bluuebunny/crossref_metadata_2025 huggingface dataset:
Practices, Perceptions, and Attitudes in the Evaluation of Critically Ill Children for Bacteremia: A National Survey*
Authors: Woods-Hill Charlotte Z. , Koontz Danielle W. , King Anne F. , Voskertchian Annie , Colantuoni Elizabeth A. , Miller Marlene R. , Fackler James C. , Bonafide Christopher P. , Milstone Aaron M. , Xie Anping
Published: November 2019

Objectives:

Sending blood cultures in children at low risk of bacteremia can contribute to a cascade of unnecessary antibiotic exposure, adverse effects, and increased costs. We aimed to describe practice variation, clinician beliefs, and attitudes about blood culture testing in critically ill children.

Design:

Cross-sectional electronic survey.

Setting:

Fifteen PICUs enrolled in the Blood Culture Improvement Guidelines and Diagnostic Stewardship for Antibiotic Reduction in Critically Ill Children collaborative, an investigation of blood culture use in critically ill children in the United States.

Subjects:

PICU clinicians (bedside nurses, resident physicians, fellow physicians, nurse practitioners, physician assistants, and attending physicians).

Interventions:

None.

Measurement and Main Results:

Survey items explored typical blood culture practices, attitudes and beliefs about cultures, and potential barriers to changing culture use in a PICU setting. Fifteen of 15 sites participated, with 347 total responses, 15–45 responses per site, and an overall median response rate of 57%. We summarized median proportions and interquartile ranges of respondents who reported certain practices or beliefs: 86% (73–91%) report that cultures are ordered reflexively; 71% (61–77%) do not examine patients before ordering cultures; 90% (86–94%) obtain cultures for any new fever in PICU patients; 33% (19–61%) do not obtain peripheral cultures when an indwelling catheter is in place; and 64% (36–81%) sample multiple (vs single) lumens of central venous catheters for new fever. When asked about barriers to reducing unnecessary cultures, 80% (73–90%) noted fear of missing sepsis. Certain practices (culture source and indication) varied by clinician type. Obtaining surveillance cultures and routinely culturing all possible sources (each lumen of indwelling catheters and peripheral specimens) are positively correlated with baseline blood culture rates.

Conclusions:

There is variation in blood culture practices in the PICU. Fear and reflexive habits are common drivers of cultures. These practices may contribute to over-testing for bacteremia. Further investigation of how to optimize blood culture use is warranted.
Conservative Treatment of Tendon Injuries
Authors: Yang Shu-Mei , Chen Wen-Shiang
Published: November 2019

Tendon injuries or tendinopathy is a common painful and disabling conditions resulting from overuse and aging. Tendinopathy remains a challenging clinical problem because response to different treatment modalities is usually unsatisfactory and recovery is slow. We performed an extensive literature review focusing on nonsurgical treatment options for tendinopathies, including nonsteroidal anti-inflammatory drugs, corticosteroid, eccentric exercise, extracorporeal shock wave therapy, therapeutic ultrasound, hyaluronic acid, platelet-rich plasma, prolotherapy, polydeoxyribonucleotide, and stem cells, aimed at providing the most updated evidence as a guideline for caregivers.
Reliability, Validity, and Sensitivity to Change of the Cochin Hand Functional Disability Scale and Testing the New 6-Item Cochin Hand Functional Disability Scale in Systemic Sclerosis
Authors: Gheorghiu Ana Maria , Gyorfi Hermina , Capotă Răzvan , Matei Alexandru , Oneaţă Raida , Bojincă Mihai , Stoica Victor , Mihai Carina
Published: November 2019

Systemic sclerosis (SSc) is a chronic autoimmune disease causing complex hand disability. A reliable tool for hand function assessment in SSc is the Cochin Hand Functional Disability Scale (CHFS). More recently, a short-form CHFS of 6 items (CHFS-6) has been developed.

Objectives

To validate the CHFS and the new CHFS-6 in Romanian patients with SSc.

Patients and Methods

Consecutive patients with SSc who completed the CHFS were included. All patients were assessed according to the recommendations of the European Scleroderma and Research Trials and also completed the Scleroderma Health Assessment Questionnaire and the Hand Mobility in Scleroderma questionnaire. Finger range-of-motion distances were measured.

Results

Seventy patients, 63 female and 7 male patients (age median, 53.0 years; interquartile range [IQR], 21.0 years), were included. Twenty seven had diffuse cutaneous involvement (dcSSc). Median CHFS and CHFS-6 at baseline were 25.0 (IQR, 37.0) and 8.0 (IQR, 13.0), respectively.

The internal consistency (Cronbach α = 0.96, respectively, 0.90, in all 70 patients) and test-retest reliability (intraclass correlation coefficient = 0.98 for both, in 38 patients) of both CHFS and CHFS-6 were excellent. The CHFS-6 had a very high correlation with the CHFS. There were moderate to good correlations with Hand Mobility in Scleroderma, Scleroderma Health Assessment Questionnaire, and the anthropometric measurements (construct validity). In patients with early dcSSc with a second evaluation, we found good to moderate sensitivity to change (standardized response mean of 0.8 and effect size of 0.4 for CHFS, and standardized response mean of 1.1 and effect size of 0.6 for CHFS-6).

Conclusions

The CHFS and CHFS-6 are valid and easy-to-use tools for hand involvement in SSc, which can be used in clinical or research setting.
Paenibacillus protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis
Authors: Heo Jun , Kim Soo-Jin , Kim Jeong-Seon , Hong Seung-Beom , Kwon Soon-Wo
Published: November 2019

A Gram-stain-positive, rod-shaped, strictly aerobic, endospore-forming and motile bacterium with peritrichous flagella was isolated from a gut sample of the larva of Protaetia brevitarsis seulensis at the National Institute of Agricultural Sciences, Wanju-gun, Republic of Korea. Growth was observed at 15–50 °C (optimum, 28–37 °C), pH 6.0–8.0 (pH 7.0) and only without NaCl. 16S rRNA gene sequence comparisons indicated that strain FW100M-2T had the highest similarity to type strains of

Paenibacillus thailandensis

S3-4AT (96.8 %) and

Paenibacillus agaridevorans

DSM 1355T (96.3 %), and had sequence similarity values less than 96.0 % to all other taxa. The phylogenetic tree showed that strain FW100M-2T fell into the genus

Paenibacillus

, and formed a cluster with

P. thailandensis

S3-4AT independent from other

Paenibacillus

species. Antesio-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 were detected as the major fatty acids. The only isoprenoid quinone was MK-7. Polar lipids of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, two unidentified phospholipids and an unidentified lipid were present. The meso-diaminopimelic acid was present in the cell-wall peptidoglycan. The genomic DNA G+C content was 51.5 mol%. Hence, strain FW100M-2T represents a novel species of the genus

Paenibacillus

, for which the name Paenibacillus protaetiae sp. nov. is proposed, with FW100M-2T (=KACC 19327T=NBRC 113071T) as the type strain.
Generation of a neutralizing antibody against RD114-pseudotyped viral vectors
Authors: Mekkaoui L. , Ferrari M. , Mattiuzzo G. , Ma B. , Nannini F. , Onuoha S. , Kotsopoulou E. , Takeuchi Y. , Pule M.
Published: November 2019

The feline endogenous RD114 glycoprotein has proved to be an attractive envelope to pseudotype both retroviral and lentiviral vectors. As a surface protein, its detection on packaging cells as well as viral particles would be useful in different fields of its use. To address this, we generated a monoclonal antibody against RD114 by immunization of rats, termed 22F10. Once seroconversion was confirmed, purified 22F10 was cloned into murine Fc and characterized with a binding affinity of 10nM. The antibody was used to detect RD114 and its variant envelopes on different stable viral packaging cell lines (FLYRD18 and WinPac-RD). 22F10 was also shown to prevent the infections of different strains of RD-pseudotyped vectors but not related envelope glycoproteins by blocking cell surface receptor binding. We are the first to report the neutralization of viral particles by a monoclonal αRD114 antibody.
Passage of influenza A/H3N2 viruses in human airway cells removes artefactual variants associated with neuraminidase-mediated binding
Authors: Brown Jonathan C. , Barclay Wendy S. , Galiano Monica , Harvey Ruth
Published: November 2019

Serological assays with modern influenza A/H3N2 viruses have become problematic due to the progressive reduction in the ability of viruses of this subtype to bind and agglutinate red blood cells (RBCs). This is due to reduced ability of the viral haemagglutinin (HA) glycoprotein to bind to the sialic acid-containing receptors presented by these cells. Additionally, as a result of reduced HA-mediated binding in cell culture, modern A/H3N2 viruses often acquire compensatory mutations during propagation that enable binding of cellular receptors through their neuraminidase (NA) surface protein. Viruses that have acquired this NA-mediated binding agglutinate RBCs through their NA, confusing the results of serological assays designed to assess HA antigenicity. Here we confirm with a large dataset that the acquisition of mutations that confer NA binding of RBCs is a culture artefact, and demonstrate that modern A/H3N2 isolates with acquired NA-binding mutations revert to a clinical-like NA sequence after a single passage in human airway epithelial (HAE) cells.
Altered motoneuron properties contribute to motor deficits in a rabbit hypoxia ischemia model of cerebral palsy
Authors: Steele P. , Cavarsan C. F. , Dowaliby L. , Westefeld M. , Drobyshevsky A. , Gorassini M. A. , Quinlan K. A.
Published: November 2019

Cerebral palsy (CP) is caused by a variety of factors attributed to early brain damage, resulting in permanently impaired motor control, marked by weakness and muscle stiffness. To find out if altered physiology of spinal motoneurons (MNs) could contribute to movement deficits, we performed whole cell patch clamp in neonatal rabbit spinal cord slices after developmental injury at 79% gestation. After preterm hypoxia-ischemia (HI), rabbits are born with motor deficits consistent with a spastic phenotype including hypertonia and hyperreflexia. There is a range in severity, thus kits are classified as severely affected, mildly affected, or unaffected based on modified Ashworth scores and other behavioral tests. At postnatal day (P)0-5, we recorded electrophysiological parameters of 40 MNs in transverse spinal cord slices using whole cell patch clamp. Using a multivariate analysis of neuronal parameters, we found significant differences between groups (severe, mild, unaffected and sham control MNs), age (P0 to P5) and spinal cord region (cervical to sacral). Severe HI MNs showed more sustained firing patterns, depolarized resting membrane potential, and a higher threshold for action potentials. These properties could contribute to both muscle stiffness and weakness, respectively, hallmarks of spastic CP. Interestingly altered persistent inward currents (PICs) and morphology in severe HI MNs would dampen excitability (reduced normalized PIC amplitude and increased dendritic length). In summary, changes we observed in spinal MN physiology likely contribute to severity of the phenotype including weakness and hypertonia, and therapeutic strategies for CP could target excitability of spinal MNs.

Key Points

Physiology of neonatal spinal motoneurons is altered after in utero hypoxia-ischemic injury

In motoneurons from severely affected animals there is more sustained firing (lower ΔI values), a depolarized resting potential, but a higher voltage threshold for action potential firing.

Altered motoneuron excitability could contribute directly to muscle stiffness and spasticity in cerebral palsy.
Primary human macrophages are polarized towards pro-inflammatory phenotypes in alginate hydrogels
Authors: Delcassian Derfogail , Malecka Anna A. , Opoku Donaldson , Palomares Cabeza Virginia , Merry Catherine , Jackson Andrew M.
Published: November 2019

Dysregulated macrophage function is implicated in a wide range of disorders. In vitro hydrogel culture systems are often used as matrices to model and explore the effect of various external stimuli on macrophage polarization and behaviour. Here, we show that 3D alginate hydrogels are not “macrophage inert” and instead help to direct the maturation of primary human macrophages towards specific phenotypes. We compared polarization of M1-like and M2-like cells activated on planar substrates or in 3D alginate hydrogels (with or without adhesion motifs (RGD)). We show that culture in 3D alginate systems selectively alters M2 polarisation following activation; cells show a 2.6-fold increase in CD86 expression compared to cells matured on planar controls, and increase IL1β cytokine secretion even in response to an M2-like stimulus (LPS alone in the absence of IFNγ). Our results suggest that alginate materials may intrinsically stimulate M2 macrophages to acquire a unique polarization state (resembling M2b), characterized by enhanced expression of CD86 and IL1β secretion while retaining low IL12 and high IL10 secretion typical for M2 macrophages. This has important implications for researchers using alginate hydrogels to study macrophage behavior in culture and co-culture systems, as alginate itself may induce direct phenotypic changes independently or in conjunction with other stimuli.
Seed plant families with diverse mycorrhizal states have higher diversification rates
Authors: Mujica María Isabel , Burin Gustavo , Pérez María Fernanda , Quental Tiago
Published: November 2019

A crucial innovation in plant evolution was the association with soil fungi during land colonization. Today, this symbiotic interaction is present in most plants species and can be classified in four types: arbuscular (AM), Ecto (EM), Orchid (OM) and Ericoid Mycorrhiza (ER). Since the AM ancestral state, some plants lineages have switched partner (EM, OM and ER) or lost the association (no-association: NM). Evolutionary transitions to a novel mycorrhizal state (MS) might allow plant lineages to access new resources, enhancing diversification rates. However, some clades are not restricted to one MS, and this variability might promote diversification. In this study we address the relationship between MS and diversification rates of seed plant families. For this, we used the recently published FungalRoot database, which compiled data for 14,870 species and their mycorrhizal partners. We assigned a MS to each plant family, calculated the MS heterogeneity and estimated their diversification rates using the method-of-moments. Families with mixed MS had the highest diversification rates and there was a positive relationship between MS heterogeneity and diversification rates. These results support the hypothesis that MS lability promotes diversification and highlight the importance of the association with soil fungi for the diversification of plants.
Real-time sampling of travelers shows intestinal colonization by multidrug-resistant bacteria to be a dynamic process with multiple transient acquisitions
Authors: Kantele Anu , Kuenzli Esther , Dunn Steven J , Dance David AB , Newton Paul N , Davong V , Mero Sointu , Pakkanen Sari H , Neumayr Andreas , Hatz Christoph , Snaith Ann , Kallonen Teemu , Corander Jukka , McNally Alan
Published: November 2019

Background

Antimicrobial resistance (AMR) is highly prevalent in low- and middle-income countries (LMIC). International travel contributes substantially to the global spread of intestinal multidrug-resistant gram-negative (MDR-GN) bacteria. Of the 100 million annual visitors to LMIC, 30–70% become colonized by MDR-GN bacteria. The phenomenon has been well documented, but since sampling has only been conducted after travelers’ return home, data on the actual colonization process are scarce. We aimed to characterize colonization dynamics by exploring stool samples abroad on a daily basis while visiting LMIC.

Methods

A group of 20 European volunteers visiting Lao People’s Democratic Republic for three weeks provided daily stool samples and filled in daily questionnaires. Acquisition of extended-spectrum beta-lactamase-producing gram-negative bacteria (ESBL-GN) was examined by selective stool cultures followed by whole-genome sequencing (WGS) of isolates.

Results

While colonization rates were 70% at the end of the study, daily sampling revealed that all participants had acquired ESBL-GN at some time point during their overseas stay, the colonization status varying day by day. WGS analysis ascribed the transient pattern of colonization to sequential acquisition of new strains, resulting in a loss of detectable colonization by the initial MDR-GN strains. All but one participant acquired multiple strains (n=2–7). Of the total of 83 unique strains identified (53 E. coli, 10 Klebsiella, 20 other ESBL-GN species), some were shared by as many as four subjects.

Conclusions

This is the first study to characterize in real time the dynamics of acquiring MDR-GN during travel. Our data show multiple transient colonization events indicative of constant microbial competition.
Genomic encryption of digital data stored in synthetic DNA
Authors: Grass Robert N. , Heckel Reinhard , Dessimoz Christophe , Stark Wendelin J.
Published: November 2019

Today, we can read human genomes and store digital data robustly in synthetic DNA. Here we report a strategy to intertwine these two technologies to enable the secure storage of valuable information in synthetic DNA, protected with personalized keys. We show that genetic short tandem repeats (STRs) contain sufficient entropy to generate strong encryption keys, and that only one technology, DNA sequencing, is required to simultaneously read key and data. Using this approach, we experimentally generated 80 bit strong keys from human DNA, and used such a key to encrypt 17kB of digital information stored in synthetic DNA. Finally, the decrypted information was recovered perfectly from a single massively parallel sequencing run.
Incipient local adaptation in a fungus: evolution of heavy metal tolerance through allelic and copy-number variation
Authors: Bazzicalupo Anna L. , Ruytinx Joske , Ke Yi-Hong , Coninx Laura , Colpaert Jan V. , Nguyen Nhu H. , Vilgalys Rytas , Branco Sara
Published: November 2019

Human-altered environments can shape the evolution of organisms. Fungi are no exception, though little is known about how they withstand anthropogenic pollution. Here, we document incipient polygenic local adaptation in the mycorrhizal fungus Suillus luteus driven by recent soil heavy metal contamination. Genome scans across individuals from recently polluted and nearby unpolluted soils in Belgium revealed no evidence of population structure but detected allelic divergence and gene copy number variation in genes involved in metal exclusion, storage, immobilization, and reactive oxygen species detoxification. Standing genetic variation included multiple alleles of small effects contributing to heavy metal tolerance, suggesting the existence of different strategies to withstand contamination. These variants were shared across the whole population but under selection in isolates exposed to pollution. Together, our results point to S. luteus undergoing the initial steps of adaptive divergence and contribute to understanding the processes underlying local adaptation under strong environmental selection.
Detecting (un)seen change: The neural underpinnings of (un)conscious prediction errors
Authors: Rowe Elise G. , Tsuchiya Naotsugu , Garrido Marta I.
Published: November 2019

Detecting changes in the environment is fundamental for our survival. According to predictive coding theory, detecting these irregularities relies both on incoming sensory information and our top-down prior expectations (or internal generative models) about the world. Prediction errors (PEs), detectable in event-related potentials (ERPs), occur when there is a mismatch between the sensory input and our internal model (i.e., a surprise event). Many changes occurring in our environment are irrelevant for survival and may remain unseen. Such changes, even if subtle, can nevertheless be detected by the brain without emerging into consciousness. What remains unclear is how these changes are processed in the brain at the network level. Here, we used a visual oddball paradigm, in which participants engaged in a central letter task during electroencephalographic (EEG) recordings while presented with task-irrelevant high- or low-coherence background, random-dot motion. Critically, once in a while, the direction of the dots changed. After the EEG session, we confirmed that changes in motion direction at high- and low-coherence were visible and invisible, respectively, using psychophysical measurements. ERP analyses revealed that changes in motion direction elicited PE regardless of the visibility, but with distinct spatiotemporal patterns. To understand these responses, we applied Dynamic Causal Modelling (DCM) to the EEG data. Bayesian Model Averaging showed visible PE relied on a release from adaptation (repetition suppression) within bilateral MT+, whereas invisible PE relied on adaptation at bilateral V1 (and left MT+). Furthermore, while feedforward upregulation was present for invisible PE, the visible change PE also included downregulation of feedback between right MT+ to V1. Our findings reveal a complex interplay of modulation in the generative network models underlying visible and invisible motion changes.
Multi-sensory integration in the mouse cortical connectome using a network diffusion model
Authors: Shadi Kamal , Dyer Eva , Dovrolis Constantine
Published: November 2019

Having a structural network representation of connectivity in the brain is instrumental in analyzing communication dynamics and information processing in the brain. In this work, we make steps towards understanding multi-sensory information flow and integration using a network diffusion approach. In particular, we model the flow of evoked activity, initiated by stimuli at primary sensory regions, using theAsynchronous Linear Threshold (ALT) diffusion model. The ALT model captures how evoked activity that originates at a given region of the cortex “ripples through” other brain regions (referred to as anactivation cascade). By comparing the model results to functional datasets based on Voltage Sensitive Dye (VSD) imaging, we find that in most cases the ALT model predicts the temporal ordering of an activation cascade correctly. Our results on the Mouse Connectivity Atlas from the Allen Institute for Brain Science show that a small number of brain regions are involved in many primary sensory streams – the claustrum and the parietal temporal cortex being at the top of the list. This suggests that the cortex relies on anhourglass architectureto first integrate and compress multi-sensory information from multiple sensory regions, before utilizing that lower-dimensionality representation in higher-level association regions and more complex cognitive tasks.
Sustained Activation of PV+ Interneurons in Core Auditory Cortex Enables Robust Divisive Gain Control for Complex and Naturalistic Stimuli
Authors: Gothner Tina , Gonçalves Pedro J. , Sahani Maneesh , Linden Jennifer F. , Hildebrandt K. Jannis
Published: November 2019

Sensory cortices must flexibly adapt their operations to internal states and external requirements. Modulation of specific inhibitory interneurons may provide a network-level mechanism for adjustments on behaviourally relevant timescales. Understanding of the computational roles of such modulation has mostly been restricted to phasic optogenetic activation and short, transient stimuli. Here, we aimed to extend the understanding of modulation of cortical inhibition by using sustained, network-wide optogenetic activation of parvalbumin-positive interneurons in core auditory cortex to study modulation of responses to transient, sustained, and naturalistic stimuli. We found highly conserved spectral and temporal tuning, despite profoundly reduced overall network activity. This reduction was predominantly divisive, and consistent across simple, complex, and naturalistic stimuli. A recurrent network model with power-law input-output functions replicated our results. We conclude that modulation of parvalbumin-positive interneurons on timescales typical of more sustained neuromodulation may provide a means for robust divisive gain control conserving stimulus representations.
The hair cycle underlies regulation of Langerhans cell renewal
Authors: Voisin Benjamin , Chartoire Dimitri , Devouassoux Caroline , Kowalczyk-Quintas Christine , Clauss François , Lezot Frédéric , Schneider Pascal , Flacher Vincent , Mueller Christopher G.
Published: November 2019

In the epidermis, Langerhans cells (LCs) provide an essential link between the innate and adaptive immune systems. They self-renew in situ and continuously transport antigen from skin to lymph node (LN) T cells in the steady state. The cyclic renewal of hair follicles (HF) causes profound alterations in the cutaneous microenvironment, however little is known about its impact on LC homeostasis. Here we show that mouse LCs developed normally in the absence of hair but perceived critical transition periods in the hair cycle. LCs underwent a proliferation burst during the HF growth phase (anagen). Reinitiation or abolishment of anagen as well as loss of the HF had direct consequences on LC self-renewal. Because dividing LCs were found close to the anagen HF, we searched for the proliferative signal within this structure and identified increased Il34 expression by HF stem cells and their progeny. Inhibition of the IL-34 receptor CSF-1R at the onset of anagen completely and specifically blocked LC proliferation. Altogether, our findings demonstrate that the hair cycle directly oversees LC self-renewal and migration.
Ecological divergence of DNA methylation patterns at distinct spatial scales
Authors: De Kort H. , Panis B. , Deforce D. , Van Nieuwerburgh F. , Honnay O.
Published: November 2019

Adaptive trait divergence between populations is regulated by genetic and non-genetic processes. Compared to genetic change, epigenetic change is unstable and short-lived, questioning its contribution to long-term adaptive potential. However, epigenetic change can accumulate over time, and may result in beneficial epigenetic memories where environments are heterogeneous. Diverging epigenetic memories have been observed across large spatial scales, and can persist through multiple generations even in the absence of the causative environmental stressor. It is unknown, however, how and to what extent epigenetic memories contribute to fine-scale population structure and evolution. Here, we performed whole genome bisulfite sequencing on 30 Fragaria vesca F1 plants originating from distinct ecological settings and grown in a controlled environment. Specifically, we compared methylation patterns between a steep, altitudinal gradient (<2 km) and a wide spatial gradient (>500 km). If epigenetic variation is random, arising from errors during replication and without evolutionary implications, one would expect similar amounts of epigenetic variation across populations and no spatial scale-effect. Here, we find that epigenetic memories arise even at fine spatial scale, and that both parallel and non-parallel biological processes underpin epigenetic divergence at distinct spatial scales. For example, demethylation of transposable elements consistently occurred at the large but not the small spatial scale, while methylation differentiation for most biological processes were shared between spatial scales. Acute drought stress did not result in significant epigenetic differentiation, indicating that repeated historical stress levels associated with heterogeneous environmental conditions are required for acquiring a stable epigenetic memory and for coping with future environmental change.
Impaired phagocytic function in CX3CR1+ tissue-resident skeletal muscle macrophages prevents muscle recovery after influenza A virus-induced pneumonia in aged mice
Authors: Runyan Constance E. , Welch Lynn C. , Lecuona Emilia , Shigemura Masahiko , Amarelle Luciano , Abdala-Valencia Hiam , Joshi Nikita , Lu Ziyan , Nam Kiwon , Markov Nikolay S. , McQuattie-Pimentel Alexandra C. , Piseaux-Aillon Raul , Politanska Yuliya , Sichizya Lango , Watanabe Satoshi , Williams Kinola J.N. , Budinger GR Scott , Sznajder Jacob I. , Misharin Alexander V.
Published: November 2019

Skeletal muscle dysfunction in survivors of pneumonia is a major cause of lasting morbidity that disproportionately affects older individuals. We found that skeletal muscle recovery was impaired in aged compared with young mice after influenza A virus-induced pneumonia. In young mice, recovery of muscle loss was associated with expansion of tissue-resident skeletal muscle macrophages and downregulation of MHC II expression, followed by a proliferation of muscle satellite cells. These findings were absent in aged mice and in mice deficient in Cx3cr1. Transcriptomic profiling of tissue-resident skeletal muscle macrophages from aged compared with young mice showed downregulation of pathways associated with phagocytosis and proteostasis, and persistent upregulation of inflammatory pathways. Consistently, skeletal muscle macrophages from aged mice failed to downregulate MHCII expression during recovery from influenza A virus induced pneumonia and showed impaired phagocytic function in vitro. Like aged animals, mice deficient in the phagocytic receptor Mertk showed no macrophage expansion, MHCII downregulation or satellite cell proliferation and failed to recover skeletal muscle function after influenza A pneumonia. Our data suggest that a loss of phagocytic function in a CX3CR1+ tissue-resident skeletal muscle macrophage population in aged mice precludes satellite cell proliferation and recovery of skeletal muscle function after influenza A pneumonia.
Estradiol-induced progesterone synthesis develops post-puberty in the rostral hypothalamus and coincides with post-pubertal changes in the steroidogenic pathway in female mouse hypothalamic astrocytes
Authors: Mohr M.A. , Keshishian T. , Falcy B.A. , Laham B.J. , Wong AM , Micevych P.E
Published: November 2019

The development of estrogen positive feedback is a hallmark of female puberty. Both estrogen and progesterone signaling are required for the functioning of this neuroendocrine feedback loop but the physiological changes that underlie the emergence of positive feedback remain unknown. Only after puberty does estradiol (E2) facilitate progesterone synthesis in the rat female hypothalamus (neuroP), an event critical for positive feedback and the LH surge. We hypothesize that prior to puberty, these astrocytes have low levels of membrane estrogen receptor alpha (ERα), which is needed for facilitation of neuroP synthesis. Thus, we hypothesized that prepubertal astrocytes are unable to respond to E2 with increased neuroP synthesis due a lack of membrane ERα. To test this, hypothalamic tissues and enriched primary hypothalamic astrocyte cultures were acquired from pre-pubertal (postnatal week 3) and post- pubertal (week 8) female mice. E2-facilitated progesterone was measured in the hypothalamus pre- and post-puberty, and hypothalamic astrocyte responses were measured after treatment with E2. Prior to puberty, E2-facilitated progesterone synthesis did not occur in the hypothalamus, and mERα expression was low in hypothalamic astrocytes, but E2-facilitated progesterone synthesis in the rostral hypothalamus and mERα expression increased post- puberty. The increase in mERα expression in hypothalamic astrocytes corresponded with an increase in caveolin-1 protein, PKA phosphorylation, and a more rapid [Ca2+]i flux in response to E2. Together, results from the present study indicate that E2-facilitated neuroP synthesis occurs in the rostral hypothalamus, develops during puberty, and corresponds to a post-pubertal increase in mERα levels in hypothalamic astrocytes.

SIGNIFICANCE STATEMENT

Estradiol facilitation of hypothalamic neuroprogesterone synthesis is necessary for the positive feedback of the LH surge. The present study localized the increase of neuroprogesterone to the rostral hypothalamus, a region that mediates estrogen positive feedback. Across pubertal development, hypothalamic astrocytes increase levels of membrane ERα and the cell signaling responses needed to facilitate neuroprogesterone synthesis that triggers the LH surge demonstrating a mechanism for pubertal maturation resulting in reproductive competence.
Facultative social exploitation amongMyxoccocusbacteria due to non-responsive local competition
Authors: smith jeff , Velicer Gregory J.
Published: November 2019

Microbes cooperate in many ways, but it is unclear to what extent they also have adaptations to detect and exploit unrelated social partners. Experimental data often cannot discriminate between social exploitation caused by complex adaptive traits and exploitation caused by simple deleterious mutations. Here we demonstrate facultative social exploitation amongMyxococcusbacteria due to simple non-responsive local competition. We show that the time dynamics of developmental exploitation by a tan phase variant are consistent with a model where cells do not respond to the presence of other genotypes but simply compete for some shared resource necessary to produce spores. The model also predicts the frequency-dependent responses of strains to genetic chimerism in multicellular fruiting bodies. Interactions between naturally occuring soil isolates, on the other hand, are consistent with strong interference competition where the winner almost completely prevents the loser from producing any spores. These results show how facultative social exploitation does not require elaborate mechanisms to detect and respond to foreign genotypes but can instead be caused by simple competition acting on a local scale.Myxococcuscells, like social insects, cooperate in some ways while simultaneously competing in others.
Resolving intrinsic ambiguities of the fMRI signal in the human brain
Authors: Liu Eulanca Y. , Haist Frank , Shin David , Buxton Richard B.
Published: November 2019

Functional magnetic resonance imaging (fMRI) using the blood oxygenation level dependent (BOLD) signal is a standard tool in human neuroscience studies. However, the BOLD signal is physiologically complex, depending on the baseline state of the brain and the balance of changes in blood flow and oxygen metabolism in response to a change in neural activity. Interpretation of the magnitude of the BOLD response is thus problematic; specifically, group differences of the BOLD response to a standard task or stimulus, or a change after administration of a drug, could be due to a change in the neural response, neurovascular coupling, or the baseline state. While changes in oxygen metabolism can serve as a biomarker of neural activity change, reflecting the energy cost of activity, oxygen metabolism cannot be estimated from BOLD measurements alone. Here we used the effects of caffeine as a test case to show that a suite of additional noninvasive measurements, requiring no manipulation of inhaled gases, makes it possible to untangle the underlying effects of caffeine on blood flow and oxygen metabolism. After caffeine administration, the BOLD response to a standard motor task was reduced, but oxygen metabolism was not reduced; rather, caffeine reduced the balance of blood flow relative to oxygen metabolism, both in the baseline state and in response to the task. The MRI methods used required only an additional 12 minutes of scanning, can be implemented on any MRI system, and painted a more complete picture of the physiological effects of caffeine. In addition to the assessment of drug effects in the human brain, these methods make it possible to resolve ambiguities of the BOLD signal in studies of development, aging, and disease. (Duplicated from first paragraph of manuscript)
Microbial community structure and ecology in sediments of a pristine mangrove forest
Authors: Santana C.O. , Spealman P. , Melo V.M.M , Gresham D. , Jesus T.B. , Chinalia F.A.
Published: November 2019

Mangrove forests are coastal intertidal ecosystems, characterized by mangrove trees growing in slow moving saline waters, that constitute a large portion of the coastline in the tropical and subtropical regions. The dynamic water regime created by the tides results in different microhabitats in which microbial communities play an essential role in the functioning and maintenance of the mangrove ecosystem. However, little is known about the diversity of taxa within these micro-habitats and their functional roles, as only a small fraction of these organisms can be cultured in the laboratory. In this study, we characterized the microbial community present in three distinct regions of mangrove sediments from the Serinhaém estuary, part of the Atlantic Forest biome within the Environmental Protection Area of Pratigi. We sampled sediments from regions below the tidal waterline (submerged), intertidal regions (intertidal), and regions above the tidal waterline (seco). More than 85% of all the sequences in the samples belonged to 6 of 42 identified phyla:Proteobacteria(30.6%),Firmicutes(30%),Chloroflexi(8.7%),Planctomycetes(5.7%),Crenarchaeota(5.4%) andActinobacteria(5.3%). Diversity indices show that the submerged regions of the mangrove forest exhibit the greatest diversity and richness relative to the other regions. Notably, the intertidal region has the least diversity, suggesting that the dynamics of environmental variables in this region has an important influence on microbial diversity. Furthermore, distance metrics indicate that submerged sediments are more homogeneous while the seco region exhibits greater variability between locations. Finally, we found that the most abundant microbial families in the sediments are associated with nutrient cycling consistent with the essential role of the microbiome in maintaining the health of the mangrove ecology.
Analysis of polyclonal vector integration sites using Nanopore sequencing as a scalable, cost-effective platform
Authors: Zhang Ping , Ganesamoorthy Devika , Nguyen Son Hoang , Au Raymond , Coin Lachlan J. , Tey Siok-Keen
Published: November 2019

Vector integration site analysis can be important in the follow-up of patients who received gene-modified cells, but current platforms based on next-generation sequencing are expensive and relatively inaccessible. We analyzed polyclonal T cells transduced by a gammaretroviral vector, SFG.iCasp9.2A.ΔCD19, from a clinical trial. Following restriction enzyme digestion, the unknown flanking genomic sequences were amplified by inverse polymerase chain reaction (PCR) or cassette ligation PCR. Nanopore sequencing could identify thousands of unique integration sites within polyclonal samples, with cassette ligation PCR showing less bias. The assay is scalable and requires minimum capital, which together enable cost-effective and timely analysis.
Genetic Genealogical Methods Used to Identify African American Diaspora Relatives in the Study of Family Identity among Ghanaian Members of the Kassena Ethnic Group
Authors: David LaKisha Tawanda , Jones Leia
Published: November 2019

Within the phenomenon of families that were separated during the Transatlantic Slave Trade reuniting using genetic genealogy, the methods for identifying ancestral extended relatives has not been explicitly agreed upon within social sciences. Our manuscript is a methodological paper that illustrates the use of autosomal genetic genealogy to identify ancestral extended relatives within the GEDmatch database. We used a sample of nine parent-offspring dyads residing in Ghana along with AncestryDNA, GEDmatch, family-based phasing, and identical by descent (IBD) segment sharing to identify African American ancestral extended relatives of our Ghanaian participants. This method supports the claim that families that were separated during the Transatlantic Slave Trade are reuniting.
Learning the properties of adaptive regions with functional data analysis
Authors: Mughal Mehreen R. , Koch Hillary , Huang Jinguo , Chiaromonte Francesca , DeGiorgio Michael
Published: November 2019

Identifying regions of positive selection in genomic data remains a challenge in population genetics. Most current approaches rely on comparing values of summary statistics calculated in windows. We present an approach termed SURFDAWave, which translates measures of genetic diversity calculated in genomic windows to functional data. By transforming our discrete data points to be outputs of continuous functions defined over genomic space, we are able to learn the features of these functions that signify selection. This enables us to confidently identify complex modes of natural selection, including adaptive introgression. We are also able to predict important selection parameters that are responsible for shaping the inferred selection events. By applying our model to human population-genomic data, we recapitulate previously identified regions of selective sweeps, such as OCA2 in Europeans, and predict that its beneficial mutation reached a frequency of 0.02 before it swept 1,802 generations ago, a time when humans were relatively new to Europe. In addition, we identify BNC2 in Europeans as a target of adaptive introgression, and predict that it harbors a beneficial mutation that arose in an archaic human population that split from modern humans within the hypothesized modern human-Neanderthal divergence range.
Evaluation of host effects on ectomycorrhizal fungal community compositions in a forest landscape in northern Japan
Authors: Matsuoka Shunsuke , Sugiyama Yoriko , Tateno Ryunosuke , Imamura Shihomi , Kawaguchi Eri , Osono Takashi
Published: November 2019

Community compositions of ectomycorrhizal (ECM) fungi are similar within the same host taxa. However, careful interpretation is required to determine whether the combination of ECM fungi and plants is explained by the host preference of ECM fungi or by the influence of neighboring conspecific and/or heterospecific hosts. In the present study, we aimed to evaluate the effects of host species on the ECM community compositions in a forest landscape (~ 10 km) where monodominant forest stands of six ECM host species belonging to three families were patchily distributed. The ECM communities were identified with DNA metabarcoding. A total of 180 ECM operational taxonomic units (OTUs) were detected. The ECM community compositions were primarily structured by host species and families, regardless of the soil environments and spatial arrangements of the sampling plots. In addition, 38 ECM OTUs were detected from particular host tree species. Furthermore, the neighboring plots harbored similar fungal compositions, although the host species were different. The relative effect of the spatial factors on the ECM compositions was weaker than that of host species. Our results suggest that the host preference of ECM fungi is a primary determinant of ECM fungal compositions in the forest landscape.
Exposure to hypomethylating agent 5-aza-2’-deoxycytidine (decitabine) causes rapid, severe DNA damage, telomere elongation and mitotic dysfunction in human WIL2-NS cells
Authors: Bull Caroline , Mayrhofer Graham , Fenech Michael
Published: November 2019

Background

5-aza-2’-deoxycytidine (5azadC, decitabine) is a DNA hypomethylating agent used in the treatment of myelodysplastic syndromes. Due to cytotoxic side effects dose optimization is essential. This study defines and quantifies the effects of 5azadC on chromosomal stability and telomere length, at clinically relevant dosages.

Methods

Human WIL2-NS cells were maintained in complete medium containing 0, 0.2 or 1.0μM 5azadC for four days, and analysed daily for telomere length (flow cytometry), chromosomal stability (cytokinesis-block micronucleus cytome (CBMN-cyt) assay), and global methylation (%5me-C).

Results

DNA methylation decreased significantly in 1.0 μM 5azadC, relative to control (p<0.0001). Exposure to 1.0μM 5azadC resulted in 170% increase in telomere length (p<0.0001), in parallel with rapid increase in biomarkers of DNA damage; (micronuclei (MN, 6-fold increase), nucleoplasmic bridges (NPB, a 12-fold increase), and nuclear buds (NBud, a 13-fold increase) (all p<0.0001). Fused nuclei (FUS), indicative of mitotic dysfunction, showed a 5- and 13-fold increase in the 0.2μM and 1.0μM conditions, respectively (p = 0.001) after 4 days.

Conclusions

These data show that (i) clinically relevant concentrations of 5azadC are highly genotoxic; (ii) hypomethylation was associated with increased TL and DNA damage; and (iii) longer TL was associated with chromosomal instability. These findings suggest that lower doses of 5azdC may be effective as a hypomethylating agent, while potentially reducing DNA damage and risk for secondary disease.
Individual housing of male C57BL/6J mice after weaning impairs growth and predisposes for obesity
Authors: Schipper Lidewij , van Heijningen Steffen , Karapetsas Giorgio , van der Beek Eline M. , van Dijk Gertjan
Published: November 2019

Individual housing from weaning onwards resulted in reduced growth rate during adolescence in male C57Bl/6J mice that were housed individually, while energy intake and energy expenditure were increased compared to socially housed counterparts. At 6 weeks of age, these mice had reduced lean body mass, but significantly higher white adipose tissue mass compared to socially housed mice. Body weight gain of individually housed animals exceeded that of socially housed mice during adulthood, with elevations in both energy intake and expenditure. At 18 weeks of age, individually housed mice showed higher adiposity and higher mRNA expression of UCP-1 in inguinal white adipose tissue. Exposure to an obesogenic diet starting at 6 weeks of age further amplified body weight gain and adipose tissue deposition. This study shows that post-weaning individual housing of male mice results in impaired adolescent growth and higher susceptibility to obesity in adulthood. Mice are widely used to study obesity and cardiometabolic comorbidities. For (metabolic) research models using mice, (social) housing practices should be carefully considered and regarded as a potential confounder due to their modulating effect on metabolic health outcomes.