bluuebunny/crossref_metadata_2025 huggingface dataset:
Epitope region identification challenges of intrinsically disordered proteins in neurodegenerative diseases: Secondary structure dependence of α‐synuclein on simulation techniques and force field parameters
Authors: Mandaci Sunay Y. , Caliskan Murat , Sariaslan M. Furkan , Uversky Vladimir N. , Coskuner‐Weber Orkid
Published: January 2020

Due to fast aggregation processes of many disordered proteins in neurodegenerative diseases, it is difficult to study their epitope regions at the monomeric and oligomeric levels. Computer simulations complement experiments and have been used to identify the epitope regions of proteins. Residues that adopt β‐sheet conformation play a central role in the oligomerization and aggregation mechanisms of such proteins, including α‐synuclein, which is at the center of Parkinson's and Alzheimer's diseases. In this study, we simulated the monomeric α‐synuclein protein in an aqueous environment to evaluate its secondary structure properties, including β‐sheet propensity, and radius of gyration by replica exchange molecular dynamics simulations. We also obtained the molecular dynamics simulation trajectories of α‐synuclein that were conducted using various force field parameters by the David E. Shaw group. Using these trajectories, we calculated the impacts of force field parameters on α‐synuclein secondary structure properties and radius of gyration values and obtained results are compared with our data from REMD simulations. This study shows that the chosen force field parameters and computer simulation techniques effect the predicted secondary structure properties and radius of gyration values of α‐synuclein in water. Herewith, we illustrate the challenges in epitope region identification of intrinsically disordered proteins in neurodegenerative diseases by current computer simulations.
Effectiveness and safety of insulin glargine 300 U/mL in insulin‐naïve patients with type 2 diabetes after failure of oral therapy in a real‐world setting
Authors: Pfohl Martin , Jornayvaz François R. , Fritsche Andreas , Pscherer Stefan , Anderten Helmut , Pegelow Katrin , Seufert Jochen
Published: January 2020

Aim

To evaluate the effectiveness and safety of initiating basal insulin‐supported oral therapy (BOT) with insulin glargine 300 U/mL (Gla‐300) in patients with type 2 diabetes inadequately controlled on oral antidiabetic drugs (OADs).

Materials and Methods

This non‐interventional, multi‐centre, prospective 52‐week study, conducted in Germany and Switzerland, documented patients with type 2 diabetes with an HbA1c of between 7.5% and 10.0%, currently treated with OADs, after the physician had decided to start a BOT regimen with Gla‐300. The primary endpoint was the rate of achievement of the individualized predefined HbA1c target.

Results

Of 1748 patients included, 1153 comprised the full analysis set, of whom 721 completed documentation of 12 months of Gla‐300 treatment. Twelve months after starting Gla‐300, 49.9% achieved their individualized HbA1c target, and 61.1% achieved either their HbA1c target or a fasting plasma glucose (FPG) of ≤110 mg/dL. Mean HbA1c decreased by −1.22% ± 1.05% to 7.28% ± 0.92% and mean FPG by −51.5 (±48.63) mg/dl to 132.9 ± 33.0 mg/dL. Median duration of HbA1c target achievement was 341 days and probability to remain on target after 6 months was 81%. Hypoglycaemia incidence and rates remained low after 12 months of Gla‐300 treatment; no severe or severe nocturnal hypoglycaemia was observed. Body weight remained unchanged.

Conclusions

Starting a BOT regimen with Gla‐300 allowed about 60% of 721 German and Swiss patients with inadequately controlled type 2 diabetes to achieve glycaemic control within 12 months in daily clinical practice. Glycaemic control was achieved without weight gain or increased risk of nocturnal or severe hypoglycaemia.
Network and cellular mechanisms underlying heterogeneous excitatory/inhibitory balanced states
Authors: Wu Jiaxing , Aton Sara J. , Booth Victoria , Zochowski Michal
Published: January 2020

Recent work has explored spatiotemporal relationships between excitatory (E) and inhibitory (I) signaling within neural networks, and the effect of these relationships on network activity patterns. Data from these studies have indicated that excitation and inhibition are maintained at a similar level across long time periods and that excitatory and inhibitory currents may be tightly synchronized. Disruption of this balance—leading to an aberrant E/I ratio—is implicated in various brain pathologies. However, a thorough characterization of the relationship between E and I currents in experimental settings is largely impossible, due to their tight regulation at multiple cellular and network levels. Here, we use biophysical neural network models to investigate the emergence and properties of balanced states by heterogeneous mechanisms. Our results show that a network can homeostatically regulate the E/I ratio through interactions among multiple cellular and network factors, including average firing rates, synaptic weights and average neural depolarization levels in excitatory/inhibitory populations. Complex and competing interactions between firing rates and depolarization levels allow these factors to alternately dominate network dynamics in different synaptic weight regimes. This leads to the emergence of distinct mechanisms responsible for determining a balanced state and its dynamical correlate. Our analysis provides a comprehensive picture of how E/I ratio changes when manipulating specific network properties, and identifies the mechanisms regulating E/I balance. These results provide a framework to explain the diverse, and in some cases, contradictory experimental observations on the E/I state in different brain states and conditions.
Characterization of a bacterial copper‐dependent lytic polysaccharide monooxygenase with an unusual second coordination sphere
Authors: Munzone Alessia , El Kerdi Bilal , Fanuel Mathieu , Rogniaux Hélène , Ropartz David , Réglier Marius , Royant Antoine , Simaan A. Jalila , Decroos Christophe
Published: January 2020

Lytic polysaccharide monooxygenases (LPMOs) are copper‐dependent enzymes involved in the degradation of recalcitrant polysaccharides such as cellulose or chitin. LPMOs act in synergy with glycoside hydrolases such as cellulases and chitinases by oxidatively cleaving a number of glycosidic bonds at the surface of their crystalline substrate(s). Besides their role in biomass degradation, some bacterial LPMOs have been found to be virulence factors in some human and insect pathogens. Photorhabdus luminescens is a nematode symbiont bacterium that is pathogenic to a wide range of insects. A single gene encoding a LPMO is found in its genome. In this work, we report the characterization of this LPMO, referred to as PlAA10. Surprisingly, PlAA10 lacks the conserved alanine residue (substituted by an isoleucine) found in the second coordination sphere of the copper‐active site in bacterial LPMOs. PlAA10 was found to be catalytically active on both α‐ and β‐chitin, and exhibits a C1‐oxidation regiospecificity, similarly to other chitin‐active LPMOs. The 1.6 Å X‐ray crystal structure confirmed that PlAA10 adopts the canonical immunoglobulin‐like fold typical for LPMOs. The geometry of the copper‐active site is not affected by the nearby isoleucine, as also supported by electron paramagnetic resonance. Nevertheless, the bulkier side chain of isoleucine protrudes from the substrate‐binding surface. A bioinformatic study on putative bacterial LPMOs unveiled that they exhibit some variability at the conserved active‐site alanine position with a substitution in about 15% of all sequences analyzed.

Database

Structural data (atomic coordinates and structure factors) reported for PlAA10 are available in the Protein Data Bank under accession number 6T5Z.

Enzymes

PlAA10, EC1.14.99.53.
Obstinate curiosity and situated solidarity in urban political ecology
Authors: Goldfischer Eric , Rice Jennifer L. , Black Sara T.
Published: January 2020

Over the past two decades, the field of urban political ecology (UPE) has developed into a robust theoretical framework for understanding the production of uneven socionatures. More recently, expanded theoretical and empirical innovations in UPE research are pushing the framework's radical roots into new and productive directions for addressing (not just critiquing) persistent inequalities and marginalizations in and beyond cities. We trace this trajectory of UPE towards its more transformative potential and argue that UPE's relevance will increase as scholars continue to embrace the power of what Povinelli calls “obstinate curiosity” to give rise to unexpected connections between people and ecologies. Specifically, we call for continued diversification of both theoretical and methodological starting points for UPE research, particularly with respect to the ways that scholars practice situated solidarity movements for social and environmental justice in cities.
Soil properties rather than plant production strongly impact soil bacterial community diversity along a desertification gradient on the Tibetan Plateau
Authors: Zong Ning , Shi Peili
Published: January 2020

Grassland desertification is an important environmental issue that has detrimental impacts on the sustainable development of grasslands and human residential environments. Soil microbial community structure might dramatically change during desertification processes because microorganisms are one of the major drivers of ecological processes through their interactions with plants and soil. However, knowledge on the driving factors of microbial diversity changes during the desertification process in alpine grasslands is still lacking. Using a spatial sequence instead of a time successional sequence method, five desertification gradients in alpine steppe were chosen to investigate the changes in soil properties, plants and microbial communities during grassland desertification and to determine the factors that drive microbial community changes. Community coverage, species diversity indices and aboveground biomass gradually decreased from potential to severely heavy desertification gradients (HDs), while species richness and belowground biomass showed unimodal patterns (p < .05). Soil water content and total nitrogen showed gradual decreasing trends, while soil bulk density and gravel content showed opposite trends (p < .05). In addition, both the Shannon diversity index and the Chao1 richness index of soil bacteria increased gradually. The structural equation model showed that of the factors, soil total nitrogen (82.3% of total effect) and soil bulk density (41.4% of total effect) were the most important soil factors affecting soil bacterial diversity. However, community aboveground (43.4% of total effect) and belowground production (13.9% of total effect) were not the primary factors affecting soil microbial diversity. This result suggests that soil microbial diversity during grassland desertification is primarily driven by changes in soil properties, and the effects of vegetation composition and production are relatively small. These findings contribute to the mechanistic understanding of soil microbial diversity by linking changes in soil properties and plant production during desertification processes in alpine ecosystems.
Optimising deproteinisation methods and effect of deproteinisation on structural and functional characteristics of flaxseed gum
Authors: Safdar Bushra , Pang Zhihua , Liu Xinqi , Jatoi Mushtaque Ahmed , Rashid Muhammad Tayyab
Published: January 2020

In the current study, deproteinisation rate (DPR) and carbohydrate loss ratio (CLR) in flaxseed gum (FSG) were compared as indexes by using four different deproteinised methods, that is sodium chloride (NaCl), trichloroacetic acid (TCA), hydrochloric acid (HCl) and calcium chloride (CaCl2). In addition, the effect of deproteinisation on physicochemical, functional and structural characteristics (FTIR, 1H NMR and SEM analysis) of deproteinised flaxseed gum (DFSG) was further examined. The results revealed that HCl and TCA methods had better ability of deproteinisation (97.83% and 96.21%) but resulted in higher CLR (27.66% and 24.19%), while CaCl2 method excelled over the NaCl method in DPR (94.7% and 88.6%) and CLR (4.90% and 4.21%), respectively. Flaxseed gum showed significant functional properties even after deproteinisation and exhibited resolved resonances for both ring and anomeric protons in 1H NMR spectra. The characteristic groups in FTIR spectra were retained after deproteinisation.
Extraction, isolation, characterisation, antioxidant and anti‐fatigue activities of Pleurotus eryngii polysaccharides
Authors: Zhao Yuanyuan , Chen Xuefeng , Jia Wei , Gong Guoli , Zhao Yanni , Li Guoliang , Zhou Jie , Li Xiaona , Zhao Yu , Ma Wenjin
Published: January 2020

Pleurotus eryngii polysaccharide (PEP) was obtained using hot water extraction and ethanol precipitation. Three purified polysaccharide fractions (namely PEP1‐A, PEP2‐A and PEP3‐A) were obtained from PEP using DEAE‐cellulose‐52 chromatography and a gel permeation Sephadex G‐100 column. Firstly, this paper examined the characterisation of PEP1‐A, PEP2‐A and PEP3‐A. The corresponding molecular weights were 5.378 × 105, 9.506 × 106 and 4.975 × 105 Da, respectively. PEP1‐A, PEP2‐A and PEP3‐A had similar monosaccharide compositions. PEP1‐A was β‐configuration, and PEP2‐A and PEP3‐A were α‐configuration. PEP1‐A, PEP2‐A and PEP3‐A had pyran‐type rings, (1 → 3) glucose and (1 → 6) galactose linkages. Secondly, PEP, PEP1‐A, PEP2‐A and PEP3‐A possessed antioxidant activities, and PEP was best. Therefore, only PEP was used to study its anti‐fatigue activity in vivo. The result proved that PEP had anti‐fatigue activity. PEP could be used as a valuable natural food supplement for preventing anti‐fatigue or functional food.
Yogurt and Streptococcus thermophilus metabolites ameliorated telomere attrition in D‐galactose‐induced ageing mice and t‐BHP‐challenged HepG2 cells
Authors: Shan Shufang , Zheng Tianli , Zhang Chaoxiong , Song Xuejiao , Chen Jiayi , Shi Ying , You Jia , Cheng Guo , Xiong Jingyuan
Published: January 2020

Antioxidant‐rich diets affect telomere length, an integrative marker associated with age‐related diseases. Yogurt exerts antioxidative capacity and is speculated to support healthy ageing. However, direct experimental evidence is missing. Here, the effects of yogurt and dairy‐fermenting bacteria on D‐galactose‐induced ageing mice and chemically challenged HepG2 cells were evaluated. Relative telomere length (RTL) in leucocyte and liver were significantly longer in yogurt (1.21 ± 0.07; 1.23 ± 0.11) and Streptococcus thermophilus group (1.18 ± 0.15; 1.13 ± 0.12). When t‐BHP‐challenged HepG2 cells were treated with digested yogurt and S. thermophilus, the senescence index (13.67 ± 3.30; 19.67 ± 2.87) were lower and RTL (1.25 ± 0.11; 1.18 ± 0.10) were longer than the model. Antioxidative effects were observed for yogurt and S. thermophilus metabolites, whereas milk and Lactobacillus rhamnosus metabolites showed minimal influence on RTL and oxidative stress. In conclusion, this study showed that yogurt and S. thermophilus metabolites ameliorated telomere attrition in ageing mice and t‐BHP‐challenged HepG2 cells, possibly by reducing oxidative stress.
In vitro evaluation of digestive enzyme inhibition and antioxidant effects of naked oat phenolic acid compound (OPC)
Authors: Yang Zhihao , Qin Chuan , Weng Peifang , Zhang Xin , Xia Qiang , Wu Zufang , Liu Lianliang , Xiao Jianbo
Published: January 2020

This research was focused on digestive enzyme inhibition and antioxidant properties of naked oat phenolic acid compound (OPC). Free and bound phenolic acid were separated from ethyl acetate fraction, n‐butanol fraction and aqueous fraction. The interactions between OPC and main digestive enzymes (α‐amylase, α‐glucosidase, pepsin and trypsin) were studied. It was shown that the semi‐purified bound phenolic acid (semi‐purified by AB‐8 column) has a competitive alpha‐glucosidase inhibitor, while OPC of the organic extract fraction exhibited the characteristics of a mixed inhibitor. Bound phenolic‐n‐butanol fraction (IC50 = 98.39 ± 0.89 µg mL−1) had the strongest ability to scavenge the 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH). Additionally, the starch hydrolysis degree of n‐butanol extraction naked oat phenolic compound was significantly lower than other fractions in vitro. The integrated results suggested that OPC could be considered as potential healthy factor to control postprandial blood glucose, and the mechanism maybe via anti‐digestion, antioxidation and interaction with diabetes‐related starch.
Effect of tea polyphenols on the quality characteristics of fresh wheat noodles in the storage
Authors: Li Hua , Ma Junting , Zhao Beibei , Pan Li , Meng Jun , Xu Baocheng
Published: January 2020

In this study, the quality properties of fresh noodles with tea polyphenols (TPs), including rheological and texture properties, were characterised. The changes of gluten protein second structure, free thiol group (‐SH) content and TPs content were evaluated in fresh noodles during storage time. The results showed that the flour farinograph and extensograph properties could be improved by 0.9% TPs. All of textural parameters exhibited significant decrease (P < 0.05) along with the storage time, including hardness, springiness and tensile force of fresh noodles, while the shelf life of noodles containing TPs was longer than that of non‐TPs noodles. In addition, TPs inhibited the transformation of glutenin macropolymer (GMP) into SDS‐soluble glutenin in the fresh noodles. Furthermore, the increase in free thiol group, the decrease of α‐helix structure and the change of TPs content mostly occurred during the first 9 days. These results indicated that TPs could prolong the shelf life of fresh noodles.
Sweetener solutions as binding agents for amaranth bars: evolution of temporal dominance of sensory attributes
Authors: Martínez‐García Nayeli , Ramírez‐Rivera Emmanuel de Jesús , Ramón‐Canul Lorena Guadalupe , Servín‐Juárez Roselia , López‐Espíndola Mirna , Herrera‐Corredor José Andrés
Published: January 2020

The objective of the study was to determine the effects of replacing binding agents with commercial low‐calorie sweetener solutions on the physicochemical and temporal dominance of sensations in amaranth bars. Five baked amaranth bar formulations (Sweetener‐Solution‐Formulated Amaranth Bars: SSFABs) were prepared using solutions of erythritol, sucralose, steviol and two sucrose concentrations (50% and 25%). A commercial bar (COMM) was used as a control. Proximal, pH, water activity, texture and colour were measured. Temporal dominance of sensations (TDS) was used to determine dominant attributes in time. In general, SSFABs showed a higher moisture, ash and protein content compared to COMM. Carbohydrates and total crude fat were lower in SSFABs than in COMM. Dominant attributes were Crispy, Dry, Sweet and Amaranth. Erythritol formulation was similar to the commercial bar in terms of maximum dominance rate. Replacement of binding agents impacted on the evolution of dominant attributes in amaranth bars.
Characterisation of sugars as the typical taste compounds in soy sauce by silane derivatisation coupled with gas chromatography–mass spectrometry and electronic tongue
Authors: Zhao Guozhong , Gao Qidou , Wang Yifei , Gao Jianbiao , Li Shu , Chen Zhenjia , Wang Xiaowen , Yao Yunping
Published: January 2020

A total of 214 taste compounds were identified in soy sauce by silane derivatisation coupled with gas chromatography–mass spectrometry (SD‐GC‐MS), including 74 kinds of sugars. The proportion of total sugars is highest from 37.24–77.24% among all taste compounds. In particular, rare sugars were detected and identified as the special compounds in soy sauce which come from the sugar metabolism. Rare sugars identified in soy sauce by traditional fermented technology were prominent than Japanese technology. Principal component analysis (PCA) investigation of these results showed that samples can be distinguished by sugars as the first principal component and the general evaluation index (GEI) of samples was consistent with the result of sensory evaluation. Meanwhile, sweetness had the maximum range (from −9.89 to 14.10) in all taste indexes by electronic tongue (E‐tongue) analysis.
Immunogenetics in stem cell donor registry work: The DKMS example (Part 1)
Authors: Schmidt Alexander H. , Sauter Jürgen , Baier Daniel M. , Daiss Jessica , Keller Andreas , Klussmeier Anja , Mengling Thilo , Rall Gabi , Riethmüller Tobias , Schöfl Gerhard , Solloch Ute V. , Torosian Tigran , Means David , Kelly Helen , Jagannathan Latha , Paul Patrick , Giani Anette S. , Hildebrand Sabine , Schumacher Stephan , Markert Jan , Füssel Monika , Hofmann Jan A. , Schäfer Thomas , Pingel Julia , Lange Vinzenz , Schetelig Johannes
Published: January 2020

Currently, stem cell donor registries include more than 35 million potential donors worldwide to provide HLA‐matched stem cell products for patients in need of an unrelated donor transplant. DKMS is a leading stem cell donor registry with more than 9 million donors from Germany, Poland, the United States, the United Kingdom, India and Chile. DKMS donors have donated hematopoietic stem cells more than 80,000 times. Many aspects of donor registry work are closely related to topics from immunogenetics or population genetics. In this two‐part review article, we describe, analyse and discuss these areas of donor registry work by using the example of DKMS. Part 1 of the review gives a general overview on DKMS and includes typical donor registry activities with special focus on the HLA system: high‐throughput HLA typing of potential stem cell donors, HLA haplotype frequencies and resulting matching probabilities, and donor file optimization with regard to HLA diversity.
Nursing interventions for adults following a mental health crisis: A systematic review guided by trauma‐informed principles
Authors: Nizum Nafsin , Yoon Rosanra , Ferreira‐Legere Laura , Poole Nancy , Lulat Zainab
Published: January 2020

There exists a growing need for health and service providers to respond to persons in a manner that recognizes the prevalence and impact of trauma in individuals and prevent inadvertent re‐traumatization in the routine process of care. The experience of mental health crisis in of itself can have traumatic and impactful effects on individuals. Trauma‐informed approaches to care offer a framework to provide crisis intervention responses that are based on the acknowledgement of the prevalence and impact of trauma and define trauma not by the event per se, but by the impact of an experience of trauma. The integration of trauma‐informed principles in the context of crisis intervention is a current practice gap. In order to inform a portion of a best‐practice guideline for registered nurses and the interprofessional team, a systematic literature review was conducted to primarily identify nursing interventions within four weeks of a mental health crisis, with a secondary focus on identifying particular interventions that included trauma‐informed principles. The systematic review yielded 21 quantitative and qualitative studies related to nursing interventions for mental health crisis, 10 of which referred to one or more principles of trauma‐informed approaches. There was a lack of studies on nursing interventions explicitly linked to implementation of trauma‐informed principles, highlighting future research needs and focused efforts to integrate trauma‐informed principles into crisis intervention practices.
Social Solidarity and Sentencing Disparities Between Ethnic Groups: The Case of Hit‐and‐Run Traffic Offenses
Authors: Factor Roni , Gur‐Arye Miriam
Published: January 2020

Studies of sentencing disparities show that in sentencing for cross‐race or cross‐ethnic violent offenses, minority defendants are likely to be sentenced to harsher punishments when the victim belongs to the majority group. Our study examines whether the same pattern of sentencing discrepancies is to be found with regard to offenses of omission, the prohibition of which imposes a legal duty to come to the aid of a victim; offenses that are based on social solidarity. The dataset includes all cases in which defendants were convicted of hit‐and‐run traffic offenses in Israel from 2001 to 2013. The surprising results show that hit‐and‐run drivers who belong to either the majority or minority ethnic group are likely to be sentenced to more severe punishments when the victim belongs to the same ethnic group than when the victim belongs to a different ethnic group.
School Climate as an Intervention to Reduce Academic Failure and Educate the Whole Child: A Longitudinal Study
Authors: Daily Shay M. , Mann Michael J. , Lilly Christa L. , Dyer Angela M. , Smith Megan L. , Kristjansson Alfgeir L.
Published: January 2020

BACKGROUND

Preventing student academic failure is crucial to student health and life success. Previous studies suggest a positive school climate may reduce students' risk for academic failure and contribute to academic success. The purpose of this study was to determine the longitudinal associations between school climate and academic grades in a group of middle school students who transition into high school.

METHODS

Parallel latent growth curve modeling was used to examine changes among study variables longitudinally using a sample of 2604 in 6th, 7th, and 8th‐grade students across 16 regional schools located in 3 counties in West Virginia.

RESULTS

Students with higher perceptions of a positive school climate exhibited sustained or improved academic achievement over time (β = 0.22 to 0.30, p < .01). Higher positive perceptions of school climate appear to sustain students who earn As/Bs (β = 0.20 to 0.27, p < .01) and strengthen students who earn Cs/Ds/Fs (β = −0.16 to −0.46, p < .05).

CONCLUSIONS

Positive student perceptions of school climate may sustain high academic performance while strengthening students who earn Cs/Ds/Fs. School climate may be useful as an intervention to support school‐based health promotion to reduce the achievement gap in the United States.
Chronic hepatitis B and non‐alcoholic fatty liver disease: Conspirators or competitors?
Authors: Zhang Jianbin , Lin Shuangzhe , Jiang Daixi , Li Mengting , Chen Yuanwen , Li Jun , Fan Jiangao
Published: January 2020

Despite the widespread use of vaccines and antiviral drugs, approximately 350‐400 million patients with chronic hepatitis B (CHB) remain worldwide, who carry high risk of cirrhosis and liver carcinoma. Moreover, owing to improvements in global living standards and lifestyle changes, non‐alcoholic fatty liver disease (NAFLD) has become the most common chronic liver disease. Coexistence of NAFLD and CHB is commonly observed, especially in Asian CHB populations; however, little is known regarding the relationship between these two diseases as comorbidities. In this review, we summarize recent advances in clinical and basic researches related to the underlying mutual interactions, as well as potential animal models to facilitate further investigation.
Heritability of interpack aggression in a wild pedigreed population of North American grey wolves
Authors: vonHoldt Bridgett M. , DeCandia Alexandra L. , Heppenheimer Elizabeth , Janowitz‐Koch Ilana , Shi Ruoyao , Zhou Hua , German Christopher A. , Brzeski Kristin E. , Cassidy Kira A. , Stahler Daniel R. , Sinsheimer Janet S.
Published: January 2020

Aggression is a quantitative trait deeply entwined with individual fitness. Mapping the genomic architecture underlying such traits is complicated by complex inheritance patterns, social structure, pedigree information and gene pleiotropy. Here, we leveraged the pedigree of a reintroduced population of grey wolves (Canis lupus) in Yellowstone National Park, Wyoming, USA, to examine the heritability of and the genetic variation associated with aggression. Since their reintroduction, many ecological and behavioural aspects have been documented, providing unmatched records of aggressive behaviour across multiple generations of a wild population of wolves. Using a linear mixed model, a robust genetic relationship matrix, 12,288 single nucleotide polymorphisms (SNPs) and 111 wolves, we estimated the SNP‐based heritability of aggression to be 37% and an additional 14% of the phenotypic variation explained by shared environmental exposures. We identified 598 SNP genotypes from 425 grey wolves to resolve a consensus pedigree that was included in a heritability analysis of 141 individuals with SNP genotype, metadata and aggression data. The pedigree‐based heritability estimate for aggression is 14%, and an additional 16% of the phenotypic variation was explained by shared environmental exposures. We find strong effects of breeding status and relative pack size on aggression. Through an integrative approach, these results provide a framework for understanding the genetic architecture of a complex trait that influences individual fitness, with linkages to reproduction, in a social carnivore. Along with a few other studies, we show here the incredible utility of a pedigreed natural population for dissecting a complex, fitness‐related behavioural trait.
Estimating dynamic origin–destination demand: A hybrid framework using license plate recognition data
Authors: Mo Baichuan , Li Ruimin , Dai Jingchen
Published: January 2020

This article proposes a hybrid framework for estimating dynamic origin–destination (OD) demand that fully exploits the information available in license plate recognition (LPR) data. A Bayesian path reconstruction model is initially developed to replenish the lost information resulting from the recognition error and insufficient coverage rate of the LPR system. The link flows, initial OD demand, left‐turning flows, and partial path flows are derived based on the reconstructed data. Subsequently, with the information derived, a two‐step ordinary least squares (OLS) OD estimation model is formulated, which incorporates the output from the Bayesian model and coestimates the OD demand and assignment matrix. The proposed framework is qualitatively validated using the real‐world LPR data collected from Langfang City, Hebei Province, China, and is quantitatively validated using the synthesized simulation data for the simplified road network of Langfang. The results show that the proposed model can estimate OD demand distribution with a mean absolute percentage error (MAPE) of about 30%. We also tested the model with different LPR coverage rates, with results showing that an LPR coverage rate of over 50% is required to obtain reasonable results.
Decisions, decisions, decisions: plant roots detect and respond to complex environmental cues
Authors: Callaway Ragan M. , Li Long
Published: January 2020

This article is a Commentary on Zhang et al. (2020), 226: 244–253.
The persuasiveness puzzle about bootstrapping
Authors: Melchior Guido
Published: January 2020

This paper aims at resolving a puzzle about the persuasiveness of bootstrapping. On the one hand, bootstrapping is not a persuasive method of settling questions about the reliability of a source. On the other hand, our beliefs that our sense apparatus is reliable is based on other empirically formed beliefs, that is, they are acquired via a presumably complex bootstrapping process. I will argue that when we doubt the reliability of a source, bootstrapping is not a persuasive method for coming to believe that the source is reliable. However, when being initially unaware of a source and its reliability, as in the case of forming beliefs about our sense apparatus, bootstrapping can be eventually persuasive.
Loose Engel structures
Authors: Casals Roger , del Pino Álvaro , Presas Francisco
Published: January 2020

This paper contributes to the study of Engel structures and their classification. The main result introduces the notion of a loose family of Engel structures and shows that two such families are Engel homotopic if and only if they are formally homotopic. This implies a complete $h$-principle when auxiliary data is fixed. As a corollary, we show that Lorentz and orientable Cartan prolongations are classified up to homotopy by their formal data.
Transient Study of the Cooling Process of a Small Cabinet
Authors: Arturo Alfaro-Ayala J. , Ramírez-Minguela J. J. , Gallegos-Muñoz A. , Hernández-Fusilier D. , Belman-Flores J. M.
Published: January 2020

A transient study of the cooling process inside a cabinet is presented in this work. Computational fluid dynamics (CFD) is used to obtain the transient temperature of the air inside a small cabinet. Three cooling levels, named Case 1, Case 2, and Case 3, were studied under different lapses of time and operational conditions. The temperature of the evaporator plate and the temperature of the room change with time through the implementation of user-defined functions (UDFs). The buoyancy effects that occur inside the cabinet (natural convection) were modeled using the approximation of all the properties fitted to temperature polynomials (PFTP). The transient temperature of the air inside the cabinet was obtained, until the second ON/OFF stage is reached, for the three cases studied. The prediction of the transient temperature of the air inside the small cabinet was validated with experimental data. The average relative errors of the transient temperatures of the air inside the cabinet were 0.49%, 0.19%, and 0.13% for Case 1, Case 2, and Case 3, respectively. The behavior of the temperature and velocity distributions of the air inside the cabinet for the ON and OFF stages is obtained. Finally, a better range of the temperature for the preservation of food, medicines, and biological matter is obtained with an increase in the thickness of the insulation material. An increment of 14.9% of the removed energy was obtained inside the cabinet with 12 cm of the insulation material, and this increment is related to the case with no insulation material. The results of this work could help in improving the design and performance of the cabinets in further works.
Chemically vapor deposited polymer nanolayers for rapid and controlled permeation of molecules and ions
Authors: Gleason Karen K.
Published: January 2020

Controlling the permeation of molecules and ions enables numerous technologies, including sensing, actuation, membrane separations, controlled drug release, and electrochemical energy storage. Rapid transport requires using ultrathin layers. Selective and switchable permeation entails the precise design of film architecture at the molecular level. Additionally, the permeation control layers must conform to the micro- and nanostructured topologies utilized to increase the surface area for permeation. This work will review the utility of highly conformal chemical vapor deposited (CVD) polymer nanolayers for permeation control. Using CVD polymerization couples the versatility of organic chemistry with the high-purity and systematic process control of all-dry vacuum processing. The full retention of organic functional groups by polymerization is essential for the fabrication of smart layers capable of switching permeation behavior in response to variations in light, pH, or temperature. Additionally, precise mechanistic control over chain formation and morphology is also essential for engineering the ionic conduction of vapor deposited polymer nanolayers.
Differential importance of trehalose in stress resistance in fermenting and nonfermenting Saccharomyces cerevisiae cells
Authors: Van Dijck P , Colavizza D , Smet P , Thevelein J M
Published: January 2020

The trehalose content in laboratory and industrial baker's yeast is widely believed to be a major determinant of stress resistance. Fresh and dried baker's yeast is cultured to obtain a trehalose content of more than 10% of the dry weight. Initiation of fermentation, e.g., during dough preparation, is associated with a rapid loss of stress resistance and a rapid mobilization of trehalose. Using specific Saccharomyces cerevisiae mutants affected in trehalose metabolism, we confirm the correlation between trehalose content and stress resistance but only in the absence of fermentation. We demonstrate that both phenomena can be dissociated clearly once the cells initiate fermentation. This was accomplished both for cells with moderate trehalose levels grown under laboratory conditions and for cells with trehalose contents higher than 10% obtained under pilot-scale conditions. Retention of a high trehalose level during fermentation also does not prevent the loss of fermentation capacity during preparation of frozen doughs. Although higher trehalose levels are always correlated with higher stress resistance before the addition of fermentable sugar, our results show that the initiation of fermentation causes the disappearance of any other factor(s) required for the maintenance of stress resistance, even in the presence of a high trehalose content.
Effects of Incubation Time and Temperature on In Vitro Selective Delignification of Silver Leaf Oak by Ganoderma colossum
Authors: Adaskaveg J E , Gilbertson R L , Dunlap M R
Published: January 2020

The effects of incubation time and temperature on the ability of isolates of the chlamydosporic and thermophilic fungus Ganoderma colossum (Fr.) C. F. Baker to cause selective delignification of Quercus hypoleucoides A. Camus were evaluated by standard in vitro agar block tests. Chemical and scanning electron microscopy studies of decayed wood were used to determine the extent of selective delignification or simultaneous decay caused by each fungal isolate. At 35 deg C, the percent weight loss increased from 6.1% after 4 weeks to a maximum of 32.5 to 33.0% after 16 and 20 weeks of incubation. The average percent Klason lignin-chlorite holocellulose ratios (PKL/CHC) decreased from 0.35 in the control wood block to 0.22 in wood blocks incubated for 12 weeks; this indicated selective delignification. The average PKL/CHC increased for the 16- and 20-week incubation periods, indicating greater removal of polysaccharides during longer incubation periods. In temperature studies, the percent weight loss after 12 weeks was 26 to 27% between 30 and 40 deg C and less than 16% for the 25 and 45 deg C treatments. The average PKL/CHC ranged from 0.18 to 0.16 between 35 and 40 deg C, whereas they were 0.23 and 0.31 for the 25 and 45 deg C treatments, respectively. Scanning electron microscopy confirmed an optimum temperature range near 35 to 40 deg C and incubation times of 8 to 12 weeks for selective delignification. Under these conditions, ray parenchyma, fiber tracheids, and vessels were devoid of middle lamella; pit regions of cells were visible with significantly enlarged apertures; and individual cells were separated and clearly delimited. Extensive delignification of wood occurred throughout the wood blocks evaluated. Incubation times longer than 12 weeks resulted in greater degradation of wood cell walls and thus in greater removal of the polysaccharide component of the wood. For incubation times of 4 weeks or a temperature of 25 deg C, limited to no degradation of cells was observed. At 45 deg C, walls of fiber tracheids were eroded and ray parenchymal cells were extensively degraded, indicating that simultaneous degradation of cell walls occurred. Thus, the incubation temperature influenced the type of decay by G. colossum observed on oak wood blocks: extensive selective delignification at 35 to 40 deg C after more than 8 weeks of incubation or simultaneous decay at 45 deg C with 14% weight loss after 12 weeks of incubation. Isolates of G. colossum may prove useful in studies on mechanisms of delignification and biotechnological applications (e.g., biopulping) of lignin-degrading fungi.
Purification and characterization of dimethylsulfoniopropionate lyase from an alcaligenes-like dimethyl sulfide-producing marine isolate
Authors: de Souza M P , Yoch D C
Published: January 2020

Dimethyl sulfide (DMS) is quantitatively the most important biogenic sulfur compound emitted from oceans and salt marshes. It is formed primarily by the action of dimethylsulfoniopropionate (DMSP) lyase which cleaves DMSP, an algal osmolyte, to equimolar amounts of DMS and acrylate. This report is the first to describe the isolation and purification of DMSP lyase. The soluble enzyme was purified to electrophoretic homogeneity from a facultatively anaerobic gram-negative rod-shaped marine bacterium identified as an Alcaligenes species by the Vitek gram-negative identification method. The key to successful purification of the enzyme was its binding to, and hydrophobic chromatography on, a phenyl-Sepharose CL-4B column. DMSP lyase biosynthesis was induced by its substrate, DMSP; its product, acrylate; and also by acrylamide. The relative effectivenesses of the inducers were 100, 90, and 204%, respectively. DMSP lyase is a 48-kDa monomer with a Michaelis-Menten constant (K(infm)) for DMSP of 1.4 mM and a V(infmax) of 408 (mu)mol/min/mg of protein. It converted DMSP to DMS and acrylate stoichiometrically. The similar K(infm) values measured for pure DMSP lyase and the axenic culture, seawater, and surface marsh sediment suggest that the microbes in these ecosystems must have enzymes similar to the one purified from our marine isolate. Anoxic sediment populations, however, have a 40-fold-lower K(infm) for this enzyme (30 (mu)M), possibly giving them the capability to metabolize much lower levels of DMSP than the aerobes.
Conservation of the genes for dissimilatory sulfite reductase from Desulfovibrio vulgaris and Archaeoglobus fulgidus allows their detection by PCR
Authors: Karkhoff-Schweizer R R , Huber D P , Voordouw G
Published: January 2020

The structural genes for dissimilatory sulfite reductase (desulfoviridin) from Desulfovibrio vulgaris Hilden-borough were cloned as a 7.2-kbp SacII DNA fragment. Nucleotide sequencing indicated the presence of a third gene, encoding a protein of only 78 amino acids, immediately downstream from the genes for the alpha and beta subunits (dsvA and dsvB). We designated this protein DsvD and the gene encoding it the dsvD gene. The alpha- and beta-subunit sequences are highly homologous to those of the dissimilatory sulfite reductase from Archaeoglobus fulgidus, a thermophilic archaeal sulfate reducer, which grows optimally at 83 degrees C. A gene with significant homology to dsvD was also found immediately downstream from the dsrAB genes of A. fulgidus. The remarkable conservation of gene arrangement and sequence across domain (bacterial versus archaeal) and physical (mesophilic versus thermophilic) boundaries indicates an essential role for DsvD in dissimilatory sulfite reduction and allowed the construction of conserved deoxyoligonucleotide primers for detection of the dissimilatory sulfite reductase genes in the environment.
Genetic diversity and geographical distribution of wild Saccharomyces cerevisiae strains from the wine-producing area of Charentes, France
Authors: Versavaud A , Courcoux P , Roulland C , Dulau L , Hallet J N
Published: January 2020

Electrophoretic karyotyping, mitochondrial DNA restriction fragment length polymorphism analysis, and PCR amplification of interspersed repeats were used to study the variability, phylogenetic affinities, and biogeographic distribution of wild Saccharomyces cerevisiae enological yeasts. The survey concentrated on 42 individual wine cellars in the Charentes area (Cognac region, France). A limited number (35) of predominant S. cerevisiae strains responsible for the fermentation process have been identified by the above molecular methods of differentiation. One strain (ACI) was found to be distributed over the entire area surveyed. There seemed to be little correlation between geographic location and genetic affinity.
Fluorescently Labeled Virus Probes Show that Natural Virus Populations Can Control the Structure of Marine Microbial Communities
Authors: Hennes K P , Suttle C A , Chan A M
Published: January 2020

Fluorescently stained viruses were used as probes to label, identify, and enumerate specific strains of bacteria and cyanobacteria in mixed microbial assemblages. Several marine virus isolates were fluorescently stained with YOYO-1 or POPO-1 (Molecular Probes, Inc.) and added to seawater samples that contained natural microbial communities. Cells to which the stained viruses adsorbed were easily distinguished from nonhost cells; typically, there was undetectable binding of stained viruses to natural microbial assemblages containing >10(sup6) bacteria ml(sup-1) but to which host cells were not added. Host cells that were added to natural seawater were quantified with 99% (plusmn) 2% (mean (plusmn) range) efficiency with fluorescently labeled virus probes (FLVPs). A marine bacterial isolate (strain PWH3a), tentatively identified as Vibrio natriegens, was introduced into natural microbial communities that were either supplemented with nutrients or untreated, and changes in the abundance of the isolate were monitored with FLVPs. Simultaneously, the concentrations of viruses that infected strain PWH3a were monitored by plaque assay. Following the addition of PWH3a, the concentration of viruses infecting this strain increased from undetectable levels (<1 ml(sup-1)) to 2.9 x 10(sup7) and 8.3 x 10(sup8) ml(sup-1) for the untreated and nutrient-enriched samples, respectively. The increase in viruses was associated with a collapse in populations of strain PWH3a from ca. 30 to 2% and 43 to 0.01% of the microbial communities in untreated and nutrient-enriched samples, respectively. These results clearly demonstrate that FLVPs can be used to identify and quantify specific groups of bacteria in mixed microbial communities. The data show as well that viruses which are present at low abundances in natural aquatic viral communities can control microbial community structure.
Production of Trichoderma reesei cellulases on glucose-containing media
Authors: Nakari-Set�l� T , Penttil� M
Published: January 2020

The filamentous fungus Trichoderma reesei was shown to secrete active cellobiohydrolase I and the endoglucanase I catalytic core domain into the culture medium when the fungus was grown on glucose-containing medium. The expression of the proteins was driven by the promoters of the elongation factor 1 alpha, tef1, and the unidentified gene for cDNA1. The cDNA1 promoter gave the best yields. The highest amounts of cellobiohydrolase I and the endoglucanase I core, being 50 to 100 mg/liter, accounted for more than half of the total protein secreted by the fungus. The levels obtained with the tef1 promoter were 20 to 50 times lower.
Evidence for indigenous Streptomyces populations in a marine environment determined with a 16S rRNA probe
Authors: Moran M A , Rutherford L T , Hodson R E
Published: January 2020

A 16S rRNA genus-specific probe was used to determine whether Streptomyces populations are an indigenous component of marine sediment bacterial communities. Previous debates have suggested that marine Streptomyces isolates are derived not from resident populations but from spores of terrestrial species which have been physically transported to marine ecosystems but remain dormant until isolation. Rigorously controlled hybridization of rRNA extracted from coastal marsh sediments with the genus-specific probe indicated that Streptomyces rRNA accounted for 2 to 5% of the sediment community rRNA and that spores are not the source of the hybridization signal. Streptomyces populations must therefore be at least the 26th most abundant genus-level source of bacterial rRNA. the relative amounts of rRNAs from Streptomyces spp. and members of the Bacteria (69 to 79%) and Archaea (4 to 7%) domains were highly consistent in these marine sediments throughout an annual cycle, indicating that the species composition of sediment bacterial communities may be more stable than recent studies suggest for marine planktonic bacterial communities. Laboratory studies designed to investigate the possible functional roles of Streptomyces populations in coastal sediments demonstrated that population levels of this genus changed relatively rapidly (within a time frame of 6 weeks) in response to manipulation of substrate availability. Amendments of intact sediment cores with two compounds (vanillic acid and succinic acid) consistently resulted in Streptomyces populations contributing an increased percentage of rRNA (6 to 15%) to the total bacterial rRNA pool.