bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneously monitoring aquatic and riparian biodiversity using riverine water eDNA
Authors: Yang Haile , Du Hao , Qi Hongfang , Yu Luxian , Hou Xindong , Zhang Hui , Li Junyi , Wu Jinming , Wang Chengyou , Zhou Qiong , Wei Qiwei 
Published: June 2020

AbstractEnvironmental DNA (eDNA) metabarcoding for biodiversity monitoring is a critical technical advance. Both aquatic and terrestrial biodiversity information can be detected in riverine water eDNA. However, it remains unverified whether riverine water eDNA can be used to simultaneously monitor aquatic and terrestrial biodiversity. Our specific objective was to assess the effectiveness of monitoring aquatic and riparian biodiversity using riverine water eDNA. We proposed that the monitoring effectiveness (the proportion of aquatic and terrestrial biodiversity information detected by riverine water eDNA samples) could be approximated by the transportation effectiveness of land-to-river and upstream-to-downstream biodiversity information flow. We conducted a case study in a watershed on the Qinghai-Tibet Plateau and estimated the effectiveness of using riverine water eDNA to monitor aquatic and riparian biodiversity based on comparing the operational taxonomic units (OTUs) and species assemblages of three taxonomic communities detected in riverine water eDNA samples and riparian soil eDNA samples in spring, summer, and autumn. The aquatic and riparian biodiversity of a watershed on the Qinghai-Tibet Plateau could be simultaneously effectively monitored using riverine water eDNA on summer or autumn rainy days. Monitoring bacterial communities was more efficient than monitoring eukaryotic communities. On summer rainy days, 43%-76% of riparian species could be detected in water eDNA samples, 92%-99% of upstream species could be detected in a 1-km downstream eDNA sample, and more than 50% of dead bioinformation (i.e., the bioinformation labeling the biological material without life activity and fertility) could be monitored 4-6 km downstream for eukaryotes and 13-19 km for bacteria. We encourage more studies on the monitoring effectiveness for each taxonomic community in other watersheds with different environmental conditions. We believe that in future ecological research, conservation and management, we could efficiently monitor and assess the aquatic and terrestrial biodiversity by simply using riverine water eDNA samples.
Sequence structure organizes items in varied latent states of working memory neural network
Authors: Huang Qiaoli , Zhang Huihui , Luo Huan 
Published: June 2020

AbstractIn memory experiences, events do not exist independently but are linked with each other via structure-based organization. Structure context largely influences memory behavior, but how it is implemented in the brain remains unknown. Here, we combined magnetoencephalogram (MEG) recordings, computational modeling, and impulse-response approaches to probe the latent states when subjects held a list of items in working memory (WM). We demonstrate that sequence context reorganizes WM items into distinct latent states, i.e., being reactivated at different latencies during WM retention, and the reactivation profiles further correlate with recency behavior. In contrast, memorizing the same list of items without sequence task requirements disrupts the recency effect and elicits comparable neural reactivations. Computational modeling further reveals a dominant function of sequence context, instead of passive memory decaying, in characterizing recency effect. Taken together, sequence structure context shapes the way WM items are stored in the human brain and essentially influences memory behavior.
High-speed single-molecule imaging reveals signal transduction by induced transbilayer raft phases
Authors: Koyama-Honda Ikuko , Fujiwara Takahiro K. , Kasai Rinshi S. , Suzuki Kenichi G. N. , Kajikawa Eriko , Tsuboi Hisae , Tsunoyama Taka A. , Kusumi Akihiro 
Published: June 2020

AbstractUsing single-molecule imaging with enhanced time resolutions down to 5 ms, we found that CD59-cluster rafts and GM1-cluster rafts stably induced in the outer leaflet of the plasma membrane (PM), which triggered the activation of Lyn, H-Ras, and ERK, continually recruited Lyn and H-Ras right beneath them in the inner leaflet, with dwell lifetimes of <0.1 s. The detection was possible due to the enhanced time resolutions employed here. The recruitment depended on the PM cholesterol and saturated alkyl chains of Lyn and H-Ras, whereas it was blocked by the non-raftophilic transmembrane protein moiety and unsaturated alkyl chains linked to the inner-leaflet molecules. Since GM1-cluster rafts recruited Lyn and H-Ras as efficiently as CD59-cluster rafts, and the protein moieties of Lyn and H-Ras were not required for the recruitment, we conclude that the transbilayer raft phases induced by the outer-leaflet stabilized rafts recruit lipid-anchored signaling molecules by lateral raft-lipid interactions, and thus serve as a key signal transduction platform.SummaryHigh-speed single-molecule imaging indicated that CD59-cluster rafts and GM1-cluster rafts stably induced in the plasma membrane outer leaflet generated nano-scale transbilayer raft phases, which continually and transiently recruited Lyn and H-Ras in the inner leaflet by cooperative raft-lipid interactions.
Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hotspots, Functional Crosstalk and Regulatory Interactions in SARS-CoV-2
Authors: Gupta Vipin , Haider Shaiza , Verma Mansi , Singhvi Nirjara , Ponnusamy Kalaiarasan , Malik Md. Zubbair , Verma Helianthous , Kumar Roshan , Sood Utkarsh , Hira Princy , Satija Shiva , Singh Yogendra , Lal Rup 
Published: June 2020

AbstractSARS-CoV-2 pandemic resulted in 92 million cases in a span of one year. The study focuses on understanding population specific variations attributing its high rate of infections in specific geographical regions particularly in USA. Rigorous phylogenomic network analysis of complete SARS-CoV-2 genomes (245) inferred five central clades named a (ancestral), b, c, d and e (subtype e1 & e2). The clade d & e2 were found exclusively comprising of USA. Clades were distinguished by 10 co-mutational combinations in Nsp3, ORF8, Nsp13, S, Nsp12, Nsp2 and Nsp6. Our analysis revealed that only 67.46% of SNP mutations were at amino acid level. T1103P mutation in Nsp3 was predicted to increase protein stability in 238 strains except 6 strains which were marked as ancestral type; whereas co-mutation (P409L & Y446C) in Nsp13 were found in 64 genomes from USA highlighting its 100% co-occurrence. Docking highlighted mutation (D614G) caused reduction in binding of Spike proteins with ACE2, but it also showed better interaction with TMPRSS2 receptor contributing to high transmissibility among USA strains. We also found host proteins, MYO5A, MYO5B, MYO5C had maximum interaction with viral proteins (N, S, M). Thus, blocking the internalization pathway by inhibiting MYO5 proteins which could be an effective target for COVID-19 treatment. The functional annotations of the HPI network were found to be closely associated with hypoxia and thrombotic conditions confirming the vulnerability and severity of infection. We also screened CpG islands in Nsp1 & N conferring ability of SARS-CoV-2 to enter and trigger ZAP activity inside host cell.ImportanceIn the current study we presented a global view of mutational pattern observed in SARS-CoV-2 virus transmission. This provided a who-infect-whom geographical model since the early pandemic. This is hitherto the most comprehensive comparative genomics analysis of full-length genomes for co-mutations at different geographical regions specially in USA strains. Compositional structural biology results suggested that mutations have balance of contrary forces effect on pathogenicity suggesting only few mutations to effective at translation level but not all. Novel HPI analysis and CpG predictions elucidates the proof of concept of hypoxia and thrombotic conditions in several patients. Thus, the current study focuses the understanding of population specific variations attributing high rate of SARS-CoV-2 infections in specific geographical regions which may eventually be vital for the most severely affected countries and regions for sharp development of custom-made vindication strategies.
Low competitive status elicits aggression in healthy young men: behavioral and neural evidence
Authors: Buades-Rotger Macià , Göttlich Martin , Weiblen Ronja , Petereit Pauline , Scheidt Thomas , Keevil Brian G. , Krämer Ulrike M. 
Published: June 2020

AbstractWinners are commonly assumed to compete more aggressively than losers. Here, we find overwhelming evidence for the opposite. We first demonstrate that low-ranking teams commit more fouls than they receive in top-tier soccer, ice hockey, and basketball men’s leagues. We replicate this effect in the laboratory, showing that male participants deliver louder sound blasts to a rival when placed in a low-status position. Using neuroimaging, we characterize brain activity patterns that encode competitive status as well as those that facilitate status-dependent aggression in healthy young men. These analyses reveal three key findings. First, anterior hippocampus and striatum contain multivariate representations of competitive status. Second, interindividual differences in status-dependent aggression are linked with a sharper status differentiation in the striatum and with greater reactivity to status-enhancing victories in the dorsal anterior cingulate cortex. Third, activity in ventromedial, ventrolateral, and dorsolateral prefrontal cortex is associated with trial-wise increases in status-dependent aggressive behavior. Taken together, our results run counter to narratives glorifying aggression in competitive situations. Rather, we show that those in the lower ranks of skill-based hierarchies are more likely to behave aggressively and identify the potential neural basis of this phenomenon.
Identification of a new geneRf9and unravelling the genetic complexity for controlling fertility restoration in hybrid wheat
Authors: Shahinnia Fahimeh , Geyer Manuel , Block Annette , Mohler Volker , Hartl Lorenz 
Published: June 2020

AbstractWheat (Triticum aestivum L.) is a self-pollinating crop whose hybrids offer the potential to provide a major boost in yield. Male sterility induced by the cytoplasm ofTriticum timopheeviiis a powerful method for hybrid seed production. Hybrids produced by this method are often partially sterile and full fertility restoration is crucial for wheat production using hybrid cultivars. To identify genetic loci controlling fertility restoration in wheat, we produced two CMS-based backcross (BC1) mapping populations. The restorer lines Gerek 79 and 71R1203 were used to pollinate the male-sterile winter wheat line CMS-Sperber. Seed set and numbers of sterile spikelets per spike were evaluated in 340 and 206 individuals of the populations derived from Gerek 79 and 71R1203, respectively. Genetic maps were constructed using 930 and 994 SNPs, spanning 2,160 and 2,328 cM over 21 linkage groups in the two populations, respectively. Twelve quantitative trait loci (QTL) controlled fertility restoration in both BC1populations, including a novelrestorer-of-fertility (Rf)locus flanked by the single nucleotide polymorphism (SNP) markersIWB72413andIWB1550on chromosome 6AS. The locus was mapped as a qualitative trait in the BC1Gerek 79 population and was designatedRf9.Ninety-three putative candidate genes were predicted for the QTL region on chromosome 6AS. Among them were genes encoding tetratricopeptide and pentatricopeptide repeat-containing proteins in rice known to be associated with fertility restoration. This finding is a promising step to better understand the functions of genes for improving hybrid wheat.
Reduced horseshoe crab abundance and feeding activity beneath intertidal oyster aquaculture structures in the Delaware Bay
Authors: Smith Joseph A.M. , Niles Lawrence J. , Feigin Stephanie 
Published: June 2020

AbstractAround the world, tidal flats play a unique ecological role in estuaries and are a primary feeding habitat for shorebirds and other benthic feeding organisms. Development and economic use of tidal flats can exclude species that depend on this habitat and disrupt ecological processes. In this study we examine patterns of abundance and feeding activity of American horseshoe crabs among oyster aquaculture structures on tidal flats that are adjacent to one of the most important horseshoe crab spawning sites in the world. We used custom-designed traps to sample horseshoe crab abundance beneath rack and bag aquaculture structures and adjacent areas without structures. In addition, we developed predictive spatial models representing three hypotheses regarding the movement of horseshoe crabs through aquaculture structures when transiting to and from spawning beaches. We tested the predictive power of each model using data from traps and found the strongest support for an avoidance model, where on average, horseshoe crabs are avoiding arrays of aquaculture structures when moving across inundated tidal flats. The best-supported spatial model also indicates that patterns of structure avoidance by horseshoe crabs can potentially affect abundance on spawning beaches, particularly with larger gear arrays that are closer to shore. We found additional support for aquaculture structure avoidance by examining an independent data set of horseshoe crab feeding pits on the tidal flats. Patterns of feeding pit density mirrored our trapping results, with fewer pits beneath and among aquaculture structures when compared to adjacent control areas. Horseshoe crabs are important constituents of the benthic food web and their displacement by aquaculture may translate to significant disruptions to the ecological function of tidal flats. This impact can be limited through deliberative spatial planning that seeks to balance ecological and economic management objectives.
Green tea and Spirulina extracts inhibit SARS, MERS, and SARS-2 spike pseudotyped virus entry in vitro
Authors: Joseph Jeswin , T Karthika , Ajay Ariya , Das V.R. Akshay , Raj V. Stalin 
Published: June 2020

AbstractCoronaviruses (CoVs) infect a wide range of animals and birds. Their tropism is primarily determined by the ability of the spike (S) protein to bind to a host cell surface receptor. The rapid outbreak of emerging novel coronavirus, SARS-CoV 2 in China inculcates the need for the development of hasty and effective intervention strategies. Medicinal plants and natural compounds have been traditionally used to treat viral infections. Here, we generated VSV based pseudotyped viruses (pvs) of SARS-, MERS-, and SARS-2 CoVs to screen entry inhibitors from natural products. In the first series of experiments, we demonstrated that pseudotyped viruses specifically bind on their receptors and enter into the cells. SARS and MERS polyclonal antibodies neutralize SARSpv and SARS-2pv, and MERSpv respectively. Incubation of soluble ACE2 inhibited entry of SARS and SARS-2 pvs but not MERSpv. In addition, expression of ACE2 and DPP4 in non-permissive BHK21 cells enabled infection by SARSpv, SARS-2pv, and MERSpv respectively. Next, we showed the antiviral properties of known enveloped virus entry inhibitors, Spirulina and Green tea extracts against CoVpvs. SARSpv, MERSpv, and SARS-2pv entry were blocked with higher efficiency when preincubated with either green tea or spirulina extracts. Green tea provided a better inhibitory effect than the spirulina extracts by binding to the S1 domain of spike and blocking the interaction of spike with its receptor. Further studies are required to understand the exact mechanism of viral inhibition. In summary, we demonstrate that pseudotyped virus is an ideal tool for screening viral entry inhibitors. Moreover, spirulina and green tea could be promising antiviral agents against emerging viruses.
DNA polymerase stalling at structured DNA constrains the expansion of Short Tandem Repeats
Authors: Murat Pierre , Guilbaud Guillaume , Sale Julian E. 
Published: June 2020

AbstractBackgroundShort tandem repeats (STRs) contribute significantly tode novomutagenesis, driving phenotypic diversity and genetic disease. Although highly diverse, their repetitive sequences induce DNA polymerase slippage and stalling, leading to length and sequence variation. However, current studies of DNA synthesis through STRs are restricted to a handful of selected sequences, limiting our broader understanding of their evolutionary behaviour and hampering the characterisation of the determinants of their abundance and stability in eukaryotic genomes.ResultsWe perform a comprehensive analysis of DNA synthesis at all STR permutations and interrogate the impact of STR sequence and secondary structure on their genomic representation and mutability. To do so, we developed a high-throughput primer extension assay that allows monitoring of the kinetics and fidelity of DNA synthesis through 20,000 sequences comprising all STR permutations in different lengths. By combining these measurements with population-scale genomic data, we show that the response of a model replicative DNA polymerase to variously structured DNA is sufficient to predict the complex genomic behaviour of STRs, including abundance and mutational constraints. We demonstrate that DNA polymerase stalling at DNA structures induces error-prone DNA synthesis, which constrains STR expansion.ConclusionsOur data support a model in which STR length in eukaryotic genomes results from a balance between expansion due to polymerase slippage at repeated DNA sequences and point mutations caused by error-prone DNA synthesis at DNA structures.
Principles for coding associative memories in a compact neural network
Authors: Pritz Chrisitian O. , Itskovits Eyal , Bokman Eduard , Ruach Rotem , Gritsenko Vladimir , Nelken Tal , Menasherof Mai , Azulay Aharon , Zaslaver Alon 
Published: June 2020

SummaryA major goal in neuroscience is to elucidate the principles by which memories are stored in a neural network. Here, we have systematically studied how the four types of associative memories (short- and long-term memories, each formed using positive and negative associations) are encoded within the compact neural network ofC. elegansworms. Interestingly, short-term, but not long-term, memories are evident in the sensory system. Long-term memories are relegated to inner layers of the network, allowing the sensory system to resume innate functionality. Furthermore, a small set of sensory neurons is allocated for coding short-term memories, a design that can increase memory capacity and limit non-innate behavioral responses. Notably, individual sensory neurons may code for the conditioned stimulus or the experience valence. Interneurons integrate these information to modulate animal behavior upon memory reactivation. This comprehensive study reveals basic principles by which memories are encoded within a neural network, and highlights the central roles of sensory neurons in memory formation.
The rice NLR pair Pikp-1/Pikp-2 initiates cell death through receptor cooperation rather than negative regulation
Authors: Zdrzałek Rafał , Kamoun Sophien , Terauchi Ryohei , Saitoh Hiromasa , Banfield Mark J 
Published: June 2020

AbstractPlant NLR immune receptors are multidomain proteins that can function as specialized sensor/helper pairs. Paired NLR immune receptors are generally thought to function via negative regulation, where one NLR represses the activity of the second and detection of pathogen effectors relieves this repression to initiate immunity. However, whether this mechanism is common to all NLR pairs is not known. Here, we show that the rice NLR pair Pikp-1/Pikp-2, which confers resistance to strains of the blast pathogenMagnaporthe oryzae(syn.Pyricularia oryzae) expressing the AVR-PikD effector, functions via receptor cooperation, with effector-triggered activation requiring both NLRs to trigger the immune response. To investigate the mechanism of Pikp-1/Pikp-2 activation, we expressed truncated variants of these proteins, and made mutations in previously identified NLR sequence motifs. We found that any domain truncation, in either Pikp-1 or Pikp-2, prevented cell death in the presence of AVR-PikD, revealing that all domains are required for activity. Further, expression of individual Pikp-1 or Pikp-2 domains did not result in cell death. Mutations in the conserved P-loop and MHD sequence motifs in both Pikp-1 and Pikp-2 prevented cell death activation, demonstrating that these motifs are required for the function of the two partner NLRs. Finally, we showed that Pikp-1 and Pikp-2 associate to form homo- and hetero-complexes in planta in the absence of AVR-PikD; on co-expression the effector binds to Pikp-1 generating a tripartite complex. Taken together, we provide evidence that Pikp-1 and Pikp-2 form a fine-tuned system that is activated by AVR-PikD via receptor cooperation rather than negative regulation.
A Geophysical and Climatological Assessment of New Guinea — Implications for the Origins ofSaccharum
Authors: Evans Dyfed Lloyd 
Published: June 2020

AbstractAny assessment of whether or notSaccharumspecies are native or introduced in New Guinea require an evolutionary (in a geological sense), geophysical and climatological assessment of the island. Like many of the land masses circling the Pacific (in the volcanically active region known as the ‘ring of fire’) New Guinea is geologically young, with the island in its modern form not pre-dating 2 Ma. Novel modelling of the 74 ka youngest Toba supereruption indicates a potential extinction level tsunami and loss of habitat. The late Pleistocene megafaunal mass extinction and the last glacial maximum (33–16 ka) are two global effects that would have significantly altered the flora on New Guinea; though the implications of these events on New Guinea have not previously been studied. Even if the genusSaccharumwas established on the island during pre-historic times the consequences of Toba and other global climate change events means that it would have been eliminated from New Guinea and would have had to be re-introduced during the period of human colonization. Indeed, given the evolution ofSaccharum’s immediate ancestors in Africa and Indochina it is most parsimonious to conclude that it was never native to New Guinea, but was introduced by humans relatively recently.Little work has been done on palaeotsunami evidence and ancient tsunami modelling in New Guinea. However, the recent recognition that the Aitape skull (dating to about 6 ka) may have been the victim of a tsunami (Goff et al. 2017) show that, in the past, tsunami have pen etrated significantly (about 10 km in this case) into the interior of the island to have a profound effect on biodiversity. This tsunami would have left the north coast of the island impoverished of plant life for several decades after.