New Books Party: books received this week | @GrrlScientist

This week, I tell you about four wonderful books; one each about the human placenta, the science of champagne, New World warblers and JK Rowling's new murder mysteryBelow the jump, I mention the books that I received recently in the mail as gifts or as review copies, or that I purchased somewhere. These are the books that I may review in more depth later, either here or in print somewhere in the world. When I get new books, I like to share them with people. Unfortunately, you are all so far away, so I cannot host a book party in my crib where you can look then over, so I'll do the next best thing. I'll host a book party on my blog each Friday of the week when I either purchase books or when they arrive in the mail. In this New Book Party, I will try to be your eyes by presenting my quick "first impression" -- almost as if we are browsing the stacks in a bookstore -- and I'll also provide relevant videos about the book and links so you can get a copy of your own. Books that arrived this week: Life's Vital Link: The astonishing role of the placenta by Y.W. Loke [Oxford University Press, 2013; Guardian Bookshop; Amazon UK; Amazon US/kindle US] Publisher's synopsis The development of the placenta was a pivotal event in evolution. The long and tortuous evolutionary road which led from egg-laying reptiles to present-day placental mammals like ourselves was an epic journey spanning over 300 million years. Without the placenta, we would still be laying eggs, instead of givi...
Source: Guardian Unlimited Science - Category: Science Authors: Tags: Birdwatching theguardian.com Blogposts Pregnancy Books Science Source Type: news

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Abstract DNA methylation is a process by which methyl groups are added to cytosine or adenine. DNA methylation can change the activity of the DNA molecule without changing the sequence. Methylation of 5-methylcytosine (5mC) is widespread in both eukaryotes and prokaryotes, and it is a very important epigenetic modification event, which can regulate gene activity and influence a number of key processes such as genomic imprinting, cell differentiation, transcriptional regulation, and chromatin remodeling. Profiling DNA methylation across the genome is critical to understanding the influence of methylation in normal ...
Source: Mol Biol Cell - Category: Molecular Biology Authors: Tags: Methods Mol Biol Source Type: research
Abstract This chapter addresses the problem of reconstructing regulatory networks in molecular biology by integrating multiple sources of data. We consider data sets measured from diverse technologies all related to the same set of variables and individuals. This situation is becoming more and more common in molecular biology, for instance, when both proteomic and transcriptomic data related to the same set of "genes" are available on a given cohort of patients.To infer a consensus network that integrates both proteomic and transcriptomic data, we introduce a multivariate extension of Gaussian graphical ...
Source: Mol Biol Cell - Category: Molecular Biology Authors: Tags: Methods Mol Biol Source Type: research
Abstract Over the last several decades, multiple recurrent chromosomal amplifications and deletions have been detected in a large number of cancers. These regions of amplification and deletion can encompass a few to several hundred genes. Determining which of these genes is causing the outgrowth of the cancer is difficult. Complicating the analysis is the fact that several genes within the affected chromosomal region may cooperate to promote tumorigenesis. In this protocol we describe a method of chromosomal engineering in mice that allows modeling of chromosomal duplications and deficiencies. This method faithful...
Source: Mol Biol Cell - Category: Molecular Biology Authors: Tags: Methods Mol Biol Source Type: research
Abstract Transposon mutagenesis has emerged as a powerful methodology for functionally annotating cancer genomes. Although in vivo transposon-mediated forward genetic screens have proven to be valuable for cancer gene identification, they are also time consuming and resource intensive. To facilitate the rapid and cost-effective identification of genes that regulate tumor-promoting pathways, we developed a complementary ex vivo transposon mutagenesis approach wherein human or mouse cells growing in culture are mutagenized and screened for the acquisition of specific phenotypes in vitro or in vivo, such as growth fa...
Source: Mol Biol Cell - Category: Molecular Biology Authors: Tags: Methods Mol Biol Source Type: research
Abstract Since the advent of large-scale, detailed descriptive cancer genomics studies at the beginning of the century, such as The Cancer Genome Atlas (TCGA), labs around the world have been working to make this data useful. Data like these can be made more useful by comparison with complementary functional genomic data. One new example is the application of CRISPR/Cas9-based library screening for cancer-related traits in cell lines. Such screens can reveal genome-wide suppressors of tumorigenesis and metastasis. Here we describe the use of widely available lentiviral libraries for such screens in cultured cell l...
Source: Mol Biol Cell - Category: Molecular Biology Authors: Tags: Methods Mol Biol Source Type: research
Abstract In this protocol, pooled sgRNA libraries targeting thousands of genes are computationally designed, generated using microarray-based synthesis techniques, and packaged into lentiviral particles. Target cells of interest are transduced with the lentiviral sgRNA pools to generate a collection of knockout mutants-via Cas9-mediated genomic cleavage-and screened for a phenotype of interest. The relative abundance of each mutant in the population can be monitored over time through high-throughput sequencing of the integrated sgRNA expression cassettes. Using this technique, we outline strategies for the identif...
Source: Mol Biol Cell - Category: Molecular Biology Authors: Tags: Methods Mol Biol Source Type: research
Abstract The tissue engineering method of decellularization and recellularization has been successfully used in a variety of regenerative medicine applications. The protocols used to de/recellularize various organs and tissues are largely different. Here we describe a method to effectively engineer a bioartificial colon by completely removing original cells from human intestinal tissues followed by repopulating the acellular tissue matrix with cell cultures. This method provides a novel approach for human intestinal regeneration and can be used to identify potential cancer driver genes. PMID: 30542993 [PubMed - in process]
Source: Mol Biol Cell - Category: Molecular Biology Authors: Tags: Methods Mol Biol Source Type: research
Abstract Here we describe a method for identifying genes and genetic pathways responsible for chemoresistance in cancer cells. The method is based on generation and characterization of matched pairs of chemotherapy-sensitive/chemotherapy-resistant cancer cell lines. In this protocol we are using endometrial cancer cell lines treated with carboplatin and paclitaxel, which are first-line chemotherapies for gynecologic malignancies. The chemoresistant cells and their chemosensitive counterparts are used for downstream applications including bulk RNA-sequencing analysis to identify a set of genes and pathways that are...
Source: Mol Biol Cell - Category: Molecular Biology Authors: Tags: Methods Mol Biol Source Type: research
Mid-infrared optical waveguides were inscribed in sapphire with femtosecond pulses at 515   nm. We show that such pulses induce a smooth negative refractive index change allowing for the inscription of a depressed cladding waveguide by closely overlapping the corresponding type I modification ...
Source: Optics Letters - Category: Physics Authors: Source Type: research
Johnson&Johnson developed a strategy in the 1970s to deal with a growing volume of research showing that talc miners had elevated rates of lung disease and cancer: Promote the positive, challenge the negative.
Source: Reuters: Health - Category: Consumer Health News Tags: healthNews Source Type: news
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