DeGiorgis
Joseph A.
DeGiorgis
Joseph A.
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PreprintA novel 65 kDa RNA-binding protein in squid presynaptic terminals( 2009-11-09) Lico, Diego T. P. ; Rosa, José C. ; DeGiorgis, Joseph A. ; de Vasconcelos, E. J. R. ; Casaletti, L. ; Tauhata, S. B. F. ; Baqui, M. M. A. ; Fukuda, M. ; Moreira, J. E. ; Larson, Roy E.A polyclonal antibody (C4), raised against the head domain of chicken myosin Va, reacted strongly towards a 65 kDa polypeptide (p65) on western blots of extracts from squid optic lobes but did not recognize the heavy chain of squid myosin V. This peptide was not recognized by other myosin Va antibodies, nor by an antibody specific for squid myosin V. In an attempt to identify it, p65 was purified from optic lobes of Loligo plei by cationic exchange and reverse phase chromatography. Several peptide sequences were obtained by mass spectroscopy from p65 cut from SDS-PAGE gels. BLAST analysis and partial matching with ESTs from a Loligo pealei data bank indicated that p65 contains consensus signatures for the hnRNP A/B family of RNA-binding proteins. Centrifugation of post mitochondrial extracts from optic lobes on sucrose gradients after treatment with RNase gave biochemical evidence that p65 associates with cytoplasmic RNP complexes in an RNA-dependent manner. Immunohistochemistry and immunofluorescence studies using the C4 antibody showed partial co-labeling with an antibody against squid synaptotagmin in bands within the outer plexiform layer of the optic lobes and at the presynaptic zone of the stellate ganglion. Also, punctate labeling by the C4 antibody was observed within isolated optic lobe synaptosomes. The data indicate that p65 is a novel RNA-binding protein located to the presynaptic terminal within squid neurons and may have a role in synaptic localization of RNA and its translation or processing.
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ArticleFarm-waste-derived recyclable photothermal evaporator(Cell Press, 2021-08-20) Tian, Yanpei ; Liu, Xiaojie ; Li, Jiansheng ; Deng, Yichen ; DeGiorgis, Joseph A. ; Zhou, Shiyu ; Caratenuto, Andrew ; Minus, Marilyn L. ; Wan, Yinsheng ; Xiao, Gang ; Zheng, YiInterfacial solar steam generation is emerging as a promising technique for efficient desalination. Although increasing efforts have been made, challenges exist for achieving a balance among a plethora of performance indicators—for example, rapid evaporation, durability, low-cost deployment, and salt rejection. Here, we demonstrate that carbonized manure can convert 98% of sunlight into heat, and the strong capillarity of porous carbon fibers networks pumps sufficient water to evaporation interfaces. Salt diffusion within microchannels enables quick salt drainage to the bulk seawater to prevent salt accumulation. With these advantages, this biomass-derived evaporator is demonstrated to feature a high evaporation rate of 2.81 kg m−2 h−1 under 1 sun with broad robustness to acidity and alkalinity. These advantages, together with facial deployment, offer an approach for converting farm waste to energy with high efficiency and easy implementation, which is particularly well suited for developing regions.
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PreprintA novel SDS-stable dimer of a heterogeneous nuclear ribonucleoprotein at presynaptic terminals of squid neurons( 2015-05) Lico, Diego T. P. ; Lopes, Gabriel S. ; Brusco, Janaina ; Rosa, José C. ; Gould, Robert M. ; DeGiorgis, Joseph A. ; Larson, Roy E.The presence of mRNAs in synaptic terminals and their regulated translation are important factors in neuronal communication and plasticity. Heterogeneous nuclear ribonucleoprotein (hnRNP) complexes are involved in the translocation, stability, and subcellular localization of mRNA and the regulation of its translation. Defects in these processes and mutations in components of the hnRNP complexes have been related to the formation of cytoplasmic inclusion bodies and neurodegenerative diseases. Despite much data on mRNA localization and evidence for protein synthesis, as well as the presence of translation machinery, in axons and presynaptic terminals, the identity of RNA-binding proteins involved in RNA transport and function in presynaptic regions is lacking. We previously characterized a strongly basic RNA-binding protein (p65), member of the hnRNP A/B subfamily, in squid presynaptic terminals. Intriguingly, in SDS-PAGE, p65 migrated as a 65 kDa protein, whereas members of the hnRNP A/B family typically have molecular masses ranging from 35 to 42 kDa. In this report we present further biochemical and molecular characterization that shows endogenous p65 to be an SDS-stable dimer composed of ~37 kDa hnRNPA/B-like subunits. We cloned and expressed a recombinant protein corresponding to squid hnRNPA/B-like protein and showed its propensity to aggregate and form SDS-stable dimers in vitro. Our data suggest that this unique hnRNPA/B-like protein co-localizes with synaptic vesicle protein 2 and RNA-binding protein ELAV and thus may serve as a link between local mRNA processing and presynaptic function and regulation.
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ArticleThe amyloid precursor protein of Alzheimer’s disease clusters at the organelle/microtubule interface on organelles that bind microtubules in an ATP dependent manner(Public Library of Science, 2016-01-27) Stevenson, James W. ; Conaty, Eliza A. ; Walsh, Rylie B. ; Poidomani, Paul J. ; Samoriski, Colin M. ; Scollins, Brianne J. ; DeGiorgis, Joseph A.The amyloid precursor protein (APP) is a causal agent in the pathogenesis of Alzheimer’s disease and is a transmembrane protein that associates with membrane-limited organelles. APP has been shown to co-purify through immunoprecipitation with a kinesin light chain suggesting that APP may act as a trailer hitch linking kinesin to its intercellular cargo, however this hypothesis has been challenged. Previously, we identified an mRNA transcript that encodes a squid homolog of human APP770. The human and squid isoforms share 60% sequence identity and 76% sequence similarity within the cytoplasmic domain and share 15 of the final 19 amino acids at the C-terminus establishing this highly conserved domain as a functionally import segment of the APP molecule. Here, we study the distribution of squid APP in extruded axoplasm as well as in a well-characterized reconstituted organelle/microtubule preparation from the squid giant axon in which organelles bind microtubules and move towards the microtubule plus-ends. We find that APP associates with microtubules by confocal microscopy and co-purifies with KI-washed axoplasmic organelles by sucrose density gradient fractionation. By electron microscopy, APP clusters at a single focal point on the surfaces of organelles and localizes to the organelle/microtubule interface. In addition, the association of APP-organelles with microtubules is an ATP dependent process suggesting that the APP-organelles contain a microtubule-based motor protein. Although a direct kinesin/APP association remains controversial, the distribution of APP at the organelle/microtubule interface strongly suggests that APP-organelles have an orientation and that APP like the Alzheimer’s protein tau has a microtubule-based function.
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ArticleEnvironmentally friendly and efficient hornet nest envelope-based photothermal absorbers(American Chemical Society, 2021-12-07) Xie, Lijia ; Liu, Xiaojie ; Caratenuto, Andrew ; Tian, Yanpei ; Chen, Fangqi ; DeGiorgis, Joseph A. ; Wan, Yinsheng ; Zheng, YiWater shortage is a critical global issue that threatens human health, environmental sustainability, and the preservation of Earth’s climate. Desalination from seawater and sewage is a promising avenue for alleviating this stress. In this work, we use the hornet nest envelope material to fabricate a biomass-based photothermal absorber as part of a desalination isolation system. This system realizes an evaporation rate of 3.98 kg m–2 h–1 under one-sun illumination, with prolonged evaporation rates all above 4 kg m–2 h–1. This system demonstrates a strong performance of 3.86 kg m–2 h–1 in 3.5 wt % saltwater, illustrating its effectiveness in evaporation seawater. Thus, with its excellent evaporation rate, great salt rejection ability, and easy fabrication approach, the hornet nest envelope constitutes a promising natural material for solar water treatment applications.
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ArticleVariation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100(Microbiology Society, 2019-12-01) Williams, Laura E. ; Cullen, Nicole ; DeGiorgis, Joseph A. ; Martinez, Karla J. ; Mellone, Justina ; Oser, Molly ; Wang, Jing ; Zhang, YingDefining phenotypic and associated genotypic variation among Bdellovibrio may further our understanding of how this genus attacks and kills different Gram-negative bacteria. We isolated Bdellovibrio sp. NC01 from soil. Analysis of 16S rRNA gene sequences and average amino acid identity showed that NC01 belongs to a different species than the type species bacteriovorus. By clustering amino acid sequences from completely sequenced Bdellovibrio and comparing the resulting orthologue groups to a previously published analysis, we defined a ‘core genome’ of 778 protein-coding genes and identified four protein-coding genes that appeared to be missing only in NC01. To determine how horizontal gene transfer (HGT) may have impacted NC01 genome evolution, we performed genome-wide comparisons of Bdellovibrio nucleotide sequences, which indicated that eight NC01 genomic regions were likely acquired by HGT. To investigate how genome variation may impact predation, we compared protein-coding gene content between NC01 and the B. bacteriovorus type strain HD100, focusing on genes implicated as important in successful killing of prey. Of these, NC01 is missing ten genes that may play roles in lytic activity during predation. Compared to HD100, NC01 kills fewer tested prey strains and kills Escherichia coli ML35 less efficiently. NC01 causes a smaller log reduction in ML35, after which the prey population recovers and the NC01 population decreases. In addition, NC01 forms turbid plaques on lawns of E. coli ML35, in contrast to clear plaques formed by HD100. Linking phenotypic variation in interactions between Bdellovibrio and Gram-negative bacteria with underlying Bdellovibrio genome variation is valuable for understanding the ecological significance of predatory bacteria and evaluating their effectiveness in clinical applications.
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ArticlePrey range and genome evolution of Halobacteriovorax marinus predatory bacteria from an estuary(American Society for Microbiology, 2018-01-10) Enos, Brett G. ; Anthony, Molly K. ; DeGiorgis, Joseph A. ; Williams, Laura E.Halobacteriovorax strains are saltwater-adapted predatory bacteria that attack Gram-negative bacteria and may play an important role in shaping microbial communities. To understand how Halobacteriovorax strains impact ecosystems and develop them as biocontrol agents, it is important to characterize variation in predation phenotypes and investigate Halobacteriovorax genome evolution. We isolated Halobacteriovorax marinus BE01 from an estuary in Rhode Island using Vibrio from the same site as prey. Small, fast-moving, attack-phase BE01 cells attach to and invade prey cells, consistent with the intraperiplasmic predation strategy of the H. marinus type strain, SJ. BE01 is a prey generalist, forming plaques on Vibrio strains from the estuary, Pseudomonas from soil, and Escherichia coli. Genome analysis revealed extremely high conservation of gene order and amino acid sequences between BE01 and SJ, suggesting strong selective pressure to maintain the genome in this H. marinus lineage. Despite this, we identified two regions of gene content difference that likely resulted from horizontal gene transfer. Analysis of modal codon usage frequencies supports the hypothesis that these regions were acquired from bacteria with different codon usage biases than H. marinus. In one of these regions, BE01 and SJ carry different genes associated with mobile genetic elements. Acquired functions in BE01 include the dnd operon, which encodes a pathway for DNA modification, and a suite of genes involved in membrane synthesis and regulation of gene expression that was likely acquired from another Halobacteriovorax lineage. This analysis provides further evidence that horizontal gene transfer plays an important role in genome evolution in predatory bacteria.
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PreprintA novel lipid binding protein is a factor required for MgATP stimulation of the squid nerve Na+/Ca2+ exchanger( 2008-11-14) Berberian, Graciela ; Bollo, Mariana ; Montich, Guillermo ; Roberts, Gretel ; DeGiorgis, Joseph A. ; DiPolo, Reinaldo ; Beauge, LuisHere we identify a cytosolic factor essential for MgATP up-regulation of the squid nerve Na+/Ca2+ exchanger. Mass spectroscopy and Western blot analysis established that this factor is a member of the lipocalin super family of lipid binding proteins of 132 amino acids in length. We named it Regulatory protein of the squid nerve sodium calcium exchanger (ReP1-NCXSQ). ReP-1-NCXSQ was cloned, over expressed and purified. Far- UV circular dichroism and infrared spectra suggest a majority of β-strand in the secondary structure. Moreover, the predicted tertiary structure indicates ten β-sheets and two short α- helices characteristic of most lipid binding proteins. Functional experiments showed that in order to be active ReP1-NCXSQ must become phosphorylated in the presence of MgATP by a kinase that is Staurosporin insensitive. Even more, the phosphorylated ReP1-NCXSQ is able to stimulate the exchanger in the absence of ATP. In addition to the identification of a new member of the lipid binding protein family, this work shows, for the first time, the requirement of a lipid binding protein for metabolic regulation of an ion transporting system.
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ArticleIsolation and ultrastructural characterization of squid synaptic vesicles(Marine Biological Laboratory, 2011-04) Pekkurnaz, Gulcin ; Fera, Andrea ; Zimmerberg-Helms, Jessica ; DeGiorgis, Joseph A. ; Bezrukov, Ludmila ; Blank, Paul S. ; Mazar, Julia ; Reese, Thomas S. ; Zimmerberg, JoshuaSynaptic vesicles contain a variety of proteins and lipids that mediate fusion with the pre-synaptic membrane. Although the structures of many synaptic vesicle proteins are known, an overall picture of how they are organized at the vesicle surface is lacking. In this paper, we describe a better method for the isolation of squid synaptic vesicles and characterize the results. For highly pure and intact synaptic vesicles from squid optic lobe, glycerol density gradient centrifugation was the key step. Different electron microscopic methods show that vesicle membrane surfaces are largely covered with structures corresponding to surface proteins. Each vesicle contains several stalked globular structures that extend from the vesicle surface and are consistent with the V-ATPase. BLAST search of a library of squid expressed sequence tags identifies 10 V-ATPase subunits, which are expressed in the squid stellate ganglia. Negative-stain tomography demonstrates directly that vesicles flatten during the drying step of negative staining, and furthermore shows details of individual vesicles and other proteins at the vesicle surface.
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ArticleMycobacteriophage Tarkin: a Cluster E Phage(American Society for Microbiology, 2022-11-21) Cleary, Katherine E. ; Fakhri, Anna M. ; Dionne, Ethan N. ; Warner, Marcie ; DeGiorgis, Joseph A. ; Cornely, KathleenMycobacteriophage Tarkin is a newly isolated phage that infects Mycobacterium smegmatis mc155. Tarkin was discovered in Providence, RI, and has a 75,998-bp genome sequence. Tarkin is predicted to have 142 protein coding genes and 2 tRNA genes. Based on gene content similarity, Tarkin is grouped with mycobacteriophages in cluster E.
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ArticleMycobacteriophage Rita: a cluster F1 phage discovered in North Easton, Massachusetts(American Society for Microbiology, 2023-08-28) Fakhri, Anna M. ; Warner, Marcie H. ; DeGiorgis, Joseph A. ; Cornely, KathleenMycobacteriophage Rita infects Mycobacterium smegmatis mc2155 and was isolated from a soil sample collected in North Easton, Massachusetts. Assigned to cluster F1 based on sequence similarity to other phages in the same cluster, Rita has a 58,771 bp genome and encodes 104 genes. Rita is 98% similar to phage Bipolar.