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https://www.readbyqxmd.com/read/29456625/alignment-of-microbial-fitness-with-engineered-product-formation-obligatory-coupling-between-acetate-production-and-photoautotrophic-growth
#1
Wei Du, Joeri A Jongbloets, Coco van Boxtel, Hugo Pineda Hernández, David Lips, Brett G Oliver, Klaas J Hellingwerf, Filipe Branco Dos Santos
Background: Microbial bioengineering has the potential to become a key contributor to the future development of human society by providing sustainable, novel, and cost-effective production pipelines. However, the sustained productivity of genetically engineered strains is often a challenge, as spontaneous non-producing mutants tend to grow faster and take over the population. Novel strategies to prevent this issue of strain instability are urgently needed. Results: In this study, we propose a novel strategy applicable to all microbial production systems for which a genome-scale metabolic model is available that aligns the production of native metabolites to the formation of biomass...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29456181/an-ultraconserved-element-containing-lncrna-preserves-transcriptional-dynamics-and-maintains-esc-self-renewal
#2
Alessandro Fiorenzano, Emilia Pascale, Miriam Gagliardi, Sara Terreri, Mariarosaria Papa, Gennaro Andolfi, Marco Galasso, Guidantonio Malagoli Tagliazucchi, Cristian Taccioli, Eduardo Jorge Patriarca, Amelia Cimmino, Maria Rosaria Matarazzo, Gabriella Minchiotti, Annalisa Fico
Ultraconserved elements (UCEs) show the peculiar feature to retain extended perfect sequence identity among human, mouse, and rat genomes. Most of them are transcribed and represent a new family of long non-coding RNAs (lncRNAs), the transcribed UCEs (T-UCEs). Despite their involvement in human cancer, the physiological role of T-UCEs is still unknown. Here, we identify a lncRNA containing the uc.170+, named T-UCstem1, and provide in vitro and in vivo evidence that it plays essential roles in embryonic stem cells (ESCs) by modulating cytoplasmic miRNA levels and preserving transcriptional dynamics...
February 8, 2018: Stem Cell Reports
https://www.readbyqxmd.com/read/29455311/accelerated-molecular-breeding-of-a-novel-p-tgms-line-with-broad-spectrum-resistance-to-rice-blast-and-bacterial-blight-in-two-line-hybrid-rice
#3
Jiaming Mi, Dabing Yang, Yi Chen, Jiefeng Jiang, Haipeng Mou, Junbin Huang, Yidan Ouyang, Tongmin Mou
BACKGROUND: Breeding two-line hybrid rice with disease resistance is an effective approach to stabilize rice yield in commercial rice production of China. RESULTS: We improved the blast and bacterial blight resistance of Guangzhan63-4S, an elite photoperiod- and thermo-sensitive male sterile (P/TGMS) line widely used in two-line hybrid rice, by introducing the R genes Pi2 and Xa7 conferring resistance to rice blast and bacterial blight, respectively. Through the backcrossing and gene pyramiding breeding coupled with molecular marker-assisted selection, a new P/TGMS line Hua1228S carrying Pi2, Xa7, and tms5 was developed...
February 17, 2018: Rice
https://www.readbyqxmd.com/read/29454346/agrobacterium-mediated-and-electroporation-mediated-transformation-of-chlamydomonas-reinhardtii-a-comparative-study
#4
Paola Mini, Olivia Costantina Demurtas, Silvia Valentini, Patrizia Pallara, Giuseppe Aprea, Paola Ferrante, Giovanni Giuliano
BACKGROUND: Chlamydomonas reinhardtii is an unicellular green alga used for functional genomics studies and heterologous protein expression. A major hindrance in these studies is the low level and instability of expression of nuclear transgenes, due to their rearrangement and/or silencing over time. RESULTS: We constructed dedicated vectors for Agrobacterium-mediated transformation carrying, within the T-DNA borders, the Paromomycin (Paro) selectable marker and an expression cassette containing the Luciferase (Luc) reporter gene...
February 17, 2018: BMC Biotechnology
https://www.readbyqxmd.com/read/29454317/oxidative-damage-and-response-to-bacillus-calmette-gu%C3%A3-rin-in-bladder-cancer-cells-expressing-sialyltransferase-st3gal1
#5
Paulo F Severino, Mariana Silva, Mylene Carrascal, Nadia Malagolini, Mariella Chiricolo, Giulia Venturi, Roberto Barbaro Forleo, Annalisa Astolfi, Mariangela Catera, Paula A Videira, Fabio Dall'Olio
BACKGROUND: Treatment with Bacillus Calmette-Guérin (BCG) is the gold standard adjuvant immunotherapy of non-muscle invasive bladder cancer (NMIBC), although it fails in one third of the patients. NMIBC expresses two tumor-associated O-linked carbohydrates: the disaccharide (Galβ1,3GalNAc) Thomsen-Friedenreich (T) antigen, and its sialylated counterpart (Siaα2,3Galβ1,3GalNAc) sialyl-T (sT), synthesized by sialyltransferase ST3GAL1, whose roles in BCG response are unknown. METHODS: The human bladder cancer (BC) cell line HT1376 strongly expressing the T antigen, was retrovirally transduced with the ST3GAL1 cDNA or with an empty vector, yielding the cell lines HT1376sT and HT1376T , that express, respectively, either the sT or the T antigens...
February 17, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29454225/low-power-lasers-on-genomic-stability
#6
Larissa Alexsandra da Silva Neto Trajano, Luiz Philippe da Silva Sergio, Ana Carolina Stumbo, Andre Luiz Mencalha, Adenilson de Souza da Fonseca
Exposure of cells to genotoxic agents causes modifications in DNA, resulting to alterations in the genome. To reduce genomic instability, cells have DNA damage responses in which DNA repair proteins remove these lesions. Excessive free radicals cause DNA damages, repaired by base excision repair and nucleotide excision repair pathways. When non-oxidative lesions occur, genomic stability is maintained through checkpoints in which the cell cycle stops and DNA repair occurs. Telomere shortening is related to the development of various diseases, such as cancer...
February 10, 2018: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/29454054/genomic-perspectives-of-spider-silk-genes-through-target-capture-sequencing-conservation-of-stabilization-mechanisms-and-homology-based-structural-models-of-spidroin-terminal-regions
#7
Matthew A Collin, Thomas H Clarke, Nadia A Ayoub, Cheryl Y Hayashi
A powerful system for studying protein aggregation, particularly rapid self-assembly, is spider silk. Spider silks are proteinaceous and silk proteins are synthesized and stored within silk glands as liquid dope. As needed, liquid dope is near-instantaneously transformed into solid fibers or viscous adhesives. The dominant constituents of silks are spidroins (spider fibroins) and their terminal domains are vital for the tight control of silk self-assembly. To better understand spidroin termini, we used target capture and deep sequencing to identify spidroin gene sequences from six species representing the araneoid families of Araneidae, Nephilidae, and Theridiidae...
February 14, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29453964/conidiogenesis-related-dna-photolyase-gene-in-beauveria-bassiana
#8
Se Jin Lee, Mi Rong Lee, Sihyeon Kim, Jong Cheol Kim, So Eun Park, Tae Young Shin, Jae Su Kim
Beauveria bassiana is an entomopathogenic fungi used in environmentally mindful pest management. Its main active ingredient, conidia, is commercially available as a fungal biopesticide. Many studies of conidia production have focused on how to optimize culture conditions for maximum productivity and stability against unfavorable abiotic factors. However, understanding of how conidiogenesis-related genes provide improved conidial production remains unclear. In this study, we focus on identifying conidiogenesis-related genes in B...
February 14, 2018: Journal of Invertebrate Pathology
https://www.readbyqxmd.com/read/29450416/a-g-quadruplex-motif-at-the-3-end-of-sgrnas-improves-crispr-cas9-based-genome-editing-efficiency
#9
Smita Nahar, Paras Sehgal, Mohd Azhar, Manish Rai, Amrita Singh, Sridhar Sivasubbu, Debojyoti Chakraborty, Souvik Maiti
Originating as a component of prokaryotic adaptive immunity, the type II CRISPR/Cas9 system has been repurposed for targeted genome editing in various organisms. Although Cas9 can bind and cleave DNA efficiently under in vitro conditions, its activity inside a cell can vary dramatically between targets owing to the differences between genomic loci and the availability of enough Cas9/sgRNA (single guide RNA) complex molecules for cleavage. Most methods have so far relied on Cas9 protein engineering or base modifications in the sgRNA sequence to improve CRISPR/Cas9 activity...
February 16, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29449677/usp35-regulates-mitotic-progression-by-modulating-the-stability-of-aurora-b
#10
Jinyoung Park, Mi-Sun Kwon, Eunice EunKyeong Kim, Hyunsook Lee, Eun Joo Song
Although approximately 100 deubiquitinating enzymes (DUBs) are encoded in the human genome, very little is known about the DUBs that function in mitosis. Here, we demonstrate that DUB USP35 functions as a mitotic regulator by controlling the protein levels and downstream signaling of Aurora B and the depletion of USP35 eventually leads to several mitotic defects including cytokinesis failures. USP35 binds to and deubiquitinates Aurora B, and inhibits the APC CDH1 -mediated proteasomal degradation of Aurora B, thus maintaining its steady-state levels during mitosis...
February 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29447390/pold3-is-required-for-genomic-stability-and-telomere-integrity-in-embryonic-stem-cells-and-meiosis
#11
Zhongcheng Zhou, Lingling Wang, Feixiang Ge, Peng Gong, Hua Wang, Feng Wang, Lingyi Chen, Lin Liu
Embryonic stem cells (ESCs) and meiosis are featured by relatively higher frequent homologous recombination associated with DNA double strand breaks (DSB) repair. Here, we show that Pold3 plays important roles in DSB repair, telomere maintenance and genomic stability of both ESCs and spermatocytes in mice. By attempting to generate Pold3 deficient mice using CRISPR/Cas9 or transcription activator-like effector nucleases, we show that complete loss of Pold3 (Pold3-/-) resulted in early embryonic lethality at E6...
February 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29444942/a-functional-link-between-rna-replication-and-virion-assembly-in-the-potyvirus-plum-pox-virus
#12
Araiz Gallo, Adrian Valli, María Calvo, Juan Antonio García
Accurate assembly of viral particles in the potyvirus Plum pox virus (PPV) has been shown to depend on the contribution of the multifunctional viral protein HCPro. In this study, we show that other viral factors, in addition to the capsid protein (CP) and HCPro, are necessary for the formation of stable PPV virions. The CP produced in Nicotiana benthamiana leaves from a subviral RNA termed LONG, which expresses a truncated polyprotein that lacks P1 and HCPro, together with HCPro supplied in trans , was assembled into virus like particles and remained stable after in vitro incubation...
February 14, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29444484/application-of-a-new-targeted-low-density-microarray-and-conventional-biomarkers-to-evaluate-the-health-status-of-marine-mussels-a-field-study-in-sardinian-coast-italy
#13
Susanna Sforzini, Caterina Oliveri, Andrea Orrù, Giannina Chessa, Beniamina Pacchioni, Caterina Millino, Awadhesh N Jha, Aldo Viarengo, Mohamed Banni
In the present study, we investigated the health status of marine mussels (Mytilus galloprovincialis) caged and deployed at three different sites on the Sardinian coastline characterized by different levels of contamination: Fornelli (F, the reference site), Cala Real (CR), and Porto Torres (PT). A new low density oligonucleotide microarray was used to investigate global gene expression in the digestive gland of mussels. Target genes were selected to cover most of the biological processes involved in the stress response in bivalve mollusks (e...
February 11, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29444437/mutations-in-cytosine-5-trna-methyltransferases-impact-mobile-element-expression-and-genome-stability-at-specific-dna-repeats
#14
Bianca Genenncher, Zeljko Durdevic, Katharina Hanna, Daniela Zinkl, Mehrpouya Balaghy Mobin, Nevcin Senturk, Bruno Da Silva, Carine Legrand, Clément Carré, Frank Lyko, Matthias Schaefer
The maintenance of eukaryotic genome stability is ensured by the interplay of transcriptional as well as post-transcriptional mechanisms that control recombination of repeat regions and the expression and mobility of transposable elements. We report here that mutations in two (cytosine-5) RNA methyltransferases, Dnmt2 and NSun2, impact the accumulation of mobile element-derived sequences and DNA repeat integrity in Drosophila. Loss of Dnmt2 function caused moderate effects under standard conditions, while heat shock exacerbated these effects...
February 13, 2018: Cell Reports
https://www.readbyqxmd.com/read/29444145/waggawagga-cli-a-command-line-tool-for-predicting-stable-single-%C3%AE-helices-sah-domains-and-the-sah-domain-distribution-across-eukaryotes
#15
Dominic Simm, Martin Kollmar
Stable single-alpha helices (SAH-domains) function as rigid connectors and constant force springs between structural domains, and can provide contact surfaces for protein-protein and protein-RNA interactions. SAH-domains mainly consist of charged amino acids and are monomeric and stable in polar solutions, characteristics which distinguish them from coiled-coil domains and intrinsically disordered regions. Although the number of reported SAH-domains is steadily increasing, genome-wide analyses of SAH-domains in eukaryotic genomes are still missing...
2018: PloS One
https://www.readbyqxmd.com/read/29442729/genomic-and-proteomic-evidences-for-exopolysaccharide-biosynthesis-in-sphingobium-chungbukense-dj77
#16
Soo Youn Lee, Simranjeet Singh Sekhon, Mihye Kim, Ji-Young Ahn, Hyung Cheol Kim, Young-Chang Kim, Yang-Hoon Kim
Sphingobium chungbukense DJ77 is a Gram-negative bacterium has metabolic capability of producing exopolysaccharide (EPS) as a potential reducing and stabilizing agent for metallic nanoparticle synthesis. In this study, we investigated the genomic and proteomic analysis to verify metabolic pathway and involved genes and enzymes related to EPS biosynthesis in S. chungbukense DJ77. End-sequencing results of randomly selected fosmid library, which were prepared from high molecular weight DNA of S. chungbukense DJ77, showed identity to sequences from genes related the EPS biosynthesis pathways in several bacteria...
June 1, 2018: Journal of Nanoscience and Nanotechnology
https://www.readbyqxmd.com/read/29439654/prospective-study-on-human-fecal-carriage-of-enterobacteriaceae-possessing-mcr-1-and-mcr-2-genes-in-a-regional-hospital-in-hong-kong
#17
Wai-Sing Chan, Chun-Hang Au, Dona N Ho, Tsun-Leung Chan, Edmond Shiu-Kwan Ma, Bone Siu-Fai Tang
BACKGROUND: Human fecal carriage of Enterobacteriaceae possessing mobilized colistin resistance genes (mcr-1 and mcr-2) remains obscure in Hong Kong. As part of routine surveillance on emerging antibiotic resistance, we conducted a prospective study on this topic in a regional hospital in Hong Kong. METHODS: From October 31 to November 25, 2016, all fecal specimens submitted for routine analysis were included in this surveillance study. These comprised 672 consecutive routine fecal specimens collected from 616 individuals...
February 13, 2018: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29435408/a-putative-rna-binding-protein-from-plasmodium-vivax-apicoplast
#18
Sofía M García-Mauriño, Antonio Díaz-Quintana, Francisco Rivero-Rodríguez, Isabel Cruz-Gallardo, Christian Grüttner, Marian Hernández-Vellisca, Irene Díaz-Moreno
Malaria is caused by Apicomplexa protozoans from the Plasmodium genus entering the bloodstream of humans and animals through the bite of the female mosquitoes. The annotation of the Plasmodium vivax genome revealed a putative RNA binding protein (apiRBP) that was predicted to be trafficked into the apicoplast, a plastid organelle unique to Apicomplexa protozoans. Although a 3D structural model of the apiRBP corresponds to a noncanonical RNA recognition motif with an additional C-terminal α-helix (α3), preliminary protein production trials were nevertheless unsuccessful...
February 2018: FEBS Open Bio
https://www.readbyqxmd.com/read/29435268/common-mental-disorders-and-association-with-telomere-length
#19
E Vakonaki, K Tsiminikaki, S Plaitis, P Fragkiadaki, D Tsoukalas, I Katsikantami, G Vaki, M N Tzatzarakis, D A Spandidos, A M Tsatsakis
Telomeres are repeated 5'-TTAGGG-3' sequences at the end of chromosomes, which maintain genomic stability. Their length is related to a number of diseases that affect humans. Apart from cancer, cardiovascular diseases, diabetes and other, telomere length has been associated with chronic diseases. Chronic mental illness includes various types of mental disorders with the most common being depression, schizophrenia and stress-anxiety. The aim of this review is to summarize the current state of knowledge on the role of telomeres in these disorders and to compare telomere length variations in patients receiving medication and patients not taking treatment...
February 2018: Biomedical Reports
https://www.readbyqxmd.com/read/29435132/suppression-of-homology-dependent-dna-double-strand-break-repair-induces-parp-inhibitor-sensitivity-in-vhl-deficient-human-renal-cell-carcinoma
#20
Susan E Scanlon, Denise C Hegan, Parker L Sulkowski, Peter M Glazer
The von Hippel-Lindau ( VHL ) tumor suppressor gene is inactivated in the vast majority of human clear cell renal carcinomas. The pathogenesis of VHL loss is currently best understood to occur through stabilization of the hypoxia-inducible factors, activation of hypoxia-induced signaling pathways, and transcriptional reprogramming towards a pro-angiogenic and pro-growth state. However, hypoxia also drives other pro-tumorigenic processes, including the development of genomic instability via down-regulation of DNA repair gene expression...
January 12, 2018: Oncotarget
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