bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiple nest entrances alter foraging and information transfer in ants
Authors: Lehue Marine , Collignon Bertrand , Detrain Claire
Published: February 2020

The ecological success of ants relies on their ability to discover and collectively exploit available resources. In this process, the nest entrances are key locations at which foragers transfer food and information about the surrounding environment. We assume that the number of nest entrances regulates social exchanges between foragers and inner-nest workers, and hence influences the foraging efficiency of the whole colony. Here, we compared the foraging responses ofMyrmica rubracolonies settled in either one-entrance or two-entrance nests. The total outflows of workers exploiting a sucrose food source were similar regardless of the number of nest entrances. However, in the two-entrance nests, the launching of recruitment was delayed, a pheromone trail was less likely to emerge between the nest and the food source, and recruits were less likely to reach the food target. As a result, an additional entrance through which information could transit decreased the efficiency of social foraging and ultimately led to a lower amount of retrieved food. Our study confirms the key-role of nest entrances in the transfer of information from foragers to potential recruits. The influence of the number of entrances on the emergence of a collective trail also highlights the spatially extended impact of the nest architecture that can shape foraging patterns outside the nest.
Mid and hindgut transcriptome profiling analysis of Atlantic salmon (
Salmon salar
) under unpredictable chronic stress
Authors: Løvmo Signe Dille , Madaro Angelico , Whatmore Paul , Bardal Tora , Ostensen Mari-Ann , Sandve Simen R. , Olsen Rolf Erik
Published: February 2020

The intestinal epithelium is a selectively permeable barrier for nutrients, electrolytes and water, while maintaining effective protection against pathogens. Combinations of stressors throughout an animal's life, especially in agriculture and aquaculture settings, may affect the regular operativity of this organ with negative consequences for animal welfare. In the current study, we report the effects of a three-week unpredictable chronic stress (UCS) period on the intestinal morphology and transcriptome response of Atlantic salmon (
Salmon salar
) parr midgut and hindgut. Midgut and hindgut from both control and UCS fish were collected for histology and RNA-sequencing analysis to identify respective changes in the membrane structures and putative genes and pathways responding to UCS. Histological analysis did not show any significant effect on morphometric parameters. In the midgut, 1030 genes were differentially expressed following UCS, resulting in 279 genes which were involved in 13 metabolic pathways, including tissue repair pathways. In the hindgut, following UCS, 591 differentially expressed genes were detected with 426 downregulated and 165 upregulated. A total of 53 genes were related to three pathways. Downregulated genes include cellular senescence pathways, p53 signalling and cytokine–cytokine receptor pathways. The overall results corroborate that salmon parr were at least partly habituating to the UCS treatment. In midgut, the main upregulation was related to cell growth and repair, while in the hindgut there were indications of the activated apoptotic pathway, reduced cell repair and inhibited immune/anti-inflammatory capacity. This may be the trade-off between habituating to UCS and health resilience. This study suggests possible integrated genetic regulatory mechanisms that are tuned when farmed Atlantic salmon parr attempt to cope with UCS.
Estimating leaf nitrogen concentration based on the combination with fluorescence spectrum and first-derivative
Authors: Yang Jian , Du Lin , Gong Wei , Shi Shuo , Sun Jia
Published: February 2020

Leaf nitrogen concentration (LNC) is a major indicator in the estimation of the crop growth status which has been diffusely applied in remote sensing. Thus, it is important to accurately obtain LNC by using passive or active technology. Laser-induced fluorescence can be applied to monitor LNC in crops through analysing the changing of fluorescence spectral information. Thus, the performance of fluorescence spectrum (FS) and first-derivative fluorescence spectrum (FDFS) for paddy rice (Yangliangyou 6 and Manly Indica) LNC estimation was discussed, and then the proposed FS + FDFS was used to monitor LNC by multivariate analysis. The results showed that the difference between FS (
R
2
= 0.781, s.d. = 0.078) and FDFS (
R
2
= 0.779, s.d. = 0.097) for LNC estimation by using the artificial neural network is not obvious. The proposed FS + FDFS can improved the accuracy of LNC estimation to some extent (
R
2
= 0.813, s.d. = 0.051). Then, principal component analysis was used in FS and FDFS, and extracted the main fluorescence characteristics. The results indicated that the proposed FS + FDFS exhibited higher robustness and stability for LNC estimation (
R
2
= 0.851, s.d. = 0.032) than that only using FS (
R
2
= 0.815, s.d. = 0.059) or FDFS (
R
2
= 0.801, s.d. = 0.065).
Gentoo penguins (Pygoscelis papua) react to underwater sounds
Authors: Sørensen K. , Neumann C. , Dähne M. , Hansen K. A. , Wahlberg M.
Published: February 2020

Marine mammals and diving birds face several physiological challenges under water, affecting their thermoregulation and locomotion as well as their sensory systems. Therefore, marine mammals have modified ears for improved underwater hearing. Underwater hearing in birds has been studied in a few species, but for the record-holding divers, such as penguins, there are no detailed data. We played underwater noise bursts to gentoo penguins (Pygoscelis papua) in a large tank at received sound pressure levels between 100 and 120 dB re 1 µPa RMS. The penguins showed a graded reaction to the noise bursts, ranging from no reactions at 100 dB to strong reactions in more than 60% of the playbacks at 120 dB re 1 µPa. The responses were always directed away from the sound source. The fact that penguins can detect and react to underwater stimuli may indicate that they make use of sound stimuli for orientation and prey detection during dives. Further, it suggests that penguins may be sensitive to anthropogenic noise, like many species of marine mammals.
Fitness differences suppress the number of mating types in evolving isogamous species
Authors: Krumbeck Yvonne , Constable George W. A. , Rogers Tim
Published: February 2020

Sexual reproduction is not always synonymous with the existence of two morphologically different sexes; isogamous species produce sex cells of equal size, typically falling into multiple distinct self-incompatible classes, termed mating types. A long-standing open question in evolutionary biology is: what governs the number of these mating types across species? Simple theoretical arguments imply an advantage to rare types, suggesting the number of types should grow consistently; however, empirical observations are very different. While some isogamous species exhibit thousands of mating types, such species are exceedingly rare, and most have fewer than 10. In this paper, we present a mathematical analysis to quantify the role of fitness variation—characterized by different mortality rates—in determining the number of mating types emerging in simple evolutionary models. We predict that the number of mating types decreases as the variance of mortality increases.
Moulding three-dimensional curved structures by selective heating
Authors: Jain Harsh , Ghosh Shankar , Nitsure Nitin
Published: February 2020

It is of interest to fabricate curved surfaces in three dimensions from homogeneous material in the form of flat sheets. The aim is not just to obtain a surface which has a desired intrinsic Riemannian metric, but to get the desired embedding in

R

3

up to translations and rotations. In this paper, we demonstrate three generic methods of moulding a flat sheet of thermo-responsive plastic by selective contraction induced by targeted heating. These methods do not involve any cutting and gluing, which is a property they share with origami. The first method is inspired by tailoring, which is the usual method for making garments out of plain pieces of cloth. Unlike usual tailoring, this method produces the desired embedding in

R

3

. The second method just aims to bring about the desired new Riemannian metric via an appropriate pattern of local contractions, without directly controlling the embedding. The third method is based on triangulation, and seeks to induce the desired local distances. This results in getting the desired embedding in

R

3

. The second and the third methods, and also the first method for the special case of surfaces of revolution, are algorithmic in nature. We explain these methods and show examples.
Regulators of an ancient polyphenism evolved through episodic protein divergence and parallel gene radiations
Authors: Biddle Joseph F. , Ragsdale Erik J.
Published: February 2020

Polyphenism is a form of developmental plasticity that transduces environmental cues into discontinuous, often disparate phenotypes. In some cases, polyphenism has been attributed to facilitating morphological diversification and even the evolution of novel traits. However, this process is predicated on the origins and evolutionary maintenance of genetic mechanisms that specify alternate developmental networks. When and how regulatory loci arise and change, specifically before and throughout the history of a polyphenism, is little understood. Here, we establish a phylogenetic and comparative molecular context for two dynamically evolving genes,
eud-1
and
seud-1
, which regulate polyphenism in the nematode
Pristionchus pacificus
. This species is dimorphic in its adult feeding-structures, allowing individuals to become microbivores or facultative predators depending on the environment. Although polyphenism regulation is increasingly well understood in
P. pacificus
, the polyphenism is far older than this species and has diversified morphologically to enable an array of ecological functions across polyphenic lineages. To bring this taxonomic diversity into a comparative context, we reconstructed the histories of
eud-1
and
seud-1
relative to the origin and diversification of polyphenism, finding that homologues of both genes have undergone lineage-specific radiations across polyphenic taxa. Further, we detected signatures of episodic diversifying selection on
eud-1
, particularly in early diplogastrid lineages. Lastly, transgenic rescue experiments suggest that the gene's product has functionally diverged from its orthologue's in a non-polyphenic outgroup. In summary, we provide a comparative framework for the molecular components of a plasticity switch, enabling studies of how polyphenism, its regulation, and ultimately its targets evolve.
Adapted dandelions trade dispersal for germination upon root herbivore attack
Authors: Bont Zoe , Pfander Marc , Robert Christelle A. M. , Huber Meret , Poelman Erik H. , Raaijmakers Ciska E. , Erb Matthias
Published: February 2020

A plant's offspring may escape unfavourable local conditions through seed dispersal. Whether plants use this strategy to escape insect herbivores is not well understood. Here, we explore how different dandelion (
Taraxacum officinale
agg.) populations, including diploid outcrossers and triploid apomicts, modify seed dispersal in response to root herbivore attack by their main root-feeding natural enemy, the larvae of the common cockchafer
Melolontha melolontha.
In a manipulative field experiment, root herbivore attack increased seed dispersal potential through a reduction in seed weight in populations that evolved under high root herbivore pressure, but not in populations that evolved under low pressure. This increase in dispersal potential was independent of plant cytotype, but associated with a reduction in germination rate, suggesting that adapted dandelions trade dispersal for establishment upon attack by root herbivores. Analysis of vegetative growth parameters suggested that the increased dispersal capacity was not the result of stress flowering. In summary, these results suggest that root herbivory selects for an induced increase in dispersal ability in response to herbivore attack. Induced seed dispersal may be a strategy that allows adapted plants to escape from herbivores.
Paraburkholderia flava sp. nov., isolated from cool temperate forest soil
Authors: Trinh Ngoc Hoang , Kim Jaisoo
Published: February 2020

A Gram-stain-negative, aerobic and short rod-shaped bacterial strain, designated LD6T, was isolated from a forest soil sample in Suwon, Gyeonggi-do, Republic of Korea. Strain LD6Tgrew at 10–37 °C (optimal temperature, 28 °C), and tolerated pH 8.0 and 2 % (w/v) NaCl. Strain LD6Twas related most closely to members of the genusParaburkholderia, namelyParaburkholderia azotifigensNF2-5-3T(98.2 % 16S rRNA gene sequence similarity),P. megapolitanaA3T(97.9 %),P. ginsengiterraeDCY85T(97.9 %) andP. caribensisMWAP64T(97.7 %). The strain grew well on R2A agar, tryptone soya agar, Mueller-Hinton agar and nutrient agar. The major polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and glycolipid. The major respiratory quinone was ubiquinone 8 (Q-8). The main fatty acids were C17 : 0cyclo, C16 : 0, C16 : 03-OH, C19 : 0cyclo ω8cand C12 : 0. The DNA G+C content of the isolated strain based on the whole genome sequence was 63.4 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain LD6Tand its reference type strains ranged from 80.3 to 82.4%, and from 23.7 to 33.7%, respectively. Based on phenotypic, chemotypic and genotypic evidence, strain LD6Tcould be differentiated phylogenetically and phenotypically from the recognized species of the genusParaburkholderia. Therefore, strain LD6Tis considered to represent a novel species, for which the nameParaburkholderia flavasp. nov. is proposed. The type strain is LD6T(=KACC 21387T=JCM 33640T).
Paracoccus aurantiacus sp. nov., isolated from shallow-sea hydrothermal systems off Kueishantao Island
Authors: Ye Jianing , Lin Dan , Zhang Mu , Lin Ta-Hui , Sun Jia , Wang Deli , Tang Kai
Published: February 2020

An orange-pigmented, short-rod-shaped, aerobic and non-motile bacterial strain, designated TK008T, was isolated from the shallow-sea hydrothermal systems off Kueishantao Island in Taiwan, China, and it was studied by using a polyphasic taxonomic approach. Cells were Gram-stain-negative, and catalase- and oxidase-positive. Strain TK008T exhibited highest 16S rRNA gene sequence similarity of 97.1 % to

Paracoccus pacificus

F14T. The phylogenetic trees based on 16S rRNA gene sequences showed that strain TK008T was a member of the genus

Paracoccus

. Digital DNA–DNA hybridization values between strain TK008T and two closely related species (

Paracoccus zhejiangensis

and

Paracoccus tegillarcae

) were 20.6 and 20.9 %. The average nucleotide identity values of strain TK008T compared with

P. zhejiangensis

and

P. tegillarcae

were 75.2 and 74.6 % respectively. The major isoprenoid quinone was ubiquinone-10. The predominant fatty acids (>10 %) were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids, two unidentified lipids and an unidentified glycolipid. The DNA G+C content of strain TK008T from genomic sequence data was 62.54 mol%. On the basis of polyphasic analysis, strain TK008T represents a novel species, for which the name Paracoccus aurantiacus sp. nov. is proposed. The type strain is TK008T (=CGMCC 1.13898T=JCM 33630T).
Estimating the serial interval of the novel coronavirus disease (COVID-19): A statistical analysis using the public data in Hong Kong from January 16 to February 15, 2020
Authors: Zhao Shi , Gao Daozhou , Zhuang Zian , Chong Marc KC , Cai Yongli , Ran Jinjun , Cao Peihua , Wang Kai , Lou Yijun , Wang Weiming , Yang Lin , He Daihai , Wang Maggie H
Published: February 2020

Backgrounds

The emerging virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a large outbreak of novel coronavirus disease (COVID-19) in Wuhan, China since December 2019. Based on the publicly available surveillance data, we identified 21 transmission chains in Hong Kong and estimated the serial interval (SI) of COVID-19.

Methods

Index cases were identified and reported after symptoms onset, and contact tracing was conducted to collect the data of the associated secondary cases. An interval censored likelihood framework is adopted to fit a Gamma distribution function to govern the SI of COVID-19.

Findings

Assuming a Gamma distributed model, we estimated the mean of SI at 4.4 days (95%CI: 2.9−6.7) and SD of SI at 3.0 days (95%CI: 1.8−5.8) by using the information of all 21 transmission chains in Hong Kong.

Conclusion

The SI of COVID-19 may be shorter than the preliminary estimates in previous works. Given the likelihood that SI could be shorter than the incubation period, pre-symptomatic transmission may occur, and extra efforts on timely contact tracing and quarantine are recommended in combating the COVID-19 outbreak.
Latent Plasticity of Effector-like Exhausted CD8 T cells contributes to memory responses
Authors: Raju Saravanan , Xia Yu , Daniel Bence , Yost Kathryn E. , Bradshaw Elliot , Tonc Elena , Verbaro Daniel J. , Satpathy Ansuman T. , Egawa Takeshi
Published: February 2020

Persistent antigen induces a dysfunctional CD8 T cell state known as T cell “exhaustion” characterized by expression of PD-1 and decreased effector functions. Nevertheless, dysfunctional CD8 T cells can mediate control of antigen burden which is long-lasting. While heterogeneity of exhausted CD8 T cells has been described, the cells which actively proliferate and exert viral control have remained elusive. Here, we define subsets of PD-1+CD8 T cells during chronic infection marked by expression of CX3CR1 with substantialin situproliferation and high expression of granzyme B. Moreover, these cells maintain the effector pool through self-renewal independently of previously defined stem-like cells. Unexpectedly, CX3CR1+CD8 T cells retain plasticity to be reprogrammed to memory cells through expression of TCF-1 and re-gain polyfunctionality. Thus, we define a subset of effector-like exhausted CD8 T cells with capacity to contribute to the memory pool, offering a prime target for novel immunotherapies.
Gender differences in patients with COVID-19: Focus on severity and mortality
Authors: Jin Jian-Min , Bai Peng , He Wei , Wu Fei , Liu Xiao-Fang , Han De-Min , Liu Shi , Yang Jin-Kui
Published: February 2020

Importance

The recent outbreak of Novel Coronavirus (SARS-CoV-2) Disease (COVID-19) has put the world on alert, that is reminiscent of the SARS outbreak seventeen years ago.

Objective

We aim to compare the severity and mortality between male and female patients with both COVID-19 and SARS, to explore the most useful prognostic factors for individualized assessment.

Design, Setting, and Participants

We extracted the data from a case series of 43 hospitalized patients we treated, a public data set of the first 37 cases died of COVID-19 in Wuhan city and 1019 survived patients from six cities in China. We also analyzed the data of 524 patients with SARS, including 139 deaths, from Beijing city in early 2003.

Main Outcomes and Measures

Severity and mortality.

Results

Older age and high number of comorbidities were associated with higher severity and mortality in patients with both COVID-19 and SARS. The percentages of older age (≥65 years) were much higher in the deceased group than in the survived group in patients with both COVID-19 (83.8 vs. 13.2, P<0.001) and SARS (37.4 vs. 4.9, P<0.001). In the case series, men tend to be more serious than women (P=0.035), although age was comparable between men and women. In the public data set, age was also comparable between men and women in the deceased group or the survived group in patients with COVID-19. Meanwhile, gender distribution was exactly symmetrical in the 1019 survivors of COVID-19. However, the percentage of male were higher in the deceased group than in the survived group (70.3 vs. 50.0, P=0.015). The gender role in mortality was also observed in SARS patients. Survival analysis showed that men (hazard ratio [95% CI] 1.47 [1.05-2.06, P= 0.025) had a significantly higher mortality rate than women in patients with SARS.

Conclusions and Relevance

Older age and male gender are risk factors for worse outcome in patients with COVID. While men and women have the same susceptibility to both SARS-CoV-2 and SARS-CoV, men may be more prone to have higher severity and mortality independent of age and susceptibility.

Key Points

Question

Are men more susceptible to getting and dying from COVID-19?

Findings

In the case series, men tend to be more serious than women. In the public data set, the percentage of men were higher in the deceased group than in the survived group, although age was comparable between men and women.

Meaning

Male gender is a risk factor for worse outcome in patients with COVID independent of age and susceptibility.
Effect of exercise and dietary intervention on serum metabolomics in men with insomnia symptoms: a 6-month randomized-controlled trial
Authors: Zhang Xiaobo , Wang Xiuqiang , Le Shenglong , Ojanen Xiaowei , Tan Xiao , Wiklund Petri , Cheng Sulin
Published: February 2020

Background

Accumulating evidences have shown that lifestyle interventions such as exercise and diet are associated with improved sleep quality. However, the underlying molecular mechanisms remain unclear. Assessing exercise and diet intervention associated changes in circulating metabolomics profile in people with insomnia symptoms may help to identify molecular biomarkers that may link lifestyle changes to improved sleep outcomes.

Methods

The present study is a part of a 6-month randomized lifestyle intervention on sleep disorder subjects. Seventy-two Finnish men (aged: 51.6 ± 10.1 years; body mass index, BMI: 29.3 ± 3.9 kg/m2) with chronic insomnia symptoms who were assigned into different intervention groups completed this study (exercise n = 24, diet n = 27 and control n = 21). The exercise group was assigned to a progressive aerobic exercise training with intensity of 60 – 75% of estimated maximum heart rate, 3 – 5 times a week. The diet group aimed to reduce their total energy intakes by 300 to 500 kcal per day for the first three months. The control group were advised to maintain their current lifestyle. Sleep was assessed by using a non-contact sleep monitoring devise (Beddit sleep tracker). Blood samples were collected in the morning between 7:00 and 9:00 a.m. after overnight fasting. Gas Chromatography Time-Of-Flight Mass Spectrometry (GC-TOF-MS) method was used to determine the serum metabolites.

Results

Twenty-one metabolites were significantly changed in the exercise group, thirty-three metabolites in the diet group and five metabolites in the control group after intervention, respectively. The differential metabolites after exercise intervention were mainly related to glycerolipids and carbohydrates metabolism, while dietary intervention altered mainly amino acids metabolism and fatty acids metabolism related metabolites. We subsequently assessed the change of those metabolites with the change of sleep parameters and found that decreased alpha-ketoisocaproic acid (r = -0.52, p = 0.026) was correlated with improved sleep efficiency (SE) in the exercise group. Change of 3-hydroxybutric acid (r = -0.47, p = 0.025) and D-glucopyranose (r = -0.54, p = 0.006) correlated negatively with SE in the diet group. On the other hand, oxalic acid (r = 0.49, p = 0.021), D-glucopyranose (r = 0.43, p = 0.048), 4-deoxyerythronic acid (r = 0.60, p = 0.004) and tagatose (r = 0.51, p = 0.016) correlated positively with change of SOL, and 2-keto-isovaleric acid (r = 0.45, p = 0.029) correlated with TST in the diet group.

Conclusion

In conclusion, this study identified circulating metabolites that may represent a part of a biological mechanism through which lifestyle interventions are associated with improved sleep quality in people with insomnia.
The anticipation and perception of affective touch in women with and recovered from Anorexia Nervosa
Authors: Crucianelli Laura , Demartini Benedetta , Goeta Diana , Nisticò Veronica , Saramandi Alkistis , Bertelli Sara , Todisco Patrizia , Gambini Orsola , Fotopoulou Aikaterini
Published: February 2020

Disruptions in reward processing and anhedonia have long being considered as possible contributors to the aetiology and maintenance of Anorexia nervosa (AN). Recently, interoceptive deficits have also been observed in AN, including reduced tactile pleasure. However, the extent to which this tactile anhedonia is specifically liked to an impairment in a specialized, interoceptive C tactile system originating at the periphery, or a more top-down mechanism in the processing of pleasant tactile stimuli remains debated. Here, we investigated two related hypotheses. First, we examined whether the differences, between patients with AN and healthy controls in the perception of pleasantness of touch stimuli delivered in a CT-optimal manner versus a CT non-optimal manner would also be observed in patients recovered from AN. This is important as tactile anhedonia in acute patients may be the secondary result of prolonged malnutrition, rather than a deficit that contributed to the development of the disorder. Second, we examined whether these three groups would also differ in their top-down, anticipatory beliefs about the perceived pleasantness of different materials touching the skin, and to what degree such top-down beliefs and related impairments in alexithymia and interoceptive sensibility would explain any differences in perceived tactile plesantness. To this end, we measured the anticipated pleasantness of various materials touching the skin and the perceived pleasantness of light, dynamic stroking touches applied to the forearm of 27 women with AN, 24 women who have recovered and 30 healthy controls using C Tactile (CT) afferents-optimal (slow) and non-optimal (fast) velocities. Our results showed that both clinical groups anticipated tactile experiences and rated delivered tactile stimuli as less pleasant than healthy controls, but the latter difference was not related to the CT optimality of the stimulation. Instead, differences in how CT optimal touch were perceived were predicted by differences in top-down beliefs, alexithymia and interoceptive sensibility. Thus, this study concludes that tactile anhedonia in AN is not the secondary result of malnutrition but persists as a trait even after otherwise successful recovery of AN and also it not linked to a bottom-up interoceptive deficit in the CT system, but rather to a learned, defective top-down anticipation of pleasant tactile experiences.
Does Vergence Affect Perceived Size?
Authors: Linton Paul
Published: February 2020

Since Kepler (1604) and Descartes (1637), it’s been suggested that ‘vergence’ (the angular rotation of the eyes) plays a key role in size constancy. However, this has never been tested divorced from confounding cues such as changes in the retinal image. In our experiment participants viewed a target which grew or shrank over 5 seconds. At the same time the fixation distance specified by vergence was reduced from 50cm to 25cm. The question was whether the reduction in the viewing distance specified by vergence biased the participants’ judgements of whether the target grew or shrank? We found no evidence of any bias, and therefore no evidence that eye movements affect perceived size. If this is correct, then this finding has three implications: First, perceived size is much more reliant on cognitive influences than previously thought. This is consistent with the argument that visual scale is purely cognitive in nature (Linton, 2017; 2018). Second, it leads us to question whether the vergence modulation of V1 contributes to size constancy. Third, given the interaction between vergence, proprioception, and the retinal image in the Taylor illusion, it leads us to ask whether this cognitive approach could also be applied to multisensory integration.
Replicated chromatin curtails 53BP1 recruitment in BRCA1-proficient and -deficient cells
Authors: Michelena Jone , Pellegrino Stefania , Spegg Vincent , Altmeyer Matthias
Published: February 2020

DNA double-strand breaks can be repaired by two competing mechanisms, non-homologous end-joining (NHEJ) and homologous recombination (HR). Whether one or the other repair pathway is favored depends on the availability of an undamaged template DNA that allows for homology-directed repair. The tumor suppressor proteins 53BP1 and BRCA1 are considered antagonistic players in this repair pathway choice, as 53BP1 restrains DNA end resection, whereas BRCA1, together with its partner protein BARD1, displaces 53BP1 from damaged replicated chromatin and promotes HR. How cells switch from a 53BP1-dominated to a BRCA1-dominated response as they progress through the cell cycle is incompletely understood. Here we reveal, using high-throughput microscopy and applying single cell normalization to control for increased genome size as cells replicate their DNA, that 53BP1 recruitment to damaged replicated chromatin is inefficient in both BRCA1-proficient and BRCA1-deficient cells, in comparison to 53BP1 accumulation at damaged unreplicated chromatin. These findings substantiate a dual switch model from a 53BP1-dominated response in unreplicated chromatin to a BRCA1-BARD1-dominated response in replicated chromatin, in which replication-coupled dilution of 53BP1’s binding mark H4K20me2 functionally cooperates with BRCA1-BARD1-mediated suppression of 53BP1 binding. More generally, we suggest that appropriate normalization of single cell data, e.g. to DNA content, provides additional layers of information, which can be critical for quantifying and interpreting cellular phenotypes.
IFN-λ4 is associated with increased risk and earlier occurrence of gastrointestinal, respiratory and malarial infections in Malian children
Authors: Prokunina-Olsson Ludmila , Morrison Robert D. , Obajemu Adeola , Mahamar Almahamoudou , Kim Sungduk , Attaher Oumar , Florez-Vargas Oscar , Sidibe Youssoufa , Onabajo Olusegun O. , Hutchinson Amy A. , Manning Michelle , Kwan Jennifer , Brand Nathan , Dicko Alassane , Fried Michal , Albert Paul S. , Mbulaiteye Sam M. , Duffy Patrick E.
Published: February 2020

Genetic polymorphisms within theIFNL3/IFNL4genomic region, which encodes type III interferons, have been strongly associated with impaired clearance of hepatitis C virus (HCV) infection. We hypothesized that type III interferons might be important for the immune response to other pathogens as well. In a cohort of 914 Malian children, we analyzed episodes of malaria, gastrointestinal and respiratory infections using information for 30,626 clinic visits from birth through up to 5 years of follow-up. Genetic polymorphismsIFNL4-rs368234815 andIFNL3-rs4803217 that functionally affect type III interferons were genotyped with TaqMan assays. For both genetic variants and each infection, we evaluated time-to-first episode and calculated odds ratios (ORs) for the risk of an infection episode during follow-up, controlling for relevant covariates. Compared to children with the rs368234815-TT/TT genotype (IFN-λ4-Null), each copy of the rs368234815-dG allele was associated with an earlier first episode of a gastrointestinal infection (p=0.003) and respiratory infection (p=0.045). The risk of experiencing an infection episode during the follow-up was also significantly increased with each copy of the rs368234815-dG allele – for gastrointestinal infections (OR=1.53, 95%CI (1.13-2.07), p=0.005) and malaria (OR=1.30, 95%CI (1.02-1.65), p=0.033).IFNL4-rs368234815 andIFNL3-rs4803217 were in moderate linkage disequilibrium in this population (r2=0.78), and all the associations for rs4803217 were weaker and lost significance after adjusting for rs368234815, implicating IFN-λ4 and not IFN-λ3 as the primary cause of these associations. We conclude that the ability to produce IFN-λ4 may have broad health-related implications by negatively affecting the immune response and clinical outcomes of several common infections.
Object selection by automatic spreading of top-down attentional signals in V1
Authors: Ekman Matthias , Roelfsema Pieter R. , de Lange Floris P.
Published: February 2020

What is selected when attention is directed to a specific location of the visual field? Theories of object-based attention have suggested that when spatial attention is directed to part of an object, attention does not simply enhance the attended location but automatically spreads to enhance all locations that comprise the object. Here, we tested this hypothesis by reconstructing the distribution of attention from population neuronal activity patterns in V1 using functional magnetic resonance imaging (fMRI) and population-based receptive field mapping. We find that attention spreads from a spatially cued location to the underlying object – and enhances all spatial locations that comprise the object. Importantly, this spreading was also evident when the object was not task-relevant. These data suggest that attentional selection automatically operates at an object level, facilitating the reconstruction of coherent objects from fragmented representations in early visual cortex.
Automatic classification of constitutive and non-constitutive metabolites with gcProfileMakeR
Authors: Pérez-Sanz Fernando , Ruiz-Hernández Victoria , Terry Marta Isabel , Arce-Gallego Sara , Weiss Julia , Navarro Pedro J , Egea-Cortines Marcos
Published: February 2020

Data analysis in non-targeted metabolomics is extremely time consuming. Genetic factors and environmental cues affect the composition and quantity of present metabolites i.e. the constitutive and non-constitutive metabolites. We developed gcProfileMakeR, an R package that uses standard output files from GC-MS for automatic data analysis using CAS numbers. gcProfileMakeR produces three outputs: a core or constitutive metabolome, a second list of compounds with high quality matches that is non-constitutive and a third set of compounds with low quality matching to MS libraries. As a proof of concept, we defined the floral scent emission ofAntirrhinum majususing wild type plants, the floral identity mutantsdeficiensandcompactaas well as RNAi lines ofAmLHY. Loss of petal identity was accompanied by appearance of aldehydes typical of green leaf volatile profiles. Decreased levels ofAmLHYcaused a major increase in volatile complexity, and activated the synthesis of benzyl acetate, absent in WT. Furthermore, some volatiles emitted in a gated fashion in WT such as methyl 3,5-dimethoxybezoate or linalool became constitutive. Using sixteen volatiles of the constitutive profile, all genotypes were classified by Machine Learning with 0% error. gcProfileMakeR may thus help define core and pan-metabolomes. It enhances the quality of data reported in metabolomic profiles as text outputs rely on CAS numbers. This is especially important for FAIR data implementation.

One sentence summary

gcProfileMakeR allows the automatic annotation of the core metabolome and non-constitutive metabolites, increasing speed and accuracy of non-targeted metabolomics.
An original structural fold underlies the multitask P1, a silencing suppressor encoded by the Rice yellow mottle virus
Authors: Poignavent Vianney , Hoh François , Terral Guillaume , Yinshan Yang , Gillet François-Xavier , Kim Jeong-Hyeon , Allemand Frédéric , Lacombe Eric , Brugidou Christophe , Cianferani Sarah , Déméné Hélène , Vignols Florence
Published: February 2020

The Rice Yellow Mottle sobemovirus (RYMV) belongs to the most damaging pathogens devastating rice fields in Africa. P1, a key protein for RYMV, was reported as a potent RNAi suppressor counteracting RNA silencing in plant reporter systems. Here we describe the complete 3D structure and dynamics of P1. Its N-terminal region contains ZnF1, a structural CCCC-type zinc finger strongly affine to zinc and a prominent short helix, rendering this region poorly amenable to structural changes. P1 C-terminal region contains ZnF2, an atypical HCHC-type ZnF that does not belong to any existing class of Zn finger proteins. ZnF2 appeared much less affine to zinc and more sensitive to oxidizing environments than ZnF1, and may serve as a sensor of plant redox status. The structure helped us to identify key residues essential for RYMV infectivity and spread in rice tissues through their participation in P1 oligomerization and folding. Altogether, our results provide the first complete structure of an antiviral silencing suppressor encoded by a virus infecting rice and highlight P1 structural and dynamical properties that may serve RYMV functions to infect and invade its host plant.
Emotional contagion of pain across different social cues shares common and process-specific neural representations
Authors: Zhou Feng , Li Jialin , Zhao Weihua , Xu Lei , Zheng Xiaoxiao , Fu Meina , Yao Shuxia , Kendrick Keith M. , Wager Tor D. , Becker Benjamin
Published: February 2020

Insular and anterior cingulate cortex activation across vicarious pain induction procedures suggests that they are core pain empathy nodes. However, pain empathic responses encompass emotional contagion as well as unspecific arousal and overlapping functional activations are not sufficient to determine shared and process-specific neural representations. We employed multivariate pattern analyses to fMRI data acquired during physical and affective vicarious pain induction and found spatially and functionally similar cross-modality (physical versus affective) whole-brain vicarious pain-predictive patterns. Further analyses consistently identified shared neural representations in the bilateral mid-insula. Mid-insula vicarious pain patterns were not sensitive to capture non-painful arousing negative stimuli but predicted self-experienced pain during thermal stimulation, suggesting process-specific representation of emotional contagion for pain. Finally, a domain-general vicarious pain pattern which predicted vicarious as well as self-experienced pain was developed. Our findings demonstrate a generalizable neural expression of vicarious pain and suggest that the mid-insula encodes emotional contagion for pain.
Caenorhabditis elegansprocesses sensory information to choose between freeloading and self-defense strategies
Authors: Schiffer Jodie , Servello Francesco , Heath William , Amrit Francis Raj Gandhi , Stumbur Stephanie , Johnsen Sean , Stanley Julian , Tam Hannah , Brennan Sarah , McGowan Natalie , Vogelaar Abigail , Xu Yuyan , Serkin William , Ghazi Arjumand , Apfeld Javier
Published: February 2020

Hydrogen peroxide is the preeminent chemical weapon that organisms use for combat. Individual cells rely on conserved defenses to prevent and repair peroxide-induced damage, but whether similar defenses might be coordinated across cells in animals remains poorly understood. Here, we identify a neuronal circuit in the nematodeCaenorhabditis elegansthat processes information perceived by two sensory neurons to control the induction of hydrogen-peroxide defenses in the organism. We found that catalases produced byEscherichia coli, the nematode’s food source, can deplete hydrogen peroxide from the local environment and thereby protect the nematodes. In the presence ofE. coli, the nematode’s neurons signal via TGFβ-insulin/IGF1 relay to target tissues to repress expression of catalases and other hydrogen-peroxide defenses. This adaptive strategy is the first example of a multicellular organism modulating its defenses when it expects to freeload from the protection provided by molecularly orthologous defenses from another species.
3D Epigenomic Characterization Reveals Insights Into Gene Regulation and Lineage Specification During Corticogenesis
Authors: Song Michael , Pebworth Mark-Phillip , Yang Xiaoyu , Abnousi Armen , Fan Changxu , Wen Jia , Rosen Jonathan D. , Choudhary Mayank NK , Cui Xiekui , Jones Ian R. , Bergenholtz Seth , Eze Ugomma C. , Juric Ivan , Li Bingkun , Maliskova Lenka , Liu Weifang , Pollen Alex A. , Li Yun , Wang Ting , Hu Ming , Kriegstein Arnold R. , Shen Yin
Published: February 2020

Lineage-specific epigenomic changes during human corticogenesis have previously remained elusive due to challenges with tissue heterogeneity and sample availability. Here, we analyze cis-regulatory chromatin interactions, open chromatin regions, and transcriptomes for radial glia, intermediate progenitor cells, excitatory neurons, and interneurons isolated from mid-gestational human brain samples. We show that chromatin looping underlies transcriptional regulation for lineage-specific genes, with transcription factor motifs, families of transposable elements, and disease-associated variants enriched at distal interacting regions in a cell type-specific manner. A subset of promoters exhibit unusually high degrees of chromatin interactivity, which we term super interactive promoters. Super interactive promoters are enriched for critical lineage-specific genes, suggesting that interactions at these loci contribute to the fine-tuning of cell type-specific transcription. Finally, we present CRISPRview, a novel approach for validating distal interacting regions in primary cells. Our study presents the first characterization of cell type-specific 3D epigenomic landscapes during human corticogenesis, advancing our understanding of gene regulation and lineage specification during human brain development.
Muscle progenitor cells are required for the regenerative response and prevention of adipogenesis after limb ischemia
Authors: Abbas Hasan , Olivere Lindsey A. , Padgett Michael E. , Schmidt Cameron A. , Gilmore Brian F. , Southerland Kevin W. , McClung Joseph M. , Kontos Christopher D.
Published: February 2020

Peripheral artery disease (PAD) is nearly as common as coronary artery disease, but few effective treatments exist, and it is associated with significant morbidity and mortality. Although PAD studies have focused on the vascular response to ischemia, skeletal muscle cells play a critically important role in determining the phenotypic manifestation of PAD. Here, we demonstrate that genetic ablation of Pax7+muscle progenitor cells (MPCs, or satellite cells) in a murine model of hind limb ischemia (HLI) resulted in a complete absence of normal muscle regeneration following ischemic injury, despite a lack of morphological or physiological changes in resting muscle. Compared to ischemic muscle of control mice (Pax7WT), the ischemic limb of Pax7-deficient mice (Pax7Δ) was unable to generate significant force 7- or 28-days after HLI inex vivoforce measurement studies. A dramatic increase in adipose infiltration was observed 28 days after HLI in Pax7Δmice, which replaced functional muscle. To investigate the mechanism of this adipogenic change, mice with inhibition of fibro/adipogenic precursors (FAPs), another pool of MPCs, were subjected to HLI. Inhibition of FAPs decreased muscle adipose fat but increased fibrosis. MPCs cultured from mouse muscle tissue failed to form myotubesin vitrofollowing depletion of satellite cellsin vivo, and they displayed an increased propensity to differentiate into fat in adipogenic medium. Importantly, this phenotype was recapitulated in patients with critical limb ischemia (CLI), the most severe form of PAD. Skeletal muscle samples from CLI patients demonstrated an increase in adipose deposition in more ischemic regions of muscle, which corresponded with a decrease in the number of satellite cells in those regions. Collectively, these data demonstrate that Pax7+MPCs are required for normal muscle regeneration after ischemic injury, and they suggest that targeting muscle regeneration may be an important therapeutic approach to prevent muscle degeneration in PAD.
Projection of orthogonal tiling from the retina to the visual cortex
Authors: Jang Jaeson , Song Min , Kim Gwangsu , Paik Se-Bum
Published: February 2020

In higher mammals, the primary visual cortex (V1) is organized into diverse tuning maps of visual features such as orientation, spatial frequency and ocular dominance. The topography of these maps is observed to intersect orthogonally, implying that a developmental principle for efficient tiling of sensory modules may exist. However, it remains unclear how such a systematic relationship among cortical tuning maps could develop. Here, we show that the orthogonal organization of tuning modules already exist in retinal ganglion cell (RGC) mosaics, and that this provides a blueprint of the orthogonal organization in V1. Firstly, from the analysis of multi-electrode recording data in V1, we found that the ON-OFF subregion distance of receptive fields varies periodically across the cortical surface, strongly correlated to ocular dominance and spatial frequency in the area. Further, the ON-OFF alignment angle, that is orthogonal to the ON-OFF distance, appears to correlate with orientation tuning. These suggest that the orthogonal organization in V1 may originate from the spatial organization of the ON-OFF receptive fields in the bottom-up projections, and this scenario was tested from analysis of the RGC mosaics data in monkeys and cats. We found that the ON-OFF RGC distance and ON-OFF angle of neighbouring RGCs are organized into a topographic tiling across mosaics, analogous to the orthogonal intersection of cortical tuning maps. These findings suggest that the regularly structured ON-OFF patterns mirrored from a retina may initiate efficient tiling of functional domains in V1.

Highlights

Orthogonal organization of visual tuning maps are observed in both V1 and the retina

Cortical tuning maps are correlated with the profile of ON-OFF feedforward projections

The profile of ON-OFF receptive fields varies periodically across the V1 surface

Regularly structured RGC patterns initiate the orthogonal tiling of sensory modules in V1
Lossless Immunocytochemistry using Photo-polymerized Hydrogel Thin-films
Authors: Lee Jeong Hyun , Santoso Aline T. , Park Emily S. , Matthews Kerryn , Duffy Simon P. , Ma Hongshen
Published: February 2020

Immunocytochemistry (ICC), or immunofluorescence microscopy, is an essential biological technique for phenotyping cells in both research and diagnostic applications. Standard ICC methods often do not work well when the cell sample contains a small number of cells (<10,000) because of the significant cell loss that occurs during washing, staining, and centrifugation steps. Cell loss is particularly relevant when working with rare cells, such as circulating tumor cells, where such losses could significantly bias experimental outcomes. In order to eliminate cell loss in ICC protocols, we present a method to encapsulate the cell sample in a photo-polymerized hydrogel thin-film. The hydrogel thin-film is permeable to antibodies and other ICC reagents, thereby allowing the use of standard ICC protocols without modification. The cell sample is physically constrained by the hydrogel at the bottom surface of a standard (unmodified) imaging microtiter plate, thereby enabling the acquisition of high-quality micrographs regardless of the properties of the cell sample or staining reagents. Furthermore, while standard ICC requires several centrifugation steps during staining and washing, our hydrogel encapsulation method requires only a single centrifugation step. This property greatly reduces the time required to perform ICC protocols and is more compatible with robotic platforms. In this study, we show that standard ICC and Cytospin protocols are extremely lossy (>70% loss) when the sample contains less than 10,000 cells, while encapsulating the cells using a permeable hydrogel thin-film results in a lossless ICC process.