Publications by authors named "Bradley Smith"

368 Publications

Biological Applications for LC-MS-Based Proteomics.

Adv Exp Med Biol 2021 ;1336:17-29

Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.

Since its inception, liquid chromatography-mass spectrometry (LC-MS) has been continuously improved upon in many aspects, including instrument capabilities, sensitivity, and resolution. Moreover, the costs to purchase and operate mass spectrometers and liquid chromatography systems have decreased, thus increasing affordability and availability in sectors outside of academic and industrial research. Processing power has also grown immensely, cutting the time required to analyze samples, allowing more data to be feasibly processed, and allowing for standardized processing pipelines. As a result, proteomics via LC-MS has become popular in many areas of biological sciences, forging an important seat for itself in targeted and untargeted assays, pure and applied science, the laboratory, and the clinic. In this chapter, many of these applications of LC-MS-based proteomics and an outline of how they can be executed will be covered. Since the field of personalized medicine has matured alongside proteomics, it has also come to rely on various mass spectrometry methods and will be elaborated upon as well. As time goes on and mass spectrometry evolves, there is no doubt that its presence in these areas, and others, will only continue to grow.
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http://dx.doi.org/10.1007/978-3-030-77252-9_2DOI Listing
October 2021

Association of Variants in the SPTLC1 Gene With Juvenile Amyotrophic Lateral Sclerosis.

JAMA Neurol 2021 Oct;78(10):1236-1248

Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom.

Importance: Juvenile amyotrophic lateral sclerosis (ALS) is a rare form of ALS characterized by age of symptom onset less than 25 years and a variable presentation.

Objective: To identify the genetic variants associated with juvenile ALS.

Design, Setting, And Participants: In this multicenter family-based genetic study, trio whole-exome sequencing was performed to identify the disease-associated gene in a case series of unrelated patients diagnosed with juvenile ALS and severe growth retardation. The patients and their family members were enrolled at academic hospitals and a government research facility between March 1, 2016, and March 13, 2020, and were observed until October 1, 2020. Whole-exome sequencing was also performed in a series of patients with juvenile ALS. A total of 66 patients with juvenile ALS and 6258 adult patients with ALS participated in the study. Patients were selected for the study based on their diagnosis, and all eligible participants were enrolled in the study. None of the participants had a family history of neurological disorders, suggesting de novo variants as the underlying genetic mechanism.

Main Outcomes And Measures: De novo variants present only in the index case and not in unaffected family members.

Results: Trio whole-exome sequencing was performed in 3 patients diagnosed with juvenile ALS and their parents. An additional 63 patients with juvenile ALS and 6258 adult patients with ALS were subsequently screened for variants in the SPTLC1 gene. De novo variants in SPTLC1 (p.Ala20Ser in 2 patients and p.Ser331Tyr in 1 patient) were identified in 3 unrelated patients diagnosed with juvenile ALS and failure to thrive. A fourth variant (p.Leu39del) was identified in a patient with juvenile ALS where parental DNA was unavailable. Variants in this gene have been previously shown to be associated with autosomal-dominant hereditary sensory autonomic neuropathy, type 1A, by disrupting an essential enzyme complex in the sphingolipid synthesis pathway.

Conclusions And Relevance: These data broaden the phenotype associated with SPTLC1 and suggest that patients presenting with juvenile ALS should be screened for variants in this gene.
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http://dx.doi.org/10.1001/jamaneurol.2021.2598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8406220PMC
October 2021

Deuterated Indocyanine Green (ICG) with Extended Aqueous Storage Shelf-Life: Chemical and Clinical Implications.

Chemistry 2021 Oct 24;27(58):14535-14542. Epub 2021 Sep 24.

Department of Chemistry & Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46545, USA.

Indocyanine Green (ICG) is a clinically approved near-infrared fluorescent dye that is used extensively for various imaging and diagnostic procedures. One drawback with ICG is its instability in water, which means that reconstituted clinical doses have to be used very shortly after preparation. Two deuterated versions of ICG were prepared with deuterium atoms on the heptamethine chain, and the spectral, physiochemical, and photostability properties were quantified. A notable mechanistic finding is that self-aggregation of ICG in water strongly favors dye degradation by a photochemical oxidative dimerization reaction that gives a nonfluorescent product. Storage stability studies showed that replacement of C-H with C-D decreased the dimerization rate constant by a factor of 3.1, and it is likely that many medical and preclinical procedures will benefit from the longer shelf-lives of these two deuterated ICG dyes. The discovery that ICG self-aggregation promotes photoinduced electron transfer can be exploited as a new paradigm for next-generation photodynamic therapies.
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http://dx.doi.org/10.1002/chem.202102816DOI Listing
October 2021

The use of transthoracic echocardiography in caesarean section surgical patients in the intensive care unit: A retrospective cohort study.

Aust N Z J Obstet Gynaecol 2021 Aug 9. Epub 2021 Aug 9.

Mater Research Institute, University of Queensland, St Lucia, Queensland, Australia.

Data regarding transthoracic echocardiography (TTE) application to obstetric patients are scant. Often, anaesthetists preparing for caesarean section are unaware of the proportion of obstetric patients who have relevant cardiac disease. This audit aimed at undertaking a retrospective analysis of TTE performed in intensive care unit patients after caesarean section. Over five years, 56 women were eligible. Echocardiographic abnormalities were deemed relevant if graded as of moderate severity. The most common reason was dyspnoea (41%). Echocardiography demonstrated structural abnormality in 29% or functional abnormality in 38%. It may be appropriate to undertake preoperative echocardiography more commonly in high-risk obstetric patients.
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http://dx.doi.org/10.1111/ajo.13414DOI Listing
August 2021

Macular Findings of Patients on Pentosan Polysulfate Sodium.

Mil Med 2021 Jul 23. Epub 2021 Jul 23.

The Retina Institute, St Louis, MO 63144, USA.

Introduction: In 2018, a unique maculopathy associated with chronic pentosan polysulfate sodium (PPS) use for the treatment of interstitial cystitis (IC) was described, where the authors detailed macular retinal pigment epithelial abnormalities in six patients. In this paper, a retrospective study of a larger patient pool at one large tertiary retina practice was undertaken to evaluate patients taking PPS and their macular findings.

Materials And Methods: A retrospective chart review was performed on all patients presenting to a single large retina practice between 2011 and 2019. Patient's macular diagnosis, findings, optical coherence tomography scans, and macular auto-fluorescent scans were assessed. This project was Institutional Review Board (IRB) approved by the St Luke's Hospital IRB board (St Louis, MO, USA).

Results: Fifty-five patients were identified as taking PPS for IC. Fifty-three patients were found to have a diagnosis consistent with changes attributable to known macular diseases to include macular degeneration and pattern dystrophies. Two (4%) of fifty-five patients had macular findings suggestive of PPS toxicity. The first was a 58-year-old female with subtle retinal pigment epithelium (RPE) deposits on optical coherence tomography that exhibited hyper-autofluorescence. The second was a 72-year-old female with 14 years of PPS use who exhibited RPE excrescences and parafoveal areas of atrophy.

Conclusions: Pentosan polysulfate sodium may be the cause of macular findings in a small percentage of patients referred to a tertiary retina practice. Although causation of macular changes with PPS use has yet to be elucidated, clinicians should be aware of this possibility when assessing patients with atypical macular findings. Future longitudinal studies are necessary to evaluate a definitive relationship. This paper should remind all clinicians of the importance of a throughout review of the patient's medication list as novel toxicities may become apparent years after initial FDA trials. The strength of this study is the larger patient population compared to earlier studies, and the main weaknesses include the retrospective nature of the study, lack of family and genetic testing, and lack of multimodal imaging for all patients.
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http://dx.doi.org/10.1093/milmed/usab301DOI Listing
July 2021

A recessive S174X mutation in Optineurin causes amyotrophic lateral sclerosis through a loss of function via allele-specific nonsense-mediated decay.

Neurobiol Aging 2021 10 4;106:351.e1-351.e6. Epub 2021 Jun 4.

Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center affiliated with the Hebrew University School of Medicine, Jerusalem, Israel. Electronic address:

Loss of function (LoF) mutations in Optineurin can cause recessive amyotrophic lateral sclerosis (ALS) with some heterozygous LoF mutations associated with dominant ALS. The molecular mechanisms underlying the variable inheritance pattern associated with OPTN mutations have remained elusive. We identified that affected members of a consanguineous Middle Eastern ALS kindred possessed a novel homozygous p.S174X OPTN mutation. Analysis of these primary fibroblast lines from family members identified that the p.S174X mutation reduces OPTN mRNA expression in an allele-dependent fashion by nonsense mediated decay. Western blotting correlated a reduced expression in heterozygote carriers but a complete absence of OPTN protein in the homozygous carrier. This data suggests that the p.S174X truncation mutation causes recessive ALS through LoF. However, functional analysis detected a significant increase in mitophagy markers TOM20 and COXIV, and higher rates of mitochondrial respiration and ATP levels in heterozygous carriers only. This suggests that heterozygous LoF OPTN mutations may not be causative in a Mendelian manner but may potentially behave as contributory ALS risk factors.
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http://dx.doi.org/10.1016/j.neurobiolaging.2021.05.009DOI Listing
October 2021

Identification of a novel interaction of FUS and syntaphilin may explain synaptic and mitochondrial abnormalities caused by ALS mutations.

Sci Rep 2021 06 30;11(1):13613. Epub 2021 Jun 30.

Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Denmark Hill, London, SE5 8AF, UK.

Aberrantly expressed fused in sarcoma (FUS) is a hallmark of FUS-related amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Wildtype FUS localises to synapses and interacts with mitochondrial proteins while mutations have been shown to cause to pathological changes affecting mitochondria, synapses and the neuromuscular junction (NMJ). This indicates a crucial physiological role for FUS in regulating synaptic and mitochondrial function that is currently poorly understood. In this paper we provide evidence that mislocalised cytoplasmic FUS causes mitochondrial and synaptic changes and that FUS plays a vital role in maintaining neuronal health in vitro and in vivo. Overexpressing mutant FUS altered synaptic numbers and neuronal complexity in both primary neurons and zebrafish models. The degree to which FUS was mislocalised led to differences in the synaptic changes which was mirrored by changes in mitochondrial numbers and transport. Furthermore, we showed that FUS co-localises with the mitochondrial tethering protein Syntaphilin (SNPH), and that mutations in FUS affect this relationship. Finally, we demonstrated mutant FUS led to changes in global protein translation. This localisation between FUS and SNPH could explain the synaptic and mitochondrial defects observed leading to global protein translation defects. Importantly, our results support the 'gain-of-function' hypothesis for disease pathogenesis in FUS-related ALS.
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http://dx.doi.org/10.1038/s41598-021-93189-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8245466PMC
June 2021

Intracellular fluorescence competition assay for inhibitor engagement of histone deacetylase.

Bioorg Med Chem Lett 2021 Sep 17;47:128207. Epub 2021 Jun 17.

School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Victoria 3216, Australia. Electronic address:

An intracellular fluorescence competition assay was developed to assess the capability of inhibitor candidates to engage histone deacetylase (HDAC) inside living cells and thus diminish cell uptake and staining by the HDAC-targeted fluorescent probe APS. Fluorescence cell microscopy and flow cytometry showed that pre-incubation of living cells with candidate inhibitors led to diminished cell uptake of the fluorescent probe. The assay was effective because the fluorescent probe (APS) possessed the required performance properties, including bright fluorescence, ready membrane diffusion, selective intracellular HDAC affinity, and negligible acute cytotoxicity. The concept of an intracellular fluorescence competition assay is generalizable and has broad applicability since it obviates the requirement to use the isolated biomacromolecule target for screening of molecular candidates with target affinity.
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http://dx.doi.org/10.1016/j.bmcl.2021.128207DOI Listing
September 2021

Cannabidiol Displays Proteomic Similarities to Antipsychotics in Cuprizone-Exposed Human Oligodendrocytic Cell Line MO3.13.

Front Mol Neurosci 2021 28;14:673144. Epub 2021 May 28.

Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.

Cannabidiol, a compound of , has been proposed as an alternative treatment of schizophrenia. Preclinical and clinical data have suggested that cannabidiol shares more similarity with atypical antipsychotics than typical, both of which are customarily used to manage schizophrenia symptoms. While oligodendrocytes are known to be relevant targets of antipsychotics, the biochemical knowledge in this regard is still limited. Here we evaluated the molecular pathways modulated by cannabidiol compared to the antipsychotics clozapine (atypical) and haloperidol (typical), additionally evaluating the effects of benztropine, a muscarinic receptor antagonist that displays a protective effect in oligodendrocytes and myelination. For this purpose, we employed nano-chromatography coupled with mass spectrometry to investigate the proteomic response to these drugs both in healthy oligodendrocytic cells and in a cuprizone-based toxicity model, using the human oligodendrocyte precursor cell line MO3.13. Cannabidiol shares similarities of biochemical pathways with clozapine and benztropine, in agreement with other studies that indicated an atypical antipsychotic profile. All drugs tested affected metabolic and gene expression pathways and cannabidiol, benztropine, and clozapine modulated cell proliferation and apoptosis when administered after cuprizone-induced toxicity. These general pathways are associated with cuprizone-induced cytotoxicity in MO3.13 cells, indicating a possible proteomic approach when acting against the toxic effects of cuprizone. In conclusion, although modeling oligodendrocytic cytotoxicity with cuprizone does not represent the entirety of the pathophysiology of oligodendrocyte impairments, these results provide insight into the mechanisms associated with the effects of cannabidiol and antipsychotics against cuprizone toxicity, offering new directions of study for myelin-related processes and deficits.
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http://dx.doi.org/10.3389/fnmol.2021.673144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8193732PMC
May 2021

Generalizable synthesis of bioresponsive near-infrared fluorescent probes: sulfonated heptamethine cyanine prototype for imaging cell hypoxia.

Org Biomol Chem 2021 May;19(18):4100-4106

Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, IN 46556, USA.

Continued advancement in bioresponsive fluorescence imaging requires new classes of activatable fluorescent probes that emit near-infrared fluorescence with wavelengths above 740 nm. Heptamethine cyanine dyes (Cy7) have suitable fluorescence properties but it is challenging to create activatable probes because Cy7 dyes have a propensity for self-aggregation and fluorescence quenching. A new synthetic strategy is employed to create a generalizable class of hydrophilic bioresponsive near-infrared fluorescent probes with appended sulfonates that provide excellent physiochemical properties. A prototype version is triggered by nitroreductase enzyme to undergo self-immolative cleavage with a large enhancement in fluorescence signal at 780 nm and the probe enables microscopic imaging of cell hypoxia with "turn on" fluorescence. Near-infrared fluorescence imaging of hypoxia is potentially useful in many different areas of biomedical research and clinical treatment.
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http://dx.doi.org/10.1039/d1ob00426cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8121178PMC
May 2021

Structural Engineering of Fluorescent Self-Threaded Peptide Probes for Targeted Cell Imaging.

Photochem Photobiol 2021 May 2. Epub 2021 May 2.

Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA.

Squaraine figure-eight (SF8) molecules are a new class of deep-red fluorescent probes that are well suited for fluorescence cell microscopy due to their very high fluorescence brightness and excellent stability. Three homologous SF8 probes, with peptidyl loops that differ by very minor changes in the peptide sequence, were synthesized and assessed for probe uptake by cancer cells. One of probes included the RGD motif that is recognized by many classes of integrin receptors that reside on the surface of the cancer cells, and it permeated the cells by receptor-mediated endocytosis. In contrast, cell microscopy showed that there was negligible cell uptake of the two homologous SF8 probes indicating differences in probe targeting capability. The synthetic method allows for easy alteration of the peptide sequence; thus, it is straightforward to develop new classes of peptidyl SF8 probes with loop sequences that target other cancer biomarkers.
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http://dx.doi.org/10.1111/php.13439DOI Listing
May 2021

Protective Action and Risky Beliefs: The Relationship Between Religion and Gambling Fallacies.

J Gambl Stud 2021 Apr 29. Epub 2021 Apr 29.

Appleton Institute, CQUniversity, 44 Greenhill Rd, Wayville, Adelaide, SA, 5034, Australia.

A number of studies have explored the relationship between religious beliefs and gambling (including gambling fallacies and gambling harm) but report seemingly contradictory findings. While some studies have found religious belief to be positively associated with gambling fallacies, others have found it to be a protective factor from gambling harms. One explanation for these differing effects is that gambling fallacies and metaphysical religious belief share properties of supernatural and magical thinking. Nevertheless, social support and moral strictures associated with religion might help protect against an unhealthy engagement with gambling. Using a multidimensional measure of religiosity, we hypothesised that only the supernatural facet of religious adherence would present a risk for gambling fallacies. We analysed two archival data sources collected in Canada (Quinte Longitudinal Study: N = 4121, M = 46, SD = 14, Female = 54%; Leisure, Lifestyle and Lifecycle Project: N = 1372, M = 37, SD = 17, Female = 56%). Using the Rohrbaugh-Jessor Religiosity Scale, we confirmed that the supernatural theistic domain of religion was a positive risk factor for gambling fallacies. However, participation in ritual (behavioural) aspects, such as churchgoing, was negatively associated with risk, and no effect was observed for the consequential (moral) domain. We conclude that multidimensional aspects in religious measures may account for conflicting prior findings.
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http://dx.doi.org/10.1007/s10899-021-10028-zDOI Listing
April 2021

Chiral figure-eight molecular scaffold for fluorescent probe development.

Org Biomol Chem 2021 Apr 24;19(14):3213-3219. Epub 2021 Mar 24.

Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA.

Targeted fluorescent molecular probes are useful for cell microscopy, diagnostics, and biological imaging. An emerging discovery paradigm is to screen libraries of fluorescent molecules and identify hit compounds with interesting targeting properties. However, a current limitation with this approach is the lack of fluorescent molecular scaffolds that can produce libraries of probe candidates with three dimensional globular shape, chiral centers, and constrained conformation. This study evaluated a new probe scaffold called squaraine figure-eight (SF8), a self-threaded molecular architecture that is comprised of an encapsulated deep-red fluorescent squaraine dye, surrounding tetralactam macrocycle, and peripheral loops. Easy synthetic variation of the loops produced four chiral isomeric SF8 probes, with the same log P values. Cell microscopy showed that subtle changes in the loop structure led to significant differences in intracellular targeting. Most notably, a comparison of enantiomeric probes revealed a large difference in mitochondrial accumulation, very likely due to differences in affinity for a chiral biomarker within the organelle. A tangible outcome of the research is a probe candidate that can be: (a) developed further as a bright and photostable, deep-red fluorescent probe for mitochondrial imaging, and (b) used as a molecular tool to identify the mitochondrial biomarker for selective targeting. It will be straightforward to expand the SF8 probe chemical space and produce structurally diverse probe libraries with high potential for selective targeting of a wide range of biomarkers.
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http://dx.doi.org/10.1039/d1ob00306bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8075008PMC
April 2021

A Rare Case of Spontaneous Splenic Rupture Secondary to Tularemia Following a Cat Bite.

Cureus 2021 Feb 8;13(2):e13218. Epub 2021 Feb 8.

Internal Medicine, University of North Dakota, Fargo, USA.

Spontaneous splenic rupture is a rare but potentially life-threatening condition. More common infectious causes include infectious mononucleosis, cytomegalovirus (CMV), human immunodeficiency virus (HIV), and malaria. We present a case of a 42-year-old male who was admitted with persistent fevers, myalgia, and a recent ulcerative lesion on the base of his left thumb after a cat bite. He developed abdominal and back pains, left axillary lymphadenopathy, and near syncope. Abdominal computed tomography (CT) scan showed splenomegaly with subcapsular splenic rupture and large hematoma requiring emergent splenic embolization. Infectious work-up revealed tularemia as a cause which was successfully treated with oral doxycycline. Though not a common cat zoonoses, tularemia should be considered in a patient with splenomegaly or spontaneous splenic rupture in the setting of cat bite.
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http://dx.doi.org/10.7759/cureus.13218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7945001PMC
February 2021

Human Blood Plasma Investigation Employing 2D UPLC-UDMS Data-Independent Acquisition Proteomics.

Methods Mol Biol 2021 ;2259:153-165

Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.

Proteomic tools are especially useful when it comes to investigating complex samples such as human blood plasma, in which protein quantities can span across up to ten orders of magnitude. Ultra definition mass spectrometry, in combination with two-dimensional liquid chromatography, provides better coverage of complex proteomes and allows for better control of collision energy, keeping the fragmentation benefits of high collision energy associated with drift time measurements from ion mobility separation. Here, we present a protocol to assist in the identification of proteins in human blood plasma and other similar samples with a large dynamic range.
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http://dx.doi.org/10.1007/978-1-0716-1178-4_9DOI Listing
April 2021

High-Performance Near-Infrared Fluorescent Secondary Antibodies for Immunofluorescence.

Anal Chem 2021 02 10;93(7):3643-3651. Epub 2021 Feb 10.

Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States.

A broad array of imaging and diagnostic technologies employs fluorophore-labeled antibodies for biomarker visualization, an experimental technique known as immunofluorescence. Significant performance advantages, such as higher signal-to-noise ratio, are gained if the appended fluorophore emits near-infrared (NIR) light with a wavelength >700 nm. However, the currently available NIR fluorophore antibody conjugates are known to exhibit significant limitations, including low chemical stability and photostability, weakened target specificity, and low fluorescence brightness. These fluorophore limitations are resolved by employing a NIR heptamethine cyanine dye named s775z whose chemical structure is very stable, charge-balanced, and sterically shielded. Using indirect immunofluorescence for imaging and visualization, a secondary IgG antibody labeled with s775z outperformed IgG analogues labeled with the commercially available NIR fluorophores, IRDye 800CW and DyLight800. Comparison experiments include three common techniques: immunocytochemistry, immunohistochemistry, and western blotting. Specifically, the secondary IgG labeled with s775z was 3-8 times brighter, 3-6 times more photostable, and still retained excellent target specificity when the degree of antibody labeling was high. The results demonstrate that antibodies labeled with s775z can emit total photon counts that are 1-2 orders of magnitude higher than those currently possible, and thus enable unsurpassed performance for NIR fluorescence imaging and diagnostics. They are especially well suited for analytical applications that require sensitive NIR fluorescence detection or use modern photon-intense methods that require high photostability.
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http://dx.doi.org/10.1021/acs.analchem.1c00276DOI Listing
February 2021

Frequency and methylation status of selected retrotransposition competent L1 loci in amyotrophic lateral sclerosis.

Mol Brain 2020 11 13;13(1):154. Epub 2020 Nov 13.

Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.

Long interspersed element-1 (LINE-1/L1) is the only autonomous transposable element in the human genome that currently mobilises in both germline and somatic tissues. Recent studies have identified correlations between altered retrotransposon expression and the fatal neurodegenerative disease amyotrophic lateral sclerosis (ALS) in a subset of patients. The risk of an individual developing ALS is dependent on an interaction of genetic variants and subsequent modifiers during life. These modifiers could include environmental factors, which can lead to epigenetic and genomic changes, such as somatic mutations, occurring in the neuronal cells that degenerate as the disease develops. There are more than 1 million L1 copies in the human genome today, but only 80-100 L1 loci in the reference genome are considered to be retrotransposition-competent (RC) and an even smaller number of these RC-L1s loci are highly active. We hypothesise that RC-L1s could affect normal cellular function through their mutagenic potential conferred by their ability to retrotranspose in neuronal cells and through DNA damage caused by the endonuclease activity of the L1-encoded ORF2 protein. To investigate whether either an increase in the genomic burden of RC-L1s or epigenetic changes to RC-L1s altering their expression, could play a role in disease development, we chose a set of seven well characterised genomic RC-L1 loci that were reported earlier to be highly active in a cellular L1 retrotransposition reporter assay or serve as major source elements for germline and/or somatic retrotransposition events. Analysis of the insertion allele frequency of five polymorphic RC-L1s, out of the set of seven, for their presence or absence, did not identify an increased number individually or when combined in individuals with the disease. However, we did identify reduced levels of methylation of RC-L1s in the motor cortex of those individuals with both familial and sporadic ALS compared to control brains. The changes to the regulation of the loci encompassing these RC-L1s demonstrated tissue specificity and could be related to the disease process.
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http://dx.doi.org/10.1186/s13041-020-00694-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7666467PMC
November 2020

Postharvest practices, challenges and opportunities for grain producers in Arequipa, Peru.

PLoS One 2020 4;15(11):e0240857. Epub 2020 Nov 4.

Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America.

Little is known about the major issues leading to postharvest losses in Peru, which are estimated to be 15-27%. We surveyed 503 farmers from the lowlands and Andean regions of Arequipa to learn more about the major grains produced and issues encountered during drying and storage. Rice, common bean, and quinoa were the most grown crops in the lowlands while starchy maize was the most cultivated crop in the highlands. Most farmers (90%) dried their crops in-field directly on the ground, which exposes them to rodents, birds, and insect pests. The majority of farmers (92%) used subjective methods to assess grain moisture content. About 77% of farmers identified insects as a major challenge during storage but only 44% said they used preventive measures such as the application of insecticides. Among farmers who stored grain, the main reason was for household consumption (61%); while among those who did not store, the main reason was the need for immediate cash at harvest (75%). Farmers who experienced insect problems, who stored seed or grain for sale, who stored longer, or farmers from the lowlands were more likely to apply insecticides on their stored products. These findings provide an opportunity for researchers, development organizations, and government agencies to improve postharvest handling and storage in Arequipa by disseminating drying technologies, moisture assessment tools and hermetic storage solutions among farmers.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0240857PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7641344PMC
December 2020

Incidence of uveitis and macular edema among patients taking fingolimod 0.5 mg for multiple sclerosis.

J Ophthalmic Inflamm Infect 2020 Sep 21;10(1):24. Epub 2020 Sep 21.

The Retina Institute in St. Louis, 2201 S Brentwood Blvd, St. Louis, MO, 63144, USA.

Background: Patients with multiple sclerosis (MS) have a higher incidence of uveitis compared with the general population. Fingolimod, a first line disease modifying drug used in multiple sclerosis, may cause macular edema and thus requires ophthalmic examination. However, murine models and anecdotal reports suggest fingolimod may reduce the incidence of uveitis.

Purpose: To report the incidence of uveitis and macular edema among those on fingolimod 0.5 mg (Gilenya®) therapy for multiple sclerosis (MS).

Methods: Retrospective review of patients on fingolimod who developed uveitis and/or macular edema.

Results: No patients had an occurrence or history of uveitis. Four of the 188 (2.13%) patients developed macular edema without ocular inflammation. One of the 188 (0.53%) patients developed Acute Macular Neuroretinopathy.

Conclusion: Patients taking fingolimod have a lower incidence of uveitis than expected in a population of MS patients.
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http://dx.doi.org/10.1186/s12348-020-00215-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7502642PMC
September 2020

Fluorescent Self-Threaded Peptide Probes for Biological Imaging.

Angew Chem Int Ed Engl 2020 12 29;59(52):23740-23747. Epub 2020 Oct 29.

Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46556, USA.

A general synthetic method creates a new class of covalently connected, self-threaded, fluorescent molecular probes with figure-eight topology, an encapsulated deep-red fluorophore, and two peripheral peptide loops. The globular molecular shape and rigidified peptide loops enhance imaging performance by promoting water solubility, eliminating probe self-aggregation, and increasing probe stability. Moreover, the peptide loops determine the affinity and selectivity for targets within complex biological samples such as cell culture, tissue histology slices, or living subjects. For example, a probe with cell-penetrating peptide loops targets the surface of cell plasma membranes, whereas, a probe with bone-targeting peptide loops selectively stains the skeleton within a living mouse. The unique combination of bright deep-red fluorescence, high stability, and predictable peptide-based targeting is ideal for photon intense fluorescence microscopy and biological imaging.
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http://dx.doi.org/10.1002/anie.202009599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7736561PMC
December 2020

C9orf72 poly GA RAN-translated protein plays a key role in amyotrophic lateral sclerosis via aggregation and toxicity.

Hum Mol Genet 2021 Apr;30(3-4):318-320

United Kingdom Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Camberwell, London SE5 9NU, UK.

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http://dx.doi.org/10.1093/hmg/ddaa181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8248939PMC
April 2021

Supramolecular Paradigm for Capture and Co-Precipitation of Gold(III) Coordination Complexes.

Chemistry 2021 Jan 27;27(2):751-757. Epub 2020 Nov 27.

Department of Chemistry & Biochemistry, University of Notre Dame, 236 Nieuwland Science Hall, Notre Dame, IN, 46545, USA.

A new supramolecular paradigm is presented for reliable capture and co-precipitation of haloauric acids (HAuX ) from organic solvents or water. Two classes of acyclic organic compounds act as complementary receptors (tectons) by forming two sets of directional non-covalent interactions, (a) hydrogen bonding between amide (or amidinium) NH residues and the electronegative X ligands on the AuX , and (b) electrostatic stacking of the electron deficient Au center against the face of an aromatic surface. X-ray diffraction analysis of four co-crystal structures reveals the additional common feature of proton bridged carbonyls as a new and predictable supramolecular design element that creates one-dimensional polymers linked by very short hydrogen bonds (CO⋅⋅⋅OC distance <2.5 Å). Two other co-crystal structures show that the amidinium-π⋅⋅⋅XAu interaction will reliably engage AuX with high directionality. These acyclic compounds are very attractive as co-precipitation agents within new "green" gold recovery processes. They also have high potential as tectons for controlled self-assembly or co-crystal engineering of haloaurate composites. More generally, the supramolecular paradigm will facilitate the design of next-generation receptors or tectons with high affinity for precious metal square planar coordination complexes for use in advanced materials, nanotechnology, or medicine.
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http://dx.doi.org/10.1002/chem.202003680DOI Listing
January 2021

Supramolecular optimization of the visual contrast for colorimetric indicator assays that release resorufin dye.

Chem Commun (Camb) 2020 Aug;56(65):9296-9299

Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA.

A tetralactam macrocycle acts as a novel supramolecular adjuvant to capture a released resorufin dye and create a higher contrasting yellow/blue color change for enhanced naked eye interpretation of a colorimetric indicator assay.
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http://dx.doi.org/10.1039/d0cc03551cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7429340PMC
August 2020

TREATMENT OF BILATERAL DIFFUSE UVEAL MELANOCYTIC PROLIFERATION WITH INTRAVITREAL STEROID IMPLANTS.

Retin Cases Brief Rep 2020 Jul 7. Epub 2020 Jul 7.

The Retina Institute of Saint Louis, St. Louis, Missouri.

Background/purpose: To report a case of bilateral diffuse uveal melanocytic proliferation (BDUMP) treated with intravitreal steroid implants.

Method: Bilateral diffuse uveal melanocytic proliferation was diagnosed and treated with intravitreal steroid implants (both dexamethasone 0.7 mg [intravitreal dexamethasone implants] and fluocinolone acetonide 0.18 mg [intravitreal fluocinolone acetonide implants]) and monitored every 2 weeks to 4 weeks with optical coherence tomography.

Results: Intravitreal dexamethasone implants improved visual acuity and central retinal thickness for 10 weeks, was best from 4 to 6 weeks, and recurred by 14 weeks after treatment. Intravitreal fluocinolone acetonide implants improved visual acuity and central retinal thickness for 20 weeks after treatment without edema recurrence. No retinal detachments were observed over 1 year of treatment.

Conclusion: Intravitreal steroid implants resulted in visual acuity improvement and central retinal thickness reduction for up to 20 weeks and may protect against retinal detachments in patients with bilateral diffuse uveal melanocytic proliferation.
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http://dx.doi.org/10.1097/ICB.0000000000001008DOI Listing
July 2020

Lymphoma masquerading as occlusive retinal vasculitis: A case study.

Am J Ophthalmol Case Rep 2020 Sep 10;19:100777. Epub 2020 Jun 10.

The Retina Institute, St. Louis, MO, USA.

Purpose: To describe a case of retinal lymphoma presenting as an occlusive retinal vasculitis without vitritis that was exquisitely responsive to intravitreal dexamethasone implant (IVDI).

Observation: A 66-year old male presented with decreased vision in the right eye and was diagnosed with occlusive retinal vasculitis and prominent cystoid macular edema though he lacked vitritis. A complete systemic workup for infectious, inflammatory, and infiltrative etiologies was unremarkable. Intravenous methylprednisolone and cyclophosphamide had no clinical effect. Due to persistent perivascular exudates and refractory macular edema, IVDI was administered with marked improvement in vision and clinical findings. Subsequent retinal vasculitis in the left eye responded to IVDI as well. The patient remained disease free for months while on weekly adalimumab. He then presented with acute vision loss in the left eye due to a lymphomatous subretinal infiltration and a new lesion in the corpus callosum. He has remained disease free for more than two years after intravitreal methotrexate injections and rituximab with an autologous stem cell transplant.

Conclusion And Importance: Lymphoma may present as an occlusive retinal vasculitis without vitritis and can be masked due to its response to IVDI.
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http://dx.doi.org/10.1016/j.ajoc.2020.100777DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320315PMC
September 2020

Cell organelle targeting of near-infrared croconaine dye controls photothermal outcome.

Chem Commun (Camb) 2020 Jun;56(51):6977-6980

Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA.

Near-infrared croconaine-peptide conjugates that target the cell nucleus promote photothermal induced cell death. In contrast, a croconaine-morpholine conjugate that targets the cell lysosomes promotes lysosome permeabilization without measurable cell phototoxicity.
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http://dx.doi.org/10.1039/d0cc02612cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319869PMC
June 2020

Addressing inequality and intolerance in human-wildlife coexistence.

Conserv Biol 2020 08 14;34(4):803-810. Epub 2020 May 14.

Evolution, Behaviour and Environment, University of Sussex, Brighton, BN1 9RH, U.K.

Millennia of human conflict with wildlife have built a culture of intolerance toward wildlife among some stakeholders. We explored 2 key obstacles to improved human-wildlife coexistence: coexistence inequality (how the costs and benefits of coexisting with wildlife are unequally shared) and intolerance. The costs of coexisting with wildlife are often disproportionately borne by the so-called global south and rural communities, and the benefits often flow to the global north and urban dwellers. Attitudes and behaviors toward wildlife (tolerance versus intolerance) vary with social and cultural norms. We suggest more empathetic advocacy is needed that, for example, promotes conservation while appropriately considering those who bear the costs of conflict with wildlife. To achieve more equitable cost-sharing, we suggest limiting the costs incurred by those most affected or by sharing those costs more widely. For example, we advocate for the development of improved wildlife compensation schemes, increasing the scale of rewilding efforts, and preventing wildlife-derived revenue leaching out of the local communities bearing the costs of coexistence.
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http://dx.doi.org/10.1111/cobi.13471DOI Listing
August 2020

Sterically Shielded Heptamethine Cyanine Dyes for Bioconjugation and High Performance Near-Infrared Fluorescence Imaging.

Angew Chem Int Ed Engl 2020 07 11;59(29):12154-12161. Epub 2020 May 11.

Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46556, USA.

The near-infrared window of fluorescent heptamethine cyanine dyes greatly facilitates biological imaging because there is deep penetration of the light and negligible background fluorescence. However, dye instability, aggregation, and poor pharmacokinetics are current drawbacks that limit performance and the scope of possible applications. All these limitations are simultaneously overcome with a new molecular design strategy that produces a charge balanced and sterically shielded fluorochrome. The key design feature is a meso-aryl group that simultaneously projects two shielding arms directly over each face of a linear heptamethine polyene. Cell and mouse imaging experiments compared a shielded heptamethine cyanine dye (and several peptide and antibody bioconjugates) to benchmark heptamethine dyes and found that the shielded systems possess an unsurpassed combination of photophysical, physiochemical, and biodistribution properties that greatly enhance bioimaging performance.
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http://dx.doi.org/10.1002/anie.202004449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7473488PMC
July 2020
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