vertical and horizontal species interactions play their role on response to stress.

The pivotal role of small non-coding RNAs in the regulation of seed development.

Seeds represent a crucial stage of the seed plants life cycle. It is during seed development that the foundations of the future plant body, and the ability to give rise to a new plant capable of growing under sometimes adverse environmental conditions, are established. Small non-coding RNAs are major regulators of gene expression both at the post-transcriptional and transcriptional levels and, not surprisingly, these elements play major roles in seed development and germination. We review here the current knowledge about small RNA expression and functions in seed development, going from the morphogenesis phase comprehending embryo development and patterning, to the several steps of the maturation phase, ending in the transition to the germination. A special focus is given to the small RNAs for which functional studies have been conducted and their participation in regulatory networks operating in seeds. Many challenges remain ahead for dissecting the complex small RNA landscape in seeds, but this is a highly relevant issue in plant biology and advances in this area will most certainly impact plant breeding.

Assessment of thiamethoxam toxicity to Chironomus riparius.

The insecticide thiamethoxam (TMX) is a systemic neonicotinoid widely used for pest control in several agricultural crops. TMX mimics the action of acetylcholine causing uncontrolled muscular contraction eventually leading to insect death. TMX is being found in freshwater ecosystems at concentrations of up to 225µg/L. Still, chronic toxicity data for freshwater invertebrates is limited. Therefore, the aim of this study was to evaluate the acute and chronic effects (at organismal and biochemical levels) of TMX on the freshwater insect Chironomus riparius. C. riparius life history responses were significantly affected by TMX exposure, namely with a decrease in growth and delay in emergence. Concerning the biochemical responses, after a short exposure (48h) to TMX, our results showed that low concentrations of TMX significantly reduced CAT activity and LPO levels of C. riparius. No effects were observed in AChE, GST and ETS activities. Effects in terms of survival, development rates and biochemical responses of C. riparius exposed to low concentrations of TMX observed in this study suggest potential deleterious effects of this neonicotinoid on aquatic insects inhabiting freshwaters environments near agricultural areas.

Assessment of DDT and Metabolites in Soil and Sediment of Potentially Contaminated Areas of Belém, Amazon Region, Brazil.

The aim of this study was to evaluate the distribution of DDT and metabolites in surface soils and soil profiles from two areas containing deposits of obsolete pesticides in Belém, Amazon Region, Brazil. DDT and metabolites were extracted by microwave assisted extraction and analyzed by gas chromatography with electron capture detection. Concentrations of total DDT in surface soil samples ranged from 64.22 mg kg-1 in area 1 (A1) to 447.84 mg kg-1 in area 2 (A2). Lower levels were found in soil profiles than at the surface (6.21-21.17 mg kg-1 in A1 and 36.13-113.66 mg kg-1 in A2). pp'-DDT, pp'-DDE and pp'-DDD were detected in sediments at levels of 2.01, 0.96 and 0.35 mg kg-1, respectively. The ratio (DDE + DDD)/ΣDDT was low indicating the recent introduction of DDT to the environment in the two study areas, through the volatilization and atmospheric deposition of the obsolete pesticides.

Assessment of discomfort in patients with cognitive failure in palliative care.

OBJECTIVE: When cognitive impairment precludes patients' report of symptoms, it becomes necessary to use other means. The purpose of our study was to evaluate the validity of the method currently in use on our service. METHOD: Two members of the team simultaneously assessed the patient and independently recorded whether the patient showed signs of discomfort, and a third questioned patients with cognitive failure who maintained some ability to respond if something was bothering them. RESULTS: Some 200 assessments were made of 116 patients. The kappa coefficient of agreement was 0.615. The sensitivity was 17% and specificity 99%. The positive predictive value was 88%, and the negative predictive value was 73%. SIGNIFICANCE OF RESULTS: Due to the low sensitivity of this method, it cannot be recommended as a screening tool.

Use of gray values in CBCT and MSCT images for determination of density: influence of variation of FOV size.

PURPOSE: To determine the effect of field of view (FOV) size on gray values in cone beam computed tomography (CBCT) and multislice computed tomography (MSCT) images. MATERIAL AND METHODS: A phantom made up of 3 cylinders containing distilled water, plaster, and motor oil was constructed and inserted into an acrylic cylinder filled with distilled water. The phantom was scanned with a CBCT and MSCT device using 3 FOV sizes. Gray value of each material was evaluated in 40 axial slices, and the comparison between the results obtained with the same FOV size was made. RESULTS: In CBCT examinations, there was significant difference between the gray values of different FOVs for the 3 materials. In the MSCT, there was significant difference for the oil. Gray values showed significant difference between the CBCT and MSCT examinations for the 3 materials in the 3 different FOV sizes. CONCLUSIONS: Gray values determined in CBCT images are significantly influenced by the FOV size. Although the gray values obtained in MSCT have shown statistically significant differences between some acquisitions, the analysis of those differences seems to indicate low clinical relevance.

De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology.

Maritime pine (Pinus pinasterAit.) is a widely distributed conifer species in Southwestern Europe and one of the most advanced models for conifer research. In the current work, comprehensive characterization of the maritime pine transcriptome was performed using a combination of two different next-generation sequencing platforms, 454 and Illumina. De novo assembly of the transcriptome provided a catalogue of 26 020 unique transcripts in maritime pine trees and a collection of 9641 full-length cDNAs. Quality of the transcriptome assembly was validated by RT-PCR amplification of selected transcripts for structural and regulatory genes. Transcription factors and enzyme-encoding transcripts were annotated. Furthermore, the available sequencing data permitted the identification of polymorphisms and the establishment of robust single nucleotide polymorphism (SNP) and simple-sequence repeat (SSR) databases for genotyping applications and integration of translational genomics in maritime pine breeding programmes. All our data are freely available at SustainpineDB, the P. pinaster expressional database. Results reported here on the maritime pine transcriptome represent a valuable resource for future basic and applied studies on this ecological and economically important pine species.

The Effectiveness of Schema Therapy in Individuals Who Committed Crimes: A Systematic Review.

Research suggests that individuals who commit crimes often exhibit various early maladaptive schemas (EMSs). EMSs are a broad and pervasive theme or pattern consisting of memories, emotions, cognitions, and bodily sensations concerning oneself and one's relationships with others. Furthermore, EMSs play a crucial role in the onset and maintenance of different types of offending behaviors, highlighting the need to implement schema therapy (ST) for perpetrators. Therefore, the present systematic review assesses the effectiveness of ST for individuals who committed crimes. Four databases (PubMed, Scopus, Web of Science, and Scielo) were searched for studies examining the effectiveness of ST for individuals who committed crimes. Seventeen studies were identified, but only 15 met the criteria for inclusion. Results showed that ST can lead to beneficial effects in EMSs, schema modes, personality symptoms, and risk factors to commit crimes (e.g., cognitive distortions). However, the studies, besides being scarce, revealed some methodological limitations. ST is a promising therapy for individuals who committed crimes, despite the studies' methodological shortcomings, which prevent us from drawing more firm conclusions. Although promising, more research is needed to enhance our understanding of the impact of ST therapies in forensic settings.

Intervention Program Dropout Among Perpetrators of Intimate Partner Violence: A Meta-Analysis of Correlated Variables.

Dropout in perpetrator intervention programs (PIPs) is extensively documented in the literature, yet findings across various studies exhibit global inconsistency. This meta-analysis aimed to identify dropout rates among individuals attending PIPs and examine sociodemographic, violence-related, intrapersonal, interpersonal, and external variables related to dropout. A search was conducted across six databases, encompassing studies published between 2010 and 2022 in English, Spanish, or Portuguese. Thirty manuscripts, comprising data from 31 independent samples, were included. Dropout rates varied from 9% to 67%. Bivariate analysis results indicated that younger age (OR = 0.69), non-White ethnicity (OR = 1.54), unemployment (OR = 1.78), offender typology other than family only (OR = 2.45), substance abuse (OR = 1.78), presenting a personality disorder (OR = 1.21), engaging in problematic leisure activities (OR = 1.28), possessing a greater criminal history (OR = 1.47), and experiencing more adversity in childhood (OR = 1.44) were significantly correlated with dropout. Additionally, the inclusion of motivational strategies in treatment (OR = 0.44) significantly decreased the likelihood of dropout. Results from multivariate analyses revealed that younger age (OR = 0.63), presenting a personality disorder (OR = 1.73), and experiencing more adversity in childhood (OR = 2.16) were significantly associated with dropout. Notably, intimate partner violence characteristics established a significant negative relation with dropout (OR = 0.59). Findings indicate that variables associated with dropout align with those related to general and intimate partner violence recidivism, suggesting that individuals requiring more intensive intervention are those who derive less benefit from it.

Photoinactivation of microorganisms using bacteriochlorins as photosensitizers.

In recent years, some microorganisms have shown resistance to conventional treatments. Considering this increase in resistant pathogens, treatment alternatives are needed to promote greater treatment efficiency. In this sense, antimicrobial photodynamic therapy (aPDT) has been an alternative treatment. This technique uses a photosensitizer that is activated by light with a specific wavelength producing reactive species, leading to the death of pathogenic microorganisms. In this study, bacteriochlorophyll derivatives such as bacteriochlorin metoxi (Bchl-M) and bacteriochlorin trizma (Bchl-T) obtained from purple bacterium (Rhodopseudomonas faecalis), were evaluated as photosensitizers in the aPDT. Photodynamic inactivation (PDI) of the microorganisms Staphylococcus aureus, Micrococcus luteus, Candida albicans and Pseudomonas aeruginosa was investigated with both bacteriochlorins (Bchl-M and Bchl-T) at different concentrations (1, 15 and 30 µM for S. aureus; 1, 15, 30, 45, 60 and 75 µM for M. luteus; 30, 60, 90, 105, 120 and 150 µM for C. albicans; and 200 µM for P. aeruginosa) and different doses of light (20 and 30 J/cm2 for S. aureus and M. luteus; 30 and 45 J/cm2 for C. albicans; and 45 J/cm2 for P. aeruginosa) to inactivate them. Both photosensitizers showed good activation against S. aureus and for M. luteus, we observed the inactivation of these microorganisms at approximately 3 log, showing to be a good photosensitizers for these microorganisms.

Transcriptomic analysis highlights epigenetic and transcriptional regulation during zygotic embryo development of Pinus pinaster.

BACKGROUND: It is during embryogenesis that the plant body plan is established and the meristems responsible for all post-embryonic growth are specified. The molecular mechanisms governing conifer embryogenesis are still largely unknown. Their elucidation may contribute valuable information to clarify if the distinct features of embryo development in angiosperms and gymnosperms result from differential gene regulation. To address this issue, we have performed the first transcriptomic analysis of zygotic embryo development in a conifer species (Pinus pinaster) focusing our study in particular on regulatory genes playing important roles during plant embryo development, namely epigenetic regulators and transcription factors. RESULTS: Microarray analysis of P. pinaster zygotic embryogenesis was performed at five periods of embryo development from early developing to mature embryos. Our results show that most changes in transcript levels occurred in the first and the last embryo stage-to-stage transitions, namely early to pre-cotyledonary embryo and cotyledonary to mature embryo. An analysis of functional categories for genes that were differentially expressed through embryogenesis highlighted several epigenetic regulation mechanisms. While putative orthologs of transcripts associated with mechanisms that target transposable elements and repetitive sequences were strongly expressed in early embryogenesis, PRC2-mediated repression of genes seemed more relevant during late embryogenesis. On the other hand, functions related to sRNA pathways appeared differentially regulated across all stages of embryo development with a prevalence of miRNA functions in mid to late embryogenesis. Identification of putative transcription factor genes differentially regulated between consecutive embryo stages was strongly suggestive of the relevance of auxin responses and regulation of auxin carriers during early embryogenesis. Such responses could be involved in establishing embryo patterning. Later in development, transcripts with homology to genes acting on modulation of auxin flow and determination of adaxial-abaxial polarity were up-regulated, as were putative orthologs of genes required for meristem formation and function as well as establishment of organ boundaries. Comparative analysis with A. thaliana embryogenesis also highlighted genes involved in auxin-mediated responses, as well as epigenetic regulation, indicating highly correlated transcript profiles between the two species. CONCLUSIONS: This is the first report of a time-course transcriptomic analysis of zygotic embryogenesis in a conifer. Taken together our results show that epigenetic regulation and transcriptional control related to auxin transport and response are critical during early to mid stages of pine embryogenesis and that important events during embryogenesis seem to be coordinated by putative orthologs of major developmental regulators in angiosperms.