Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.

The ability to reliably and reproducibly measure any protein of the human proteome in any tissue or cell type would be transformative for understanding systems-level properties as well as specific pathways in physiology and disease. Here, we describe the generation and verification of a compendium of highly specific assays that enable quantification of 99.7% of the 20,277 annotated human proteins by the widely accessible, sensitive, and robust targeted mass spectrometric method selected reaction monitoring, SRM. This human SRMAtlas provides definitive coordinates that conclusively identify the respective peptide in biological samples. We report data on 166,174 proteotypic peptides providing multiple, independent assays to quantify any human protein and numerous spliced variants, non-synonymous mutations, and post-translational modifications. The data are freely accessible as a resource at http://www.srmatlas.org/, and we demonstrate its utility by examining the network response to inhibition of cholesterol synthesis in liver cells and to docetaxel in prostate cancer lines.

CCT and Cullin1 Regulate the TORC1 Pathway to Promote Dendritic Arborization in Health and Disease.

The development of cell-type-specific dendritic arbors is integral to the proper functioning of neurons within their circuit networks. In this study, we examine the regulatory relationship between the cytosolic chaperonin CCT, key insulin pathway genes, and an E3 ubiquitin ligase (Cullin1) in dendritic development. CCT loss of function (LOF) results in dendritic hypotrophy in Drosophila Class IV (CIV) multi-dendritic larval sensory neurons, and CCT has recently been shown to fold components of the TOR (Target of Rapamycin) complex 1 (TORC1) in vitro. Through targeted genetic manipulations, we confirm that an LOF of CCT and the TORC1 pathway reduces dendritic complexity, while overexpression of key TORC1 pathway genes increases the dendritic complexity in CIV neurons. Furthermore, both CCT and TORC1 LOF significantly reduce microtubule (MT) stability. CCT has been previously implicated in regulating proteinopathic aggregation, thus, we examine CIV dendritic development in disease conditions as well. The expression of mutant Huntingtin leads to dendritic hypotrophy in a repeat-length-dependent manner, which can be rescued by Cullin1 LOF. Together, our data suggest that Cullin1 and CCT influence dendritic arborization through the regulation of TORC1 in both health and disease.

CCT and Cullin1 regulate the TORC1 pathway to promote dendritic arborization in health and disease.

The development of cell-type-specific dendritic arbors is integral to the proper functioning of neurons within their circuit networks. In this study, we examine the regulatory relationship between the cytosolic chaperonin CCT, key insulin pathway genes, and an E3 ubiquitin ligase (Cullin1) in homeostatic dendritic development. CCT loss of function (LOF) results in dendritic hypotrophy in Drosophila Class IV (CIV) multidendritic larval sensory neurons, and CCT has recently been shown to fold components of the TOR (Target of Rapamycin) complex 1 (TORC1), in vitro. Through targeted genetic manipulations, we have confirmed that LOF of CCT and the TORC1 pathway reduces dendritic complexity, while overexpression of key TORC1 pathway genes increases dendritic complexity in CIV neurons. Both CCT and TORC1 LOF significantly reduce microtubule (MT) stability. CCT has been previously implicated in regulating proteinopathic aggregation, thus we examined CIV dendritic development in disease conditions as well. Expression of mutant Huntingtin leads to dendritic hypotrophy in a repeat-length-dependent manner, which can be rescued by TORC1 disinhibition via Cullin1 LOF. Together, our data suggest that Cullin1 and CCT influence dendritic arborization through regulation of TORC1 in both health and disease.

Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses.

Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. Based on the prevalence of these species, at least two likely coexist in the nasal microbiota of 82% of adults. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the functional protein repertoire and metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the U.S. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution across Africa and North America. All four species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent (core) compared to the accessory genome of each species indicating limited strain-level variability in metabolic capacity. Moreover, core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in the Botswanan clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.

Senescent and disease-associated microglia are modifiable features of aged brain white matter.

Brain white matter tracts undergo structural and functional changes linked to late-life cognitive decline, but the cellular and molecular contributions to their selective vulnerability are not well defined. In naturally aged mice, we demonstrate that senescent and disease-associated microglia (DAM) phenotypes converge in hippocampus-adjacent white matter. Through gold-standard gene expression and immunolabeling combined with high-dimensional spatial mapping, we identified microglial cell fates in aged white matter characterized by aberrant morphology, microenvironment reorganization, and expression of senescence and DAM markers, including galectin 3 (GAL3/Lgals3), B-cell lymphoma 2 (Bcl2), and cyclin dependent kinase inhibitors, including Cdkn2a/p16ink4a. Pharmacogenetic or pharmacological targeting of p16ink4a or BCL2 reduced white matter GAL3+ DAM abundance and rejuvenated microglial fimbria organization. Our results demonstrate dynamic changes in microglial identity in aged white matter that can be reverted by senotherapeutic intervention to promote homeostatic maintenance in the aged brain.

2-month ketogenic diet preferentially alters skeletal muscle and augments cognitive function in middle aged female mice.

The effect of a ketogenic diet (KD) on middle aged female mice is poorly understood as most of this work have been conducted in young female mice or diseased models. We have previously shown that an isocaloric KD started at middle age in male mice results in enhanced mitochondrial mass and function after 2 months on diet and improved cognitive behavior after being on diet for 14 months when compared with their control diet (CD) fed counterparts. Here, we aimed to investigate the effect of an isocaloric 2-month KD or CD on healthy 14-month-old female mice. At 16 months of age cognitive behavior tests were performed and then serum, skeletal muscle, cortex, and hippocampal tissues were collected for biochemical analysis. Two months on a KD resulted in enhanced cognitive behavior associated with anxiety, memory, and willingness to explore. The improved neurocognitive function was associated with increased PGC1α protein in the gastrocnemius (GTN) muscle and nuclear fraction. The KD resulted in a tissue specific increase in mitochondrial mass and kynurenine aminotransferase (KAT) levels in the GTN and soleus muscles, with a corresponding decrease in kynurenine and increase in kynurenic acid levels in serum. With KAT proteins being responsible for converting kynurenine into kynurenic acid, which is unable to cross the blood brain barrier and be turned into quinolinic acid-a potent neurotoxin, this study provides a potential mechanism of crosstalk between muscle and brain in mice on a KD that may contribute to improved cognitive function in middle-aged female mice.

COVID-19 among Minority Children in Detroit, Michigan during the Early National Surge of the Pandemic.

Background. The COVID-19 pandemic has shed light on communities of racial/ethnic minority groups in the US where long-standing health issues and structural inequities are now known to have resulted in increased risk for infection, severe illness, and death from the virus. The objective of our study was to describe demographic characteristics, clinical presentations, medical interventions and outcomes of pediatric patients with COVID-19 treated at Children's Hospital of Michigan (CHM), a tertiary care center in urban Detroit, an early hotspot during the initial surge of the SARS-CoV-2 pandemic. Methods. A retrospective chart review was performed of children ≤18 years of age who had polymerase chain reaction (RT-PCR) testing via NP swab or serum IgG antibody testing for SARS-CoV-2 during March 1, 2020-June 30, 2020. Results. Seventy-eight COVID-19 infected children were identified of whom 85.8% (67/78) were from minority populations (African American, Hispanic). Hospitalization rate was 82% (64/78). About 44% (34/78) had an associated comorbidity with asthma and obesity being most common. Although all ages were affected, infants <1 year of age had the highest hospitalization rate (19/64, 30%). In all disease severity categories, dichotomized non-whites had more severe disease by percentage within race/ethnicity than Whites, and also within percent disease severity (P-value = .197). Overall, 37% of hospitalized patients required intensive care. Conclusions. Extremely high rates of COVID-19 hospitalization and requirement of ICU care were identified in our patient population. Further studies are needed to better understand the contributing factors to this health disparity in disadvantaged communities.

Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome.

Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of D. pigrum is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into D. pigrum's chromosomal structure, pangenome, and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate D. pigrum prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites, including one RM system hot spot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which D. pigrum defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in D. pigrum this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms. IMPORTANCE Dolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels of D. pigrum nasal colonization in adults predicts the absence of Staphylococcus aureus nasal colonization. Also, D. pigrum nasal colonization in young children is associated with healthy control groups in studies of middle ear infections. Our analysis of 28 genomes revealed a remarkable stability of D. pigrum strains colonizing people in the United States across a 20-year span. We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation, and defenses against MGEs. Finally, these D. pigrum strains also lacked predicted virulence factors. Overall, these findings add additional support to the potential for D. pigrum as a therapeutic bacterium.

A beneficial kinetic effect of an η(5)-C5Me4H ligand.

C-H activation of benzene at 26 °C by (η(5)-C(5)Me(5))W(NO)(CH(2)CMe(3))(η(3)-CH(2)CHCHMe) results after 4 h in the production of five new organometallic complexes, only two of which are isomers of the desired (η(5)-C(5)Me(5))W(NO)(C(6)H(5))(η(3)-CH(2)CHCHMe) compound. In contrast, the identical reaction involving the η(5)-C(5)Me(4)H analogue affords only the phenyl complexes during the first 24 h, thereby facilitating their isolation in good yields. This striking difference in reactivity can be attributed to the lesser steric demands of the η(5)-C(5)Me(4)H ligand that result in its complexes reacting at a significantly slower rate.

Evaluating Outcomes of Stand-Alone Anterior Lumbar Interbody Fusion: A Systematic Review.

BACKGROUND: Stand-alone anterior lumbar interbody fusion (ALIF) is an effective surgical approach for selected spinal pathologies. It avoids the morbidity and complications associated with instrumented ALIF, such as plate fixation and the traditionally used posterior approach. Despite improved disc space visualization and clearance, the associated posterior instability and increased risk of nonfusion present major challenges to this approach. The integral cage design aims to address these challenges by providing the necessary stabilization through intracorporeal screws. However, there is limited and controversial data available for stand-alone ALIF and integral cage fixation. To our knowledge, this is the first systematic review to evaluate recent findings on outcomes of stand-alone ALIF devices to explore areas of controversy and identify directions for future research. METHODS: Two reviewers conducted independent, systematic literature searches for appropriate studies in 5 electronic databases as per Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Studies were filtered by the use of specified selection criteria, particularly exclusion of studies with supplementary fixation to ALIF and studies published before the year 2000. A total of 17 studies met the criteria, and their data were comprehensively extracted and analyzed. RESULTS: The current literature is supportive of stand-alone ALIF due to acceptable clinical outcomes, promising fusion rates and disc height restoration. However, data and outcomes remain preliminary, and there are numerous areas of controversy. CONCLUSIONS: There is evidence for the efficacy and safety of stand-alone ALIF. However, the extent of improvement based on specific indications for surgery remains unclear. Further investigation utilizing more methodologically rigorous studies of long-term outcomes is necessary to address these issues.

Impact of Elderly Age on Complications and Clinical Outcomes Following Anterior Lumbar Interbody Fusion Surgery.

BACKGROUND: Anterior lumbar interbody fusion (ALIF) is a surgical technique used to treat patients with a variety of lumbar pathologies. Identification of risk factors leading to complication following ALIF surgery may allow surgeons to better judge candidacy and optimize care for high-risk patients. METHODS: A retrospective analysis was conducted on a prospectively collected database of 137 patients who all underwent ALIF surgery by a single primary spine surgeon. Patients were separated into age-based cohorts (≤49, 50-63, and ≥64 years of age). Chi-squared, Fisher exact test, and multivariate logistic regression models were used to identify independent risk factors. RESULTS: A total of 137 patients met the inclusion criteria. Patients were divided into age-based tertiles as follows: Group 1 (<49 years old, n = 45, 32.8%), Group 2 (50-63 years old, n = 46, 33.6%), and Group 3 (64 years old, n = 46, 33.6%). Univariate analysis revealed increasing age (relative to Group 1) to be an independent risk factor for postoperative hematoma and delayed subsidence at 6 weeks and 12 weeks postoperatively compared with immediately post operation (all P < 0.05). No significant differences were found among the groups in terms of clinical outcome. Multivariate analysis also demonstrated increased age to be independently associated with greater prevalence of delayed subsidence (odds ratio 9.174, P = 0.029). CONCLUSIONS: Increased age was not associated with adverse perioperative outcomes and complications of ALIF. However, there was an increased incidence of delayed subsidence in patients ≥64 years old.

Image-Guided Lateral Mass Osteotomy for En Bloc Resection of Cervical Ewing Sarcoma: A Technical Note.

BACKGROUND: En bloc resection of Ewing sarcoma in the cervical spine according to Enneking's principles is technically challenging owing to the proximity of important neurovascular structures, the complex local anatomy, and the biomechanical instability of radical resection. The rarity of Ewing sarcoma and variability of its presentation justifies ongoing exploration and compilation of the surgical nuances and subtleties of en bloc resection in the cervical spine. CASE DESCRIPTION: We present a 34-year-old male with Ewing sarcoma of the neck who underwent successful en bloc resection using a novel technique of splitting the laminae and osteomizing the lateral masses under imaging guidance. CONCLUSIONS: This novel and successful approach of en bloc resection in the cervical spine can add to the spinal surgeon's repertoire when dealing with complex cervical tumor masses.

Systematic review of cortical bone trajectory versus pedicle screw techniques for lumbosacral spine fusion.

Fusion of the lumbosacral spine is a common surgical procedure to address a range of spinal pathologies. Fixation in lumbar fusion has traditionally been performed using pedicle screw (PS) augmentation. However, an alternative method of screw insertion via cortical bone trajectory (CBT) has been advocated as a less invasive approach which improves initial fixation and reduces neurovascular injury. There is a paucity of robust clinical evidence to support these claims, particularly in comparison to traditional pedicle screws. This study aims to review the available evidence to assess the merits of the CBT approach. Six electronic databases were searched for original published studies which compared CBT with traditional PS and their findings reviewed. Nine comparative studies were identified through a comprehensive literature search. Studies were classified as retrospective cohort, prospective cohort or case control studies with medium quality as assessed by the GRADE criteria. The available literature is not cohesive regarding outcomes and complications of CBT versus PT procedures. Most studies found no difference in operative time, but reported less blood loss during CBT. Radiological outcomes show no difference in slippage at one year although CBT is associated with greater bone-density compared to PT. Results for post-operative pain are inconclusive.

Multisite accelerometry for sleep and wake classification in children.

Actigraphy is a useful alternative to the gold standard polysomnogram for non-invasively measuring sleep and wakefulness. However, it is unable to accurately assess sleep fragmentation due to its inability to differentiate restless sleep from wakefulness and quiet wake from sleep. This presents significant limitations in the assessment of sleep-related breathing disorders where sleep fragmentation is a common symptom. We propose that this limitation may be caused by hardware constraints and movement representation techniques. Our objective was to determine if multisite tri-axial accelerometry improves sleep and wake classification. Twenty-four patients aged 6-15 years (median: 8 years, 16 male) underwent a diagnostic polysomnogram while simultaneously recording motion from the left wrist and index fingertip, upper thorax and left ankle and great toe using a custom accelerometry system. Movement was quantified using several features and two feature selection techniques were employed to select optimal features for restricted feature set sizes. A heuristic was also applied to identify movements during restless sleep. The sleep and wake classification performance was then assessed and validated against the manually scored polysomnogram using discriminant analysis. Tri-axial accelerometry measured at the wrist significantly improved the wake detection when compared to uni-axial accelerometry (specificity at 85% sensitivity: 71.3(14.2)% versus 55.2(24.7)%, p < 0.01). Multisite accelerometry significantly improved the performance when compared to the single wrist placement (specificity at 85% sensitivity: 82.1(12.5)% versus 71.3(14.2)%, p < 0.05). Our results indicate that multisite accelerometry offers a significant performance benefit which could be further improved by analysing movement in raw multisite accelerometry data.

Illness perceptions and quality of life in Japanese and Dutch patients with non-small-cell lung cancer.

This study examined quality of life (QOL) and illness perceptions in Dutch and Japanese patients with non-small-cell lung cancer, thereby extending the body of knowledge on cultural differences and psychosocial aspects of this illness. 24 Dutch and 22 Japanese patients with non-small-cell lung cancer filled out questionnaires on three occasions: immediately before chemotherapy, 1 week later, and 8 weeks after the initial chemotherapy. The European Organization for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ-C30) assessed QOL, and the Brief Illness Perception Questionnaire (B-IPQ) illness perceptions. Scores on several QOL measures indicated (a) major impact of first chemotherapy sessions, and (b) some tendency to returning to baseline measures at 8 weeks. Differences between Japanese and Dutch samples were found on five EORTC QLQ-C30 dimensions: global health status, emotional functioning, social functioning, constipation, and financial difficulties, with the Dutch patients reporting more favorable scores. Regarding illness perceptions, Japanese patients had higher means on perceived treatment control and personal control, expressing a higher sense of belief in the success of medical treatment than Dutch patients. In both Japanese and Dutch patients, impact of chemotherapy on QOL was evident. Some differences in illness perceptions and QOL between the two samples were observed, with implications for integral medical management. Both samples reported illness perceptions that reflect the major consequences of non-small-cell lung cancer. Incorporating symptom reports, illness perceptions, and QOL into medical management may have positive consequences for patients with non-small-cell lung cancer.