bluuebunny/crossref_metadata_2025 huggingface dataset:
Photoinduced charge carrier dynamics in a ZnSe quantum dot-attached CdTe system
Authors: Saeed Shomaila , Iqbal Azhar , Iqbal Azhar
Published: March 2020

A new nanohybrid material is prepared by attaching CdTe nanoneedles (NNs) to surface-modified ZnSe quantum dots (QDs). The NNs and QDs are prepared by a colloidal synthesis method in an aqueous alkaline medium. The surface modification and the attachment of nanostructures are achieved by a bifunctional ligand 3-mercaptopropionic acid (3-MPA). The band gap of the ZnSe QDs is varied by controlling the size of the QDs in order to get the maximum overlap between the absorption band of the CdTe NNs and the emission band of the ZnSe QDs, which is a prerequisite for effective charge/energy transfer. The possibility of photoinduced charge transfer (PCT) and Förster resonance energy transfer (FRET) from the donor (QDs) to the acceptor (NNs) has been assessed. Very fast (less than 800 ps) PCT and FRET from QDs to NNs occur because the emission band of QDs overlaps with the absorption band of NNs. The calculated large value of the overlapping integral,
J
(
λ
) ∼4.5 × 10
19 
M
−1 
cm
−1 
nm
4
, of the donor and the acceptor bands proves the feasibility of energy transfer. These findings suggest that the ZnSe QDs can exchange photoinduced energy with the CdTe NNs effectively over a wide distance in a CdTe–ZnSe nanohybrid.
Insecticide exposure during brood or early-adult development reduces brain growth and impairs adult learning in bumblebees
Authors: Smith Dylan B. , Arce Andres N. , Ramos Rodrigues Ana , Bischoff Philipp H. , Burris Daisy , Ahmed Farah , Gill Richard J.
Published: March 2020

For social bees, an understudied step in evaluating pesticide risk is how contaminated food entering colonies affects residing offspring development and maturation. For instance, neurotoxic insecticide compounds in food could affect central nervous system development predisposing individuals to become poorer task performers later-in-life. Studying bumblebee colonies provisioned with neonicotinoid spiked nectar substitute, we measured brain volume and learning behaviour of 3 or 12-day old adults that had experienced in-hive exposure during brood and/or early-stage adult development. Micro-computed tomography scanning and segmentation of multiple brain neuropils showed exposure during either of the developmental stages caused reduced mushroom body calycal growth relative to unexposed workers. Associated with this was a lower probability of responding to a sucrose reward and lower learning performance in an olfactory conditioning test. While calycal volume of control workers positively correlated with learning score, this relationship was absent for exposed workers indicating neuropil functional impairment. Comparison of 3- and 12-day adults exposed during brood development showed a similar degree of reduced calycal volume and impaired behaviour highlighting lasting and irrecoverable effects from exposure despite no adult exposure. Our findings help explain how the onset of pesticide exposure to whole colonies can lead to lag-effects on growth and resultant dysfunction.
Mate selection based on labile traits affects short-term fitness in a long-lived seabird
Authors: González-Medina Erick , Castillo-Guerrero José Alfredo , Masero José A. , Fernández Guillermo
Published: March 2020

In long-lived monogamous social species, partner compatibility can play a crucial role in reproductive success. We evaluated assortative mating based on body condition (plasma triglyceride concentration), diet (δ15N), and foraging habitat (δ13C) in the blue-footed boobySula nebouxii, a long-lived monogamous seabird. We investigated the effects of assortative mating (sum of triglycerides in a pair) and asymmetry within pairs (residuals from regression of female–male triglycerides) on reproductive performance and offspring growth (alkaline phosphatase, ALP). We found that strong assortative mating determined by body condition and diet seemed to be related to a signalling mechanism (nutritional state). This mating pattern had a substantial effect on the breeding parameters and influenced offspring ALP. Within-pair asymmetry did not influence any reproductive parameters, but the ALP of offspring was related to the within-pair relative female condition. Overall, our results indicate that individuals seek the best possible match to maximize their breeding investment and/or individuals are limited in their mate options by their current body condition, which has consequences for offspring fitness in the short term. Our findings show that assortative mating based on body condition produces notable variation in the joint condition of the pair, which determines their breeding success.
Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark
Authors: Dierickx Elisa G. , Sin Simon Yung Wa , van Veelen H. Pieter J. , Brooke M. de L. , Liu Yang , Edwards Scott V. , Martin Simon H.
Published: March 2020

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.
Where to rewild? A conceptual framework to spatially optimize ecological function
Authors: Thierry Hugo , Rogers Haldre
Published: March 2020

Rewilding is an approach aiming at restoring ecosystems to a self-sustaining state by restoring ecological function through active reintroductions or passive management. Locations for most rewilding-through-reintroduction efforts today are selected based on the suitability of the habitat for the reintroduced species, often with little consideration of where the ecological function is most needed. We developed the Spatial Planning of Rewilding Effort (Spore) framework to identify priority locations for rewilding projects through simultaneous consideration of habitat suitability and provisioning of ecological function. We use the island of Guam as a case study for a potential rewilding project, as the island has functionally lost all native seed dispersers as a result of the invasive brown treesnake (Boiga irregularis). The Såli (Micronesian starling,Aplonis opaca) is a good candidate for rewilding to restore ecological function, because it is an effective seed disperser with a localized remnant population. Using Spore, we identify three priority areas for the restoration of seed dispersal, each subdivided into management units. By recognizing the influence of landscape structure and the behaviour of the reintroduced species on the spatial pattern of the function provided by that species, this approach should lead to improved ecological outcomes.
Motif analysis in co-expression networks reveals regulatory elements in plants: The peach as a model
Authors: Ksouri Najla , Castro-Mondragón Jaime A. , Montardit-Tardà Francesc , van Helden Jacques , Contreras-Moreira Bruno , Gogorcena Yolanda
Published: March 2020

Identification of functional regulatory elements encoded in plant genomes is a fundamental need to understand gene regulation. While much attention has been given to model species asArabidopsis thaliana, little is known about regulatory motifs in other plant genera. Here, we describe an accurate bottom-up approach using the online workbench RSAT::Plants for a versatile ab-initio motif discovery takingPrunus persicaas a model. These predictions rely on the construction of a co-expression network to generate modules with similar expression trends and assess the effect of increasing upstream region length on the sensitivity of motif discovery. Applying two discovery algorithms, 18 out of 45 modules were found to be enriched in motifs typical of well-known transcription factor families (bHLH, bZip, BZR, CAMTA, DOF, E2FE, AP2-ERF, Myb-like, NAC, TCP, WRKY) and a novel motif. Our results indicate that small number of input sequences and short promoter length are preferential to minimize the amount of uninformative signals in peach. The spatial distribution of TF binding sites revealed an unbalanced distribution where motifs tend to lie around the transcriptional start site region. The reliability of this approach was also benchmarked inArabidopsis thaliana, where it recovered the expected motifs from promoters of genes containing ChIPseq peaks. Overall, this paper presents a glimpse of the peach regulatory components at genome scale and provides a general protocol that can be applied to many other species. Additionally, a RSAT Docker container was released to facilitate similar analyses on other species or to reproduce our results.

One sentence summary

Motifs prediction depends on the promoter size. A proximal promoter region defined as an interval of -500 bp to +200 bp seems to be the adequate stretch to predictde novoregulatory motifs in peach
Corticospinal excitability remains unchanged in the presence of residual force enhancement and does not contribute to increased torque production
Authors: Frischholz Jasmin , Raiteri Brent J. , Cresswell Andrew G. , Hahn Daniel
Published: March 2020

Following active muscle stretch, muscle force is enhanced, which is known as residual force enhancement (rFE). As earlier studies found apparent corticospinal excitability modulations in the presence of rFE, this study aimed to test whether corticospinal excitability modulations contribute to rFE. Fourteen participants performed submaximal plantar flexion stretch-hold and fixed-end contractions at 30% of their maximal voluntary soleus muscle activity in a dynamometer. During the steady state of the contractions, participants either received subthreshold or suprathreshold transcranial magnetic stimulation (TMS) of their motor cortex, while triceps surae muscle responses to stimulation were obtained via electromyography (EMG), and net ankle joint torque was recorded. B-mode ultrasound imaging was used to confirm muscle fascicle stretch during stretch-hold contractions in a subset of participants. Following stretch of the plantar flexors, an average rFE of 7% and 11% was observed for contractions with subthreshold and suprathreshold TMS, respectively. 41-46 ms following subthreshold TMS, triceps surae muscle activity was suppressed by 19-25%, but suppression was not significantly different between stretch-hold and fixed-end contractions. Similarly, the reduction in plantar flexion torque following subthreshold TMS was not significantly different between contraction conditions. Motor evoked potentials, silent periods and superimposed twitches following suprathreshold TMS were also not significantly different between contraction conditions. As TMS of the motor cortex did not result in any differences between stretch-hold and fixed-end contractions, we conclude that rFE is not linked to changes in corticospinal excitability, making rFE a muscle mechanical property rather than a combined neuro-muscular property.
Implementing an algorithm for controlling for female MC phase for clinical neuroscience
Authors: Herrold Amy A. , Gallagher Virginia T. , Chen Yufen , Majaanes Jeffery , Kramer Natalie , Vesci Brian , Colegrove Danielle , Reilly James , McCloskey Leanne , Breiter Hans
Published: March 2020

Background

Recent research suggests that hormones and/or menstrual cycle (MC) phase at time of study may significantly affect clinical neuroscience outcomes of interest. Prior research puts forth sound methods for characterizing MC phase in women not using hormonal contraceptives (HC). However, an estimated 40% of premenopausal women in the United States use some form of HC. We developed an algorithm for characterizing hormone levels and MC phase among women both using and not using HC. We have employed this algorithm among female collegiate athletes post-mild traumatic brain injury (mTBI) as female athletes are understudied in the sports mTBI field, MC phase may have important effects on mTBI-related outcomes and controlling for MC phase has not been employed in this population.

Methods

Thirty female collegiate athletes were studied. Fifteen incurred a mTBI 3-10 days prior to assessment and sixteen were age, ethnicity, and menstrual cycle (MC) phase matched to the injured athletes. MC matching was conducted with retrospective and prospective self-report MC tracking, self-report of HC use, and serum progesterone testing.

Results

53% (16/30) of females were on HC and 47% (14/30) were not. Of the non-HC users, seven female pairs were in the follicular and one was in the luteal phase. Among the non-HC users, there was 50% agreement in MC phase identification between self-report and progesterone measures and a κ = 0.138. Of the HC users, eight were in the inactive and six were in the active phase of their medication. Among the HC users, average progesterone levels indicated medication compliance (.58ng/mL).

Conclusions

This study provides important methodology and proof-of-concept that MC phase can be used as a control variable for time-sensitive prospective clinical neuroscience studies including those involving brain injury. When studying females, it is important to properly examine and control for the sex-specific factor of MC phase in order to have a full understanding of brain behavior relationships in translational research.
Applying a gene-suite approach to examine the physiological status of wild-caught walleye (Sander vitreus)
Authors: Jeffrey Jennifer D. , Carlson Hunter , Wrubleski Dale , Enders Eva C. , Treberg Jason R. , Jeffries Ken M.
Published: March 2020

Molecular techniques have been increasingly used in a conservation physiology framework to provide valuable information regarding the mechanisms underlying responses of wild organisms to environmental and anthropogenic stressors. In the present study, we developed a reference gill transcriptome for walleye (Sander vitreus) allowing us to pair a gene-suite approach with multivariate statistics to examine the physiological status of wild-caught walleye. For molecular analyses of wild fish, the gill is a useful target for conservation studies, not only because of its importance as an indicator of the physiological status of fish but also because it can be biopsied non-lethally. Walleye were non-lethally sampled following short- (∼1.5 month) and long-term (∼3.5 month) holding in the Delta Marsh, that is located south of Lake Manitoba in Manitoba, Canada. Large-bodied walleye are held in the Delta Marsh from late April to early August by exclusion screens used to protect the marsh from invasive common carp (Cyprinus carpio), exposing fish to potentially stressful water quality conditions. Principal components analysis (PCA) revealed patterns of transcript abundance consistent with exposure of fish to increasingly high temperature and low oxygen conditions with longer holding in the marsh. For example, longer-term holding in the marsh was associated with increases in the mRNA levels of heat shock proteins and a shift in the mRNA abundance of aerobic to anaerobic metabolic genes. Overall, the results of the present study suggest that walleye held in the Delta Marsh may be exhibiting sub-lethal responses to high temperature and low oxygen conditions and provides valuable information for managers invested in mediating these impacts to a local species of conservation concern. More broadly, we highlight the usefulness of pairing transcriptomic techniques with multivariate statistics to address potential confounding factors that can affect measured physiological responses of wild-caught fish.

Lay summary

Non-lethal molecular techniques were used to assess the physiological status of wild-caught walleye confined in the Delta Marsh, Manitoba, Canada, because of common carp exclusion screens. Walleye sampled during the warmest months of the year exhibited responses to elevated temperature and low oxygen conditions, suggesting sub-lethal effects of local conditions.
Heme A-containing oxidases evolved in the ancestors of iron oxidizing bacteria
Authors: Degli Esposti Mauro , Garcia-Meza Viridiana , Ceniceros Gómez Agueda E. , Moya-Beltrán Ana , Quatrini Raquel , Hederstedt Lars
Published: March 2020

The origin of oxygen respiration in bacteria has long intrigued biochemists, microbiologists and evolutionary biologists. The earliest enzymes that consume oxygen to extract energy did not evolve in the same lineages of photosynthetic bacteria that released oxygen on primordial earth, leading to the great oxygenation event (GOE). A widespread type of such enzymes is proton pumping cytochromecoxidase (COX) that contains heme A, a unique prosthetic group for these oxidases. Here we show that the most ancestral proteins for the biosynthesis of heme A are present in extant acidophilic Fe2+-oxidizing Proteobacteria. Acidophilic Fe2+-oxidizers lived on emerged land around the time of the GOE, as suggested by the earliest geochemical evidence for aerobic respiration on paleoproterozoic earth. The gene for heme A synthase in acidophilic Fe2+-oxidizing Proteobacteria is associated with the COX gene cluster for iron oxidation. Compared to many other soil bacteria, the COX subunits encoded by this gene cluster are early diverging. Our data suggest that the ancient bacterial lineage which first evolved heme A-containing COX was related to the ancestors of present acidophilic Fe2+-oxidizers such asAcidiferrobacterandAcidithiobacillusspp. The copper leaching activity of such bacteria might have constituted a key ecological factor to promote COX evolution.
Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution
Authors: Georgakopoulos-Soares Ilias , Barnea Ofer Yizhar , Mouratidis Ioannis , Hemberg Martin , Ahituv Nadav
Published: March 2020

Nullomers and nullpeptides are short DNA or amino acid sequences that are absent from a genome or proteome, respectively. One potential cause for their absence could be that they have a detrimental impact on an organism. Here, we identified all possible nullomers and nullpeptides in the genomes and proteomes of over thirty species and show that a significant proportion of these sequences are under negative selection. We assign nullomers to different functional categories (coding sequences, exons, introns, 5’UTR, 3’UTR and promoters) and show that nullomers from coding sequences and promoters are most likely to be selected against. Utilizing variants in the human population, we annotate variant-associated nullomers, highlighting their potential use as DNA ‘fingerprints’. Phylogenetic analyses of nullomers and nullpeptides across evolution shows that they could be used to build phylogenetic trees. Our work provides a catalog of genomic and proteome derived absent k-mers, together with a novel scoring function to determine their potential functional importance. In addition, it shows how these unique sequences could be used as DNA ‘fingerprints’ or for phylogenetic analyses.
Dynamic cell wall modifications in brassicas during clubroot disease
Authors: Badstöber Julia , Ciaghi Stefan , Neuhauser Sigrid
Published: March 2020

Biotic interactions of plants and microbial pathogens can cause drastic changes in cell wall composition in response to developmental reprogramming caused as consequence of an infection. Clubroot disease, caused by the biotrophic plant pathogenPlasmodiophora brassicae(Phytomyxea, Rhizaria), is the economically most important disease of Brassica crops worldwide. The disease is best known by the characteristic hypertrophied roots (root galls, clubroots). Amongst a series of physiological changes of the host tissue, the formation of the characteristic root galls leads to cell wall modification and reorganization. Cell wall chemistry and the hosts genetic repertoire are discussed to play a role in the resilience of plants against clubroot disease. Plant cells infected withP. brassicaeare markedly enlarged, and look very differently from uninfected, healthy cells. Here we systematically review cell wall related processes that lead to the typical clubroot phenotype and provide novel insights howP. brassicaeuses these modifications to benefit its own development. An infection withP. brassicaeimpacts on nearly all cell wall related processes, but all alterations are meaningful for successful growth and development ofP. brassicae.Processes related to cell wall stability and rigidity (e.g. cellulose, pectin or lignin synthesis) are down-regulated, while cell wall degrading enzymes or processes that increase the flexibility of the host cell wall (e.g. expansin) are up-regulated. The here presented findings indicate thatP. brassicaeweakens the structural stability of its host cell while it increases its elasticity, which in consequence allowsP. brassicaeto grow bigger and ultimately to develop more resting spores. Consequently, the understanding of the modification of the host cell wall is important for the formation of the characteristic root galls but also to better understand clubroot disease.
Bridging parametric and nonparametric measures of species interactions unveils new insights of non-equilibrium dynamics
Authors: Song Chuliang , Saavedra Serguei
Published: March 2020

A central theme in ecological research is to understand how species interactions contribute to community dynamics. Species interactions are the basis of parametric (model-driven) and nonpara-metric (model-free) approaches in theoretical and empirical work. However, despite their different interpretations across these approaches, these measures have occasionally been used interchangeably, limiting our opportunity to use their differences to gain new insights about ecological systems. Here, we revisit two of the most used measures across these approaches: species interactions measured asconstant directeffects (typically used in parametric approaches) andlocal aggregatedeffects (typically used in nonparametric approaches). We show two fundamental properties of species interactions that cannot be revealed without bridging these definitions. First, we show that the local aggregated intraspecific effect summarizes all potential pathways through which one species impacts itself, which are likely to be negative even without any constant direct self-regulation mechanism. This property has implications for the long-held debate on how communities can be stabilized when little evidence of self-regulation has been found among higher-trophic species. Second, we show that a local aggregated interspecific effect between two species is correlated with the constant direct interspecific effect if and only if the population dynamics do not have any higher-order direct effects. This other property provides a rigorous methodology to detect direct higher-order effects in the field and experimental data. Overall, our findings illustrate a practical route to gain further insights about non-equilibrium ecological dynamics and species interactions.
UC2 – A Versatile and Customizable low-cost 3D-printed Optical Open-Standard for microscopic imaging
Authors: Diederich Benedict , Lachmann René , Carlstedt Swen , Marsikova Barbora , Wang Haoran , Uwurukundo Xavier , Mosig Alexander , Heintzmann Rainer
Published: March 2020

With UC2 (You-See-Too) we present an inexpensive 3D-printed microscopy toolbox. The system is based on concepts of modular development, rapid-prototyping and all-time accessibility using widely available off-the-shelf optic and electronic components. We aim to democratize microscopy, reduce the reproduction crisis and enhance trust into science by making it available to everyone via an open-access public repository. Due to its versatility the aim is to boost creativity and non-conventional approaches. In this paper, we demonstrate a development cycle from basic blocks to different microscopic techniques. First, we build a bright-field system and stress-test it by observing macrophage cell differentiation, apoptosis and proliferation incubator-enclosed for seven days with automatic focussing to minimize axial drift. We prove versatility by assembling a system using the same components to a fully working fluorescence light-sheet system and acquire a 3D volume of a GFP-expressing living drosophila larvae. Finally, we sketch and demonstrate further possible setups to draw a picture on how the system can be used for reproducible prototyping in scientific research. All design files for replicating the experimental setups are provided via an open-access online repository (https://github.com/bionanoimaging/UC2-GIT) to foster widespread use.
A Decoy Library Uncovers U-box E3 Ubiquitin Ligases that Regulate Flowering Time in Arabidopsis
Authors: Feke Ann M. , Hong Jing , Liu Wei , Gendron Joshua M.
Published: March 2020

Targeted degradation of proteins is mediated by E3 ubiquitin ligases and is important for the execution of many biological processes. Previously, we created and employed a large library of E3 ubiquitin ligase decoys to identify regulators of the circadian clock (Feke et al., 2019). In tandem with the screen for circadian regulators, we performed a flowering time screen using our U-box-type E3 ubiquitin ligase decoy transgenic library. We identified five U-box decoy transgenic populations that have defects in flowering time or the floral development program. We used additional genetic and biochemical studies to validatePLANT U-BOX 14(PUB14),MOS4-ASSOCIATED COMPLEX 3A (MAC3A),andMAC3Basbona fideregulators of flowering time. This work reinforces the utility of the decoy library in identifying regulators of important developmental transitions in plants and expands the scope of the technique beyond our previous studies.
CDKN2Chomozygous loss identifies a distinct subtype ofTP53/RB1-wildtype leiomyosarcoma with frequentCICgenomic alterations and 1p/19q-codeletion
Authors: Williams Erik A. , Sharaf Radwa , Decker Brennan , Werth Adrienne J. , Toma Helen , Montesion Meagan , Sokol Ethan S. , Pavlick Dean C. , Shah Nikunj , Venstrom Jeff M. , Alexander Brian M. , Ross Jeffrey S. , Albacker Lee A. , Lin Douglas I , Ramkissoon Shakti H. , Elvin Julia A.
Published: March 2020

Purpose

Leiomyosarcomas (LMS) harbor frequent inactivation ofTP53andRB1, and extensive DNA copy number alterations. Here, we describe a distinct recurrent genomic signature inTP53/RB1-wildtype uterine LMS.

Methods

Tissues from 276,645 unique advanced cancers, including 2,570 uterine and soft tissue LMS were sequenced by hybrid-capture-based next-generation DNA and RNA sequencing/comprehensive genomic profiling of up to 406 genes. We characterized clinicopathologic features of relevant cases.

Results

We identified 77 LMS with homozygous copy loss ofCDKN2Cat chromosome 1p32.3 (3.0% of LMS). Genomic alterations (GAs) inTP53, RB1, andATRXwere rare in comparison with the remainder of the LMS cohort (11.7% vs 73.4%, 0% vs 54.5%, 2.6% vs 24.5%, all p<0.0001).CDKN2C-null LMS cases were significantly enriched for GAs inCIC(40.3% vs 1.4%) at 19q13.2,CDKN2A(46.8% vs 7.0%), andRAD51B(16.9% vs 1.7%; all p<0.0001). Chromosome arm-level aneuploidy analysis of available LMS cases (n=1,251) found that 85% (n=33/39) ofCDKN2C-null LMS cases exhibited 1p/19q-codeletion, with significant enrichment in comparison to the remainder of the evaluated LMS cohort (85% vs. 5.1%, p<0.0001).

99% ofCDKN2C-null cases were in females; median age was 61 years at surgery (range, 36-81 years). 55 cases were of uterine primary, 4 cases non-uterine, and the remaining 18 of uncertain primary site. 6 patients had a prior history of leiomyomatosis or uterine smooth muscle tumor of uncertain malignant potential. 60% of cases showed at least focal epithelioid variant histology. Most cases were of known advanced stage, with 62% of confirmed uterine primary cases at FIGO stage IVB.

Conclusion

The identification of this novel genomic subset may have prognostic and/or therapeutic clinical relevance, including use of specific cyclin-dependent kinase inhibitors.
Ongoing exposure to peritoneal dialysis fluid alters resident peritoneal macrophage phenotype and activation propensity
Authors: Sutherland Tara E. , Shaw Tovah N. , Lennon Rachel , Herrick Sarah E. , Rückerl Dominik
Published: March 2020

Peritoneal dialysis (PD) is a more continuous alternative to haemodialysis, for patients with chronic kidney disease, with considerable initial benefits for survival, patient independence and healthcare costs. However, longterm PD is associated with significant pathology, negating the positive effects over haemodialysis. Importantly, peritonitis and activation of macrophages is closely associated with disease progression and treatment failure. However, recent advances in macrophage biology suggest opposite functions for macrophages of different cellular origins. While monocyte-derived macrophages promote disease progression in some models of fibrosis, tissue resident macrophages have rather been associated with protective roles. Thus, we aimed to identify the relative contribution of tissue resident macrophages to PD induced inflammation in mice. Unexpectedly, we found an incremental loss of homeostatic characteristics, anti-inflammatory and efferocytic functionality in peritoneal resident macrophages, accompanied by enhanced inflammatory responses to external stimuli. Moreover, presence of glucose degradation products within the dialysis fluid led to markedly enhanced inflammation and almost complete disappearance of tissue resident cells. Thus, alterations in tissue resident macrophages may render longterm PD patients sensitive to developing peritonitis and consequently fibrosis/sclerosis.
Full quantum mechanical modeling of the enzyme-substrate system: how laccase detoxifies aflatoxin
Authors: Zaccaria Marco , Dawson William , Kish Darius , Reverberi Massimo , Domin Marek , Dellafiora Luca , Nakajima Takahito , Genovese Luigi , Momeni Babak
Published: March 2020

This work focuses on: 1) the development of a methodology to perform a full Quantum Mechanics (QM) characterization of enzymatic activity; 2) the development of a rational approach to laccase engineering as a food bioremediator. Aflatoxins are among the most dangerous natural carcinogens, and regularly contaminate reserves of staple crops worldwide. Decontamination of aflatoxin-polluted food is of great interest for ensuring food safety, and bioremediation is regarded as the most promising solution. The fungal isoforms of laccase display the rare potential to detoxify aflatoxin by tackling its aromatic moieties.. Yet, because of a generally low efficiency, large-scale application of naturally occurring isoforms has so far been unfeasible. We perform a combination of quantitative experimentation and quantum mechanical modeling on aflatoxin and reveal that: (1) detoxification efficiency is limited by the low enzymatic affinity for the substrate; and (2) aflatoxin is not detoxified by oxidative activity of laccase alone, but requires additional stimulation from the environment. QM modeling also allowed identification of the residues in the laccase tertiary structure that determine affinity of the enzymatic pocket for aflatoxin. We conclude that, for our case-study, a full QM approach is mandatory as a first step towards rational optimization. We detail a feasible approach towards this endeavor and argue that our full QM characterization can serve as a roadmap for enzyme development in other applications pertaining laccase as well as other enzymes.
Visuospatial n-back test for early detection of mild cognitive impairment in patients with Parkinson’s Disease : an fMRI study
Authors: Kawashima Shoji , Shimizu Yoko , Ueki Yoshino , Matsukawa Noriyuki
Published: March 2020

Background

Cognitive impairment is a common symptom in the patients with Parkinson’s disease (PD). In delineating a therapeutic plan, the early diagnosis of mild cognitive impairment in PD (PD-MCI) is important. Patients with PD-MCI have severe impairment in frontal executive function and/or visuospatial recognition. However, the clinical assessment of these functions is not routinely performed.

Method

In this study, we aimed to clarify the advantage of visuospatial version of the n-back test as a tool for the early detection of neuropsychological change in the patients with PD-MCI. The score of 0-back test reflects visuospatial recognition, and the scores of 1-back and 2-back reflect visuospatial working memory. PD-MCI was classified according to the criteria provided by the Movement Disorder Society Task Force for mild cognitive impairment in PD. We recruited 13 patients with PD-MCI, and 15 patients with cognitive normal PD. Using functional MRI (fMRI), we also aimed to clarify the specific brain regions associated with the impairment of visuospatial working memory.

Result

We demonstrated that the correct answer rate of patients with PD-MCI was lower in the 2-back test than patients with PD-CN. However, we did not find statistical difference in the 0-back test. These results indicate the preservation of visuospatial recognition and the impairment of visuospatial working memory in the patients with PD-MCI. We revealed the reduced activation within the middle frontal gyrus (MFG) and the inferior parietal lobule (IPL) during the 2-back test in the patients with PD-MCI. It may be associated with the severity of cortico-striatal dysfunction in the dopaminergic neural network which is associated with Lewy body pathology.

Conclusion

The visuospatial n-back test has advantages for use in rapid and early detection of impaired visual recognition and working memory. The combination of functional neuroimaging and neuropsychological tests may provide markers for the increased risk of dementia before the development of an irreversible disease-specific pathology.
SLC45A2 protein stability and regulation of melanosome pH determine melanocyte pigmentation
Authors: Le Linh , Escobar Iliana E. , Ho Tina , Lefkovith Ariel J. , Latteri Emily , Dennis Megan K. , Haltaufderhyde Kirk D. , Sviderskaya Elena V. , Bennett Dorothy C. , Oancea Elena , Marks Michael S.
Published: March 2020

SLC45A2encodes a putative transporter expressed primarily in pigment cells.SLC45A2mutations and polymorphisms cause oculocutaneous albinism (OCA) and pigmentation variation, but neither SLC45A2 localization and function nor how gene variants affect these properties are known. We show that SLC45A2 localizes to mature melanosomes that only partially overlap with a cohort expressing the chloride channel OCA2. SLC45A2 expressed ectopically in HeLa cells localizes to lysosomes and raises lysosomal pH, suggesting that, like OCA2, SLC45A2 in melanocytes de-acidifies maturing melanosomes to support melanin synthesis. Analyses of SLC45A2- and OCA2-deficient mouse melanocytes show that SLC45A2 functions later during melanosome maturation than OCA2, and that OCA2 overexpression compensates for loss of SLC45A2 expression in pigmentation. The light skin-associated SLC45A2 allelic F374 variant restores only moderate pigmentation to SLC45A2-deficient melanocytes because of low level expression in melanosomes due to rapid proteasome-independent degradation. Our data indicate that SLC45A2 maintains melanosome neutralization – initially orchestrated by transient OCA2 activity – to support melanization at late stages of melanosome maturation, and that a common variant imparts reduced activity due to protein instability.
Proteomics support the threespine stickleback egg coat as a protective oocyte envelope
Authors: Killingbeck Emily E. , Wilburn Damien B. , Merrihew Gennifer E. , MacCoss Michael J. , Swanson Willie J.
Published: March 2020

After the end of the last ice age, ancestrally marine threespine stickleback fish (Gasterosteus aculeatus) have undergone an adaptive radiation into freshwater environments throughout the Northern Hemisphere, creating an excellent model system for studying molecular adaptation and speciation. Stickleback populations are reproductively isolated to varying degrees, despite the fact that they can be crossed in the lab to produce viable offspring. Ecological and behavioral factors have been suggested to underlie incipient stickleback speciation. However, reproductive proteins represent a previously unexplored driver of speciation. As mediators of gamete recognition during fertilization, reproductive proteins both create and maintain species boundaries. Gamete recognition proteins are also frequently found to be rapidly evolving, and their divergence may culminate in reproductive isolation and ultimately speciation. As an initial investigation into the contribution of reproductive proteins to stickleback reproductive isolation, we characterized the egg coat proteome of threespine stickleback eggs. In agreement with other teleosts, we find that stickleback egg coats are comprised of homologs to the zona pellucida (ZP) proteins ZP1 and ZP3. We explore aspects of stickleback ZP protein biology, including glycosylation, disulfide bonding, and sites of synthesis, and find many substantial differences compared to their mammalian homologs. Furthermore, molecular evolutionary analyses indicate thatZP3, but notZP1, has experienced positive Darwinian selection across teleost fish. Taken together, these changes to stickleback ZP protein architecture suggest that the egg coats of stickleback fish, and perhaps fish more generally, have evolved to fulfill a more protective functional role than their mammalian counterparts. Data are available via ProteomeXchange with identifiers PXD017488 and PXD017489.
Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. elegans to mammals
Authors: Rowley M. Jordan , Poulet Axel , Nichols Michael H. , Bixler Brianna J. , Sanborn Adrian L. , Brouhard Elizabeth A. , Hermetz Karen , Linsenbaum Hannah , Csankovszki Gyorgyi , Lieberman Aiden Erez , Corces Victor G.
Published: March 2020

Chromatin loops are a major component of 3D nuclear organization, visually apparent as intense point-to-point interactions in Hi-C maps. Identification of these loops is a critical part of most Hi-C analyses. However, current methods often miss visually evident CTCF loops in Hi-C data sets from mammals, and they completely fail to identify high intensity loops in other organisms. We present SIP, Significant Interaction Peak caller, and SIPMeta, which are platform independent programs to identify and characterize these loops in a time- and memory-efficient manner. We show that SIP is resistant to noise and sequencing depth, and can be used to detect loops that were previously missed in human cells as well as loops in other organisms. SIPMeta corrects for a common visualization artifact by accounting for Manhattan distance to create average plots of Hi-C and HiChIP data. We then demonstrate that the use of SIP and SIPMeta can lead to biological insights by characterizing the contribution of several transcription factors to CTCF loop stability in human cells. We also annotate loops associated with the SMC component of the dosage compensation complex (DCC) in Caenorhabditis elegans and demonstrate that loop anchors represent bidirectional blocks for symmetrical loop extrusion. This is in contrast to the asymmetrical extrusion until unidirectional blockage by CTCF that is presumed to occur in mammals. Using HiChIP and multiway ligation events, we then show that DCC loops form a network of strong interactions that may contribute to X Chromosome–wide condensation in C. elegans hermaphrodites.
Design of hybrid electric heavy fuel MALE ISR UAV enabling technologies for military operations
Authors: Fioriti Marco , Vaschetto Silvio , Corpino Sabrina , Premoli Giovanna
Published: March 2020

Purpose

This paper aims to present the main results achieved in the frame of the TIVANO national-funded project which may anticipate, in a stepped approach, the evolution and the design of the enabling technologies needed for a hybrid/electric medium altitude long endurance (MALE) unmanned aerial vehicle (UAV) to perform persistent intelligence surveillance reconnaissance (ISR) military operations.

Design/methodology/approach

Different architectures of hybrid-propulsion system are analyzed pointing out their operating modes to select the more suitable architecture for the reference aircraft. The selected architecture is further analyzed together with its electric power plant branch focusing on electric system architecture and the selected electric machine. A final comparison between the hybrid and standard propulsion is given at aircraft level.

Findings

The use of hybrid propulsion may lead to a reduction of the total aircraft mass and an increase in safety level. However, this result comes together with a reduced performance in climb phase.

Practical implications

This study can be used as a reference for similar studies and it provides a detailed description of propulsion operating modes, power management, electric system and machine architecture.

Originality/value

This study presents a novel application of hybrid propulsion focusing on a three tons class MALE UAV for ISR missions. It provides new operating modes of the propulsion system and a detailed electric architecture of its powertrain branch and machine. Some considerations on noise emissions and infra-red traceability of this propulsion, at aircraft level.
The power of an intersectionality framework in teacher education
Authors: Leckie Alisa , Buser De Maya
Published: March 2020

Purpose

The purpose of this study is to describe the use of an intersectionality framework to analyze and incorporate teachers’ lived experiences into critical professional development.

Design/methodology/approach

Researchers used qualitative coding based on the matrix of oppression and privilege (Ferber and O’Reilly Herrera, 2013) to analyze teachers’ multicultural autobiographies. Connections between multicultural autobiographies were then made between other course reflections and lesson plans that were developed throughout the 150 h of professional development.

Findings

Findings evidence the multiple sites of oppression and privilege, the importance of spaces and relationships in locating ourselves and others on the matrix and the possibilities for transferring knowledge to professional practice.

Research limitations/implications

The authors do recognize the limitations of their study. Although the participants were from differing educational contexts and backgrounds, the sample size was small. Additional studies of this nature can expand our understanding of privilege, oppression and the impact of critical professional development for educators. Our society, and therefore the education system, continues to become more culturally and linguistically diverse, and it is incumbent upon us as educators and researchers to identify effective approaches for preparing both teachers and students for a changing world.

Practical implications

The power of the matrix framework in pedagogical settings is that it facilitates the recognition and analysis of individual social locations and their relationships to various systems of inequality. Most importantly, analyzing both privilege and oppression allows individuals and instructors to reflect on their own experiences and initiate conversations that reduce the animosity toward those who have different experiences.

Originality/value

This study is significant, in that it offers a framework that addresses the perceived disconnect between teachers and their increasingly culturally and linguistically diverse student population (Banks and Banks, 2013; Darling-Hammond and Bransford, 2005).
Configurational crop heterogeneity increases within‐field plant diversity
Authors: Alignier Audrey , Solé‐Senan Xavier O. , Robleño Irene , Baraibar Bàrbara , Fahrig Lenore , Giralt David , Gross Nicolas , Martin Jean‐Louis , Recasens Jordi , Sirami Clélia , Siriwardena Gavin , Bosem Baillod Aliette , Bertrand Colette , Carrié Romain , Hass Annika , Henckel Laura , Miguet Paul , Badenhausser Isabelle , Baudry Jacques , Bota Gerard , Bretagnolle Vincent , Brotons Lluis , Burel Françoise , Calatayud François , Clough Yann , Georges Romain , Gibon Annick , Girard Jude , Lindsay Kathryn , Minano Jesus , Mitchell Scott , Patry Nathalie , Poulin Brigitte , Tscharntke Teja , Vialatte Aude , Violle Cyrille , Yaverscovski Nicole , Batáry Péter
Published: March 2020

Increasing landscape heterogeneity by restoring semi‐natural elements to reverse farmland biodiversity declines is not always economically feasible or acceptable to farmers due to competition for land. We hypothesized that increasing the heterogeneity of the crop mosaic itself, hereafter referred to as crop heterogeneity, can have beneficial effects on within‐field plant diversity.

Using a unique multi‐country dataset from a cross‐continent collaborative project covering 1,451 agricultural fields within 432 landscapes in Europe and Canada, we assessed the relative effects of compositional and configurational crop heterogeneity on within‐field plant diversity components. We also examined how these relationships were modulated by the position within the field.

We found strong positive effects of configurational crop heterogeneity on within‐field plant alpha and gamma diversity in field interiors. These effects were as high as the effect of semi‐natural cover. In field borders, effects of crop heterogeneity were limited to alpha diversity. We suggest that a heterogeneous crop mosaic may overcome the high negative impact of management practices on plant diversity in field interiors, whereas in field borders, where plant diversity is already high, landscape effects are more limited.

Synthesis and applications. Our study shows that increasing configurational crop heterogeneity is beneficial to within‐field plant diversity. It opens up a new effective and complementary way to promote farmland biodiversity without taking land out of agricultural production. We therefore recommend adopting manipulation of crop heterogeneity as a specific, effective management option in future policy measures, perhaps adding to agri‐environment schemes, to contribute to the conservation of farmland plant diversity.