bluuebunny/crossref_metadata_2025 huggingface dataset:
Concordance of various chromosomal errors among different parts of the embryo and the value of re-biopsy in embryos with segmental aneuploidies
Authors: Navratil Rostislav , Horak Jakub , Hornak Miroslav , Kubicek David , Balcova Maria , Tauwinklova Gabriela , Travnik Pavel , Vesela Katerina
Published: January 2020

Chromosomal mosaicism detected during preimplantation genetic testing for aneuploidy (PGT-A) and its impact on embryo implantation have been widely discussed, and healthy live births from mosaic embryos were reported by many groups. On the other hand, only very few studies have focused on segmental chromosome aneuploidies and their clinical impact. Eighty-nine embryos with various PGT-A results (trophectoderm 1: TE1) were re-analysed using a second trophectoderm biopsy (TE2) and the rest of the embryo (RE) for testing. Of 19 euploid TE1 biopsies, 18 were concordant across TE2 and RE. Similarly, whole chromosomal aneuploidies were concordant in 59 of 62 TE1-TE2 and 58 TE1-RE. In contrast, from 31 segmental aneuploidies detected in TE1, only 15 were observed again in TE2 and 14 in RE. If a TE1 segmental abnormality appeared again in TE2, it was almost always present in RE (17/18) as well. Moreover, when a TE1 segmental abnormality was not detected in TE2, in 12 out of 13 cases RE was also unaffected. Similarly, only 1 of 26 TE1 whole chromosome mosaics were repeated in TE2 and 7 in RE. Our study confirms that euploid and whole chromosomal aneuploidy results are highly predictive of the embryo. In contrast, mosaicism has a very low concordance rate. Most importantly, re-biopsy of embryos with segmental aneuploidies demonstrated that they are mostly not uniform across the embryo. Finally, in the case of segmental aneuploidy, the second biopsy enables an accurate prediction of the real status of the embryo and could be offered to patients undergoing PGT-A.
Enhancer occlusion transcripts regulate the activity of human enhancer domains via transcriptional interference: a computational perspective
Authors: Pande Amit , Makalowski Wojciech , Brosius Jürgen , Raabe Carsten A
Published: January 2020

Analysis of ENCODE long RNA-Seq and ChIP-seq (Chromatin Immunoprecipitation Sequencing) datasets for HepG2 and HeLa cell lines uncovered 1647 and 1958 transcripts that interfere with transcription factor binding to human enhancer domains. TFBSs (Transcription Factor Binding Sites) intersected by these ‘Enhancer Occlusion Transcripts’ (EOTrs) displayed significantly lower relative transcription factor (TF) binding affinities compared to TFBSs for the same TF devoid of EOTrs. Expression of most EOTrs was regulated in a cell line specific manner; analysis for the same TFBSs across cell lines, i.e. in the absence or presence of EOTrs, yielded consistently higher relative TF/DNA-binding affinities for TFBSs devoid of EOTrs. Lower activities of EOTr-associated enhancer domains coincided with reduced occupancy levels for histone tail modifications H3K27ac and H3K9ac. Similarly, the analysis of EOTrs with allele-specific expression identified lower activities for alleles associated with EOTrs. ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag Sequencing) and 5C (Carbon Copy Chromosome Conformation Capture) uncovered that enhancer domains associated with EOTrs preferentially interacted with poised gene promoters. Analysis of EOTr regions with GRO-seq (Global run-on) data established the correlation of RNA polymerase pausing and occlusion of TF-binding. Our results implied that EOTr expression regulates human enhancer domains via transcriptional interference.
Pipeline Embolization Device Versus Stent-Assisted Coiling for Intracranial Aneurysm Treatment: A Retrospective Propensity Score-Matched Study
Authors: Salem Mohamed M , Ravindran Krishnan , Enriquez-Marulanda Alejandro , Ascanio Luis C , Jordan Noah , Gomez-Paz Santiago , Foreman Paul M , Ogilvy Christopher S , Thomas Ajith J , Moore Justin M
Published: January 2020

Background

Pipeline embolization device (PED; Medtronic) and stent-assisted coiling (SAC) are established modalities for treatment of intracranial aneurysms.

Objective

To comparatively assess the efficacy of these techniques.

Methods

We conducted a retrospective analysis of patients with aneurysms treated at our institution with either PED from 2013 to 2017 or SAC from 2009 to 2015. All large (>10 mm), ruptured, fusiform, anterior communicating artery, posterior circulation aneurysms, and patients with no available follow-up imaging were eliminated before running the propensity score matching (PSM). Patients were matched using nearest neighbor controlling for: age, gender, smoking, exact location, maximal diameter, and presence of multiple aneurysms. Total hospital costs for equipment and implants were calculated from procedure product and hospital billing records, and compared between the propensity-matched pairs.

Results

Out of 165 patients harboring 202 aneurysms; 170 (84.2%) were treated with the PED, and 32 (15.8%) were treated using SAC. PSM resulted in 23 matched pairs; with significantly longer follow up in the SAC group (mean 29.8 vs 14.1 mo; P = .0002). Complete occlusion rates were not different (82.6 vs 87%; P = .68), with no difference between the groups for modified Rankin Scale on last clinical follow-up, procedural complications or retreatment rates. Average total costs calculated from the hospital records, including equipment and implants, were not different between propensity-score matched pairs (P = .48).

Conclusion

PED placement and SAC offer equally efficacious occlusion rates, functional outcomes, procedural complication rates, and cost profiles for small unruptured anterior circulation saccular aneurysms which do not involve the anterior communicating artery.
Disparities in Shigellosis Incidence by Census Tract Poverty, Crowding, and Race/Ethnicity in the United States, FoodNet, 2004–2014
Authors: Libby Tanya , Clogher Paula , Wilson Elisha , Oosmanally Nadine , Boyle Michelle , Eikmeier Dana , Nicholson Cynthia , McGuire Suzanne , Cieslak Paul , Golwalkar Mugdha , Geissler Aimee , Vugia Duc
Published: January 2020

Background

Shigella causes an estimated 500 000 enteric illnesses in the United States annually, but the association with socioeconomic factors is unclear.

Methods

We examined possible epidemiologic associations between shigellosis and poverty using 2004–2014 Foodborne Diseases Active Surveillance Network (FoodNet) data. Shigella cases (n = 21 246) were geocoded, linked to Census tract data from the American Community Survey, and categorized into 4 poverty and 4 crowding strata. For each stratum, we calculated incidence by sex, age, race/ethnicity, and FoodNet site. Using negative binomial regression, we estimated incidence rate ratios (IRRs) comparing the highest to lowest stratum.

Results

Annual FoodNet Shigella incidence per 100 000 population was higher among children <5 years old (19.0), blacks (7.2), and Hispanics (5.6) and was associated with Census tract poverty (incidence rate ratio [IRR], 3.6; 95% confidence interval [CI], 3.5–3.8) and household crowding (IRR, 1.8; 95% CI, 1.7–1.9). The association with poverty was strongest among children and persisted regardless of sex, race/ethnicity, or geographic location. After controlling for demographic variables, the association between shigellosis and poverty remained significant (IRR, 2.3; 95% CI, 2.0–2.6).

Conclusions

In the United States, Shigella infections are epidemiologically associated with poverty, and increased incidence rates are observed among young children, blacks, and Hispanics.
High-Cost, High-Need Users of Acute Unscheduled HIV Care: A Cross-Sectional Study
Authors: Grant Conor , Bergin Colm , O’Connell Sarah , Cotter John , Ní Cheallaigh Clíona
Published: January 2020

Background

High-cost, high-need users are defined as patients who accumulate large numbers of emergency department visits and hospital admissions that might have been prevented by relatively inexpensive early interventions and primary care. This phenomenon has not been previously described in HIV-infected individuals.

Methods

We analyzed the health records of HIV-infected individuals using scheduled or unscheduled inpatient or outpatient health care in St James’s Hospital, Dublin, Ireland, from October 2014 to October 2015.

Results

Twenty-two of 2063 HIV-infected individuals had a cumulative length of stay >30 days in the study period. These individuals accrued 99 emergency department attendances and 1581 inpatient bed days, with a direct cost to the hospital of >€1 million during the study period. Eighteen of 22 had potentially preventable requirements for unscheduled care. Two of 18 had a late diagnosis of HIV. Sixteen of 18 had not been successfully engaged in outpatient HIV care and presented with consequences of advanced HIV. Fourteen of 16 of those who were not successfully engaged in care had ≥1 barrier to care (addiction, psychiatric disease, and/or homelessness).

Conclusions

A small number of HIV-infected individuals account for a high volume of acute unscheduled care. Intensive engagement in outpatient care may prevent some of this usage and ensuing costs.
Should We Sacrifice the Utilitarians First?
Authors: Smilansky Saul
Published: January 2020

It is commonly thought that morality applies universally to all human beings as moral targets, and our general moral obligations to people will not, as a rule, be affected by their views. I propose and explore a radical, alternative normative moral theory, ‘Designer Ethics’, according to which our views are pro tanto crucial determinants of how, morally, we ought to be treated. For example, since utilitarians are more sympathetic to the idea that human beings may be sacrificed for the greater good, perhaps it is permissible (or, even under certain conditions, obligatory) to give them ‘priority’ as potential victims. This odd idea has manifold drawbacks but I claim that it also has substantial advantages, that it has some affinities to more commonly accepted moral positions, and that it should be given a significant role in our ethical thinking.
Effect of a pine enhanced biochar on growth performance, carcass quality, and feeding behavior of feedlot steers1
Authors: Terry Stephanie A , Redman Abby-Ann P , Ribeiro Gabriel O , Chaves Alex V , Beauchemin Karen A , Okine Erasmus , McAllister Tim A
Published: January 2020

The objective of this study was to evaluate the effect of enhanced biochar (EB) on growth performance, carcass quality, and feeding behavior of feedlot steers fed high-forage and high-grain diets. A total of 160 crossbred steers (initial 286 ± 26 kg body weight [BW]) were blocked by BW and randomly assigned to 16 pens (10 steers per pen), 8 of which were equipped with the GrowSafe system for monitoring feeding behavior. Treatments were EB included in the diet at 0% (control), 0.5%, 1.0%, or 2.0% (dry matter [DM] basis) with four pens per treatment. The backgrounding phase (84 d) was divided into four 21-d periods, and the finishing phase (112 d) was divided into four 28-d periods, with a 28-d transition period for dietary adaptation. Pen was the experimental unit for all parameters except for feeding behavior, where steer was considered the experimental unit. Treatment was included as a fixed effect, and period was considered a repeated measure. Total weight gain and overall average daily gain (ADG) tended to decrease (P = 0.06) with 2.0% EB. There was no effect (P ≥ 0.13) of EB on dry matter intake (DMI), gain-to-feed ratio (G:F), net energy for gain, ADG, or final BW for the backgrounding or finishing phases. There was a treatment × period effect (P < 0.05) of EB on DMI, ADG, and G:F for both backgrounding and finishing phases. Hot carcass weight, dressing %, back fat, rib-eye area, and meat yield were not affected (P ≥ 0.26) by EB. Lean meat yield was increased (P = 0.03) by 2.0% EB compared to all other treatments. Compared to the control, 2.0% EB increased (P = 0.02) the number of carcasses that achieved Canada 1 grade. More (P = 0.05) carcasses from control steers were graded as Canada 3 as compared to those fed 0.5% or 2.0% EB. Quality grade and incidences of liver abscesses were not affected (P ≥ 0.44) by EB. Enhanced biochar had no effect (P ≥ 0.11) on feeding behavior during backgrounding or finishing phases. In conclusion, EB did not result in changes in growth rate, feed efficiency, or feeding behavior in feedlot cattle, but 2.0% EB increased lean carcass yield grade.
Feeling Out of Place: Internalized Age Stereotypes Are Associated With Older Employees’ Sense of Belonging and Social Motivation
Authors: Rahn Georg , Martiny Sarah E , Nikitin Jana
Published: January 2020

Older employees are not only confronted with subtle negative stereotypes about cognitive decline, but they also tend to internalize these negative stereotypes (i.e., they agree with the idea that intellectual performance declines in old age and they feel affected by this decline). Previous research has shown that internalizing negative age stereotypes has detrimental effects on work-related outcomes. Little is known about how internalized negative stereotypes shape older employees’ social emotions and social motivation. In the present research, we argue that older adults who internalize negative age stereotypes feel insecure about their belongingness in the workplace and this has negative motivational consequences. Four out of five studies and an aggregate analysis with a total of N = 1,306 older employees (age 50–76 years) supported this hypothesis. Internalized age stereotypes were negatively related to social approach motivation toward coworkers through reduced sense of belonging in the workplace and low positive affect. In addition, internalized age stereotypes were positively related to social avoidance motivation. Investigations of the causality of these relationships revealed mixed results. We discuss these findings from the perspective of socioemotional aging and the need to belong. In sum, the present research adds to knowledge on the role of internalized negative stereotypes for older employees’ social lives and, potentially, their success in the work domain.
Advancing Diabetes-Related Equity Through Diabetes Self-Management Education and Training: Existing Coverage Requirements and Considerations for Increased Participation
Authors: Carr Derek , Kappagoda Manel , Boseman Letia , Cloud Lindsay K. , Croom Brittany
Published: January 2020

America is in the grips of a diabetes epidemic. Underserved communities disproportionately bear the burden of diabetes and associated harms. Diabetes self-management education and training (DSME/T) may help address the epidemic. By empowering patients to manage their diabetes, DSME/T improves health outcomes and reduces medical expenditures. However, participation in DSME/T remains low. Insurance coverage offers 1 approach for increasing participation in DSME/T. The impact of DSME/T insurance coverage on advancing diabetes-related health equity depends on which types of insurers must cover DSME/T and the characteristics of such coverage. We conducted a legal survey of DSME/T coverage requirements for private insurers, Medicaid programs, and Medicare, finding that substantial differences exist. Although 43 states require that private insurers cover DSME/T, only 30 states require such coverage for most or all Medicaid beneficiaries. Public health professionals and decision makers may find this analysis helpful in understanding and evaluating patterns and gaps in DSME/T coverage.
State Preemption: Impacts on Advances in Tobacco Control
Authors: Kang Joann Yoon , Kenemer Brandon , Mahoney Margaret , Tynan Michael A.
Published: January 2020

Context:

Policy is an effective tool for reducing the health harms caused by tobacco use. State laws can establish baseline public health protections. Preemptive legislation at the state level, however, can prohibit localities from enacting laws that further protect their citizens from public health threats.

Approach:

Preemptive state tobacco control laws were assessed using the Centers for Disease Control and Prevention's State Tobacco Activities Tracking and Evaluation System. Based on the assessments, the Centers for Disease Control and Prevention quantified the number of states with certain types of preemptive tobacco control laws in place. In addition, 4 different case examples were presented to highlight the experiences of 4 states with respect to preemption.

Discussion:

Tracking and reporting on preemptive state tobacco control laws through the Centers for Disease Control and Prevention's State Tobacco Activities Tracking and Evaluation System provide an understanding of the number and scope of preemptive laws. Case examples from Hawaii, North Carolina, South Carolina, and Washington provide a detailed account of how preemption affects tobacco control governance at state and local levels within these 4 states.
The antibiofilm effects of docosahexaenoic acid
Authors: Brady Jonathan
Published: January 2020

The ability of bacteria to form biofilms allows for recalcitrance against conventional antibiotic therapies (Potera, 1999). Therefore, this has contributed to the prevalence of biofilm acquired infections (BAI) clinically (Percival and Kite, 2018) which has resulted in increased morbidity and mortality amongst patients, with immunocompromised patients at risk in particular (Donlan, 2002). Biofilm formation on abiotic and biotic surfaces has enabled bacteria to colonise major organs and medical devices, such as within the lungs, on implant surfaces, contact lenses, and urinary catheters (Vinh and Embil, 2005; Percival et al., 2012; Seth et al., 2012). Docosahexaenoic acid (DHA) is a poly-unsaturated fatty acid known to exhibit antibiofilm and antimicrobial effects (Sun et al., 2017; Kim et al., 2018). Our research has found that DHA possesses strong anti-biofilm effects against Klebsiella pneumoniae and Enterococcus faecalis at low mM concentrations. DHA was capable of reducing biofilm formation by both K. pneumoniae and E. faecalis by approximately 60%. It is believed that this is the first time these effects have been reported. We have also have evidence that DHA in conjunction with an antibiotic is better at reducing biofilm formation by these strains better then either alone.

To date, there is much debate into how DHA exerts these anti-biofilm effects. DHA has been reported to distort bacterial membrane’s therefore, impacting biofilm formation (Sun et al., 2017). We aim to elucidate the precise mechanism of action by utilising a number of genetic approaches alongside the dynamic flow cell system and confocal microscopy.
Understanding selection of antimicrobial resistance in biofilms through experimental evolution
Authors: Wickham Gregory , Trampari Eleftheria , Webber Mark
Published: January 2020

Background. Biofilms possess several important properties which differentiate them from free-living cells, including their response to selective pressures. This work demonstrates a link between exposure to non-therapeutic antimicrobials and selection for antibiotic resistance in experimentally evolved biofilms of Pseudomonas aeruginosa.

Methods. Biofilms of P. aeruginosa PA14 were experimentally evolved through successive subculture under periodically increasing antimicrobial stress. Beginning at 0.25-times MIC, biofilms were exposed to benzalkonium chloride, ciprofloxacin, colistin, zinc or copper sulfate. When the antimicrobial stress resulted in growth failure, the last successful passage was phenotyped. Biofilm formation was quantified via crystal violet uptake and MICs determined by broth microdilution according to EUCAST guidelines.

Results. Experimental evolution selected for mutants which produced approximately four-fold more biomass than the parenteral strain. Both ciprofloxacin and chloramphenicol readily selected for mutants able to survive >1024-times MIC. Conversely, no change in susceptibility was observed for either metal. However, despite zinc sulfate not selecting for decreased susceptibility to itself, cross-resistance to both colistin and meropenem was observed in the zinc-passaged lineages. Benzalkonium chloride did not select for a significant change in susceptibility when grown planktonically. However, when assayed as a biofilm, a 5-fold decrease in benzalkonium chloride susceptibility was observed, indicating a biofilm-specific mechanism of antimicrobial tolerance.

Conclusion. Mutants with an increased capacity to form biofilms and decreased antimicrobial susceptibility were successfully selected. Furthermore, zinc sulfate, a common feed additive, was able to select for decreased susceptibility to clinically-relevant antibiotics, lending to concerns that ubiquitous non-therapeutic antimicrobials may act as non-canonical drivers of antibiotic resistance.
Sox2 and canonical Wnt signaling interact to activate a developmental checkpoint coordinating morphogenesis with mesodermal fate acquisition
Authors: Kinney Brian A. , Row Richard H. , Tseng Yu-Jung , Weidmann Maxwell D. , Knaut Holger , Martin Benjamin L.
Published: January 2020

Animal embryogenesis requires a precise coordination between morphogenesis and cell fate specification. It is unclear if there are mechanisms that prevent uncoupling of these processes to ensure robust development. During mesoderm induction, mesodermal fate acquisition is tightly coordinated with the morphogenetic process of epithelial to mesenchymal transition (EMT). In zebrafish, cells exist transiently in a partial EMT state during mesoderm induction. Here we show that cells expressing the neural inducing transcription factor Sox2 are held in the partial EMT state, stopping them from completing the EMT and joining the mesodermal territory. This is critical for preventing ectopic neural tissue from forming. The mechanism involves specific interactions between Sox2 and the mesoderm inducing canonical Wnt signaling pathway. When Wnt signaling is inhibited in Sox2 expressing cells trapped in the partial EMT, cells are now able to exit into the mesodermal territory, but form an ectopic spinal cord instead of mesoderm. Our work identifies a critical developmental checkpoint that ensures that morphogenetic movements establishing the mesodermal germ layer are accompanied by robust mesodermal cell fate acquisition.
Immunophenotyping of HER4/YAP axis in breast cancer brain metastasis
Authors: Kalita-de Croft Priyakshi , Lim Malcolm , de Luca Xavier M , Day Bryan W , Saunus Jodi M , Lakhani Sunil R
Published: January 2020

Brain metastasis (BrM) is a devastating diagnosis for patients with breast cancer. Identification of immunophenotypical features specific to BrM is crucial for developing effective new therapeutic interventions. Yes-associated protein (YAP) mediates downstream effects of the neuregulin receptor, HER4, on breast cancer cell proliferationin vitro. HER4 is frequently over-expressed in BrM, but the relationship with YAP has not been investigated. This study examined the HER4/YAP axis in patient samples (n=41) from matched primary breast and metastatic brain tumours. Immunohistochemistry analysis revealed HER4 was highly phosphorylated in BrM compared to matched primary tumours (p=0.0022), and this was strongly associated with expression and phosphorylation of dimerization partners HER2 and HER3 (p<0.0001). When compared to a general breast cancer cohort (n=373), we found HER4 activation to be brain metastasis specific (p<0.0001). However, YAP was frequently phosphorylated in both HER4-activated primary breast tumours and brain metastases, suggesting that pro-proliferative YAP signaling is not a major consequence of HER4 activation in these tumours. These results display the complexity of expression of the HER family receptors and the downstream pathways in BrM and suggest simultaneous targeting of multiple receptors might be more advantageous.
MinION-based DNA barcoding of preserved and non-invasively collected wildlife samples
Authors: Seah Adeline , Lim Marisa C.W. , McAloose Denise , Prost Stefan , Seimon Tracie
Published: January 2020

The ability to sequence a variety of wildlife samples with portable, field-friendly equipment will have significant impacts on wildlife conservation and health applications. However, the only currently available field-friendly DNA sequencer, the MinION by Oxford Nanopore Technologies, has a high error rate compared to standard laboratory-based sequencing platforms and has not been systematically validated for DNA barcoding accuracy for preserved and non-invasively collected tissue samples.

We tested whether various wildlife sample types, field-friendly methods, and our clustering-based bioinformatics pipeline, SAIGA, can be used to generate consistent and accurate consensus sequences for species identification. Here, we systematically evaluate variation in cytochrome b sequences amplified from scat, hair, feather, fresh frozen liver, and formalin-fixed paraffin-embedded (FFPE) liver. Each sample was processed by three DNA extraction protocols.

For all sample types tested, the MinION consensus sequences matched the Sanger references with 99.29-100% sequence similarity, even for samples that were difficult to amplify, such as scat and FFPE tissue extracted with Chelex resin. Sequencing errors occurred primarily in homopolymer regions, as identified in previous MinION studies.

We demonstrate that it is possible to generate accurate DNA barcode sequences from preserved and non-invasively collected wildlife samples using portable MinION sequencing, creating more opportunities to apply portable sequencing technology for species identification.
Growth of theFucusembryo: insights into wall-mediated cell expansion through mechanics and transcriptomics
Authors: Linardić Marina , Cokus Shawn J. , Pellegrini Matteo , Braybrook Siobhan A.
Published: January 2020

Morphogenesis in walled organisms represents a highly controlled process that involves cell proliferation and expansion; cell growth is regulated through changes in the structure and mechanics of the cells’ walls. Despite taking different evolutionary paths, land plants and some brown algae exhibit developmental and morphological similarities; however, the role of the algal cell wall in morphogenesis remains heavily underexplored. Cell expansion in plants is hypothesized to involve modifications of hemicellulose linkages and pectin gelation in the cell wall. Little is known about the wall-based control of cell expansion in brown algae; however, the algal analog to pectin, alginate, exhibits different gelation depending on its biochemistry. Here we show that cell wall mechanics and alginate biochemistry are correlated with cell expansion versus proliferation in the developingFucus serratusembryo. In the elongating cells of the embryo rhizoid, we found a reduced cell wall stiffness and lower amounts of ‘stiffer’ alginate epitopes. In comparison, the early embryo thallus was shown to undergo cleavage-type cell proliferation, without expansion, and this was correlated with higher amounts of ‘stiff’ alginate epitopes and increased wall stiffness. An embryo development RNAseq dataset was generated to characterize differential gene expression during development. This data set allowed for identification of many enriched GO functions through developmental time. In addition, the transcriptome allowed for the identification of cell-wall related genes whose differential expression may underlie our observed growth phenotypes. We propose that differential gene expression of genes involved in alginate stiffness are strong candidates underlying differential wall stiffness and cell elongation in the developingFucusembryo. Our results show that wall-driven cellular expansion mechanisms in brown algae are similar to those observed in plants. In addition, our data show that cleavage-type cell proliferation exists in brown algae similar to that seen in plant and animal systems indicating a possible conserved developmental phenomenon across the branches of multicellular life.
Loss and recovery of transcriptional plasticity after long-term adaptation to global change conditions in a marine copepod
Authors: Brennan Reid S. , deMayo James A. , Dam Hans G. , Finiguerra Michael , Baumann Hannes , Pespeni Melissa H.
Published: January 2020

Adaptive evolution from standing genetic variation and physiological plasticity will fuel resilience in the geologically unprecedented warming and acidification of the earth’s oceans. For marine animals, however, we have much to learn about the mechanisms, interactions, and costs of adaptation. Here, using 20 generations of experimental evolution followed by three generations of reciprocal transplantation, we investigate the relationship between adaptation and plasticity in the marine copepod,Acartia tonsa, in future greenhouse conditions (high temperature, high CO2). We find highly parallel genetic adaptation to greenhouse conditions in genes related to stress response, gene expression regulation, actin regulation, developmental processes, and energy production. However, reciprocal transplantation showed that genetic adaptation resulted in a loss of transcriptional plasticity, reduced fecundity, and reduced population growth when greenhouse animals were returned to ambient conditions or reared in low food conditions, suggestive of genetic assimilation after 20 generations of adaptation. Despite the loss of plasticity at F21, after three successive transplant generations, greenhouse-adapted animals were able to match the ambient-adaptive transcriptional profile. Concurrent changes in allele frequencies and erosion of nucleotide diversity suggest that this recovery occurred via adaptation back to ancestral conditions. These results demonstrate the power of experimental evolution from natural populations to reveal the mechanisms, timescales of responses, consequences, and reversibility of complex, physiological adaptation. While plasticity facilitated initial survival in global change conditions, it eroded after 20 generations as populations genetically adapted, limiting resilience to new stressors and previously benign environments.
Germinal center B cells separate signals for selection and division like compact discs
Authors: Meyer-Hermann Michael
Published: January 2020

Selection of B cells in germinal center (GC) reactions is pivotal to the generation of high affinity antibodies and memory B cells. Knowledge about B cell selection is limited to individual interactions and lacks global understanding. Here, seemingly contradictory experiments are unified in a common concept by separation of signals for the frequency of fate decision from the strength of cell division, which can then be controlled independently, similar to the separation of frequency and amplitude in digital audio signals. Based on this concept of information processing, three theories of B cell selection are developed that can be distinguish by predicted experiments drawn from computer simulations. Understanding encoding of information in molecular states is critical for targeted immune interventions.
Two-photon voltage imaging of spontaneous activity from multiple neurons reveals network activity in brain tissue
Authors: Li Binglun , Chavarha Mariya , Kobayashi Yuho , Yoshinaga Satoshi , Nakajima Kazunori , Lin Michael Z. , Inoue Takafumi
Published: January 2020

Recording the electrical activity of multiple neurons simultaneously would greatly facilitate studies on the structure and function of neuronal circuits. Using fluorescent genetically encoded voltage indicators (GEVI) would be especially desirable, as it would allow cell type-selectivity, longitudinal recordings, and further optical manipulations. By expressing the GEVI ASAP3 viain uteroelectroporation and rapidly imaging neurons in densely labelled tissues via random-access multi-photon microscopy, we achieve voltage recording of multiple neurons in brain slice with single-trial single-voxel resolution. This approach enables monitoring of subthreshold membrane potential changes and action potentials from multiple locations in soma and dendrites for tens of minutes. By optically recording spontaneous electrical activities in somatosensory cortex neurons, we provide evidence for the development of intralaminar horizontal connections in layer 2/3 with greater sensitivity than calcium imaging. Single-trial optical voltage recordings using ASAP3 thus enables the investigation of network connectivity at cellular resolution.
Cannabinoid Biosynthesis using Noncanonical Cannabinoid Synthases
Authors: Go Maybelle K. , Lim Kevin Jie Han , Yew Wen Shan
Published: January 2020

We have found enzymes from the berberine-bridge enzyme (BBE) superfamily (IPR012951) that catalyze the oxidative cyclization of the monoterpene moiety in cannabigerolic acid (CBGA) to form cannabielsoic acid B (CBSA). The enzymes are from a variety of organisms and are previously uncharacterized. This is the first report that describes enzymes that did not originate from theCannabisplant that catalyze the production of cannabinoids. Out of 72 homologues chosen from the enzyme superfamily, six orthologues were shown to accept CBGA as a substrate and catalyze the biosynthesis of CBSA. The six enzymes discovered in this study are the first report of heterologous expression of BBEs that did not originate from theCannabisplant that catalyze the production of cannabinoids using CBGA as substrate. This study details a new avenue for discovering and producing natural and unnatural cannabinoids.
Inducible epithelial resistance improves survival of Sendai virus pneumonia in mice by both inactivating virus and preventing CD8+T cell-mediated immunopathology
Authors: Wali S. , Flores J. R. , Jaramillo A.M. , Goldblatt D. L. , Pantaleón García J. , Tuvim M. J. , Dickey B. F. , Evans S. E.
Published: January 2020

Viral pneumonias remain a global health threat necessitating novel strategies to prevent and treat these lower respiratory tract infections. We have reported that mice treated with a combination of inhaled Toll-like receptor (TLR) 2/6 and TLR 9 agonists (Pam2-ODN) are broadly protected against respiratory pathogens. Although a single inhalation of Pam-ODN prevents acute morbidity and chronic complications associated with viral pneumonias, the mechanisms underlying this protection remain incompletely elucidated. Here, we show in a lethal paramyxovirus model that Pam2-ODN-enhanced survival is associated with robust virus inactivation that occurs prior to internalization by lung epithelial cells. However, it was also noted that viral mortality in sham-treated mice temporally corresponded with CD8+T cell-enriched lung inflammation that peaks after the viral burden wanes. Pam2-ODN treatment also blocked this injurious inflammation, but the attenuation of lymphocytic inflammation and the reduction in virus burden were both lost when inducible reactive oxygen species generation was inhibited. Depleting CD8+T cells before or after viral challenge underscored the balanced roles of CD8+T cells in antiviral immunity and fatal immunopathology, but did not obviate the Pam2-ODN antiviral protection. These findings identify multifunctional inducible antiviral mechanisms and may reveal means to protect susceptible individuals against respiratory infections.
Intrinsically disordered domain of kinesin-3 Kif14 enables unique functional diversity
Authors: Zhernov Ilia , Diez Stefan , Braun Marcus , Lansky Zdenek
Published: January 2020

In addition to their force-generating motor domains, kinesin motor proteins feature various accessory domains enabling them to fulfil a variety of functions in the cell. Human kinesin-3, Kif14, localizes to the midbody of the mitotic spindle and is involved in the progression of cytokinesis. The specific motor properties enabling Kif14’s cellular functions, however, remain unknown. Here, we show in vitro that it is the intrinsically disordered N-terminal domain of Kif14 that enables unique functional diversity of the motor. Using single molecule TIRF microscopy we observed that the presence of the disordered domain i) increased the Kif14 run-length by an order of magnitude, rendering the motor super-processive and enabling the motor to pass through highly crowded microtubule areas shielded by cohesive layers of microtubule-associated protein tau, which blocks less processive motors ii) enabled robust, autonomous Kif14 tracking of growing microtubule tips, independent of microtubule end-binding (EB) proteins and iii) enabled Kif14 to crosslink parallel microtubules and to drive the relative sliding of antiparallel ones. We explain these features of Kif14 by the observed increased affinity of the disordered domain for GTP-like tubulin and the observed diffusible interaction of the disordered domain with the microtubule lattice. We hypothesize that the disordered domain tethers the motor domain to the microtubule forming a diffusible foothold. We suggest that the intrinsically disordered N-terminal anchoring domain of Kif14 is a regulatory hub supporting the various cellular functions of Kif14 by tuning the motor’s interaction with microtubules.
Germline genetic contribution to the immune landscape of cancer
Authors: Sayaman Rosalyn W. , Saad Mohamad , Thorsson Vésteinn , Hendrickx Wouter , Roelands Jessica , Mokrab Younes , Farshidfar Farshad , Kirchhoff Tomas , Sweis Randy F. , Bathe Oliver F. , Porta-Pardo Eduard , Campbell Michael J. , Stretch Cynthia , Hu Donglei , Huntsman Scott , Graff Rebecca E. , Syed Najeeb , Radvanyi Laszlo , Shelley Simon , Wolf Denise , Marincola Francesco M. , Ceccarelli Michele , Galon Jérôme , Ziv Elad , Bedognetti Davide
Published: January 2020

The role of germline genetics in shaping the tumor immune landscape is largely unknown. Using genotypes from >9,000 individuals in The Cancer Genome Atlas, we investigated the association of common and rare variants with 139 well-defined immune traits. Our analysis of common variants identified 10 immune traits with significant heritability estimates, and an additional 23 with suggestive heritability, including estimates of T-cell subset abundance and interferon signaling. We performed genome-wide association on the 33 heritable traits and identified 23 genome-wide significant loci associated with at least one immune trait, including SNPs in theIFIH1locus previously associated with several autoimmune diseases. We also found significant associations between immune traits and pathogenic or likely-pathogenic rare variants inBRCA1and in genes functionally linked to telomere stabilization, and Wnt/Beta-catenin signaling. We conclude that germline genetic variants significantly impact the composition and functional orientation of the tumor immune microenvironment.
CRISPR Mutants of Three Y Chromosome Genes Suggest Gradual Evolution of Fertility Functions inDrosophila melanogaster
Authors: Hafezi Yassi , Sruba Samantha R. , Tarrash Steven R. , Wolfner Mariana F. , Clark Andrew G.
Published: January 2020

Gene-poor, repeat-rich regions of the genome are poorly understood and have been understudied due to technical challenges and the misconception that they are degenerating “junk”. Yet multiple lines of evidence indicate these regions may be an important source of variation that could drive adaptation and species divergence, particularly through regulation of fertility. The ∼40 Mb Y chromosome ofDrosophila melanogastercontains only 16 known protein-coding genes and is highly repetitive and entirely heterochromatic. Most of the genes originated from duplication of autosomal genes and have reduced nonsynonymous substitution rates, suggesting functional constraint. We devised a genetic strategy for recovering and retaining stocks with sterile Y-linked mutations and combined it with CRISPR to create mutants with deletions that disrupt three Y-linked genes. Two genes,PRYandFDY, had no previously identified functions. We found thatPRYmutant males are sub-fertile, butFDYmutant males had no detectable fertility defects.FDY, the newest known gene on the Y chromosome, may have fertility effects that are conditional or too subtle to detect. The third gene,CCY, had been predicted but never formally shown to be required for male fertility. CRISPR-targeting and RNAi ofCCYcaused male sterility. Surprisingly, however, ourCCYmutants were sterile even in the presence of an extra wild-type Y chromosome, suggesting that perturbation of the Y chromosome can lead to dominant sterility. Our approach provides an important step toward understanding the complex functions of the Y chromosome and parsing which functions are accomplished by genes versus repeat elements.
Too Close to Eat? Solidarity with Animals, Animal Welfare and Meat Consumption
Authors: Boaitey Albert , Eden Michaela , Jette-Nantel Simon
Published: January 2020

Meat consumption is influenced by a variety of factors including of empathy and feelings on affinity towards farm animals. The goal of this study was to examine the role of solidarity with animals on meat consumption and attitudes towards the treatment of animals. Data was drawn from a sample of 265 respondents in the US. Correlation and mediation analyses were performed. The results of the correlation analysis indicate a moderate but positive correlation between solidarity with animals and proecological beliefs. The association between attitudes towards the treatment of farm animals and antibiotic use and solidarity with animals was also positive. Relative to meat consumption, the results indicate that proecological beliefs and concerns about the treatment of farm animals negatively influenced consumption. The effect of attitudes towards antibiotic use and solidarity with animals on consumption were however fully mediated by proecological beliefs. The results indicate that social identification with animals can play a significant role in food choice. However, its relationship with proecological beliefs implies that holistic approaches are required to address current livestock production practices that are considered unnatural.
Passive acoustic methods for tracking the 3D movements of small cetaceans around marine structures
Authors: Gillespie Douglas , Palmer Laura , Macaulay Jamie , Sparling Carol , Hastie Gordon
Published: January 2020

A wide range of anthropogenic structures exist in the marine environment with the extent of these set to increase as the global offshore renewable energy industry grows. Many of these pose acute risks to marine wildlife; for example, tidal energy generators have the potential to injure or kill seals and small cetaceans through collisions with moving turbine parts. Information on fine scale behaviour of animals close to operational turbines is required to understand the likely impact of these new technologies. There are inherent challenges associated with measuring the underwater movements of marine animals which have, so far, limited data collection. Here, we describe the development and application of a system for monitoring the three-dimensional movements of cetaceans in the immediate vicinity of a subsea structure. The system comprises twelve hydrophones and software for the detection and localisation of vocal marine mammals. We present data demonstrating the systems practical performance during a deployment on an operational tidal turbine between October 2017 and October 2019. Three-dimensional locations of cetaceans were derived from the passive acoustic data using time of arrival differences on each hydrophone. Localisation accuracy was assessed with an artificial sound source at known locations and a refined method of error estimation is presented. Calibration trials show that the system can accurately localise sounds to 2m accuracy within 20m of the turbine but that localisations become highly inaccurate at distances greater than 35m. The system is currently being used to provide data on rates of encounters between cetaceans and the turbine and to provide high resolution tracking data for animals close to the turbine. These data can be used to inform stakeholders and regulators on the likely impact of tidal turbines on cetaceans.
Arginine-vasopressin mediates counter-regulatory glucagon release and is diminished in type 1 diabetes
Authors: Kim Angela , Knudsen Jakob G. , Madara Joseph C. , Benrick Anna , Hill Thomas , Abdul Kadir Lina , Kellard Joely A. , Mellander Lisa , Miranda Caroline , Lin Haopeng , James Timothy , Suba Kinga , Spigelman Aliya F. , Wu Yanling , MacDonald Patrick E. , Wernstedt Asterholm Ingrid , Magnussen Tore , Christensen Mikkel , Visboll Tina , Salem Victoria , Knop Filip K. , Rorsman Patrik , Lowell Bradford B. , Briant Linford J.B.
Published: January 2020

Insulin-induced hypoglycemia is a major barrier to the treatment of type-1 diabetes (T1D). Accordingly, it is important that we understand the mechanisms regulating the circulating levels of glucagon – the body’s principal blood glucose-elevating hormone which is secreted from alpha-cells of the pancreatic islets. Varying glucose over the range of concentrations that occur physiologically between the fed and fuel-deprived states (from 8 to 4 mM) has no significant effect on glucagon secretion in isolated islets (in vitro) and yet associates with dramatic changes in plasma glucagonin vivo. The identity of the systemic factor(s) that stimulates glucagon secretion remains unknown. Here, we show that arginine-vasopressin (AVP), secreted from the posterior pituitary, stimulates glucagon secretion. Glucagon-secreting alpha-cells express high levels of the vasopressin 1b receptor gene (Avpr1b). Activation of AVP neuronsin vivoincreased circulating copeptin (the C-terminal segment of the AVP precursor peptide, a stable surrogate marker of AVP) and increased blood glucose; effects blocked by pharmacological antagonism of either the glucagon receptor or vasopressin 1b receptor. AVP also mediates the stimulatory effects of hypoglycemia produced by exogenous insulin and 2-deoxy-D-glucose on glucagon secretion. We show that the A1/C1 neurons of the medulla oblongata drive AVP neuron activation in response to insulin-induced hypoglycemia. Exogenous injection of AVPin vivoincreased cytoplasmic Ca2+in alpha-cells (implanted into the anterior chamber of the eye) and glucagon release. Hypoglycemia also increases circulating levels of AVP in humans and this hormone stimulates glucagon secretion from isolated human islets. In patients with T1D, hypoglycemia failed to increase both plasma copeptin and glucagon levels. These findings suggest that AVP is a physiological systemic regulator of glucagon secretion and that this mechanism becomes impaired in T1D.
Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes
Authors: Niu Yiming , Suzuki Hiroshi , Hosford Christopher J. , Walz Thomas , Chappie Joshua S.
Published: January 2020

McrBC complexes are motor-driven nucleases functioning in bacterial self-defense by cleaving foreign DNA. The GTP-specific AAA+ protein McrB powers translocation along DNA and its hydrolysis activity is stimulated by its partner nuclease McrC. Here, we report cryo-EM structures ofThermococcus gammatoleransMcrB and McrBC, andE. coliMcrBC. The McrB hexamers, containing the necessary catalytic machinery for basal GTP hydrolysis, are intrinsically asymmetric. This asymmetry directs McrC binding so that it engages a single active site, where it then uses an arginine/lysine-mediated hydrogen-bonding network to reposition the asparagine in the McrB signature motif for optimal catalytic function. While the two McrBC complexes use different DNA-binding domains, these contribute to the same general GTP-recognition mechanism employed by all G proteins. Asymmetry also induces distinct inter-subunit interactions around the ring, suggesting a coordinated and directional GTP-hydrolysis cycle. Our data provide novel insights into the conserved molecular mechanisms governing McrB family AAA+ motors.