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تعليم الأطفال ذوي الحاجات الخاصة
يعد كتاب تعليم الأطفال ذوي الحاجات الخاصة للمؤلف صموئيل كيرك وزملائه من المراجع القيمة حيث يشتمل على آخر التطورات والمستجدات في مجال تخصص التربية الخاصة. ويمكن للقارئ إن يلاحظ بأن الكتاب تطرق لمجالات وفئات التربية الخاصة من خلال مناح ونماذج عدة أهمها : نموذج معالجة المعلومات، وآخر الأبحاث والدراسات العصبية والجينية، أهمية التدخل المبكر ومرحلة الطفولة المبكرة، بالإضافة إلى موضوع الدمج الشامل وأهمية توظيف منحى الاستجابة للتدخل، ويمكن للقارئ وعبر الدخول إلى الموقع الالكتروني للكتاب إن يتفحص آخر المستجدات المتعلقة بالأساليب التربوية والتكنولوجيا المساندة.
BOOK
Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria
The co-selective pressure of heavy metals is a contributor to the dissemination and persistence of antibiotic resistance genes in environmental reservoirs. The overlapping range of antibiotic and metal contamination and similarities in their resistance mechanisms point to an intertwined evolutionary history. Metal resistance genes are known to be genetically linked to antibiotic resistance genes, with plasmids, transposons, and integrons involved in the assembly and horizontal transfer of the resistance elements. Models of co-selection between metals and antibiotics have been proposed, however, the molecular aspects of these phenomena are in many cases not defined or quantified and the importance of specific metals, environments, bacterial taxa, mobile genetic elements, and other abiotic or biotic conditions are not clear. Co-resistance is often suggested as a dominant mechanism, but interpretations are beset with correlational bias. Proof of principle examples of cross-resistance and co-regulation has been described but more in-depth characterizations are needed, using methodologies that confirm the functional expression of resistance genes and that connect genes with specific bacterial hosts. Here, we comprehensively evaluate the recent evidence for different models of co-selection from pure culture and metagenomic studies in environmental contexts and we highlight outstanding questions.
Co-selection between metal and antibiotics results in the persistence of resistance genes, but more work is needed to understand the relative roles of co-resistance, cross-resistance and co-regulation mechanisms in causing co-selection in the environment.
Journal Article
The landscape of somatic mutation in normal colorectal epithelial cells
The colorectal adenoma–carcinoma sequence has provided a paradigmatic framework for understanding the successive somatic genetic changes and consequent clonal expansions that lead to cancer
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. However, our understanding of the earliest phases of colorectal neoplastic changes—which may occur in morphologically normal tissue—is comparatively limited, as for most cancer types. Here we use whole-genome sequencing to analyse hundreds of normal crypts from 42 individuals. Signatures of multiple mutational processes were revealed; some of these were ubiquitous and continuous, whereas others were only found in some individuals, in some crypts or during certain periods of life. Probable driver mutations were present in around 1% of normal colorectal crypts in middle-aged individuals, indicating that adenomas and carcinomas are rare outcomes of a pervasive process of neoplastic change across morphologically normal colorectal epithelium. Colorectal cancers exhibit substantially increased mutational burdens relative to normal cells. Sequencing normal colorectal cells provides quantitative insights into the genomic and clonal evolution of cancer.
Genome sequencing of hundreds of normal colonic crypts from 42 individuals sheds light on mutational processes and driver mutations in normal colorectal epithelial cells.
Journal Article
Aerobic biodegradation of the chloroethenes: pathways, enzymes, ecology, and evolution
Extensive use and inadequate disposal of chloroethenes have led to prevalent groundwater contamination worldwide. The occurrence of the lesser chlorinated ethenes [i.e. vinyl chloride (VC) and cis-1,2-dichloroethene (cDCE)] in groundwater is primarily a consequence of incomplete anaerobic reductive dechlorination of the more highly chlorinated ethenes (tetrachloroethene and trichloroethene). VC and cDCE are toxic and VC is a known human carcinogen. Therefore, their presence in groundwater is undesirable. In situ cleanup of VC- and cDCE-contaminated groundwater via oxidation by aerobic microorganisms is an attractive and potentially cost-effective alternative to physical and chemical approaches. Of particular interest are aerobic bacteria that use VC or cDCE as growth substrates (known as the VC- and cDCE-assimilating bacteria). Bacteria that grow on VC are readily isolated from contaminated and uncontaminated environments, suggesting that they are widespread and influential in aerobic natural attenuation of VC. In contrast, only one cDCE-assimilating strain has been isolated, suggesting that their environmental occurrence is rare. In this review, we will summarize the current knowledge of the physiology, biodegradation pathways, genetics, ecology, and evolution of VC- and cDCE-assimilating bacteria. Techniques (e.g. PCR, proteomics, and compound-specific isotope analysis) that aim to determine the presence, numbers, and activity of these bacteria in the environment will also be discussed.
Journal Article
Development of a whole‐cell biosensor for ethylene oxide and ethylene
Ethylene and ethylene oxide are widely used in the chemical industry, and ethylene is also important for its role in fruit ripening. Better sensing systems would assist risk management of these chemicals. Here, we characterise the ethylene regulatory system in Mycobacterium strain NBB4 and use these genetic parts to create a biosensor. The regulatory genes etnR1 and etnR2 and cognate promoter Petn were combined with a fluorescent reporter gene (fuGFP) in a Mycobacterium shuttle vector to create plasmid pUS301‐EtnR12P. Cultures of M. smegmatis mc2‐155(pUS301‐EtnR12P) gave a fluorescent signal in response to ethylene oxide with a detection limit of 0.2 μM (9 ppb). By combining the epoxide biosensor cells with another culture expressing the ethylene monooxygenase, the system was converted into an ethylene biosensor. The co‐culture was capable of detecting ethylene emission from banana fruit. These are the first examples of whole‐cell biosensors for epoxides or aliphatic alkenes. This work also resolves long‐standing questions concerning the regulation of ethylene catabolism in bacteria. The regulatory genes and promoter from an ethylene‐utilising bacterium were used to construct a biosensor which was capable of detecting epoxyethane with high sensitivity. By combining this biosensor with a culture expressing a monooxygenase enzyme, the epoxide biosensor could be converted into an ethylene biosensor.
Journal Article
Embryonal precursors of Wilms tumor
Adult cancers often arise from premalignant clonal expansions. Whether the same is true of childhood tumors has been unclear. To investigate whether Wilms tumor (nephroblastoma; a childhood kidney cancer) develops from a premalignant background, we examined the phylogenetic relationship between tumors and corresponding normal tissues. In 14 of 23 cases studied (61%), we found premalignant clonal expansions in morphologically normal kidney tissues that preceded tumor development. These clonal expansions were defined by somatic mutations shared between tumor and normal tissues but absent from blood cells. We also found hypermethylation of the H19 locus, a known driver of Wilms tumor development, in 58% of the expansions. Phylogenetic analyses of bilateral tumors indicated that clonal expansions can evolve before the divergence of left and right kidney primordia. These findings reveal embryonal precursors from which unilateral and multifocal cancers develop.
Journal Article
Stromal oncostatin M cytokine promotes breast cancer progression by reprogramming the tumor microenvironment
The tumor microenvironment (TME) is reprogrammed by cancer cells and participates in all stages of tumor progression. The contribution of stromal cells to the reprogramming of the TME is not well understood. Here, we provide evidence of the role of the cytokine oncostatin M (OSM) as central node for multicellular interactions between immune and nonimmune stromal cells and the epithelial cancer cell compartment. OSM receptor (OSMR) deletion in a multistage breast cancer model halted tumor progression. We ascribed causality to the stromal function of the OSM axis by demonstrating reduced tumor burden of syngeneic tumors implanted in mice lacking OSMR. Single-cell and bioinformatic analysis of murine and human breast tumors revealed that OSM expression was restricted to myeloid cells, whereas OSMR was detected predominantly in fibroblasts and, to a lower extent, cancer cells. Myeloid-derived OSM reprogrammed fibroblasts to a more contractile and tumorigenic phenotype and elicited the secretion of VEGF and proinflammatory chemokines CXCL1 and CXCL16, leading to increased myeloid cell recruitment. Collectively, our data support the notion that the stromal OSM/OSMR axis reprograms the immune and nonimmune microenvironment and plays a key role in breast cancer progression.
Journal Article
Mesoporous Platinum Films from Lyotropic Liquid Crystalline Phases
The lyotropic liquid crystalline phases of surfactants exhibit a rich polymorphism of structures that have long-range periodicities and whose characteristic repeat distances range from 2 to 15 nanometers. The electrochemical reduction of platinum salts confined to the aqueous environments of these phases leads to the deposition of platinum films that have a well-defined long-ranged porous nanostructure and high specific surface areas. These results suggest that the use of liquid crystalline plating solutions could be a versatile way to create mesoporous electrodes for batteries, fuel cells, electrochemical capacitors, and sensors.
Journal Article
PymiRa: A rapid and accurate classification tool for small non-coding RNAs, including microRNAs
Small non-coding RNAs (sncRNA; < 200 nucleotide length) are of increasing research interest due to their key regulatory roles in a host of fundamental biological processes. For example, microRNAs (miRNAs), a specific class of sncRNAs, regulate gene expression through messenger RNA (mRNA) interactions, and their dysregulation is associated with disease. Classifying sncRNAs is an important bioinformatic task in small RNA-sequencing pipelines. Here we have developed an aligner called PymiRa, written in Python, to identify and quantify miRNAs from FASTA/FASTQ sequencing files. Unlike other approaches, PymiRa utilises a Burrows-Wheeler algorithm to align an input file against a reference hairpin precursor FASTA file derived from miRBase, the online miRNA registry, permitting up to two mismatches at the 3’ end of a read. Previous tools used either a Burrows-Wheeler genome alignment or dynamic programming alignment to precursors; we demonstrate that combining both approaches yields improved results and efficiency. Importantly, the PymiRa aligner accounts for 3’ post-transcriptional modifications to miRNAs that typically occur. PymiRa is a fast, accurate, and publicly accessible aligner available via GitHub and/or a webserver for sncRNA identification, including miRNAs, enabling accurate counts to be produced as part of a small RNA-sequencing pipeline. PymiRa will undergo relevant revisions over time e.g., with miRBase version updates. The PymiRa aligner will facilitate a deeper biological understanding of the landscape of sncRNA expression in normal physiological conditions and their dysregulation in disease states, including cancer.
Journal Article
Seasonal total methane depletion in limestone caves
Methane concentration in caves is commonly much lower than the external atmosphere, yet the cave CH
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depletion causal mechanism is contested and dynamic links to external diurnal and seasonal temperature cycles unknown. Here, we report a continuous 3-year record of cave methane and other trace gases in Jenolan Caves, Australia which shows a seasonal cycle of extreme CH
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depletion, from ambient ~1,775 ppb to near zero during summer and to ~800 ppb in winter. Methanotrophic bacteria, some newly-discovered, rapidly consume methane on cave surfaces and in external karst soils with lifetimes in the cave of a few hours. Extreme bacterial selection due to the absence of alternate carbon sources for growth in the cave environment has resulted in an extremely high proportion 2–12% of methanotrophs in the total bacteria present. Unexpected seasonal bias in our cave CH
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depletion record is explained by a three-step process involving methanotrophy in aerobic karst soil above the cave, summer transport of soil-gas into the cave through epikarst, followed by further cave CH
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depletion. Disentangling cause and effect of cave gas variations by tracing sources and sinks has identified seasonal speleothem growth bias, with implied palaeo-climate record bias.
Journal Article