bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep-sea plastisphere: long-term colonization by plastic-associated bacterial and archaeal communities in the Southwest Atlantic Ocean
Authors: Agostini Luana , Moreira Julio Cezar Fornazier , Bendia Amanda Gonçalves , Kmit Maria Carolina Pezzo , Waters Linda Gwen , Santana Marina Ferreira Mourão , Sumida Paulo Yukio Gomes , Turra Alexander , Pellizari Vivian Helena
Published: January 2021

Marine plastic pollution is a global concern because of continuous release into the oceans over the last several decades. Although recent studies have made efforts to characterize the so-called plastisphere, or microbial community inhabiting plastic substrates, it is not clear whether the plastisphere is defined as a core community or as a random attachment of microbial cells. Likewise, little is known about the influence of the deep-sea environment on the plastisphere. In our experimental study, we evaluated the microbial colonization on polypropylene pellets and two types of plastic bags: regular high density polyethylene (HDPE) and HDPE with the oxo-biodegradable additive BDA. Gravel was used as control. Samples were deployed at three sites at 3,300 m depth in the Southwest Atlantic Ocean and left for microbial colonization for 719 days. For microbial communities analysis, DNA was extracted from the biofilm on plastic and gravel substrates, and then the 16S rRNA was sequenced through the Illumina Miseq platform. Cultivation was performed to isolate strains from the plastic and gravel substrates. Substrate type strongly influenced the microbial composition and structure, while no difference between sites was detected. Although several taxa were shared among plastics, we observed some groups specific for each plastic substrate. These communities comprised taxa previously reported from both epipelagic zones and deep-sea benthic ecosystems. The core microbiome (microbial taxa shared by all plastic substrates) was exclusively composed by low abundance taxa, with some members well-described in the plastisphere and with known plastic-degradation capabilities. Additionally, we obtained bacterial strains that have been previously reported inhabiting plastic substrates and/or degrading hydrocarbon compounds, which corroborates our metabarcoding data and suggests the presence of microbial members potentially active and involved with degradation of these plastics in the deep sea.
A Rapid and Low-Cost protocol for the detection of B.1.1.7 lineage of SARS-CoV-2 by using SYBR Green-Based RT-qPCR
Authors: Sater Fadi Abdel , Younes Mahmoud , Nassar Hassan , Nguewa Paul , Hamze Kassem
Published: January 2021

Background

The new SARS-CoV-2 variant VUI (202012/01), identified recently in the United Kingdom (UK), exhibits a higher transmissibility rate compared to other variants, and a reproductive number 0.4 higher. In the UK, scientists were able to identify the increase of this new variant through the rise of false negative results for the spike (S) target using a three-target RT-PCR assay (TaqPath kit).

Methods

To control and study the current coronavirus pandemic, it is important to develop a rapid and low-cost molecular test to identify the aforementioned variant. In this work, we designed primer sets specific to SARS-CoV-2 variant VUI (202012/01) to be used by SYBR Green-based RT-PCR. These primers were specifically designed to confirm the deletion mutations Δ69/Δ70 in the spike and the Δ106/Δ107/Δ108 in the NSP6 gene. We studied 20 samples from positive patients, 16 samples displayed an S-negative profile (negative for S target and positive for N and ORF1ab targets) and four samples with S, N and ORF1ab positive profile.

Results

Our results emphasized that all S-negative samples harbored the mutations Δ69/Δ70 and Δ106/Δ107/Δ108. This protocol could be used as a second test to confirm the diagnosis in patients who were already positive to COVID-19 but showed false negative results for S-gene.

Conclusions

This technique may allow to identify patients carrying the VUI (202012/01) variant or a closely related variant, in case of shortage in sequencing.
Objective adherence to an online FAVAS therapeutic game for treating amblyopia in children
Authors: Bocqué Catheline , Wang Jingyun , Rickmann Annekatrin , Julich-Haertel Henrike , Kaempf Uwe , Januschowski Kai
Published: January 2021

Aim

This retrospective study was to evaluate whether an updated version of attention binding digital therapeutic games based on the principle of Focal Ambient Visual Acuity Stimulation (FAVAS) would result in an improved patient adherence of patching in 4- to 12-year-old patients with amblyopia.

Methods

We analyzed pseudonymised electronically recorded data from patients treated with two different versions of attention binding digital therapeutic games in 2015 and 2020. Two groups of children treated with occlusion therapy and attention binding digital therapeutic games, divided in treatment version, were compared. Patients in Group 2015 used the old version of therapeutic games without tablet computer functionality, while Group 2020 used more attractive therapeutic games with tablet computer functionality. Objective adherence was calculated by comparing the amount of minutes using the therapeutic games as monitored in the automatized logbook versus prescribed minutes of using the games.

Results

Children in Group 2015 spent on average 2009.3±1372.1 (36 to 5472) minutes using FAVAS; children in Group 2020 spent on average 2695.5±1526.8 (37.5 to 5672) minutes using the improved therapy. Meaning, Group 2020 spent 686.2 more minutes on FAVAS than Group 2015 (t=3.87, P<0.001). Although patient adherence was very variable, it significantly improved up to 78% ± 46% in Group 2020 compared to the 57% ± 34% in Group 2015 (t=4.3, P<0.001).

Conclusion

FAVAS 2020 with an improved gamification aspect as well as tablet computer functionality increased adherence significantly compared to the earlier version FAVAS 2015, indicating that FAVAS 2020 could be an effective approach to support patching amblyopia treatment.
Diagnostic accuracy and utility of SARS-CoV-2 antigen lateral flow assays in medical admissions with possible COVID-19
Authors: Houston Hamish , Gupta-Wright Ankur , Toke-Bjolgerud Edward , Biggin-Lamming James , John Laurence
Published: January 2021

We evaluated diagnostic accuracy of the Innova SARS-CoV-2 Antigen Rapid Qualitative Test compared to SARS-CoV-2 RT-PCR from nasopharyngeal swabs in adult admissions who met the COVID-19 case definition at a busy acute hospital in the UK. We found the Innova SARS-CoV-2 Antigen Rapid Qualitative Test had a good specificity in patients with symptoms of COVID-19 presenting to hospital. The Innova LFA can be used to rapidly identify COVID-19 cases amongst hospital admissions meeting the COVID-19 case definition, allowing patients to be allocated to COVID-19 cohort areas.
Baseline functional connectivity in resting state networks associated with depression and remission status after 16 weeks of pharmacotherapy: A CAN-BIND Report
Authors: van der Wijk Gwen , Harris Jacqueline K. , Hassel Stefanie , Davis Andrew D. , Zamyadi Mojdeh , Arnott Stephen R. , Milev Roumen , Lam Raymond W. , Frey Benicio N. , Hall Geoffrey B. , Müller Daniel J. , Rotzinger Susan , Kennedy Sidney H. , Strother Stephen C. , MacQueen Glenda M. , Protzner Andrea B.
Published: January 2021

Understanding the neural underpinnings of major depressive disorder (MDD) and its treatment could improve treatment outcomes. While numerous studies have been conducted, findings are variable and large sample replications scarce. We aimed to replicate and extend altered functional connectivity findings in the default mode, salience and cognitive control networks (DMN, SN, and CCN respectively) associated with MDD and pharmacotherapy outcomes in a large, multi-site sample. Resting-state fMRI data were collected from 129 patients and 99 controls through the Canadian Biomarker Integration Network in Depression (CAN-BIND) initiative. Symptoms were assessed with the Montgomery-Åsberg Depression Rating Scale (MADRS). Connectivity was measured as correlations between four seeds (anterior and posterior DMN, SN and CCN) and all other brain voxels across participants. Partial least squares, a multivariate statistical technique, was used to compare connectivity prior to treatment between patients and controls, and between patients reaching remission early (MADRS ≤ 10 within 8 weeks), late (MADRS ≤ 10 within 16 weeks) or not at all. We replicated previous findings of altered connectivity in the DMN, SN and CCN in patients. In addition, baseline connectivity of the anterior/posterior DMN and SN seeds differentiated patients with different treatment outcomes. Weaker connectivity within the anterior DMN and between the anterior DMN and the SN and CCN characterised early remission; stronger connectivity within the SN and weaker connectivity between the SN and the DMN and CCN was related to late remission, of which the weaker SN – anterior DMN connectivity might specifically be associated with remission to dual pharmacotherapy; and connectivity strength between the posterior DMN and cingulate areas distinguished all three groups, with early remitters showing the strongest connections and non-remitters the weakest. The stability of these baseline patient differences was established in the largest single-site subsample of the data. Our replication and extension of altered connectivity within and between the DMN, SN and CCN highlighted previously reported and new differences between patients with MDD and controls, and revealed features that might predict remission prior to pharmacotherapy.

Trial registration

ClinicalTrials.gov:NCT01655706.
New-Onset IgG Autoantibodies in Hospitalized Patients with COVID-19
Authors: Chang Sarah Esther , Feng Allan , Meng Wenzhao , Apostolidis Sokratis A. , Mack Elisabeth , Artandi Maja , Barman Linda , Bennett Kate , Chakraborty Saborni , Chang Iris , Cheung Peggie , Chinthrajah Sharon , Dhingra Shaurya , Do Evan , Finck Amanda , Gaano Andrew , Geßner Reinhard , Giannini Heather M. , Gonzalez Joyce , Greib Sarah , Gündisch Margrit , Hsu Alex Ren , Kuo Alex , Manohar Monali , Mao Rong , Neeli Indira , Neubauer Andreas , Oniyide Oluwatosin , Powell Abigail Elizabeth , Puri Rajan , Renz Harald , Schapiro Jeffrey M. , Weidenbacher Payton A , Wittman Rich , Ahuja Neera , Chung Ho-Ryun , Jagannathan Pras , James Judith , Kim Peter S. , Meyer Nuala J. , Nadeau Kari , Radic Marko , Robinson William H. , Singh Upinder , Wang Taia T. , Wherry E. John , Skevaki Chrysanthi , Prak Eline T. Luning , Utz PJ
Published: January 2021

Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), is associated with a wide range of clinical manifestations, including autoimmune features and autoantibody production. We developed three different protein arrays to measure hallmark IgG autoantibodies associated with Connective Tissue Diseases (CTDs), Anti-Cytokine Antibodies (ACA), and anti-viral antibody responses in 147 hospitalized COVID-19 patients in three different centers. Autoantibodies were identified in approximately 50% of patients, but in <15% of healthy controls. When present, autoantibodies largely targeted autoantigens associated with rare disorders such as myositis, systemic sclerosis and CTD overlap syndromes. Anti-nuclear antibodies (ANA) were observed in ∼25% of patients. Patients with autoantibodies tended to demonstrate one or a few specificities whereas ACA were even more prevalent, and patients often had antibodies to multiple cytokines. Rare patients were identified with IgG antibodies against angiotensin converting enzyme-2 (ACE-2). A subset of autoantibodies and ACA developed de novo following SARS-CoV-2 infection while others were transient. Autoantibodies tracked with longitudinal development of IgG antibodies that recognized SARS-CoV-2 structural proteins such as S1, S2, M, N and a subset of non-structural proteins, but not proteins from influenza, seasonal coronaviruses or other pathogenic viruses. COVID-19 patients with one or more autoantibodies tended to have higher levels of antibodies against SARS-CoV-2 Nonstructural Protein 1 (NSP1) and Methyltransferase (ME). We conclude that SARS-CoV-2 causes development of new-onset IgG autoantibodies in a significant proportion of hospitalized COVID-19 patients and are positively correlated with immune responses to SARS-CoV-2 proteins.
Operational response simulation tool for epidemics within refugee and IDP settlements
Authors: Aylett-Bullock Joseph , Cuesta-Lazaro Carolina , Quera-Bofarull Arnau , Katta Anjali , Pham Katherine Hoffmann , Hoover Benjamin , Strobelt Hendrik , Jimenez Rebeca Moreno , Sedgewick Aidan , Evers Egmond Samir , Kennedy David , Harlass Sandra , Kahindo Maina Allen Gidraf , Hussien Ahmad , Luengo-Oroz Miguel
Published: January 2021

The spread of infectious diseases such as COVID-19 presents many challenges to healthcare systems and infrastructures across the world, exacerbating inequalities and leaving the world’s most vulnerable populations most affected. Given their density and available infrastructure, refugee and internally displaced person (IDP) settlements can be particularly susceptible to disease spread. Non-pharmaceutical public health interventions can be used to mitigate transmission, and modeling efforts can provide crucial insights on the potential effectiveness of such interventions to help inform decision making processes. In this paper we present an agent-based modeling approach to simulating the spread of disease in refugee and IDP settlements. The model, based on the JUNE open-source framework, is informed by data on geography, demographics, comorbidities, physical infrastructure and other parameters obtained from real-world observations and previous literature. Furthermore, we present a visual analytics tool which allows decision makers to distill insights by comparing the results of different simulations and scenarios. Through simulating their effects on the epidemiological development of COVID-19, we evaluate several public health interventions ranging from increasing mask wearing compliance to the reopening of learning institutions. The development and testing of this approach focuses on the Cox’s Bazar refugee settlement in Bangladesh, although our model is designed to be generalizable to other informal settings.
High current production ofShewanella oneidensiswith electrospun carbon nanofiber anodes is directly linked to biofilm formation
Authors: Erben Johannes , Wang Xinyu , Kerzenmacher Sven
Published: January 2021

1

We study the current production ofShewanella oneidensisMR-1 with electro-spun carbon fiber anode materials and analyze the effect of the anode morphology on the micro-, meso-and macroscale. The materials feature fiber diameters in the range between 108 nm and 623 nm, resulting in distinct macropore sizes and surface roughness factors. A maximum current density of (255± 71) µA cm−2was obtained with 286 nm fiber diameter material. Additionally, micro-and mesoporosity were introduced by CO2and steam activation which did not improve the current production significantly. The current production is directly linked to the biofilm dry mass under anaerobic and micro-aerobic conditions. Our findings suggest that either the surface area or the pore size related to the fiber diameter determines the attractiveness of the anodes as habitat and there-fore biofilm formation and current production. Reanalysis of previous works supports these findings.
Identifying drivers of spatio-temporal variation in survival in four blue tit populations
Authors: Bastianelli Olivier , Robert Alexandre , Doutrelant Claire , de Franceschi Christophe , Giovannini Pablo , Charmantier Anne
Published: January 2021

In a context of rapid climate change, the influence of large-scale and local climate on population demography is increasingly scrutinized, yet studies are usually focused on one population. Demographic parameters, including survival, can vary significantly across populations of a given species, depending on global or local climatic fluctuations but also on many other population-specific parameters such as breeding density, habitat naturalness, predation or parasitism. Such ecological differences between populations could lead to different paces-of-life (POL), whereby populations where individuals display higher reproductive investment and bolder behaviours would have lower survival probabilities. We use here long-term (19 to 38 years) monitoring datasets from four Mediterranean populations of blue tits (Cyanistes caeruleus) to investigate the effects of sex, age class, large-scale and local climate temporal variation and population breeding density, on adult survival, using Capture-Mark-Recapture modelling. Environment heterogeneity in these four populations (two in evergreen and two in deciduous forests) has been linked to strong multi-trait phenotypic variation, suggesting blue tits in deciduous forests display faster POL compared to their conspecifics in evergreen habitats. The present results show heterogeneity in average survival probabilities across the four populations, with, as predicted, lower survival in the ‘fast’ blue tits occupying deciduous habitats. Interestingly, the year-to-year variation in survival probabilities was synchronous among populations. This suggests that regional environmental conditions could drive survival fluctuations across populations. However, breeding densities were not correlated across populations, and we found no evidence that adult survival is correlated with either large-scale or local, climate temporal variation in these four blue tit populations. Finally, two of the focal populations displayed a linear temporal decrease in adult survival over the study period, calling for further investigation to explain this decline. Overall, this multi-site study shows that blue tit parental survival from one spring to the next can vary substantially across years, in a synchronous way across populations, yet the climate indices we used are not correlated with the temporal variation. This calls for further investigations in other potential drivers such as resource (in particular insect) abundance, predation or parasitism.
Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model
Authors: Hosoda Shion , Fukunaga Tsukasa , Hamada Michiaki
Published: January 2021

Motivation

Accumulating evidence has highlighted the importance of microbial interaction networks. Methods have been developed for estimating microbial interaction networks, of which the generalized Lotka-Volterra equation (gLVE)-based method can estimate a directed interaction network. The previous gLVE-based method for estimating microbial interaction networks did not consider time-varying interactions.

Results

In this study, we developedunsupervised learning basedmicrobialinteraction inference method usingBayesian estimation (Umibato), a method for estimating time-varying microbial interactions. The Umibato algorithm comprises Gaussian process regression (GPR) and a new Bayesian probabilistic model, the continuous-time regression hidden Markov model (CTRHMM). Growth rates are estimated by GPR, and interaction networks are estimated by CTRHMM. CTRHMM can estimate time-varying interaction networks using interaction states, which are defined as hidden variables. Umibato outperformed the existing methods on synthetic datasets. In addition, it yielded reasonable estimations in experiments on a mouse gut microbiota dataset, thus providing novel insights into the relationship between consumed diets and the gut microbiota.

Availability

The C++ and python source codes of the Umibato software are available athttps://github.com/shion-h/Umibato

Contact

shion_hosoda@asagi.waseda.jp,mhamada@waseda.jp
Statistical learning as reinforcement learning phenomena
Authors: Orpella J , Mas-Herrero E , Ripollés P , Marco-Pallarés J , de Diego-Balaguer R
Published: January 2021

Statistical learning (SL) is the ability to extract regularities from the environment. In the domain of language, this ability is fundamental in the learning of words and structural rules. In lack of reliable online measures, statistical word and rule learning have been primarily investigated using offline (post-familiarization) tests, which gives limited insights into the dynamics of SL and its neural basis. Here, we capitalize on a novel task that tracks theonlinestatistical learning of language rules combined with computational modelling to show that online SL responds to reinforcement learning principles rooted in striatal function. Specifically, we demonstrate - on two different cohorts - that a Temporal Difference model, which relies on prediction errors, accounts for participants’ online learning behavior. We then show that the trial-by-trial development of predictions through learning strongly correlates with activity in both ventral and dorsal striatum. Our results thus provide a detailed mechanistic account of language-related SL and an explanation for the oft-cited implication of the striatum in SL tasks. This work, therefore, bridges the longstanding gap between language learning and reinforcement learning phenomena.
Estimating the societal disease burden of East Coast fever among rural cattle keeping households of Namwala District, Zambia
Authors: Mwila Natasha , Mumba Chisoni , Salih Omran , Sichibalo Karen , Simulundu Edgar , Changula Katendi , Chitanga Simbarashe
Published: January 2021

The study aimed to estimate the disease burden of East Coast fever (ECF) among rural cattle keeping households of Namwala District of Zambia using Productivity Adjusted Life Years (PALYs). We modified Disability Adjusted Life Year (DALY) equations for humans to PALYs to estimate the societal burden of animal diseases. We used a structured questionnaire to collect data on parameters that feed into PALY equations. We coded and entered data from questionnaires directly into Statistical Package of Social Sciences (IBM SPSS Version 20), and entered the estimated values of PALY parameters into Mathematical Calculus Software called Integral Calculator (https://www.integral-calculator.com/). We then used the integral calculator to calculate PALY equations, which we used to estimate the societal disease burden of ECF in cattle. PALYs calculations were done in three categories; PALYs without discounting and age weighting, PALYs with only discounting, and PALYs with discounting and age weighting.

Results revealed that the years of productivity lost by a cow, bull, and ox that suffered from ECF were estimated at 15, 10, and 15 years, respectively. In the second category, the years of productivity lost by a cow, bull, and ox were seven, six, and seven years, respectively. In the final category, the years of productivity lost by a cow, bull, and ox were five years.

ECF caused a total of 517,165 PALYs in Namwala District. The quality of life reduced in years due to disability (YLD) caused by ECF per cow, bull, and ox was 0.07, 0.07, and 0.02 percent of their life expectancy, respectively. The estimated values for the years of a lifetime lost due to mortality (YLL) caused by ECF were 35, 49, and 35 percent of the life expectancy per cow, bull, and ox. These results are important for measuring outcomes of animal health problems in terms of PALYs. The findings are helpful in future projections for the future burden of any disease and can be used as a basis in policy-making and decision-making, particularly on priorities in animal health research. We recommend that a classification of animal diseases of national economic importance should consider both the societal burden and economic impact instead of the common practice of only considering the economic impact.
Multiomics single-cell analysis of human pancreatic islets reveals novel cellular states in health and type 1 diabetes
Authors: Fasolino Maria , Schwartz Gregory W. , Golson Maria L. , Wang Yue J. , Morgan Ashleigh , Liu Chengyang , Schug Jonathan , Liu Jinping , Wu Minghui , Traum Daniel , Kondo Ayano , May Catherine L. , Goldman Naomi , Wang Wenliang ,   the HPAP Consortium, Feldman Michael , Moore Jason H. , Japp Alberto S. , Betts Michael R. , Faryabi Robert B. , Naji Ali , Kaestner Klaus H. , Vahedi Golnaz
Published: January 2021

Type 1 diabetes (T1D) is an autoimmune disease of only partially defined etiology in which immune cells destroy insulin-producing beta cells. Using single-cell transcriptomics and an advanced analytical strategy to assess pancreatic islets of T1D, autoantibody-positive, and non-diabetic organ donors, we identified both canonical cell types and rare insulin-expressing cells with a hybrid mixture of endocrine and exocrine gene signatures within all donors. We further found elevated expression of MHC Class II pathway genes in exocrine ductal cells of T1D donors, which we confirmed through CyTOF, in situ imaging mass cytometry, and immunofluorescence analysis. Taken together, our multimodal analyses identify novel cell types and processes that may contribute to T1D immunopathogenesis and provide new cellular and molecular insights into human pancreas function.
Encephalitis patient derived monoclonal GABAAreceptor antibodies cause catatonia and epileptic seizures
Authors: Kreye Jakob , Wright Sukhvir K. , van Casteren Adriana , Machule Marie-Luise , Reincke S. Momsen , Nikolaus Marc , Stöffler Laura , van Hoof Scott , Sanchez-Sendin Elisa , Kornau Hans-Christian , Kaindl Angela M. , Wilson Max A. , Greenhill Stuart , Woodhall Gavin , Turko Paul , Vida Imre , Garner Craig C. , Wickel Jonathan , Geis Christian , Fukata Yuko , Fukata Masaki , Prüss Harald
Published: January 2021

Autoantibodies targeting the GABAAreceptor (GABAAR) hallmark an autoimmune encephalitis presenting with frequent seizures and psychomotor abnormalities. Their pathogenic role is still not well-defined, given the common overlap with further autoantibodies and the lack of patient derived monoclonal antibodies (mAbs). We cloned and recombinantly produced five affinity-maturated GABAAR IgG1 mAbs from cerebrospinal fluid cells, which bound to various epitopes involving α1 and γ2 receptor subunits, with variable binding strength and partial competition. mAbs selectively reduced GABAergic currents in neuronal cultures without causing receptor internalization. Cerebroventricular infusion of GABAAR mAbs and Fab fragments into rodents induced a severe phenotype with catatonia, seizures and increased mortality, reminiscent of encephalitis patients’ symptoms. Our results prove direct functional effects of autoantibodies on GABAARs and provide an animal model for GABAAR encephalitis. They further provide the scientific rationale for clinical treatments using antibody depletion and pave the way for future antibody-selective immunotherapies.
Genome-wide DNA methylation predicts environmentally-driven life history variation in a marine fish
Authors: Cayuela Hugo , Rougeux Clément , Laporte Martin , Mérot Claire , Normandeau Eric , Leitwein Maëva , Dorant Yann , Præbel Kim , Kenchington Ellen , Clément Marie , Sirois Pascal , Bernatchez Louis
Published: January 2021

The molecular mechanisms underlying intraspecific variation in life history strategies are still poorly understood, despite the importance of this question for understanding of organism’s responses to environmental variability. Theoretical work proposed that epigenetic mechanisms such as DNA methylation might regulate intraspecific variation in life history strategies, however this assumption has rarely been verified empirically in wild populations. We examined associations between genome-wide methylation changes and environmentally-driven life history variation in two lineages of a marine fish that diverged approximatively 2.5 Mya, the capelin (Mallotus villosus), from North America and Europe. In both lineages, capelin harbour two contrasted life history strategies: some are strictly semelparous, experience fast actuarial senescence, but benefit from high hatching success by spawning on demersal sites where water temperature is low and relatively stable. In contrast, others are facultative iteroparous, have slower actuarial senescence, and suffer from lower hatching success by breeding in the intertidal zone where temperature is warmer, thermohaline parameters are less stable, and egg desiccation risk is high. Performing whole genome and epigenome sequencing, we showed that these contrasted life history strategies are more likely governed by epigenetic changes than by differences in DNA sequence. While genetic differentiation between the capelin harbouring different life history strategies was negligible, we detected parallel genome-wide methylation changes across lineages. We identified 1,067 differentially methylated regions (DMRs) comprising 15,818 CpGs, with 22% of them located within 5-kb around genes comprising promotor regions. We found that all DMRs were hypermethylated in demersal-spawning individuals. This striking result suggests that lower water temperature at demersal sites leads to an overall hypermethylation of the genome determined during the epigenetic reprogramming occurring over embryonic development. Our study emphasizes that parallel epigenetics changes in lineages with divergent genetic background could have a functional role in the regulation of intraspecific life history variation.
The coral symbiontCandidatusAquarickettsia is variably abundant in threatened Caribbean acroporids and transmitted horizontally
Authors: Baker Lydia J. , Reich Hannah G. , Kitchen Sheila A. , Klinges J. Grace , Koch Hanna R. , Baums Iliana B. , Muller Erinn , Thurber Rebecca Vega
Published: January 2021

The aquatic symbiont “Candidatus Aquarickettsia rohweri” infects a diversity of non-bilaterian metazoan phyla. In the threatened coralAcropora cervicornis,Aquarickettsiaproliferates in response to increased nutrient exposure, resulting in suppressed growth and increased disease susceptibility and mortality. This study evaluated the extent, as well as the ecology and evolution ofAquarickettsiainfecting the Caribbean corals:Ac. cervicornisandAc. palmataand their hybrid (‘Ac. prolifera’). The bacterial parasiteAquarickettsiawas found in all acroporids, with host and sampling location impacting infection magnitude. Phylogenomic and genome-wide single nucleotide variant analysis foundAquarickettsiaclustering by region, not by coral taxon. Fixation analysis suggested within coral colonies,Aquarickettsiaare genetically isolated to the extent that reinfection is unlikely. Relative to other Rickettsiales,Aquarickettsiais undergoing positive selection, with Florida populations experiencing greater positive selection relative to the other Caribbean locations. This may be due toAquarickettsiaresponse to increased nutrient stress in Florida, as indicated by greaterin situreplication rates in these corals.Aquarickettsiadid not significantly codiversify with either coral animal nor algal symbiont, and qPCR analysis of gametes and juveniles from susceptible coral genotypes indicated absence in early life stages. Thus, despite being an obligate parasite,Aquarickettsiamust be horizontally transmitted via coral mucocytes, an unidentified secondary host, or a yet unexplored environmentally mediated mechanism. Importantly, the prevalence ofAquarickettsiainAc. cervicornisand high abundance in Florida populations suggests that disease mitigation efforts in the US and Caribbean should focus on preventing early infection via horizontal transmission.
RSC primes the quiescent genome for hypertranscription upon cell cycle re-entry
Authors: Cucinotta Christine E. , Dell Rachel H. , Braceros Keean C.A. , Tsukiyama Toshio
Published: January 2021

Quiescence is a reversible G0state essential for differentiation, regeneration, stem cell renewal, and immune cell activation. Necessary for long-term survival, quiescent chromatin is compact, hypoacetylated, and transcriptionally inactive. How transcription activates upon cell-cycle re-entry is undefined. Here we report robust, widespread transcription within the first minutes of quiescence exit. During quiescence, the chromatin-remodeling enzyme RSC was already bound to the genes induced upon quiescence exit. RSC depletion caused severe quiescence exit defects: a global decrease in RNA polymerase II (Pol II) loading, Pol II accumulation at transcription start sites, initiation from ectopic upstream loci, and aberrant antisense transcription. These phenomena were due to a combination of highly robust Pol II transcription and severe chromatin defects in the promoter regions and gene bodies. Together, these results uncovered multiple mechanisms by which RSC facilitates initiation and maintenance of large-scale, rapid gene expression despite a globally repressive chromatin state.
Selectivity of Protein Interactions along the Aggregation Pathway of α-Synuclein
Authors: Leitão André D. G. , Soto Paulina Rudolffi , Chappard Alexandre , Bhumkar Akshay , Hunter Dominic J. B. , Sierecki Emma , Gambin Yann
Published: January 2021

The aggregation of α-SYN follows a cascade of oligomeric, prefibrillar and fibrillar forms, culminating in the formation of Lewy Bodies (LB), the pathological hallmarks of Parkinson’s Disease in neurons. Whilst α-synuclein is a major contributor to LB, these dense accumulations of protein aggregates and tangles of fibrils contain over 70 different proteins. However, the potential for interactions between these proteins and the different aggregated species of α-SYN is largely unknown. We hypothesized that the proteins present in the Lewy Bodies are trapped or pulled into the aggregates in a hierarchical manner, by binding at specific stages of the aggregation of α-SYN.

In this study we uncover a map of interactions of a total of 65 proteins, against different species formed by α-SYN. We measured binding to monomeric α-SYN using AlphaScreen, a sensitive nano-bead assay for detection of protein-protein interactions. To access different oligomeric species, we made use of the pathological mutants of α-SYN (A30P, G51D and A53T), which form oligomeric species with distinct properties. Finally, we used bacterially expressed recombinant α-SYN to generate amyloid fibrils and measure interactions with a pool of GFP-tagged potential partners. Binding to oligomers and fibrils was measured by two-color coincidence detection (TCCD) on a single molecule spectroscopy setup. Overall, we demonstrate that LB components are selectively recruited to specific steps in the formation of the LB, explaining their presence in the inclusions. Only a few proteins were found to interact with α-SYN monomers at detectable levels, and only a subset recognizes the oligomeric α-SYN including autophagosomal proteins. We therefore propose a new model for the formation of Lewy Bodies, where selectivity of protein partners at different steps drives the arrangement of these structures, uncovering new ways to modulate aggregation.

Significance Statement

The molecular complexity of the Lewy Bodies has been a major hindrance to a bottom-up reconstruction of these inclusions, protein by protein. This work presents an extensive dataset of protein-protein interactions, showing that despite its small size and absence of structure, α-SYN binds to specific partners in the LB, and that there is a clear selectivity of interactions between the different α-SYN species along the self-assembly pathway. We use single-molecule methods to deconvolute number and size of the co-aggregates, to gain detailed information about the mechanisms of interaction. These observations constitute the basis for the elaboration of a global interactome of α-SYN.
Extension of Hall symbols of crystallographic space groups to magnetic space groups
Authors: González-Platas Javier , Katcho Nebil A. , Rodríguez-Carvajal Juan
Published: January 2021

The Hall symbols for describing unambiguously the generators of space groups have been extended to describe any setting of the 1651 types of magnetic space groups (Shubnikov groups). A computer program called MHall has been developed for parsing the Hall symbols, generating the full list of symmetry operators and identifying the transformation to the standard setting.
crystIT: complexity and configurational entropy of crystal structures via information theory
Authors: Kaußler Clemens , Kieslich Gregor
Published: January 2021

The information content of a crystal structure as conceived by information theory has recently proved an intriguing approach to calculate the complexity of a crystal structure within a consistent concept. Given the relatively young nature of the field, theory development is still at the core of ongoing research efforts. This work provides an update to the current theory, enabling the complexity analysis of crystal structures with partial occupancies as frequently found in disordered systems. To encourage wider application and further theory development, the updated formulas are incorporated into crystIT (crystal structure and information theory), an open-source Python-based program that allows for calculating various complexity measures of crystal structures based on a standardized *.cif file.
Synthesis and structure of (E)-N-(4-methoxyphenyl)-2-[4-(3-oxo-3-phenylprop-1-en-1-yl)phenoxy]acetamide
Authors: Nguyen Tien Cong , Vu Quoc Trung , Nguyen Dang Dat , Le Duc Giang , Van Meervelt Luc
Published: January 2021

The title compound N-(4-methoxyphenyl)-2-[4-(3-oxo-3-phenylprop-1-en-1-yl)phenoxy]acetamide, C24H21NO4, was prepared from reaction of N-(4-methoxyphenyl)-2-chloroacetamide and (E)-3-(4-hydroxyphenyl)-1-phenylprop-2-en-1-one, which was obtained from the reaction of 4-hydroxybenzaldehyde and acetophenone. The structure of the title compound was determined by IR, 1H-NMR, 13C-NMR and HR–MS spectroscopic data and further characterized by single-crystal X-ray diffraction. The asymmetric unit contains four molecules, each displaying an E-configuration of the C=C bond. The dihedral angle between the phenyl rings in each molecule varies between 14.9 (2) and 45.8 (2)°. In the crystal, C—H...O hydrogen-bonding interactions link the molecules into chains running along the [001] direction. In addition, C—H...π interactions further stabilize the crystal packing. A Hirshfeld analysis indicates that the most important contributions to the surface contacts are from H...H (43.6%), C...H/H...C (32.1%) and O...H/H...O (18.1%) interactions.
{4,4′-Dibromo-2,2′-[cyclohexane-1,2-diylbis(nitrilomethanylylidene)]diphenolato-κ4
O,N,N′,O′}nickel(II)
Authors: Ha Kwang
Published: January 2021

In the title compound, [Ni(C20H18Br2N2O2)], the NiII ion is four-coordinated in a slightly distorted square-planar coordination geometry defined by two N atoms and two O atoms of the tetradentate dianionic 4,4′-dibromo-2,2′-[cyclohexane-1,2-diylbis(nitrilomethanylylidene)]diphenolato ligand. Pairs of complex molecules are assembled by intermolecular C—H...O hydrogen bonds with d(C...O) = 3.247 (4) Å.
Synchronization of seasonal acclimatization and short‐term heat hardening improves physiological resilience in a changing climate
Authors: Zhang Wen‐yi , Storey Kenneth B. , Dong Yun‐wei
Published: January 2021

Animal survival and species distribution in the face of global warming and increasing occurrences of heatwave largely depend on how heat tolerance shifts with plastic responses at different spatiotemporal scales, including long‐term acclimation/acclimatization and short‐term heat hardening. However, knowledge about the interaction of these plastic responses is still unclear.

To understand how plastic responses at different time‐scales work together to adjust heat tolerance of organisms, we examined the effect of heat hardening on the upper thermal limits of an intertidal mudflat bivalve, the razor clam Sinonovacula constricta, for different seasons using heart rate as a proxy.

We observed a stronger heat hardening response of S. constricta in warm seasons, implying that heat hardening worked synchronously with seasonal acclimatization to increase resistance of the clams to high temperatures in warm seasons. In warm seasons, heat hardening increased heat tolerance by 2–4°C and showed a 24‐hr temporal dependence, suggesting an adaptation to the diel fluctuation of thermal regimes in summer.

Furthermore, thermal stress resembling seasonal maximum environmental temperature induced stronger heat hardening effects, indicating that heat hardening is an essential plastic response to extreme hot weather, complementing seasonal acclimatization.

Our results suggest that high temperature risk can be alleviated jointly by seasonal acclimatization and heat hardening, and emphasize the importance of considering physiological plasticity on both long‐term and short‐term temporal scales in evaluating and forecasting vulnerability of organisms to climate change.

A free Plain Language Summary can be found within the Supporting Information of this article.
Functional diversity and trait composition of vascular plant and Sphagnum moss communities during peatland succession across land uplift regions
Authors: Laine Anna M. , Lindholm Tapio , Nilsson Mats , Kutznetsov Oleg , Jassey Vincent E. J. , Tuittila Eeva‐Stiina
Published: January 2021

Most of the carbon accumulated into peatlands is derived from Sphagnum mosses. During peatland development, the relative share of vascular plants and Sphagnum mosses in the plant community changes, which impacts ecosystem functions. Little is known on the successional development of functional plant traits or functional diversity in peatlands, although this could be a key for understanding the mechanisms behind peatland resistance to climate change. Here we aim to assess how functionality of successive plant communities change along the autogenic peatland development and the associated environmental gradients, namely peat thickness and pH, and to determine whether trait trade‐offs during peatland succession are analogous between vascular plant and moss communities.

We collected plant community and trait data on successional peatland gradients from post‐glacial rebound areas in coastal Finland, Sweden and Russia, altogether from 47 peatlands. This allowed us to analyse the changes in community‐weighted mean trait values and functional diversity (diversity of traits) during peatland development.

Our results show comparative trait trade‐offs from acquisitive species to conservative species in both vascular plant and Sphagnum moss communities during peatland development. However, mosses had higher resistance to environmental change than vascular plant communities. This was seen in the larger proportion of intraspecific trait variation than species turnover in moss traits, while the proportions were opposite for vascular plants. Similarly, the functional diversity of Sphagnum communities increased during the peatland development, while the opposite occurred for vascular plants. Most of the measured traits showed a phylogenetic signal. More so, the species common to old successional stages, namely Ericacae and Sphagna from subgroup Acutifolia were detected as most similar to their phylogenetic neighbours.

Synthesis. During peatland development, vegetation succession leads to the dominance of conservative plant species accustomed to high stress. At the same time, the autogenic succession and ecological engineering of Sphagna leads to higher functional diversity and intraspecific variability, which together indicate higher resistance towards environmental perturbations.
Overyielding in young tree communities does not support the stress‐gradient hypothesis and is favoured by functional diversity and higher water availability
Authors: Belluau Michaël , Vitali Valentina , Parker William C. , Paquette Alain , Messier Christian
Published: January 2021

Biodiversity effects on productivity and other ecosystem functions are strongly dependent on climate and resource availability. Based on the stress‐gradient hypothesis, under conditions of greater abiotic stress, diversity effects on plant performance are intensified due to the increased relative importance of positive plant interactions. However, whether this hypothesis is consistently applicable in forest systems remains unclear. A field trial was established to test the stress‐gradient hypothesis and examine diversity effects on above‐ground biomass production of young trees in mixtures exposed to different water availability.

Six native tree species of northern temperate forests (Acer saccharum, Betula papyrifera, Larix laricina, Picea glauca, Pinus strobus and Quercus rubra) were planted as monocultures and as mixtures of two, four and six species. For five growing seasons, four replicates of each community were exposed to conditions of either low‐ or high‐water availability created by rainfall exclusion and weekly irrigation, respectively. Growth‐years 4 and 5 were significantly different when the climatic water balance of the growing seasons was compared. We tested the effects of functional diversity on: (a) total growth of mixtures under low‐ and high‐water availability, and (b) annual growth in years 4 (higher water availability, 2017) and 5 (lower water availability, 2018).

Annual growth of most species in both years was greater under high‐ versus low‐water availability. Functional diversity had a significant positive effect on total biomass production and annual growth, and this effect was more strongly expressed under high‐water availability. Functional diversity effects on annual growth did not differ between years 4 and 5 regardless of their climatic water balance. Functional and species identity were key to understanding productivity responses to mixture and treatment effects.

Synthesis. Contrary to the stress‐gradient hypothesis, the positive effects of functional diversity on productivity were enhanced by high‐water availability and were independent of seasonal water balance.
Dynamic feedbacks among tree functional traits, termite populations and deadwood turnover
Authors: Guo Chao , Tuo Bin , Ci Hang , Yan En‐Rong , Cornelissen Johannes H. C.
Published: January 2021

Changes in the composition of plant functional traits may affect ecosystem processes through influencing trophic interactions. Bottom‐up control by plant species through food availability to animals may vary with time. However, such dynamics and their consequences for deadwood turnover are poorly known for detrital food webs.

We introduce a dynamic conceptual model of the feedback of tree functional traits, (deadwood‐feeding) termite populations and deadwood decomposition. We hypothesized that tree functional diversity (in terms of a wood resource economic spectrum [WES]) supports the sustenance of termite populations via complementary food supplied through time, as deadwood varies in traits both initially across species and because of different decomposition rates. Simultaneously, driven by this temporal dynamics of food quality, the consumption of deadwood by termites should hypothetically sustain deadwood turnover in a functionally diverse forest over time.

We tested our hypothesis through an 18‐month termite‐exclusion decomposition experiment by incubating coarse (i.e. 5 cm diameter) deadwood of 34 woody species in two subtropical forests in East China. One site still sustained a healthy population of pangolins as the keystone termite predator, whereas another had lost its pangolins due to hunting and illegal wildlife trade.

The results supported our hypothesis: in the first 12 months, termites amplified the positive linear relationship between % wood mass loss and initial wood quality (WES). In contrast, between 12 and 18 months, termite‐mediated consumption, and associated wood mass loss, showed a humpback relation with the initial WES. This shift in termite preference of deadwood species along the WES reflects complementary food availability to termites through time.

Synthesis. Our findings imply that tree functional composition, with variation in deadwood quality through decomposition time, can help to sustain termite populations and thereby forest carbon turnover. Future studies need to test whether and how our conceptual model may apply to other detrital systems and food webs. In general, food web research would benefit from a stronger focus on temporal patterns for better understanding the interactions of basal resource functional traits and consumers on ecosystem functions.