Genomic Point Of View Research Articles

Potential effect on molecular pathways in different targeted genes in the VEGF family in retina - From the genomic point of view

This study's goal is to determine similarities and differences in the molecular pathways or potential functions of the various targeted regions or genes of the Vegf family—VegfA, VegfB, VegfC, and Pgf—using the BXD genetic reference panel. Data from whole genome expression profiles of retinas from the well-characterized mouse recombinant inbred (RI) strain population derived from C57BL/6J X DBA/2J (BXD) were analyzed. Multiple analytical tools and statistical strategies were used to investigate the expression level. The expression Quantitative Trait Loci (QTLs) of these probes were mapped and compared. Our data showed that VegfA2 has the highest expression levels among all probes of Vegf genes. The expression levels of Vegf family genes are not significantly correlated. In the overall comparison, expression levels of VegfA1 and VegfA2 are positively correlated (R = 0.540). The expression levels of VegfB and VegfC are weakly correlated (R = 0.360). VegfC is also weakly correlated with the expression levels of Pgf (R = 0.324). The interaction of VegfB- and VegfA2-associated 50a2 genes was very weak (R50 ab = 0.3129). The interaction of top VegfB-associated 50b genes with VegfA2 has a reciprocal negative impact (R50ba = −0.42758). The VegfC-associated top 50c genes are strongly correlated with VegfB (R50 cb = 0.8159), while they are negatively correlated with VegfA2 (R50ca = −0.1450). Expression quantitative trait loci (eQTL) analysis suggested that the regulatory mechanisms for the expression levels of these genes in the Vegf family are different from each other. The expression level of VegfA associates with a group of genes that are not associated with other genes in the Vegf family.

Role of Salt Valency in the Switch of H-NS Proteins between DNA-Bridging and DNA-Stiffening Modes

This work investigates the interactions of H-NS proteins and bacterial genomic DNA through computer simulations performed with a coarse-grained model. The model was developed specifically to study the switch of H-NS proteins from the DNA-stiffening to the DNA-bridging mode, which has been observed repeatedly upon addition of multivalent cations to the buffer but is still not understood. Unraveling the corresponding mechanism is all the more crucial, as the regulation properties of H-NS proteins, as well as other nucleoid proteins, are linked to their DNA-binding properties. The simulations reported here support a mechanism, according to which the primary role of multivalent cations consists in decreasing the strength of H-NS/DNA interactions compared to H-NS/H-NS interactions, with the latter ones becoming energetically favored with respect to the former ones above a certain threshold of the effective valency of the cations of the buffer. Below the threshold, H-NS dimers form filaments, which stretch along the DNA molecule but are quite inefficient in bridging genomically distant DNA sites (DNA-stiffening mode). In contrast, just above the threshold, H-NS dimers form three-dimensional clusters, which are able to connect DNA sites that are distant from the genomic point of view (DNA-bridging mode). The model provides clear rationales for the experimental observations that the switch between the two modes is a threshold effect and that the ability of H-NS dimers to form higher order oligomers is crucial for their bridging capabilities.

New protocol based on massive parallel sequencing for aneuploidy screening of preimplantation human embryos

ABSTRACTNovel next-generation sequencing procedures have rapidly emerged into the preimplantation genetic screening framework. This work presents the design and validation of a new low-coverage whole-genome sequencing assay for aneuploidy detection in single blastomeres and trophectodermal samples from preimplantation embryos. The validation ensures analytical sensitivity, specificity, robustness, precision, limit of detection, resolution, and reproducibility. Specific parameters to measure the performance are defined, and the results are compared with a standardized array-based method to stablish the concordance. From the single cell genomics point of view, the main novelties are the length of reads of the libraries (150 nucleotides) together with a paired-end strategy and the design of an original algorithm and copy number viewer. A total of 129 samples were included in six experimental runs using a MiSeq Illumina platform. Samples included: single amniocytes, single blastomeres (cleavage-stage embryos), trophectoderm samples (blastocyst), and diluted DNA. Sensitivity and specificity were calculated per chromosome yielding 96% and 99%, respectively. The percentage of concordant samples was 98.2% and all of the aneuploid samples were confirmed. In conclusion, the validation yields highly reliable and reproducible results, representing an accurate and cost-effective strategy for the routine detection of aneuploidy in human embryos.

PI3K-AKT-mTOR inhibitors in breast cancers: From tumor cell signaling to clinical trials.

Breast cancer (BC) is the most common women cancer and second most common cause of cancer death in women. A woman living in the United States has 12.3% lifetime risk of being diagnosed with BC. From the genomics point of view, the most common three subtypes of BC encountered in clinics are HR+, HER2+, and TNBC or basal-like BC. Estrogen receptor (ER) status or HER2 amplification or chemotherapy is not sufficient to understand the underlying mechanisms of disease progression and resistance (de novo or acquire). Although hormonal therapy and HER2-directed therapies have produced a considerable positive outcome in HR+ and HER2+ BC respectively, there are no established targeted agents for TNBC and basal-like BC. While PARP inhibitors have shown promising activity in BRCA-related cancers, its value in the treatment of TNBC remains to be demonstrated. The PI3K-AKT-mTOR signaling pathway plays a crucial role in the initiation and progress in tumorigenesis including breast tumorigenesis and regulates critical cellular functions including survival, proliferation, and metabolism. This article aims to understand the role of PI3K-mTORC1/C2 alterations in determining the clinical outcome in the specific breast cancer subtypes. The understanding of the tumor cell signaling will help us in the decision-making the process for obtaining the treatment modalities towards further advancement of the precision medicine. In this review, we will restrict our discussion to a basic understanding of the biology of subtype-specific BC and several targeted agents under development for the treatment of BC.

Biochemical Modulation of Lipid Pathway in Microalgae Dunaliella sp. for Biodiesel Production.

Exploitation of renewable sources of energy such as algal biodiesel could turn energy supplies problem around. Studies on a locally isolated strain of Dunaliella sp. showed that the mean lipid content in cultures enriched by 200 mg L−1 myoinositol was raised by around 33% (1.5 times higher than the control). Similarly, higher lipid productivity values were achieved in cultures treated by 100 and 200 mg L−1 myoinositol. Fluorometry analyses (microplate fluorescence and flow cytometry) revealed increased oil accumulation in the Nile red-stained algal samples. Moreover, it was predicted that biodiesel produced from myoinositol-treated cells possessed improved oxidative stability, cetane number, and cloud point values. From the genomic point of view, real-time analyses revealed that myoinositol negatively influenced transcript abundance of AccD gene (one of the key genes involved in lipid production pathway) due to feedback inhibition and that its positive effect must have been exerted through other genes. The findings of the current research are not to interprete that myoinositol supplementation could answer all the challenges faced in microalgal biodiesel production but instead to show that “there is a there there” for biochemical modulation strategies, which we achieved, increased algal oil quantity and enhanced resultant biodiesel quality.

Metabolic network motifs can provide novel insights into evolution: The evolutionary origin of Eukaryotic organelles as a case study

Phylogenetic trees are typically constructed using genetic and genomic data, and provide robust evolutionary relationships of species from the genomic point of view. We present an application of network motif mining and analysis of metabolic pathways that when used in combination with phylogenetic trees can provide a more complete picture of evolution. By using distributions of three-node motifs as a proxy for metabolic similarity, we analyze the ancestral origin of Eukaryotic organelles from the metabolic point of view to illustrate the application of our motif mining and analysis network approach. Our analysis suggests that the hypothesis of an early proto-Eukaryote could be valid. It also suggests that a δ- or ϵ-Proteobacteria may have been the endosymbiotic partner that gave rise to modern mitochondria. Our evolutionary analysis needs to be extended by building metabolic network reconstructions of species from the phylum Crenarchaeota, which is considered to be a possible archaeal ancestor of the eukaryotic cell. In this paper, we also propose a methodology for constructing phylogenetic trees that incorporates metabolic network signatures to identify regions of genomically-estimated phylogenies that may be spurious. We find that results generated from our approach are consistent with a parallel phylogenetic analysis using the method of feature frequency profiles.

Tissue proteomics and imaging mass spectrometry

Tissue proteomics and imaging mass spectrometry

Stellate cells and the development of liver cancer: Therapeutic potential of targeting the stroma

Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) are the most common types of primary tumors in the liver. Although major advances have been made in understanding the cellular and molecular mechanisms underlying liver carcinogenesis, HCC and ICC are still deadly cancers worldwide waiting for innovative therapeutic options. Growing evidence from the literature highlight the critical role of the tumor cell microenvironment in the pathogenesis of cancer diseases. Thus, targeting the microenvironment, particularly the crosstalk between tumor cells and stromal cells, has emerged as a promising therapeutic strategy. This strategy would be particularly relevant for liver cancers which frequently develop in a setting of chronic inflammation and microenvironment remodeling associated with hepatic fibrosis and cirrhosis, such processes in which hepatic stellate cells (HSC) greatly contribute. This review brings a genomic point of view on the alterations of the cellular microenvironment in liver cancers, particularly the stromal tissue within tumor nodules, emphasizing the importance of the crosstalk between tumor cells and stromal cells, notably activated HSC, in tumor onset and progression. Furthermore, potential therapeutic modalities of targeting the stroma and HSC are discussed.

Genome‐wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds

Italy counts several sheep breeds, arisen over centuries as a consequence of ancient and recent genetic and demographic events. To finely reconstruct genetic structure and relationships between Italian sheep, 496 subjects from 19 breeds were typed at 50K single nucleotide polymorphism loci. A subset of foreign breeds from the Sheep HapMap dataset was also included in the analyses. Genetic distances (as visualized either in a network or in a multidimensional scaling analysis of identical by state distances) closely reflected geographic proximity between breeds, with a clear north-south gradient, likely because of high levels of past gene flow and admixture all along the peninsula. Sardinian breeds diverged more from other breeds, a probable consequence of the combined effect of ancient sporadic introgression of feral mouflon and long-lasting genetic isolation from continental sheep populations. The study allowed the detection of previously undocumented episodes of recent introgression (Delle Langhe into the endangered Altamurana breed) as well as signatures of known, or claimed, historical introgression (Merino into Sopravissana and Gentile di Puglia; Bergamasca into Fabrianese, Appenninica and, to a lesser extent, Leccese). Arguments that would question, from a genomic point of view, the current breed classification of Bergamasca and Biellese into two separate breeds are presented. Finally, a role for traditional transhumance practices in shaping the genetic makeup of Alpine sheep breeds is proposed. The study represents the first exhaustive analysis of Italian sheep diversity in an European context, and it bridges the gap in the previous HapMap panel between Western Mediterranean and Swiss breeds.

Azoospermia Related Genes and the Detection Kit for Y Chromosome Micro Deletion

Azoospermia is caused by abnormality in the various genes involved in spermatogenesis. However, the crucial genes for spermatogenesis have not yet been identified. Recently, targeted knockout and transgenic mice have been generated and considerable knowledge has been accumulated about their phenotype patterns, and a wide variety of genes are known to be associated with sperm formation. First, we review the meiotic and post-meiotic phases and genes expressed during spermatogenesis. Many genes corresponding to various clinical features of azoospermia exist, and we also review azoospermia related genes from clinical aspects. The AZF (azoospermia factor) regions on the Y chromosome long arm are thought to show a major correlation with spermatogenesis. From the genomic point of view, their deletion due to intrachromosomal recombimation is reviewed as a constitutional feature of the Y chromosome. Moreover, we explain how to use a detection kit for the Y chromosome micro deletion which we developed.

Why We Still Need HBV Population-Based Epidemiologic Studies

As a practicing physician, I face clinical problems every day. To solve them, I use clinical decision making skills including reaching the most accurate diagnosis and deciding on the next step or steps to manage the problem. A clinician is a pragmatic person; i.e., s/he needs practical, implementable data to guide reasoning or decision making and nothing else! In this environment, why is Mohammad Reza Ghadir's article on the epidemiology of Hepatitis B virus infection in this issue of the journal at all? [1]. Of course it is a Socratic question, and you may find me to be the author of similar articles [2]. Description and research on epidemiology from the aspects of incidence and prevalence will affect pre-test likelihood in clinical decision-making. When a doctor encounters a patient in daily practice, s/he needs to know the possibility of the presence of a condition or disease when a sign or symptom is present; therefore the background epidemiology of the disease in the population that the patient comes from is important. It is especially important when there are limited data regarding the population; for example when there is a demographic shift due to immigration to a new area or a change of transmission-related factors after universal HBV vaccination. In terms of infectious disease, these epidemiologic shifts may be rapid and may necessitate surveillance and trend analysis through point estimation studies. In the context Ghadir reported, there is a dynamic, ever-migrating population and a disease whose epidemiology changes frequently. Epidemiologic studies may help indicate possible risk factors, especially when using methodologies that include attributable risk calculations. The risk factors may be manageable in a clinical setting or may be used by health authorities to plan preventive projects for the community. This approach may be combined with an estimation of risk factor manipulation in the patient as a single case as well as in the community. For example, if there is an established attributable risk of intravenous drug use with needle sharing that could disseminate the infection in the community, you may put an HBV patient on Methadone maintenance therapy (MMT). On the other hand, in a case of monogamous sexual contact with an HBcAb-positive sex partner at the age of 50, you may conclude that there is no need to recommend barrier methods. Along these lines, the risk factor tables in the Ghadir articles attempt to guide us. This is a methodological change and results in a nested case-control type of plan within a large cross-sectional study. When the prevalence of a disease is low and consequently the cases within a sample of population are limited, analyzing risk factors will result in methodological problems. This is the problem that Ghadir encounters in some rows of his table, for example when analyzing tattooing as a risk factor. On other hand, when there is a shared risk factor in the majority of the sample and there is no measurement of higher or lower exposure rates, the researcher cannot conclude that this factor is essentially a risk or not. Consider unsafe barber practices within a male population and its effect on HBV transmission. The last evidence-gathering step before concluding on clinical guidelines would be a decision analysis study. The formal methodology in such studies is to draw a decision tree and conduct reverse calculations. To enable the calculation, probabilities are needed for each arm, and to define the probabilities, it is essential to know the prevalence and incidence of each subgroup, which are extractable from epidemiologic studies. Even when a researcher intends to do a sensitivity analysis as part of the decision analysis, the ideal conclusion will be reached when the epidemiologic variations are known and a systematic review performed, such as that done by Alavian et al. in their publication on HBV epidemiology [3]. In terms of data consistency, a new piece of information on the same HBV epidemiology surely does not add anything to our current preventive and clinical practice; in such circumstances when associated with limited manpower and financial support, resources are better shifted toward other studies. Along with the importance of population based epidemiologic studies, I would like to note that, in terms of scientific reasoning, dissociating such studies from other biomedical studies on infectious transmission and risk factors may result in a reductionist philosophy. Without knowing the etiopathogenesis of the disease, variations in humans from the viewpoint of genomics, proteomics, and even metabolomics will result in pitfalls that have happened throughout the history of medicine.

FISH mapping of microsatellite loci from Drosophila subobscura and its comparison to related species

Microsatellites are highly polymorphic markers that are distributed through all the genome being more abundant in non-coding regions. Whether they are neutral or under selection, these markers if localized can be used as co-dominant molecular markers to explore the dynamics of the evolutionary processes. Their cytological localization can allow identifying genes under selection, inferring recombination from a genomic point of view, or screening for the genomic reorganizations occurring during the evolution of a lineage, among others. In this paper, we report for the first time the localization of microsatellite loci by fluorescent in situ hybridization on Drosophila polytene chromosomes. In Drosophila subobscura, 72 dinucleotide microsatellite loci were localized by fluorescent in situ hybridization yielding unique hybridization signals. In the sex chromosome, microsatellite distribution was not uniform and its density was higher than in autosomes. We identified homologous segments to the sequence flanking the microsatellite loci by browsing the genome sequence of Drosophila pseudoobscura and Drosophila melanogaster. Their localization supports the conservation of Muller's chromosomal elements among Drosophila species and the existence of multiple intrachromosomal rearrangements within each evolutionary lineage. Finally, the lack of microsatellite repeats in the homologous D. melanogaster sequences suggests convergent evolution for high microsatellite density in the distal part of the X chromosome.

Genomics of deep‐sea and sub‐seafloor microbes

Over two‐thirds of the surface of the earth is covered by oceans, which have an average depth of about 3800 m. As each drop of ocean water contains > 105 cells, the > 1030 microbial cells in the ocean represent the largest reservoir of microbes on earth (Whitman et al., 1998). Communities of bacteria, archaea, protists and unicellular fungi account for most of the oceanic biomass and metabolism. Marine microbes are known to play an essential role in the global cycling of nitrogen, carbon, oxygen, phosphorous, iron, sulfur and trace elements (Karl, 2007).

Understanding the regulatory genome

The sequencing of the whole genome of multiple species provides us with the instruction book of how to build an organism and make it work, plus a detailed history of how diversity was generated during evolution. Unfortunately, we still understand only a small fraction, which is locating where genes are and deciphering the proteins they code for. The next step is to understand how the correct amount of gene products are produced in space and time to obtain a fully functioning organism, from the egg to the adult. This is what is known as the regulatory genome, a term coined by Eric H. Davidson. In this review, we examine what we know about gene regulation from a genomic point of view, revise the current in silico, in vitro and in vivo methodological approaches to study transcriptional regulation, and point to the power of phylogenetic footprinting as a guide to regulatory element discovery. The advantages and limitations of each approach are considered, with the emerging view that only large-scale studies and data-crunching will give us insight into the language of genomic regulatory systems, and allow the discovery of regulatory codes in the genome.

Genomics and premalignant breast lesions: clues to the development and progression of lobular breast cancer

Advances in genomic technology have improved our understanding of the genetic events that parallel breast cancer development. Because almost all mammary carcinomas develop in the terminal duct lobular units of the breast, understanding the events involved in mammary gland development make it possible to recognize those events that, when altered, contribute to breast neoplasia. In this review we focus on lobular carcinomas, discussing the pathology, development, and progression of premalignant lobular lesions from a genomic point of view. We highlight studies utilizing genomic approaches and describe how these investigations have furthered our understanding of the complexity of premalignant breast lesions.

Piezophilic adaptation: a genomic point of view

Two-thirds of Earth's surface is covered by oceans, yet the study of this massive integrated living system is still in its infancy. Various environmental variables, such as high salinity, low and changeable nutrient availability and depth-correlated gradients of light, temperature, nutrients and pressure shape the diversity, physiology and ecology of marine species. As oceans present an average depth of 3800 m, deep-sea ecosystems represent the most common marine ecological niche. One of the key environment variables that influences the life and evolution of deep-sea organisms is high pressure. This extreme widespread condition requires specific adaptations, the nature of which remains largely unknown. Recent advances in genomic approaches, such as in sequencing technologies and global expression profiling, are rapidly increasing the data available to understand microbial evolution, biochemistry, physiology and diversity. This review summarises the analysis of the results published so far about microbial high pressure adaptation from a genomic point of view. Understanding high pressure adaptation mechanisms is not just a scientific exercise but has important biotechnological implications. For example, hydrostatic pressure is a reality for food science and technology, both for food preparation and preservation. An understanding of the effects of pressure on biomolecules will expand its use in the medical, industrial and biotechnological fields.

Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains

BackgroundOceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, thus a large part of the biosphere is occupied by high pressure environments. Piezophilic (pressure-loving) organisms are adapted to deep-sea life and grow optimally at pressures higher than 0.1 MPa. To better understand high pressure adaptation from a genomic point of view three different Photobacterium profundum strains were compared. Using the sequenced piezophile P. profundum strain SS9 as a reference, microarray technology was used to identify the genomic regions missing in two other strains: a pressure adapted strain (named DSJ4) and a pressure-sensitive strain (named 3TCK). Finally, the transcriptome of SS9 grown under different pressure (28 MPa; 45 MPa) and temperature (4°C; 16°C) conditions was analyzed taking into consideration the differentially expressed genes belonging to the flexible gene pool.ResultsThese studies indicated the presence of a large flexible gene pool in SS9 characterized by various horizontally acquired elements. This was verified by extensive analysis of GC content, codon usage and genomic signature of the SS9 genome. 171 open reading frames (ORFs) were found to be specifically absent or highly divergent in the piezosensitive strain, but present in the two piezophilic strains. Among these genes, six were found to also be up-regulated by high pressure.ConclusionThese data provide information on horizontal gene flow in the deep sea, provide additional details of P. profundum genome expression patterns and suggest genes which could perform critical functions for abyssal survival, including perhaps high pressure growth.

Comparative and evolutionary genomics of Yersinia pestis

Yersinia pestis is the causative agent of plague, causing three human plague pandemics in history. Comparative and evolutionary genomics of Y. pestis are extensively discussed in this review. Understanding the genomic variability and the adaptive evolution of Y. pestis from the genomic point of view will contribute greatly to plague detection, identification, control and prevention.

Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view.

Methylotrophy is defined as the ability to “grow at the expense of reduced carbon compounds containing one or more carbon atoms but containing no carbon-carbon bonds” (3). It is an intriguing example of microbial metabolic agility, with the use of a class of chemicals disregarded by the majority of organisms. Even though the ability to grow methylotrophically was first discovered in the early 1900s (cited in reference 3), it was not until the 1960s to 1970s that an understanding of the biochemical nature of this capability started to emerge. Fascination with methylotrophy in those years was fueled by the commercial interest in single-cell protein production, and as a result, the specific details of the biochemistry of methylotrophy began to be revealed. Enzymes for the primary oxidation of C1 substrates such as methanol dehydrogenase and methylamine dehydrogenase were characterized, and distinct modes of C1 assimilation, such as the ribulose monophosphate cycle and the serine cycle were discovered. The biochemical processes involved in methylotrophy that were known by 1982 are described in detail in the now classic book Biochemistry of Methylotrophs by Christopher Anthony (3). In the 20 years following the publication of Biochemistry of Methylotrophs, a few additional methylotrophy biochemical pathways have been discovered, such as the pathway for C1 transfer linked to methanopterin and methanofuran, which solved the long-standing mystery of formaldehyde oxidation in many methylotrophs (15, 53), and novel pathways for primary C1 oxidation, such as the pathways for degradation of chlorinated methanes and methanesulfonic acid (21, 50). The knowledge concerning the biochemistry and physiology of methylotrophic organisms accumulated over the past three decades suggests a new framework for understanding methylotrophy as a novel metabolic mode. In this framework, methylotrophy is envisioned as a set of specific metabolic functional modules, with different combinations of such modules being present in different methylotrophs (Fig. ​(Fig.11 for the methylotrophic metabolic modules in Methylobacterium extorquens AM1). However, until recently, a number of important details of these modules were missing, and so the picture remained incomplete. The availability of two unfinished genome sequences for the important model organisms M. extorquens AM1 (http://www.integratedgenomics.com/genomereleases.html#list6)and Methylococcus capsulatus Bath (http://tigrblast.tigr.org/ufmg/) is transforming our understanding of methylotrophy. Annotation of these two genomes combined with functional analysis will delineate the set of genes and functions that is both sufficient and necessary to define a methylotroph. Expanding genomic analyses to include other groups of methylotrophs will in turn provide clues to the origins of methylotrophy and the evolution of various methylotrophic pathways. In this publication, we summarize the existing knowledge of the genes involved in methylotrophic pathways in M. extorquens AM1, analyze its yet unfinished genome with respect to location and clustering of methylotrophy genes, and present a comprehensive list of methylotrophy genes and enzymes known at this time in M. extorquens AM1 (Table ​(Table11). FIG. 1. Methylotrophy metabolic modules in M. extorquens AM1. Known genes are in italic. For simplicity, redox reactions in the assimilatory pathways are not indicated. For details, refer to the references given in Table ​Table11. TABLE 1. Methylotrophy genes in M. extorquens AM1

Pharmacogenetic and Pharmacogenomic Studies

The topics discussed in this article are concerned with studying genomic polymorphism and identifying new therapeutic targets, the role of genetics in preclinical and clinical drug development, and cultural, regulatory and logistical aspects of the development of pharmacogenetics in France. The conclusions are that from a physiological, biochemical or genomic point of view, the study of human genetic polymorphism has obvious potential value for drug development, because it can help to identify new therapeutic targets, and to predict drug efficacy and tolerability more effectively. There are already several examples of the latter approach, which relies on studying the genetic variability of enzymes involved in drug metabolism, and that of the effector molecules of the pharmacological activity. Pharmacogenetics could eventually make it possible to personalise drug treatments, as methods for analysing genes are simplified and their cost reduced. To help attain this still far-off goal, certain recommendations have been proposed.