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An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi.

Genetics 2021 May 4. Epub 2021 May 4.

Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA.

Aspergillosis is an important opportunistic human disease caused by filamentous fungi in the genus Aspergillus. Roughly 70% of infections are caused by Aspergillus fumigatus, with the rest stemming from approximately a dozen other Aspergillus species. Several of these pathogens are closely related to A. Read More

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Using CRISPR-Cas9-based genome engineering tools in Drosophila melanogaster.

Authors:
Deepti Trivedi

Prog Mol Biol Transl Sci 2021 15;180:85-121. Epub 2021 Feb 15.

National Centre for Biological Sciences-TIFR, Bengaluru, India. Electronic address:

Drosophila melanogaster has been used as a model organism for over a century. Mutant-based analyses have been used extensively to understand the genetic basis of different cellular processes, including development, neuronal function and diseases. Most of the earlier genetic mutants and specific tools were generated by random insertions and deletion strategies and then mapped to specific genomic loci. Read More

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February 2021

AAV-HDV: An Attractive Platform for the In Vivo Study of HDV Biology and the Mechanism of Disease Pathogenesis.

Viruses 2021 Apr 28;13(5). Epub 2021 Apr 28.

Programa de Terapia Génica y Regulación de la Expresión Génica, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Avenida Pío XII, 31080 Pamplona, Spain.

Hepatitis delta virus (HDV) infection causes the most severe form of viral hepatitis, but little is known about the molecular mechanisms involved. We have recently developed an HDV mouse model based on the delivery of HDV replication-competent genomes using adeno-associated vectors (AAV), which developed a liver pathology very similar to the human disease and allowed us to perform mechanistic studies. We have generated different AAV-HDV mutants to eliminate the expression of HDV antigens (HDAgs), and we have characterized them both in vitro and in vivo We confirmed that S-HDAg is essential for HDV replication and cannot be replaced by L-HDAg or host cellular proteins, and that L-HDAg is essential to produce the HDV infectious particle and inhibits its replication. Read More

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Mind the Gap: LRRK2 Phenotypes in the Clinic vs. in Patient Cells.

Cells 2021 Apr 22;10(5). Epub 2021 Apr 22.

UMR-S 1172-LilNCog-Lille Neuroscience & Cognition, Université de Lille, Inserm, CHU Lille, F-59000 Lille, France.

Mutations in the Parkinson's disease (PD) protein Leucine Rich Repeat Kinase 2 (LRRK2) have been under study for more than 15 years and our understanding of the cellular phenotypes for the pathogenic mutant forms of LRRK2 has significantly advanced. In parallel to research on LRRK2 mutations in experimental systems, clinical characterization of patients carrying LRRK2 mutations has advanced, as has the analysis of cells that are derived from these patients, including fibroblasts, blood-derived cells, or cells rendered pluripotent. Under the hypothesis that patient clinical phenotypes are a consequence of a cascade of underlying molecular mechanisms gone astray, we currently have a unique opportunity to compare findings from patients and patient-derived cells to ask the question of whether the clinical phenotype of LRRK2 Parkinson's disease and cellular phenotypes of LRRK2 patient-derived cells may be mutually informative. Read More

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Extremely Thermostabilizing Core Mutations in Coiled-Coil Mimetic Proteins of HIV-1 gp41 Produce Diverse Effects on Target Binding but Do Not Affect Their Inhibitory Activity.

Biomolecules 2021 Apr 12;11(4). Epub 2021 Apr 12.

Departamento de Química Física, Instituto de Biotecnología, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.

A promising strategy to neutralize HIV-1 is to target the gp41 spike subunit to block membrane fusion with the cell. We previously designed a series of single-chain proteins (named covNHR) that mimic the trimeric coiled-coil structure of the gp41 N-terminal heptad repeat (NHR) region and potently inhibit HIV-1 cell infection by avidly binding the complementary C-terminal heptad repeat (CHR) region. These proteins constitute excellent tools to understand the structural and thermodynamic features of this therapeutically important interaction. Read More

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Development in the Mammalian Auditory System Depends on Transcription Factors.

Int J Mol Sci 2021 Apr 18;22(8). Epub 2021 Apr 18.

Department of Biology, University of Iowa, Iowa City, IA 52242, USA.

We review the molecular basis of several transcription factors (, ), including the three related genes coding basic helix-loop-helix (bHLH; see abbreviations) proteins (, , ) during the development of spiral ganglia, cochlear nuclei, and cochlear hair cells. Neuronal development requires followed by its downstream target , to cross-regulate expression. In contrast, hair cells and cochlear nuclei critically depend on and require expression for interactions with . Read More

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Alternative σ Factors Regulate Overlapping as Well as Distinct Stress Response and Metabolic Functions in under Stationary Phase Stress Condition.

Pathogens 2021 Apr 1;10(4). Epub 2021 Apr 1.

Department of Food Science, Cornell University, Ithaca, NY 14853, USA.

can regulate and fine-tune gene expression, to adapt to diverse stress conditions encountered during foodborne transmission. To further understand the contributions of alternative sigma (σ) factors to the regulation of gene expression, RNA-Seq was performed on strain 10403S and five isogenic mutants (four strains bearing in-frame null mutations in three out of four alternative σ factor genes, ΔCHL, ΔBHL, ΔBCL, and ΔBCH, and one strain bearing null mutations in all four genes, ΔBCHL), grown to stationary phase. Our data showed that 184, 35, 34, and 20 genes were positively regulated by σ, σ, σ, and σ (posterior probability > 0. Read More

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Fitness selection of hyperfusogenic measles virus F proteins associated with neuropathogenic phenotypes.

Proc Natl Acad Sci U S A 2021 May;118(18)

Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029;

Measles virus (MeV) is resurgent and caused >200,000 deaths in 2019. MeV infection can establish a chronic latent infection of the brain that can recrudesce months to years after recovery from the primary infection. Recrudescent MeV leads to fatal subacute sclerosing panencephalitis (SSPE) or measles inclusion body encephalitis (MIBE) as the virus spreads across multiple brain regions. Read More

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A complex genetic architecture in zebrafish relatives Danio quagga and D. kyathit underlies development of stripes and spots.

PLoS Genet 2021 Apr 26;17(4):e1009364. Epub 2021 Apr 26.

Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America.

Vertebrate pigmentation is a fundamentally important, multifaceted phenotype. Zebrafish, Danio rerio, has been a valuable model for understanding genetics and development of pigment pattern formation due to its genetic and experimental tractability, advantages that are shared across several Danio species having a striking array of pigment patterns. Here, we use the sister species D. Read More

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Genome Sequence of Lactiplantibacillus plantarum DmPark25_157, a Bacterial Strain Isolated from Drosophila melanogaster.

Microbiol Resour Announc 2021 Apr 22;10(16). Epub 2021 Apr 22.

Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA

We present the genome sequence of a bacterial strain isolated from mutants of as part of efforts to better understand the microbial communities in We isolated and sequenced a strain. We present a preliminary comparative analysis with a closely related strain. Read More

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Mechanosensitive myosin II but not cofilin primarily contributes to cyclic cell stretch-induced selective disassembly of actin stress fibers.

Am J Physiol Cell Physiol 2021 Apr 21. Epub 2021 Apr 21.

Division of Bioengineering, Graduate School of Engineering Science, Osaka University, Japan.

Cells adapt to applied cyclic stretch (CS) to circumvent chronic activation of proinflammatory signaling. Currently, the molecular mechanism of the selective disassembly of actin stress fibers (SFs) in the stretch direction, which occurs at the early stage of the cellular response to CS, remains controversial. Here we suggest that the mechanosensitive behavior of myosin II, a major cross-linker of SFs, primarily contributes to the directional disassembly of the actomyosin complex SFs in bovine vascular smooth muscle cells and human U2OS osteosarcoma cells. Read More

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N-Acyl Homoserine Lactone-Mediated Quorum Sensing Regulates Species Interactions in Multispecies Biofilm Communities.

Front Cell Infect Microbiol 2021 18;11:646991. Epub 2021 Mar 18.

Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.

Bacterial biofilms are important medically, environmentally and industrially and there is a need to understand the processes that govern functional synergy and dynamics of species within biofilm communities. Here, we have used a model, mixed-species biofilm community comprised of PAO1, Pf-5 and KP1. This biofilm community displays higher biomass and increased resilience to antimicrobial stress conditions such as sodium dodecyl sulfate and tobramycin, compared to monospecies biofilm populations. Read More

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Design for Systems-Based Metabolic Engineering for the Bioconversion of Valuable Compounds From Industrial By-Products.

Front Genet 2021 26;12:633073. Epub 2021 Mar 26.

Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia.

Selecting appropriate metabolic engineering targets to build efficient cell factories maximizing the bioconversion of industrial by-products to valuable compounds taking into account time restrictions is a significant challenge in industrial biotechnology. Microbial metabolism engineering following a rational design has been widely studied. However, it is a cost-, time-, and laborious-intensive process because of the cell network complexity; thus, it is important to use tools that allow predicting gene deletions. Read More

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Functional analysis of two novel TBX5 variants present in individuals with Holt-Oram syndrome with different clinical manifestations.

Mol Genet Genomics 2021 Apr 17. Epub 2021 Apr 17.

Centre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal.

Holt-Oram syndrome (HOS) is a rare disorder characterized by cardiac and upper-limb defects. Pathogenic variants in TBX5-a gene encoding a transcription factor important for heart and skeletal development-are the only known cause of HOS. Here, we present the identification and functional analysis of two novel TBX5 pathogenic variants found in two individuals with HOS presenting distinct phenotypes. Read More

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A new model for regulation of sphingosine kinase 1 translocation to the plasma membrane in breast cancer cells.

J Biol Chem 2021 Apr 15:100674. Epub 2021 Apr 15.

Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE Scotland, UK. Electronic address:

The translocation of sphingosine kinase 1 (SK1) to the plasma membrane (PM) is crucial in promoting oncogenesis. We have previously proposed that SK1 exists as both a monomer and dimer in equilibrium, although it is unclear whether these species translocate to the PM via the same or different mechanisms. We therefore investigated the structural determinants involved to better understand how translocation might potentially be targeted for therapeutic intervention. Read More

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RTKN-1/Rhotekin shields endosome-associated F-actin from disassembly to ensure endocytic recycling.

J Cell Biol 2021 May;220(5)

Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.

Cargo sorting and the subsequent membrane carrier formation require a properly organized endosomal actin network. To better understand the actin dynamics during endocytic recycling, we performed a genetic screen in C. elegans and identified RTKN-1/Rhotekin as a requisite to sustain endosome-associated actin integrity. Read More

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Genetics animates structure: leveraging genetic interactions to study the dynamics of ribosome biogenesis.

Curr Genet 2021 Apr 12. Epub 2021 Apr 12.

Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.

The assembly of eukaryotic ribosomes follows an assembly line-like pathway in which numerous trans-acting biogenesis factors act on discrete pre-ribosomal intermediates to progressively shape the nascent subunits into their final functional architecture. Recent advances in cryo-electron microscopy have led to high-resolution structures of many pre-ribosomal intermediates; however, these static snapshots do not capture the dynamic transitions between these intermediates. To this end, molecular genetics can be leveraged to reveal how the biogenesis factors drive these dynamic transitions. Read More

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Plasmodium falciparum Atg18 localizes to the food vacuole via interaction with the multi-drug resistance protein 1 and phosphatidylinositol 3-phosphate.

Biochem J 2021 Apr 12. Epub 2021 Apr 12.

Centre for Cellular and Molecular Biology, Hyderabad, India.

Autophagy, a lysosome-dependent degradative process, does not appear to be a major degradative process in malaria parasites and has a limited repertoire of genes. To better understand the autophagy process, we investigated Plasmodiumfalciparum Atg18 (PfAtg18), a PROPPIN family protein, whose members like S. cerevisiae Atg18 (ScAtg18) and human WIPI2 bind PI3P and play an essential role in autophagosome formation. Read More

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An MHV macrodomain mutant predicted to lack ADP-ribose binding activity is severely attenuated, indicating multiple roles for the macrodomain in coronavirus replication.

bioRxiv 2021 Mar 31. Epub 2021 Mar 31.

All coronaviruses (CoVs) contain a macrodomain, also termed Mac1, in non-structural protein 3 (nsp3) which binds and hydrolyzes ADP-ribose covalently attached to proteins. Despite several reports demonstrating that Mac1 is a prominent virulence factor, there is still a limited understanding of its cellular roles during infection. Currently, most of the information regarding the role of CoV Mac1 during infection is based on a single point mutant of a highly conserved asparagine-to-alanine mutation, which is known to largely eliminate Mac1 ADP-ribosylhydrolase activity. Read More

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Probing the Diacylglycerol Binding Site of Presynaptic Munc13-1.

Biochemistry 2021 Apr 5;60(16):1286-1298. Epub 2021 Apr 5.

Department of Pharmacological & Pharmaceutical Sciences, College of Pharmacy, Health 2, University of Houston, Houston, Texas 77204, United States.

Munc13-1 is a presynaptic active zone protein that acts as a master regulator of synaptic vesicle priming and neurotransmitter release in the brain. It has been implicated in the pathophysiology of several neurodegenerative diseases. Diacylglycerol and phorbol ester activate Munc13-1 by binding to its C1 domain. Read More

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Optical Switching Between Long-lived States of Opsin Transmembrane Voltage Sensors.

Photochem Photobiol 2021 Apr 4. Epub 2021 Apr 4.

Molecular Biophysics Laboratory, Photonics Center, Department of Physics, Boston University, Boston, Massachusetts, 02215, USA.

Opsin-based transmembrane voltage sensors (OTVSs) are membrane proteins increasingly used in optogenetic applications to measure voltage changes across cellular membranes. In order to better understand the photophysical properties of OTVSs, we used a combination of UV-Vis absorption, fluorescence and FT-Raman spectroscopy to characterize QuasAr2 and NovArch, two closely related mutants derived from the proton pump archaerhodopsin-3 (AR3). We find both QuasAr2 and NovArch can be optically cycled repeatedly between O-like and M-like states using 5-min exposure to red (660 nm) and near-UV (405 nm) light. Read More

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Structural Insights into a Bifunctional Peptide Methionine Sulfoxide Reductase MsrA/B Fusion Protein from .

Antioxidants (Basel) 2021 Mar 5;10(3). Epub 2021 Mar 5.

Department of Biotechnology, Korea University, Seoul 02841, Korea.

Methionine sulfoxide reductase (Msr) is a family of enzymes that reduces oxidized methionine and plays an important role in the survival of bacteria under oxidative stress conditions. MsrA and MsrB exist in a fusion protein form (MsrAB) in some pathogenic bacteria, such as (), , and . To understand the fused form instead of the separated enzyme at the molecular level, we determined the crystal structure of MsrAB at 2. Read More

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Genome-wide analysis of manganese homeostasis in .

J Microbiol Biotechnol 2021 Mar 26. Epub 2021 Mar 26.

National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.

Manganese is a crucial cofactor for a wide range of enzymes in many living cells. However, excessive manganese can induce cellular toxicity by affecting a number of metabolic reactions and even cause severe neurological diseases in humans. To understand manganese homeostasis fully, a genome-scale screen was performed using the homozygous diploid yeast deletion mutant library. Read More

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Three common symbiotic ABC-B transporters in Medicago truncatula are regulated by a NIN-independent branch of the symbiosis signalling pathway.

Mol Plant Microbe Interact 2021 Mar 29. Epub 2021 Mar 29.

John Innes Centre, 15549, Norwich, Norfolk, United Kingdom of Great Britain and Northern Ireland.

Several ATP-Binding Cassette (ABC) transporters involved in the arbuscular mycorrhizal symbiosis and nodulation have been identified. We describe three previously-unreported ABC subfamily-B transporters, named ABCB for Mycorrhization and Nodulation (AMN1, AMN2, and AMN3), that are expressed early during infection by rhizobia and arbuscular mycorrhizal fungi. These ABCB transporters are strongly expressed in symbiotically infected tissues, including in root hair cells with rhizobial infection threads and arbusculated cells. Read More

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The transcription factor FvHmg1 negatively regulates fruiting body development in Winter Mushroom Flammulina velutipes.

Gene 2021 Jun 26;785:145618. Epub 2021 Mar 26.

Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China. Electronic address:

Fruiting body formation in Agaricomycetes represents the most complex and unclear process in the fungi. Mating type pathways (matA and matB) and transcription factors are important regulators in the process. Here, we report a new High-mobility-group (HMG) box domain protein FvHmg1 that acts as a negative transcription regulator in fruiting body development in Winter Mushroom Flammulina velutipes. Read More

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Bok binds to a largely disordered loop in the coupling domain of type 1 inositol 1,4,5-trisphosphate receptor.

Biochem Biophys Res Commun 2021 May 24;553:180-186. Epub 2021 Mar 24.

Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY, USA. Electronic address:

Bcl-2-related ovarian killer (Bok) binds tightly to inositol 1,4,5-trisphosphate receptors (IPRs). To better understand this interaction, we sought to elucidate the Bok binding determinants in IPR1, focusing on the ∼75 amino acid loop (residues 1882-1957) between α helices 72 and 73. Bioinformatic analysis revealed that the majority of this loop is intrinsically disordered, with two flanking regions of high disorder next to a low disorder central region (∼residues 1914-1926) that is predicted to contain two fused, disjointed transient helical elements. Read More

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Glia actively sculpt sensory neurons by controlled phagocytosis to tune animal behavior.

Elife 2021 03 24;10. Epub 2021 Mar 24.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.

Glia in the central nervous system engulf neuron fragments to remodel synapses and recycle photoreceptor outer segments. Whether glia passively clear shed neuronal debris or actively prune neuron fragments is unknown. How pruning of single-neuron endings impacts animal behavior is also unclear. Read More

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Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data.

J Cell Physiol 2021 Mar 23. Epub 2021 Mar 23.

Department of Bioinformatics and Biological Statistics, Shanghai Jiao Tong University, Shanghai, P.R. China.

The evolution of the SARS-CoV-2 new variants reported to be 70% more contagious than the earlier one is now spreading fast worldwide. There is an instant need to discover how the new variants interact with the host receptor (ACE2). Among the reported mutations in the Spike glycoprotein of the new variants, three are specific to the receptor-binding domain (RBD) and required insightful scrutiny for new therapeutic options. Read More

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Effect of Met/Leu substitutions on the stability of NAD+-dependent formate dehydrogenases from Gossypium hirsutum.

Appl Microbiol Biotechnol 2021 Apr 22;105(7):2787-2798. Epub 2021 Mar 22.

Department of Molecular Biology and Genetics, Faculty of Arts and Science, Yildiz Technical University, Istanbul, Turkey.

NAD-dependent formate dehydrogenases (FDHs) are extensively used in the regeneration of NAD(P)H and the reduction of CO to formate. In addition to their industrial importance, FDHs also play a crucial role in the maintenance of a reducing environment to combat oxidative stress in plants. Therefore, it is important to investigate the response of NAD-dependent FDH against both temperature and HO, to understand the defense mechanisms, and to increase its stability under oxidative stress conditions. Read More

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The microcephaly gene Donson is essential for progenitors of cortical glutamatergic and GABAergic neurons.

PLoS Genet 2021 Mar 19;17(3):e1009441. Epub 2021 Mar 19.

Institute of Pharmacology and Toxicology, Jena University Hospital, Jena, Germany.

Biallelic mutations in DONSON, an essential gene encoding for a replication fork protection factor, were linked to skeletal abnormalities and microcephaly. To better understand DONSON function in corticogenesis, we characterized Donson expression and consequences of conditional Donson deletion in the mouse telencephalon. Donson was widely expressed in the proliferation and differentiation zones of the embryonic dorsal and ventral telencephalon, which was followed by a postnatal expression decrease. Read More

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