Skip to main content
Phase III+: The University is open for expanded research operations; only authorized personnel will be admitted on campus. More info here.

Publications search

Found 36319 matches. Displaying 31-40
Johnson DS, Deneau T, Toledo-Crow R, Simon SM
Show All Authors

Microscope Enclosure for Temperature Regulation and Light Isolation

APPLIED SCIENCES-BASEL 2021 AUG; 11(15):? Article 6812
Featured Application Here we present the design of a temperature regulation and light isolation microscope enclosure. This design can be readily adapted to the specific configurations of a custom imaging system. Light isolation and temperature regulation are often required for microscopic imaging. Commercial enclosures are available to satisfy these requirements, but they are often not flexible to the variety of custom systems found in research laboratories. We present the design for an affordable enclosure which utilizes aluminum t-slot profiles to support opaque expanded PVC panels. Temperature is regulated by exchanging the enclosure air with an external heater. In addition, we demonstrate baffles integrated into the enclosure improve temperature uniformity. Example designs for both upright and inverted microscopes are given, providing a starting point for creating a system-specific custom enclosure.
Mak T, Jones AW, Nurse P
Show All Authors

The TOR-dependent phosphoproteome and regulation of cellular protein synthesis

EMBO JOURNAL 2021 AUG 16; 40(16):? Article e107911
Cell growth is orchestrated by a number of interlinking cellular processes. Components of the TOR pathway have been proposed as potential regulators of cell growth, but little is known about their immediate effects on protein synthesis in response to TOR-dependent growth inhibition. Here, we present a resource providing an in-depth characterisation of Schizosaccharomyces pombe phosphoproteome in relation to changes observed in global cellular protein synthesis upon TOR inhibition. We find that after TOR inhibition, the rate of protein synthesis is rapidly reduced and that notable phosphorylation changes are observed in proteins involved in a range of cellular processes. We show that this reduction in protein synthesis rates upon TOR inhibition is not dependent on S6K activity, but is partially dependent on the S. pombe homologue of eIF4G, Tif471. Our study demonstrates the impact of TOR-dependent phospho-regulation on the rate of protein synthesis and establishes a foundational resource for further investigation of additional TOR-regulated targets both in fission yeast and other eukaryotes.
Zhou W, Melamed D, Banyai G, Meyer C, Tuschl T, Wickens M, Cao JY, Fields S
Show All Authors

Expanding the binding specificity for RNA recognition by a PUF domain

NATURE COMMUNICATIONS 2021 AUG 24; 12(1):? Article 5107
The PUF RNAbinding domain has an eight-repeat structure with the ability to bind an eight-base RNA sequence. Here the authors generate a comprehensive library of variants of a PUF domain to find an RNA binding code and design PUF domains that recognize an arbitrary RNA sequence. The ability to design a protein to bind specifically to a target RNA enables numerous applications, with the modular architecture of the PUF domain lending itself to new RNA-binding specificities. For each repeat of the Pumilio-1 PUF domain, we generate a library that contains the 8,000 possible combinations of amino acid substitutions at residues critical for RNA contact. We carry out yeast three-hybrid selections with each library against the RNA recognition sequence for Pumilio-1, with any possible base present at the position recognized by the randomized repeat. We use sequencing to score the binding of each variant, identifying many variants with highly repeat-specific interactions. From these data, we generate an RNA binding code specific to each repeat and base. We use this code to design PUF domains against 16 RNAs, and find that some of these domains recognize RNAs with two, three or four changes from the wild type sequence.
Hu JJ, Molinari E, Darmon S, Zhang L, Patrizio P, Barad DH, Gleicher N
Show All Authors

Valor predictivo de los patrones de granulacion del citoplasma durante Fecundacion in vitro en ovocitos en metafase II: Parte I, pacientes con mal pronostico

FERTILITY AND STERILITY 2021 AUG; 116(2):431-443
Objective: To determine whether 4 cytoplasmic granulation patterns of human metaphase II oocytes have a predictive value for in vitro fertilization outcomes. Design: A retrospective cohort study. Setting: An academically affiliated private clinical infertility and research center. Patient(s): A total of 2,690 consecutive fresh autologous oocytes collected from women aged 41.2 + 5.0 years between 2017 and 2019. Intervention(s): Determination of granulation pattern in every oocyte during intracytoplasmic sperm injection as fine, central, dispersed, and newly introduced uneven granulations. Main Outcome Measure(s): Fertilization outcomes (2 pronuclei [2PN], <2PN, and >2PN rates), pregnancy, and live birth rates for different granulation patterns at different ages. Result(s): Fine granulation produced the highest 2PN rate, followed by central, uneven, and dispersed granulation (91.8%, 83.9%, 77.9%, and 54.8%, respectively). Differences in fertilization were surprisingly relatively independent of age and other variables. Overall, compared with fine granulation, dispersed granulation resulted in lower pregnancy rates (4.6% vs. 10.7%) and known-outcome analysis (1.3% vs. 5.6%) as well as lower live birth rates (3.0% vs. 8.9%) and known-outcome analysis (0.6% vs. 5.6%). The known-outcome analysis demonstrated that uneven granulation had lower live birth rates than fine granulation (2.3% vs. 5.6%). Unexpectedly, the ooplasm granulation patterns were largely disassociated from embryo morphologic grades. Conclusion(s): We, for the first time, demonstrated that 4 distinct cytoplasmic granulation patterns in metaphase II oocytes had, largely independent of age and other variables, a predictive value for fertilization, pregnancy, and live birth outcomes in in vitro fertilization cycles of poor-prognosis patients. These data suggest that upstream ooplasm granulation patterns deserve closer attention in terms of embryo selection.
Niu YM, Tao X, Vaisey G, Olinares PDB, Alwaseem H, Chait BT, MacKinnon R
Show All Authors

Analysis of the mechanosensor channel functionality of TACAN

ELIFE 2021 AUG 10; 10(?):? Article e71188
Mechanosensitive ion channels mediate transmembrane ion currents activated by mechanical forces. A mechanosensitive ion channel called TACAN was recently reported. We began to study TACAN with the intent to understand how it senses mechanical forces and functions as an ion channel. Using cellular patch-recording methods, we failed to identify mechanosensitive ion channel activity. Using membrane reconstitution methods, we found that TACAN, at high protein concentrations, produces heterogeneous conduction levels that are not mechanosensitive and are most consistent with disruptions of the lipid bilayer. We determined the structure of TACAN using single-particle cryo-electron microscopy and observed that it is a symmetrical dimeric transmembrane protein. Each protomer contains an intracellular-facing cleft with a coenzyme A cofactor, confirmed by mass spectrometry. The TACAN protomer is related in three-dimensional structure to a fatty acid elongase, ELOVL7. Whilst its physiological function remains unclear, we anticipate that TACAN is not a mechanosensitive ion channel.
Li XL, Fetter R, Schwabe T, Jung C, Liu LR, Steller H, Gaul U
Show All Authors

The cAMP effector PKA mediates Moody GPCR signaling in Drosophila blood-brain barrier formation and maturation

ELIFE 2021 AUG 12; 10(?):? Article e68275
The blood-brain barrier (BBB) of Drosophila comprises a thin epithelial layer of subperineural glia (SPG), which ensheath the nerve cord and insulate it against the potassium-rich hemolymph by forming intercellular septate junctions (SJs). Previously, we identified a novel Gi/Go protein-coupled receptor (GPCR), Moody, as a key factor in BBB formation at the embryonic stage. However, the molecular and cellular mechanisms of Moody signaling in BBB formation and maturation remain unclear. Here, we identify cAMP-dependent protein kinase A (PKA) as a crucial antagonistic Moody effector that is required for the formation, as well as for the continued SPG growth and BBB maintenance in the larva and adult stage. We show that PKA is enriched at the basal side of the SPG cell and that this polarized activity of the Moody/PKA pathway finely tunes the enormous cell growth and BBB integrity. Moody/PKA signaling precisely regulates the actomyosin contractility, vesicle trafficking, and the proper SJ organization in a highly coordinated spatiotemporal manner. These effects are mediated in part by PKA's molecular targets MLCK and Rho1. Moreover, 3D reconstruction of SJ ultrastructure demonstrates that the continuity of individual SJ segments, and not their total length, is crucial for generating a proper paracellular seal. Based on these findings, we propose that polarized Moody/PKA signaling plays a central role in controlling the cell growth and maintaining BBB integrity during the continuous morphogenesis of the SPG secondary epithelium, which is critical to maintain tissue size and brain homeostasis during organogenesis.
Prabhu M, Murphy EA, Sukhu AC, Yee J, Singh S, Eng D, Zhao Z, Riley LE, Yang YWJ
Show All Authors

Antibody Response to Coronavirus Disease 2019 (COVID-19) Messenger RNA Vaccination in Pregnant Women and Transplacental Passage Into Cord Blood

Halford B
Show All Authors

Proteomics path paver is using organic chemistry to glean information on immune system proteins

CHEMICAL & ENGINEERING NEWS 2021 AUG 16; 99(30):48-49
Rowan DJ, Yasir S, Chen ZME, Mounajjed T, Damgard SE, Cummins L, Zhang LZ, Whitcomb E, Falck V, Simon SM, Singhi AD, Torbenson MS
Show All Authors

Morphologic and Molecular Findings in Myxoid Hepatic Adenomas

Myxoid hepatic adenomas are a rare subtype of hepatic adenomas with distinctive deposition of extracellular myxoid material between the hepatic plates. A total of 9 cases were identified in 6 women and 3 men with an average of 59 +/- 12 years. The myxoid adenomas were single tumors in 5 cases and multiple in 4 cases. In 1 case with multiple adenomas, the myxoid adenoma arose in the background of GNAS-mutated hepatic adenomatosis. Myxoid hepatic adenomas had a high frequency of malignant transformation (N=5 cases). They were characterized at the molecular level by HNF1A inactivating mutations, leading to loss of LFABP protein expression. In addition, myxoid adenomas had recurrent mutations in genes within the protein kinase A (PKA) pathway or in genes that regulate the PKA pathway: GNAS, CDKN1B (encodes p27), and RNF123. In sum, myxoid adenomas are rare, occur in older-aged persons, have a high risk of malignant transformation, and are characterized by the combined inactivation of HNF1A and additional mutations that appear to cluster in the PKA pathway.
Muecksch F, Weisblum Y, Barnes CO, Schmidt F, Schaefer-Babajew D, Wang ZJ, Lorenzi JCC, Flyak AI, DeLaitsch AT, Huey-Tubman KE, Hou SR, Schiffer CA, Gaebler C, Da Silva J, Poston D, Finkin S, Cho A, Cipolla M, Oliveira TY, Millard KG, Ramos V, Gazumyan A, Rutkowska M, Caskey M, Nussenzweig MC, Bjorkman PJ, Hatziioannou T, Bieniasz PD
Show All Authors

Affinity maturation of SARS-CoV-2 neutralizing antibodies confers potency, breadth, and resilience to viral escape mutations

IMMUNITY 2021 AUG 10; 54(8):1853-1868.e7
Antibodies elicited by infection accumulate somatic mutations in germinal centers that can increase affinity for cognate antigens. We analyzed 6 independent groups of clonally related severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) Spike receptor-binding domain (RBD)-specific antibodies from 5 individuals shortly after infection and later in convalescence to determine the impact of maturation over months. In addition to increased affinity and neutralization potency, antibody evolution changed the mutational pathways for the acquisition of viral resistance and restricted neutralization escape options. For some antibodies, maturation imposed a requirement for multiple substitutions to enable escape. For certain antibodies, affinity maturation enabled the neutralization of circulating SARS-CoV-2 variants of concern and heterologous sarbecoviruses. Antibody-antigen structures revealed that these properties resulted from substitutions that allowed additional variability at the interface with the RBD. These findings suggest that increasing antibody diversity through prolonged or repeated antigen exposure may improve protection against diversifying SARS-CoV-2 populations, and perhaps against other pandemic threat coronaviruses.