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Forward genetics

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https://www.readbyqxmd.com/read/28546435/a-simple-pipeline-for-mapping-point-mutations
#1
Guy Wachsman, Jennifer L Modliszewski, Manuel Valdes, Philip N Benfey
A forward genetic screen is one of the best methods for revealing the function of genes. In plants, this technique is highly efficient as it is relatively easy to grow and screen hundreds or thousands of individuals. The cost-efficiency and ease of data production afforded by next-generation sequencing has created new opportunities for rapid mapping of induced mutations. Current mapping tools are often not user-friendly, complicated, or require extensive preparation steps. To simplify the process of mapping new mutations, we developed a pipeline that takes next generation sequencing fastq files as input, calls on several well-established and freely available genome-analysis tools, and outputs the most likely causal DNA changes...
May 25, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28540471/genetic-characterization-of-the-honeybee-ectoparasitic-mite-varroa-destructor-from-benin-west-africa-using-mitochondrial-and-microsatellite-markers
#2
Aude E Kelomey, Armand Paraiso, Haziz Sina, Hélène Legout, Lionel Garnery, Lamine Baba-Moussa
Varroa destructor is one of the scourges of global beekeeping. It was detected for the first time in Benin in 2011 on the honeybee Apis mellifera adansonii. The aim of this study was to identify the strain of Varroa sp. found and study its genetic diversity. In total 183 Varroa mites were sampled in 21 municipalities in Benin. The COI intergenic region of each mite mtDNA was amplified by PCR. The SacI restriction enzyme was used to determine the strains of Varroa sp. Only the Korean (K) haplotype, identical to the most prevalent strain in Africa, was detected...
May 24, 2017: Experimental & Applied Acarology
https://www.readbyqxmd.com/read/28540163/dissecting-the-role-of-amp-activated-protein-kinase-in-human-diseases
#3
REVIEW
Jin Li, Liping Zhong, Fengzhong Wang, Haibo Zhu
AMP-activated protein kinase (AMPK), known as a sensor and a master of cellular energy balance, integrates various regulatory signals including anabolic and catabolic metabolic processes. Accompanying the application of genetic methods and a plethora of AMPK agonists, rapid progress has identified AMPK as an attractive therapeutic target for several human diseases, such as cancer, type 2 diabetes, atherosclerosis, myocardial ischemia/reperfusion injury and neurodegenerative disease. The role of AMPK in metabolic and energetic modulation both at the intracellular and whole body levels has been reviewed elsewhere...
May 2017: Acta Pharmaceutica Sinica. B
https://www.readbyqxmd.com/read/28536847/an-empirical-investigation-of-the-possibility-of-adaptability-of-arbuscular-mycorrhizal-fungi-to-new-hosts
#4
Akihiro Koyama, Olivia Pietrangelo, Laura Sanderson, Pedro M Antunes
Little is known about the adaptive capacity of arbuscular mycorrhizal (AM) fungi to novel hosts. Here we assessed the possibility of two heterospecific AM fungal isolates to adaptively change, in terms of host biomass response, as a function of host plant identity, over the course of a growing season. First, we produced pure inocula of Rhizophagus clarus and Rhizophagus intraradices, each starting from a single spore. Second, we "trained" each isolate individually in a community with two plants, sudangrass (Sorgum bicolour subsp...
May 24, 2017: Mycorrhiza
https://www.readbyqxmd.com/read/28535375/morc-1-integrates-nuclear-rnai-and-transgenerational-chromatin-architecture-to-promote-germline-immortality
#5
Natasha E Weiser, Danny X Yang, Suhua Feng, Natallia Kalinava, Kristen C Brown, Jayshree Khanikar, Mallory A Freeberg, Martha J Snyder, Györgyi Csankovszki, Raymond C Chan, Sam G Gu, Taiowa A Montgomery, Steven E Jacobsen, John K Kim
Germline-expressed endogenous small interfering RNAs (endo-siRNAs) transmit multigenerational epigenetic information to ensure fertility in subsequent generations. In Caenorhabditis elegans, nuclear RNAi ensures robust inheritance of endo-siRNAs and deposition of repressive H3K9me3 marks at target loci. How target silencing is maintained in subsequent generations is poorly understood. We discovered that morc-1 is essential for transgenerational fertility and acts as an effector of endo-siRNAs. Unexpectedly, morc-1 is dispensable for siRNA inheritance but is required for target silencing and maintenance of siRNA-dependent chromatin organization...
May 22, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28533456/colour-vision-and-coevolution-in-avian-brood-parasitism
#6
REVIEW
Mary Caswell Stoddard, Mark E Hauber
The coevolutionary interactions between avian brood parasites and their hosts provide a powerful system for investigating the diversity of animal coloration. Specifically, reciprocal selection pressure applied by hosts and brood parasites can give rise to novel forms and functions of animal coloration, which largely differ from those that arise when selection is imposed by predators or mates. In the study of animal colours, avian brood parasite-host dynamics therefore invite special consideration. Rapid advances across disciplines have paved the way for an integrative study of colour and vision in brood parasite-host systems...
July 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28533440/identification-and-characterization-of-caenorhabditis-elegans-rnai-inheritance-machinery
#7
George Spracklin, Brandon Fields, Gang Wan, Diveena Vijayendran, Ashley Wallig, Aditi Shukla, Scott Kennedy
Gene silencing mediated by dsRNA (RNAi) can persist for multiple generations in Caenorhabditis elegans (termed RNAi inheritance). Here we describe the results of a forward genetic screen in C. elegans that has identified six factors required for RNAi inheritance: GLH-1/VASA, PUP-1/CDE-1, MORC-1, SET-32, and two novel nematode specific factors that we term here (heritable RNAi defective) HRDE-2 and HRDE-4. The new RNAi inheritance factors exhibit mortal germline (Mrt) phenotypes, which we show is likely caused by epigenetic deregulation in germ cells...
May 22, 2017: Genetics
https://www.readbyqxmd.com/read/28532592/extending-the-scope-of-eco-labelling-in-the-food-industry-to-drive-change-beyond-sustainable-agriculture-practices
#8
Marco A Miranda-Ackerman, Catherine Azzaro-Pantel
New consumer awareness is shifting industry towards more sustainable practices, creating a virtuous cycle between producers and consumers enabled by eco-labelling. Eco-labelling informs consumers of specific characteristics of products and has been used to market greener products. Eco-labelling in the food industry has yet been mostly focused on promoting organic farming, limiting the scope to the agricultural stage of the supply chain, while carbon labelling informs on the carbon footprint throughout the life cycle of the product...
May 19, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28530678/the-complex-genetics-of-hypoplastic-left-heart-syndrome
#9
Xiaoqin Liu, Hisato Yagi, Shazina Saeed, Abha S Bais, George C Gabriel, Zhaohan Chen, Kevin A Peterson, You Li, Molly C Schwartz, William T Reynolds, Manush Saydmohammed, Brian Gibbs, Yijen Wu, William Devine, Bishwanath Chatterjee, Nikolai T Klena, Dennis Kostka, Karen L de Mesy Bentley, Madhavi K Ganapathiraju, Phillip Dexheimer, Linda Leatherbury, Omar Khalifa, Anchit Bhagat, Maliha Zahid, William Pu, Simon Watkins, Paul Grossfeld, Stephen A Murray, George A Porter, Michael Tsang, Lisa J Martin, D Woodrow Benson, Bruce J Aronow, Cecilia W Lo
Congenital heart disease (CHD) affects up to 1% of live births. Although a genetic etiology is indicated by an increased recurrence risk, sporadic occurrence suggests that CHD genetics is complex. Here, we show that hypoplastic left heart syndrome (HLHS), a severe CHD, is multigenic and genetically heterogeneous. Using mouse forward genetics, we report what is, to our knowledge, the first isolation of HLHS mutant mice and identification of genes causing HLHS. Mutations from seven HLHS mouse lines showed multigenic enrichment in ten human chromosome regions linked to HLHS...
May 22, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28530119/update-in-sleep-disordered-breathing-2016
#10
Najib T Ayas, Luciano F Drager, Mary J Morrell, Vsevolod Y Polotsky
The field of sleep disordered breathing has continued to evolve with many important articles published in the last year. In this review, we have summarized some of the key articles relevant to sleep disordered breathing that have been published in the Journal and selected articles published elsewhere in the last year; these have included landmark randomized trials concerning sleep apnea treatment in the prevention of adverse cardiac outcomes, basic science and animal studies, genetic studies, and analyses of epidemiologic cohorts...
May 21, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28527809/accuracy-of-genomic-predictions-in-gyr-bos-indicus-dairy-cattle
#11
S A Boison, A T H Utsunomiya, D J A Santos, H H R Neves, R Carvalheiro, G Mészáros, Y T Utsunomiya, A S do Carmo, R S Verneque, M A Machado, J C C Panetto, J F Garcia, J Sölkner, M V G B da Silva
Genomic selection may accelerate genetic progress in breeding programs of indicine breeds when compared with traditional selection methods. We present results of genomic predictions in Gyr (Bos indicus) dairy cattle of Brazil for milk yield (MY), fat yield (FY), protein yield (PY), and age at first calving using information from bulls and cows. Four different single nucleotide polymorphism (SNP) chips were studied. Additionally, the effect of the use of imputed data on genomic prediction accuracy was studied...
May 17, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28522215/blocking-voltage-gated-sodium-channels-as-a-strategy-to-suppress-pathological-cough
#12
REVIEW
Hui Sun, Marian Kollarik, Bradley J Undem
Pathological cough is thought to be secondary to inappropriate activation of vagal sensory nerves. Sensory nerves can be activated by a large number of disparate stimuli. The most relevant stimuli to block for effective anti-tussive therapy likely depend on the specific underlying pathology that is leading to the coughing. Blocking voltage-gated sodium channels (NaV) will prevent action potential initiation and conduction and therefore prevent sensory communication between the airways and brainstem. In so doing, they would be expected to inhibit evoked cough independently of the nature of the stimulus and underlying pathology...
May 15, 2017: Pulmonary Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28520773/development-of-the-highly-sensitive-dog-questionnaire-to-evaluate-the-personality-dimension-sensory-processing-sensitivity-in-dogs
#13
Maya Braem, Lucy Asher, Sibylle Furrer, Isabel Lechner, Hanno Würbel, Luca Melotti
In humans, the personality dimension 'sensory processing sensitivity (SPS)', also referred to as "high sensitivity", involves deeper processing of sensory information, which can be associated with physiological and behavioral overarousal. However, it has not been studied up to now whether this dimension also exists in other species. SPS can influence how people perceive the environment and how this affects them, thus a similar dimension in animals would be highly relevant with respect to animal welfare. We therefore explored whether SPS translates to dogs, one of the primary model species in personality research...
2017: PloS One
https://www.readbyqxmd.com/read/28515773/building-a-multipurpose-insertional-mutant-library-for-forward-and-reverse-genetics-in-chlamydomonas
#14
Xi Cheng, Gai Liu, Wenting Ke, Lijuan Zhao, Bo Lv, Xiaocui Ma, Nannan Xu, Xiaoling Xia, Xuan Deng, Chunlei Zheng, Kaiyao Huang
BACKGROUND: The unicellular green alga, Chlamydomonas reinhardtii, is a classic model for studying flagella and biofuel. However, precise gene editing, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas9) system, is not widely used in this organism. Screening of random insertional mutant libraries by polymerase chain reaction provides an alternate strategy to obtain null mutants of individual gene. But building, screening, and maintaining such a library was time-consuming and expensive...
2017: Plant Methods
https://www.readbyqxmd.com/read/28514493/the-narrow-road-to-the-deep-past
#15
Jack W Szostak
The sequence of events that gave rise to the first life on our planet took place in the Earth's deep past, seemingly forever beyond our reach. Perhaps for that very reason the idea of reconstructing our ancient story is tantalizing, almost irresistible. Understanding the processes that led to synthesis of the chemical building blocks of biology and the ways in which these molecules self-assembled into cells that could grow, divide and evolve, nurtured by a rich and complex environment, seems at times insurmountably difficult...
May 17, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28512313/a-rapid-capillary-pressure-driven-micro-channel-to-demonstrate-newtonian-fluid-behavior-of-zebrafish-blood-at-high-shear-rates
#16
Juhyun Lee, Tzu-Chieh Chou, Dongyang Kang, Hanul Kang, Junjie Chen, Kyung In Baek, Wei Wang, Yichen Ding, Dino Di Carlo, Yu-Chong Tai, Tzung K Hsiai
Blood viscosity provides the rheological basis to elucidate shear stress underlying developmental cardiac mechanics and physiology. Zebrafish is a high throughput model for developmental biology, forward-genetics, and drug discovery. The micro-scale posed an experimental challenge to measure blood viscosity. To address this challenge, a microfluidic viscometer driven by surface tension was developed to reduce the sample volume required (3μL) for rapid (<2 min) and continuous viscosity measurement. By fitting the power-law fluid model to the travel distance of blood through the micro-channel as a function of time and channel configuration, the experimentally acquired blood viscosity was compared with a vacuum-driven capillary viscometer at high shear rates (>500 s(-1)), at which the power law exponent (n) of zebrafish blood was nearly 1 behaving as a Newtonian fluid...
May 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28510361/chlamydia-trachomatis-transformation-and-allelic-exchange-mutagenesis
#17
Konrad E Mueller, Katerina Wolf, Kenneth A Fields
Gene inactivation is essential for forward and reverse genetic approaches to establish protein function. Techniques such as insertion or chemical mutagenesis have been developed to mutagenize chlamydiae via targeted or random mutagenesis, respectively. Both of these approaches require transformation of chlamydiae to either introduce insertion elements or complement mutants. We have recently developed a targeted mutagenesis strategy, fluorescence-reported allelic exchange mutagenesis (FRAEM), to delete Chlamydia trachomatis L2 genes...
May 16, 2017: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/28509909/experimental-evolution-and-the-dynamics-of-adaptation-and-genome-evolution-in-microbial-populations
#18
Richard E Lenski
Evolution is an on-going process, and it can be studied experimentally in organisms with rapid generations. My team has maintained 12 populations of Escherichia coli in a simple laboratory environment for >25 years and 60 000 generations. We have quantified the dynamics of adaptation by natural selection, seen some of the populations diverge into stably coexisting ecotypes, described changes in the bacteria's mutation rate, observed the new ability to exploit a previously untapped carbon source, characterized the dynamics of genome evolution and used parallel evolution to identify the genetic targets of selection...
May 16, 2017: ISME Journal
https://www.readbyqxmd.com/read/28509084/whole-exome-sequencing-identifies-a-novel-homozygous-frameshift-mutation-in-the-mtmr2-gene-as-a-causative-mutation-in-a-patient-with-charcot-marie-tooth-disease-type-4b1
#19
Tameemi Abdalla-Moady, Amir Peleg, Orit Sadeh, Khader Badarneh, Fuad Fares
Charcot-Marie-Tooth (CMT) disease refers to a heterogeneous group of axonal and demyelinating polyneuropathies, characterized by chronic motor and sensory dysfunction. CMT is the most common genetic cause of neuropathy. The present study aimed to identify the gene mutation responsible for CMT in Ashkenazi Jew (AJ) patient. Genomic DNA was extracted from whole blood leukocytes of affected family and normal subject. Whole-exome sequencing was performed using the Illumina HiSeq2500. The DNA region containing the identified mutation was amplified by PCR and sequenced using dye-terminator chemistry and the forward primer...
May 16, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28508221/rapid-reverse-genetics-systems-for-rhabdoviruses-from-forward-to-reverse-and-back-again
#20
Tobias Nolden, Stefan Finke
Methods to recover recombinant negative strand RNA viruses (rNSVs) from cloned cDNAs have been significantly improved in more than two decades of NSV reverse genetics . In particular, for non-segmented negative strand RNA viruses (NNSVs ) like rhabdoviruses , time-consuming generation of reverse genetics systems by stitching PCR subfragments of genomic rhabdovirus cDNAs using ligase-based conventional cloning approaches limited the number of available recombinant virus cDNA clones. As genetic variability is considered an intrinsic feature of RNA viruses, it is thus reasonable to conclude that reverse genetics approaches to investigate natural virus functions and pathogenesis require improved systems that reflect the complexity of naturally occurring wild-type viruses, and that largely exclude adaption to cell culture conditions...
2017: Methods in Molecular Biology
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