bluuebunny/crossref_metadata_2025 huggingface dataset:
Propagation of Activated B Cells by In Vitro Severe Fever With Thrombocytopenia Syndrome Virus Infection of Human Peripheral Blood Mononuclear Cells
Authors: Wada Yuji , Miyamoto Sho , Iida Shun , Sano Kaori , Sato Yuko , Ainai Akira , Saito Kumpei , Katano Harutaka , Hasegawa Hideki , Suzuki Tadaki
Published: July 2021

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging, life-threatening tick-borne viral hemorrhagic fever caused by SFTS virus (SFTSV). Transient appearance of plasmablastic lymphocytes in the peripheral blood of SFTS cases has been reported; however, the pathological significance of this transient burst in peripheral blood plasmablastic lymphocytes is unclear. Here, we show that SFTSV infection of human peripheral blood mononuclear cells in vitro induced propagation of atypical lymphocytes. These atypical lymphocytes were activated B cells, which were induced by secretory factors other than viral particles; these factors were secreted by SFTSV-infected B cells. Activated B cells shared morphological and immunophenotypic characteristics with B cells of plasmablast lineage observed in peripheral blood and autopsy tissues of SFTS cases. This suggests that SFTSV-infected B cells secrete factors that induce B-cell differentiation to plasmablasts, which may play an important role in pathogenesis of SFTS through the SFTSV-B cell axis.
Flooding mechanism of biolithite based on progressive ion exchange model: an example of the Wangxuzhuang biolithite reservoir in the Dagang oilfield
Authors: Sun Jianmeng , Lv Xindi , Zong Jie , Ma Shuiping , Wu Yong , Huang Xiaodi , Chi Ming , Feng Xueyin , Yan Weichao
Published: July 2021

The biolithite reservoir has a strong heterogeneity and complex pore structure, and the changing trend of formation resistivity is complicated during the waterflood development process. In the logging interpretation of a water-flooded layer, mixed-formation water resistivity is a critical parameter and its accurate calculation heavily influences the evaluation of logging water saturation. The commonly used mixed liquid resistivity models have not taken into account the contribution of irreducible clay water and, thus, they are not suitable for biolithite reservoirs with high shale contents. In this paper, a new 3D digital core was constructed based on CT scanning, and a progressive ion exchange model of the mixed-formation water compatible with the biolithite reservoir put forward. Compared with experimental data from core water flooding, the progressive ion exchange model conforms to the resistivity change law of biolithite reservoirs. Through numerical simulation and analysis of the resistivity of biolithite reservoir, it is concluded that the salinity of injected water and the formation water saturation are the main factors affecting the resistivity characteristics of water-flooded layer. In terms of the interpretation of the water-flooded layer, the water saturation was calculated using the progressive ion exchange model through finite element modelling of formation resistivity. The particular mechanism of water flooding and changing law of rock electrical properties during reservoir water injection development are presented, which provide a new reliable basis for optimization of the biolithite reservoir development plan.
Vibration and horizontal directivity analysis of transmitting transducer for acoustic logging while drilling
Authors: Gou Yang , Fu Xin
Published: July 2021

Radially polarized open-cylindrical piezoelectric transducers are widely used in the field of acoustic logging while drilling (LWD). Unlike the wireline logging transducer, the structure of the acoustic LWD transducer is an open structure; in this case, its radial vibration is accompanied by apparent circumferential vibration. In this paper, based on the two-dimensional wave equations and electrostatic charge equation, according to the free boundary conditions of the transducer, the resonance frequency equation of radial-circumferential coupled vibration for the acoustic LWD transducer is obtained. The vibration modal and resonance frequency for transducers of several typical sizes are simulated using COMSOL software. The results show that when the geometrical size of the transducer satisfies certain conditions, the theoretical calculation and the numerical analysis are in good agreement and the relative error is controlled below 3%. Meanwhile, the horizontal directivity of the LWD transducer after actual installation is discussed, and it is found that adding appropriate coupling materials can improve the monopole sound field radiation. So, it is expected that this work can serve as a reference for the acoustic LWD transducer design and install.
Effect of orbital trapping by bar resonances in the local U–V velocity field
Authors: Moreno Edmundo , Fernández-Trincado José G , Schuster William J , Pérez-Villegas Angeles , Chaves-Velasquez Leonardo
Published: July 2021

The effects in the local U–V velocity field due to orbital trapping by bar resonances have been studied computing 15 resonant families in a non-axisymmetric Galactic potential, considering the bar’s angular velocity between 35 and 57.5 ${\rm \, km\, s^{-1}{kpc}^{-1}}$. Only cases in the low, 37.5, 40 ${\rm \, km\, s^{-1}{kpc}^{-1}}$, and high, 55, 57.5 ${\rm \, km\, s^{-1}{kpc}^{-1}}$, velocity ranges give trapping structures that have some similarity with observed features in the velocity distribution. The resulting structures in the local U–V plane form resonant bands appearing at various levels in velocity V. Cases with angular velocity 40 and 55 ${\rm \, km\, s^{-1}{kpc}^{-1}}$ show the greatest similarity with observed branches. Our best approximation to the local velocity field by orbital trapping is obtained with a bar angular velocity of 40 ${\rm \, km\, s^{-1}{kpc}^{-1}}$ and a bar angle of 40°. With this solution, three main observed features can be approximated: (i) the Hercules branch at V = $-50\, {\rm \, km\, s^{-1}}$ produced by the resonance 8/1 outside corotation, and the close features produced by resonances 5/1 and 6/1, (ii) the newly detected low-density arch at V ≃ 40 ${\rm \, km\, s^{-1}}$ produced approximately by the resonance 4/3, (iii) the inclined structure below the Hercules branch, also observed in the Gaia DR2 data, produced by tube orbits around Lagrange point L5 at corotation. Some predicted contributions due to orbital trapping in regions of the U–V plane corresponding to the Galactic halo are given, which could help to further restrict the value of the angular velocity of the Galactic bar. No support by orbital trapping is found for the Arcturus stream at V$\approx \, -100\, {\rm \, km\, s^{-1}}$.
GmPIN-dependent polar auxin transport is involved in soybean nodule development
Authors: Gao Zhen , Chen Zhiwei , Cui Yuanyuan , Ke Meiyu , Xu Huifang , Xu Qinzhen , Chen Jiaomei , Li Yang , Huang Laimei , Zhao Hong , Huang Dingquan , Mai Siyuan , Xu Tao , Liu Xiao , Li Shujia , Guan Yuefeng , Yang Wenqiang , Friml Jiří , Petrášek Jan , Zhang Jing , Chen Xu
Published: July 2021

To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that are fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed the impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that the establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia.
The mediating role of epigenetic clocks underlying educational inequalities in mortality: a multi-cohort study
Authors: Fiorito Giovanni , Pedron Sara , Ochoa-Rosales Carolina , McCrory Cathal , Polidoro Silvia , Zhang Yan , Dugué Pierre-Antoine , Ratliff Scott , Zhao Wei , McKay Gareth J , Costa Giuseppe , Solinas Maria Giuliana , Harris Kathleen Mullan , Tumino Rosario , Grioni Sara , Ricceri Fulvio , Panico Salvatore , Brenner Hermann , Schwettmann Lars , Waldenberger Melanie , Matias-Garcia Pamela R , Peters Annette , Hodge Allison , Giles Graham G , Schmitz Lauren L. , Levine Morgan , Smith Jennifer , Liu Yongmei , Kee Frank , Young Ian , McGuinness Bernadette , McKnight Amy Jayne , van Meurs Joyce , Voortman Trudy , Kenny Rose A ,   Lifepath consortium, Vineis Paolo , Carmeli Cristian
Published: July 2021

Educational inequalities in mortality have been observed for decades, however the underlying biological mechanisms are not well known. We assessed the mediating role of altered aging of immune cells functioning captured by DNA methylation changes in blood (known as epigenetic clocks) in educational associated all-cause mortality. Data were from eight prospective population-based cohort studies, representing 13,021 participants. We found educational inequalities in mortality were larger for men than for women, estimated by hazard differences and ratios. Epigenetic clocks explained approximately 50% of educational inequalities in mortality for men, while the proportion was small for women. Most of this mediation was explained by differential effects of unhealthy lifestyles and morbidities of the WHO risk factors for premature mortality. These results support DNA methylation-based epigenetic aging as a signature of educational inequalities in life expectancy emphasizing the need for policies to address the unequal social distribution of these WHO risk factors.
Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages
Authors: Petrone Mary E. , Rothman Jessica E. , Breban Mallery I. , Ott Isabel M. , Russell Alexis , Lasek-Nesselquist Erica , Kelly Kevin , Omerza Greg , Renzette Nicholas , Watkins Anne E. , Kalinich Chaney C. , Alpert Tara , Brito Anderson F. , Earnest Rebecca , Tikhonova Irina R. , Castaldi Christopher , Kelly John P. , Shudt Matthew , Plitnick Jonathan , Schneider Erasmus , Murphy Steven , Neal Caleb , Laszlo Eva , Altajar Ahmad , Pearson Claire , Muyombwe Anthony , Downing Randy , Razeq Jafar , Niccolai Linda , Wilson Madeline S. , Anderson Margaret L. , Wang Jianhui , Liu Chen , Hui Pei , Mane Shrikant , Taylor Bradford P. , Hanage William P. , Landry Marie L. , Peaper David R. , Bilguvar Kaya , Fauver Joseph R. , Vogels Chantal B.F. , Gardner Lauren M. , Pitzer Virginia E. , George Kirsten St. , Adams Mark D. , Grubaugh Nathan D.
Published: July 2021

Emerging SARS-CoV-2 variants have shaped the second year of the COVID-19 pandemic and the public health discourse around effective control measures. Evaluating the public health threat posed by a new variant is essential for appropriately adapting response efforts when community transmission is detected. However, this assessment requires that a true comparison can be made between the new variant and its predecessors because factors other than the virus genotype may influence spread and transmission. In this study, we develop a framework that integrates genomic surveillance data to estimate the relative effective reproduction number (Rt) of co-circulating lineages. We use Connecticut, a state in the northeastern United States in which the SARS-CoV-2 variants B.1.1.7 and B.1.526 co-circulated in early 2021, as a case study for implementing this framework. We find that the Rt of B.1.1.7 was 6-10% larger than that of B.1.526 in Connecticut in the midst of a COVID-19 vaccination campaign. To assess the generalizability of this framework, we apply it to genomic surveillance data from New York City and observe the same trend. Finally, we use discrete phylogeography to demonstrate that while both variants were introduced into Connecticut at comparable frequencies, clades that resulted from introductions of B.1.1.7 were larger than those resulting from B.1.526 introductions. Our framework, which uses open-source methods requiring minimal computational resources, may be used to monitor near real-time variant dynamics in a myriad of settings.
Machine learning of all Mycobacterium tuberculosis H37Rv RNA-seq data reveals a structured interplay between metabolism, stress response, and infection
Authors: Yoo Reo , Rychel Kevin , Poudel Saugat , Al-bulushi Tahani , Yuan Yuan , Chauhan Siddharth , Lamoureux Cameron , Palsson Bernhard O. , Sastry Anand
Published: July 2021

Mycobacterium tuberculosis is one of the most consequential human bacterial pathogens, posing a serious challenge to 21st century medicine. A key feature of its pathogenicity is its ability to adapt its transcriptional response to environmental stresses through its transcriptional regulatory network (TRN). While many studies have sought to characterize specific portions of the M. tuberculosis TRN, a systems level characterization and analysis of interactions among the controlling transcription factors remains to be achieved. Here, we applied an unsupervised machine learning method to modularize the M. tuberculosis transcriptome and describe the role of transcription factors (TFs) in the TRN. By applying Independent Component Analysis (ICA) to over 650 transcriptomic samples, we obtained 80 independently modulated gene sets known as “iModulons,” many of which correspond to known regulons. These iModulons explain 61% of the variance in the organism’s transcriptional response. We show that iModulons: 1) reveal the function of previously unknown regulons, 2) describe the transcriptional shifts that occur during environmental changes such as shifting carbon sources, oxidative stress, and virulence events, and 3) identify intrinsic clusters of transcriptional regulons that link several important metabolic systems, including lipid, cholesterol, and sulfur metabolism. This transcriptome-wide analysis of the M. tuberculosis TRN informs future research on effective ways to study and manipulate its transcriptional regulation, and presents a knowledge-enhanced database of all published high-quality RNA-seq data for this organism to date.
Behaviourally modulated hippocampal theta oscillations in the ferret persist during both locomotion and immobility
Authors: Dunn S.L.S. , Town S.M. , Bizley J.K. , Bendor D.
Published: July 2021

Theta oscillations are a hallmark of hippocampal activity across mammals and play a critical role in many hippocampal models of memory and spatial navigation. To reconcile the cross-species differences observed in the presence and properties of theta, we recorded hippocampal local field potentials in rats and ferrets during auditory and visual localisation tasks designed to vary locomotion and sensory attention. Here, we show that theta oscillations occur during locomotion in both ferrets and rats, however during periods of immobility, theta oscillations persisted in the ferret, contrasting starkly with the switch to large irregular activity (LIA) in the rat. Theta during immobility in the ferret was identified as analogous to Type 2 theta that has been observed in rodents due to its sensitivity to atropine, and was modulated by behavioural state, with the strongest theta observed during reward epochs. These results demonstrate that even under similar behavioural conditions, differences exist between species in the relationship between theta and behavioural state.
High confidence identification of intra-host single nucleotide variants for person-to-person influenza transmission tracking in congregate settings
Authors: Berry Irina Maljkovic , Treangen Todd , Fung Christian , Tai Sheldon , Pollett Simon , Hong Filbert , Li Tao , Pireku Papa , Thomanna Ashley , German Jennifer , de Mesquita P. Jacob Bueno , Rutvisuttinunt Wiriya , Panciera Michael , Lidl Grace , Frieman Matthew , Jarman Richard G , Milton Donald K ,   Prometheus@UMD Consortium
Published: July 2021

Influenza within-host viral populations are the source of all global influenza diversity and play an important role in driving the evolution and escape of the influenza virus from human immune responses, antiviral treatment, and vaccines, and have been used in precision tracking of influenza transmission chains. Next Generation Sequencing (NGS) has greatly improved our ability to study these populations, however, major challenges remain, such as accurate identification of intra-host single nucleotide variants (iSNVs) that represent within-host viral diversity of influenza virus. In order to investigate the sources and the frequency of called iSNVs in influenza samples, we used a set of longitudinal influenza patient samples collected within a University of Maryland (UMD) cohort of college students in a living learning community. Our results indicate that technical replicates aid in removal of random RT-PCR, PCR, and platform sequencing errors, while the use of clonal plasmids for removal of systematic errors is more important in samples of low RNA abundance. We show that the choice of reference for read mapping affects the frequency of called iSNVs, with the sample self-reference resulting in the lowest amount of iSNV noise. The importance of variant caller choice is also highlighted in our study, as we observe differential sensitivity of variant callers to the mapping reference choice, as well as the poor overlap of their called iSNVs. Based on this, we develop an approach for identification of highly probable iSNVs by removal of sequencing and bioinformatics algorithm-associated errors, which we implement in phylogenetic analyses of the UMD samples for a greater resolution of transmission links. In addition to identifying closely related transmission connections supported by the presence of highly confident shared iSNVs between patients, our results also indicate that the rate of minor variant turnover within a host may be a limiting factor for utilization of iSNVs to determine patient epidemiological links.
Uncontrolled CD21low age-associated and B1 B cell accumulation caused by failure of an EGR2/3 tolerance checkpoint
Authors: Masle-Farquhar Etienne , Peters Timothy J. , Miosge Lisa A. , Parish Ian A. , Weigel Christoph , Oakes Christopher C. , Reed Joanne H. , Goodnow Christopher C.
Published: July 2021

CD21low age-associated or atypical memory B cells, enriched for autoantibodies and poised for plasma cell differentiation, accumulate in large numbers in chronic infections, autoimmune disease and immunodeficiency, posing the question of what checkpoints normally oppose their excessive accumulation. Here, we reveal a critical role for the calcium-NFAT-regulated transcription factors EGR2 and EGR3. In the absence of EGR2 and EGR3 within B cells, CD21low and B1 B cells accumulate and circulate in young mice in numbers 10-20 times greater than normal, over-express a large set of EGR2 ChIP-seq target genes including known drivers of plasma cell differentiation and under-express drivers of follicular germinal centers. Most follicular B cells constitutively express Egr2 proportionally to surface IgM down-regulation by self-antigens, and EGR2/3 deficiency abolishes this characteristic anergy response. These results define a key transcriptional checkpoint repressing CD21low B cell formation and inform how NFATC1 or EGR2 mutations promote B1 cell-derived chronic lymphocytic leukemias.
Identifying components that vary in space and time from resting-state functional MRI
Authors: Scott Gregory , Leech Rob
Published: July 2021

A widespread assumption of fMRI-derived large-scale intrinsic connectivity networks (ICNs) is that they are spatially static over time. However, the assumption of spatial stationarity of ICNs has been challenged by a range of techniques that allow for time-varying connectivity between brain regions and demonstration that canonical networks like the default model network (DMN) can be fractionated according to time-varying connectivity relationships of their subcomponents. Previously, we developed a simple spatiotemporal ICA (stICA) technique to allow the discovery of patterns of spatiotemporal evolution in task fMRI data in a way that avoided the traditional constraint of spatial stationarity on brain networks, and we validated the approach in fMRI of task-to-rest transitions. Here, we apply our stICA technique to resting-state fMRI datasets to explore whether spatiotemporally evolving components of brain activity can be identified in the absence of an overt behavioural task. We found that stICA components could generally be described in terms of graded onsets and offsets of ICNs that had been calculated based on techniques that assumed spatial stationarity. Our results suggest that, to a reasonable approximation, stable ICNs can be taken to be building blocks of the spatiotemporal patterns measured with resting-state fMRI.
Using stationary vital rates in impact assessments may underestimate potential threat
Authors: Horswill C. , Miller J.A.O. , Wood M. J.
Published: July 2021

Population viability analysis (PVA) is commonly used to assess future potential risks to threatened species. These models are typically based on mean vital rates, such as survival and fecundity, with some level of environmental stochasticity. However, the vital rates of wild populations, especially those already exhibiting declining trajectories, may be nonstationary, such that the mean or variance changes over time. In this study, we examined whether including observed temporal trends in vital rates affects the predictive accuracy of PVA, as well as the projected impact associated with a hypothetical threat. To achieve this, we ran a series of simulations using Leslie matrix PVA models that included different combinations of environmental stochasticity, temporal trends in vital rates, and threat. We apply our analysis to a long-lived colonial species of seabird, the black-legged kittiwake Rissa tridactyla, that is classified as globally Vulnerable and is potentially highly sensitive to offshore renewable energy development. We found that including observed temporal trends in vital rates was (i) crucial for the accurate reconstruction of observed population dynamics and (ii) had a dramatic effect on the projected impact from the hypothetical threat. In an era when many animal and plant populations are declining due to long-term trends in their vital rates, we identify that including this demographic structure is essential for robustly evaluating potential threats using PVA models. Omitting observed temporal trends in vital rates from impact assessments is highly likely to yield unreliable results that could misinform conservation and management decision making. This result has immediate application for conducting impact assessments on protected species and populations.
Time to recover from daily caffeine intake
Authors: Lin Yu-Shiuan , Weibel Janine , Landolt Hans-Peter , Santini Francesco , Garbazza Corrado , Kistler Joshua , Rehm Sophia , Rentsch Katharina , Borgwardt Stefan , Cajochen Christian , Reichert Carolin
Published: July 2021

Caffeine elicits widespread effects in the central nervous system and is the most frequently consumed psychostimulant worldwide. First evidence indicates that, during daily intake, the elimination of caffeine may slow down and the primary metabolite, paraxanthine, may accumulate. The neural impact of such adaptions is virtually unexplored. In this report, we leveraged the data of a laboratory study with N= 20 participants and three within-subject conditions: caffeine (150 mg caffeine x 3/day x 10 days), placebo (150 mg mannitol x 3/day x 10 days), and withdrawal (caffeine x 9 days, afterwards placebo x 1 day). Using liquid chromatography–mass spectrometry coupled with tandem mass spectrometry, we determined the course of salivary caffeine and paraxanthine, measured regularly at day 10. We assessed grey matter (GM) intensity and cerebral blood flow (CBF) in the withdrawal condition as compared to their changes in caffeine in our previous report. The results indicate high remaining levels of paraxanthine and of caffeine carried overnight during daily intake, and the levels of paraxanthine remained higher than in placebo during withdrawal. After 36 h of withdrawal, the previously reported caffeine-induced GM reduction was partially mitigated, while CBF was elevated compared to placebo. Our findings unveil that conventional daily caffeine intake does not provide sufficient time to clear up psychoactive compounds and restore cerebral responses, even after 36 hours of abstinence. They also suggest investigating consequences of a paraxanthine accumulation during daily caffeine intake.
Sulfated agarans from red seaweed Gracilaria cornea induce macrophages polarization to an antitumor M1 phenotype
Authors: Teles Felipe Barros , Assef Alexia Nathália Brígido , Andrade Renato Martins , Soares Vitória Virgínia Magalhães , da Silva Alves Antônio Willame , Lima-Júnior Roberto César Pereira , Benevides Norma Maria Barros , Wilke Diego Veras
Published: July 2021

Marine seaweeds are a rich source of sulfated polysaccharides with several biological activities, including antitumor effect. Some polysaccharides are also described to activate macrophages (Mϕs) to an antitumor M1-like phenotype. Here, we evaluated the capacity of sulfated galactans (SGs) extracts obtained from three seaweed species, Gracilaria cornea (Gc-E), Gracilaria birdiae (Gb-E), and Solieria filiformis (Sf-E), to activate the Mϕs antitumor M1 phenotype. The nitric oxide production, MHCII, and CD86 (M1 markers) were evaluated to screening the bioactive SGs profile on murine Mϕs (RAW 264.7 cells). The direct SGs antiproliferative effect was tested on melanoma B16-F10 cells. In another experimental setting, B16-F10 cells were incubated with a conditioned medium obtained from Mϕs exposed to SGs. The three SGs tested induced NO release. Sf-E directly inhibited B16-F10 cells proliferation compared with the saline group, but Gc-E and Gb-E failed to inhibit cell proliferation. Notably, a conditioned medium (CM) of Mϕs incubated with Gc-E and Sf-E, but not of Gb-E, inhibited the proliferation of B16-F10 cells. Gc-E also induced TNF-α release and increase of M1 markers such as iNOS, MHCII, and CD86. Therefore, Gc-E activates Mϕs to M1 phenotype, which in turn releases a factor that inhibits B16-F10 proliferation.
Understanding hydropower impacts on Amazonian wildlife is limited by a lack of robust evidence: results from a systematic review
Authors: dos Santos Eduardo Rodrigues , Michalski Fernanda , Norris Darren
Published: July 2021

Background and Research Aims

Although hydropower provides energy to fuel economic development across Amazonia, strategies to minimize or mitigate impacts in highly biodiverse Amazonian environments remain unclear. The growing number of operational and planned hydroelectrics requires robust scientific evidence to evaluate impacts of these projects on Amazonian vertebrates. Here we investigated the existing scientific knowledge base documenting impacts of hydropower developments on vertebrates across Brazilian Amazonia.

Methods

We reviewed the scientific literature from 1945 to 2020 published in English, Spanish and Portuguese to assess the temporal and spatial patterns in publications and the types of study design adopted as well as scientific evidence presented.

Results

A total of 24 published articles documented impacts on fish (n = 20), mammals (n = 3) and freshwater turtles (n = 1). Most study designs (87.5%) lacked appropriate controls and only three studies adopted more robust Before-After-Control-Impact designs. The published evidence did not generally support causal inference with only two studies (8.3%) including appropriate controls and/or confounding variables.

Conclusion

Decades of published assessments (54.2% of which were funded by hydropower developers or their subsidiaries) do not appear to have established robust evidence of impacts of hydropower developments on Amazonian vertebrates. This lack of robust evidence could limit the development of effective minimization and mitigation actions for the diverse vertebrate groups impacted by hydroelectrics across Brazilian Amazonia.

Implications for Conservation

To avoid misleading inferences there is a need to integrate more robust study designs into impact assessments of hydropower developments in the Brazilian Amazon.
The Effect of a Fennel Extract on the STAT Signaling and Intestinal Barrier Function
Authors: Rabalais John , Kozan Philip , Lu Tina , Durali Nassim , Okamoto Kevin , Das Barun , McGeough Matthew D. , Lee Jae Beom , Barrett Kim E. , Marchelletta Ronald , Sivagnanam Mamata
Published: July 2021

Background

Foeniculum vulgare,F. vulgare, commonly known as fennel, is believed to be one of the world’s oldest medicinal herbs and has been exploited by people for centuries as a nutritional aid for digestive disorders. In many southeast Asian countries it is ingested as an after-meal snack, mukhvas, due to its breath-freshening and digestive aid properties.F. vulgareis used in some countries, such as Iran, as a complementary and alternative treatment for inflammatory bowel disease (IBD).

Methods

This study investigated the effects ofF. vulgareon the barrier function of the intestinal epithelium Signal Transducer and Activator of Transcription (STAT) pathway, which is active in inflammatory bowel disease.

To study the protective effects ofF. vulgareextractin vitro, monolayers derived from the T84 colonic cell line were challenged with interferon-gamma (IFN-γ) and monitored with and withoutF. vulgareextract. To complement ourin vitrostudies, the dextran sodium sulfate induced murine colitis model was employed to ascertain whether the protective effect ofF. vulgareextract can be recapitulatedin vivo.

Results

F. vulgareextract was shown to exert a protective effect on TEER in both T84 and murine models and showed increases in tight junction-associated mRNA in T84 cell monolayers. Both models demonstrated significant decreases in phosphorylated STAT1 (pSTAT1), indicating reduced activation of the STAT pathway. Additionally, mice treated withF. vulgareshowed significantly lower ulcer indices than control mice.

Conclusions

We conclude barrier function of the gastrointestinal tract is improved byF. vulgare, suggesting the potential utility of this agent as an alternative or adjunctive therapy in IBD.
Environmental transmission of Pseudogymnoascus destructans to hibernating little brown bats
Authors: Hicks Alan C. , Darling Scott , Flewelling Joel , von Linden Ryan , Meteyer Carol U. , Redell Dave , White J. Paul , Redell Jennifer , Smith Ryan , Blehert David , Rayman Noelle , Hoyt Joseph R. , Okoniewski Joseph C. , Langwig Kate E.
Published: July 2021

Pathogens with persistent environmental stages can have devastating effects on wildlife communities. White-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans, has caused widespread declines in bat populations of North America. In 2009, during the early stages of the WNS investigation and before molecular techniques had been developed to readily detect P. destructans in environmental samples, we initiated this study to assess whether P. destructans can persist in the hibernaculum environment in the absence of its conclusive bat host and cause infections in naive bats. We transferred little brown bats (Myotis lucifugus) from an unaffected winter colony in northwest Wisconsin to two P. destructans contaminated hibernacula in Vermont where native bats had been excluded. Infection with P. destructans was apparent on some bats within 8 weeks following the introduction of unexposed bats to these environments, and mortality from WNS was confirmed by histopathology at both sites 14 weeks following introduction. These results indicate that environmental exposure to P. destructans is sufficient to cause the infection and mortality associated with WNS in naive bats, which increases the probability of winter colony extirpation and complicates conservation efforts.
Postsynaptic plasticity of cholinergic synapses underlies the induction and expression of appetitive memories in Drosophila
Authors: Pribbenow Carlotta , Chen Yi-chun , Heim Michael-Marcel , Laber Desiree , Reubold Silas , Reynolds Eric , Balles Isabella , Grimalt Raquel Suárez , Rauch Carolin , Rösner Jörg , Lichtner Gregor , Jagannathan Sridhar R. , Alquicira Tania Fernández-d.V. , Owald David
Published: July 2021

In vertebrates, several forms of memory-relevant synaptic plasticity involve postsynaptic rearrangements of glutamate receptors. In contrast, previous work indicates that Drosophila and other invertebrates store memories using presynaptic plasticity of cholinergic synapses. Here, we provide evidence for postsynaptic plasticity at cholinergic output synapses from the Drosophila mushroom bodies (MBs). We find that the nicotinic acetylcholine receptor (nAChR) subunit α5 is required within specific MB output neurons (MBONs) for appetitive memory induction, but is dispensable for aversive memories. In addition, nAChR α2 subunits mediate memory expression and likely functions downstream of α5 and the postsynaptic scaffold protein Dlg. We show that postsynaptic plasticity traces can be induced independently of the presynapse, and that in vivo dynamics of α2 nAChR subunits are changed both in the context of associative and non-associative memory formation, underlying different plasticity rules. Therefore, regardless of neurotransmitter identity, key principles of postsynaptic plasticity support memory storage across phyla.
Amino acid and nucleotide metabolism shape the selection of trophic levels in animals
Authors: Yu Rosemary , Wang Hao , Nielsen Jens
Published: July 2021

What an animal eats determines its trophic level (TL) in the food web. The diet of high-TL animals is thought to contain more energy because it contains higher levels of lipids. This however has not been systematically examined in the context of comprehensive metabolic networks of different animals. Here, we reconstruct species-specific genome-scale metabolic models (GEMs) of 32 animals, and calculate the maximum ATP production per unit of food for each animal. Surprisingly, we find that ATP production is closely associated with metabolic flux through central carbon metabolism and amino acid metabolism, while correlation with lipid metabolism is low. Further, metabolism of specific amino acids and nucleotides underlie maximum ATP production from food. Our analyses indicate that amino acid and nucleotide metabolism, rather than lipid metabolism, are major contributors to the selection of animal trophic levels, demonstrating that species-level metabolic flux plays key roles in trophic interactions and evolution.
Effects of warming winter embryo incubation temperatures on larval cisco (Coregonus artedi) survival, growth, and critical thermal maximum
Authors: Stewart Taylor R. , Vinson Mark R. , Stockwell Jason D.
Published: July 2021

Freshwater whitefishes, Salmonidae Coregoninae, are cold stenothermic fishes of ecological and socio-economic importance in northern hemisphere lakes that are warming in response to climate change. To address the effect of warming waters on coregonine reproduction we experimentally evaluated different embryo incubation temperatures on post-hatching survival, growth, and critical thermal maximum of larval cisco (Coregonus artedi) sampled from lakes Superior and Ontario. Embryos were incubated at water temperatures of 2.0, 4.4, 6.9, and 8.9°C to simulate present and increased winter temperatures, and hatched larvae were reared in a common environment. For both populations, larval survival and critical thermal maximum were negatively related to incubation temperature, and larval growth was positively related to incubation temperature. The magnitude of change across incubation temperatures was greater in the population sampled from Lake Superior than Lake Ontario for all traits examined. The more rapid decrease in survival and critical thermal maximum across incubation temperatures for larval cisco in Lake Superior, compared to those from Lake Ontario, suggests that Lake Superior larvae may possess a more limited ability to acclimate to and cope with increasing winter water temperatures. However, the rapid increase in growth rates across incubation temperatures in Lake Superior larvae suggests they could recover better from hatching at a small length induced by warm winters, as compared to Lake Ontario larvae. Our results suggest propagation and restoration programs may want to consider integrating natural habitat preferences and maximizing phenotypic variability to ensure offspring are set up for success upon stocking.
Regulatory small RNA, Qrr2, is expressed independently of sigma factor-54 and functions autonomously inVibrio parahaemolyticusto control quorum sensing
Authors: Tague J.G. , Hong J. , Kalburge S.S. , Boyd E.F.
Published: July 2021

Bacterial cells alter gene expression in response to changes in population density in a process called quorum sensing (QS). InVibrio harveyi, LuxO, a low cell density activator of sigma factor-54 (RpoN), is required for transcription of five non-coding regulatory sRNAs, Qrr1-Qrr5, which each repress translation of the master QS regulator LuxR.Vibrio parahaemolyticus, the leading cause of bacterial seafood-borne gastroenteritis, also contains five Qrr sRNAs that control OpaR (the LuxR homolog), required for capsule polysaccharide (CPS) and biofilm production, motility, and metabolism. We show that in a ΔluxOdeletion mutant,opaRwas de-repressed and CPS and biofilm were produced. However, in a ΔrpoNmutant,opaRwas repressed, no CPS was produced, and less biofilm production was observed compared to wild type. To determine whyopaRwas repressed, expression analysis in ΔluxOshowed all fiveqrrgenes were repressed, while in ΔrpoNtheqrr2gene was significantly de-repressed. Reporter assays and mutant analysis showed Qrr2 sRNA can act autonomously to control OpaR. Bioinformatics analysis identified a sigma-70 (RpoD) -35 -10 promoter overlapping the canonical sigma-54 (RpoN) promoter in theqrr2regulatory region. Mutagenesis of the sigma-70 -10 promoter site in the ΔrpoNmutant background, resulted in repression ofqrr2.Analysis ofqrrquadruple deletion mutants, in which only a singleqrrgene is present, showed that only Qrr2 sRNA can act autonomously to regulateopaR. Mutant and expression data also demonstrated that RpoN and the global regulator Fis act additively to repressqrr2. Our data has uncovered a new mechanism ofqrrexpression and shows that Qrr2 sRNA is sufficient for OpaR regulation.

Importance

The quorum sensing non-coding sRNAs are present in allVibriospecies but vary in number and regulatory roles among species. In the Harveyi clade, all species contain fiveqrrgenes that, inV. harveyi, are additive in function to control LuxR. In the Cholerae clade, fourqrrgenes are present, and inV. choleraetheqrrgenes are redundant in function to control HapR (the LuxR homolog). Here, we show that inV. parahaemolyticus, onlyqrr2can function autonomously to control OpaR, and it is controlled by two overlapping promoters. Theqrr2sigma-70 promoter is present in all strains ofV. parahaemolyticusand in other members of the Harveyi clade suggesting a conserved mechanism of regulation.
Extracellular ribosomal RNA provides a window into taxon-specific microbial lysis
Authors: Zhong Kevin Xu , Wirth Jennifer F. , Chan Amy M. , Suttle Curtis A.
Published: July 2021

Microbes are by far the dominant biomass in the world’s oceans and drive biogeochemical cycles that are critical to life on Earth. The composition of marine microbial communities is highly dynamic spatially and temporally, with consequent effects on their functional roles. In part, these changes in composition result from viral lysis, which is taxon-specific and estimated to account for about half of marine microbial mortality. Here we determined taxon-specific cell lysis of prokaryotes in coastal seawater by sequencing extracellular and cellular ribosomal RNA (rRNA). We detected lysis in about 15% of the 16946 prokaryotic amplicon sequence variants (ASVs) identified, and lysis of up to 34% of the ASVs within a water sample. High lysis was most commonly associated with rare but typically highly productive bacteria, while relatively low lysis was more common in taxa that are often abundant, consistent with the proposed model of “kill the winner”, and the idea that less abundant taxa generally experience higher relative lysis than dominant taxa. These results provide an explanation to the long-standing conundrum of why highly productive bacteria that are readily isolated from seawater are often in very low abundance.

One Sentence Summary

Extracellular rRNA shows wide variation in cell lysis among prokaryotic taxa.
ionbot: a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identification
Authors: Degroeve Sven , Gabriels Ralf , Velghe Kevin , Bouwmeester Robbin , Tichshenko Natalia , Martens Lennart
Published: July 2021

Mass spectrometry-based proteomics generates vast amounts of signal data that require computational interpretation to obtain peptide identifications. Dozens of algorithms for this task exist, but all exploit only part of the acquired data to judge a peptide-to-spectrum match (PSM), ignoring important information such as the observed retention time and fragment ion peak intensity pattern. Moreover, only few identification algorithms allow open modification searches that can substantially increase peptide identifications.

We here therefore introduce ionbot, a novel open modification search engine that is the first to fully merge machine learning with peptide identification. This core innovation brings the ability to include a much larger range of experimental data into PSM scoring, and even to adapt this scoring to the specifics of the data itself. As a result, ionbot substantially increases PSM confidence for open searches, and even enables a further increase in peptide identification rate of up to 12% by also considering lower-ranked, co-eluting matches for a fragmentation spectrum. Moreover, the exclusive use of machine learning for scoring also means that any future improvements to predictive models for peptide behavior will also result in more sensitive and accurate peptide identification.
Gradient-mixing LEGO robots for purifying DNA origami nanostructures of multiple components by rate-zonal centrifugation
Authors: Sentosa Jason , Horne Brian , Djutanta Franky , Showkeir Dominic , Rezvani Robert , Hariadi Rizal F.
Published: July 2021

DNA origami purification is critical in emerging applications of functionalized DNA nanostructures from basic fundamental biophysics, nanorobots to therapeutics. Advances in DNA origami purification have led to the establishment of rate-zonal centrifugation (RZC) as a scalable, high-yield, and contamination-free approach to purifying DNA origami nanostructures. In RZC purification, a linear density gradient is created using viscous agents, such as glycerol and sucrose, to separate molecules based on their mass and shape during high-rpm centrifugation. However, current methods for creating density gradients are typically time-consuming because of their reliance on slow passive diffusion. Here, we built a LEGO gradient mixer to rapidly create a quasi-continuous density gradient with minimal layering of concentrations using simple rotational motion. We found that rotating two layers of different concentrations at an angle can reduce the diffusion time from a few hours to mere minutes. The instrument needed to perform the movement can be constructed from low-cost components, such as Arduino and LEGO Mindstorms pieces, and has comparable efficacy to commercial gradient mixers currently available. Our results demonstrate that the creation of a linear density gradient can be achieved with minimal labor, time, and cost with this machine. With the recent advances in DNA origami production, we anticipate our findings to further improve the viability of scaling up DNA origami purification in grams quantities. Our simple process enables automated large-scale purification of functionalized DNA origami more feasible in resource-constrained settings.
Behavioral and fMRI evidence that arousal enhances bottom-up attention and memory selectivity in young but not older adults
Authors: Gallant Sara N. , Kennedy Briana L. , Bachman Shelby L. , Huang Ringo , Lee Tae-Ho , Mather Mara
Published: July 2021

During a challenge or emotional experience, increases in arousal help us focus on the most salient or relevant details and ignore distracting stimuli. The noradrenergic system integrates signals about arousal states throughout the brain and helps coordinate this adaptive attentional selectivity. However, age-related changes in the noradrenergic system and attention networks in the brain may reduce the efficiency of arousal to modulate selective processing in older adults. In the current neuroimaging study, we examined age differences in how arousal affects bottom-up attention to category-selective stimuli differing in perceptual salience. We found a dissociation in how arousal modulates selective processing in the young and older brain. In young adults, emotionally arousing sounds enhanced selective incidental memory and brain activity in the extrastriate body area for salient versus non-salient images of bodies. Older adults showed no such advantage in selective processing under arousal. These age differences could not be attributed to changes in the arousal response or less neural distinctiveness in old age. Rather, our results suggest that, relative to young adults, older adults become less effective at focusing on salient over non-salient details during increases in emotional arousal.
Differential impact of TNFRSF co-stimulation on CD8+T cell cytokine production by feedback control of surface receptor expression
Authors: Nguyen John , Pettmann Johannes , Kruger Philipp , Dushek Omer
Published: July 2021

T cell responses towards infections and cancers are regulated by a host of co-signalling receptors that are largely grouped into the binary categories of co-stimulation and co-inhibition. The TNF receptor superfamily (TNFRSF) members 4-1BB, CD27, GITR, and OX40 are well-established co-stimulation receptors with largely shared molecular pathways raising the question of whether they also have a similar impact on quantitative T cell responses, such as the efficacy, sensitivity, and duration of T cell responses. Here, we systematically stimulated primary human CD8+T cell blasts with dose ranges of antigen and ligands for TNFRSF members to screen for their quantitative effects on cytokine production. Although both 4-1BB and CD27 increased efficacy, only 4-1BB was able to prolong the duration of cytokine production, and both had only a modest impact on antigen sensitivity. An operational model could explain these divergent quantitative phenotypes using a shared signalling mechanism based on the surface expression of 4-1BB, but not CD27, being regulated through a signalling feedback. The model predicted that CD27 co-stimulation would increase 4-1BB expression and subsequent 4-1BB co-stimulation, which we confirmed experimentally. Although GITR and OX40 produced only minor changes in cytokine production on their own, we found that like 4-1BB, CD27 could enhance GITR expression and subsequent GITR co-stimulation. Thus, feedback control of induced TNFRSF surface expression explains both synergy and differential impact on cytokine production. The work highlights that different co-stimulation receptors can have different quantitative phenotypes on the same output allowing for highly regulated control of T cell responses.