@article{fleischman_kaskar_shams_zhang_olson_zdanski_thorp_kuznetsov_grace_lee_2019, title={A Novel Porcine Model for the Study of Cerebrospinal Fluid Dynamics: Development and Preliminary Results}, volume={10}, ISSN={["1664-2295"]}, DOI={10.3389/fneur.2019.01137}, abstractNote={Idiopathic intracranial hypertension, space-flight associated neuro-ocular syndrome (SANS), and glaucoma are conditions that are among a spectrum of cerebrospinal fluid (CSF)-related ophthalmologic disease. This implies that local CSF pressures at the level of the optic nerve are involved to variable extent in these disease processes. However, CSF pressure measurements are problematic due to invasiveness and interpretation. The pressure measured by a lumbar puncture is likely not the same as the orbital CSF pressure. It is believed this is at least in part due to the flow restrictive properties of the optic canal. To investigate CSF flow within the orbit, a model for CSF dynamics was created using three medium-sized pigs. Contrast was administered through a lumbar subarachnoid space access. The contrast front was imaged with repeated computed tomographic (CT) imaging. Once contrast entered the orbit, rapid, sequential CT imaging was performed until the contrast reached the posterior globe. Head tilting was performed to highlight the role of gravitational dependence within the subarachnoid space.}, journal={FRONTIERS IN NEUROLOGY}, author={Fleischman, David and Kaskar, Omkar and Shams, Rayad and Zhang, Xinxin and Olson, Daniel and Zdanski, Carlton and Thorp, Brian D. and Kuznetsov, Andrey V and Grace, Landon and Lee, Yueh Z.}, year={2019}, month={Oct} }
 @article{zhang_zhu_sun_yuan_cheng_argyropoulos_2019, title={Extraction and characterization of lignin from corncob residue after acid-catalyzed steam explosion pretreatment}, volume={133}, ISSN={["1872-633X"]}, url={https://doi.org/10.1016/j.indcrop.2019.03.027}, DOI={10.1016/j.indcrop.2019.03.027}, abstractNote={Corncob residue after acid catalyzed steam explosion (CRSE) is rich in cellulose and lignin. However, the structure of the lignin present in the CRSE has not been studied in detail and this hinders its application. An enzymatic mild acidolysis lignin (EMAL) extraction is adopted to process the CRSE where the extraction conditions are modified to improve lignin recovery and purity. Extraction severity factor is calculated and correlations between it and lignin recovery, lignin purity and total phenolic groups are evaluated. The best extraction condition produces lignin with a purity of 99.0% and a yield of 57.3%. A comparative study between lignin samples extracted under the best condition from the CRSE and untreated corncob (CC) is conducted. The structures of extracted lignin samples are investigated by using 31P NMR, 2D-HSQC NMR, FTIR and GPC. Although SE pretreatment caused degradation of lignin, the abundance per 100 aromatic units of β-O-4′ linkages is 46.0, which is higher than most technical lignins. The molecular weight of CRSE EMAL is found to be higher than that of CC EMAL due to condensation reactions. Antioxidant property of CC EMAL and CRSE EMAL is measured and compared. The data shows that CRSE EMAL possesses better antioxidant activity (IC50 = 128 μg/mL) than CC EMAL (IC50 = 238 μg/mL), which makes CRSE EMAL an ideal additive for polymer composites.}, journal={INDUSTRIAL CROPS AND PRODUCTS}, publisher={Elsevier BV}, author={Zhang, Xin and Zhu, Jiadeng and Sun, Lu and Yuan, Qipeng and Cheng, Gang and Argyropoulos, Dimitris S.}, year={2019}, month={Jul}, pages={241–249} }
 @article{gagnon_biswas_zhang_brown_wollenzien_mattos_maxwell_2012, title={Structurally Conserved Nop56/58 N-terminal Domain Facilitates Archaeal Box C/D Ribonucleoprotein-guided Methyltransferase Activity}, volume={287}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.m111.323253}, abstractNote={Background: Box C/D RNPs direct site-specific 2′-O-methylation of rRNA. Results: The Nop56/58 and fibrillarin core proteins establish a very stable dimer with Nop56/58 contributing to methyltransferase activity. Conclusion: The Nop56/58 core protein plays a role not only in RNP assembly, but also methyltransferase activity. Significance: Our observations reveal a novel role for the Nop56/58 core protein in box C/D RNP function. Box C/D RNA-protein complexes (RNPs) guide the 2′-O-methylation of nucleotides in both archaeal and eukaryotic ribosomal RNAs. The archaeal box C/D and C′/D′ RNP subcomplexes are each assembled with three sRNP core proteins. The archaeal Nop56/58 core protein mediates crucial protein-protein interactions required for both sRNP assembly and the methyltransferase reaction by bridging the L7Ae and fibrillarin core proteins. The interaction of Methanocaldococcus jannaschii (Mj) Nop56/58 with the methyltransferase fibrillarin has been investigated using site-directed mutagenesis of specific amino acids in the N-terminal domain of Nop56/58 that interacts with fibrillarin. Extensive mutagenesis revealed an unusually strong Nop56/58-fibrillarin interaction. Only deletion of the NTD itself prevented dimerization with fibrillarin. The extreme stability of the Nop56/58-fibrillarin heterodimer was confirmed in both chemical and thermal denaturation analyses. However, mutations that did not affect Nop56/58 binding to fibrillarin or sRNP assembly nevertheless disrupted sRNP-guided nucleotide modification, revealing a role for Nop56/58 in methyltransferase activity. This conclusion was supported with the cross-linking of Nop56/58 to the target RNA substrate. The Mj Nop56/58 NTD was further characterized by solving its three-dimensional crystal structure to a resolution of 1.7 Å. Despite low primary sequence conservation among the archaeal Nop56/58 homologs, the overall structure of the archaeal NTD domain is very well conserved. In conclusion, the archaeal Nop56/58 NTD exhibits a conserved domain structure whose exceptionally stable interaction with fibrillarin plays a role in both RNP assembly and methyltransferase activity.}, number={23}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Gagnon, Keith T. and Biswas, Shyamasri and Zhang, Xinxin and Brown, Bernard A., II and Wollenzien, Paul and Mattos, Carla and Maxwell, E. Stuart}, year={2012}, month={Jun}, pages={19418–19428} }
 @article{gagnon_zhang_qu_biswas_suryadi_brown_maxwell_2010, title={Signature amino acids enable the archaeal L7Ae box C/D RNP core protein to recognize and bind the K-loop RNA motif}, volume={16}, ISSN={["1469-9001"]}, DOI={10.1261/rna.1692310}, abstractNote={The archaeal L7Ae and eukaryotic 15.5kD protein homologs are members of the L7Ae/15.5kD protein family that characteristically recognize K-turn motifs found in both archaeal and eukaryotic RNAs. In Archaea, the L7Ae protein uniquely binds the K-loop motif found in box C/D and H/ACA sRNAs, whereas the eukaryotic 15.5kD homolog is unable to recognize this variant K-turn RNA. Comparative sequence and structural analyses, coupled with amino acid replacement experiments, have demonstrated that five amino acids enable the archaeal L7Ae core protein to recognize and bind the K-loop motif. These signature residues are highly conserved in the archaeal L7Ae and eukaryotic 15.5kD homologs, but differ between the two domains of life. Interestingly, loss of K-loop binding by archaeal L7Ae does not disrupt C′/D′ RNP formation or RNA-guided nucleotide modification. L7Ae is still incorporated into the C′/D′ RNP despite its inability to bind the K-loop, thus indicating the importance of protein–protein interactions for RNP assembly and function. Finally, these five signature amino acids are distinct for each of the L7Ae/L30 family members, suggesting an evolutionary continuum of these RNA-binding proteins for recognition of the various K-turn motifs contained in their cognate RNAs.}, number={1}, journal={RNA}, author={Gagnon, Keith T. and Zhang, Xinxin and Qu, Guosheng and Biswas, Shyamasri and Suryadi, Jimmy and Brown, Bernard A., II and Maxwell, E. Stuart}, year={2010}, month={Jan}, pages={79–90} }
 @article{xue_wang_yang_terns_terns_zhang_maxwel_li_2010, title={Structural Basis for Substrate Placement by an Archaeal Box C/D Ribonucleoprotein Particle}, volume={39}, ISSN={["1097-4164"]}, DOI={10.1016/j.molcel.2010.08.022}, abstractNote={<h2>Summary</h2> Box C/D small nucleolar and Cajal body ribonucleoprotein particles (sno/scaRNPs) direct site-specific 2′-O-methylation of ribosomal and spliceosomal RNAs and are critical for gene expression. Here we report crystal structures of an archaeal box C/D RNP containing three core proteins (fibrillarin, Nop56/58, and L7Ae) and a half-mer box C/D guide RNA paired with a substrate RNA. The structure reveals a guide-substrate RNA duplex orientation imposed by a composite protein surface and the conserved GAEK motif of Nop56/58. Molecular modeling supports a dual C/D RNP structure that closely mimics that recently visualized by electron microscopy. The substrate-bound dual RNP model predicts an asymmetric protein distribution between the RNP that binds and methylates the substrate RNA. The predicted asymmetric nature of the holoenzyme is consistent with previous biochemical data on RNP assembly and provides a simple solution for accommodating base-pairing between the C/D guide RNA and large ribosomal and spliceosomal substrate RNAs.}, number={6}, journal={MOLECULAR CELL}, author={Xue, Song and Wang, Ruiying and Yang, Fangping and Terns, Rebecca M. and Terns, Michael P. and Zhang, Xinxin and Maxwel, E. Stuart and Li, Hong}, year={2010}, month={Sep}, pages={939–949} }
 @misc{gagnon_zhang_maxwell_2007, title={In vitro reconstitution and affinity purification of catalytically active archaeal box C/D sRNP complexes}, volume={425}, DOI={10.1016/s0076-6879(07)25012-8}, abstractNote={Archaeal box C/D RNAs guide the site-specific 2'-O-methylation of target nucleotides in ribosomal RNAs and tRNAs. In vitro reconstitution of catalytically active box C/D RNPs by use of in vitro transcribed box C/D RNAs and recombinant core proteins provides model complexes for the study of box C/D RNP assembly, structure, and function. Described here are protocols for assembly of the archaeal box C/D RNP and assessment of its nucleotide modification activity. Also presented is a novel affinity purification scheme that uses differentially tagged core proteins and a sequential three-step affinity selection protocol that yields fully assembled and catalytically active box C/D RNPs. This affinity selection protocol can provide highly purified complex in sufficient quantities not only for biochemical analyses but also for biophysical approaches such as cryoelectron microscopy and X-ray crystallography.}, journal={RNA modification}, publisher={San Diego: Elsevier academic press inc}, author={Gagnon, K. and Zhang, X. X. and Maxwell, E. S.}, year={2007}, pages={263–282} }
 @article{gagnon_zhang_agris_maxwell_2006, title={Assembly of the archaeal box C/D sRNP can occur via alternative pathways and requires temperature-facilitated sRNA remodeling}, volume={362}, DOI={10.1016/j.jmb.2006.07.091}, abstractNote={Archaeal dual-guide box C/D small nucleolar RNA-like RNAs (sRNAs) bind three core proteins in sequential order at both terminal box C/D and internal C'/D' motifs to assemble two ribonuclear protein (RNP) complexes active in guiding nucleotide methylation. Experiments have investigated the process of box C/D sRNP assembly and the resultant changes in sRNA structure or "remodeling" as a consequence of sRNP core protein binding. Hierarchical assembly of the Methanocaldococcus jannaschii sR8 box C/D sRNP is a temperature-dependent process with binding of L7 and Nop56/58 core proteins to the sRNA requiring elevated temperature to facilitate necessary RNA structural dynamics. Circular dichroism (CD) spectroscopy and RNA thermal denaturation revealed an increased order and stability of sRNA folded structure as a result of L7 binding. Subsequent binding of the Nop56/58 and fibrillarin core proteins to the L7-sRNA complex further remodeled sRNA structure. Assessment of sR8 guide region accessibility using complementary RNA oligonucleotide probes revealed significant changes in guide region structure during sRNP assembly. A second dual-guide box C/D sRNA from M. jannaschii, sR6, also exhibited RNA remodeling during temperature-dependent sRNP assembly, although core protein binding was affected by sR6's distinct folded structure. Interestingly, the sR6 sRNP followed an alternative assembly pathway, with both guide regions being continuously exposed during sRNP assembly. Further experiments using sR8 mutants possessing alternative guide regions demonstrated that sRNA folded structure induced by specific guide sequences impacted the sRNP assembly pathway. Nevertheless, assembled sRNPs were active for sRNA-guided methylation independent of the pathway followed. Thus, RNA remodeling appears to be a common and requisite feature of archaeal dual-guide box C/D sRNP assembly and formation of the mature sRNP can follow different assembly pathways in generating catalytically active complexes.}, number={5}, journal={Journal of Molecular Biology}, author={Gagnon, K. T. and Zhang, X. X. and Agris, P. F. and Maxwell, E. S.}, year={2006}, pages={1025–1042} }
 @article{tran_zhang_lackey_maxwell_2005, title={Conserved spacing between the box C/D and C '/D ' RNPs of the archaeal box C/D sRNP complex is required for efficient 2 '-O-methylation of target RNAs}, volume={11}, ISSN={["1469-9001"]}, DOI={10.1261/rna.7223405}, abstractNote={RNA-guided nucleotide modification complexes direct the post-transcriptional nucleotide modification of both archaeal and eukaryotic RNAs. We have previously demonstrated that efficient 2′-O-methylation activity guided by an in vitro reconstituted archaeal box C/D sRNP requires juxtaposed box C/D and C′/D′ RNP complexes. In these experiments, we investigate the importance of spatially positioning the box C/D and C′/D′ RNPs within the sRNP complex for nucleotide modification. Initial sequence analysis of 245 archaeal box C/D sRNAs from both Eukyarchaeota and Crenarchaeota kingdoms revealed highly conserved spacing between the box C/D and C′/D′ RNA motifs. Distances between boxes C to D′ and C′ to D (D′ and D spacers, respectively) exhibit highly constrained lengths of 12 nucleotides (nt). Methanocaldococcus jannaschii sR8 sRNA, a model box C/D sRNA with D and D′ spacers of 12 nt, was mutated to alter the distance between the two RNA motifs. sRNAs with longer or shorter spacer regions could still form sRNPs by associating with box C/D core proteins, L7, Nop56/58, and fibrillarin, comparable to wild-type sR8. However, these reconstituted box C/D sRNP complexes were severely deficient in methylation activity. Alteration of the D and D′ spacer lengths disrupted the guided methylation activity of both the box C/D and C′/D′ RNP complexes. When only one spacer region was altered, methylation activity of the corresponding RNP was lost. Collectively, these results demonstrate the importance of box C/D and C′/D′ RNP positioning for preservation of critical inter-RNP interactions required for efficient box C/D sRNP-guided nucleotide methylation.}, number={3}, journal={RNA}, author={Tran, E and Zhang, XX and Lackey, L and Maxwell, ES}, year={2005}, month={Mar}, pages={285–293} }
 @article{tran_zhang_maxwell_2003, title={Efficient RNA 2 '-O-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C '/D ' RNPs}, volume={22}, ISSN={["0261-4189"]}, DOI={10.1093/emboj/cdg368}, abstractNote={Box C/D ribonucleoprotein (RNP) complexes direct the nucleotide‐specific 2′‐O‐methylation of ribonucleotide sugars in target RNAs. In vitro assembly of an archaeal box C/D sRNP using recombinant core proteins L7, Nop56/58 and fibrillarin has yielded an RNA:protein enzyme that guides methylation from both the terminal box C/D core and internal C′/D′ RNP complexes. Reconstitution of sRNP complexes containing only box C/D or C′/D′ motifs has demonstrated that the terminal box C/D RNP is the minimal methylation‐competent particle. However, efficient ribonucleotide 2′‐O‐methylation requires that both the box C/D and C′/D′ RNPs function within the full‐length sRNA molecule. In contrast to the eukaryotic snoRNP complex, where the core proteins are distributed asymmetrically on the box C/D and C′/D′ motifs, all three archaeal core proteins bind both motifs symmetrically. This difference in core protein distribution is a result of altered RNA‐binding capabilities of the archaeal and eukaryotic core protein homologs. Thus, evolution of the box C/D nucleotide modification complex has resulted in structurally distinct archaeal and eukaryotic RNP particles.}, number={15}, journal={EMBO JOURNAL}, author={Tran, EJ and Zhang, XX and Maxwell, ES}, year={2003}, month={Aug}, pages={3930–3940} }