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1.
Crit Rev Clin Lab Sci ; 61(2): 89-106, 2024 Mar.
Article in English | MEDLINE | ID: mdl-37776898

ABSTRACT

Great strides have been made in the past decade to lower barriers to clinical pharmacogenomics implementation. Nevertheless, PGx consultation prior to prescribing therapeutics is not yet mainstream. This review addresses the current climate surrounding PGx implementation, focusing primarily on strategies for implementation at academic institutions, particularly at The University of Chicago, and provides an up-to-date guide of resources supporting the development of PGx programs. Remaining challenges and recent strategies for overcoming these challenges to implementation are discussed.


Subject(s)
Pharmacogenetics , Precision Medicine , Humans
2.
Am J Clin Pathol ; 159(1): 6-9, 2023 01 04.
Article in English | MEDLINE | ID: mdl-36413387

ABSTRACT

OBJECTIVES: We sought to replace the highly hemolysis-susceptible diazo conjugated bilirubin (Bc) assay with the more robust vanadate oxidation method and determine its impact on test cancellation in the pediatric population. METHODS: Analytical validation of the Randox vanadate assay and comparison with the Roche diazo method were performed. The frequency of pediatric sample cancellation because of hemolysis was compared between the diazo and vanadate methods by retrospective analysis of clinical test data. RESULTS: The vanadate assay demonstrated no clinically significant interference from hemolysis up to a hemolysis index of 1,300 (approximately 13 g/L hemoglobin). There was a strong correlation with the diazo method (r2 = 0.97) but with a positive slope bias of 1.27. Implementing the vanadate method resulted in a significantly lower proportion of pediatric samples cancelled because of hemolysis compared with the diazo method (0.6% of 688 patients vs 30.6% of 10,464 patients, respectively; P < .001), with a 0.6% (n = 513) vs 43.2% (n = 6,464) reduction in test cancellations (P < .001) for children younger than 6 months of age. CONCLUSIONS: The vanadate method showed robust performance against hemolysis. Its implementation resulted in a significant decrease in pediatric tests cancelled because of hemolysis.


Subject(s)
Hemolysis , Vanadates , Humans , Child , Retrospective Studies , Bilirubin , Bias
3.
Semin Thromb Hemost ; 48(6): 690-699, 2022 Sep.
Article in English | MEDLINE | ID: mdl-36223772

ABSTRACT

Von Willebrand factor (VWF) level and/or function is altered in von Willebrand disease (VWD), the most common heritable bleeding disorder worldwide. Laboratory assessment of VWF is continually evolving. Historically, the primary method for the assessment of VWF platelet-binding activity was the ristocetin cofactor assay (VWF:RCo). Contemporary alternative measures of VWF platelet-binding activity include VWF:GPIbR (recombinant; using ristocetin), VWF:GPIbM (recombinant; gain-of-function mutant), and monoclonal antibody. Recently, the American Society of Hematology, International Society on Thrombosis and Haemostasis, National Hemophilia Foundation, and World Federation of Hemophilia collaboration issued guidelines recommending the use of newer assays of VWF platelet-binding activity (VWF: GPIbM, VWF: GPIbR) over VWF:RCo, given known limitations of the VWF:RCo assay. Despite this recommendation, the newer VWF:GPIbM and VWF:GPIbR assays are not United States Food and Drug Administration cleared, limiting their availability in the United States. We sought to assess assay utilization trends, agreement of VWF testing methods, and imprecision of VWF testing (based on assigned sample type) from the College of American Pathologists Proficiency Testing Surveys. The analysis confirms that, while VWF antigen testing has low imprecision, the various VWF activity assays have significant interassay variability, with VWF:RCo showing greater imprecision than the newer GPIb-binding assays. The overall trends in assay utilization reflect the barriers to complete compliance with modern VWD diagnostic guidelines in North America.


Subject(s)
Hemophilia A , von Willebrand Diseases , Antibodies, Monoclonal , Humans , Pathologists , Ristocetin , von Willebrand Diseases/diagnosis , von Willebrand Factor
4.
Semin Thromb Hemost ; 2022 Sep 02.
Article in English | MEDLINE | ID: mdl-36055272

ABSTRACT

Von Willebrand factor (VWF) level and/or function is altered in von Willebrand disease (VWD), the most common heritable bleeding disorder worldwide. Laboratory assessment of VWF is continually evolving. Historically, the primary method for the assessment of VWF platelet-binding activity was the ristocetin cofactor assay (VWF:RCo). Contemporary alternative measures of VWF platelet-binding activity include VWF:GPIbR (recombinant; using ristocetin), VWF:GPIbM (recombinant; gain-of-function mutant), and monoclonal antibody. Recently, the American Society of Hematology, International Society on Thrombosis and Haemostasis, National Hemophilia Foundation, and World Federation of Hemophilia collaboration issued guidelines recommending the use of newer assays of VWF platelet-binding activity (VWF: GPIbM, VWF: GPIbR) over VWF:RCo, given known limitations of the VWF:RCo assay. Despite this recommendation, the newer VWF:GPIbM and VWF:GPIbR assays are not United States Food and Drug Administration cleared, limiting their availability in the United States. We sought to assess assay utilization trends, agreement of VWF testing methods, and imprecision of VWF testing (based on assigned sample type) from the College of American Pathologists Proficiency Testing Surveys. The analysis confirms that, while VWF antigen testing has low imprecision, the various VWF activity assays have significant interassay variability, with VWF:RCo showing greater imprecision than the newer GPIb-binding assays. The overall trends in assay utilization reflect the barriers to complete compliance with modern VWD diagnostic guidelines in North America.

5.
Am J Hematol ; 97(5): 519-526, 2022 05.
Article in English | MEDLINE | ID: mdl-35132672

ABSTRACT

Rare cases of COVID-19 vaccinated individuals develop anti-platelet factor 4 (PF4) antibodies that cause thrombocytopenia and thrombotic complications, a syndrome referred to as vaccine-induced immune thrombotic thrombocytopenia (VITT). Currently, information on the characteristics and persistence of anti-PF4 antibodies that cause VITT after Ad26.COV2.S vaccination is limited, and available diagnostic assays fail to differentiate Ad26.COV2.S and ChAdOx1 nCoV-19-associated VITT from similar clinical disorders, namely heparin-induced thrombocytopenia (HIT) and spontaneous HIT. Here we demonstrate that while Ad26.COV2.S-associated VITT patients are uniformly strongly positive in PF4-polyanion enzyme-linked immunosorbent assays (ELISAs); they are frequently negative in the serotonin release assay (SRA). The PF4-dependent p-selectin expression assay (PEA) that uses platelets treated with PF4 rather than heparin consistently diagnosed Ad26.COV2.S-associated VITT. Most Ad26.COV2.S-associated VITT antibodies persisted for >5 months in PF4-polyanion ELISAs, while the PEA became negative earlier. Two patients had otherwise unexplained mild persistent thrombocytopenia (140-150 x 103 /µL) 6 months after acute presentation. From an epidemiological perspective, differentiating VITT from spontaneous HIT, another entity that develops in the absence of proximate heparin exposure, and HIT is important, but currently available PF4-polyanion ELISAs and functional assay are non-specific and detect all three conditions. Here, we report that a novel un-complexed PF4 ELISA specifically differentiates VITT, secondary to both Ad26.COV2.S and ChAdOx1 nCoV-19, from both spontaneous HIT, HIT and commonly-encountered HIT-suspected patients who are PF4/polyanion ELISA-positive but negative in functional assays. In summary, Ad26.COV2.S-associated VITT antibodies are persistent, and the un-complexed PF4 ELISA appears to be both sensitive and specific for VITT diagnosis.


Subject(s)
COVID-19 , Thrombocytopenia , Vaccines , Ad26COVS1 , COVID-19/diagnosis , COVID-19 Vaccines/adverse effects , ChAdOx1 nCoV-19 , Heparin/adverse effects , Humans , Platelet Factor 4 , Thrombocytopenia/chemically induced , Thrombocytopenia/diagnosis
6.
J Clin Apher ; 37(1): 117-121, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34672380

ABSTRACT

Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a newly described hematologic disorder, which presents as acute thrombocytopenia and thrombosis after administration of the ChAdOx1 nCov-19 (AstraZeneca) and Ad26.COV2.S (Johnson & Johnson) adenovirus-based vaccines against COVID-19. Due to positive assays for antibodies against platelet factor 4 (PF4), VITT is managed similarly to autoimmune heparin-induced thrombocytopenia (HIT) with intravenous immunoglobulin (IVIG) and non-heparin anticoagulation. We describe a case of VITT in a 50-year-old man with antecedent alcoholic cirrhosis who presented with platelets of 7 × 103 /µL and portal vein thrombosis 21 days following administration of the Ad26.COV2.S COVID-19 vaccine. The patient developed progressive thrombosis and persistent severe thrombocytopenia despite IVIG, rituximab and high-dose steroids and had persistent anti-PF4 antibodies over 30 days after his initial presentation. As such, delayed therapeutic plasma exchange (TPE) was pursued on day 32 of admission as salvage therapy, with a sustained improvement in his platelet count. Our case serves as proof-of-concept of the efficacy of TPE in VITT.


Subject(s)
Ad26COVS1/adverse effects , Plasma Exchange/methods , Purpura, Thrombocytopenic, Idiopathic/therapy , Vaccination/adverse effects , Humans , Male , Middle Aged , Platelet Count , Platelet Factor 4/immunology , Purpura, Thrombocytopenic, Idiopathic/etiology
7.
Am J Clin Pathol ; 157(1): 109-118, 2022 01 06.
Article in English | MEDLINE | ID: mdl-34463315

ABSTRACT

OBJECTIVES: To analytically and clinically evaluate the semiquantitative Elecsys anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein antibody (S-Ab) assay on the Roche cobas e602 analyzer. METHODS: The S-Ab assay is a 1-step, double-antigen sandwich electrochemiluminescent immunoassay that semiquantitatively measures total IgG, IgM, and IgA antibodies specific for the receptor binding domain of SARS-CoV-2 spike protein in serum or plasma. The S-Ab assay was evaluated for precision, linearity, interference (by hemoglobin, bilirubin, triglycerides, and biotin), cross-reactivity, and clinical performance, and was compared to the qualitative Elecsys anti-nucleocapsid (N-Ab) immunoassay, a lateral flow device that qualitatively detects S-Ab and N-Ab, and an anti-spike enzyme-linked immunosorbent assay (ELISA). RESULTS: S-Ab assay is precise, exhibits linearity from 0.4 to 250 U/mL, is unaffected by significant cross-reactivity or interferences, and qualitatively demonstrates greater than 90% concordance with N-Ab assay and lateral flow device. Readouts of S-Ab assay correlate with ELISA, which in turn correlates strongly with SARS-CoV-2 virus neutralization assay, and exhibit 100% sensitivity and specificity for COVID-19 patient samples obtained at or more than 14 days after PCR positivity. CONCLUSIONS: The S-Ab assay is a robust clinical test for qualitative and semiquantitative detection of seropositivity following SARS-CoV-2 infection or spike-encoding mRNA COVID-19 vaccination.


Subject(s)
COVID-19 , Spike Glycoprotein, Coronavirus , Antibodies, Viral , COVID-19 Vaccines , Humans , SARS-CoV-2 , Sensitivity and Specificity
8.
Acad Pathol ; 8: 23742895211010275, 2021.
Article in English | MEDLINE | ID: mdl-34192135

ABSTRACT

As students do not qualify as essential health care workers, medical education faced severe disruptions during the COVID-19 pandemic including initial suspension of all in-person lectures and on-site rotations. Our Pathology Department was among the first at Northwestern to offer a completely virtual rotation with the goals of: (1) providing a comprehensive introduction to the practice of anatomic and clinical pathology, (2) emphasizing uninterrupted and continued excellence in education, and (3) minimizing exposure risk during the pandemic. The innovative 2-week curriculum incorporated diverse teaching modalities including live and recorded lectures; live and recorded video demonstrations; interactive small group discussions; interactive virtual sign-outs; and written and multimedia assignments, quizzes, and projects. The virtual elective ran from March to July 2020 with 52 total participating medical students. On post-rotation evaluations, students rated the pathology virtual elective 4.7/5.0 compared to other virtual rotations and 4.0/5.0 compared to all rotations (including in-person and virtual). Furthermore, continual improvements were made to the established framework based on rotation feedback such that curriculum content was more abundant and more favorably rated by the last cohort when compared to the first. Finally, although students identified interest in over 10 different medical specialties, all participants expressed increased interest in choosing pathology as a specialty and better understanding of pathology's role in patient care. We hope our detailed description of creating and evaluating a completely virtual elective rotation serves as a model for other departments to improve pathology education and visibility.

9.
Am J Clin Pathol ; 156(1): 15-23, 2021 06 17.
Article in English | MEDLINE | ID: mdl-33978164

ABSTRACT

OBJECTIVES: To report our institutional experience in devising and implementing a pooling protocol and process for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription polymerase chain reaction (RT-PCR) testing over a 3-month period in the fall of 2020. METHODS: The widespread testing implemented in the United States for detecting SARS-CoV-2 infection in response to the coronavirus disease 2019 pandemic has led to a significant shortage of testing supplies and therefore has become a major impediment to the public health response. To date, several institutions have implemented sample pooling, but publications documenting these experiences are sparse. Nasal and nasopharyngeal samples collected from low-positivity (<5%) areas were tested in pools of five on the Roche cobas 6800 analyzer system. Routine SARS-CoV-2 RT-PCR turnaround times between sample collection to result reporting were monitored and compared before and after sample pooling implementation. RESULTS: A total of 4,131 sample pools were tested over a 3-month period (during which 39,770 RT-PCR results were reported from the Roche system), allowing our laboratory to save 13,824 tests, equivalent to a conservation rate of 35%. A 48-hour or less turnaround time was generally maintained throughout the pooling period. CONCLUSIONS: Sample pooling offers a viable means to mitigate shortfalls of PCR testing supplies in the ongoing pandemic without significantly compromising overall turnaround times.


Subject(s)
COVID-19 Testing , COVID-19/diagnosis , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , COVID-19/genetics , Clinical Laboratory Techniques/methods , Humans , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/pathogenicity , Specimen Handling/methods
10.
PLoS One ; 16(3): e0247797, 2021.
Article in English | MEDLINE | ID: mdl-33661960

ABSTRACT

Since the initial identification of the novel coronavirus SARS-CoV-2 in December of 2019, researchers have raced to understand its pathogenesis and begun devising vaccine and treatment strategies. An accurate understanding of the body's temporal immune response against SARS-CoV-2 is paramount to successful vaccine development and disease progression monitoring. To provide insight into the antibody response against SARS-CoV-2, plasma samples from 181 PCR-confirmed COVID-19 patients collected at various timepoints post-symptom onset (PSO) were tested for the presence of anti-SARS-CoV-2 IgM and IgG antibodies via lateral flow. Additionally, 21 donors were tracked over time to elucidate patient-specific immune responses. We found sustained levels of anti-SARS-CoV-2 antibodies past 130 days PSO, with 99% positivity observed at 31-60 days PSO. By 61-90 days PSO, the percentage of IgM-/IgG+ results were nearly equal to that of IgM+/IgG+ results, demonstrating a shift in the immune response with a decrease in IgM antibody levels. Results from this study not only provide evidence that the antibody response to COVID-19 can persist for over 4 months, but also demonstrates the ability of Easy Check™ to monitor seroconversion and antibody response of patients. Easy Check was sufficiently sensitive to detect antibodies in patient samples as early as 1-4 days PSO with 86% positivity observed at 5-7 days PSO. Further studies are required to determine the longevity and efficacy of anti-SARS-CoV-2 antibodies, and whether they are protective against re-infection.


Subject(s)
Antibodies, Viral/blood , COVID-19/blood , Immunoglobulin G/blood , Immunoglobulin M/blood , SARS-CoV-2/immunology , Adolescent , Adult , Aged , Aged, 80 and over , Antibodies, Viral/immunology , COVID-19/immunology , COVID-19 Serological Testing/instrumentation , COVID-19 Serological Testing/methods , Equipment Design , Female , Humans , Immunoglobulin G/immunology , Immunoglobulin M/immunology , Longitudinal Studies , Male , Middle Aged , SARS-CoV-2/isolation & purification , Young Adult
12.
Am J Clin Pathol ; 155(2): 286-295, 2021 02 04.
Article in English | MEDLINE | ID: mdl-33135049

ABSTRACT

OBJECTIVES: To evaluate the analytical and clinical performance of the Truvian Easy Check coronavirus disease 2019 (COVID-19) IgM/IgG anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody test.Serologic assays have become increasingly available for surveillance through the Food and Drug Administration emergency use authorization in the ongoing COVID-19 global pandemic. However, widespread application of serologic assays has been curbed by reports of faulty or inaccurate tests. Therefore, rapid COVID-19 antibody tests need to be thoroughly validated prior to their implementation. METHODS: The Easy Check device was analytically evaluated and its performance was compared with the Roche Elecsys anti-SARS-CoV-2 antibody assay. The test was further characterized for cross-reactivity using sera obtained from patients infected by other viruses. Clinical performance was analyzed with polymerase chain reaction-confirmed samples and a 2015 prepandemic reference sample set. RESULTS: The Easy Check device showed excellent analytical performance and compares well with the Roche Elecsys antibody assay, with an overall concordance of 98.6%. Clinical performance showed a sensitivity of 96.6%, a specificity of 98.2%, and an overall accuracy of 98.1%. CONCLUSIONS: The Easy Check device is a simple, reliable, and rapid test for detection of SARS-CoV-2 seropositivity, and its performance compares favorably against the automated Roche Elecsys antibody assay.


Subject(s)
Antibodies, Viral/blood , COVID-19 Serological Testing/instrumentation , COVID-19/diagnosis , SARS-CoV-2/immunology , Cross Reactions , Humans , Immunoglobulin G/blood , Immunoglobulin M/blood , Sensitivity and Specificity
13.
Am J Clin Pathol ; 154(5): 620-626, 2020 10 13.
Article in English | MEDLINE | ID: mdl-32814955

ABSTRACT

OBJECTIVES: To evaluate the analytical and clinical performance of the automated Elecsys anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody (Elecsys Ab) assay on the Roche cobas e602 analyzer. With the ongoing global coronavirus disease 2019 (COVID-19) pandemic, widespread and routine serologic testing of SARS-CoV-2 remains a pressing need. To better understand its epidemiologic spread and to support policies aimed at curtailing further infections, reliable serologic testing is crucial for providing insight into the dynamics of the spread of COVID-19 on a population level. METHODS: The presence of anti-SARS-CoV-2 antibodies in polymerase chain reaction-positive, confirmed COVID-19 patient samples was determined using the Elecsys Ab assay on the Roche cobas e602 analyzer. The precision and cross-reactivity of the Elecsys Ab assay were characterized and its performance was compared against the EuroImmun IgA/IgG antibody (EuroImmun Ab) assay. Calculated sensitivity, specificity, and positive and negative predictive values were assessed. RESULTS: The Elecsys Ab assay demonstrated good precision, had no cross-reactivity with other viral samples, and showed 100% concordance with the EuroImmun Ab assay. Excellent clinical performance with respect to sensitivity, specificity, and positive and negative predictive values was observed. CONCLUSIONS: The Elecsys Ab assay is a precise and highly reliable automated platform for clinical detection of seropositivity in SARS-CoV-2 infection.


Subject(s)
Automation, Laboratory , Betacoronavirus/pathogenicity , Serologic Tests , Automation, Laboratory/methods , Clinical Laboratory Techniques , Female , Humans , Immunoglobulin G/analysis , Male , SARS-CoV-2 , Sensitivity and Specificity , Serologic Tests/instrumentation , Serologic Tests/methods
14.
Nucleic Acids Res ; 48(13): 7569-7583, 2020 07 27.
Article in English | MEDLINE | ID: mdl-32544228

ABSTRACT

Cobalamin riboswitches encompass a structurally diverse group of cis-acting, gene regulatory elements found mostly in bacterial messenger RNA and are classified into subtypes based on secondary and tertiary characteristics. An unusual variant of the cobalamin riboswitch with predicted structural features was identified in Bacillus subtilis over a decade ago, but its structure and mechanisms of cobalamin selectivity and translational control have remained unsolved. We present the crystal structure of the aptamer domain of this atypical cobalamin riboswitch and a model for the complete riboswitch, including its expression platform domain. We demonstrate that this riboswitch binds to multiple cobalamin derivatives and correlate its promiscuous behavior to its structure and unique arrangement of peripheral elements. Comparative structural analyses between conventional cobalamin riboswitches and the B. subtilis cobalamin riboswitch reveal that the likely basis for this promiscuous ligand binding is intrinsic structural adaptability encoded in the RNA structure. It suggests that cobalamin selectivity might ultimately be viewed as existing on a spectrum of affinity for each derivative rather than as belonging to distinct types based on ligand specificities. Our work provides an interesting and notable example of functional coupling of ligand-sensing and adaptive folding by a structured RNA molecule.


Subject(s)
Aptamers, Nucleotide/chemistry , Cobamides/chemistry , RNA Folding , Riboswitch , Vitamin B 12/chemistry , Bacillus subtilis
15.
RNA ; 26(3): 278-289, 2020 03.
Article in English | MEDLINE | ID: mdl-31848215

ABSTRACT

Ubiquitous across all domains of life, tRNAs constitute an essential component of cellular physiology, carry out an indispensable role in protein synthesis, and have been historically the subject of a wide range of biochemical and biophysical studies as prototypical folded RNA molecules. Although conformational flexibility is a well-established characteristic of tRNA structure, it is typically regarded as an adaptive property exhibited in response to an inducing event, such as the binding of a tRNA synthetase or the accommodation of an aminoacyl-tRNA into the ribosome. In this study, we present crystallographic data of a tRNA molecule to expand on this paradigm by showing that structural flexibility and plasticity are intrinsic properties of tRNAs, apparent even in the absence of other factors. Based on two closely related conformations observed within the same crystal, we posit that unbound tRNAs by themselves are flexible and dynamic molecules. Furthermore, we demonstrate that the formation of the T-loop conformation by the tRNA TΨC stem-loop, a well-characterized and classic RNA structural motif, is possible even in the absence of important interactions observed in fully folded tRNAs.


Subject(s)
Nucleic Acid Conformation , RNA, Transfer, Amino Acyl/ultrastructure , RNA, Transfer/ultrastructure , Anticodon/chemistry , Anticodon/genetics , Crystallography , Escherichia coli/chemistry , Escherichia coli/ultrastructure , Nucleotide Motifs/genetics , RNA, Transfer/chemistry , RNA, Transfer, Amino Acyl/chemistry , Ribosomes/genetics , Ribosomes/ultrastructure
16.
J Mol Biol ; 430(10): 1403-1416, 2018 05 11.
Article in English | MEDLINE | ID: mdl-29625199

ABSTRACT

Ribonuclease P (RNase P) catalyzes the removal of 5' leaders of tRNA precursors and its central catalytic RNA subunit is highly conserved across all domains of life. In eukaryotes, RNase P and RNase MRP, a closely related ribonucleoprotein enzyme, share several of the same protein subunits, contain a similar catalytic RNA core, and exhibit structural features that do not exist in their bacterial or archaeal counterparts. A unique feature of eukaryotic RNase P/MRP is the presence of two relatively long and unpaired internal loops within the P3 region of their RNA subunit bound by a heterodimeric protein complex, Rpp20/Rpp25. Here we present a crystal structure of the human Rpp20/Rpp25 heterodimer and we propose, using comparative structural analyses, that the evolutionary divergence of the single-stranded and helical nucleic acid binding specificities of eukaryotic Rpp20/Rpp25 and their related archaeal Alba chromatin protein dimers, respectively, originate primarily from quaternary level differences observed in their heterodimerization interface. Our work provides structural insights into how the archaeal Alba protein scaffold was adapted evolutionarily for incorporation into several functionally-independent eukaryotic ribonucleoprotein complexes.


Subject(s)
Autoantigens/chemistry , Autoantigens/metabolism , RNA/metabolism , Ribonuclease P/chemistry , Ribonuclease P/metabolism , Archaeal Proteins/chemistry , Archaeal Proteins/metabolism , Crystallography, X-Ray , Evolution, Molecular , Fungal Proteins/chemistry , Fungal Proteins/metabolism , Humans , Models, Molecular , Multienzyme Complexes/chemistry , Multienzyme Complexes/metabolism , Protein Domains , Protein Multimerization , Protein Structure, Quaternary , Protein Structure, Secondary
17.
Proc Natl Acad Sci U S A ; 112(28): E3669-78, 2015 Jul 14.
Article in English | MEDLINE | ID: mdl-26124119

ABSTRACT

Acetylation is correlated with chromatin decondensation and transcriptional activation, but its regulation by histone deacetylase (HDAC)-bearing corepressor complexes is poorly understood. Here, we describe the mechanism of assembly of the mammalian Sin3L/Rpd3L complex facilitated by Sds3, a conserved subunit deemed critical for proper assembly. Sds3 engages a globular, helical region of the HDAC interaction domain (HID) of the scaffolding protein Sin3A through a bipartite motif comprising a helix and an adjacent extended segment. Sds3 dimerizes through not only one of the predicted coiled-coil motifs but also, the segment preceding it, forming an ∼ 150-Å-long antiparallel dimer. Contrary to previous findings in yeast, Sin3A rather than Sds3 functions in recruiting HDAC1 into the complex by engaging the latter through a highly conserved segment adjacent to the helical HID subdomain. In the resulting model for the ternary complex, the two copies of the HDACs are situated distally and dynamically because of a natively unstructured linker connecting the dimerization domain and the Sin3A interaction domain of Sds3; these features contrast with the static organization described previously for the NuRD (nucleosome remodeling and deacetylase) complex. The Sds3 linker features several conserved basic residues that could potentially maintain the complex on chromatin by nonspecific interactions with DNA after initial recruitment by sequence-specific DNA-binding repressors.


Subject(s)
Histone Deacetylases/metabolism , Repressor Proteins/chemistry , Amino Acid Sequence , Animals , Dimerization , Magnetic Resonance Spectroscopy , Molecular Sequence Data , Protein Conformation , Repressor Proteins/metabolism , Sequence Homology, Amino Acid
18.
Wiley Interdiscip Rev RNA ; 4(5): 507-22, 2013.
Article in English | MEDLINE | ID: mdl-23754657

ABSTRACT

The T-loop is a frequently occurring five-nucleotide motif found in the structure of noncoding RNAs where it is commonly assumed to play an important role in stabilizing the tertiary RNA structure by facilitating long-range interactions between different regions of the molecule. T-loops were first identified in tRNA(Phe) and a formal consensus sequence for this motif was formulated and later revised based on analyses of the crystal structures of prokaryotic ribosomal RNAs and RNase P and the corresponding primary sequence of their orthologues. In the past decade, several new structures of large RNA molecules have been added to the RCSB Protein Data Bank, including the eukaryotic ribosome, a self-splicing group II intron, numerous synthetases in complex with their cognate transfer RNAs (tRNAs), transfer-messenger RNA (tmRNA) in complex with SmpB, several riboswitches, and a complex of bacterial RNase P bound to its tRNA substrate. In this review, the search for T-loops is extended to these new RNA molecules based on the previously established structure-based criteria. The review highlights and discusses the function and additional roles of T-loops in four broad categories of RNA molecules, namely tRNAs, ribosomal RNAs (rRNAs), P RNAs, and RNA genetic elements. Additionally, the potential application for T-loops as interaction modules is also discussed.


Subject(s)
Nucleic Acid Conformation , RNA Stability , RNA, Untranslated/chemistry , RNA, Untranslated/metabolism
19.
Curr Opin Struct Biol ; 21(3): 319-26, 2011 Jun.
Article in English | MEDLINE | ID: mdl-21474301

ABSTRACT

Extensive networks of tertiary interactions give rise to unique, highly organized domain architectures that characterize the three-dimensional structure of large RNA molecules. Formed by stacked layers of a near-planar arrangement of contiguous coaxial helices, large RNA molecules are relatively flat in overall shape. The functional core of these molecules is stabilized by a diverse set of tertiary interaction motifs that often bring together distant regions of conserved nucleotides. Although homologous RNAs from different organisms can be structurally diverse, they adopt a structurally conserved functional core that includes preassembled active and/or substrate binding sites. These findings broaden our understanding of RNA folding and tertiary structure stabilization, illustrating how large, complex RNAs assemble into unique structures to perform recognition and catalysis.


Subject(s)
Nucleic Acid Conformation , RNA/chemistry , Adenosine/metabolism , Binding Sites/genetics , Consensus Sequence/genetics , RNA/genetics , RNA/metabolism , Ribonucleoproteins/metabolism
20.
Methods Cell Biol ; 92: 11-30, 2009.
Article in English | MEDLINE | ID: mdl-20409796

ABSTRACT

We describe the protocol through which we identify and characterize dynein subunit genes in the ciliated protozoan Tetrahymena thermophila. The gene(s) of interest is found by searching the Tetrahymena genome, and it is characterized in silico including the prediction of the open reading frame and identification of likely introns. The gene is then characterized experimentally, including the confirmation of the exon-intron organization of the gene and the measurement of the expression of the gene in nondeciliated and reciliating cells. In order to understand the function of the gene product, the gene is modified-for example, deleted, overexpressed, or epitope-tagged-using the straightforward gene replacement strategies available with Tetrahymena. The effect(s) of the dynein gene modification is evaluated by examining transformants for ciliary traits including cell motility, ciliogenesis, cell division, and the engulfment of particles through the oral apparatus. The multistepped protocol enables undergraduate students to engage in short- and long-term experiments. In our laboratory during the last 6 years, more than two dozen undergraduate students have used these methods to investigate dynein subunit genes.


Subject(s)
Computational Biology/methods , Dyneins/genetics , Genes, Protozoan/genetics , Tetrahymena/genetics , Animals , Biological Assay , Cilia/metabolism , Dyneins/metabolism , Gene Expression Regulation , Gene Targeting , Phenotype , Phylogeny , Protein Subunits/genetics , Protein Subunits/metabolism , Sequence Analysis, DNA
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