bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of Automated Sample Preparation for Mycotoxin Analysis in Foods
Authors: Zhang Kai
Published: January 2020

Background

In the present study, we developed a novel automated sample preparation workflow for the determination of mycotoxins in foods.

Objective

This workflow integrates off-line devices such as a centrifuge, shaker, liquid and solid dispensing units into a unified platform to perform gravimetric and volumetric dispensing, capping/decapping, extraction, shaking, filtration, and centrifugation. Two robotic arms provide sample transportation without human assistance.

Method

Critical method performance attributes were characterized using spiked corn, milk and peanut butter containing aflatoxins, deoxynivalenol, fumonisins, ochratoxin A, HT-2 and T-2 toxins and zearalenone and certified reference materials. Prepared samples were analyzed by liquid chromatography mass spectrometry (LC-MS).

Results

Recoveries of spiked samples range 100–120% with RSD<20% and the majority of measured values of certified reference materials are consistent with certified values within ±20%. Within- and between-batch variabilities of QC samples range 5–9% and 7–12% respectively.

Conclusions

Our workflow introduces a straightforward and automated sample preparation procedure for LC-MS-based multimycotoxin analysis. Further, it demonstrates how individual sample preparation devices, that are conventionally used off-line, can be integrated together.

Highlights

This study shows automated sample preparation will replace manual operations and significantly increase the degree of automation and standardization for sample preparation.
Determination of Lutein, β-Carotene, and Lycopene in Infant Formula and Adult Nutritionals by Ultra-High Performance Liquid Chromatography: Collaborative Study, Final Action 2016.13 for β-Carotene and Lycopene Only
Authors: Hostetler Gregory L ,   Collaborators, Benét S , Buis R , Campos-Giménez E , Christiansen S , Daniel A , DeBorde J-L , de Haan E , Eckes J , Gill B , Griffin E , Joseph G , LeCours L , Mazzega R , McGrail I , McMahon A , Malaviole I , Perra D , Schattner A , Schierle J , Staffas A , Tsang T , Vermeulen M
Published: January 2020

Background

Lutein, β-carotene, and lycopene are among the most common carotenoids present in human milk and are frequently added to infant formula and adult nutritionals.

Objective

A collaborative study was conducted to assess the interlaboratory performance of AOAC Official MethodSM2016.13 for the determination of lutein, β-carotene, and lycopene in infant formula and adult nutritionals.

Methods

Thirteen laboratories agreed to participate in the study and 10 laboratories from seven different countries reported results. The study samples included blind duplicates of 6 matrices fortified with lutein, 7 matrices fortified with β-carotene, and 1 fortified with lycopene. NIST SRM 1869 was included in the sample set as a reference material.

Results

After the removal of outliers and invalid data, the repeatability (RSDr) data was ≤10.0% for all-trans-lutein, ≤12.0% for total lutein, ≤4.2% for all-trans-β-carotene, ≤6.0% for total β-carotene, and 1.6% for total lycopene. Reproducibility (RSDR) was ≤14.8% for all-trans-lutein, ≤19.9% for total lutein, ≤15.3% for all-trans-β-carotene, ≤13.7% for total β-carotene, and 7.4% for total lycopene.

Conclusions

The repeatability and reproducibility values met the criteria in the Standard Method Performance Requirements (SMPRs) for β-carotene and lycopene and it was recommended that the method be approved as a Final Action for these analytes. Since the method did not meet the SMPR for lutein, it was recommended that it remain a First Action method for this analyte.

Highlights

AOAC Official MethodSM2016.13 was validated through a collaborative study to be accurate and reproducible for the determination of β-carotene and lycopene in infant formula and adult nutritionals.
Reuse of Food Waste and Wastewater as a Source of Polyphenolic Compounds to Use as Food Additives
Authors: Barbera Marcella
Published: January 2020

The problem of waste and byproducts generated from agro-industrial activities worldwide is an increasing concern in terms of environmental sustainability. In this ambit, the quantity of food wastes—produced in all steps of the whole food chain—is enormous, and it may be forecasted that food waste could amount to more than 120 billion tonnes by 2020. The reuse of food waste and wastewater as source of polyphenolic compounds could be an interesting discussion in this ambit. In fact, polyphenols obtained in this way might be used for food and non-food purposes by means of new, improved, and safe extraction methods. In light of the opportunity represented by the treatment of agro-industrial waste, different systems concerning the winemaking and olive oil production industries have also been discussed as describing approaches applicable to other sectors. More research is needed before considering recovery of phenolic compounds from wastewater as an economically convenient choice for the food sector.
Northeastern Family Forest Owner Gender Differences in Land-Based Estate Planning and the Role of Self-Efficacy
Authors: Markowski-Lindsay Marla , Catanzaro Paul , Zimmerer Rebekah , Kittredge David , Markowitz Ezra , Chapman Daniel A
Published: January 2020

Understanding family forest owner (FFO) estate planning decisionmaking is fundamental to ensuring the survival of landscapes that provide many public goods, but little is known about how land-based estate planning differs by gender. Analyses of a survey of FFOs in northeastern United States indicated that female FFOs rate themselves with lower levels of land-based estate planning self-efficacy—being less prepared, confident, and financially able to move forward with planning the future of their land than males. Of the FFOs who had positive levels of land-based estate planning self-efficacy, females were more likely to want to keep their land undeveloped than males. Our research suggests that increasing land-based estate planning self-efficacy of female FFOs may lead to higher rates of keeping land undeveloped for regions with FFOs similar to those of the northeast. We recommend ways in which foresters and programs could play an important role in increasing land-based estate planning self-efficacy.
Neighborhood Disparities in the Availability, Advertising, Promotion, and Youth Appeal of Little Cigars and Cigarillos, United States, 2015
Authors: Kong Amanda Y , Queen Tara L , Golden Shelley D , Ribisl Kurt M
Published: January 2020

Introduction

Between 2012 and 2016, sales of cigars increased by 29% in the United States. In small local studies, greater little cigar and cigarillo (LCC) availability and marketing has been documented in neighborhoods with a greater proportion of Hispanic or Latino and black residents, and near schools. This national study of cigarette retailers assesses whether LCC availability and marketing at the point of sale is associated with neighborhood racial, ethnic, income, and percent youth demographics.

Methods

In 2015, we collected LCC availability and marketing data through retailer audits of a nationally representative sample of 2128 cigarette retailers. Using 2011–2015 American Community Survey census tract estimates, we modeled associations of neighborhood demographics (in quartiles) with availability of LCC-flavored products, and presence of exterior advertisements, youth marketing, and promotions.

Results

Nearly 90% of retailers sold LCCs, 83.0% sold flavored LCCs, and 30.9% had youth marketing. Controlling for retailer type and other neighborhood characteristics, neighborhoods with the highest proportion of black residents had significantly higher odds of flavored LCC availability (adjusted odds ratio [AOR] = 2.24, 95% confidence interval [CI] = 1.52, 3.30); exterior advertisements (AOR = 2.84, 95% CI = 1.94, 4.16); price promotions (AOR = 1.62; 95% CI = 1.07–2.45), and youth appeal (AOR = 1.49, 95% CI 1.08–2.08) compared to the lowest. Disparities in flavored LCC availability, exterior advertising, and youth appeal were also present for lower income neighborhoods.

Conclusion

Neighborhoods with a greater proportion of black or lower income residents have greater flavored LCCs availability and LCC marketing. Without stronger LCC regulation, residents of these neighborhoods may be at a greater risk of LCC use.

Implications

LCCs are harmful combustible tobacco products that are less regulated than cigarettes (eg, lower taxation, cheaper outlay due to small package sizes, availability of flavors), which makes them an affordable and appealing product to youth. This study documents greater availability, advertising, and marketing of LCCs in neighborhoods with a higher proportion of black or lower-income residents, potentially putting these populations at a greater risk of using or switching to these products in the face of increasing cigarette regulations. These findings underscore the need for local, state, and federal LCC regulatory action.
Measuring Opioid Withdrawal in a Phase 3 Study of a New Analgesic, NKTR-181 (Oxycodegol), in Patients with Moderate to Severe Chronic Low Back Pain
Authors: Henningfield Jack E , Gudin Jeffrey , Rauck Richard , Gimbel Joseph , Tagliaferri Mary , Doberstein Stephen K , Di Fonzo Carlo , Lu Lin , Katz Nathaniel , Siddhanti Suresh , Schnoll Sidney
Published: January 2020

Objective

To evaluate the SUMMIT-07 trial opioid withdrawal results of NKTR-181 (oxycodegol), a new molecular entity mu-opioid receptor agonist.

Design

Phase 3, enriched-enrollment, double-blind, randomized-withdrawal study in patients with chronic low back pain (CLBP).

Setting

Conducted in the United States at multiple sites.

Methods

SUMMIT-07 was comprised of five periods: screening; NKTR-181 open-label titration (100 to 400 mg twice daily); 12-week randomized, double-blind study drug (NKTR-181 or placebo); one-week study drug taper; and two-week safety follow-up. Permitted rescue medication included hydrocodone 5 mg/acetaminophen 300 mg (two tablets daily) for two weeks after randomization, then acetaminophen 1.0 gm daily for the remainder of the trial. Signs and symptoms of drug withdrawal were evaluated using the Clinical Opiate Withdrawal Scale (COWS); Subjective Opiate Withdrawal Scale (SOWS); Misuse, Abuse, and Diversion Drug Event Reporting System (MADDERS); and withdrawal-related adverse events.

Results

Of 1,190 patients entering titration, one patient had moderate withdrawal (COWS score 13/48 maximum) three days after discontinuing NKTR-181. Of 610 patients randomized (N = 309, NKTR-181; N = 301, placebo), no COWS scores indicating withdrawal at a moderate level or greater (i.e., score ≥13) were observed at any time point. At day 8 after randomization, week 12, and the end of tapering, COWS scores indicating mild withdrawal (<13) were observed in seven (2.4%), one (0.4%), and one (0.5%) placebo patients, respectively, and three (1.0%), one (0.4%), and five (2.3%) NKTR-181 patients, respectively. Mean SOWS scores in both arms were ≤2.8 of 64 possible points at all time points. During the randomized period, of 35 events identified by MADDERS, adjudicators identified 20 possible “withdrawal” events (9 [2.9%] NKTR-181 and 11 [3.7%] placebo).

Conclusions

NKTR-181 exhibited a low rate and severity of opioid withdrawal in SUMMIT-07 patients with CLBP.
Leeuwenhoekiella aestuarii sp. nov., isolated from salt-water sediment and first insights in the genomes of Leeuwenhoekiella species
Authors: Tahon Guillaume , Lebbe Liesbeth , De Troch Marleen , Sabbe Koen , Willems Anne
Published: January 2020

Four Gram-negative, aerobic, rod-shaped and yellow-orange pigmented bacteria (R-46770, R-48165T, R-50232 and R-50233) were isolated from intertidal sediment and water of the Westerschelde estuary between 2006 and 2012. Analysis of their 16S rRNA gene sequences revealed that the four strains form a separate cluster between validly described type strains of the genus

Leeuwenhoekiella

. DNA–DNA reassociation values of two representative strains (i.e. R-48165T and R-50232) of the new group with type strains of

Leeuwenhoekiella

species ranged from 18.7 to 56.6 %. A comparative genome analysis of the two strains and the type strains confirmed average nucleotide identity values from 75.6 to 94.4 %. The G+C contents of the genomic DNA of strains R-48165T and R-50232 were 37.80 and 37.83 mol%, respectively. The predominant cellular fatty acids of the four novel strains were summed feature 3 (i.e. C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The four new

Leeuwenhoekiella

-like strains grew with 0.5–12 % (w/v) NaCl, at pH 5.5–9.0 and displayed optimum growth between 20 and 30 °C. Based on the results of phenotypic, genomic, phylogenetic and chemotaxonomic analyses, the four new strains represent a novel species of the genus

Leeuwenhoekiella

for which the name Leeuwenhoekiella aestuarii sp. nov. is proposed. The type strain is LMG 30908T (=R-48165T=CECT 9775T=DSM 107866T). Genome analysis of type strains of the genus

Leeuwenhoekiella

revealed a large number of glycosyl hydrolases, peptidases and carboxyl esterases per Mb, whereas the number of transporters per Mb was low compared to other bacteria. This confirmed the environmental role of

Leeuwenhoekiella

species as (bio)polymer degraders, with a specialization on degrading proteins and high molecular weight compounds. Additionally, the presence of a large number of genes involved in gliding motility and surface adhesion, and large numbers of glycosyl transferases per Mb confirmed the importance of these features for

Leeuwenhoekiella

species.
Cerebellar Purkinje cell activity modulates aggressive behavior
Authors: Jackman Skyler L. , Chen Christopher H. , Offermann Heather L. , Drew Iain R. , Harrison Bailey M. , Bowman Anna M. , Flick Katelyn M. , Flaquer Isabella , Regehr Wade G.
Published: January 2020

Although the cerebellum is traditionally associated with balance and motor function, it also plays wider roles in affective and cognitive behaviors. Evidence suggests that the cerebellar vermis may regulate aggressive behavior, though the cerebellar circuits and patterns of activity that influence aggression remain unclear. We used optogenetic methods to bidirectionally modulate the activity of spatially-delineated cerebellar Purkinje cells to evaluate the impact on aggression in mice. Increasing Purkinje cell activity in the vermis significantly reduced the frequency of attacks in a resident-intruder assay. Reduced aggression was not a consequence of impaired motor function, because optogenetic stimulation did not alter motor performance. In complementary experiments, optogenetic inhibition of Purkinje cells in the vermis increased the frequency of attacks. These results establish Purkinje cell activity in the cerebellar vermis regulates aggression, and further support the importance of the cerebellum in driving affective behaviors that could contribute to neurological disorders.
Individual variability in functional organization of the human and monkey auditory cortex
Authors: Ren Jianxun , Liu Hesheng , Xu Ting , Wang Danhong , Li Meiling , Lin Yuanxiang , Ramirez Julian S.B. , Lu Jie , Li Luming , Ahveninen Jyrki
Published: January 2020

Accumulating evidence shows that auditory cortex (AC) of humans, and other primates, is involved in more complex cognitive processes than feature segregation only, which are shaped by experience-dependent plasticity and thus likely show substantial individual variability. However, thus far, individual variability of ACs has been considered a methodological impediment rather than a phenomenon of theoretical importance. Here, we examined the variability of ACs using intrinsic functional connectivity patterns in humans and macaques. Our results demonstrate that in humans, functional variability is 1) greater near the non-primary than primary ACs, 2) greater in ACs than comparable visual areas, and 3) greater in the left than right ACs. Remarkably similar modality differences and lateralization of variability were observed in macaques. These connectivity-based findings are consistent with a confirmatory task-based fMRI analysis. The quantitative proof of the exceptional variability of ACs has implications for understanding the evolution of advanced auditory functions in humans.
EngineeringE. colifor magnetic control and the spatial localization of functions
Authors: Aubry Mary , Wang Wei-An , Guyodo Yohan , Delacou Eugénia , Guignier Jean Michel , Espeli Olivier , Lebreton Alice , Guyot François , Gueroui Zoher
Published: January 2020

The fast-developing field of synthetic biology enables broad applications of programmed microorganisms including the development of whole-cell biosensors, delivery vehicles for therapeutics, or diagnostic agents. However, the lack of spatial control required for localizing microbial functions could limit their use and induce their dilution leading to ineffective action or dissemination. To overcome this limitation, the integration of magnetic properties into living systems enables a contact-less and orthogonal method for spatiotemporal control. Here, we generated a magnetic-sensingEscherichia coliby driving the formation of iron-rich bodies into bacteria. We found that these bacteria could be spatially controlled by magnetic forces and sustained cell growth and division, by transmitting asymmetrically their magnetic properties to one daughter cell. We combined the spatial control of bacteria with genetically encoded-adhesion properties to achieve the magnetic capture of specific target bacteria as well as the spatial modulation of human cell invasions.
Unraveling the aggregation dynamics of amyloidogenesis: A data-driven mathematical modeling approach
Authors: Tikader Baishakhi , Maji Samir K. , Kar Sandip
Published: January 2020

Proteins often get misfolded into highly ordered amyloid aggregates that are found to be associated with various neurodegenerative diseases. However, the dynamical events that lead to such self organization of different types of proteins are still poorly understood due to the experimentally untractable complex molecular mechanism, which governs the process of amyloidogenesis. Herein, we propose a generic and data-driven mathematical modeling approach that enables us to decipher a most probable molecular mechanism responsible for amyloidogensis in a context dependent manner. The preferred model efficiently elucidates various aspects of amyloid forming kinetics as a function of initial protein concentration, and qualitatively predicts the dynamics of amyloidogenesis for point mutated proteins. Importantly, the model analysis reveals that intermediate aggregates formed just after the primary necleation steps plays a vital role in dictating the nature of amyloid forming kinetics. Moreover, our model makes experimentally feasible insightful predictions to formulate better therapeutic measures in future to counter unwanted amyloidogenesis by just fine-tuning the molecular interactions related to amyloidogenesis.

Author Summary

In cells, proteins mostly function by being in a native folded conformation. However, under certain circumstances, some of these proteins undergo high degree of aggregation and eventually misfold to form highly stable amyloid aggregates that are often involved in different neurodegenerative disease progression and pathogenesis. To develop appropriate therapeutic strategies to resist such oligomerazation of protein, it is imperative to unravel the molecular interactions that essentially organize the dynamical events of amyloidogenesis. We have proposed a generic computational modeling framework to elucidate the important molecular events that govern the dynamics of amyloid formation. Our model reconciles diverse set of experimental observations including different mutant phenotyes from a dynamical perspective, and predicts possible ways to control the kinetics of amyloid formation experimentally. In future, these insights will be helpful to design drugs to treat patients with neurodegenerative disorders. Importantly, our model, in general, will be quite useful to figure out the important molecular events that are orchestrating the amyloidogenesis of different amyloid forming proteins.
Platelet, erythrocyte, endothelial, and monocyte microparticles in coagulation activation and propagation
Authors: Lipets E.N. , Antonova O.A. , Shustova O.N. , Losenkova K.V. , Mazurov A.V. , Ataullakhanov F.I.
Published: January 2020

Background and objective

For many pathological states, microparticles are supposed to be one of the causes of hypercoagulation. Although there are some indirect data about microparticles participation in coagulation activation and propagation, the integral hemostasis test Thrombodynamics allows to measure micropaticles participation in these two coagulation phases directly by influence on the appearance of coagulation centers in plasma volume and on the rate of clot grown from surface with immobilized tissue factor.

Methods

Microparticles were obtained from platelets and erythrocytes by stimulation with SFLLRN and A23187, respectively, from monocytes, endothelial HUVEC culture and monocytic THP cell culture by stimulation with lipopolysaccharides. Microparticles were counted by flow cytometry and titrated in microparticle-depleted normal plasma in the Thrombodynamics test.

Results

Monocyte microparticles induced the appearance of clotting centres through the TF pathway at concentrations approximately 100-fold lower than platelet and erythrocyte microparticles, which activated plasma by the contact pathway. For endothelial microparticles, both activation pathways were essential, and their activity was intermediate. Monocyte microparticles induced plasma clotting by the appearance of hundreds of clots with an extremely slow growth rate, while erythrocyte microparticles induced the appearance of a few clots with a growth rate similar to that from surface covered with high-density tissue factor. Patterns of clotting induced by platelet and endothelial microparticles were intermediate. Platelet, erythrocyte and endothelial microparticles impacts on the rate of clot growth from the surface with tissue factor did not differ significantly within the 0-200·103/ul range of microparticles concentrations. However, at concentrations greater than 500·103/ul, erythrocyte microparticles increased the stationary clot growth rate to significantly higher levels than do platelet microparticles or artificial phospholipid vesicles consisting of phosphatidylcholine and phosphatidylserine.

Conclusion

Microparticles of different origins demonstrated qualitatively different characteristics related to coagulation activation and propagation.
Constructing early diagnosis model of colorectal cancer based on expression profile
Authors: Wang shaoqiang , Wang Yifan , Wang Shudong
Published: January 2020

purpose

In order to break through the restrictive factors such as the fecal occult blood test (FOBT) in the routine detection of bowel cancer, which is susceptible to diet and drugs, and the high cost and inconvenience of microscopy, Seeking a possible FOBT alternative.

Methods

An error back propagation neural network (BPNN) algorithm was used to construct a CRC diagnosis model based on expression profiles.

Results

The accuracy of the model on the training and test sets is 0.943 and 0.935, respectively. AUC all reached above 0.95.

Conclusion

The CRC molecular detection model based on expression profiles provides a possible alternative to FOBT. It provides a new approach and method for the clinical diagnosis of bowel cancer.
RFDTI: Using Rotation Forest with Feature Weighted for Drug-Target Interaction Prediction from Drug Molecular Structure and Protein Sequence
Authors: Wang Lei , You Zhu-Hong , Li Li-Ping , Yan Xin
Published: January 2020

The identification and prediction of Drug-Target Interactions (DTIs) is the basis for screening drug candidates, which plays a vital role in the development of innovative drugs. However, due to the time-consuming and high cost constraints of biological experimental methods, traditional drug target identification technologies are often difficult to develop on a large scale. Therefore,in silicomethods are urgently needed to predict drug-target interactions in a genome-wide manner. In this article, we design a newin silicoapproach, named RFDTI to predict the DTIs combine Feature weighted Rotation Forest (FwRF) classifier with protein amino acids information. This model has two outstanding advantages: a) using the fusion data of protein sequence and drug molecular fingerprint, which can fully carry information; b) using the classifier with feature selection ability, which can effectively remove noise information and improve prediction performance. More specifically, we first use Position-Specific Score Matrix (PSSM) to numerically convert protein sequences and utilize Pseudo Position-Specific Score Matrix (PsePSSM) to extract their features. Then a unified digital descriptor is formed by combining molecular fingerprints representing drug information. Finally, the FwRF is applied to implement onEnzyme,Ion Channel,GPCR, andNuclear Receptordata sets. The results of the five-fold cross-validation experiment show that the prediction accuracy of this approach reaches 91.68%, 88.11%, 84.72% and 78.33% on four benchmark data sets, respectively. To further validate the performance of the RFDTI, we compare it with other excellent methods and Support Vector Machine (SVM) model. In addition, 7 of the 10 highest predictive scores in predicting novel DTIs were validated by relevant databases. The experimental results of cross-validation indicated that RFDTI is feasible in predicting the relationship among drugs and target, and can provide help for the discovery of new candidate drugs.
“Pain in my heart”: Understanding perinatal depression among women living with HIV in Malawi
Authors: LeMasters Katherine , Dussault Josée , Barrington Clare , Bengtson Angela , Gaynes Bradley , Go Vivian , Hosseinipour Mina C. , Kulisewa Kazione , Kutengule Anna , Meltzer-Brody Samantha , Midiani Dalitso , Mphonda Steve , Udedi Michael , Pence Brian
Published: January 2020

Background

Perinatal depression (PND) can interfere with HIV care engagement and outcomes. We examined experiences of PND among women living with HIV (WLWH) in Malawi.

Methods

We screened 73 WLWH presenting for perinatal care in Lilongwe, Malawi using the Edinburgh Postnatal Depression Scale (EPDS). We conducted interviews with 24 women experiencing PND and analyzed data using inductive and deductive coding and narrative analysis.

Results

Women experienced a double burden of physical and mental illness, expressed as pain in one’s heart. Receiving an HIV diagnosis unexpectedly during antenatal care was a key contributor to developing PND. This development was influenced by stigmatization and social support.

Conclusions

These findings highlight the need to recognize the mental health implications of routine screening for HIV and to routinely screen and treat PND among WLWH. Culturally appropriate mental health interventions are needed in settings with a high HIV burden.
Lumbar corticospinal tract in rodents modulates sensory inputs but does not convey motor command
Authors: Moreno-Lopez Yunuen , Bichara Charlotte , Delbecq Gilles , Isope Philippe , Cordero-Erausquin Matilde
Published: January 2020

It is generally assumed that the main function of the corticospinal tract (CST) is to convey motor commands to bulbar or spinal motoneurons. Yet the CST has also been shown to modulate sensory signals at their entry point in the spinal cord, through presynaptic inhibition. By sequentially investigating different routes of corticofugal pathways through electrophysiological recordings and an intersectional viral strategy, we here demonstrate that motor and sensory modulation commands in mice belong to segregated paths within the CST. Sensory modulation is excuted exclusively by the CST via a population of lumbar interneurons located in the deep dorsal horn. In contrast, the cortex conveys the motor command via a relay in the upper spinal cord or supraspinal motor centers. At lumbar level, the main role of the CST is thus the modulation of sensory inputs, which is an essential component of the selective tuning of sensory feedback, to ensure well-coordinated and skilled movement.

Impact statement

While the corticospinal tract is often considered exclusively as a motor path, this study demonstrates that, in the mouse lumbar cord, its main role is the modulation of sensory inputs.
Genome-wide comparison of DNA methylation between life cycle stages ofDrosophila melanogasterusing high-throughput sequencing techniques
Authors: Deshmukh Saniya , Abhyankar Varada , Vellarikkal Shamsudheen Karuthedath , Sivasubbu Sridhar , Scaria Vinod , Deobagkar Deepti
Published: January 2020

Drosophila melanogasterundergoes holometabolous development, has very low levels of DNA methylation, and is known to possess a single known methyltransferase, dDNMT2. This study compares the DNA methylation patterns between the two life cycle stages ofD. melanogasterusing a combination of DNA immunoprecipitation and high throughput sequencing techniques.

Our results indicate, a change in the chromosomal distribution of the sparse DNA methylation concerning genes and natural transposable elements between in the embryo and the adult stages ofD. melanogaster. The differentially methylated regions localised on genes involved in the regulation of cell cycle processes of mitotic cell divisions and chromosomal segregation. dDNMT2 knockout flies exhibited altered patterns of DNA methylation. The observed differences in DNA methylation were in genes involved in cellular communication and cytoskeletal functions. The variation in DNA methylation between the two life cycle stages is indicative that it could have a role in regulatory processes during development and, dDNMT2 may have a role as a co-factor for the hitherto undiscovered DNA methyltransferase inD. melanogaster.
barCoder: a tool to generate unique, orthogonal genetic tags for qPCR detection
Authors: Bernhards Casey B. , Lux Matthew W. , Katoski Sarah E. , Goralski Tyler D. P. , Liem Alvin T. , Gibbons Henry S.
Published: January 2020

Background

Tracking dispersal of microbial populations in the environment requires specific detection methods that discriminate between the target strain and all potential natural and artificial interferents, including previously utilized tester strains. Recent work has shown that genomic insertion of short identification tags, called “barcodes” here, allows detection of chromosomally tagged strains by real-time PCR. Manual design of these barcodes is feasible for small sets, but expansion of the technique to larger pools of distinct and well-functioning assays would be significantly aided by software-guided design.

Results

Here we introduce barCoder, a bioinformatics tool that facilitates the process of creating sets of uniquely identifiable barcoded strains. barCoder utilizes the genomic sequence of the target strain and a set of user-specified PCR parameters to generate a list of suggested barcode “modules” that consist of binding sites for primers and probes and appropriate spacer sequences. Each module is designed to yield optimal PCR amplification and unique identification. Optimal amplification includes metrics such as ideal Tmand G+C-content, appropriate spacing, and minimal stem-loop formation; unique identification includes low BLAST hits against the target organism, previously generated barcode modules, and databases, such as NCBI. We tested the ability of our algorithm to suggest appropriate barcodes by generating 12 modules forBacillus thuringiensisserovarkurstaki, a simulant for the potential biowarfare agentBacillus anthracis, and three each for other potential target organisms with variable G+C content. Real-time PCR detection assays directed at barcodes were specific and yielded minimal cross-reactivity with a panel of near-neighbor and potential contaminant materials.

Conclusions

The barCoder algorithm facilitates the generation of barcoded biological simulants by (a) eliminating the task of creating modules by hand, (b) minimizing optimization of PCR assays, and (c) reducing effort wasted on non-unique barcode modules.
Hybridization capture of larch (LarixMill) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forests
Authors: Schulte Luise , Bernhardt Nadine , Stoof-Leichsenring Kathleen R. , Zimmermann Heike H. , Pestryakova Luidmila A. , Epp Laura S. , Herzschuh Ulrike
Published: January 2020

Siberian larch (LarixMill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches, in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA – metabarcoding – focuses on small fragments which cannot resolveLarixto species level nor allow the detailed study of population dynamics. Here we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the completeLarixchloroplast genome to studyLarixpopulations from a sediment core reaching back up to 6700 years in age from the Taymyr region in northern Siberia. In comparison to shotgun sequencing, hybridization capture results in an increase of taxonomically classified reads by several orders of magnitude and the recovery of near-complete chloroplast genomes ofLarix. Variation in the chloroplast reads corroborate an invasion ofLarix gmeliniiinto the range ofLarix sibiricabefore 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied to ancient DNA from lake sediments can provide genome-scale information and is a viable tool for studying past changes of a specific taxon.
Single-cell epigenomic identification of inherited risk loci in Alzheimer’s and Parkinson’s disease
Authors: Corces M. Ryan , Shcherbina Anna , Kundu Soumya , Gloudemans Michael J. , Frésard Laure , Granja Jeffrey M. , Louie Bryan H. , Shams Shadi , Bagdatli S. Tansu , Mumbach Maxwell R. , Liu Bosh , Montine Kathleen S. , Greenleaf William J. , Kundaje Anshul , Montgomery Stephen B. , Chang Howard Y. , Montine Thomas J.
Published: January 2020

Genome-wide association studies (GWAS) have identified thousands of variants associated with disease phenotypes. However, the majority of these variants do not alter coding sequences, making it difficult to assign their function. To this end, we present a multi-omic epigenetic atlas of the adult human brain through profiling of the chromatin accessibility landscapes and three-dimensional chromatin interactions of seven brain regions across a cohort of 39 cognitively healthy individuals. Single-cell chromatin accessibility profiling of 70,631 cells from six of these brain regions identifies 24 distinct cell clusters and 359,022 cell type-specific regulatory elements, capturing the regulatory diversity of the adult brain. We develop a machine learning classifier to integrate this multi-omic framework and predict dozens of functional single nucleotide polymorphisms (SNPs), nominating gene and cellular targets for previously orphaned GWAS loci. These predictions both inform well-studied disease-relevant genes, such asBIN1in microglia for Alzheimer’s disease (AD) and reveal novel gene-disease associations, such asSTAB1in microglia andMALin oligodendrocytes for Parkinson’s disease (PD). Moreover, we dissect the complex inverted haplotype of theMAPT(encoding tau) PD risk locus, identifying ectopic enhancer-gene contacts in neurons that increaseMAPTexpression and may mediate this disease association. This work greatly expands our understanding of inherited variation in AD and PD and provides a roadmap for the epigenomic dissection of noncoding regulatory variation in disease.
A comprehensive and comparative study on the action of pentacyclic triterpenoids onVibrio choleraebiofilms
Authors: Bhattacharya Sudipta Paul , Bhattacharya Arijit , Sen Aparna
Published: January 2020

While serving as environmental reservoir forV. choleraeinfection, biofilms are also crucial for intestinal colonization of the pathogen. Triterpenoids, a group of bioactive phytochemicals, have been tested for antibiofilm activity against model biofilm forming bacteria in recent times. In this context, glycyrrhetinic acid (GRA), ursolic acid (UA) and betulinic acid (BA), representing three categorically distinct groups of pentacyclic triterpenoids, are targeted for profiling their impact onVibrio choleraeC6709 biofilms. The triterpenoids substantially affected biofilm associated attributes like formation, substratum adherence and dispersion from preformed biofilms. Though at variable degree, the compounds decreased cell surface hydrophobicity and composition in terms of macromolecular content. Not only EPS-associated extracellular enzyme activities were estimated to be reduced by triterpenoid exposure, ultra structural analysis also revealed that GRA, UA and BA can affect extracellular polymeric substance (EPS) content. Albeit total extracellular proteolytic activity remained unaffected by the triterpenoids, GRA treatment resulted in considerable reduction of extracellular gelatinase activity. Molecular docking analysis indicated potential interaction with cyclic di-GMP sensor VpsT, autoinducer-2 sensor kinase LuxP-LuxQ and transcriptional activator HapR, component of complex quorum sensing networks modulating biofilm formation. Comprehensive analysis of antibiotic action revealed accentuation of cephalosporin antibiotics with GRA and UA while BA potentiated action of fluoroquinolones, widening the scope of combinatorial therapeutic strategy.
Uncovering antibody cross-reaction dynamics in influenza A infections
Authors: Hernandez-Mejia Gustavo , Hernandez-Vargas Esteban A.
Published: January 2020

Uncovering the hidden pathways of how antibodies induced by one influenza strain is effective against another, cross-reaction, is the central dogma for the design of universal flu vaccines. Here, we conceive a stochastic model that successfully represents the antibody cross-reactive data from mice infected with H3N2 influenza strains and further validation with cross-reaction data of H1N1 strains. After modifying several aspects and parameters in the model, our computational simulations highlight that changes in time of infection and the B-cells population are relevant, however, the affinity threshold of B-cells between consecutive infections is a necessary condition for the successful Abs cross-reaction. Our results suggest a reformulation in 3-D of the current antibody influenza landscape.
Overexpression ofThalassiosira pseudonanaviolaxanthin de-epoxidase-like 2 (VDL2) increases fucoxanthin while stoichiometrically reducing diadinoxanthin cycle pigment abundance
Authors: Gaidarenko Olga , Mills Dylan W. , Vernet Maria , Hildebrand Mark
Published: January 2020

Despite the ubiquity and ecological importance of diatoms, much remains to be understood about their physiology and metabolism, including their carotenoid biosynthesis pathway. Early carotenoid biosynthesis steps are well-conserved, while the identity of the enzymes that catalyze the later steps and their order remain unclear. Those steps lead to the biosynthesis of the final pathway products: the main accessory light-harvesting pigment fucoxanthin (Fx) and the main photoprotective pigment pool comprised of diadinoxanthin (Ddx) and its reversibly de-epoxidized form diatoxanthin (Dtx). We used sequence comparison to known carotenoid biosynthesis enzymes to identify novel candidates in the diatomThalassiosira pseudonana. Microarray and RNA-seq data was used to select candidates with transcriptomic responses similar to known carotenoid biosynthesis genes and to create full-length gene models, and we focused on those that encode proteins predicted to be chloroplast-localized. We identified a violaxanthin de-epoxidase-like gene (Thaps3_11707, VDL2) that when overexpressed results in increased Fx abundance while stoichiometrically reducing Ddx+Dtx. Based on transcriptomics, we hypothesize that Thaps3_10233 may also contribute to Fx biosynthesis, in addition to VDL2. Separately using antisense RNA to target VDL2, VDL1, and both LUT1-like copies (hypothesized to catalyze an earlier step in the pathway) simultaneously, reduced the overall cellular photosynthetic pigment content, including chlorophylls, suggesting destabilization of light-harvesting complexes by Fx deficiency. Based on transcriptomic and physiological data, we hypothesize that the two predictedT. pseudonanazeaxanthin epoxidases have distinct functions and that different copies of phytoene synthase and phytoene desaturase may serve to initiate carotenoid biosynthesis in response to different cellular needs. Finally, nine carotene cis/trans isomerase (CRTISO) candidates identified based on sequence identity to known CRTISO proteins were narrowed to two most likely to be part of theT. pseudonanacarotenoid biosynthesis pathway based on transcriptomic responses and predicted chloroplast targeting.
Dysregulation of excitatory neural firing replicates physiological and functional changes in aging visual cortex
Authors: Talyansky Seth , Brinkman Braden A. W.
Published: January 2020

The mammalian visual system has been the focus of countless experimental and theoretical studies designed to elucidate principles of neural computation and sensory coding. Most theoretical work has focused on networks intended to reflect developing or mature neural circuitry, in both health and disease. Few computational studies have attempted to model changes that occur in neural circuitry as an organism ages non-pathologically. In this work we contribute to closing this gap, studying how physiological changes correlated with advanced age impact the computational performance of a spiking network model of primary visual cortex (V1). Our results demonstrate that deterioration of homeostatic regulation of excitatory firing, coupled with long-term synaptic plasticity, is a sufficient mechanism to reproduce features of observed physiological and functional changes in neural activity data, specifically declines in inhibition and in selectivity to oriented stimuli. This suggests a potential causality between dysregulation of neuron firing and age-induced changes in brain physiology and performance. While this does not rule out deeper underlying causes or other mechanisms that could give rise to these changes, our approach opens new avenues for exploring these underlying mechanisms in greater depth and making predictions for future experiments.
Simulation of the Gαq /Phospholipase Cβ1 Signaling Pathway Returns Differentiated PC12 Cells to a Stem-like State
Authors: Garwain Osama , Pearce Katherine M. , Jackson Lela , Carley Samuel , Rosati Barbara , Scarlata Suzanne
Published: January 2020

Phospholipase Cβ1 is activated by Gαq to generate calcium signals in response to hormones and neurotransmitters, and is found at high levels in mammalian neuronal tissue. Besides carrying out this key plasma membrane function, PLCβ1 has a cytosolic population that helps, in part, to drive the differentiation of PC12 cells by inhibiting a nuclease that promotes RNA-induced silencing (C3PO). Here, we show that down-regulating PLCβ1 or reducing its cytosolic population by activating Gαq to drive it to the plasma membrane, returns differentiated PC12 cells to an undifferentiated state. In this state, the cells return to a spherical morphology, resume proliferation and express the stem cell transcription factors nanog and Oct4. Similar changes are seen with C3PO down-regulation. This return to a stem-like state is accompanied by shifts in multiple miR populations, such as increased levels of rno-miR-21 and rno-miR-26a. Surprisingly, we find that de-differentiation can also be induced by extended stimulation of the Gαq. In this case, the neurites completely retract over a 10-minute period, and while levels of nanog remain unchanged, the levels of some miRs begin to return to their undifferentiated values. In complementary studies, we followed the real time hydrolysis of a fluorescent-tagged miR in cells where PLCβ1 or C3PO were down-regulated. These samples showed substantial differences in miR processing in cells both the undifferentiated and differentiated states. Taken together, our studies suggest that PLCβ1, through its ability to regulate C3PO and endogenous miR populations, plays a key role in mediating PC12 cell differentiation.
Structural basis for catalysis and substrate specificity of human ACAT1
Authors: Qian Hongwu , Zhao Xin , Yan Renhong , Gao Shuai , Sun Xue , Wong Catherine C. L. , Yan Nieng
Published: January 2020

Acyl-coenzyme A: cholesterol acyltransferases (ACATs) catalyze acyl transfer from acyl-coenzyme A (CoA) to cholesterol to generate cholesteryl ester, which is the primary form for cellular storage and plasma transport of cholesterol. Because of their close relationship with cholesterol metabolism, ACATs represent potential drug target for the treatment of atherosclerosis and other cholesterol-related disorders. Here we present the cryo-EM structure of human ACAT1 at 3.3 Å resolution for dimer of dimers and 3.0 Å for a dimer. Each protomer consists of nine transmembrane segments that enclose a cytosolic (C) and a transmembrane (T) tunnel. The tunnels, each accommodating an elongated density, converge at the predicted catalytic site. Structure-guided mutational analyses suggest the cytosolic and lateral entry for acyl-CoA and cholesterol, respectively. Our structural, biochemical, and mass spectrometric characterizations reveal the catalytic mechanism and substrate preference for unsaturated acyl chain by ACAT1.
Long-term warming weakens stabilizing effects of biodiversity in aquatic ecosystems
Authors: Chang Chun-Wei , Ye Hao , Miki Takeshi , Deyle Ethan R. , Souissi Sami , Anneville Orlane , Adrian Rita , Chiang Yin-Ru , Ichise Satoshi , Kumagai Michio , Matsuzaki Shin-ichiro S. , Shiah Fuh-Kwo , Wu Jiunn-Tzong , Hsieh Chih-hao , Sugihara George
Published: January 2020

Despite the consensus that warming will affect biodiversity, alter physicochemical environments, and disrupt biological interactions, the relative importance of these key processes and how they interact to determine overall ecosystem function is poorly understood. Here, we analyze long-term (16∼39 years) time series data from ten aquatic ecosystems and use convergent cross mapping (CCM) to quantify the hidden causal network linking species diversity, ecosystem function, and physicochemical factors. We observe that aquatic ecosystems subject to stronger warming exhibit decreased stability (larger fluctuations in phytoplankton biomass). We further show that this effect can be attributed to a weakening of stabilizing causal pathways between biodiversity, nutrient cycling, and phytoplankton biomass. Thus, rather than thinking in terms of separate factors, a more holistic view, that causally links biodiversity and the other ecosystem components, is required to understand and predict climate impacts on the temporal stability of aquatic ecosystems.