Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota.

The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.

Appearance and resolution of numerous bilateral gass plaques in probable Susac syndrome.

Purpose: To describe a patient with a unique retinal phenotype of probable Susac syndrome. Observations: A 47-year-old female who presented with bilateral tinnitus and vision changes was found to have bilateral sensorineural hearing loss and many bilateral retinal arteriolar Gass plaques. She had bilateral scotomas corresponding with temporal thinning and atrophy of the inner nuclear layer (INL) on OCT. Retinal examination and fluorescein angiography demonstrated minimal arteriolar wall hyperfluorescence with no evidence of acute branch retinal artery occlusion. She developed daily headaches. MRI of the brain was normal with no corpus callosal lesions. She was diagnosed with probable Susac syndrome based on the above findings. Conclusions and importance: Our patient's bilateral high frequency sensorineural hearing loss, numerous bilateral Gass plaques, and headaches are most likely attributable to Susac syndrome. While BRAO is considered a cornerstone of retinal involvement in Susac syndrome, it may only be appreciable angiographically in the acute setting, and it is important to recognize Gass plaques as a significant diagnostic marker of disease.

Fluorescein Angiography Findings in Susac Syndrome: A Multicenter Retrospective Case Series.

BACKGROUND: Susac syndrome is a vasculopathy, resulting in the classic triad of branch retinal artery occlusion (BRAO), inner ear ischemia, and brain ischemia. In this retrospective chart review, we characterize fluorescein angiography (FA) findings and other ancillary studies in Susac syndrome, including the appearance of persistent disease activity and the occurrence of new subclinical disease on FA. METHODS: This multicenter, retrospective case series was institutional review board-approved and included patients with the complete triad of Susac syndrome evaluated with FA, contrasted MRI of the brain, and audiometry from 2010 to 2020. The medical records were reviewed for these ancillary tests, along with demographics, symptoms, visual acuity, visual field defects, and findings on fundoscopy. Clinical relapse was defined as any objective evidence of disease activity during the follow-up period after initial induction of clinical quiescence. The main outcome measure was the sensitivity of ancillary testing, including FA, MRI, and audiometry, to detect relapse. RESULTS: Twenty of the 31 (64%) patients had the complete triad of brain, retinal, and vestibulocochlear involvement from Susac syndrome and were included. Median age at diagnosis was 43.5 years (range 21-63), and 14 (70%) were women. Hearing loss occurred in 20 (100%), encephalopathy in 13 (65%), vertigo in 15 (75%), and headaches in 19 (95%) throughout the course of follow-up. Median visual acuity at both onset and final visit was 20/20 in both eyes. Seventeen (85%) had BRAO at baseline, and 10 (50%) experienced subsequent BRAO during follow-up. FA revealed nonspecific leakage from previous arteriolar damage in 20 (100%), including in patients who were otherwise in remission. Of the 11 episodes of disease activity in which all testing modalities were performed, visual field testing/fundoscopy was abnormal in 4 (36.4%), MRI brain in 2 (18.2%), audiogram in 8 (72.7%), and FA in 9 (81.8%). CONCLUSIONS: New leakage on FA is the most sensitive marker of active disease. Persistent leakage represents previous damage, whereas new areas of leakage suggest ongoing disease activity that requires consideration of modifying immunosuppressive therapy.

Splenium of the Corpus Callosum Infarct Associated With COVID-19: Case Report.

INTRODUCTION: Coronavirus disease 2019 (COVID-19) has been recently associated with infarction of the central splenium of the corpus callosum. These are described as cytotoxic lesions, and imaging rarely reveals enhancement. They have not been described in the body or head of the corpus callosum. Few diseases affect the corpus callosum, but the most common include multiple sclerosis, aquaporin-4 disease, and Susac syndrome. There is also emerging literature on Mild Encephalopathy with Reversible Splenial lesions associated with central and not basal lesions. The reason for the location of these lesions in acute COVID-19 infection is unknown. CASE REPORT: A 22-year-old female presented to the ED for altered mental status after being found down. A brief history review indicated that the patient had been altered for 2-3 days before being found naked and covered in her own feces and urine by her family after they had not heard from her. As she lived alone, a clear history of the events preceding her admission remains unclear. On initial assessment, the patient was found to be somnolent and nonverbal, though she could follow simple commands. On admission, testing for SARS CoV-2 RNA PCR was positive. Patient was admitted to the hospital for further work up to determine the cause of the altered mental status. CONCLUSION: We present a new case of a young woman who developed a central splenium lesion during acute COVID-19 infection and explain the predilection for the callosum in these patients, as well as literature to show that COVID-19 was most likely the cause.

Flash Oxidation (FOX) System: A Novel Laser-Free Fast Photochemical Oxidation Protein Footprinting Platform.

Hydroxyl radical protein footprinting (HRPF) is a powerful and flexible technique for probing changes in protein topography. With the development of the fast photochemical oxidation of proteins (FPOP), it became possible for researchers to perform HRPF in their laboratory on a very short time scale. While FPOP has grown significantly in popularity since its inception, adoption remains limited due to technical and safety issues involved in the operation of a hazardous Class IV UV laser and irreproducibility often caused by improper laser operation and/or differential radical scavenging by various sample components. Here, we present a new integrated FOX (Flash OXidation) Protein Footprinting System. This platform delivers sample via flow injection to a facile and safe-to-use high-pressure flash lamp with a flash duration of 10 µs fwhm. Integrated optics collect the radiant light and focus it into the lumen of a capillary flow cell. An inline radical dosimeter measures the hydroxyl radical dose delivered and allows for real-time compensation for differential radical scavenging. A programmable fraction collector collects and quenches only the sample that received the desired effective hydroxyl radical dose, diverting the carrier liquid and improperly oxidized sample to waste. We demonstrate the utility of the FOX Protein Footprinting System by determining the epitope of TNFα recognized by adalimumab. We successfully identify the surface of the protein that serves as the epitope for adalimumab, identifying four of the five regions previously noted by X-ray crystallography while seeing no changes in peptides not involved in the epitope interface. The FOX Protein Footprinting System allows for FPOP-like experiments with real-time dosimetry in a safe, compact, and integrated benchtop platform.

Posterior Cortical Atrophy: Characteristics From a Clinical Data Registry.

Background: Posterior cortical atrophy (PCA) is a neurodegenerative syndrome that presents with higher-order visual dysfunction with relative sparing of memory and other cognitive domains, and it is most commonly associated with Alzheimer's disease pathology. There is a lack of data regarding the presentation of PCA to non-cognitive specialists. Therefore, we collected clinical data from neuro-ophthalmologists regarding the presentation of PCA to their practices and compared data to published cohorts and a published survey of cognitive specialists. Methods: Members of the North American Neuro-Ophthalmology Society Listserv (NANOSnet) were invited to complete an online, retrospective, chart-review data-entry survey regarding their patients with PCA, and REDCap was used for data collection. Results: Data for 38 patients were entered by 12 neuro-ophthalmologists. Patient mean age at presentation was 67.8 years, and 74% of patients were women. Difficulty reading was reported at presentation by 91% of patients, and poor performance on color vision, stereopsis, and visual field testing (performed reliably by 36/38 patients) were common findings. Most patients who were treated were treated with donepezil and/or memantine. Conclusions: Compared to published data from cognitive specialists, patients presenting to neuro-ophthalmology with PCA were more likely to be older and female and have a reading complaint. Reliable visual field testing was the norm with homonymous defects in the majority of patients. The neuro-ophthalmologist plays an important role in diagnosing PCA in older adults with unexplained visual signs and symptoms, and future studies of PCA should involve multiple specialists in order to advance our understanding of PCA and develop effective treatments.

Asymmetric Inferior Predilection of Lisch Nodules With Unilateral Ptosis.

Lisch nodules are melanocytic hamartomas that have been hypothesized to grow larger in the presence of sunlight. A 17-year-old boy with neurofibromatosis Type 1 and congenital ptosis in one eye presented and was found to have a distinct asymmetry of Lisch nodules between eyes with less under the ptotic lid. This case supports the theory that Lisch nodules form at least partially due to a direct trophic effect of sunlight.

Prevalence of Retinal Emboli and Acute Retinal Artery Occlusion in Acute Ischemic Stroke.

OBJECTIVE: In population-based studies asymptomatic retinal emboli occur in .32%-2.9% of people. Retinal artery occlusion (RAO) may occur concurrently with cerebral stroke but the frequency is unknown. No study has examined how commonly retinal emboli occur in the acute stroke population. We aimed to assess the prevalence of retinal emboli and RAO at the time of carotid territory ischemic stroke. METHODS: Patients were enrolled prospectively after onset of symptoms consistent with the diagnosis of carotid territory ischemic stroke. Every participant underwent pharmacologic dilation of both pupils and bedside funduscopic examination. Emboli were classified as cholesterol, calcific, platelet/fibrin, or other and categorized by the side of occurrence. Stroke was classified as atheroembolic, cardioembolic, embolic stroke of undetermined source, lacunar, or other. Acute RAO was diagnosed by direct visualization of ischemic retinal whitening. RESULTS: Sixty-five patients were enrolled with a mean age of 59.2 years; 23 were female (35.4%). Eleven of 65 subjects (16.9%) had retinal emboli visible on funduscopy; all were cholesterol emboli except a single platelet/fibrin embolus in a patient with atheroembolic source. Six patients (9%) had acute RAO and no RAO was seen in the lacunar or undetermined source subgroups. CONCLUSIONS: Retinal emboli occurred more than 10 times more frequently in the acute stroke patient than in large population-based studies. RAOs also occurred concurrently with ischemic stroke. Although emboli were seen in patients with atheroembolic and cardioembolic sources, all patients with carotid disease had emboli in the ipsilateral eye. Future studies are required to determine if the presence of retinal emboli or RAO may help elucidate an etiology in patients suffering from embolic stroke of undetermined source.

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.

Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel.

Diagnostic Criteria and Treatment Algorithm for Susac Syndrome.

BACKGROUND: Susac syndrome (SS) classically presents with the clinical triad of retinal artery occlusion, sensorineural hearing loss, and encephalopathy and the neuroimaging triad of white matter lesions, deep gray matter lesions, and leptomeningeal disease. However, patients can present with an incomplete clinical or neuroimaging triads making diagnosis difficult in certain situations. A standard treatment paradigm also is lacking in this illness. It is important for neuro-ophthalmologists to recognize clinical and radiographic findings that are pathognomonic for this syndrome and have a basic understanding of the available treatment options. EVIDENCE ACQUISITION: Review of medical literature. RESULTS: A definite diagnosis of SS is made when the clinical triad or the neuroimaging triad is present. There are numerous reports of 2 other imaging findings in this condition: arteriolar wall hyperfluorescence (AWH) on fluorescein angiography in retinal arterioles remote from retinal ischemia and central callosal lesions on MRI. Both of these imaging findings are diagnostic of SS. Gass plaques in retinal arterioles are almost always seen in the acute phase of the illness but are not pathognomonic for SS. The most common medications used in this syndrome are corticosteroids and intravenous immunoglobulin. A number of other medications have been used including mycopheolate, rituximab, azathioprine, and cyclophosphamide. CONCLUSIONS: In the absence of the clinical triad or magnetic resonance imaging triad for SS, AWH remote from retinal vascular injury and central callosal lesions are confirmatory of the diagnosis because they have never been described in any other condition. The presence of Gass plaques in retinal arterioles should strongly suggest the diagnosis. Despite the lack of clinical trial data, patients with SS must be treated promptly and aggressively. In more fulminant cases, addition of mycophenolate mofetil or rituximab is required, followed by cyclophosphamide when disease is refractory to other medications.

Real Time Normalization of Fast Photochemical Oxidation of Proteins Experiments by Inline Adenine Radical Dosimetry.

Hydroxyl radical protein footprinting (HRPF) is a powerful method for measuring protein topography, allowing researchers to monitor events that alter the solvent accessible surface of a protein (e.g., ligand binding, aggregation, conformational changes, etc.) by measuring changes in the apparent rate of reaction of portions of the protein to hydroxyl radicals diffusing in solution. Fast Photochemical Oxidation of Proteins (FPOP) offers an ultrafast benchtop method for radical generation for HRPF, photolyzing hydrogen peroxide using a UV laser to generate high concentrations of hydroxyl radicals that are consumed on roughly a microsecond time scale. The broad reactivity of hydroxyl radicals means that almost anything added to the solution (e.g., ligands, buffers, excipients, etc.) will scavenge hydroxyl radicals, altering their half-life and changing the effective radical concentration experienced by the protein. Similarly, minute changes in peroxide concentration, laser fluence, and buffer composition can alter the effective radical concentration, making reproduction of data challenging. Here, we present a simple method for radical dosimetry that can be carried out as part of the FPOP workflow, allowing for measurement of effective radical concentration in real time. Additionally, by modulating the amount of radical generated, we demonstrate that effective hydroxyl radical yields in FPOP HRPF experiments carried out in buffers with widely differing levels of hydroxyl radical scavenging capacity can be compensated on the fly, yielding statistically indistinguishable results for the same conformer. This method represents a major step in transforming FPOP into a robust and reproducible technology capable of probing protein structure in a wide variety of contexts.

Retinal Arterio-Arterial Collaterals in Susac Syndrome.

BACKGROUND: The ophthalmic findings of Susac syndrome (SS) consist of visual field defects related to branch retinal artery occlusion (BRAO), and fluorescein angiography (FA) reveals a unique staining pattern. To date, retinal arterial collateral development has been described only in a single patient. Given that the immunopathological process in SS induces retinal ischemia, it is conceivable that abnormal blood vessel development may occur in affected individuals. METHODS: This is a retrospective observational study. The medical records including fundus photography and FA of all patients with SS were reviewed, and those with any type of retinal arterial collateral were identified. RESULTS: A total of 11 patients were identified with retinal collaterals. Five were men. Age ranged from 20 to 50 years. Ten patients had arterio-arterial (A-A) collaterals and 1 had arterio-venous (A-V) collaterals, and all had collaterals remote from the optic disc. No collaterals were present at onset of illness and the first developed at 9 months. CONCLUSIONS: The literature reveals scant evidence for the association between BRAO and retinal arterial collaterals. Our findings indicate that retinal arterial collaterals in SS are usually A-A and not A-V and may be more common in this disorder than previously believed. Collaterals do not develop early in the disease, and there may be a predilection toward development in men. The chronic inflammatory state of SS may be the stimulus for the development of these arterial collaterals.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.

Functional Vision Disorder.

Functional vision disorder (FVD) is a common problem seen in many neurologic and ophthalmologic practitioners' offices and may occur in isolation or in the presence of medical illness. This disorder presents with visual or oculomotor symptoms and manifests as vision loss in one or both eyes, visual field loss, double vision, oscillopsia, anisocoria, blepharospasm, or ptosis. Manual perimetry is the most effective method for determining functional visual loss, and the presence of a central scotoma in a functional visual field signifies that a neuropathophysiologic process is almost certainly present. The exact neuropathophysiologic mechanism of this disorder is unknown; however, information can be drawn from the small studies of FVD samples and studies examining neuropsychiatric factors in other conversion disorder semiologies. Psychological and psychiatric interventions can be useful in treating these patients.