bluuebunny/crossref_metadata_2025 huggingface dataset:
The association of body composition with the risk of gestational diabetes mellitus in Chinese pregnant women
Authors: Wang Yan , Luo Bi-Ru
Published: October 2019

Studies have found that the measurement of body composition can be used to identify the gestational diabetes mellitus (GDM) risk in pregnant women. However, few studies focused on the relationship between body composition and GDM development in low GDM risk population. Thus, the objective of this study was to examine the association between body composition and the development of GDM in pregnant women with low risk of gestational diabetes.

A retrospective case-control study was conducted. We reviewed the medical records of 3965 pregnant women who had body composition measurement from March, 2016 to May, 2018 in our hospital. Their sociodemographic, clinical data, and body composition information were collected from medical record. Multiple logistic regression analyses were used.

A total of 2698 subjects were eligible for the study. The mean age of the gravidas was 30.95 ± 4.01 years old. Of all gravidas, 462 had gestational diabetes. Percentage body fat was the strongest risk factor for gestational diabetes after adjusting pre-pregnancy body mass index (BMI) (odds ratio = 1.786, 95% confidence interval = 1.112–2.866, P = .02). The age and extracellular water/intracellular water ratio were independently associated with gestational diabetes.

Percentage body fat was the strongest risk factor for gestational diabetes after adjusting pre-pregnancy BMI. Assessment of body composition may provide important guidance to identify gestational diabetes in pregnant women with low gestational diabetes risk.
Endometrial carcinoma complicated by malignant pericardial effusion
Authors: Liu Guang , Zhang Qianqian , Li Ze , Chen Xiaojun , Zhang Ning , Zhang Jinli
Published: October 2019

Rationale:

High-stage endometrial carcinoma is an aggressive tumor with a high propensity for distant spread. However, metastases to the pericardium are rare in gynecological cancer, and are usually fatal.

Patient concerns:

A 69-year-old woman was diagnosed with endometrial carcinoma with pericardium metastasis. The symptoms at presentation were panic and shortness of breath.

Diagnoses:

The cytologic examination of pericardial fluid obtained by pericardiocentesis confirmed metastasis.

Interventions:

In addition to cisplatin instilled into the pericardial space, for systemic chemotherapy, we chose that gemcitabine and lobaplatin regimen be preferred.

Outcomes:

The patient has been participating in telephone follow-up for 8 months and has generally remained in a good condition.

Lessons:

Endometrial carcinoma can have pericardial metastases. When this happens, we recommend ultrasound-guided pericardial puncture and the pericardial injection of cisplatin, in combination with systemic chemotherapy that consists of gemcitabine and lobaplatin.
Efficacy and safety of tenofovir disoproxil fumarate in Chinese patients with chronic hepatitis B virus infection
Authors: Zheng Shuqin , Liu Longgen , Lu Jianchun , Zhang Xiujun , Shen Hongyu , Zhang Hongyu , Xue Yuan , Lin Lin
Published: October 2019

To date, a small number of studies concerning the effects and safety of tenofovir disoproxil fumarate (TDF) in Chinese individuals were conducted. In this study, we aimed to assess the antiviral effects and nephrotoxicity of TDF in Chinese patients with chronic hepatitis B virus (HBV) infection.

Patients with chronic HBV infection were prospectively recruited and TDF treatment was given for 96 weeks. HBV serologic markers, HBV DNA, creatinine and phosphorus were collected.

Fifty-seven treatment-naïve and 48 treatment-experienced patients were recruited. Irrespective of the prior treatment history, more than 95% of patients achieved virological response during 96 weeks treatment with TDF. Estimated glomerular filtration rate (eGFR) significantly declined in the first year of treatment in patients with chronic hepatitis B or younger age (<65 years old) (both P < .05), while that was not achieved in patients with liver cirrhosis or older age (≥65 years old) (both P > .05). For patients who were treatment-naïve or treated previously with adefovir dipivoxil, eGFR declined at the 48th week; however, eGFR was partially recovered at the 96th week. Furthermore, multivariable analysis showed that basal eGFR <90 mL/min/1.73 m2 (P = .001; odds ratio: 4.821; 95% confidence interval: 1.904–12.206) is the only independent risk factor for eGFR <90 mL/min/1.73 m2 at the 96th week.

TDF has potent antiviral effect in both treatment-naïve and treatment-experienced patients.
The peculiarities of Kawasaki disease at the extremes of age
Authors: Mărginean Cristina Oana , Meliţ Lorena Elena , Mărginean Maria Oana
Published: October 2019

Rationale:

Extremes of age is an important risk factor for the development of coronary arteries aneurysms (CAAs) associated to Kawasaki disease (KD) along with male gender, prolonged fever and a delay in diagnosis or treatment.

Patient concerns:

We report two cases of KD in the extremes of age, a 5-month-old male infant and a 9-year-old child in order to underline the features of this disorder outside the typical age range of 1 to 4 years. The 5-month-old male was admitted in our clinic for generalized polymorphous exanthema and fever for approximately 7 days. The laboratory test pointed out leukocytosis and increased inflammatory biomarkers. The 9-year-old male child was admitted in our clinic for fever and submandibular adenopathy. The onset was approximately 5 days before the admission with a sudden development of unilateral, painless, submandibular lymphadenopathy for which the ENT specialist recommended antibiotics and nonsteroid anti-inflammatory drugs. In the 2nd day of admission, he presented severe desquamation of hands and soles.

Diagnosis:

Both cases were diagnosed with KD. The echocardiography showed no cardiac impairment in the infant, while in the older patient it revealed mild dilation of the left coronary artery.

Interventions:

Both patients received intravenously immunoglobulin and pulsed methylprednisolone.

Outcomes:

The evolution was favorable in both cases, but in the infant, the C-reactive protein levels persisted mildly elevated for approximately 2 months after the diagnosis.

Lessons:

The peculiarities of KD in the extremes of age are related to a higher frequency of incomplete features and an increased incidence of coronary artery lesions resulting in a delay of the diagnosis, and subsequent poorer outcomes.
Circular RNA expression profile in peripheral whole blood of lung adenocarcinoma by high
Authors: Mu Yinyu , Xie Fuyi , Huang YunFei , Yang Dongdong , Xu Guodong , Wang Chunnian , Wu Qiaoping
Published: October 2019

Background:

Lung adenocarcinoma (LA) is a most common form of non-small cell lung cancer (NSCLC). To date, there are still no effective early diagnosis methods for patients to be cured in time. Noncoding RNA plays an important role in oncogenesis and tumor development. The expression profile of circular RNA (circRNA) in peripheral whole blood (PWB) of LA has not been systematically investigated. In this study, we identified the differentially expressed (DE) circRNAs in PWB of LA by high-throughput sequencing.

Methods:

Five paired LA and normal participants PWB samples were chosen to investigate the expression profile of circRNAs by high-throughput sequencing. Twenty LA and 10 normal controls PWB samples were subjected to reverse-transcription polymerase chain reaction (RT-PCR) for validation of circRNAs expression profile. Gene Ontology (GO) functional analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and circRNA-miRNA network analysis was also performed to predict the function of circRNAs in PWB.

Results:

A total of 10566 circRNAs were identified and annotated, most of the circRNAs were exonic (78.14%). Statistical analysis revealed 4390 DE circRNAs, in which were 3009 upregulated circRNAs and1381downregulated circRNAs in LA. RT-PCR results showed that circRNA expression in LA was higher than that in controls. GO functional analysis, KEGG pathway analysis, and circRNA-miRNA network analysis all showed that circRNAs correlated with tumor development and progression to a certain degree. The current study is the first to systematically characterize and annotate circRNA expression in PWB of LA. Some host genes of the DE circRNAs were involved in tumor signaling pathway and had complicated correlations with tumor related miRNAs, indicating that circRNAs might involve in development and progression of LA.

Conclusions:

Our study revealed that circRNAs were abnormally expressed in PWB of LA, which might offer potential targets for the early diagnosis of the disease and new genetic insights into LA.
Outcomes of pathologically localized high-grade prostate cancer treated with radical prostatectomy
Authors: Heo Ji Eun , Park Jee Soo , Lee Jong Soo , Kim Jongchan , Jang Won Sik , Rha Koon Ho , Choi Young Deuk , Hong Sung Joon , Ham Won Sik
Published: October 2019

Adjuvant radiation therapy (ART) is recommended without consideration of radical prostatectomy Gleason score (RP GS) for cases with adverse features. We compared the outcomes of pathologically localized high-grade (GS 8–10) prostate cancer (PC) with those of pT3 GS 7 PC.

A total of 1585 men who underwent RP between 1995 and 2015 comprised the cohort, which was divided into group 1 (RP GS 7(3 + 4) and pT3; n = 760), group 2 (RP GS 7(4 + 3) and pT3; n = 565), and group 3 (RP GS 8–10 and pT2; n = 260). Biochemical recurrence (BCR), all-cause mortality (ACM), and PC-specific mortality (PCSM) risk were compared among groups using Cox regression and competing risk analysis.

At a median follow-up of 58 months (interquartile range: 37–85), 721 men experienced BCR and 84 died (22 due to PC). BCR-free survival rates were lower in group 3 than in group 1 (P < .001); nevertheless, no difference was observed between groups 2 and 3 (P = .638). Furthermore, no difference in ACM was noted among groups. PCSM rates were higher in group 3 than in groups 1 and 2 (P = .001 and P = .005, respectively). This association persisted in multivariate models after adjustment for clinicopathological variables.

Patients with RP GS 8–10 and pT2 PC had higher BCR and PCSM rates than those with RP GS 7 and pT3 PC. Localized high-grade PC should be considered in decision-making for ART.
Fall prevention initiative: A fall screening and intervention pilot study on the ambulatory setting
Authors: Kartiko Susan , Jeremitsky Elan , Cripps Michael W. , Konderwicz Ida , Jarosz Erin , Minshall Christian T.
Published: October 2019

BACKGROUND

Falling is the most common cause of trauma in the geriatric population. To identify patients that were at-risk for falling, we implemented a provider-directed fall prevention screening initiative in the ambulatory setting of a large tertiary care referral center. We used three clinician-directed questions from the Stopping Elderly Accidents, Death and Injuries toolkit. Our goal was to intervene on patients who were screened as at-risk for falling by referring them to our physical therapy program and evaluating its effects to these patients.

METHODS

Patients 55 years or older who live in the community were screened from June 2017 to June 2018. Patients who answered yes to any of the three questions were identified as at-risk for falling, and referred to the Fall Prevention Initiative Physical Therapy Program (FPIPTP). The FPIPTP is a program that establishes a quantifiable fall risk using the Time Up and Go (TUG) test, which then initiates PT treatments, designed to prevent future falls by improving, gait, balance, and fitness. The Wilcoxon signed rank test was used to determine significance (p < 0.05).

RESULTS

We identified 112 patients with a median age of 76.5 years (IQR, 68–82 years) to be at-risk for falling. The initial median TUG score in this group of patients is 15.85 seconds (12–20.33 seconds), which is consistent with a high fall-risk (time >12 seconds). After completing the FPIPTP, the median TUG score significantly improved to 12 seconds (9–15 seconds, p < 0.0001).

CONCLUSION

We conclude that a provider can use the three specific questions from the Stopping Elderly Accidents, Death and Injuries toolkit to identify patients (≥55 years) that are at-risk for falling. Additionally, the FPIPTP is able to significantly improve the TUG score in this group. We will need to confirm this conclusion with a larger population study.

LEVEL OF EVIDENCE

Therapeutic, Level IV.
Endophenotypes of executive functions in obsessive compulsive disorder? A meta-analysis in unaffected relatives
Authors: Zartaloudi Eirini , Laws Keith R. , Bramon Elvira
Published: October 2019

Endophenotypes are mediator traits between genetic influences and clinical phenotypes. Meta-analyses have consistently shown modest impairments of executive functioning in obsessive compulsive disorder (OCD) patients compared to healthy controls. Similar deficits have also been reported in unaffected relatives of OCD patients, but have not been quantified. We conducted the first meta-analysis combining all studies investigating executive functioning in unaffected relatives of individuals with OCD to quantify any deficits. A search of Pubmed, Medline and PsychInfo databases identified 21 suitable papers comprising 707 unaffected relatives of OCD patients and 842 healthy controls. Effect sizes were calculated using random effects models. Unaffected relatives displayed a significant impairment in global executive functioning. Analyses of specific executive functioning subdomains revealed impairments in: planning, visuospatial working memory and verbal fluency. Deficits in executive functioning are promising endophenotypes for OCD. To identify further biomarkers of disease risk/resilience in OCD, we suggest examining specific executive functioning domains.
SMART: Statistical Mitogenome Assembly with Repeats
Authors: Alqahtani Fahad , Măndoiu Ion I.
Published: October 2019

By using next-generation sequencing technologies it is possible to quickly and inexpensively generate large numbers of relatively short reads from both the nuclear and mitochondrial DNA contained in a biological sample. Unfortunately, assembling such whole-genome sequencing (WGS) data with standard de novo assemblers often fails to generate high quality mitochondrial genome sequences due to the large difference in copy number (and hence sequencing depth) between the mitochondrial and nuclear genomes. Assembly of complete mitochondrial genome sequences is further complicated by the fact that many de novo assemblers are not designed for circular genomes, and by the presence of repeats in the mitochondrial genomes of some species.

In this paper we describe the Statistical Mitogenome Assembly with Repeats (SMART) pipeline for automated assembly of complete circular mitochondrial genomes from WGS data. SMART uses an efficient coverage-based filter to first select a subset of reads enriched in mtDNA sequences. Contigs produced by an initial assembly step are filtered using BLAST searches against a comprehensive mitochondrial genome database, and used as “baits” for an alignment-based filter that produces the set of reads used in a second de novo assembly and scaffolding step. In the presence of repeats, the possible paths through the assembly graph are evaluated using a maximum-likelihood model. Additionally, the assembly process is repeated a user-specified number of times on re-sampled subsets of reads to select for annotation the reconstructed sequences with highest bootstrap support.

Experiments on WGS datasets from a variety of species show that the SMART pipeline produces complete circular mitochondrial genome sequences with a higher success rate than current state-of-the art tools, even from low coverage WGS data. The pipeline is available through an easy-to-use web interface at https://neo.engr.uconn.edu/?tool_id=SMART.
Integrating healthcare and research genetic data empowers the discovery of 28 novel developmental disorders
Authors: Kaplanis Joanna , Samocha Kaitlin E. , Wiel Laurens , Zhang Zhancheng , Arvai Kevin J. , Eberhardt Ruth Y. , Gallone Giuseppe , Lelieveld Stefan H. , Martin Hilary C. , McRae Jeremy F. , Short Patrick J. , Torene Rebecca I. , de Boer Elke , Danecek Petr , Gardner Eugene J. , Huang Ni , Lord Jenny , Martincorena Iñigo , Pfundt Rolph , Reijnders Margot R. F. , Yeung Alison , Yntema Helger G. , Study DDD , Vissers Lisenka E. L. M. , Juusola Jane , Wright Caroline F. , Brunner Han G. , Firth Helen V. , FitzPatrick David R. , Barrett Jeffrey C. , Hurles Matthew E. , Gilissen Christian , Retterer Kyle
Published: October 2019

De novomutations (DNMs) in protein-coding genes are a well-established cause of developmental disorders (DD). However, known DD-associated genes only account for a minority of the observed excess of such DNMs. To identify novel DD-associated genes, we integrated healthcare and research exome sequences on 31,058 DD parent-offspring trios, and developed a simulation-based statistical test to identify gene-specific enrichments of DNMs. We identified 285 significantly DD-associated genes, including 28 not previously robustly associated with DDs. Despite detecting more DD-associated genes than in any previous study, much of the excess of DNMs of protein-coding genes remains unaccounted for. Modelling suggests that over 1,000 novel DD-associated genes await discovery, many of which are likely to be less penetrant than the currently known genes. Research access to clinical diagnostic datasets will be critical for completing the map of dominant DDs.
Pitch of Harmonic Complex Tones: Rate-Place Coding of Resolved Components in Harmonic and Inharmonic Complex Tones in Auditory Midbrain
Authors: Su Yaqing , Delgutte Bertrand
Published: October 2019

Harmonic complex tones (HCT) commonly occurring in speech and music evoke a strong pitch at their fundamental frequency (F0), especially when they contain harmonics individually resolved by the cochlea. When all frequency components of an HCT are shifted by the same amount, the pitch of the resulting inharmonic tone (IHCT) also shifts although the envelope repetition rate is unchanged. A rate-place code whereby resolved harmonics are represented by local maxima in firing rates along the tonotopic axis has been characterized in the auditory nerve and primary auditory cortex, but little is known about intermediate processing stages. We recorded single neuron responses to HCT and IHCT with varying F0 and sound level in the inferior colliculus (IC) of unanesthetized rabbits. Many neurons showed peaks in firing rates when a low-numbered harmonic aligned with the neuron’s characteristic frequency, demonstrating “rate-place” coding. The IC rate-place code was most prevalent for F0>800 Hz, was only moderately dependent on sound level over a 40 dB range, and was not sensitive to stimulus harmonicity. A spectral receptive-field model incorporating broadband inhibition better predicted the neural responses than a purely excitatory model, suggesting an enhancement of the rate-place representation by inhibition. Some IC neurons showed facilitation in response to HCT, similar to cortical “harmonic template neurons” (Feng and Wang 2017), but to a lesser degree. Our findings shed light on the transformation of rate-place coding of resolved harmonics along the auditory pathway, and suggest a gradual emergence of harmonic templates from low to high processing centers.

Significance statement

Harmonic complex tones are ubiquitous in speech and music and produce strong pitch percepts in human listeners when they contain frequency components that are individually resolved by the cochlea. Here, we characterize a “rate-place” code for resolved harmonics in the auditory midbrain that is more robust across sound levels than the peripheral rate-place code and insensitive to the harmonic relationships among frequency components. We use a computational model to show that inhibition may play an important role in shaping the rate-place code. We also show that midbrain auditory neurons can demonstrate similar properties as cortical harmonic template neurons. Our study fills a gap in understanding the transformation in neural representations of resolved harmonics along the auditory pathway.
Detecting dipicolinic acid production and biosynthesis pathways in Bacilli and Clostridia
Authors: Gordon Benjamin , Duellman Paul , Salvucci Anthony , De Lorme Marthah
Published: October 2019

Bacterial endospores are highly resistant structures and dipicolinic acid is a key component of their resilience and stability. Due to the difficulty in controlling endospore contaminants, they are of interest in clean rooms, food processing, and production industries, while benefical endospore-formers are sought for potential utility. Dipicolinic acid production has traditionally been recognized in Bacilli, Clostridia, and Paenibacilli. Here, sixty-seven strains of aerobic and anaerobic endospore-forming bacteria belonging to the generaBacillus, Brevibacillus, Clostridium, Fontibacillus, Lysinibacillus, Paenibacillus, Rummeliibacillus, andTerribacilluswere grown axenically and sporulated biomasses were assayed for dipicolinic acid production using fluorimetric detection. Strains testing positive were sequenced and the genomes analyzed to identify dipicolinic acid biosynthesis genes. The well-characterized biosynthesis pathway was conserved in 59 strains of Bacilli and Paenibacilli as well as two strains of Clostridia; six strains of Clostridia lacked homologs to genes recognized as involved in dipicolinic acid biosynthesis. Our results confirm dipicolinic acid production across different classes and families of Firmicutes. We find that members ofClostridium(cluster I) lack recognized dipicolinic acid biosynthesis genes and propose an alternate genetic pathway in these strains. Finally, we explore why the extent and mechanism of dipicolinic acid production in endospore-forming bacteria should be fully understood. We believe that understanding the mechanism by which dipicolinic acid is produced can expand the methods to utilize endospore-forming bacteria, such as novel bacterial strains added to products, for genes to create inputs for the polymer industry and to be better equipped to control contaminating spores in industrial processes.
A sparse, spatially biased subtype of mature granule cell is preferentially recruited in hippocampal-associated behaviors
Authors: Erwin Sarah R. , Sun Weinan , Copeland Monique , Lindo Sarah , Spruston Nelson , Cembrowski Mark S.
Published: October 2019

Animals can store information about experiences by activating specific neuronal populations, and subsequent reactivation of these neural ensembles can lead to recall of salient experiences. In the hippocampus, granule cells of the dentate gyrus participate in such memory engrams; however, whether there is an underlying logic to granule cell participation has not been examined. Here, we found that a broad range of novel experiences preferentially activates granule cells of the suprapyramidal blade relative to the infrapyramidal blade. Motivated by this, we identified a suprapyramidal-blade-enriched population of granule cells with distinct spatial, morphological, physiological, and developmental properties. Via transcriptomics, we mapped these traits onto a sparse and discrete granule cell subtype that was recruited at a ten-fold greater frequency than expected by subtype prevalence, constituting the majority of all recruited granule cells. Thus, a rare and spatially localized granule cell subtype is intrinsically predisposed to activation during hippocampal memory formation.
Cardiomyocyte-Specific Deletion of GCN5L1 in Mice Limits Ex Vivo Cardiac Functional Decline in Response to a High Fat Diet
Authors: Thapa Dharendra , Manning Janet R , Stoner Michael W. , Zhang Manling , Xie Bingxian , Sack Michael N. , Scott Iain
Published: October 2019

Reduced substrate flexibility, and a shift towards increased cardiac fatty acid utilization, is a key feature of obesity and diabetes. We previously reported that increased acetylation of several mitochondrial FAO enzymes, regulated in part via increased abundance of the mitochondrial acetyltransferase GCN5L1, correlated with increased FAO enzyme activity in the heart. The focus of the current study was to investigate whether decreased acetylation, via cardiomyocyte-specific deletion of GCN5L1 (GCN5L1 cKO), regulates cardiac energy metabolism following exposure to a high fat diet (HFD). Excess dietary fat led to similar cardiac hypertrophy in wildtype and GCN5L1 cKO mice. We show that acetylation of pyruvate dehydrogenase (PDH) was significantly reduced in HFD GCN5L1 cKO hearts, which correlated with its increased enzymatic activity relative to HFD wildtype controls. The acetylation of both electron transport chain Complex I protein NDUFB8, and manganese superoxide dismutase 2 (SOD2), was significantly reduced by GCN5L1 deletion in HFD animals, resulting in decreased lipid peroxidation. Finally, we show that in contrast to wildtype mice, GCN5L1 cKO hearts maintain ex vivo contractility and workload in response to a HFD. In summary, we show that GCN5L1 deletion limits cardiac functional decline observed in HFD mice, by increasing fuel substrate flexibility and limiting reactive oxygen species damage.
Stimulus-specific neural encoding of a persistent, internal defensive state in the hypothalamus
Authors: Kennedy Ann , Kunwar Prabhat S. , Li Lingyun , Wagenaar Daniel , Anderson David J.
Published: October 2019

Persistent neural activity has been described in cortical, hippocampal, and motor networks as mediating short-term working memory of transiently encountered stimuli1–4. Internal emotion states such as fear also exhibit persistence following exposure to an inciting stimulus5,6, but such persistence is typically attributed to circulating stress hormones7–9; whether persistent neural activity also plays a role has not been established. SF1+/Nr5a1+ neurons in the dorsomedial and central subdivision of the ventromedial hypothalamus (VMHdm/c) are necessary for innate and learned defensive responses to predators10–13. Optogenetic activation of VMHdmSF1 neurons elicits defensive behaviors that can outlast stimulation11,14, suggesting it induces a persistent internal state of fear or anxiety. Here we show that VMHdmSF1 neurons exhibit persistent activity lasting tens of seconds, in response to naturalistic threatening stimuli. This persistent activity was correlated with, and required for, persistent thigmotaxic (anxiety-like) behavior in an open-field assay. Microendoscopic imaging of VMHdmSF1 neurons revealed that persistence reflects dynamic temporal changes in population activity, rather than simply synchronous, slow decay of simultaneously activated neurons. Unexpectedly, distinct but overlapping VMHdmSF1 subpopulations were persistently activated by different classes of threatening stimuli. Computational modeling suggested that recurrent neural networks (RNNs) incorporating slow excitation and a modest degree of neurochemical or spatial bias can account for persistent activity that maintains stimulus identity, without invoking genetically determined “labeled lines”15. Our results provide causal evidence that persistent neural activity, in addition to well-established neuroendocrine mechanisms, can contribute to the ability of emotion states to outlast their inciting stimuli, and suggest a mechanism that could prevent over-generalization of defensive responses without the need to evolve hardwired circuits specific for each type of threat.
The Development, Function, and Plasticity of the Immune Macroenvironment in Cancer
Authors: Allen Breanna M. , Hiam Kamir J. , Burnett Cassandra E. , Venida Anthony , DeBarge Rachel , Carmi Yaron , Spitzer Matthew H.
Published: October 2019

Harnessing immune defense mechanisms has revolutionized cancer therapy, but our understanding of the factors governing immune responses in cancer remains incomplete, limiting patient benefit. Here, we use mass cytometry to define the organism-wide immune landscape in response to tumor development across five tissues in eight tumor models. Systemic immunity was dramatically altered across mouse models and cancer patients, with changes in peripheral tissues differing from those in the tumor microenvironment and taking place in phases during tumor growth. This tumor-experienced immune system mounted dampened responses to orthogonal challenges, including reduced T cell activation during viral or bacterial infection. Disruptions in T cell responses were not cell-intrinsic but rather due to reduced responses in antigen-presenting cells (APCs). Promoting APC activation was sufficient to restore T cell responses to orthogonal infection. All systemic immune changes were reversed with surgical tumor resection, revealing remarkable plasticity in the systemic immune state, which contrasts with terminal immune dysfunction in the tumor microenvironment. These results demonstrate that tumor development dynamically reshapes the composition and function of the immune macroenvironment.
3D projection electrophoresis for single-cell immunoblotting
Authors: Grist Samantha M. , Mourdoukoutas Andoni P. , Herr Amy E.
Published: October 2019

While immunoassays and mass spectrometry are powerful single-cell protein analysis tools, bottlenecks remain in interfacing and throughput. Here, we introduce highly parallel, synchronous, three-dimensional single-cell immunoblots to detect both cytosolic and nuclear proteins. The novel threedimensional microfluidic device is a photoactive polyacrylamide gel with a high-density microwell array patterned on one face (x-y) for cell isolation and lysis. From each microwell, single-cell lysate is ‘electrophoretically projected’ into the 3rddimension (z-axis), separated by size, and photo-captured for immunoprobing and three-dimensional interrogation by confocal/light sheet microscopy. Design guidelines for throughput and separation performance are informed by simulation, analyses, and deconvolution postprocessing based on physics of 3D diffusion. Importantly, separations are nearly synchronous, whereas serial analyses can impart hours of delay between the first and last cell. We achieve an electrophoresis throughput of >2.5 cells/s (70X faster than serial sampling) and perform 25 immunoblots/mm2device area (>10X increase over previous immunoblots). A straightforward device for parallel single-cell immunoblotting, projection electrophoresis promises to advance integration of protein-level profiles into the emerging single-cell atlas of genomic and transcriptomic profiles.
Encephalitic alphaviruses exploit caveolae-mediated transcytosis at the blood-brain barrier for CNS entry
Authors: Salimi Hamid , Cain Matthew D. , Jiang Xiaoping , Roth Robyn A. , Beatty Wandy , Sun Chengqun , Klimstra William B. , Hou Jianghui , Klein Robyn S.
Published: October 2019

Venezuelan and Western equine encephalitis viruses (VEEV and WEEV) invade the CNS early during infection, via neuronal and hematogenous routes (1, 2). While viral replication mediates host-shut off, including expression of type I interferons (IFN) (3, 4), few studies have addressed how alphaviruses gain access to the CNS during established infection or the mechanisms of viral crossing at the blood-brain barrier (BBB). Here, we show that hematogenous dissemination of VEEV and WEEV into the CNS occurs via caveolin (Cav)-1-mediated transcytosis (Cav-MT) across an intact BBB, which is impeded by IFN and inhibitors of RhoA GTPase. Use of reporter and non-replicative strains also demonstrates that IFN signaling mediates viral restriction within cells comprising the neurovascular unit (NVU), differentially rendering brain endothelial cells, pericytes and astrocytes permissive to viral replication. Transmission and immunoelectron microscopy revealed early events in virus internalization and Cav-1-association within brain endothelial cells. Cav-1-deficient mice exhibit diminished CNS VEEV and WEEV titers during early infection, whereas viral burdens in peripheral tissues remained unchanged. Our findings show that alphaviruses exploit Cav-MT to enter the CNS, and that IFN differentially restricts this process at the BBB.

Importance

VEEV, WEEV and EEEV are emerging infectious diseases in the Americas, and they have caused several major outbreaks in the human and horse population during the past few decades. Shortly after infection, these viruses can infect the CNS, resulting in severe long-term neurological deficits or death. Neuroinvasion has been associated with virus entry into the CNS directly from the blood-stream, however the underlying molecular mechanisms have remained largely unknown. Here we demonstrate that following peripheral infection alphavirus augments vesicular formation/trafficking at the BBB and utilizes Cav-MT to cross an intact BBB, a process regulated by activators of Rho GTPAses within brain endothelium.In vivoexamination of early viral entry in Cav-1-deficient mice revealed significantly lower viral burdens than in similarly infected wild-type animals. These studies identify a potentially targetable pathway to limit neuroinvasion by alphaviruses.
Biasing the perception of spoken words with tACS
Authors: Kösem Anne , Bosker Hans Rutger , Jensen Ole , Hagoort Peter , Riecke Lars
Published: October 2019

Recent neuroimaging evidence suggests that the frequency of entrained oscillations in auditory cortices influences the perceived duration of speech segments, impacting word perception (Kösem et al. 2018). We further tested the causal influence of neural entrainment frequency during speech processing, by manipulating entrainment with continuous transcranial alternating current stimulation (tACS) at distinct oscillatory frequencies (3 Hz and 5.5 Hz) above the auditory cortices. Dutch participants listened to speech and were asked to report their percept of a target Dutch word, which contained a vowel with an ambiguous duration. Target words were presented either in isolation (first experiment) or at the end of spoken sentences (second experiment). We predicted that the frequency of the tACS current would influence neural entrainment and therewith how speech is perceptually sampled, leading to a perceptual over- or underestimation of the vowel duration. Experiment 1 revealed no significant result. In contrast, results from experiment 2 showed a significant effect of tACS frequency on target word perception. Faster tACS lead to more long-vowel word percepts, in line with previous findings suggesting that neural oscillations are instrumental in the temporal processing of speech. The different results from the two experiments suggest that the impact of tACS is dependent on the sensory context. tACS may have a stronger effect on spoken word perception when the words are presented in a continuous stream of speech as compared to when they are isolated, potentially because prior (stimulus-induced) entrainment of brain oscillations might be a prerequisite for tACS to be effective.
Comparing dopamine release, uptake, and D2 autoreceptor function across the ventromedial to dorsolateral striatum in adolescent and adult rats
Authors: Pitts Elizabeth G. , Stowe Taylor A. , Christensen Brooke , Ferris Mark J.
Published: October 2019

Adolescents have increased vulnerability for the development of a range of psychiatric disorders, including substance abuse disorders (SUD) and mood disorders. Adolescents also have increased rates of sensation seeking and risk taking. The mesolimbic dopamine system plays a role in all these behaviors and disorders and reorganization of the dopamine system during adolescence may be important in mediating these developmental changes in behavior and vulnerability. Here, we usedex vivofast scan cyclic voltammetry to examine developmental differences in dopamine release and its local circuitry regulation across the striatum. We found that adolescents have significantly decreased dopamine release in the nucleus accumbens core across a range of stimulation frequencies that model tonic and phasic firing of mesolimbic dopamine neurons. We show this is not mediated by differences in rate of dopamine uptake, but may be driven by hypersensitive dopamine autoreceptors, indicated by increased inhibition in dopamine release following agonism of D2/D3 receptors, in the adolescent nucleus accumbens core. Additionally, we observed increases in dopamine uptake in the dorsomedial striatum. No other significant differences between release, uptake, or D2 autoreceptor function was observed between adolescent and adult rats in all brain areas tested (nucleus accumbens shell, nucleus accumbens core, dorsomedial striatum, and dorsolateral striatum). These developmental differences in dopamine release may be important in mediating some of the unique behavioral repertoire seen in adolescents, such as increases in sensation seeking, and its associated vulnerabilities.
Ribosome dimerization prevents loss of essential ribosomal proteins during quiescence
Authors: Feaga Heather A. , Kopylov Mykhailo , Kim Jenny Kim , Jovanovic Marko , Dworkin Jonathan
Published: October 2019

The formation of ribosome dimers during periods of quiescence is widespread among bacteria and some higher eukaryotes. However, the mechanistic importance of dimerization is not well understood. In bacteria ribosome dimerization is mediated by the Hibernation Promoting Factor (HPF). Here, we report that HPF from the Gram-positive bacterium Bacillus subtilis preserves active ribosomes by preventing the loss of essential ribosomal proteins. Ribosomes isolated from strains either lacking HPF (Δhpf) or encoding a mutant allele of HPF that binds the ribosome but does not mediate dimerization were substantially depleted of the small subunit proteins S2 and S3. Strikingly, these proteins are located at the ribosome dimer interface. We used single particle cryo-EM to further characterize ribosomes isolated from a Δhpf mutant strain and observed that many were missing S2, S3, or both. These data support a model in which the ribosome dimerization activity of HPF evolved to protect labile proteins that are essential for ribosome function.

Significance Statement

When nutrients become scarce, many bacterial species enter an extended state of quiescence. A major challenge of this state is how to attenuate protein synthesis, the most energy consuming cellular process, while preserving ribosomes for the return to favorable conditions. Here, we show that the ribosome-binding protein HPF which dimerizes ribosomes functions to protect essential ribosomal proteins at the dimer interface. HPF is almost universally conserved in bacteria and HPF deletions in diverse species exhibit decreased viability under nutrient limitation. Our data provide mechanistic insight into this phenotype and establish a role for HPF in maintaining translationally competent ribosomes during quiescence.
Beyond traditional biodiversity fish monitoring: environmental DNA metabarcoding and simultaneous underwater visual census detect different sets of a complex fish community at a marine biodiversity hotspot
Authors: Valdivia-Carrillo Tania , Rocha-Olivares Axayácatl , Reyes-Bonilla Héctor , Domínguez-Contreras José Francisco , Munguia-Vega Adrian
Published: October 2019

Significant advances in the study of marine fish communities have been achieved with traditional monitoring methods and recently with novel genetic approaches. eDNA metabarcoding is one of them and a powerful tool for the study of biodiversity still in continuous development. Its applicability in marine ecology and conservation studies may be gauged by comparing its results with those of traditional methods. In the present investigation, we compare results from the underwater visual census (UVC) with eDNA metabarcoding (eDNA) carried out simultaneously in 24 rocky reef sites along the Gulf of California. We developed a two-PCR library preparation protocol followed by high throughput sequencing aimed at teleost fish. Our results show that both methods had different detection capabilities, and each registered different sets of fish taxa from rocky reefs, with some overlap. In particular, eDNA identified taxa from pelagic, demersal, and estuarine habitats beyond the rocky reef itself, suggesting differences in detection mainly attributed to the transport and permanence time of the eDNA in the ocean. Overlap in the detection with both methods increased with taxonomic level. We argue that substantial gaps in sequence reference databases for teleost are at the root of major discrepancies. Our results also confirm that PCR-based eDNA metabarcoding of seawater samples does not reflect patterns in abundance and biomass of species estimated from traditional methods. We discuss how to reconcile the results of eDNA metabarcoding and traditional methods in marine hotspots.
Integrated Proteomics Reveals Brain-Based Cerebrospinal Fluid Biomarkers in Asymptomatic and Symptomatic Alzheimer’s Disease
Authors: Higginbotham Lenora , Ping Lingyan , Dammer Eric B. , Duong Duc M. , Zhou Maotian , Gearing Marla , Johnson Erik C.B. , Hajjar Ihab , Lah James J. , Levey Allan I. , Seyfried Nicholas T.
Published: October 2019

Alzheimer’s disease (AD) features a complex web of pathological processes beyond amyloid accumulation and tau-mediated neuronal death. To meaningfully advance AD therapeutics, there is an urgent need for novel biomarkers that comprehensively reflect these disease mechanisms. Here we applied an integrative proteomics approach to identify cerebrospinal fluid (CSF) biomarkers linked to a diverse set of pathophysiological processes in the diseased brain. Using multiplex proteomics, we identified >3,500 proteins across 40 CSF samples from control and AD patients and >12,000 proteins across 48 postmortem brain tissues from control, asymptomatic AD (AsymAD), AD, and other neurodegenerative cases. Co-expression network analysis of the brain tissues resolved 44 protein modules, nearly half of which significantly correlated with AD neuropathology. Fifteen modules robustly overlapped with proteins quantified in the CSF, including 271 CSF markers highly altered in AD. These 15 overlapping modules were collapsed into five panels of brain-linked fluid markers representing a variety of cortical functions. Neuron-enriched synaptic and metabolic panels demonstrated decreased levels in the AD brain but increased levels in diseased CSF. Conversely, glial-enriched myelination and immunity panels were highly increased in both the brain and CSF. Using high-throughput proteomic analysis, proteins from these panels were validated in an independent CSF cohort of control, AsymAD, and AD samples. Remarkably, several validated markers were significantly altered in AsymAD CSF and appeared to stratify subpopulations within this cohort. Overall, these brain-linked CSF biomarker panels represent a promising step toward a physiologically comprehensive tool that could meaningfully enhance the prognostic and therapeutic management of AD.
A Mechanism for Neurofilament Transport Acceleration through Nodes of Ranvier
Authors: Ciocanel Maria-Veronica , Jung Peter , Brown Anthony
Published: October 2019

Abstract

Neurofilaments are abundant space-filling cytoskeletal polymers in axons that are transported along microtubule tracks. Neurofilament transport is accelerated at nodes of Ranvier, where axons are locally constricted. Strikingly, these constrictions are accompanied by a sharp decrease in neurofilament number but no decrease in microtubule number, bringing neurofilaments closer to their microtubule tracks. We hypothesize this leads to an increase in the proportion of the time that the filaments spend moving and that this can explain the local acceleration. To test this, we developed a stochastic model of neurofilament transport that tracks their number, kinetic state and proximity to nearby microtubules in space and time. The model assumes that the probability of a neurofilament moving is dependent on its distance from the nearest available microtubule track. Taking into account experimentally reported numbers and densities for neurofilaments and microtubules in nodes and internodes, we show that the model is sufficient to explain the local acceleration of neurofilaments across nodes of Ranvier. This suggests that proximity to microtubule tracks may be a key regulator of neurofilament transport in axons, which has implications for the mechanism of neurofilament accumulation in development and disease.
Arabidopsis ENHANCED DISEASE RESISTANCE1 Protein Kinase Regulates the Association of ENHANCED DISEASE SUSCEPTIBILITY1 and PHYTOALEXIN DEFICIENT4 to Inhibit Cell Death
Authors: Neubauer Matthew , Serrano Irene , Rodibaugh Natalie , Bhandari Deepak D. , Bautor Jaqueline , Parker Jane E. , Innes Roger W.
Published: October 2019

ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) and PHYTOALEXIN DEFICIENT4 (PAD4) are sequence-related lipase-like proteins that function as a complex to regulate defense responses in Arabidopsis by both salicylic acid-dependent and independent pathways. Here we describe a gain-of-function mutation in PAD4 (S135F) that enhances resistance and cell death in response to infection by the powdery mildew pathogenGolovinomyces cichoracearum.The mutant PAD4 protein accumulates to wild-type levels in Arabidopsis cells, thus these phenotypes are unlikely to be due to PAD4 over accumulation. The phenotypes are similar to loss of function mutations in the protein kinase Enhanced Disease Resistance1 (EDR1), and previous work has shown that loss ofPAD4orEDS1suppressesedr1-mediated phenotypes, placing these proteins downstream ofEDR1. Here we show that EDR1 directly associates with EDS1 and PAD4 and inhibits their interaction in yeast and plant cells. We propose a model whereby EDR1 negatively regulates defense responses by interfering with the heteromeric association of EDS1 and PAD4. Our data indicate that the S135F mutation likely alters an EDS1-independent function of PAD4, potentially shedding light on a yet unknown PAD4 signaling function.
A model to study NMDA receptors in early nervous system development
Authors: Zoodsma Josiah , Chan Kelvin , Golann David , Bhandiwad Ashwin , Napoli Amalia , Liu Guangmei , Syed Shoaib , Burgess Harold , Sirotkin Howard , Wollmuth Lonnie P.
Published: October 2019

NMDA receptors (NMDARs) are glutamate-gated ion channels that play critical roles in neuronal development and nervous system function. Pharmacological antagonism is an invaluable tool to study NMDARs, but is experimentally limited. Here, we developed a model to study NMDARs in early development in zebrafish, by generating CRISPR-mediated lesions in the NMDAR genes,grin1aandgrin1b, which encode the obligatory GluN1 subunits. While receptors containinggrin1aorgrin1bshow high Ca2+permeability, like their mammalian counterpart,grin1ais expressed earlier and more broadly in development thangrin1b. Bothgrin1a−/−andgrin1b−/−zebrafish are viable as adults. Unlike in rodents, where thegrin1knockout is embryonic lethal,grin1double mutant fish (grin1a−/−; grin1b−/−), which lack all NMDAR-mediated synaptic transmission, survive until about 10 days post fertilization, providing a unique opportunity to explore NMDAR function during development and in generating behaviors. Many behavioral defects in thegrin1double mutant larvae, including abnormal evoked responses to light and acoustic stimuli, prey capture deficits and a failure to habituate to acoustic stimuli, are replicated by short-term treatment with the NMDAR antagonist MK-801, suggesting they arise from acute effects of compromised NMDAR-mediated transmission. Other defects, however, such as periods of hyperactivity and alterations in place preference, are not phenocopied by MK-801, suggesting a developmental origin. Taken together, we have developed a unique model to study NMDARs in the developing vertebrate nervous system.