bluuebunny/crossref_metadata_2025 huggingface dataset:
Employing NaChBac for cryo-EM analysis of toxin action on voltage-gated Na+channels in nanodisc
Authors: Gao Shuai , Valinsky William C , On Nguyen Cam , Houlihan Patrick R , Qu Qian , Liu Lei , Pan Xiaojing , Clapham David E. , Yan Nieng
Published: April 2020

NaChBac, the first bacterial voltage-gated Na+(Nav) channel to be characterized, has been the prokaryotic prototype for studying the structure-function relationship of Navchannels. Discovered nearly two decades ago, the structure of NaChBac has not been determined. Here we present the cryo-EM analysis of NaChBac in both detergent micelles and nanodiscs. Under both conditions, the conformation of NaChBac is nearly identical to that of the potentially inactivated NavAb. Determining the structure of NaChBac in nanodiscs enabled us to examine gating modifier toxins (GMTs) of Navchannels in lipid bilayers. To study GMTs in mammalian Navs, we generated a chimera in which the extracellular fragment of the S3 and S4 segments in the second voltage-sensing domain from Nav1.7 replaces the corresponding sequence in NaChBac. Cryo-EM structures of the nanodisc-embedded chimera alone and in complex with HuwenToxin IV (HWTX-IV) were determined to 3.5 Å and 3.2 Å resolutions, respectively. Compared to the structure of HWTX-IV-bound human Nav1.7, which was obtained at an overall resolution of 3.2 Å, the local resolution of the toxin has been improved from ~ 6 Å to ~ 4 Å. This resolution enabled visualization of toxin docking. NaChBac can thus serve as a convenient surrogate for structural studies of the interactions between GMTs and Navchannels in a membrane environment.
Responses to Visual Speech in Human Posterior Superior Temporal Gyrus Examined with iEEG Deconvolution
Authors: Metzger Brian A. , Magnotti John F. , Wang Zhengjia , Nesbitt Elizabeth , Karas Patrick J. , Yoshor Daniel , Beauchamp Michael S.
Published: April 2020

Experimentalists studying multisensory integration compare neural responses to multisensory stimuli with responses to the component modalities presented in isolation. This procedure is problematic for multisensory speech perception since audiovisual speech and auditory-only speech are easily intelligible but visual-only speech is not. To overcome this confound, we developed intracranial encephalography (iEEG) deconvolution. Individual stimuli always contained both auditory and visual speech but jittering the onset asynchrony between modalities allowed for the time course of the unisensory responses and the interaction between them to be independently estimated. We applied this procedure to electrodes implanted in human epilepsy patients (both male and female) over the posterior superior temporal gyrus (pSTG), a brain area known to be important for speech perception. iEEG deconvolution revealed sustained, positive responses to visual-only speech and larger, phasic responses to auditory-only speech. Confirming results from scalp EEG, responses to audiovisual speech were weaker than responses to auditory- only speech, demonstrating a subadditive multisensory neural computation. Leveraging the spatial resolution of iEEG, we extended these results to show that subadditivity is most pronounced in more posterior aspects of the pSTG. Across electrodes, subadditivity correlated with visual responsiveness, supporting a model in visual speech enhances the efficiency of auditory speech processing in pSTG. The ability to separate neural processes may make iEEG deconvolution useful for studying a variety of complex cognitive and perceptual tasks.

Significance statement

Understanding speech is one of the most important human abilities. Speech perception uses information from both the auditory and visual modalities. It has been difficult to study neural responses to visual speech because visual-only speech is difficult or impossible to comprehend, unlike auditory-only and audiovisual speech. We used intracranial encephalography (iEEG) deconvolution to overcome this obstacle. We found that visual speech evokes a positive response in the human posterior superior temporal gyrus, enhancing the efficiency of auditory speech processing.
Fungi of the Fortuna Forest Reserve: Taxonomy and ecology with emphasis on ectomycorrhizal communities
Authors: Corrales Adriana , Ovrebo Clark L.
Published: April 2020

Panamanian montane forests harbor a high diversity of fungi, particularly of ectomycorrhizal (ECM) fungi, however their taxonomy and diversity patterns remain for the most part unexplored. Here we present state of the art fungal taxonomy and diversity patterns at Fortuna Forest Reserve based on morphological and molecular identification of over 1,000 fruiting body collections of macromycetes made over a period of five years. We compare these new results with previously published work based on environmental sampling ofOreomunnea mexicanaroot tips. We compiled a preliminary list of species and report 22 new genera and 29 new fungal species for Panama. Based on fruiting body collection data we compare the species composition of ECM fungal communities associated withOreomunneastands across sites differing in soil fertility and amount of rainfall. We also examine the effect of a long-term nitrogen addition treatment on the fruiting body production of ECM fungi. Finally, we discuss the biogeographic importance of Panama collections which fill in the knowledge gap of ECM fungal records between Costa Rica and Colombia. Given that the isthmus of Panama was an important migration route of ECM tree and fungal species from northern temperate areas to South America, the ECM fungal communities of Panama might show a high degree of isolation and therefore a high level of endemism. We expect that the forests at Fortuna will continue to yield new ECM macromycete data as we continue to study the collected specimens and describe new species.
Optimal sampling design for spatial capture-recapture
Authors: Dupont Gates , Royle J. Andrew , Nawaz Muhammad Ali , Sutherland Chris
Published: April 2020

Spatial capture-recapture (SCR) has emerged as the industry standard for estimating population density by leveraging information from spatial locations of repeat encounters of individuals. The precision of density estimates depends fundamentally on the number and spatial configuration of traps. Despite this knowledge, existing sampling design recommendations are heuristic and their performance remains untested for most practical applications. To address this issue, we propose a genetic algorithm that minimizes any sensible, criteria-based objective function to produce near-optimal sampling designs. To motivate the idea of optimality, we compare the performance of designs optimized using three model-based criteria related to the probability of capture. We use simulation to show that these designs out-perform those based on existing recommendations in terms of bias, precision, and accuracy in the estimation of population size. Our approach allows conservation practitioners and researchers to generate customized and improved sampling designs for wildlife monitoring.
First evidence of virus-like particles in the bacterial symbionts of Bryozoa
Authors: Vishnyakov A.E. , Karagodina N.P. , Lim-Fong G. , Ivanov P.A. , Schwaha T.F. , Letarov A.V. , Ostrovsky A.N.
Published: April 2020

Bacteriophage communities associated with humans and vertebrate animals have been extensively studied, but the data on phages living in invertebrates remain scarce. In fact, they have never been reported for most animal phyla. Our ultrastructural study showed for the first time a variety of virus-like particles (VLPs) and supposed virus-related structures inside symbiotic bacteria in two marine species from the phylum Bryozoa, the cheilostomesBugula neritinaandParalicornia sinuosa. We also documented the effect of VLPs on bacterial hosts: we explain different bacterial ‘ultrastructural types’ detected in bryozoan tissues as stages in the gradual destruction of prokaryotic cells caused by viral multiplication during the lytic cycle. We speculate that viruses destroying bacteria regulate symbiont numbers in the bryozoan hosts, a phenomenon known in some insects. We develop two hypotheses explaining exo- and endogenous circulation of the viruses during the life-cycle ofB. neritina. Finally, we compare unusual ‘sea-urchin’-like structures found in the collapsed bacteria inP. sinuosawith so-called metamorphosis associated complexes (MACs) known to trigger larval metamorphosis in a polychaete worm.

Importance

Complex symbiotic systems, including metazoan hosts, their bacterial symbionts and bacteriophages are widely studied using vertebrate models whereas much less is known about invertebrates. Our ultrastructural research revealed replication of the viruses and/or activation of virus related elements in the bacterial symbionts inhabiting tissues of the marine colonial invertebrates (phylum Bryozoa). The virus activity in the bacterial cells that are believed to be transmitted exclusively vertically is of a special importance. In addition, in the bacterial symbionts of one of the bryozoan hosts we observed the massive replication of the structures seemingly related to the Metamorphosis associated complexes (MAC). To our knowledge, MACs were never reported in the animal prokaryotic symbionts. Our findings indicate that Bryozoa may be new suitable model to study the role of bacteriophages and phage-related structures in the complex symbiotic systems hosted by marine invertebrates.
Transplantation of Muscle Stem Cell Mitochondria Rejuvenates the Bioenergetic Function of Dystrophic Muscle
Authors: Mohiuddin Mahir , Choi Jeongmoon J. , Lee Nan Hee , Jeong Hyeonsoo , Anderson Shannon E. , Han Woojin M. , Aliya Berna , Peykova Tsvetomira Z. , Verma Sumit , García Andrés J. , Aguilar Carlos A. , Jang Young C.
Published: April 2020

Mitochondrial dysfunction has been implicated in various pathologies, including muscular dystrophies. During muscle regeneration, resident stem cells, also known as muscle satellite cells (MuSCs), undergo myogenic differentiation to formde novomyofibers or fuse to existing syncytia. Leveraging this cell-cell fusion process, we postulated that mitochondria stemming from MuSCs could be transferred to myofibers during muscle regeneration to remodel the mitochondrial network and restore bioenergetic function. Here, we report that dystrophic MuSCs manifest significant mitochondrial dysfunction and fuse with existing dystrophic myofibers to propagate mitochondrial dysfunction during muscle repair. We demonstrate that by transplanting healthy donor MuSCs into dystrophic host muscle, the mitochondrial network (reticulum) and bioenergetic function can be rejuvenated. Conversely, when bioenergetically-compromised donor MuSCs are transplanted, improvements in mitochondrial organization and bioenergetic function were ablated in the dystrophic recipient. Overall, these data reveal a unique role of muscle stem cells as an essential regulator of myofiber mitochondrial homeostasis and a potential therapeutic target against mitochondrial myopathies.
Phosphoproteomics Reveals a Distinct Mode of Mec1/ATR Signaling in Response to DNA End Hyper-Resection
Authors: Sanford Ethan J. , Faça Vitor M. , Vega Stephanie C. , Comstock William J. , Smolka Marcus B.
Published: April 2020

The Mec1/ATR kinase is crucial for genome maintenance in response to a range of genotoxic insults, although how it promotes context-dependent signaling and DNA repair remains elusive. Here we uncovered a specialized mode of Mec1/ATR signaling triggered by the extensive nucleolytic processing (resection) of DNA ends. Cells lackingRAD9, a checkpoint activator and an inhibitor of resection, exhibit a selective increase in Mec1-dependent phosphorylation of proteins associated with single strand DNA transactions, including the ssDNA binding protein Rfa2, the translocase/ubiquitin ligase Uls1 and the HR-regulatory Sgs1-Top3-Rmi1 (STR) complex. Extensive Mec1-dependent phosphorylation of the STR complex, mostly on the Sgs1 helicase subunit, promotes an interaction between STR and the DNA repair scaffolding protein Dpb11. Fusion of Sgs1 to phosphopeptide-binding domains of Dpb11 strongly impairs HR-mediated repair, supporting a model whereby Mec1 signaling regulates STR upon hyper-resection to influence recombination outcomes. Overall, the identification of a distinct mode of Mec1 signaling triggered by hyper-resection highlights the multi-faceted action of this kinase in the coordination of checkpoint signaling and HR-mediated DNA repair.
Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication
Authors: Yurtman Erinç , Özer Onur , Yüncü Eren , Dağtaş Nihan Dilşad , Koptekin Dilek , Çakan Yasin Gökhan , Özkan Mustafa , Akbaba Ali , Kaptan Damla , Atağ Gözde , Vural Kıvılcım Başak , Gündem Can Yümni , Martin Louise , Kılınç Gülşah Merve , Ghalichi Ayshin , Açan Sinan Can , Yaka Reyhan , Sağlıcan Ekin , Lagerholm Vendela Kempe , Krzewinska Maja , Pişkin Evangelia , Şevketoğlu Müge , Bilgin C. Can , Atakuman Çiğdem , Erdal Yılmaz Selim , Sürer Elif , Lenstra Johannes , Yorulmaz Sevgi , Abazari Foad , Hoseinzadeh Javad , Baird Douglas , Bıçakçı Erhan , Çevik Özlem , Gerritsen Fokke , Özbal Rana , Götherström Anders , Somel Mehmet , Togan İnci , Özer Füsun
Published: April 2020

Sheep was among the first domesticated animals, but its demographic history is little understood. Here we present combined analyses of mitochondrial and nuclear polymorphism data from ancient central and west Anatolian sheep dating to the Late Glacial and early Holocene. We observe loss of mitochondrial haplotype diversity around 7500 BCE during the early Neolithic, consistent with a domestication-related bottleneck. Post-7000 BCE, mitochondrial haplogroup diversity increases, compatible with admixture from other domestication centres and/or from wild populations. Analysing archaeogenomic data, we further find that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds, and especially those from central and north Europe. Our results indicate that Asian contribution to south European breeds in the post-Neolithic era, possibly during the Bronze Age, may explain this pattern.
NPC1L1 inhibition disturbs lipid trafficking and induces large lipid droplet formation in intestinal absorptive epithelial cells
Authors: Nakano Takanari , Inoue Ikuo , Takenaka Yasuhiro , Ito Rina , Kotani Norihiro , Sato Sawako , Nakano Yuka , Hirasaki Masataka , Shimada Akira , Murakoshi Takayuki
Published: April 2020

Ezetimibe inhibits Niemann-Pick C1-like 1 (NPC1L1) protein, which mediates intracellular cholesterol trafficking from the brush border membrane to the endoplasmic reticulum, where chylomicron assembly takes place in enterocytes or in the intestinal absorptive epithelial cells. Cholesterol is a minor lipid component of chylomicrons; however, whether or not a shortage of cholesterol attenuates chylomicron assembly is unknown. The aim of this study was to examine the effect of NPC1L1 inhibition on trans-epithelial lipid transport, and chylomicron assembly and secretion in enterocytes. Caco-2 cells, an absorptive epithelial model, grown onto culture inserts were given lipid micelles from the apical side, and chylomicron-like triacylglycerol-rich lipoprotein secreted basolaterally were analyzed after a 24-h incubation period in the presence of ezetimibe up to 50 μM. The secretion of lipoprotein and apolipoprotein B48 were reduced by adding ezetimibe (30%,p<0.01 and 34%,p<0.05, respectively). Additionally, ezetimibe accelerated intracellular apoB protein degradation by approximately 2.8-fold and activated sterol regulatory element binding protein 2 by approximately 1.5-fold: These are indicators whether the cells are sensing cellular cholesterol shortage. Thus, ezetimibe appeared to limit cellular cholesterol mobilization required for lipoprotein assembly. In such conditions, large lipid droplet formation in Caco-2 cells and the enterocytes in mice were induced, implying that unprocessed triglyceride was sheltered in these compartments. Although ezetimibe did not reduce the post-prandial lipid surge appreciably in triolein-infused mice, the results of the present study indicated that NPC1L1-mediated supply chylomicron with cholesterol may participate in a novel regulatory mechanism for the efficient chylomicron assembly and secretion.
Conservation and divergence of vulnerability and responses to stressors between human and mouse astrocytes
Authors: Li Jiwen , Pan Lin , Godoy Marlesa I. , Pembroke William G. , Rexach Jessica E. , Condro Michael C. , Alvarado Alvaro G. , Harteni Mineli , Chen Yen-Wei , Stiles Linsey , Chen Angela Y. , Wanner Ina B. , Yang Xia , Goldman Steven A. , Geschwind Daniel H. , Kornblum Harley I. , Zhang Ye
Published: April 2020

Human-mouse differences are a major barrier in translational research. Astrocytes play important roles in neurological disorders such as stroke, injury, and neurodegeneration. However, the similarities and differences between human and mouse astrocytes are largely unknown. Combining analyses of acutely purified astrocytes, experiments using serum-free cultures of primary astrocytes, and xenografted chimeric mice, we found extensive conservation in astrocytic gene expression between human and mouse. However, genes involved in defense response and metabolism showed species differences. Human astrocytes exhibited greater susceptibility to oxidative stress than mouse astrocytes, due to differences in mitochondria physiology and detoxification pathways. Mouse astrocytes, but not human astrocytes, activate a molecular program for neural repair under hypoxia. Human astrocytes, but not mouse astrocytes, activate the antigen presentation pathway under inflammatory conditions. These species-dependent properties of astrocytes may contribute to differences between mouse models and human neurological and psychiatric disorders.
gwaRs: an R shiny web application for visualizing genome-wide association studies data
Authors: Nkambule Lethukuthula L
Published: April 2020

Although there is an exponential increase and extensive availability of genome-wide association studies data, the visualization of this data remains difficult for non-specialist users. Current software and packages for visualizing GWAS data are intended for specialists and have been developed to accomplish specific functions, favouring functionality over user experience. To facilitate this, we have developed an R shiny web application, gwaRs, that allows any general user to visualize GWAS data efficiently and effortlessly. The gwaRs web-browser interface allows users to visualize GWAS data using SNP-density, quantile-quantile, Manhattan, and Principal Component Analysis plots.

Availability

The gwaRs web application is publicly hosted athttps://gwasviz.shinyapps.io/gwaRs/and R source code is released under the GNU General Public License and freely available at GitHub:https://github.com/LindoNkambule/gwaRs.

Contact

lindonkambule116@gmail.com
c-Fos-MMP-9 pathway in central amygdala mediates approach motivation but not reward consumption
Authors: Lebitko T. , Nowicka K. , Dzik J. , Kanigowski D. , Jędrzejewska-Szmek J. , Chaturvedi M. , Jaworski T. , Nikolaev T. , Gorkiewicz T. , Meyza K. , Urban-Ciecko J. , Kaczmarek L. , Knapska E.
Published: April 2020

Although impaired motivational and consummatory aspects of reward behavior are core symptoms of several psychiatric disorders, the underlying neural and molecular mechanisms remain poorly understood. c-Fos, as a component of AP-1 transcription factor, regulates the expression of matrix metalloproteinase 9 (MMP-9), an enzyme involved in synaptic remodeling and plasticity. Both proteins are expressed in the central amygdala (CeA) that orchestrates appetitive and aversive responses. We have examined the role of c-Fos and MMP-9 in CeA in reward and punishment processing. We have manipulated c-Fos and MMP-9 levels in vivo using: RNAi-based approach to block c-Fos expression, inhibitor-releasing nanoparticles to block MMP-9 activity, and lentiviral vector to increase MMP-9 expression. To assess motivation, consumption and learning reinforced by either a sweet or bitter-tasting solution, we employed automated behavioral tests in the IntelliCage cystem. We have used transgenic mouse lines to identify CeA cells expressing c-Fos and a specific fluorescently labelled substrate peptide to measure MMP-9 activity. Excitability of neurons was measured with patch-clamp. Blocking c-Fos expression has been found to disrupt both reward processing components, motivational and consummatory, while inhibition of MMP-9 activity has impaired only motivational aspects of the behavior. On the other hand, punishment processing has not been affected by those manipulations. Furthermore, we have observed that reward training induces c-Fos expression in both somatostatin (SST)+, and SST-neurons, while MMP-9 activity is increased in SST- subpopulation only. We have further linked SST+ population to consummatory reactions by showing that reward consumption increases excitability of the SST+ neurons. These findings reveal molecular mechanisms of motivational anhedonia, linking it to c-Fos-MMP-9 pathway and CeA SST- neurons, and consummatory anhedonia, linking it to c-Fos and CeA SST+ neurons.
Mortality of native and invasive ladybirds co-infected by ectoparasitic and entomopathogenic fungi
Authors: Haelewaters Danny , Hiller Thomas , Kemp Emily A. , van Wielink Paul S. , Shapiro-Ilan David I. , Aime M. Catherine , Nedvěd Oldřich , Pfister Donald H. , Cottrell Ted E.
Published: April 2020

Harmonia axyridisis an invasive alien ladybird in North America and Europe. Studies show that multiple natural enemies are usingHa. axyridisas a new host. However, thus far, no research has been undertaken to study the effects of simultaneous infections of multiple natural enemies onHa. axyridis. We hypothesized that high thallus densities of the ectoparasitic fungusHesperomyces virescenson a ladybird weaken the host’s defenses, thereby making it more susceptible to infection by other natural enemies. We examined mortality of the North American-nativeOlla v-nigrumandHa. axyridisco-infected withHe. virescensand an entomopathogenic fungus—eitherBeauveria bassianaorMetarhizium anisopliae. Laboratory assays revealed thatHe. virescens-infectedO. v-nigrumindividuals are more susceptible to entomopathogenic fungi, butHa. axyridisdoes not suffer the same effects. This is in line with the enemy release hypothesis, which predicts that invasive alien species in new geographic areas experience reduced regulatory effects from natural enemies compared to native species. Considering our results, we can ask howHe. virescensaffects survival when confronted by other pathogens that previously had little impact onHa. axyridis.
Membrane-bound flurophore-labelled vectors for Targeted DamID allow simultaneous profiling of expression domains and DNA binding
Authors: Delandre Caroline , McMullen John PD , Marshall Owen J
Published: April 2020

Targeted DamID (TaDa) allows highly efficient cell-type-specific profiling of protein-DNA interactions. Cell-type-specificity, however, is governed by the GAL4/UAS system, which can exhibit differences in expression patterns depending upon the genomic insertion site and the UAS promoter strength. The TaDa system uses a bicistronic transcript to reduce the translation rates of Dam-fusion proteins, presenting the possibility of using the primary ORF within in the transcript to label expression domains and precisely identified the profiled cell populations in experimental samples. Here, we describe new TaDa vectors, pTaDaG, pTaDaG2 and pTaDaM, that use myristoylated-GFP or myristoylated-mCherry as the primary ORF. Differing lengths of the myristoylation sequence between the two GFP plasmids allows additional translational control. The mCherry plasmid allows profiled cells to be visualised when using the NanoDam system, in which an anti-GFP nanobody is fused to Dam to profile the localisation of GFP-fusion proteins. Fly lines created with this system allow easy visualisation of expression domains under both fluorescent dissecting and confocal microscopes without the use of antibody staining, whilst faithfully profiling protein-DNA interactions via Targeted DamID.
Dissociable electrophysiological measures of natural language processing reveal differences in speech comprehension strategy in healthy ageing
Authors: Broderick Michael P. , Di Liberto Giovanni M. , Anderson Andrew J. , Rofes Adrià , Lalor Edmund C.
Published: April 2020

Healthy ageing leads to changes in the brain that impact upon sensory and cognitive processing. It is not fully clear how these changes affect the processing of everyday spoken language. Prediction is thought to play an important role in language comprehension, where information about upcoming words is pre-activated across multiple representational levels. However, evidence from electrophysiology suggests differences in how older and younger adults use context-based predictions, particularly at the level of semantic representation. We investigate these differences during natural speech comprehension by presenting older and younger subjects with continuous, narrative speech while recording their electroencephalogram. We use linear regression to test how distinct computational measures of 1) semantic dissimilarity and 2) lexical surprisal are processed in the brains of both groups. Our results reveal dissociable neural correlates of these two measures that suggest differences in how younger and older adults successfully comprehend speech. Specifically, our results suggest that, while younger and older subjects both employ context-based lexical predictions, older subjects are significantly less likely to pre-activate the semantic features relating to upcoming words. Furthermore, across our group of older adults, we show that the weaker the neural signature of this semantic pre-activation mechanism, the lower a subject’s semantic verbal fluency score. We interpret these findings as prediction playing a generally reduced role at a semantic level in the brains of older listeners during speech comprehension and that these changes may be part of an overall strategy to successfully comprehend speech with reduced cognitive resources.
Disordered Proteins Enable Histone Chaperoning on the Nucleosome
Authors: Heidarsson Pétur O. , Mercadante Davide , Sottini Andrea , Nettels Daniel , Borgia Madeleine B. , Borgia Alessandro , Kilic Sinan , Fierz Beat , Best Robert B. , Schuler Benjamin
Published: April 2020

Proteins with highly charged disordered regions are abundant in the nucleus, where many of them interact with nucleic acids and control key processes such as transcription. The functional advantages conferred by protein disorder, however, have largely remained unclear. Here we show that disorder can facilitate a remarkable regulatory mechanism involving molecular competition. Single-molecule experiments demonstrate that the human linker histone H1 binds to the nucleosome with ultra-high affinity. However, the large-amplitude dynamics of the positively charged disordered regions of H1 persist on the nucleosome and facilitate the interaction with the highly negatively charged and disordered histone chaperone prothymosin α. Consequently, prothymosin α can efficiently invade the H1-nucleosome complex and displace H1 via competitive substitution. By integrating experiments and simulations, we establish a molecular model that rationalizes this process structurally and kinetically. Given the abundance of charged disordered regions in the nuclear proteome, this mechanism may be widespread in cellular regulation.
Simple attributes predict the importance of plants as hosts to the richness of fungi and arthropods
Authors: Bruun Hans Henrik , Brunbjerg Ane Kirstine , Dalby Lars , Fløjgaard Camilla , Frøslev Tobias G. , Haarder Simon , Heilmann-Clausen Jacob , Høye Toke T. , Læssøe Thomas , Ejrnæs Rasmus
Published: April 2020

Consumers constitute the vast majority of global terrestrial biodiversity. Yet, local consumer richness is poorly understood. Plant species richness offers a simple hypothesis to how the diversification of carbon substrates may promote the diversity of arthropods and fungi. We took this one step further and used databases on plant-consumer interaction links to derive the richness of associated biota per plant species (link score). Using a species inventory of 130 sites we investigated 1) how well the link score could be predicted by plant attributes and 2) if the sum of plant species’ observed or predicted link scores could predict site richness of arthropods and macrofungi better than plant species richness alone. We found plant link scores to be positively related to plant size, abundance, nativeness and ectomycorrhizal status. Link based indices generally improved prediction of richness, stressing the importance of plants as niche space for the megadiverse groups of insects and fungi.
Optimizing athlete assessment of maximal force and rate of development: A comparison of the isometric squat and mid-thigh pull
Authors: Silva Joao Renato , Sideris Vasileios , Chrismas Bryna C.R. , Read Paul J.
Published: April 2020

This study compared force-time characteristics and muscle activity between the isometric squat (ISQ) and mid-thigh pull (IMTP) in both bilateral (ISQBI andIMTPBI) and unilateral (ISQUNI andIMTPUNI) stance. Peak force (PF), rate-of-force (RFD) (e.g. 0-300ms) and EMG of the multifidus, erector spinae (ES), gluteus maximus (GM), biceps femoris (BF), semitendinosus (ST), vastus medialis (VM), vastus lateralis (VL) and soleus were recorded in ten recreationally trained males. PF was significantly greater during the ISQBIvs. IMTPBI(p=0.016, ES=1.08) but not in the unilateral test mode although effects remained moderate (ES=0.62). A trend indicated heightened RFD300ms(p = 0.083; ES=0.81) during the IMTPBIvs. the ISQBI, but these effects were smaller in the unilateral test (ES = 0.51). Greater (p<0.0001) EMG for VL (ES=1.00-1.13) and VM were recorded during the ISQ compared to IMTP modes in both modes (ES = 0.97 – 1.18). Greater BF EMG (p = 0.030, ES = 0.31) was shown in IMTPBIvs. ISQBIand these effects were stronger in the unilateral modes (p = < 0.05; ES = 0.81 – 0.83). Significantly greater ST activation was shown in both IMTPUNI(p < 0.05; ES = 0.69-0.76) and IMTPBI(p < 0.001; ES = 1.08). These findings indicate that ISQ results in elevated PF, whereas, RFD is heightened during the IMTP and these differences are more pronounced in bilateral modes. Greater activation of the quadriceps and hamstring muscles are expected in ISQ and IMPT respectively.
Human-lineage-specific genomic elements: relevance to neurodegenerative disease andAPOEtranscript usage
Authors: Chen Zhongbo , Zhang David , Reynolds Regina H. , Gustavsson Emil K. , Ruiz Sonia García , D’Sa Karishma , Fairbrother-Browne Aine , Vandrovcova Jana ,   International Parkinson’s Disease Genomics Consortium (IPDGC), Hardy John , Houlden Henry , Taliun Sarah A. Gagliano , Botía Juan , Ryten Mina
Published: April 2020

Knowledge of genomic features specific to the human lineage may provide insights into brain-related diseases. We leverage high-depth whole genome sequencing data to generate a combined annotation identifying regions simultaneously depleted for genetic variation (constrained regions) and poorly conserved across primates. We propose that these constrained, non-conserved regions (CNCRs) have been subject to human-specific purifying selection and are enriched for brain-specific elements. We find that CNCRs are depleted from protein-coding genes but enriched within lncRNAs. We demonstrate that per-SNP heritability of a range of brain-relevant phenotypes are enriched within CNCRs. We find that genes implicated in neurological diseases have high CNCR density, includingAPOE, highlighting an unannotated intron-3 retention event. Using human brain RNA-sequencing data, we show the intron-3-retaining transcript/s to be more abundant in Alzheimer’s disease with more severe tau and amyloid pathological burden. Thus, we demonstrate the importance of human-lineage-specific sequences in brain development and neurological disease. We release our annotation through vizER (https://snca.atica.um.es/browser/app/vizER).
Controls on and consequences of specific leaf area variation with permafrost depth in a boreal forest
Authors: Anderson Carolyn G. , Bond-Lamberty Ben , Stegen James C.
Published: April 2020

Specific leaf area (SLA, leaf area per unit dry mass) is a key canopy structural characteristic, a measure of photosynthetic capacity, and an important input into many terrestrial process models. Although many studies have examined SLA variation, relatively few data exist from high latitude, climate-sensitive permafrost regions. We measured SLA and soil and topographic properties across a boreal forest permafrost transition, in which forest composition changed as permafrost deepened from 54 to >150 cm over 75 m hillslope transects in Caribou-Poker Creeks Research Watershed, Alaska. We characterized both linear and threshold relationships between topographic and edaphic variables and SLA and developed a conceptual model of these relationships. We found that the depth of the soil active layer above permafrost was significantly and positively correlated with SLA for both coniferous and deciduous boreal tree species. Intraspecific SLA variation was associated with a fivefold increase in net primary production, suggesting that changes in active layer depth due to permafrost thaw could strongly influence ecosystem productivity. While this is an exploratory study to begin understanding SLA variation in a non-contiguous permafrost system, our results indicate the need for more extensive evaluation across larger spatial domains. These empirical relationships and associated uncertainty can be incorporated into ecosystem models that use dynamic traits, improving our ability to predict ecosystem-level carbon cycling responses to ongoing climate change.
Stress reactivity elicits a tissue-specific reduction in telomere length in ageing zebrafish (Danio rerio)
Authors: Evans James R. , Torres-Pérez Jose V. , Miletto Petrazzini Maria Elena , Riley Riva , Brennan Caroline H.
Published: April 2020

Telomere length reflects cellular ageing. Increased telomere shortening in leukocytes is associated with a range of neurodegenerative and cardiovascular diseases, the onset and progression of which may be mediated by behavioural traits such as anxiety and stress reactivity. However, the effects of the hypothalamus-pituitary-adrenal axis stress response are shown to be tissue specific. As such, leukocyte telomere length may not give an accurate measure of the relationship between stress-reactivity and telomere length in disease relevant tissues. To test the hypothesis that stress-reactivity contributes to age-related telomere shortening in a tissue specific manner, we examined the correlation between telomere length in heart and brain tissue and stress-reactivity in a population of young (6-9 month) and ageing (18 month) zebrafish. Stress-reactivity was assessed by tank diving, a zebrafish version of the rodent open-field test, and through gene expression. Telomere length was assessed using quantitative polymerase chain reaction. We show that ageing zebrafish have shorter telomeres in both heart and brain. Telomere length is inversely related to stress-reactivity in heart but not brain of ageing individuals. These data support the hypotheses that an anxious predisposition contributes to telomere shortening in heart tissue, and by extension age-related heart disease, and that stress-reactivity contributes to age-related telomere shortening in a tissue-specific manner.
New genetic insights about hybridization and population structure of hawksbill and loggerhead turtles from Brazil
Authors: Arantes Larissa S. , Vilaça Sibelle T. , Mazzoni Camila J. , Santos Fabrício R.
Published: April 2020

An extremely high incidence of hybridization among sea turtles is found along the Brazilian coast. To understand this atypical phenomenon and its impact on sea turtle conservation, research focused in the evolutionary history of sea turtles is fundamental. We assessed high quality multilocus haplotypes of 143 samples of the five species of sea turtles that occur along the Brazilian coast to investigate the hybridization process and the population structure of hawksbill (Eretmochelys imbricata) and loggerhead turtles (Caretta caretta). The multilocus data were initially used to characterize interspecific hybrids. Introgression (F2 hybrids) was only confirmed in hatchlings of F1 hybrid females (hawksbill × loggerhead), indicating that introgression was either previously overestimated and F2 hybrids may not survive to adulthood, or the first-generation hybrid females nesting in Brazil were born as recent as few decades ago. Phylogenetic analyses using nuclear markers recovered the mtDNA-based Indo-Pacific and Atlantic lineages for hawksbill turtles, demonstrating a deep genetic divergence dating from the early Pliocene. In addition, loggerhead turtles that share a common feeding area and belong to distinct Indo-Pacific and Atlantic mtDNA clades present no clear genetic differentiation at the nuclear level. Finally, our results indicate that hawksbill and loggerhead rookeries along the Brazilian coast are likely connected by male-mediated gene flow.
Goslin - A Grammar of Succinct Lipid Nomenclature
Authors: Kopczynski Dominik , Hoffmann Nils , Peng Bing , Ahrends Robert
Published: April 2020

We introduce Goslin, a polyglot grammar for common lipid shorthand nomenclatures based on the LipidMaps nomenclature and the shorthand nomenclature established by Liebischet al. and used by LipidHome and SwissLipids. Goslin was designed to address the following pressing issues in the lipidomics field: 1) to simplify the implementation of lipid name handling for developers of mass spectrometry-based lipidomics tools; 2) to offer a tool that unifies and normalizes the main existing lipid name dialects enabling a lipidomics analysis in a high-throughput fashion. We provide implementations of Goslin in four major programming languages, namely C++, Java, Python 3, and R to kick-start adoption and integration. Further, we set up a web service for users to work with Goslin directly. All implementations are available free of charge under a permissive open source license.
Classes for the masses: Systematic classification of unknowns using fragmentation spectra
Authors: Dührkop Kai , Nothias Louis Felix , Fleischauer Markus , Ludwig Marcus , Hoffmann Martin A. , Rousu Juho , Dorrestein Pieter C. , Böcker Sebastian
Published: April 2020

Metabolomics experiments can employ non-targeted tandem mass spectrometry to detect hundreds to thousands of molecules in a biological sample. Structural annotation of molecules is typically carried out by searching their fragmentation spectra in spectral libraries or, recently, in structure databases. Annotations are limited to structures present in the library or database employed, prohibiting a thorough utilization of the experimental data. We present a computational tool for systematic compound class annotation: CANOPUS uses a deep neural network to predict 1,270 compound classes from fragmentation spectra, and explicitly targets compounds where neither spectral nor structural reference data are available. CANOPUS even predicts classes for which no MS/MS training data are available. We demonstrate the broad utility of CANOPUS by investigating the effect of the microbial colonization in the digestive system in mice, and through analysis of the chemodiversity of different Euphorbia plants; both uniquely revealing biological insights at the compound class level.
Osmotic and ionic regulation by hololimnetic freshwater crustaceans: a molecular role for gill ion transporters
Authors: Mantovani Milene , McNamara John Campbell
Published: April 2020

Owing to their extraordinary niche diversity, the Crustacea are ideal for comprehending the evolution of osmoregulation. The processes that effect systemic hydro-electrolytic homeostasis maintain hemolymph ionic composition via membrane transporters located in highly specialized gill ionocytes. We evaluated physiological and molecular hyper- and hypo-osmoregulatory mechanisms in two phylogenetically distant, freshwater crustaceans, the crabDilocarcinus pageiand the shrimpMacrobrachium jelskii, when osmotically challenged for up to 10 days. When in distilled water, hemolymph osmolality and [Cl−] increased briefly inD. pagei, stabilizing at initial values, while [Na+] decreased continually. Gill V(H+)-ATPase, Na+/K+-ATPase and Na+/K+/2Cl−gene expressions were unchanged. InM. jelskii, hemolymph osmolality, [Cl−] and [Na+] decreased continually for 12 h, the shrimps no longer surviving. Gill transporter gene expressions increased 2- to 5-fold. After 10-days exposure to brackish water,D. pageiwas isosmotic, iso-chloremic and iso-natriuremic. Gill V(H+)-ATPase expression decreased while Na+/K+-ATPase and Na+/K+/2Cl−expressions were unchanged. InM. jelskii, the hemolymph was hypo-regulated, particularly [Cl−]. Transporter expressions initially increased 3- to 12-fold, declining to control values. Gill V(H+)-ATPase expression underlies the ability ofD. pageito survive in fresh water while Na+/K+-ATPase and Na+/K+/2Cl−expressions enableM. jelskiito deal with osmotic challenge. These findings reveal divergent responses in two unrelated crustaceans habiting a similar osmotic niche. WhileD. pageihas maintained the capacity to tolerate elevated cellular isosmoticity despite its inability to secrete salt,M. jelskiidisplays clear hypo-osmoregulatory ability. Each species has developed distinct strategies at the transcription and systemic levels during adaptation to fresh water.

Summary statement

During their evolutionary adaptation to fresh water, unrelated hololimnetic crustaceans have developed physiological strategies like tolerating elevated cellular isosmoticity or regulating hypo-osmoregulatory ability at the gene transcription level.
Towards resilient beef cattle production systems: Impact of truck contamination and information sharing on foot-and-mouth disease spreading
Authors: Yang Qihui , Gruenbacher Don M. , Heier Stamm Jessica L. , Amrine David E. , Brase Gary L. , DeLoach Scott A. , Scoglio Caterina M.
Published: April 2020

As cattle movement data in the United States are scarce due to the absence of mandatory traceability programs, previous epidemic models for U.S. cattle production systems heavily rely on contact rates estimated based on expert opinions and survey data. These models are often based on static networks and ignore the sequence of movement, possibly overestimating the epidemic sizes. In this research, we adapt and employ an agent-based model that simulates beef cattle production and transportation in southwest Kansas to analyze the between-premises transmission of a highly contagious disease, the foot-and-mouth disease. First, we assess the impact of truck contamination on the disease transmission with the truck agent following an independent clean-infected-clean cycle. Second, we add an information-sharing functionality such that producers/packers can trace back and forward their trade records to inform their trade partners during outbreaks. Scenario analysis results show that including indirect contact routes between premises via truck movements can significantly increase the amplitude of disease spread, compared with equivalent scenarios that only consider animal movement. Mitigation strategies informed by information sharing can dramatically improve the system resilience against epidemics, highlighting the benefit of promoting information sharing in the cattle industry. In addition, we identify salient characteristics that must be considered when designing an information-sharing strategy, including the number of days to trace back and forward in the trade records and the role of different cattle supply chain stakeholders. Sensitivity analysis results show that epidemic sizes are sensitive to variations in parameters of fomite survival time and indirect contact transmission probability and future studies can focus on a more accurate estimation of these parameters.
Genetic variations (eQTLs) in muscle transcriptome and mitochondrial genes, and trans-eQTL molecular pathways in feed efficiency from Danish breeding pigs
Authors: Carmelo Victor AO. , Kadarmideen Haja N.
Published: April 2020

Feed efficiency (FE) is a key trait in pig production, as it has both high economic and environmental impact. FE is a challenging phenotype to study, as it is complex and affected by many factors, such as metabolism, growth and activity level. Furthermore, testing for FE is expensive, as it requires costly equipment to measure feed intake of individual animals, making FE biomarkers valuable. Therefore, there has been a desire to find single nucleotide polymorphisms (SNPs) as biomarkers, to assist with improved selection and improve our biological understanding of FE. We have done a cis- and trans-eQTL (expressed quantitative trait loci) analysis, in a population of Danbred Durocs (N=11) and Danbred Landrace (N=27) using both a linear and Anova model. We used bootstrapping and enrichment analysis to validate and analyze our detected eQTLs. We identified 15 eQTLs with FDR < 0.01, affecting several genes found in previous studies of commercial pig breeds. Examples include IFI6, PRPF39, TMEM222, CSRNP1,PARK7 and MFF. The bootstrapping results showed statistically significant enrichment of eQTLs with p-value < 0.01 (p-value < 2.2×0-16) in both cis and trans-eQTLs. Based on this, enrichment analysis of top trans-eQTLs revealed high enrichment for gene categories and gene ontologies associated with genomic context and expression regulation. This includes transcription factors (p-value=1.0×10-13), DNA-binding (GO:0003677, p-value=8.9×10-14), DNA-binding transcription factor activity (GO:0003700,) nucleus gene (GO:0005634, p-value<2.2×10-16), positive regulation of expression (GO:0010628), negative regulation of expression (GO:0010629, p-value<2.2×10-16). These results would be useful for future genome assisted breeding of pigs to improve FE, and in the improved understanding of the functional mechanism of trans-eQTLs.
Spatially Resolved Measurement of Dynamic Glucose Uptake in Live Ex Vivo Tissues
Authors: Dunn Austin F. , Catterton Megan A. , Dixon Drake D. , Pompano Rebecca R.
Published: April 2020

Highly proliferative cells depend heavily on glycolysis as a source of energy and biological precursor molecules, and glucose uptake is a useful readout of this aspect of metabolic activity. Glucose uptake is commonly quantified by using flow cytometry for cell cultures and positron emission tomography for organs in vivo. However, methods to detect spatiotemporally resolved glucose uptake in intact tissues are far more limited, particularly those that can quantify changes in uptake over time in specific tissue regions and cell types. Using lymph node metabolism as a case study, we developed a novel assay of dynamic and spatially resolved glucose uptake in living tissue by combining ex vivo tissue slice culture with a fluorescent glucose analogue. Live slices of murine lymph node were treated with the glucose analogue 2-[N-(7-nitrobenz-2-oxa-1,3-dia-xol-4-yl)amino]-2-deoxyglucose (2-NBDG). Incubation parameters were optimized to differentiate glucose uptake in activated versus naïve lymphocytes. Regional glucose uptake could be imaged at both the tissue level, by widefield microscopy, and at the cellular level, by confocal microscopy. Furthermore, the assay was readily multiplexed with live immunofluorescence labelling to generate maps of 2-NBDG uptake across tissue regions, revealing highest uptake in T cell-dense regions. The signal was predominantly intracellular and localized to lymphocytes rather than stromal cells. Finally, we demonstrated that the assay was repeatable in the same slices, and imaged the dynamic distribution of glucose uptake in response to ex vivo T cell stimulation for the first time. We anticipate that this assay will serve as a broadly applicable, user-friendly platform to quantify dynamic metabolic activities in complex tissue microenvironments.