bluuebunny/crossref_metadata_2025 huggingface dataset:
Sleep in unnatural times: illuminated night negatively affects sleep and associated hypothalamic gene expressions in diurnal zebra finches
Authors: Batra Twinkle , Malik Indu , Prabhat Abhilash , Bhardwaj Sanjay Kumar , Kumar Vinod
Published: June 2020

We investigated the effects of exposure at ecologically relevant levels of dim light at night (dLAN) on sleep and the 24 h hypothalamic expression pattern of genes involved in the circadian timing (
per2, bmal1
,
reverb-β
,
cry1
,
ror-α
,
clock
) and sleep regulatory pathways (cytokines:
tlr4
,
tnf
-
α
,
il-1β
,
nos
; Ca
2+
-dependent pathway:
camk2
,
sik3
,
nr3a
; cholinergic receptor,
achm3
) in diurnal female zebra finches. Birds were exposed to 12 h light (150 lux) coupled with 12 h of absolute darkness or of 5 lux dim light for three weeks. dLAN fragmented the nocturnal sleep in reduced bouts, and caused sleep loss as evidenced by reduced plasma oxalate levels. Under dLAN, the 24 h rhythm of
per2
, but not
bmal1
or
reverb-β
, showed a reduced amplitude and altered peak expression time; however,
clock
,
ror-α
and
cry1
expressions showed an abolition of the 24 h rhythm. Decreased
tlr4
,
il-1β
and
nos
, and the lack of diurnal difference in
achm3
messenger RNA levels suggested an attenuated inhibition of the arousal system (hence, awake state promotion) under dLAN. Similarly, changes in
camk2
,
sik3
and
nr3a
expressions suggested dLAN-effects on Ca
2+
-dependent sleep-inducing pathways. These results demonstrate dLAN-induced negative effects on sleep and associated hypothalamic molecular pathways, and provide insights into health risks of illuminated night exposures to diurnal animals.
Urban moth communities suggest that life in the city favours thermophilic multi-dimensional generalists
Authors: Franzén Markus , Betzholtz Per-Eric , Pettersson Lars B. , Forsman Anders
Published: June 2020

Biodiversity is challenged worldwide by exploitation, global warming, changes in land use and increasing urbanization. It is hypothesized that communities in urban areas should consist primarily of generalist species with broad niches that are able to cope with novel, variable, fragmented, warmer and unpredictable environments shaped by human pressures. We surveyed moth communities in three cities in northern Europe and compared them with neighbouring moth assemblages constituting species pools of potential colonizers. We found that urban moth communities consisted of multi-dimensional generalist species that had larger distribution ranges, more variable colour patterns, longer reproductive seasons, broader diets, were more likely to overwinter as an egg, more thermophilic, and occupied more habitat types compared with moth communities in surrounding areas. When body size was analysed separately, results indicated that city occupancy was associated with larger size, but this effect disappeared when body size was analysed together with the other traits. Our findings indicate that urbanization imposes a spatial filtering process in favour of thermophilic species characterized by high intraspecific diversity and multi-dimensional generalist lifestyles over specialized species with narrow niches.
The evolution of high-fidelity social learning
Authors: Montrey Marcel , Shultz Thomas R.
Published: June 2020

A defining feature of human culture is that knowledge and technology continually improve over time. Such cumulative cultural evolution (CCE) probably depends far more heavily on how reliably information is preserved than on how efficiently it is refined. Therefore, one possible reason that CCE appears diminished or absent in other species is that it requires accurate but specialized forms of social learning at which humans are uniquely adept. Here, we develop a Bayesian model to contrast the evolution of high-fidelity social learning, which supports CCE, against low-fidelity social learning, which does not. We find that high-fidelity transmission evolves when (1) social and (2) individual learning are inexpensive, (3) traits are complex, (4) individual learning is abundant, (5) adaptive problems are difficult and (6) behaviour is flexible. Low-fidelity transmission differs in many respects. It not only evolves when (2) individual learning is costly and (4) infrequent but also proves more robust when (3) traits are simple and (5) adaptive problems are easy. If conditions favouring the evolution of high-fidelity transmission are stricter (3 and 5) or harder to meet (2 and 4), this could explain why social learning is common, but CCE is rare.
Cuckoos use host egg number to choose host nests for parasitism
Authors: Wang Longwu , Yang Canchao , He Gangbin , Liang Wei , Møller Anders Pape
Published: June 2020

To maximize their offspring success common cuckoo (
Cuculus canorus
) females should lay their eggs into host nests before incubation has begun. This ensures that the parasite chick hatches before all host chicks and can evict its foster siblings to monopolize host parental care. Many studies have demonstrated that most cuckoo eggs are indeed laid before the onset of host incubation. But cues used by female cuckoos to choose the right nest at the right time remain unclear. Here, we combine field observations with a field experiment to test whether female cuckoos use the number of eggs in the nests of their Oriental reed warbler (
Acrocephalus orientalis
) hosts to direct their choice. Over 8 years of field observations and 5 years of experiments, cuckoo females placed the majority of their eggs in nests with fewer than three host eggs, i.e. early in the laying sequence. For natural nests, the cuckoos may use information gleaned from the activity and behaviour of the host parents to make their choice. In our sets of experimental nests containing different numbers of model eggs, the vast majority of parasitism events occurred in nests containing a single egg. To our knowledge, this is the first field experiment showing that cuckoos choose host nests for parasitism based on the number of host eggs they contain. It appears that cuckoo females use the egg number to estimate the appropriate host nest stage for timely parasitism.
Chytrid rhizoid morphogenesis resembles hyphal development in multicellular fungi and is adaptive to resource availability
Authors: Laundon Davis , Chrismas Nathan , Wheeler Glen , Cunliffe Michael
Published: June 2020

Key to the ecological prominence of fungi is their distinctive cell biology, our understanding of which has been principally based on dikaryan hyphal and yeast forms. The early-diverging Chytridiomycota (chytrids) are ecologically important and a significant component of fungal diversity, yet their cell biology remains poorly understood. Unlike dikaryan hyphae, chytrids typically attach to substrates and feed osmotrophically via anucleate rhizoids. The evolution of fungal hyphae appears to have occurred from rhizoid-bearing lineages and it has been hypothesized that a rhizoid-like structure was the precursor to multicellular hyphae. Here, we show in a unicellular chytrid,Rhizoclosmatium globosum, that rhizoid development exhibits striking similarities with dikaryan hyphae and is adaptive to resource availability. Rhizoid morphogenesis exhibits analogous patterns to hyphal growth and is controlled by β-glucan-dependent cell wall synthesis and actin polymerization. Chytrid rhizoids growing from individual cells also demonstrate adaptive morphological plasticity in response to resource availability, developing a searching phenotype when carbon starved and spatial differentiation when interacting with particulate organic matter. We demonstrate that the adaptive cell biology and associated developmental plasticity considered characteristic of hyphal fungi are shared more widely across the Kingdom Fungi and therefore could be conserved from their most recent common ancestor.
Superorganismal anisogamy: queen–male dimorphism in eusocial insects
Authors: Lehtonen Jussi , Helanterä Heikki
Published: June 2020

Colonies of insects such as ants and honeybees are commonly viewed as ‘superorganisms’, with division of labour between reproductive ‘germline-like’ queens and males and ‘somatic’ workers. On this view, properties of the superorganismal colony are comparable with those of solitary organisms to such an extent that the colony itself can be viewed as a unit analogous to an organism. Thus, the concept of a superorganism can be useful as a guide to thinking about life history and allocation traits of colonies as a whole. A pattern that seems to reoccur in insects with superorganismal societies is size dimorphism between queens and males, where queens tend to be larger than males. It has been proposed that this is analogous to the phenomenon of anisogamy at the level of gametes in organisms with separate sexes; more specifically, it is suggested that this caste dimorphism may have evolved via similar selection pressures as gamete dimorphism arises in the ‘gamete competition’ theory for the evolution of anisogamy. In this analogy, queens are analogous to female gametes, males are analogous to male gametes, and colony survival is analogous to zygote survival in gamete competition theory. Here, we explore if this question can be taken beyond an analogy, and whether a mathematical model at the superorganism level, analogous to gamete competition at the organism level, may explain the caste dimorphism seen in superorganismal insects. We find that the central theoretical idea holds, but that there are also significant differences between the way this generalized ‘propagule competition’ theory operates at the levels of solitary organisms and superorganisms. In particular, we find that the theory can explain superorganismal caste dimorphism, but compared with anisogamy evolution, a central coevolutionary link is broken, making the requirements for the theory to work less stringent than those found for the evolution of anisogamy.
Adaptive reshaping of the hormonal phenotype after social niche transition in adulthood
Authors: Mutwill Alexandra M. , Zimmermann Tobias D. , Hennicke Antonia , Richter S. Helene , Kaiser Sylvia , Sachser Norbert
Published: June 2020

Phenotypic plasticity allows individuals to adjust traits to the environment. Whether long-term adjustments of the phenotype occur during later life stages is largely unknown. To address this question, we examined whether hormonal phenotypes that are shaped by the environment during adolescence can still be reshaped in full adulthood. For this, guinea pig males were either housed in mixed-sex colonies or in heterosexual pairs. In adulthood, males were individually transferred to pair housing with a female. This way, a social niche transition was induced in colony-housed males, but not in pair-housed males. Before transfer, corresponding to findings in adolescence, adult colony-housed males showed significantly higher baseline testosterone levels and lower cortisol responsiveness than pair-housed males. One month after transfer, the hormonal phenotype of colony-housed males was changed towards that of pair-housed males: animals showed comparable baseline testosterone levels and cortisol responsiveness was significantly increased in colony-housed males. This endocrine readjustment builds the basis for an adaptive behavioural tactic in the new social situation. Thus, an adaptive change of the behavioural phenotype may still occur in adulthood via modification of underlying mechanisms. This suggests a greater role for developmental plasticity in later life stages than is commonly presumed.
Cooperative policing behaviour regulates reproductive division of labour in a termite
Authors: Sun Qian , Hampton Jordan D. , Merchant Austin , Haynes Kenneth F. , Zhou Xuguo
Published: June 2020

Reproductive conflicts are common in insect societies where helping castes retain reproductive potential. One of the mechanisms regulating these conflicts is policing, a coercive behaviour that reduces direct reproduction by other individuals. In eusocial Hymenoptera (ants, bees and wasps), workers or the queen act aggressively towards fertile workers, or destroy their eggs. In many termite species (order Blattodea), upon the death of the primary queen and king, workers and nymphs can differentiate into neotenic reproductives and inherit the breeding position. During this process, competition among neotenics is inevitable, but how this conflict is resolved remains unclear. Here, we report a policing behaviour that regulates reproductive division of labour in the eastern subterranean termite,
Reticulitermes flavipes
. Our results demonstrate that the policing behaviour is a cooperative effort performed sequentially by successful neotenics and workers. A neotenic reproductive initiates the attack of the fellow neotenic by biting and displays alarm behaviour. Workers are then recruited to cannibalize the injured neotenic. Furthermore, the initiation of policing is age-dependent, with older reproductives attacking younger ones, thereby inheriting the reproductive position. This study provides empirical evidence of policing behaviour in termites, which represents a convergent trait shared between eusocial Hymenoptera and Blattodea.
Terrilactibacillus tamarindi sp. nov., isolated from bark of Tamarindus indica
Authors: Kingkaew Engkarat , Nuhwa Ratthanatda , Piluk Jirabhorn , Thitiprasert Sitanan , Thongchul Nuttha , Tanasupawat Somboon
Published: June 2020

A Gram-stain-positive, catalase-positive, facultatively anaerobic, terminal-spore-forming rod, designated strain BCM23-1T, was isolated from bark ofTamarindus indicacollected from Chiang Mai Province, Thailand. This strain producedd-lactic acid from glucose. It grew at 20–45 °C (optimum, 30 °C), pH 3.5–9 (optimum, pH 7.0) and in the presence of 1–4 % (w/v) NaCl. The cell-wall peptidoglycan containedmeso-diaminopimelic acid (A1γ). The major isoprenoid quinone was menaquinone 7 (MK-7). Polar lipids analysis revealed the presence of diphosphatidylglycerol, phosphatidylglycerol, an unidentified aminophospholipid, an unidentified phospholipid and an unidentified lipid. The predominant cellular fatty acids were anteiso-C17 : 0, anteiso-C15:0,and iso-C16 : 0when cultivated on GYP agar plates. The 16S rRNA gene sequence similarity between strain BCM23-1TandTerrilactibacillus laevilacticusNK26-11Twas 98.3 %. The draft genome of BCM23-1Twas 3.24 Mb in size and contained 3088 coding sequences with anin silicoDNA G+C content of 37.1 mol%. The values of ANIb, ANIm and digital DNA–DNA hybridization between strain BCM23-1TandT. laevilacticusNK26-11Twere 89.9, 90.8 and 40.4 %, respectively. The results of phenotypic and chemotaxonomic, 16S rRNA gene sequence similarity, and whole genome analyses support strain BCM23-1Tas representing a novel species ofTerrilactibacillusfor which the nameTerrilactibacillus tamarindisp. nov. is proposed. The type strain is BCM23-1T(=LMG 31662T=JCM 33748T=TISTR 2841T).
Towards an understanding of the avian virome
Authors: François Sarah , Pybus Oliver G
Published: June 2020

The last two decades have seen the rise of viromics, the study of viral communities through the detection and characterization of virus genome sequences. Here we systematically review and summarize the scope and limitations of our current understanding of avian viromes, in both domesticated and wild-bird populations. We compare this viromic work to the broader literature on avian prokaryotic microbiomes, and highlight the growing importance of structured sampling and experimental design for testing explanatory hypotheses. We provide a number of recommendations for sample collection and preliminary data analysis to guide the development of avian viromics. Avian viromes have the potential to inform disease surveillance in poultry and improve our understanding of the risk of zoonotic viruses to human health.
Diversity of avian influenza A(H5N6) viruses in wild birds in southern China
Authors: Zhang Tao , Fan Kai , Zhang Xue , Xu Yujuan , Xu Jian , Xu Bing , Li Ruiyun
Published: June 2020

The predominance of H5N6 in ducks and continuous human cases have heightened its potential threat to public health in China. Therefore, the detection of emerging variants of H5N6 avian influenza viruses has become a priority for pandemic preparedness. Questions remain as to its origin and circulation within the wild bird reservoir and interactions at the wild–domestic interface. Samples were collected from migratory birds in Poyang Lake, Jiangxi Province, PR China during the routine bird ring survey in 2014–16. Phylogenetic and coalescent analyses were conducted to uncover the evolutionary relationship among viruses circulating in wild birds. Here, we report the potential origin and phylogenetic diversity of H5N6 viruses isolated from wild birds in Poyang Lake. Sequence analyses indicated that Jiangxi H5N6 viruses most likely evolved from Eurasian-derived H5Nx and H6N6 viruses through multiple reassortment events. Crucially, the diversity of the HA gene implies that these Jiangxi H5N6 viruses have diverged into two primary clades − clade 2.3.4.4 and clade 2.3.2.1 c. Phylogenetic analysis revealed two independent pathways of reassortment during 2014–16 that might have facilitated the generation of emerging variants within wild bird populations as well as inter-species infections. Our findings contribute to our understanding of the genetic diversification of H5N6 viruses in the wild bird population. These results highlight the necessity of large-scale surveillance of wild birds in the Poyang Lake area to address the threat of regional epizootic epidemics and attendant pandemics.
Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands
Authors: Wyrsch Ethan R. , Chowdhury Piklu Roy , Wallis Louise , Cummins Max L. , Zingali Tiziana , Brandis Kate J. , Djordjevic Steven P.
Published: June 2020

Wildlife, and birds in particular, play an increasingly recognized role in the evolution and transmission of

Escherichia coli

that pose a threat to humans. To characterize these lineages and their potential threat from an evolutionary perspective, we isolated and performed whole-genome sequencing on 11 sequence types (STs) of

E. coli

recovered from the desiccated faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands located in geographically different regions of New South Wales, Australia. Carriage of virulence-associated genes was limited, and no antimicrobial resistance genes were detected, but novel variants of an insertion element that plays an important role in capturing and mobilizing antibiotic resistance genes, IS26, were identified and characterized. The isolates belonged to phylogroups B1 and D, including types known to cause disease in humans and animals. Specifically, we found

E. coli

ST58, ST69, ST162, ST212, ST446, ST906, ST2520, ST6096 and ST6241, and a novel phylogroup D strain, ST10208. Notably, the ST58 strain hosted significant virulence gene carriage. The sequences of two plasmids hosting putative virulence-associated factors with incompatibility groups I1 and Y, an extrachromosomal integrative/conjugative element, and a variant of a large

Escherichia

phage of the family Myoviridae, were additionally characterized. We identified multiple epidemiologically relevant gene signatures that link the ibis isolates to sequences from international sources, plus novel variants of IS26 across different sequence types and in different contexts.
The hypothalamus as a hub for SARS-CoV-2 brain infection and pathogenesis
Authors: Nampoothiri Sreekala , Sauve Florent , Ternier Gaëtan , Fernandois Daniela , Coelho Caio , Imbernon Monica , Deligia Eleonora , Perbet Romain , Florent Vincent , Baroncini Marc , Pasquier Florence , Trottein François , Maurage Claude-Alain , Mattot Virginie , Giacobini Paolo , Rasika S. , Prevot Vincent
Published: June 2020

Most patients with COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), display neurological symptoms, and respiratory failure in certain cases could be of extra-pulmonary origin. Hypothalamic neural circuits play key roles in sex differences, diabetes, hypertension, obesity and aging, all risk factors for severe COVID-19, besides being connected to olfactory/gustative and brainstem cardiorespiratory centers. Here, human brain gene-expression analyses and immunohistochemistry reveal that the hypothalamus and associated regions express angiotensin-converting enzyme 2 and transmembrane proteinase, serine 2, which mediate SARS-CoV-2 cellular entry, in correlation with genes or pathways involved in physiological functions or viral pathogenesis. A post-mortem patient brain shows viral invasion and replication in both the olfactory bulb and the hypothalamus, while animal studies indicate that sex hormones and metabolic diseases influence this susceptibility.
Characterization of the exopolysaccharide biosynthesis pathway inMyxococcus xanthus
Authors: Pérez-Burgos María , García-Romero Inmaculada , Jung Jana , Schander Eugenia , Valvano Miguel A. , Søgaard-Andersen Lotte
Published: June 2020

Myxococcus xanthusarranges into two morphologically distinct biofilms depending on its nutritional status, i.e. coordinately spreading colonies in the presence of nutrients and spore-filled fruiting bodies in the absence of nutrients. A secreted polysaccharide referred to as exopolysaccharide (EPS) is a structural component of both biofilms and is also important for type IV pili-dependent motility and fruiting body formation. Here, we characterize the biosynthetic machinery responsible for EPS biosynthesis using bioinformatics, genetics, heterologous expression, and biochemical experiments. We show that this machinery constitutes a Wzx/Wzy-dependent pathway dedicated to EPS biosynthesis. Our data support that EpsZ (MXAN_7415) is the polyisoprenyl-phosphate hexose-1-phosphate transferase responsible for initiation of the repeat unit synthesis. Heterologous expression experiments support that EpsZ has galactose-1-P transferase activity. Moreover, MXAN_7416, renamed WzxEPS, and MXAN_7442, renamed WzyEPS, are the Wzx flippase and Wzy polymerase responsible for translocation and polymerization of the EPS repeat unit, respectively. Also, in this pathway, EpsV (MXAN_7421) is the polysaccharide co-polymerase and EpsY (MXAN_7417) the outer membrane polysaccharide export (OPX) protein. Mutants with single in-frame deletions in the five corresponding genes had defects in type IV pili-dependent motility and a conditional defect in fruiting body formation. Furthermore, all five mutants were deficient in type IV pili formation and genetic analyses suggest that EPS and/or the EPS biosynthetic machinery stimulates type IV pili extension. Additionally, we identify a polysaccharide biosynthesis gene cluster, which together with an orphan gene encoding an OPX protein make up a complete Wzx/Wzy-dependent pathway for synthesis of an unknown polysaccharide.

Importance

The secreted polysaccharide referred to as exopolysaccharide (EPS) has important functions in the social life cycle ofM. xanthus; however, little is known about how EPS is synthesized. Here, we characterized the EPS biosynthetic machinery and show that it makes up a Wzx/Wzy-dependent pathway for polysaccharide biosynthesis. Mutants lacking a component of this pathway had reduced type IV pili-dependent motility and a conditional defect in development. Also, these analysis suggest that EPS and/or the EPS biosynthetic machinery is important for type IV pili formation.
Combining Mechanistic Models and Machine Learning for Personalized Chemotherapy and Surgery Sequencing in Breast Cancer
Authors: Axenie Cristian , Kurz Daria
Published: June 2020

Mathematical and computational oncology has increased the pace of cancer research towards the advancement of personalized therapy. Serving the pressing need to exploit the large amounts of currently underutilized data, such approaches bring a significant clinical advantage in tailoring the therapy. CHIMERA is a novel system that combines mechanistic modelling and machine learning for personalized chemotherapy and surgery sequencing in breast cancer. It optimizes decision-making in personalized breast cancer therapy by connecting tumor growth behaviour and chemotherapy effects through predictive modelling and learning. We demonstrate the capabilities of CHIMERA in learning simultaneously the tumor growth patterns, across several types of breast cancer, and the pharmacokinetics of a typical breast cancer chemotoxic drug. The learnt functions are subsequently used to predict how to sequence the intervention. We demonstrate the versatility of CHIMERA in learning from tumor growth and pharmacokinetics data to provide robust predictions under two, typically used, chemotherapy protocol hypotheses.
Structural basis of a public antibody response to SARS-CoV-2
Authors: Yuan Meng , Liu Hejun , Wu Nicholas C. , Lee Chang-Chun D. , Zhu Xueyong , Zhao Fangzhu , Huang Deli , Yu Wenli , Hua Yuanzi , Tien Henry , Rogers Thomas F. , Landais Elise , Sok Devin , Jardine Joseph G. , Burton Dennis R. , Wilson Ian A.
Published: June 2020

Molecular-level understanding of human neutralizing antibody responses to SARS-CoV-2 could accelerate vaccine design and facilitate drug discovery. We analyzed 294 SARS-CoV-2 antibodies and found that IGHV3-53 is the most frequently used IGHV gene for targeting the receptor binding domain (RBD) of the spike (S) protein. We determined crystal structures of two IGHV3-53 neutralizing antibodies +/- Fab CR3022 ranging from 2.33 to 3.11 Å resolution. The germline-encoded residues of IGHV3-53 dominate binding to the ACE2 binding site epitope with no overlap with the CR3022 epitope. Moreover, IGHV3-53 is used in combination with a very short CDR H3 and different light chains. Overall, IGHV3-53 represents a versatile public VH in neutralizing SARS-CoV-2 antibodies, where their specific germline features and minimal affinity maturation provide important insights for vaccine design and assessing outcomes.
The epidemiological signature of pathogen populations that vary in the relationship between free-living survival and virulence
Authors: Gomez Lourdes M. , Meszaros Victor A , Turner Wendy C. , Ogbunugafor C. Brandon
Published: June 2020

The relationship between parasite virulence and transmission is a pillar of evolutionary theory that has specific implications for public health. Part of this canon involves the idea that virulence and free-living survival (a key component of transmission) may have different relationships in different host-parasite systems. Most examinations of the evolution of virulence-transmission relationships—theoretical or empirical in nature—tend to focus on the evolution of virulence, with transmission a secondary consideration. And even within transmission studies, the focus on free-living survival is a smaller subset, though recent studies have examined its importance in the ecology of infectious diseases. Few studies have examined the epidemic-scale consequences of variation in survival across different virulence-survival relationships. In this study, we utilize a mathematical model motivated by aspects of SARS-CoV-2 natural history to investigate how evolutionary changes in survival may influence several aspects of disease dynamics at the epidemiological scale. Across virulence-survival relationships (where these traits are positively or negatively correlated), we found that small changes (5% above and below the nominal value) in survival can have a meaningful effect on certain outbreak features, including theR0, and the size of the infectious peak in the population. These results highlight the importance of properly understanding the mechanistic relationship between virulence and parasite survival, as evolution of increased survival across different relationships with virulence will have considerably different epidemiological signatures.
Quantitative data independent acquisition glycoproteomics of sparkling wine
Authors: Pegg Cassandra L. , Phung Toan K. , Caboche Christopher H. , Niamsuphap Suchada , Bern Marshall , Howell Kate , Schulz Benjamin L.
Published: June 2020

Sparkling wine is an alcoholic beverage enjoyed around the world. The sensory properties of sparkling wine depend on a complex interplay between the chemical and biochemical components in the final product. Glycoproteins have been linked to positive and negative qualities in sparkling wine, but the glycosylation profiles of sparkling wine have not been previously investigated in detail. We analysed the glyco/proteome of sparkling wines using protein- and glycopeptide-centric approaches. We developed an automated workflow that created ion libraries to analyse Sequential Window Acquisition of all THeoretical mass spectra (SWATH) Data Independent Acquisition (DIA) mass spectrometry data based on glycopeptides identified by Byonic. We applied our workflow to three pairs of experimental sparkling wines to assess the effects of aging on lees and of different yeast strains used in the Liqueur de Tirage for secondary fermentation. We found that aging a cuvée on lees for 24 months compared to 8 months led to a dramatic decrease in overall protein abundance and an enrichment in large glycans at specific sites in some proteins. Secondary fermentation of a Riesling wine withSaccharomyces cerevisiaeyeast strain Siha4 produced more yeast proteins and glycoproteins than withS. cerevisiaeyeast strain DV10. The abundance and glycosylation profiles of grape glycoproteins were also different between grape varieties. This work represents the first in-depth study into protein- and peptide-specific glycosylation in sparkling wines and describes a quantitative glycoproteomic SWATH/DIA workflow that is broadly applicable to other sample types.
Epigenetic Consequences of Hormonal Interactions between Opposite-sex Twin Fetuses
Authors: Kong Siming , Peng Yong , Chen Wei , Ma Xinyi , Wei Yuan , Zhao Yangyu , Li Rong , Yan Liying , Qiao Jie
Published: June 2020

In human opposite-sex twins, certain phenotypic traits of the female are affected negatively by testosterone transfer from the male, while the male may or may not be affected by the femalein utero. However, no study was carried out to uncover the epigenetic basis of these effects. Here, we generated DNA methylation data from 54 newborn twins and histone modification data from 14 newborn twins, including female-female (FF), female-male (FM), and male-male (MM) newborn twins, to exclude the effects of postnatal environment and socialization, and investigated the epigenetic consequences of prenatal interactions between female and male gonadal hormones. We found that FM-Fs (female in FM twins) were distinguishable from FF twins by their DNA methylome, as were FM-Ms (male in FM twins) from MM twins. The correlation between genome-wide DNA methylation of females and males showed that FM-Fs, but not FFs, were closer to males from FM-Ms and MMs. Interestingly, the DNA methylomic differences between FM-Fs and FFs, but not those between FM-Ms and MMs, were linked to cognition and the nervous system. Meanwhile, FM-Ms and MMs, but not FM-Fs and FFs, displayed differential histone modification of H3K4me3, which were linked to immune responses. These findings provide epigenetic evidence for the twin testosterone transfer hypothesis and explain how prenatal hormone exposure is linked to reported and novel traits of childhood and adult through the epigenome in opposite-sex twins.

Author Summary

Prenatal exposure to testosterone may affect physiological, cognitive, and behavioral traits in females with male co-twins, while the males in opposite-sex twins present weak and inconsistent influences. In this study, we systematically investigated the hormonal interactions between opposite-sex twins in newborns from epigenetics including DNA methylation and histone modifications. We show that DNA methylome in FM-Fs (female in FM twins) was different from FF twins and their DNA methylomic differences were associated with cognition and the nervous system. We also suggest that FM-Ms (male in FM twins) were distinguishable from MM twins by their DNA methylome and FM-MsversusMMs displayed differential histone modification of H3K4me3, which were linked to immune responses. Our study provides insight into the epigenetic explanation for hormonal influences between opposite-sex fetuses.
Hippocampal hyperactivity in a rat model of Alzheimer’s disease
Authors: Sosulina Liudmila , Mittag Manuel , Geis Hans-Rüdiger , Hoffmann Kerstin , Klyubin Igor , Qi Yingjie , Steffen Julia , Friedrichs Detlef , Henneberg Niklas , Fuhrmann Falko , Justus Daniel , Keppler Kevin , Cuello A. Claudio , Rowan Michael J. , Fuhrmann Martin , Remy Stefan
Published: June 2020

Neuronal network dysfunction is a hallmark of Alzheimer’s disease (AD). However, the underlying pathomechanisms remain unknown. We analyzed the hippocampal micronetwork in a rat model of AD at an early disease stage at the beginning of extracellular amyloid beta (Aβ) deposition. We established two-photon Ca2+-imagingin vivoin the hippocampus of rats and found hyperactivity of CA1 neurons. Patch-clamp recordings in brain slicesin vitrorevealed changes in the passive properties and intrinsic excitability of CA1 pyramidal neurons. Furthermore, we observed increased neuronal input resistance and prolonged action potential width in CA1 pyramidal neurons. Surprisingly, all parameters measured to quantify synaptic inhibition and excitation onto CA1 pyramidal neurons were intact suggesting a cell immanent deficit. Our data support the view that altered intrinsic excitability of CA1 neurons may precede inhibitory dysfunction at an early stage of disease progression.
Modulation of Early Mitotic Inhibitor 1 (EMI1) Depletion on the Sensitivity of PARP Inhibitors in BRCA1 Mutated Triple-Negative Breast Cancer Cells
Authors: Moustafa Dina , Abd Elwahed Maha R. , Elsaid Hanaa H. , Parvin Jeffrey D.
Published: June 2020

Triple negative breast cancer (TNBC) represents approximately 10–15% of all breast cancers and has a poor outcome as it lacks a receptor target for therapy, and TNBC is frequently associated with a germline mutation ofBRCA1. Poly (ADP-ribose) polymerase inhibitor (PARPi) drugs have demonstrated some effectiveness in treatingBRCA1orBRCA2mutated breast and ovarian cancers but resistance to PARPi is common. Published results found that resistance to Olaparib, a PARPi, can be due to downregulation of EMI1 and the consequent upregulation of the RAD51 recombinase. Using a tissue culture-based cell viability assay, we extended those observations to another PARPi and to other chemotherapy drugs that affect DNA repair or the cell cycle. As we expected, EMI1 downregulation resulted in resistance to another PARPi drug, Talazoparib. EMI1 downregulation also led to resistance to other cytotoxic drugs, Cisplatin and CHK1 inhibitor. Surprisingly, EMI1 depletion also led to resistance to a MEK inhibitor, though this inhibitor blocks cells in G1 phase of the cell cycle and would not be expected to be sensitive to EMI1 levels. Notably, increasing the RAD51 protein expression only partially recapitulated the effects of EMI1 depletion in causing resistance to different PARPi and the other cytotoxic drugs. These results suggest that the downstream effects of EMI1 downregulation that contribute to PARPi resistance are increasing the concentration of RAD51 protein in the cell and blocking mitotic entry. We found that combining CHK1 inhibitor with olaparib results in restoration of sensitivity even when EMI1 expression is downregulated. This combination therapy may be a means to overcome the PARPi resistance in BRCA1-deficient TNBC cells.
(3S,6E)-Nerolidol-mediated rendezvous of Cyclocephalini beetles,Cyclocephala paraguayensis, in bottle gourd flowers
Authors: Favaris Arodí P. , Túler Amanda C. , Silva Weliton D. , Rodrigues Sérgio R. , Leal Walter S. , Bento José M. S.
Published: June 2020

Cyclocephalini beetles of genusCyclocephala(Coleoptera: Melolonthidae: Dynastinae) use flowers of some plants as food, shelter, and mating stands. However, little is known about floral scent chemistry involved in this interaction. Here we show that a sesquiterpene alcohol mediates attraction ofCyclocephala paraguayensisArrow on bottle gourd flowers,Lagenaria siceraria(Curcubitaceae). Both males and females started to aggregate on flowers at twilight; after that, mating began and remained for the entire night. The major constituent of the airborne volatiles fromL. sicerariawas fully characterized as(3S,6E)-nerolidol, which elicited electroantennographic responses on male and female antennae. Field bioassays showed that traps baited with the natural stereoisomer or a mix of nerolidol isomers captured significantly more males and females ofC. paraguayensisthan control traps. Analysis from the gut content of these Cyclocephalini beetles showed the presence of pollen, suggesting that they also use bottle gourd flowers for their nourishment. Taken together, these results suggest that(3S,6E)-nerolidol plays an essential role in the reproductive behavior ofC. paraguayensisby eliciting aggregation, mating, and feeding.
Organization of cortico-hippocampal networks in the human brain
Authors: Barnett Alexander J. , Reilly Walter , Dimsdale-Zucker Halle R. , Mizrak Eda , Reagh Zachariah , Ranganath Charan
Published: June 2020

Episodic memory depends on interactions between the hippocampus and the interconnected regions comprising default mode network (DMN). Here, using data-driven analyses of resting-state fMRI data, we identified the networks that interact with the hippocampus—the DMN and a “Medial Temporal Network” (MTN) that included regions in the medial temporal lobe and retrosplenial cortex. We observed that the MTN plays a critical role in connecting the visual network to the DMN and hippocampus. The DMN could be further divided into three subnetworks: a “Posterior-Medial” Subnetwork comprised of posterior cingulate, and lateral parietal cortices, an “Anterior-Temporal” Subnetwork comprised of regions in the temporopolar, and dorsomedial prefrontal cortex, and a “Medial-Prefrontal” Subnetwork comprised of regions primarily in the medial prefrontal cortex. These networks vary in their functional connectivity along the hippocampal long-axis and represent different kinds of information during memory-guided decision-making. Finally, a Neurosynth meta-analysis of fMRI studies suggests new hypotheses regarding the functions of the MTN and DMN subnetworks, providing a framework to guide future research on the neural architecture of episodic memory.
Assessing the JEOL CRYO ARM 300 for high-throughput automated single-particle cryo-EM in a multiuser environment
Authors: Fislage Marcus , Shkumatov Alexander V. , Stroobants Annelore , Efremov Rouslan G.
Published: June 2020

Single-particle cryo-EM has become an indispensable structural biology method. It requires regular access to high-resolution electron cryogenic microscopes. To fully utilize the capacity of the expensive high-resolution instruments, the time used for data acquisition and the rate of data collection have to be maximized. This in turn requires high stability and high uptime of the instrument. One of the first 300 kV JEOL CRYO ARM 300 microscopes has been installed at the cryo-EM facility BECM at VIB-VUB, Brussels, where the microscope is used for continuous data collection on multiple projects. Here, the suitability and performance of the microscope is assessed for high-throughput single-particle data collection. In particular, the properties of the illumination system, the stage stability and ice contamination rates are reported. The microscope was benchmarked using mouse heavy-chain apoferritin which was reconstructed to a resolution of 1.9 Å. Finally, uptime and throughput statistics of the instrument accumulated during the first six months of the facility operation in user access mode are reported.
Premium misrating in federal crop insurance programs: scale, geography, and fiscal impacts
Authors: Chen Zhangliang , Dall'Erba Sandy , Sherrick Bruce J.
Published: June 2020

Purpose

Federal crop insurance programs are the primary risk management programs of the US farm programs. Currently, these programs have been criticized for being disproportionally in favor of the riskier areas. Despite previous researchers having widely speculated its existence, a formal study of the scale, spatial pattern and fiscal impacts of such misrating phenomenon is still missing in the literature.

Design/methodology/approach

This paper first purposes an empirically testable definition of misrating, and then detects the scale of the misrating phenomenon by using over two million actuarial records collected by United States Department of Agriculture (USDA's) risk management agency since 1989. Furthermore, multiple spatial statistics methods have been adopted to study the spatial patterns of the misrating statuses. Finally, the paper builds a simple theoretical model to study the potential fiscal impacts of any policy attempts to mitigate the misrating issue.

Findings

The result reveals that roughly 40% of the counties display some degree of misrating. Furthermore, the distribution of misrating displays a significant pattern of positive global spatial autocorrelation, which reflects the existence of regional clusters of premium rate mispricing. Last but not least, the paper concludes that whether an attempt toward fair rating decreases the total program outlay or not relies on the demand elasticity of crop insurance in both overrated and underrated regions.

Originality/value

This paper offers the first attempt to quantify the scale, identify the spatial pattern and evaluate the fiscal impact of the premium misrating in federal crop insurance programs.
Innovation capability: a systematic literature review
Authors: Mendoza-Silva Andrea
Published: June 2020

Purpose

Innovation is considered an important stage in the process of competitiveness of companies. While there is an extensive literature in the management and innovation field that shows the characteristics that enhance a firm's ability to innovate, there is still no consensus on its determinants and nature. This study aims to advance the understanding of innovation capability (IC) by conducting a systematic review of relevant literature at the firm level.

Design/methodology/approach

The study reviews the literature by applying the categorization and contextualization of qualitative strategies. The study gathered 137 peer-reviewed papers from Scopus and Web of Science databases.

Findings

The papers were analysed and synthesized into an integrated framework that links IC with its internal and external determinants, and its consequences. In doing this, this study proposes directions for future investigations that might enlighten a better understanding of IC.

Practical implications

The study provides elements that can be useful during the design and implementation of innovative initiatives in a firm.

Originality/value

The paper jointly examines in the same model the nature, antecedents and consequences of IC. In the same vein, the framework provides the little-researched links between those themes in the IC literature.
The efficacy of campus wayfinding signage: a comparative study from Hong Kong and Pakistan
Authors: Iftikhar Hassan , Asghar Salman , Luximon Yan
Published: June 2020

Purpose

Complex environments have a paucity of visual wayfinding information creating a strenuous situation for the new visitors. University campuses situated in the central urban areas with multi-storey structures and complex spatial layouts have poor environmental legibility. International students and visitors with diverse cultural backgrounds feel disoriented during wayfinding in these environments. The purpose of this paper is to investigate the cultural and individual differences affecting wayfinding behaviour.

Design/methodology/approach

An online wayfinding survey has been conducted through a questionnaire from 170 university students and visitors from Hong Kong and Pakistan. A five-point bipolar Likert scale has been used to evaluate wayfinding problems and ascribed behaviour.

Findings

The results enunciated a substantial influence of culture on the decision-making process and wayfinding behaviour. Critical differences have been documented based on the country of origin and native language. Individual-related differences (age, gender, spatial familiarity, education, etc.) were computed, where age and spatial familiarity being noted as key factors impacting the respondents’ opinion. Future exploration has been discussed for the pivotal elements regarding wayfinding information signage using computer simulations.

Research limitations/implications

The investigation can be further moved towards the other complex environments with fused facilities for a better understanding of wayfinding behaviour.

Practical implications

The findings can be instrumental for improved access to user facilities and can reinforce the user’s trust and dependence on the institutional facility management.

Originality/value

In the wayfinding study, no cross-cultural (individualists vs collectivists) study has been conducted in a university campus to investigate the wayfinding difficulty and ascribed behaviour, especially when the environment is unfamiliar.
The Geographical imagination of Israeli tourists to Turkey
Authors: Shmuel Irit , Cohen Nir
Published: June 2020

Purpose

This study aims to examine changes in the discourse concerning Israeli tourism to Turkey between 2000 and 2014.

Design/methodology/approach

Drawing on the concept of geographic imagination and using a critical cultural discourse analysis of travel stories published in the Israeli media, the authors analyze the extent to which changes have both reflected and resulted from changing relations between the two countries.

Findings

The analysis reveals that before 2010, Turkey was depicted in largely positive geo-cultural terms, imagined as a desired cosmopolitan, culturally “authentic” destination, which elicits feelings of joy and peacefulness. More recent narratives, however, highlighted its negative geopolitical qualities, underscoring its anti-Israel stance and invoking a fearful discourse of political and ethno-religious radicalization.

Originality/value

The study makes three contributions. First, by attending to the significance of perceptions in the social construction of tourist destinations it brings the fields of tourism and cognitive geography into a closer dialogue. Second, by using a critical discourse analysis it highlights the changing cultural contexts within which places are imagined and constructed by tourists. Finally, by uncovering the geographic complexities that undergird the discursive construction of places as tourist destinations, it illustrates how everyday narratives change over time, reflecting the dynamic nature of inter-state relations.