bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification and expression ofLactobacillus paracaseigenes for adaptation to desiccation and rehydration
Authors: Palud Aurore , Salem Karima , Cavin Jean-François , Beney Laurent , Licandro Hélène
Published: November 2018

Lactobacillus paracaseiis able to persist in a variety of natural and technological environments despite physico-chemical perturbations, in particular alternations between desiccation and rehydration. However, the way in which it adapts to hydric fluctuations and in particular the genetic determinants involved are not clearly understood. To identify the genes involved in adaptation to desiccation, an annotated library ofL. paracaseirandom transposon mutants was screened for viability after desiccation (25% relative humidity, 25°C). Subsequently, the expression of the identified genes was measured at five stages of the dehydration-rehydration process to formulate the chronology of gene expression. The 24 identified genes were related to metabolism and transport, membrane function and structure, regulation of stress response, DNA related enzymes and environmental sensing. They were classified into four different transcriptomic profiles, in particular genes upregulated during both desiccation and rehydration phases and genes upregulated during the desiccation phase only. Thus, genetic response to hydric fluctuations seems to occur during desiccation and can continue or not during rehydration. The genes identified should contribute to improving the stabilization of lactobacillus starters in dry state.

Importance

Since water is the fundamental component of all living organisms, desiccation and rehydration alternation is one of the most prevalent and severe stresses for most microorganisms. Adaptation to this stress occurs via a combination of mechanisms which depend on the genetic background of the microorganism. InL. paracasei,we developed a strategy to identify genes involved in the adaptation to hydric fluctuations using random transposon mutagenesis and targeted transcriptomics. Both dehydration and rehydration were studied to decipher the chronology of genetic mechanisms. We found 24 as yet unidentified genes involved in this response. Most of them are linked to either the transport of molecules or to cell wall structure and function. Our screening also identified genes for environment sensing and two alarmones necessary forL. paracaseisurvival. Furthermore, our results show that desiccation is a critical phase for inducing stress response inL. paracasei.
Natural copy number differences of tandemly repeated small nucleolar RNAs in the Prader-Willi syndrome genomic region regulate individual behavioral responses in mammals
Authors: Keshavarz Maryam , Krebs-Wheaton Rebecca , Refki Peter , Savriama Yoland , Zhang Yi , Guenther Anja , Brückl Tanja M. , Binder Elisabeth B. , Tautz Diethard
Published: November 2018

The Prader-Willi Syndrome (PWS) gene region is an imprinted gene complex involved in behavioral, metabolic and osteogenic functions. We have analyzed here the variation of two families of regulatory small nucleolar RNAs (SNORD115 and SNORD116) that are coded within the PWS and are expressed from the paternal chromosome. They are organized in two tandemly repeated clusters which are naturally copy number variable between individuals. We find that the copy numbers at these loci correlate with repeatable individual test scores for anxiety that are considered to constitute a component of the “personality” of individuals. We show this for different populations and species of mice, cavies and for the anxiety component of personality tests in humans. This is also the case for an inbred mouse strain (C57Bl6) implying that copy number variation creates phenotypic variability even in an isogenic background. In transcriptome data from brain samples of this strain we find SNORD copy-number correlated regulation of target genes that are known to be involved in influencing behavior. SNORD115 has previously been suggested to regulate splicing of the serotonin receptor Htr2c and we confirm this in our data. For SNORD116 we provide evidence that it regulates the expression level of the chromatin regulator Ankrd11, which itself regulates GABA receptors, metabolic pathways, cell differentiation and osteogenesis. Intriguingly, we find that craniofacial shapes in mice correlate also with SNORD116 copy numbers. New copy number variants are generated at very high rates in mice, possibly at every generation, explaining why conventional genetic mapping could not detect this association. Our results suggest that the variable dosage of two regulatory RNAs are major determinants of individual behavioral differences and correlated traits in mammals.
Dispersal increases the resilience of tropical savanna and forest distributions
Authors: Goel Nikunj , Guttal Vishwesha , Levin Simon A. , Staver Carla A.
Published: November 2018

Global change may induce changes in savanna and forest distributions, but the dynamics of these changes remain unclear. Classical biome theory suggests that climate is predictive of biome distributions, such that shifts will be continuous and reversible. This view, however, cannot explain a widely observed mismatch between climate and tree cover, which some argue results from fire-vegetation feedbacks maintaining savanna and forest as bistable states, such that, instead, shifts will be discontinuous and irreversible. This bistable model, however, cannot reproduce the spatial aggregation of biomes. Here, we suggest that both models are limited in that they ignore spatial processes, such as dispersal. We examine the contributions of dispersal to determining savanna and forest distributions using a reaction-diffusion model, comparing results qualitatively to empirical savanna and forest distributions in Africa. The diffusion model induces spatially aggregated distributions, separated by a stable savanna-forest boundary. The equilibrium position of that boundary depends not only on precipitation but also on the curvature of precipitation contours with some history dependence (although less than in the bistable model). This model predicts different dynamics in response to global change: the boundary continuously tracks climate, recovering following disturbances, unless remnant biome patches are too small.
Topological gene-expression networks recapitulate brain anatomy and function
Authors: Patania Alice , Selvaggi Pierluigi , Veronese Mattia , Dipasquale Ottavia , Expert Paul , Petri Giovanni
Published: November 2018

Understanding how gene expression translates to and affects human behaviour is one of the ultimate aims of neuroscience. In this paper, we present a pipeline based on Mapper, a topological simplification tool, to produce and analyze genes co-expression data. We first validate the method by reproducing key results from the literature on the Allen Human Brain Atlas, and the correlations between resting-state fMRI and gene co-expression maps. We then analyze a dopamine-related gene-set and find that co-expression networks produced by Mapper returned a structure that matches the well-known anatomy of the dopaminergic pathway. Our results suggest that topological network descriptions can be a powerful tool to explore the relationships between genetic pathways and their association with brain function and its perturbation due to illness and/or pharmacological challenge.
The coast-wide collapse in marine survival of west coast Chinook and steelhead: slow-moving catastrophe or deeper failure?
Authors: Welch David W. , Porter Aswea D. , Rechisky Erin L.
Published: November 2018

Accelerating decreases in survival are evident for northern Hemisphere salmon populations. We collated smolt survival and smolt-to-adult (marine) survival data for all regions of the Pacific coast of North America excluding California to examine the forces shaping salmon returns. A total of 3,055 years of annual survival estimates were available for Chinook (Oncorhynchus tshawytscha) and steelhead (O. mykiss). This dataset provides a fundamentally different perspective on west coast salmon conservation problems from the previously accepted view. We found that marine survival collapsed over the past half century by a factor of at least 4-5 fold to similar low levels (~1%) for most regions of the west coast. The size of the decline is too large to be compensated by freshwater habitat remediation or cessation of harvest, and too large-scale to be attributable to specific anthropogenic impacts such as dams in the Columbia River or salmon farming in British Columbia. Within the Columbia River, both smolt survivals during downstream migration in freshwater and adult return rates (SARs) of Snake River populations, often singled out as exemplars of poor survival, appear unexceptional and are in fact higher than estimates reported from other regions of the west coast lacking dams. Formal Columbia River rebuilding targets of 2-6% SARs may therefore be unachievable if regions with nearly pristine freshwater conditions also fail to achieve these targets. Finally, we present case studies demonstrating that the historical response to evidence that the salmon problems are primarily ocean-related was to re-emphasize freshwater actions and to stop work on ocean issues. With ocean temperatures forecast to increase far further, the failure of management to identify the drivers of salmon collapse and respond appropriately suggest that the future of most west coast salmon populations is bleak.
Structural insights into SETD3-mediated histidine methylation on β-actin
Authors: Guo Qiong , Liao Shanhui , Kwiatkowski Sebastian , Tomaka Weronika , Yu Huijuan , Wu Gao , Tu Xiaoming , Min Jinrong , Drozak Jakub , Xu Chao
Published: November 2018

SETD3 is a member of SET (Su(var)3-9, Enhancer of zeste, and Trithorax) domain protein superfamily and plays important roles in hypoxic pulmonary hypertension, muscle differentiation, and carcinogenesis. Recently, we have identified SETD3 as the actin-specific methyltransferase that methylates the N3 of His73 on β-actin. Here we present two structures of S-adenosyl-L-homocysteine-bound SETD3 in complex with either an unmodified β-actin peptide or its His-methylated variant. Structural analyses supported by the site-directed mutagenesis experiments and the enzyme activity assays indicated that the recognition and methylation of β-actin by SETD3 is highly sequence specific, and both SETD3 and β-actin adopt pronounce conformational changes upon binding to each other. In conclusion, the data show for the first time a catalytic mechanism of SETD3-mediated histidine methylation in β-actin, which not only throws light on protein histidine methylation phenomenon, but also facilitates the design of small molecule inhibitors of SETD3.
Role of geography and climatic oscillations in governing into-India dispersal of freshwater snails of the family: Viviparidae
Authors: Sil Maitreya , Aravind N. A. , Karanth K. Praveen
Published: November 2018

The Indian subcontinent has experienced numerous paleogeological and paleoclimatic events during the Cenozoic which shaped the biotic assembly over time in the subcontinent. The role of these events in governing the biotic exchange between Southeast Asia and Indian subregion is underexplored. We aimed to uncover the effects the collision of the Indian and Asian plate, marine transgression in the Bengal basin as well as the paleoclimatic changes in the subcontinent and adjoining regions, on the dispersal of freshwater snail family Viviparidae from Southeast Asia (SEA) to Indian subregion. Extensive sampling was carried out throughout the Indian subcontinent to capture the current diversity of the targeted lineages. Three mitochondrial and two nuclear markers were sequenced from these samples and combined with published sequences to reconstruct a near complete global phylogeny of Viviparidae. Molecular dating and ancestral range estimation were undertaken to obtain the time frame for the dispersal events. Results from these analyses were contrasted with paleoclimate and paleogeology to better understand the biogeography of Indian viviparids. Results support at least two dispersal events into India from Southeast Asia. The earlier event is likely to have occurred during a warm and humid Eocene period before a permanent land connection was established between the two landmasses. While the more recent dispersal occurred post-suturing and overlapped with a time in late Tertiary to Quaternary when arid climate prevailed. However, we could not firmly establish how the marine transgressions influenced the dispersal events. Even though most biotic exchange between India and SEA are noted to be post-suturing, our results add to a growing body of work that suggests faunal exchange pre-suturing probably mediated by intermittent land connections.
Production of very-high-amylose cassava by post-transcriptional silencing of branching enzyme genes
Authors: Zhou Wenzhi , Zhao Shanshan , He Shutao , Ma Qiuxiang , Lu Xinlu , Hao Xiaomeng , Wang Hongxia , Yang Jun , Zhang Peng
Published: November 2018

High amylose starch, a desired raw material in the starch industry, can be produced by plants deficient in the function of branching enzymes (BEs). Here we report the production of transgenic cassava plants with starches containing up to 50% amylose due to the constitutive expression of hair-pin dsRNAs targeting the BE1 or BE2 genes. A significant decrease in BE transcripts was confirmed in these transgenic plants by quantitative real-time RT-PCR. The absence of BE1 protein in the BE1-RNAi plant lines (BE1i) and a dramatically lower level of BE2 protein in the BE2-RNAi plant lines (BE2i) were further confirmed by Western blot assays. All transgenic plant lines were grown up in the field, but with reduced biomass production of the above-ground parts and storage roots compared to wild type (WT). Considerably high amylose content in the storage roots of BE2i plant lines was achieved, though not in BE1i plant lines. Storage starch granules of BE1i and BE2i plants had similar morphology as WT, however, the size of BE1i starch granules were bigger than that of WT. Comparisons of amylograms and thermograms of all three sources of storage starches revealed dramatic changes to the pasting properties and a higher melting temperature for BE2i starches. Glucan chain length distribution analysis showed a slight increase in chains of DP>36 in BE1i lines and a dramatic increase in glucan chains between DP 10-20 and DP>40 in BE2i lines, compared to that of WT starch. Furthermore, BE2i starches displayed a B-type X-ray diffraction pattern instead of the A-type pattern found in BE1i and WT starches. Therefore, cassava BE1 and BE2 function differently in storage root starch biosynthesis; silencing of cassava BE1 or BE2 caused various changes to starch physico-chemical properties and amylopectin structure. We also report that remarkably high amylose content in cassava starch has been first obtained in transgenic cassava by silencing of BE2 expression, thus showing a high potential for future industrial utilization.
DrugCombDB: a comprehensive database of drug combinations toward network medicine and combination therapy
Authors: Deng Lei , Zou Bo , Zhang Wenhao , Liu Hui
Published: November 2018

Drug combinations have demonstrated high efficacy and low adverse side effects compared to single drug administrations in cancer therapies, and thus draw intensive attentions from researchers and pharmaceutical enterprises. Thanks to the fast development of high-throughput screening (HTS) methods, the amount of available drug combination datasets has tremendously increased. However, existing drug combination databases are lack of indications of the drug combinations and quantitative dose-responses. Therefore, there is an urgent need for a comprehensive database that is crucial to both experimental and computational screening of drug combinations. In this paper, we present DrugCombDB, a comprehensive database dedicated to integrating drug combinations from various data sources. Concretely, the data sources include 1) high-throughput screening assays of drug combinations, 2) external databases, and 3) manual curations from PubMed literature. In total, DrugCombDB includes 1,127,969 experimental data points with quantitative dose response and concentrations of drug combinations covering 561 unique drugs and 104 human cancer cell lines, and 1,875 FDA approved or literature-supported drug combinations. In particular, we adopted the zero interaction potency (ZIP) model [2] to compute the scores determining the synergy or antagonism of two drugs. To facilitate the downstream usage of our data resource, we prepared multiple datasets that are ready for building prediction models of classification and regression analysis. A website with user-friendly data visualization is provided to help users access the wealth of data. Users can input a drug of interest to retrieve associated drug combinations, together with the supporting evidence sources and drug targets. Our database is available at http://drugcombdb.denglab.org/.
The Pupillary Light Response Reflects Visual Working Memory Content
Authors: Hustá Cecília , Dalmaijer Edwin , Belopolsky Artem , Mathôt Sebastiaan
Published: November 2018

Recent studies have shown that the pupillary light response (PLR) is modulated by higher cognitive functions, presumably through activity in visual sensory brain areas. Here we use the PLR to test the involvement of sensory areas in visual working memory (VWM). In two experiments, participants memorized either bright or dark stimuli. We found that pupils were smaller when a pre-stimulus cue indicated that a bright stimulus should be memorized; this reflects a covert shift of attention during encoding of items into VWM. Crucially, we obtained the same result with a post-stimulus cue, which shows that internal shifts of attention within VWM affect pupil size as well. Strikingly, pupil size reflected VWM content only briefly. This suggests that a shift of attention within VWM momentarily activates an “active” memory representation, but that this representation quickly transforms into a “hidden” state that does not rely on sensory areas.
Garcinia cambogia extract removes calcium oxalate kidney stones in both genetic and non-genetic Drosophila models of nephrolithiasis
Authors: Fan Qiuxia , Feng Xiaoming , Hong Xizhen , Gong Siqiao , Tian Jianwei , Hou Fanfan , Zhang Fujian
Published: November 2018

Kidney stone formers with family history have a high rate of stone recurrence after kidney stone removal surgery and there is no effective medication available for treatment. Here, we show that Garcinia cambogia extract (GCE) efficiently removes calcium oxalate kidney stones from Malpighian tubules in both genetic and non-genetic Drosophila models of nephrolithiasis, and hydroxycitrate -a major component of GCE, directly dissolves calcium oxalate stones in Drosophila Malpighian tubules ex vivo. Our study discovers a potential novel therapeutic strategy for the clinical treatment of nephrolithiasis and suggests that clinical-grade Garcinia cambogia extract could be used to treat patients with nephrolithiasis in the future.
Cyfip1 haploinsufficiency is associated with white matter changes, myelin thinning, reduction of mature oligodendrocytes and behavioural inflexibility:
Authors: Silva Ana I. , Haddon Josephine E. , Trent Simon , Syed Yasir Ahmed , Lin Tzu-Ching E. , Patel Yateen , Carter Jenny , Haan Niels , Honey Rob C. , Humby Trevor , Assaf Yaniv , Linden David E.J. , Owen Michael J. , Hall Jeremy , Wilkinson Lawrence
Published: November 2018

The biological basis of the increased risk for psychiatric disorders due to the pathogenic 15q11.2 copy number deletion is unknown. Previous work has shown disturbances in white matter tracts in human carriers of the deletion at this locus. Using a novel rat model, we have recapitulated low dosage of the candidate risk gene CYFIP1 present within the 15q11.2 interval to reveal alterations in white matter microstructure. Using diffusion tensor imaging, we first showed extensive white matter changes in Cyfip1 mutants that were most pronounced in the corpus callosum and external capsule. Transmission electron microscopy showed that these changes were associated with thinning of the myelin sheath in the corpus callosum. Myelin thinning was independent of changes in axon number or diameter but was associated with a reduction in the number of mature oligodendrocytes. Finally, we demonstrated functional effects on cognitive phenotypes sensitive to both disruptions in myelin and callosal circuitry.
Impact of high phosphorous and sodium on productivity and stress tolerance of Arundo donax plants
Authors: Cocozza Claudia , Brilli Federico , Miozzi Laura , Pignattelli Sara , Rotunno Silvia , Brunetti Cecilia , Giordano Cristiana , Pollastri Susanna , Centritto Mauro , Accotto Gian Paolo , Tognetti Roberto , Loreto Francesco
Published: November 2018

Arundo donax L. is an invasive species recently employed for biomass production that emits large amounts of isoprene, a volatile compound having important defensive role. Here, the potential of A. donax to grow in degraded soils, characterized by poor fertility, eutrophication and/or salinization, has been evaluated at morphological, biochemical and transcriptional level. Our results highlight sensitivity of A. donax to P deficiency. Moreover, we show that A. donax response to salt stress (high sodium, Na+), which impaired plant performance causing detrimental effects on leaf cells ultrastructure, is characterized by enhanced biosynthesis of antioxidant carotenoids and sucrose. Differently from Na+, high phosphorous (P) supply did not hamper photosynthesis although it affected carbon metabolism through reduction of starch content and by lowering isoprene emission. In particular, we revealed on salt-stress leaves that high P enhanced the expression of genes involved in abiotic stress tolerance, but further increased diffusive limitations to photosynthesis and slowed-down sugar turnover without modifying isoprene emission. Therefore, despite limiting productivity, high P improved A. donax tolerance to salinity by favouring the accumulation of carbohydrates that protect cells and increase osmotic potential, and by stimulating the synthesis of antioxidants that improves photo-protection and avoids excessive accumulation of reactive oxygen species.

Highlights

Arundo donax is sensitive to elevated salinity. High phosphorous supply to salt-stressed A. donax enhances transcriptomic changesthat induce the onset of physiological mechanisms of stress tolerance but limits productivity.
Social determinants of health, the family, and children's personal hygiene: a comparative study
Authors: Ramos-Morcillo Antonio Jesús , Moreno-Martínez Francisco José , Hernández-Susarte Ana María , Ruzafa-Martínez María
Published: November 2018

Aims

To examine differences in personal hygiene and in the perception of social rejection between children in reception centers and children living in a family setting.

Background

Little attention has been paid to the influence of the family as a unit on the personal hygiene behaviors of children.

Design

Cross-sectional study.

Methods

Children aged between 7-12 years were recruited from 2015 through 2017 from two centers in the Network of State Care Centers and from three schools selected from a rural, suburban and urban setting in the same region. A validated questionnaire on child personal hygiene habits was completed by 51 children in reception centers and 454 in normal families.

Results

Data shows worse results for the majority personal hygiene habits studied in children in reception centers than in children living in families. Multiple logistic regressions showed lower frequency of body washing, hand washing after defecating, use of soap in hand washing, tooth brushing, and dentist visits during the previous year. Also, a significantly higher proportion of children in reception centers had experienced social rejection for being dirty and smelling bad in comparison to the children living in families.

Conclusions

Deficient hygiene habits were observed in the offspring of families affected by the main features of social inequality, who were more likely to perceive social rejection for this reason and less likely to consider their family as the greatest influence on their personal hygiene practices. Promoting family practices designed to improve personal hygiene habits are needed specially in vulnerable families.
The genomic and epigenomic evolutionary history of papillary renal cell carcinomas
Authors: Zhu Bin , Poeta Maria Luana , Costantini Manuela , Zhang Tongwu , Shi Jianxin , Sentinelli Steno , Zhao Wei , Pompeo Vincenzo , Cardelli Maurizio , Alexandrov Boian S. , Otlu Burcak , Hua Xing , Jones Kristine , Brodie Seth , Toro Jorge R. , Yeager Meredith , Wang Mingyi , Hicks Belynda , Alexandrov Ludmil B. , Brown Kevin M. , Wedge David C. , Chanock Stephen , Fazio Vito Michele , Gallucci Michele , Landi Maria Teresa
Published: November 2018

Intratumor heterogeneity (ITH) and tumor evolution have been well described for clear cell renal cell carcinomas (ccRCC), but they are less studied for other kidney cancer subtypes. Here we investigate ITH and clonal evolution of papillary renal cell carcinoma (pRCC) and rarer kidney cancer subtypes, integrating whole-genome sequencing and DNA methylation data. In 29 tumors, up to 10 samples from the center to the periphery of each tumor, and metastatic samples in 2 cases, enable phylogenetic analysis of spatial features of clonal expansion, which shows congruent patterns of genomic and epigenomic evolution. In contrast to previous studies of ccRCC, in pRCC driver gene mutations and most arm-level somatic copy number alterations (SCNAs) are clonal. These findings suggest that a single biopsy would be sufficient to identify the important genetic drivers and targeting large-scale SCNAs may improve pRCC treatment, which is currently poor. While type 1 pRCC displays near absence of structural variants (SVs), the more aggressive type 2 pRCC and the rarer subtypes have numerous SVs, which should be pursued for prognostic significance.
Powerful statistical method to detect disease associated genes using publicly available GWAS summary data
Authors: Zhang Jianjun , Zhao Zihan , Guo Xuan , Guo Bin , Wu Baolin
Published: November 2018

Genome-wide association studies (GWAS) have thus far achieved substantial success. In the last decade a large number of common variants underlying complex diseases have been identified through GWAS. In most existing GWAS, the identified common variants are obtained by single marker based tests, that is, testing one single nucleotide polymorphisms (SNP) at a time. Generally the basic functional unit of inheritance is a gene, rather than a SNP. Thus, results from gene level association test can be more readily integrated with downstream functional and pathogenic investigation. In this paper, we propose a general gene-based p-value adaptive combination approach (GPA) which can integrate association evidence of multiple genetic variants using only GWAS summary statistics (either p-value or other test statistics). The proposed method could be used to test both continuous and binary traits through not only a single but also multiple studies, which helps overcome the limitation of existing methods that only can be applied to specific type of data. We conducted thorough simulation studies to verify that the proposed method controls type I errors well, and performs favorably compared to single-marker analysis and other existing methods. We demonstrated the utility of our proposed method through analysis of GWAS meta-analysis results for fasting glucose and lipids from the international MAGIC consortium and Global Lipids Consortium, respectively. The proposed method identified some novel traits associated genes which can improve our understanding of the mechanisms involved in β-cell function, glucose homeostasis and lipids traits.
Increased prediction ability in Norway spruce trials using a marker x environment interaction and non-additive genomic selection model
Authors: Chen Zhi-Qiang , Baison John , Pan Jin , Westin Johan , Rosario García Gil María , Wu Harry X.
Published: November 2018

A genomic selection (GS) study of growth and wood quality traits is reported based on control-pollinated Norway spruce families established in two Northern Swedish trials at two locations using exome capture as a genotyping platform. Non-additive effects including dominance and first-order epistatic interactions (including additive by additive, dominance by dominance, and additive by dominance) and marker-by-environment interaction (M×E) effects were dissected in genomic and phenotypic selection models. GS models partitioned additive and non-additive genetic variances more precisely compared with pedigree-based models. In addition, predictive ability (PA) in GS was substantially increased by including dominance and slightly increased by including M×E effects when these effects are significant. For velocity, response to GS (RGS) per year increased 91.3/43.7%, 86.9/82.9%, and 78.9/80.8% compared with response to phenotypic selection (RPS) per year when GS was based on 1) main marker effects (M), 2) M + M×E effects (A), and 3) A + dominance effects (AD) for site 1/site 2, respectively. This indicates that including M×E and dominance effects not only improves genetic parameter estimates but also may improve the genetic gain when they are significant. For tree height, Pilodyn, and modulus of elasticity (MOE), RGS per year improved up to 84.2%, 91.3%, and 92.6% compared with RPS per year, respectively.
Statistical physics of liquid brains
Authors: Piñero Jordi , Solé Ricard
Published: November 2018

Liquid neural networks (or “liquid brains”) are a widespread class of cognitive living networks characterised by a common feature: the agents (ants or immune cells, for example) move in space. Thus, no fixed, long-term agent-agent connections are maintained, in contrast with standard neural systems. How is this class of systems capable of displaying cognitive abilities, from learning to decision-making? In this paper, the collective dynamics, memory and learning properties of liquid brains is explored under the perspective of statistical physics. Using a comparative approach, we review the generic properties of three large classes of systems, namely: standard neural networks (“solid brains”), ant colonies and the immune system. It is shown that, despite their intrinsic physical differences, these systems share key properties with standard neural systems in terms of formal descriptions, but strongly depart in other ways. On one hand, the attractors found in liquid brains are not always based on connection weights but instead on population abundances. However, some liquid systems use fluctuations in ways similar to those found in cortical networks, suggesting a relevant role of criticality as a way of rapidly reacting to external signals.
Age-associated different transcriptome profiling in zebrafish and rat: insight into diversity of vertebrate aging
Authors: Kijima Yusuke , Wantong Wang , Igarashi Yoji , Yoshitake Kazutoshi , Asakawa Shuichi , Suzuki Yutaka , Watabe Shugo , Kinoshita Shigeharu
Published: November 2018

Background

Aging and death are inevitable for most species and are of intense interest for human beings. Most mammals, including humans, show obvious aging phenotypes, for example, loss of tissue plasticity and sarcopenia. In this regard, fish provide attractive models because of their unique aging characteristics. First, the lifespan of fish is highly varied and some long-lived fish can live for over 200 years. Second, some fish show anti-aging features and indeterminate growth throughout their life. Because these characteristics are not found in mammalian model organisms, exploring mechanisms of senescence in fish is expected to provide new insights into vertebrate aging. Therefore, we conducted transcriptome analysis for brain, gill, heart, liver and muscle from 2-month-, 7-month-, 16month- and 39-month-old zebrafish. In addition, we downloaded RNA-seq data for sequential age related gene expression in brain, heart, liver and muscle of rat (1). These RNA-seq data from two species were compared, and common and species-specific features of senescence were analyzed.

Results

Screening of differentially expressed genes (DEGs) in all zebrafish tissues examined revealed up-regulation of circadian genes and down-regulation ofhmgb3a. Comparative analysis of DEG profiles associated with aging between zebrafish and rat showed both conserved and clearly different aging phenomena. Furthermore, up-regulation of circadian genes with aging and down-regulation of collagen genes were observed in both species. On the other hand, in zebrafish, up-regulation of autophagy related genes in muscle andatf3in various tissues suggested fish-specific anti- aging characteristics. Consistent with our knowledge of mammalian aging, a tissue deterioration-related DEG profile was observed in rat. We also detected aging-associated down-regulation of muscle development and ATP metabolism-related genes in zebrafish gill. Correspondingly, hypoxia-related genes were systemically up-regulated in aged zebrafish, suggesting age-related hypoxia as a senescence modulator in fish.

Conclusions

Our results indicate both common and different aging profiles between fish and mammals. Gene expression profiles specific to fish will provide new insight for future translational research.
Network dynamics of Broca’s area during word selection
Authors: Conner Christopher R , Kadipasaoglu Cihan M , Shouval Harel Z , Hickok Gregory , Tandon Nitin
Published: November 2018

Current models of word-production in Broca’s area posit that sequential and staggered semantic, lexical, phonological and articulatory processes precede articulation. Using millisecond-resolution intra-cranial recordings, we evaluated spatiotemporal dynamics and high frequency functional interconnectivity between ventro-lateral prefrontal regions during single-word production. Through the systematic variation of retrieval, selection, and phonological loads, we identified specific activation profiles and functional coupling patterns between these regions that fit within current psycholinguistic theories of word production. However, network interactions underpinning these processes activate in parallel (not sequentially), while the processes themselves are indexed by specific changes in network state. We found evidence that suggests that pars orbitalis is coupled with pars triangularis during lexical retrieval, while lexical selection in Broca’s area is terminated via coupled activity with M1 at articulation onset. Taken together, this work reveals that speech production relies on very specific inter-regional couplings in rapid sequence in the language dominant hemisphere.
Lin28B is involved in curcumin-reversed paclitaxel chemoresistance and associated with poor prognosis in hepatocellular carcinoma
Authors: Tian Nan , Shangguan Wenbing , Zhou Zuolin , yao Yao , Fan Chunlei , Cai Lijun
Published: November 2018

Chemoresistance remains a big challenge in hepatocellular carcinoma (HCC) treatment. Several studies indicated that RNA-binding protein Lin28B serves an oncogenic role in HCC, but its activity in HCC chemotherapy has never been assessed. In this study, we found that overexpression of Lin28B significantly increased the paclitaxel chemoresistance in two different HCC cells lines while silencing Lin28B reduced the chemoresistance in paclitaxel-resistance HCC cells. Curcumin, a natural anti-cancer agent, increased the sensitivity of HCC cells to paclitaxel through inhibiting NF-κB stimulated Lin28B expression both in vitro and in vivo. Furthermore, by analyzing TCGA (The Cancer Genome Atlas) LIHC (liver hepatocellular carcinoma) and GSE14520 databases, we found that Lin28B was highly up-regulated in HCC tissue compared with that in normal tissue and associated with α-fetoprotein levels, and that patients with Lin28B higher expression had a significant shorter overall survival time than those with Lin28B lower expression. Our data reveal that Lin28B may serve as a predictive biomarker and a treatment target to reverse HCC chemotherapy resistance in future clinical practice.

Summary statement

upregulation of Lin28B not only confers poor prognosis in HCC patients but also increases chemoresistance in HCC cells. Thus, Lin28B may serve as a predictive biomarker for use to reverse chemoresistance in clinical practice.
Effects of food restriction on body mass, energy metabolism and thermogenesis in a tree shrew (Tupaia belangeri)
Authors: Gong Xue-na , Zhang Hao , Zhang Di , Zhu Wan-long
Published: November 2018

This study investigates the energy strategies of a small mammal in response to food shortages as a function of food restriction (FR), metabolic rate and ambient temperature. We subjected tree shrews (Tupaia belangeri) to FR and measured body mass, survival rate, resting metabolic rate (RMR), nonshivering thermogenesis (NST) and cytochromecoxidase (COX) activity of brown adipose tissue (BAT). Cold-exposed animals restricted to 80% ofad libitumfood intake had significantly increased RMR and NST and decreased body mass and survival rates compared with those kept at room temperature on the same FR level. Animals classified has having a high RMR consumed 30.69% more food than those classified as having a low RMR, but showed no differences in body mass or survival when restricted to 80% ofad libitumfood intake. These results indicate that tree shrews, known for their relatively high metabolic rates, are sensitive to periods of FR, which supports the metabolic switch hypothesis. Our findings are also consistent with the prediction that small mammals with food hoarding behaviors, like tree shrews, may have a lower tolerance for food shortages than non-hoarding species.
Dynamic brain interactions during picture naming
Authors: Saravani Aram Giahi , Forseth Kiefer J. , Tandon Nitin , Pitkow Xaq
Published: November 2018

Brain computations involve multiple processes by which sensory information is encoded and transformed to drive behavior. These computations are thought to be mediated by dynamic interactions between populations of neurons. Here we demonstrate that human brains exhibit a reliable sequence of neural interactions during speech production. We use an autoregressive hidden Markov model to identify dynamical network states exhibited by electrocorticographic signals recorded from human neurosurgical patients. Our method resolves dynamic latent network states on a trial-by-trial basis. We characterize individual network states according to the patterns of directional information flow between cortical regions of interest. These network states occur consistently and in a specific, interpretable sequence across trials and subjects: a fixed-length visual processing state is followed by a variable-length language state, and then by a terminal articulation state. This empirical evidence validates classical psycholinguistic theories that have posited such intermediate states during speaking. It further reveals these state dynamics are not localized to one brain area or one sequence of areas, but are instead a network phenomenon.
Females facilitate male patch discovery in a wild fish population
Authors: Snijders Lysanne , Kurvers Ralf H. J. M. , Krause Stefan , Tump Alan N. , Ramnarine Indar W. , Krause Jens
Published: November 2018

When individuals are more socially responsive to one sex than the other, the benefits they get from foraging socially are likely to depend on the sex composition of the social environment. We tested this hypothesis by performing experimental manipulations of guppy,Poecilia reticulata, sex compositions in the wild. Males found fewer novel food patches in the absence of females than in mixed-sex compositions, while female patch discovery did not differ between compositions. We argue that these results were driven by sex-dependent mechanisms of social association: Markov chain-based fission-fusion modeling revealed that males reduced sociality when females were absent, while less social individuals found fewer patches. Females were similarly social with or without males. Finally, males, but not females, preferred to join females over males at patches. Our findings reveal the relevance of considering how individual and population-level traits interact in shaping the adaptive value of social living in the wild.
The effect of chemical distances, physical distances, and the presence of sexuals on aggression inCataglyphisdesert ants
Authors: Inbar Shani , Privman Eyal
Published: November 2018

In social insects, non-nestmates interactions are typically agonistic and many factors may influence the degree of exhibited aggression. Two of these factors are the physical proximity between nests and the chemical dissimilarity between colonies’ chemical signatures. We studied a population sample of 43 colonies ofCataglyphis nigerants distributed along a transect of ∼4KM. This geographic distribution allowed us to examine correlations of aggression levels with physical and chemical distances. Ants were collected before mating season, when sexuals (unmated gynes and drones) could be found in nests. In our sample, colonies had either gynes or drones but never both. The presence of sexuals, therefore, was another factor we took into account in our behavioral analyses. Workers from nests with sexuals were more aggressive towards conspecifics than workers from nests where sexuals were absent. We also found those workers to be more vigorously active towards colonies with greater chemical distances, while workers from nests without sexuals were indifferent to chemical distances. We therefore concluded that ants are able to detect differences in chemical dissimilarity, but their aggression levels are mainly determined by other mechanisms. A possible additional mechanism is associative learning and long term memory of the chemical signatures of neighboring colonies. Such learning is supported by our finding that aggression is higher towards neighboring nests, which is in line with the previously reported ‘nasty neighbour’ effect inCataglyphisants. These results suggest that previous experience and learning of neural templates representing neighbors’ chemical cues is a stronger component than chemical dissimilarity in the mechanisms which determine aggression towards conspecifics in this species. We discuss possible explanations for the observed effect of the presence of sexuals on agonistic behavior and responsiveness to chemical distances.
Gut microbiota features of the geographically diverse Indian population
Authors: Shetty Sudarshan A.
Published: November 2018

Population-level microbial profiling allows for identifying the overarching features of the microbiome. Knowledge of population specific base-line gut microbiome features is important due to the widely reported impact of geography, lifestyle and dietary patterns on the microbiome composition, structure and function. Here, the gut microbiota of more than 1000 subjects across the length and breadth of India is presented. The publicly available 16S rRNA gene profiling data of faecal microbiota from the Landscape Of Gut Microbiome - Pan-India Exploration (LogMPIE) study representing 14 major cities, covering populations from northern, southern, eastern and western part of India analyzed. Majority of the dominant OTUs belonged to the Firmicutes, Bacteroidetes and Proteobacteria phyla. The rarer fraction was comprised of OTUs mainly from the phyla Verrucomicrobia and Spirochaetes. The median core size was estimated to consist of 12 OTUs (>80% prevalence) dominated by representing generaPrevotella,Faecalibacterium, Bacteroides, Roseburia, Megasphaera,EubacteriumandGemmiger. Geographic location explained majority of the variation in the gut microbiota community structure. The observations of the present study support the previous reports ofPrevotelladominance in the Indian population. ThePrevotella/Bacteroidesratio was high for the overall population irrespective of geographic location and did not correlate with BMI or age of the participants. Despite a rapid transition towards a western lifestyle, high prevalence ofTreponemain the Indian gut microbiota suggests that the urban population still harbors signatures of the traditional gut microbiome. The results presented here improve the knowledge of baseline microbiota in the Indian population across the length and breadth of the country. This study provides a base for future studies which need to incorporate numerous other confounding factors and their impact on the observed characteristics of the Indian gut microbiome.
It takes extremes to be robust
Authors: Rocha Felipe Bastos , Vibranovski Maria Dulcetti , Klaczko Louis Bernard
Published: November 2018

Phenotypic robustness is a central property of life, manifested in the ability of organisms to endure perturbing conditions throughout their development and often yield rather constant phenotypes. Fundamental questions on robustness (canalization) remain to be answered (see [1]). Do alleles that confer robustness against one perturbation also confer robustness to others? Is the robustness observed in multiple traits/taxa achieved through shared or specific mechanisms? Here, we describe an elementary model of trait development that yields phenotypic robustness without dedicated systems of developmental or transcriptional buffering. Robustness emerges when extremely low or high levels of gene activity lead to either depletion or saturation of the developmental system. We use this model to show that experimental results associating robustness to apparently redundantcis-regulatory sequences (from [2]) probably reflect a similar elementary system of saturation/depletion. We then analyze a large dataset of phenotypic responses of diverse traits of animals, plants and bacteria (from [3]) and show that the amount of response is mostly determined by the distance to the phenotypic extremes. Moreover, the most robust genotypes are often those that yield either extremely low or high phenotypes. Our results help reframing the concepts of canalization and plasticity, suggesting that phenotypic responses are mainly the result of variation in the very systems controlling each trait, rather than being attributable to either “plasticity genes” or “canalization genes”. Furthermore, they provide a hint on the causes of the genomic ubiquity of apparently redundantcis-regulatory sequences [4,5].