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Deaminase base editing has emerged as a tool to install or correct point mutations in the genomes of living cells in a wide range of organisms. However, the genome-wide off-target effects introduced by base editors in the mammalian genome have been examined in only one study. Here, we have investigated the fidelity of cytosine base editor 4 (BE4) and adenine base editors (ABE) in mouse embryos using unbiased whole-genome sequencing of a family-based trio cohort. The same sgRNA was used for BE4 and ABE. We demonstrate that BE4-edited mice carry an excess of single-nucleotide variants and deletions compared to ABE-edited mice and controls. Therefore, an optimization of cytosine base editors is required to improve its fidelity. While the remarkable fidelity of ABE has implications for a wide range of applications, the occurrence of rare aberrant C-to-T conversions at specific target sites needs to be addressed. Hye Kyung Lee, Harold E. Smith et al. examined the fidelity of cytosine base editor 4 (BE4) and adenine base editors (ABEs) in mouse embryos using whole-genome sequencing of a family-based trio cohort. They show that BE4-edited mice carry more single-nucleotide variants and deletions than ABE-edited mice. [ABSTRACT FROM AUTHOR]

This text is an obituary for Andy Golden, a Senior Investigator and Section Chief of Genetics of Early Development at the National Institutes of Health. The author reflects on Andy's dedication to mentorship and his contributions to the field of developmental biology. Andy's research focused on using worms as a model for understanding human development and rare diseases. The author also includes testimonials from Andy's former postdoctoral fellows, highlighting his kindness, generosity, and sense of humor as a mentor. The text is a collection of personal reflections and tributes from individuals who had a close relationship with Andy Golden, a mentor and scientist. The authors highlight Andy's support and encouragement in both their professional and personal lives. They describe him as a kind, supportive, and humble person who valued the well-being and success of his mentees. Andy's legacy is remembered through his dedication to his work, his ability to create a positive and inclusive lab environment, and his impact on the scientific community. [Extracted from the article]

Most genes in higher eukaryotes express isoforms with distinct 3' untranslated regions (3' UTRs), generated by alternative polyadenylation (APA). Since 3' UTRs are predominant locations of post-transcriptional regulation, APA can render such programs conditional, and can also alter protein sequences via alternative last exon (ALE) isoforms. We previously used 3'-sequencing from diverse Drosophila samples to define multiple tissue-specific APA landscapes. Here, we exploit comprehensive single nucleus RNA-sequencing data (Fly Cell Atlas) to elucidate cell-type expression of 3' UTRs across >250 adult Drosophila cell types. We reveal the cellular bases of multiple tissue-specific APA/ALE programs, such as 3' UTR lengthening in differentiated neurons and 3' UTR shortening in spermatocytes and spermatids. We trace dynamic 3' UTR patterns across cell lineages, including in the male germline, and discover new APA patterns in the intestinal stem cell lineage. Finally, we correlate expression of RNA binding proteins (RBPs), miRNAs and global levels of cleavage and polyadenylation (CPA) factors in several cell types that exhibit characteristic APA landscapes, yielding candidate regulators of transcriptome complexity. These analyses provide a comprehensive foundation for future investigations of mechanisms and biological impacts of alternative 3' isoforms across the major cell types of this widely-studied model organism. Single cell data provides cellular resolution on gene expression, but is rarely mined for isoforms. Analysis of 3' isoforms across ~250 Drosophila cell types reveals the cellular bases for numerous tissue-specific 3' programs, identifies new 3' programs, and nominates candidate trans-acting factors [ABSTRACT FROM AUTHOR]

Within contemporary developments of Asian regional security, a core undertone of conflict catalysts and motivations for territorial claims is directly motivated through archaeological findings. These findings include artefacts and settlements, which are utilised to justify political and territorial claims in the region. This overlooked factor will be analysed using three regional case studies through an archaeological and security studies lens. The research aims to further understand Asia Pacific regional security and political disputes and reflect conflict motivation undertones of each interacting nation-state. The article assesses core case studies of Chinese claims in the South China Sea, Japanese and Korean island claims, and Thai-Cambodian temple disputes. The research will analyse how site evidence becomes politicised to justify territorial claims in Asia- Pacific. Through interdisciplinary research, the article will conclude with a greater understanding of assessing conflict development and motivations between state actors in the Asia Pacific region. [ABSTRACT FROM AUTHOR]

Copyright of Research in Educational & Human Sciences Arts & Languages is the property of Research & Development of Human Recourses Center (REMAH) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Given their copy number differences and unique modes of inheritance, the evolved gene content and expression of sex chromosomes is unusual. In many organisms the X and Y chromosomes are inactivated in spermatocytes, possibly as a defense mechanism against insertions into unpaired chromatin. In addition to current sex chromosomes, Drosophila has a small gene-poor X-chromosome relic (4th) that re-acquired autosomal status. Here we use single cell RNA-Seq on fly larvae to demonstrate that the single X and pair of 4th chromosomes are specifically inactivated in primary spermatocytes, based on measuring all genes or a set of broadly expressed genes in testis we identified. In contrast, genes on the single Y chromosome become maximally active in primary spermatocytes. Reduced X transcript levels are due to failed activation of RNA-Polymerase-II by phosphorylation of Serine 2 and 5. [ABSTRACT FROM AUTHOR]

Ciliary microtubules are subject to post-translational modifications that act as a "Tubulin Code" to regulate motor traffic, binding proteins and stability. In humans, loss of CCP1, a cytosolic carboxypeptidase and tubulin deglutamylating enzyme, causes infantile-onset neurodegeneration. In C. elegans, mutations in ccpp-1, the homolog of CCP1, result in progressive degeneration of neuronal cilia and loss of neuronal function. To identify genes that regulate microtubule glutamylation and ciliary integrity, we performed a forward genetic screen for suppressors of ciliary degeneration in ccpp-1 mutants. We isolated the ttll-5(my38) suppressor, a mutation in a tubulin tyrosine ligase-like glutamylase gene. We show that mutation in ttll-4, ttll-5, or ttll-11 gene suppressed the hyperglutamylation-induced loss of ciliary dye filling and kinesin-2 mislocalization in ccpp-1 cilia. We also identified the nekl-4(my31) suppressor, an allele affecting the NIMA (Never in Mitosis A)-related kinase NEKL-4/NEK10. In humans, NEK10 mutation causes bronchiectasis, an airway and mucociliary transport disorder caused by defective motile cilia. C. elegans NEKL-4 localizes to the ciliary base but does not localize to cilia, suggesting an indirect role in ciliary processes. This work defines a pathway in which glutamylation, a component of the Tubulin Code, is written by TTLL-4, TTLL-5, and TTLL-11; is erased by CCPP-1; is read by ciliary kinesins; and its downstream effects are modulated by NEKL-4 activity. Identification of regulators of microtubule glutamylation in diverse cellular contexts is important to the development of effective therapies for disorders characterized by changes in microtubule glutamylation. By identifying C. elegans genes important for neuronal and ciliary stability, our work may inform research into the roles of the tubulin code in human ciliopathies and neurodegenerative diseases. Author summary: Cilia are microtubule-based organelles that play essential roles in human development and health. Ciliopathies are caused by abnormalities in the structure or function of primary cilia, with polycystic kidney disease (PKD) being a common clinical phenotype. As cilia are found on most non-dividing cells in the human body, ciliopathies often display extrarenal manifestations including neurological disorders and retinal degeneration. The Tubulin Code–combinatorial use of tubulin isotypes and post-translational modifications–dictates ciliary structure, motor-based transport, and function. Mutation in the tubulin deglutamylase ccpp-1 (cytosolic carboxypeptidase) results in ciliary hyperglutamylation and degeneration. C. elegans ccpp-1 ciliary degeneration is suppressed by a mutation in any of three TTLL (tubulin tyrosine ligase-like) glutamylase genes, indicating that regulated glutamylation is critically important for ciliary homeostasis. Pathological hyperglutamylation caused by CCP deglutamylase mutations are associated with human retinal degeneration and murine progressive neurodegeneration and sperm immotility. ccpp-1 ciliary degeneration is also suppressed by a mutation in the kinase NEKL-4/NEK10. NEK kinases are implicated in polycystic kidney disease and other ciliopathies and NEKL-4/NEK10 is important for ciliary stability in C. elegans. By identifying C. elegans genes important for neuronal and ciliary stability, "the worm" may inform research into human ciliopathies and neurodegenerative diseases. [ABSTRACT FROM AUTHOR]

The article lists several books received by the May 1952 issue of the journal Social Forces. Some of the books are, Formal and Informal Participation in a New York Village, by W.A. Anderson and Harold E. Smith, Willow Run: A Study of Industrialization and Cultural Inadequacy, by Lowell Juilliard Carr and James Edson Stermer, The American Government and Its Work, by Edward W. Carter and Charles C. Rohlfing, Closing the Ring, by Winston S. Churchill, Community Development in the South, The March of Methodism. The Story of Methodist Missionary Work Overseas, by Cyril J. Davey, And Crown Thy Good, by Philip Davis, The Story of the Rockefeller Foundation, by Raymond B. Fosdick, A Sex Guide to Happy Marriage, by Edward F. Griffith, Law and Contemporary Problems, Jefferson, by Saul K. Padover, Social Science and Psychotherapy for Children, by Otto Pollak, Social Problems and Social Policy, by James M. Reinhardt, Personality Development, by J.S. Slotkin, Public Administration and Policy Development, edited by Harold Stein, etc.

The article presents information on a Philippines Studies Conference that will be organized by the Southeast Asia Summer Studies Institute, Ann Arbor, Michigan, from August 2-4, 1984. The panels for the Conference include: "Studies on Philippine Society and Culture," Philippine Social Structure and Colonial Politics at the Turn-of-the-Century," "Language and Literature in the Philippines Under Martial Law," "Critical Perspective on Recent Trends and Developments in the Southern Philippines," "Filipino Americans: 1984," and "The Effects of the Economic Crisis and the Aquino Assassination on Philippine Politics." Some of the papers that will be discussed during the conference are "Doctors in the Western Philippines: Their Views on Herbal Medicine," by Harold E. Smith, "Macao Insik, and Half-Breed: Ethnic Rhetoric and Ethnic Consciousness Among the Chinese-Igorot Mestizos in Bagulo-Benguet," by Julia K. Ko, "Black Asians in the Philippines: The 'Negrito Problem' Revisited," by Charles P. Waren, "Bisayan Swardspeak," by Harriett Hart, "Women in the Philippine Bureaucracy," by Proserpina D. Tapales.

Copyright of Larq Journal for Philosophy, Linguistics & Social Sciences is the property of Republic of Iraq Ministry of Higher Education & Scientific Research (MOHESR) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Whole-genome sequencing is a powerful tool for analyzing genetic variation on a global scale. One particularly useful application is the identification of mutations obtained by classical phenotypic screens in model species. Sequence data from the mutant strain is aligned to the reference genome, and then variants are called to generate a list of candidate alleles. A number of software pipelines for mutation identification have been targeted to C. elegans, with particular emphasis on ease of use, incorporation of mapping strain data, subtraction of background variants, and similar criteria. Although success is predicated upon the sensitive and accurate detection of candidate alleles, relatively little effort has been invested in evaluating the underlying software components that are required for mutation identification. Therefore, we have benchmarked a number of commonly used tools for sequence alignment and variant calling, in all pair-wise combinations, against both simulated and actual datasets. We compared the accuracy of those pipelines for mutation identification in C. elegans, and found that the combination of BBMap for alignment plus FreeBayes for variant calling offers the most robust performance. [ABSTRACT FROM AUTHOR]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2009.06.044 Byline: Antonio del Castillo-Olivares (a), Madhura Kulkarni (b)(c), Harold E. Smith (a)(d) Keywords: Germ line; Spermatogenesis; GATA factor; Gene expression Abstract: Cell fate specification is mediated primarily through the expression of cell-type-specific genes. The regulatory pathway that governs the sperm/egg decision in the hermaphrodite germ line of Caenorhabditis elegans has been well characterized, but the transcription factors that drive these developmental programs remain unknown. We report the identification of ELT-1, a GATA transcription factor that specifies hypodermal fate in the embryo, as a regulator of sperm-specific transcription in the germ line. Computational analysis identified a conserved bipartite sequence element that is found almost exclusively in the promoters of a number of sperm genes. ELT-1 was recovered in a yeast one-hybrid screen for factors that bind to that sperm consensus site. In vitro assays defined the sperm consensus sequence as an optimal binding site for ELT-1. We determined that expression of elt-1 is elevated in the sperm-producing germ line, and that ELT-1 is required for sperm function. Deletion of the ELT-1 binding site from a sperm promoter abrogates sperm-specific expression of a reporter transgene. This work demonstrates a role for the ELT-1 transcription factor in sperm, and provides a critical link between the germ line sex determination program and gamete-specific gene expression. Author Affiliation: (a) Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MD 20850, USA (b) Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA (c) Massachusetts General Hospital Cancer Center and Department of Cell Biology, Harvard Medical School, Charlestown, MA 02129, USA (d) National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA Article History: Received 13 March 2009; Revised 14 May 2009; Accepted 30 June 2009

Background The production of multiple transcript isoforms from one gene is a major source of transcriptome complexity. RNA-Seq experiments, in which transcripts are converted to cDNA and sequenced, allow the resolution and quantification of alternative transcript isoforms. However, methods to analyze splicing are underdeveloped and errors resulting in incorrect splicing calls occur in every experiment. Results We used RNA-Seq data to develop sequencing and aligner error models. By applying these error models to known input from simulations, we found that errors result from false alignment to minor splice motifs and antisense stands, shifted junction positions, paralog joining, and repeat induced gaps. By using a series of quantitative and qualitative filters, we eliminated diagnosed errors in the simulation, and applied this to RNA-Seq data from Drosophila melanogaster heads. We used high-confidence junction detections to specifically interrogate local splicing differences between transcripts. This method out-performed commonly used RNA-seq methods to identify known alternative splicing events in the Drosophila sex determination pathway. We describe a flexible software package to perform these tasks called Splicing Analysis Kit (Spanki), available at http://www.cbcb.umd.edu/software/spanki. Conclusions Splice-junction centric analysis of RNA-Seq data provides advantages in specificity for detection of alternative splicing. Our software provides tools to better understand error profiles in RNA-Seq data and improve inference from this new technology. The splicejunction centric approach that this software enables will provide more accurate estimates of differentially regulated splicing than current tools. [ABSTRACT FROM AUTHOR]

Before Guy Madison became famous as a 1950s Western hero on television, the handsome but untrained actor was under contract to David O. Selznick. The producer heavily promoted Madison in fan magazines, then loaned him out for a lead role in an A-picture. Madison made little impression there or in subsequent low-budget releases. Finally, his five years under Selznick attested to the limitations of star-making in the troubled postwar studio system. [ABSTRACT FROM AUTHOR]

Bacterial production of recombinant proteins offers several advantages over alternative expression methods and remains the system of choice for many structural genomics projects. However, a large percentage of targets accumulate as insoluble inclusion bodies rather than soluble protein, creating a significant bottleneck in the protein production pipeline. Numerous strategies have been reported that can improve in vivo protein solubility, but most do not scale easily for high-throughput expression screening. To understand better the host cell response to the accumulation of insoluble protein, we determined genome-wide changes in bacterial gene expression upon induction of either soluble or insoluble target proteins. By comparing transcriptional profiles for multiple examples from the soluble or insoluble class, we identified a pattern of gene expression that correlates strongly with protein solubility. Direct targets of the σ32 heat shock sigma factor, which includes genes involved in protein folding and degradation, were highly expressed in response to induction of insoluble protein. This same group of genes was also upregulated by insoluble protein accumulation under a different growth regime, indicating that σ32-mediated gene expression is a general response to protein insolubility. This knowledge provides a starting point for the rational design of growth parameters and host strains with improved protein solubility characteristics. Summary Problems with protein solubility are frequently encountered when recombinant proteins are expressed in E. coli. The bacterial host responds to this problem by increasing expression of the protein folding machinery via the heat shock sigma factor σ32. Manipulation of the σ32 regulon might provide a general mechanism for improving recombinant protein solubility. [ABSTRACT FROM AUTHOR]

With increasing vigor since the events of September 11, 2001, police institutions across the globe have proliferated their counterterrorism strategies, including participation in international police organizations such as the International Criminal Police Organization (Interpol). This article discusses some of these developments in light of the prospects of the development toward a global rule of law. Based on the theory of police bureaucratization, it is shown that police institutions have independently developed international structures and practices irrespective of international accords. This article reveals the dynamics of such international police efforts by examining the counterterrorist policies of Interpol. It is argued that the outcome of the relative separation between international police practices, on one hand, and global legal developments, on the other, will be critical in assessing any efforts to counteract the societal processes and conditions that may facilitate the development of terrorism on a global scale. [ABSTRACT FROM AUTHOR]

Intermediate Care Programs were jointly established by the New York State Office of Mental Health and Department of Correctional Services to reduce risk and better manage inmates with psychiatric disorders. In an earlier study, we collected data from the mental health and corrections records of 209 inmates who were admitted to Intermediate Care Programs. Our analysis of those data showed there were significant reductions in the mean number of serious problem behaviors, correctional restrictions, and mental health crisis services during the six months before and after admission. In the present study, we used Wilcoxon tests to assess changes in the distribution of scores on variables assessed by the earlier study. The Wilcoxon tests showed there were significant changes in the distribution of scores on most of the variables. We then focused on inmates who scored positive on the respective variables, either before admission or after admission, and determined the percentage who improved, stayed the same, or worsened on those variables. The highest reductions occurred in mental health observations (65%), suicide attempts (63%), and emergency medications (43%). Lower reductions occurred in correctional infractions and restrictions (26% to 31%). Overall, the data from this study and our earlier one suggest that Intermediate Care Programs are effective in reducing risk and managing inmates with psychiatric disorders. [ABSTRACT FROM AUTHOR]