Skip to main content

Publications search

Found 37443 matches. Displaying 861-870
Carlson AL, Floyd RJ, Arbona RJR, Henderson KS, Perkins C, Lipman NS
Show All Authors

Assessing Elimination of Mouse Kidney Parvovirus from Cages by Mechanical Washing (opens in new window)

JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE 2022 JAN; 61(1):61-66
Show Abstract
Mouse kidney parvovirus (MKPV), a newly identified parvovirus of the genus Chaphamaparvovirus, causes inclusion body nephropathy in severely immunocompromised mice and is prevalent in research mouse colonies. As nonenveloped viruses, mammalian parvoviruses are stable and generally resist thermal inactivation; however, as a novel and highly divergent parvovirus, the thermal stability of MKPV is undefined. This study aimed to evaluate the ability of cage sanitization in a mechanical washer to eliminate MKPV. Cages contaminated by MKPV-infected mice were assigned to 1 of 3 treatment groups: 1) control (bedding change only); 2) sanitization in a tunnel washer (88 degrees C final rinse for 20 s); or 3) sanitization in a tunnel washer followed by autoclave sterilization (121 degrees C for 20 min). The presence of MKPV on the cage's interior surface was assessed by PCR of cage swab extracts collected before and after cage treatment. After treatment and swabbing, each cage housed 4 MKPV-negative CD1 mice. Each group of naive CD1 mice was assigned to one of the treatment groups and was housed in a cage from this group for two, 1 wk periods. At 12, 17, and 20 wk after the first exposure, renal tissue was collected from 1 test mouse per cage and assessed for MKPV by PCR. MKPV was detected by PCR on the surface of 63% of the pretreatment cages. All cages sanitized in a tunnel washer with or without sterilization were PCR negative after treatment. Seven of 10 mice housed in untreated cages contained a mouse positive for MKPV by 20 wk after exposure. None of the mice housed in cages sanitized in a tunnel washer with or without sterilization tested positive for MKPV at any time point. This study indicates that MKPV contaminated caging can result in MKPV infection of mice, and the use of a tunnel washer at the temperature and duration evaluated was sufficient to remove MKPV nucleic acid and prevent MKPV transmission.
Cho A, Gaebler C, Olveira T, Ramos V, Saad M, Lorenzi JCC, Gazumyan A, Moir S, Caskey M, Chun TW, Nussenzweig MC
Show All Authors

Longitudinal clonal dynamics of HIV-1 latent reservoirs measured by combination quadruplex polymerase chain reaction and sequencing (opens in new window)

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2022 JAN 25; 119(4):? Article e2117630119
Show Abstract
HIV-1 infection produces a long-lived reservoir of latently infected CD4(+) T cells that represents the major barrier to HIV-1 cure. The reservoir contains both intact and defective proviruses, but only the proviruses that are intact can reinitiate infection upon cessation of antiretroviral therapy (ART). Here we combine four-color quantitative PCR and next-generation sequencing (Q4PCR) to distinguish intact and defective proviruses and measure reservoir content longitudinally in 12 infected individuals. Q4PCR differs from other PCR-based methods in that the amplified proviruses are sequence verified as intact or defective. Samples were collected systematically over the course of up to 10 y beginning shortly after the initiation of ART. The size of the defective reservoir was relatively stable with minimal decay during the 10-y observation period. In contrast, the intact proviral reservoir decayed with an estimated half-life of 4.9 y. Nevertheless, both intact and defective proviral reservoirs are dynamic. As a result, the fraction of intact proviruses found in expanded clones of CD4(+) T cells increases over time with a concomitant decrease in overall reservoir complexity. Thus, reservoir decay measurements by Q4PCR are quantitatively similar to viral outgrowth assay (VOA) and intact proviral DNA PCR assay (IPDA) with the addition of sequence information that distinguishes intact and defective proviruses and informs reservoir dynamics. The data are consistent with the notion that intact and defective proviruses are under distinct selective pressure, and that the intact proviral reservoir is progressively enriched in expanded clones of CD4(+) T cells resulting in diminishing complexity over time.
Cridland JM, Majane AC, Zhao L, Begun DJ
Show All Authors

Population biology of accessory gland-expressed de novo genes in Drosophila melanogaster (opens in new window)

GENETICS 2022 JAN; 220(1):? Article iyab207
Show Abstract
Early work on de novo gene discovery in Drosophila was consistent with the idea that many such genes have male-biased patterns of expression, including a large number expressed in the testis. However, there has been little formal analysis of variation in the abundance and properties of de novo genes expressed in different tissues. Here, we investigate the population biology of recently evolved de novo genes expressed in the Drosophila melanogaster accessory gland, a somatic male tissue that plays an important role in male and female fertility and the post mating response of females, using the same collection of inbred lines used previously to identify testis-expressed de novo genes, thus allowing for direct cross tissue comparisons of these genes in two tissues of male reproduction. Using RNA-seq data, we identify candidate de novo genes located in annotated intergenic and intronic sequence and determine the properties of these genes including chromosomal location, expression, abundance, and coding capacity. Generally, we find major differences between the tissues in terms of gene abundance and expression, though other properties such as transcript length and chromosomal distribution are more similar. We also explore differences between regulatory mechanisms of de novo genes in the two tissues and how such differences may interact with selection to produce differences in D. melanogaster de novo genes expressed in the two tissues.
Barrangou R, Marraffini LA
Show All Authors

Turning CRISPR on with antibiotics (opens in new window)

CELL HOST & MICROBE 2022 JAN 12; 30(1):12-14
Show Abstract
CRISPR-Cas systems have the ability to integrate invasive DNA sequences to build adaptive immunity in bacteria. In this issue Dimitriu et al. show bacteriostatic antibiotics prompt CRISPR acquisition events, illustrating how environmental conditions affect complex dynamics between host and virus and the corresponding biological and genetic arms race.
Gross A, Zhou BH, Bewersdorf L, Schwarz N, Schacht GM, Boor P, Hoeft K, Hoffmann B, Fuchs E, Kramann R, Merkel R, Leube RE, Strnad P
Show All Authors

Desmoplakin Maintains Transcellular Keratin Scaffolding and Protects From Intestinal Injury (opens in new window)

CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY 2022; 13(4):1181-1200
Show Abstract
BACKGROUND & AIMS: Desmosomes are intercellular junctions connecting keratin intermediate filaments of neighboring cells. The cadherins desmoglein 2 (Dsg2) and desmocollin 2 mediate cell-cell adhesion, whereas desmoplakin (Dsp) provides the attachment of desmosomes to keratins. Although the importance of the desmosome-keratin network is well established in mechanically challenged tissues, we aimed to assess the currently understudied function of desmosomal proteins in intestinal epithelia.& nbsp;METHODS: We analyzed the intestine-specific villin-Cre DSP (DSP delta IEC) and the combined intestine-specific DSG2/DSP delta IEC (delta Dsg2/Dsp) knockout mice. Cross-breeding with keratin 8-yellow fluorescent protein knock-in mice and generation of organoids was performed to visualize the keratin network. A Dsp-deficient colorectal carcinoma HT29-derived cell line was generated and the role of Dsp in adhesion and mechanical stress was studied in dispase assays, after exposure to uniaxial cell stretching and during scratch assay.& nbsp;RESULTS: The intestine of DSP delta IEC mice was histopathologically inconspicuous. Intestinal epithelial cells, however, showed an accelerated migration along the crypt and an enhanced shedding into the lumen. Increased intestinal permeability and altered levels of desmosomal proteins were detected. An inconspicuous phenotype also was seen in delta Dsg2/Dsp mice. After dextran sodium sulfate treatment, DSP delta IEC mice developed more pronounced colitis. A retracted keratin network was seen in the intestinal epithelium of DSP delta IEC/keratin 8-yellow fluorescent protein mice and organoids derived from these mice presented a collapsed keratin network. The level, phosphorylation status, and solubility of keratins were not affected. Dsp-deficient HT29 cells had an impaired cell adhesion and suffered from increased cellular damage after stretch.& nbsp;CONCLUSIONS: Our results show that Dsp is required for proper keratin network architecture in intestinal epithelia, mechanical resilience, and adhesion, thereby protecting from injury.
Navrazhina K, Garcet S, Zheng XZ, Hur HB, Frew JW, Krueger JG
Show All Authors

High inflammation in hidradenitis suppurativa extends to perilesional skin and can be subdivided by lipocalin-2 expression (opens in new window)

JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY 2022 JAN; 149(1):135-+
Show Abstract
Background: Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease presenting with diverse manifestations ranging from nodules and abscesses to draining tunnels. Whether the underlying inflammation from lesions extends to relatively healthy-appearing adjacent perilesional and distant nonlesional skin has not been systematically evaluated. Objective: We sought to characterize lesional, perilesional, and nonlesional skin in patients with HS. Methods: Skin biopsy samples were collected under ultrasound guidance from patients with active, untreated moderate-tosevere HS. Site-matched control biopsy samples from healthy volunteers were used for comparison. Results: RNA sequencing demonstrated that HS skin clustered separately from healthy control skin, with perilesional and lesion skin clustering together and away from nonlesional skin. Immunohistochemistry analysis identified psoriasiform hyperplasia with keratin 16 positivity in both perilesional and lesional skin, with comparable levels of CD3(+), CD11c(+), and neutrophil elastase-positive cellular infiltration. There was a marked upregulation of IL-17 signaling in perilesional and lesional skin. HS samples clustered on the basis of expression of lipocalin-2 (LCN2), with samples characterized by high LCN2 expression in the skin exhibiting a differing transcriptomic profile with significantly higher overall inflammation than that of skin characterized by low LCN2 levels. Conclusions: Perilesional HS skin has a transcriptomic and molecular profile comparable to that of lesional skin. HS can be grouped into 2 distinct subtypes based on molecular levels of LCN2 in the skin, with the LCN2-high subtype exhibiting an overall higher inflammatory burden and an upregulation of targetable cytokines. To our knowledge, this is the first study to characterize a unique HS subtype (and a potential endotype) that may guide future therapeutic targets.
Farris S, Hacisuleyman E, Donlin-Asp P, Cioni JM
Show All Authors

Editorial: RNA Localization and Localized Translation in Neurons (opens in new window)

FRONTIERS IN INTEGRATIVE NEUROSCIENCE 2022 JAN 12; 15(?):? Article 831038
Show Abstract
Gleicher N, Orvieto R
Show All Authors

Transferring more than one embryo simultaneously is justifiable in most patients (opens in new window)

REPRODUCTIVE BIOMEDICINE ONLINE 2022 JAN; 44(1):1-4
Show Abstract
Elective single embryo transfer (eSET) was first introduced to IVF in 1999, and its subsequent integration into mainstream reproductive endocrinology and infertility has been hugely consequential. It can be viewed as the first (among many since) 'add-ons' to IVF that has significantly and adversely affected how IVF is practised, resulting in astonishing declines in live birth rates after fresh non-donor IVF cycles worldwide. We propose that, like most 'addons' to IVF over recent years, the almost universal use of eSET worldwide lacks proper validation of its underlying hypothesis and is based on statistically incorrect assumptions and incorrect data interpretation. As with most recent 'add-ons' to IVF, eSET lacks evidentiary support, and, therefore, its remarkable success in the marketplace must be based on expert opinions, the lowest level of evidence in medicine and widely recognized as frequently biased. Like other 'add-ons' to IVF, eSET-practice must be reassessed because it does not offer the benefits it has widely claimed to provide, prolongs time to conception and adversely affects live birth chances for many women. Moreover, by ignoring that infertile women value quick conception over most other considerations, provider-insistence on eSET frequently deprives them of the right to self-determination.
Dahan N, Bykov YS, Boydston EA, Fadel A, Gazi Z, Hochberg-Laufer H, Martenson J, Denic V, Shav-Tal Y, Weissman JS, Aviram N, Zalckvar E, Schuldiner M
Show All Authors

Peroxisome function relies on organelle-associated mRNA translation (opens in new window)

SCIENCE ADVANCES 2022 JAN; 8(2):? Article eabk2141
Show Abstract
Crucial metabolic functions of peroxisomes rely on a variety of peroxisomal membrane proteins (PMPs). While mRNA transcripts of PMPs were shown to be colocalized with peroxisomes, the process by which PMPs efficiently couple translation with targeting to the peroxisomal membrane remained elusive. Here, we combine quantitative electron microscopy with proximity-specific ribosome profiling and reveal that translation of specific PMPs occurs on the surface of peroxisomes in the yeast Saccharomyces cerevisiae. This places peroxisomes alongside chloroplasts, mitochondria, and the endoplasmic reticulum as organelles that use localized translation for ensuring correct insertion of hydrophobic proteins into their membranes. Moreover, the correct targeting of these transcripts to peroxisomes is crucial for peroxisomal and cellular function, emphasizing the importance of localized translation for cellular physiology.
Dahn HA, Mountcastle J, Balacco J, Winkler S, Bista I, Schmitt AD, Pettersson OV, Formenti G, Oliver K, Smith M, Tan WH, Kraus A, Mac S, Komoroske LM, Lama T, Crawford AJ, Murphy RW, Brown S, Scott AF, Morin PA, Jarvis ED, Fedrigo O
Show All Authors

Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing (opens in new window)

GIGASCIENCE 2022; 11(?):? Article giac068
Show Abstract
Background Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. Results We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4 degrees C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4 degrees C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield. Conclusion We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all similar to 70,000 extant vertebrate species.