bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic and molecular analysis of trichome development in
Arabis alpina
Authors: Chopra Divykriti , Mapar Mona , Stephan Lisa , Albani Maria C. , Deneer Anna , Coupland George , Willing Eva-Maria , Schellmann Swen , Schneeberger Korbinian , Fleck Christian , Schrader Andrea , Hülskamp Martin
Published: May 2019

Significance

Typically, comparative developmental studies focus on the question whether key genes are conserved over large evolutionary distances. How the gene regulatory network of a whole developmental process evolves is virtually unknown. This requires a functional comparison of homologous processes in species closely related enough to find similarities and distant enough to see functional changes. We approach this question by genetically and molecularly comparing trichome development in
Arabidopsis thaliana
with that in
Arabis
alpina
. We show which steps are regulated similarly and which are different. A closer analysis of trichome patterning revealed fascinating changes in the gene regulatory network; in particular, the finding that overexpression of one key regulator leads to opposite phenotypes in the two species suggested fundamental changes.
Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives
Authors: Hao Yan , Xiong Ying , Cheng Yalin , Song Gang , Jia Chenxi , Qu Yanhua , Lei Fumin
Published: May 2019

High-altitude environments present strong stresses for living organisms, which have driven striking phenotypic and genetic adaptations. While previous studies have revealed multiple genetic adaptations in high-altitude species, how evolutionary history (i.e., phylogenetic background) contributes to similarity in genetic adaptations to high-altitude environments is largely unknown, in particular in a group of birds. We explored this in 3 high-altitude passerine birds from the Qinghai-Tibet Plateau and their low-altitude relatives in lowland eastern China. We generated transcriptomic data for 5 tissues across these species and compared sequence changes and expression shifts between high- and low-altitude pairs. Sequence comparison revealed that similarity in all 3 high-altitude species was high for genes under positive selection (218 genes) but low in amino acid substitutions (only 4 genes sharing identical amino acid substitutions). Expression profiles for all genes identified a tissue-specific expression pattern (i.e., all species clustered by tissue). By contrast, an altitude-related pattern was observed in genes differentially expressed between all 3 species pairs and genes associated with altitude, suggesting that the high-altitude environment may drive similar expression shifts in the 3 high-altitude species. Gene expression level, gene connectivity, and the interactions of these 2 factors with altitude were correlated with evolutionary rates. Our results provide evidence for how gene sequence changes and expression shifts work in a concerted way in a group of high-altitude birds, leading to similar evolution routes in response to high-altitude environmental stresses.
Emission characteristics for a single CdSe quantum dot on an optical nanofiber at cryogenic temperatures
Authors: Shafi K Muhammed , Luo Wei , Yalla Ramachandrarao , Hakuta Kohzo
Published: May 2019

We investigate the emission characteristics of a single CdSe quantum dot on an optical nanofiber at cryogenic temperatures from the viewpoint of quantum photonics. We show that the charged exciton (trion) of the quantum dot is a promising quantum emitter for both aspects of spectral and temporal characteristics. The nanofiber/quantum-dot system may give a promising work bench for the future quantum photonic network.
Absorption and photoluminescence properties of CdSe quantum dots prepared by hydrothermal method
Authors: Lee TaeGi , Noguchi Kaito , Nishimura Hisaaki , Kim DaeGwi
Published: May 2019

Herein, we investigated the preparation and optical properties of water-soluble CdSe quantum dots (QDs). CdSe QDs with a narrow size distribution were hydrothermally prepared by reacting Cd2+ with NaHSe in the presence of N-acetyl-L-cysteine as ligand. Furthermore, photoluminescence quantum yield increased to ∼47% when a ZnS shell was applied to prepare the CdSe/ZnS core/shell QDs.
Formation of a single poly(N,N-diethylacrylamide) micro-droplet in water by coupling of photothermal effects and an optical force
Authors: Matsumoto M , Asoh T , Shoji T , Nishiyama T , Horibe Hideo , Katsumoto Yukiteru , Tsuboi Yasuyuki
Published: May 2019

Poly(N-isopropylacrylamide) (PNIPAM) exhibits phase separation with lower critical solution temperature (LCST). In the 1990s, Masuhara and co-workers reported the first demonstration of optical trapping of PNIPAM forming a micrometer-sized polymer droplet. Since then, this technique has attracted much attention to create a molecular assembly in a microspace. In the present study, we targeted poly(N,N-diethylacrylamide) (PDEA), which has an analogous chemical structure to PNIPAM. We demonstrated that optical tweezers formed the unique micro-morphologies of a phase separated PDEA droplet. Fluorescence microscopic images and Raman spectra of the PDEA droplet showed that a lot of smaller-sized water-rich micro-domains were inhomogeneously formed in the droplet. Such unique phase separation behavior was never observed in steady-state heating of an aqueous PDEA solution above its LCST. Our results indicate that a novel micro-structure can be formed by coupling of an optical gradient force and a local temperature elevation.
Potential effect in Balmer light emission near surface irradiated with highly charged ions
Authors: Nishida N , Hori Y , Yamauchi A , Sakurai M , Kato D , Sakaue H A
Published: May 2019

The interaction between highly charged ions (HCIs) and the solid surface causes various phenomena due to high potential energy of HCIs. Luminescence is also included in them. In order to investigate the origin of the light emission from the surface irradiated with HCIs, we conducted spectroscopic measurements and then we investigated characteristics of Balmer light emission because potential effect of HCI was remarkable in Balmer light emitted from hydrogen atoms desorbed from the surface. In the present study, the Balmer light intensity was revealed to increase rapidly with the charge state of HCIs.
Pump-probe study of β’-(BEDT-TTF)(TCNQ) crystal near antiferromagnetic transition
Authors: Mino Hirofumi , Tokuda Shiho , Sakai Masatoshi
Published: May 2019

The photo-excited state properties of an organic Mott-insulator β’-(BEDT-TTF)(TCNQ) crystal were investigated by pump-probe measurements. Considerable change in the pump-probe reflection signal with a wide spectral range was observed near the antiferromagnetic (AF) transition temperature of the TCNQ layers. In the time response, approach to the AF temperature induced the appearance of a slow decay signal whose lifetime was estimated to be about 3 msec maximum. These results indicate that a sustained mechanism exists for photo-excited states near the AF transition, which is probably related to a critical slowing down phenomenon.
Optical characterization of MoS2 sputtered thin films
Authors: Hasuike N , Yamauchi S , Seki K , Kamoi S , Nishio K , Kisoda K
Published: May 2019

We studied on the crystallinity of as-sputtered and annealed MoS2 thin films by Raman scattering. The samples were prepared by RF magnetron sputtering, and the thermal annealing was carried out under sulfurous atmosphere. Although as-sputtered MoS2 thin films clearly showed the deterioration of the lattice ordering, it was drastically improved by the thermal annealing due to the sulfurization of the sample. And since the sulfurization occurred remarkably on the top surface of MoS2 sputtered thin films, it was expected to be an effective method to realize a few-layer MoS2 sputtered thin films with high crystallinity.
New implications for the recurrence mechanism of an upper septal ventricular tachycardia: a case report
Authors: Yamaguchi Junji , Nagata Yasutoshi , Yamauchi Yasuteru , Hirao Kenzo
Published: May 2019

Background

Verapamil-sensitive fascicular ventricular tachycardia (VT) is the most common type of idiopathic left ventricular tachycardia, and it is divided into three types. Upper septal ventricular tachycardia (US-VT) is likely in patients with prior episodes of left posterior fascicular (LPF)-VT ablation, however, little is known about the recurrence mechanism of US-VT.

Case summary

A 53-year-old man had an US-VT after two catheter ablation sessions for a common idiopathic LPF-VT. The US-VT was successfully treated by ablating the proximal site of the LPF without making any further branch or fascicular block. This successful ablation point corresponded completely with the earliest pre-systolic potential (P2) site of the LPF-VT during the 1st session of catheter ablation.

Discussion

An US-VT recurrence could occur if a critical slow conduction is not affected by the catheter ablation. This recurrence might be the result of changing the re-entrant circuit after damage to the LPF. In order to eliminate the LPF-VT and prevent an US-VT recurrence, the earliest P2 site should be investigated carefully and ablated sufficiently.
Are Donors Afraid of Core Costs? Economies of Scale and Contestability in Charity Markets*
Authors: Perroni Carlo , Pogrebna Ganna , Sandford Sarah , Scharf Kimberley
Published: May 2019

We study contestability in charity markets where non-commercial, not-for-profit providers supply a homogeneous collective good through increasing-returns-to-scale technologies. Unlike in the case of for-profit competition, the absence of price-based sales contracts for charities means that fixed costs can translate into entry barriers, protecting the position of an inefficient incumbent; or, conversely, they can make it possible for inefficient newcomers to contest the position of a more efficient incumbent. Evidence from laboratory experiments show that fixed-cost driven tradeoffs between efficiency and perceived risk can lead to inefficient technology adoption.
Bacterial community changes with granule size in cryoconite and their susceptibility to exogenous nutrients on NW Greenland glaciers
Authors: Uetake Jun , Nagatsuka Naoko , Onuma Yukihiko , Takeuchi Nozomu , Motoyama Hideaki , Aoki Teruo
Published: May 2019

Cryoconite granules are dark-colored biological aggregates on glaciers. Bacterial community varies with granule size, however, community change in space and their susceptibility to environmental factors has not been described yet. Therefore, we focused on bacterial community from four different granule sizes (30–249 μm, 250–750 μm, 750–1599 μm, more than 1600 μm diameter) in 10 glaciers in northwestern Greenland and their susceptibility to exogenous nutrients in cryoconite hole. A filamentous cyanobacterium Phormidesmis priestleyi, which has been frequently reported from glaciers in Arctic was abundant (10%–26%) across any size of granules on most of glaciers. Bacterial community across glaciers became similar with size increase, and whence smallest size fractions contain more unique genera in each glacier. Multivariate analysis revealed that effect of nutrients to beta diversity is larger in smaller granules (30–249 μm and 250–750 μm diameter), suggesting that bacterial susceptibility to nutrients changes with growth of granule (i.e. P. priestleyi was affected by nitrate in early growth stage).
Transfer of a lincomycin-resistant plasmid between coagulase-negative staphylococci during soybean fermentation and mouse intestine passage
Authors: Heo Sojeong , Bae Taeok , Lee Jong-Hoon , Jeong Do-Won
Published: May 2019

Staphylococcus equorum is a benign bacterium and the predominant species in high-salt fermented food. Some strains of S. equorum contain antibiotic-resistance plasmids, such as pSELNU1 that contains a lincosamide nucleotidyltransferase (lnuA) gene and confers resistance to lincomycin. Previously, we showed that pSELNU1 is transferred to other bacteria under laboratory growth conditions. However, it is not known if the plasmid can be transferred to other bacteria during food fermentation (in situ) or during passage through animal intestines (in vivo). In this study, we examined the in situ and in vivo transfer of pSELNU1 using Staphylococcus saprophyticus as a recipient. During soybean fermentation, pSELNU1 was transferred to S. saprophyticus at a rate of 1.9 × 10−5–5.6 × 10−6 per recipient in the presence of lincomycin. However, during passage through murine intestines, the plasmid was transferred at similar rates (1.3 × 10−5 per recipient) in the absence of lincomycin, indicating that the plasmid transfer is much more efficient under in vivo conditions. Based on these results, we conclude that it is prudent to examine food fermentation starter candidates for the presence of mobile genetic elements containing antibiotic resistance genes and to select candidates lacking these genes.
Expression of a stress-responsive gene cluster for mycosporine-2-glycine confers oxidative stress tolerance in Synechococcus elongatus PCC7942
Authors: Pingkhanont Panwad , Tarasuntisuk Supamate , Hibino Takashi , Kageyama Hakuto , Waditee-Sirisattha Rungaroon
Published: May 2019

Mycosporine-like amino acids (MAAs) are a class of well-documented UV-screening compounds produced by taxonomically diverse organisms. Extensive studies revealed that a rare MAA, mycosporine-2-glycine (M2G), possesses unique biological activities and functions. M2G is not only a potent antioxidant, but also suppresses protein glycation in vitro, and production of inflammatory mediators in RAW 264.7 macrophages. The present study evaluates vital functions of M2G in a heterologous expression system. The stress-sensitive fresh water cyanobacterium Synechococcus elongatus PCC7942, carrying a M2G biosynthetic gene cluster, was generated. The M2G-expressing cells were more tolerant to H2O2-induced oxidative stress than the wild type, with a half-maximal inhibitory concentration (IC50) value of 2.3 ± 0.06 mM. Transcriptional analysis revealed that all M2G biosynthetic genes were highly up-regulated under oxidative stress. Further, expression of vital genes in the cellular antioxidant defense system, including sodB, cat and tpxA were modulated and up-regulated. Elevated M2G was detected under oxidative stress as well as salt stress treatments. This study provides insight into the molecular and cellular effects of the M2G biosynthetic gene cluster, contributing to understanding of the mechanism behind physiological plasticity under this heterologous expression system.
When Does Form Reflect Function? Acknowledging and Supporting Ecomorphological Assumptions
Authors: Feilich Kara L , López-Fernández Hernán
Published: May 2019

Ecomorphology is the study of relationships between organismal morphology and ecology. As such, it is the only way to determine if morphometric data can be used as an informative proxy for ecological variables of interest. To achieve this goal, ecomorphology often depends on, or directly tests, assumptions about the nature of the relationships among morphology, performance, and ecology. We discuss three approaches to the study of ecomorphology: morphometry-driven, function-driven, and ecology-driven and study design choices inherent to each approach. We also identify 10 assumptions that underlie ecomorphological research: 4 of these are central to all ecomorphological studies and the remaining 6 are variably applicable to some of the specific approaches described above. We discuss how these assumptions may impact ecomorphological studies and affect the interpretation of their findings. We also point out some limitations of ecomorphological studies, and highlight some ways by which we can strengthen, validate, or eliminate systematic assumptions.
Evaluation of the optimal standardized ileal digestible threonine:lysine ratio in lactating sow diets
Authors: Greiner Laura , Graham Amanda , Goncalves Marcio , Orlando Uiseli , Touchette Kevin J
Published: May 2019

Camborough PIC sows (n = 291) were fed 1 of 5 dietary treatments to evaluate the standardized ileal digestible (SID) Thr:Lys requirement during lactation. Sows were blocked by parity (1, 2, and 3+) and randomly allotted to 1 of 5 SID Thr:Lys ratios (52, 60, 68, 76, and 84). SID Lys was formulated to 1.03% and SID methionine and cystine (M + C):Lys was 55%. Sows were allowed 5.45 kg feed/day starting on the day of farrowing. All other nutrients met or exceeded the NRC (2012) requirements. Sows were allowed ad libitum access to water, and piglets were cross-fostered within treatment within 24 h of birth. Data collected during the study included sow prefarrow BW, sow weaning weight, starting litter weight, weaning litter weight, piglet mortality, weaning-to-estrus interval, and subsequent total born piglets. Data were analyzed as a randomized complete block design using PROC MIXED with sow as the experimental unit and treatment and parity as fixed effects. Requirement estimation models evaluated were quadratic polynomial, broken-line linear, and broken-line quadratic (BLQ) using PROC NLMIXED. Models that differed in their Bayesian information criterion (BIC) values by at least 2 points were considered to have meaningful differences in their data fit. The best-fit model was based on the best BIC value. As the SID Thr:Lys ratio increased, there was a quadratic response on ADFI (4.73, 4.57, 4.67, 4.55, and 4.60 kg/d; P = 0.001) and percent of sow BW loss (−6.4, −7.89, −7.35, −6.19, and −5.81; P = 0.004). In addition, there was a trend for weaning-to-estrus interval to be affected by the ratio (5.4, 4.4, 4.6, 4.5, and 4.8; P = 0.07). Daily litter gain was also quadratically improved as the SID Thr:Lys ratio increased (2.67, 2.67, 2.78, 2.77, and 2.68 kg/d; P-value = 0.001). For daily litter gain, the BLQ model was determined to be the best fit with an estimated SID Thr:Lys requirement of 65%. In conclusion, the optimal SID Thr:Lys ratio for litter growth was 65.
Recurrent abdominal liposarcoma presenting with intestinal obstruction
Authors: Abufkhaida Belal S , Alsalameh Barah K
Published: May 2019

Liposarcoma is the most common retroperitoneal sarcoma and mesenchymal tumor in the abdomen. Usually, it presents with vague symptoms due to its large size and slow growth at the time of diagnosis. Liposarcoma is associated with a high local recurrence rate according to its histology, size and growth rate. Up till now, surgical resection is the only effective treatment for primary and recurrent abdominal liposarcoma.

Secondary mesenteric liposarcoma is an extremely rare entity and so far a small number of cases have been reported in the literature. In this article, we present a rare case of a 63-year-old female patient who was diagnosed with mesenteric liposarcoma after 3 years of complete excision of retroperitoneal liposarcoma, presenting primarily as abdominal mass causing mechanical intestinal obstruction.
Joint Space Narrowing in Patients with Femoroacetabular Impingement: A Matched Cohort Study of Military versus Civilian Patients
Authors: Dumont Guillaume D , Antosh Ivan J , Carmon Philip
Published: May 2019

Introduction

Decreased hip joint space has been associated with poorer outcomes after hip arthroscopy. The purpose of this study was to determine if a difference exists in hip joint degenerative findings in military versus civilian patients with FAI.

Methods

A single surgeon’s case series was reviewed to identify all patients undergoing primary hip arthroscopy for treatment of FAI. All active duty military personnel were included in the study group. A cohort of civilian patients matched for age, gender, lateral center edge (LCE) angle, and alpha angle was identified and included as the control group. The hip joint space was measured at the medial and lateral extents of the acetabular sourcil and the center of the sourcil. The Tonnis grade for osteoarthritis was recorded for each patient. Labral tear size as well as femoral head and acetabular chondromalacia grading were obtained from operative records.

Results

A total of 229 patients that underwent primary hip arthroscopy for FAI were identified. 46(20.1%) were active duty military personnel. A well-matched cohort of 46 civilian patients was identified. There was no statistical difference in age (35.0, 34.7 years), gender (31 males, 15 females in both groups), BMI (26.8, 27.6), LCE angle (31.0, 31.5), and alpha angle (64.9, 64.9) between the civilian and military groups. Joint space was narrower in the military group in each of the three measured locations (Superomedial 3.8 mm vs 4.2 mm, p = 0.025; Superior 4.0 mm vs 4.4 mm, p = 0.013; Superolateral 4.4 mm vs 4.9 mm, p = 0.043).

Conclusion

Military patients with FAI may have increased joint space narrowing compared to otherwise similar civilian patients. Femoral and acetabular chondromalacia are found in similar frequencies in military and civilian populations, however the grading system utilized accounts for the presence but not the size of high grade lesions.

Level of Evidence

Level 3.
Histiotus magellanicus (Chiroptera: Vespertilionidae)
Authors: Díaz M Mónica , Ossa Gonzalo , Barquez Rubén M
Published: May 2019

Histiotus magellanicus (Philippi, 1866) is a vespertilionid bat called the southern big-eared brown bat. The dark color of the ears and the absence of a connecting band between the ears are the characters that clearly differentiate this species from all other species of Histiotus. It is a little-known species with a distribution restricted to the southern portions of Argentina and Chile. H. magellanicus is listed as “Least Concern” by the International Union for Conservation of Nature and Natural Resources.
Hepatitis B Virus Prevalence and Vaccination in Men Who Have Sex With Men in West Africa (CohMSM ANRS 12324—Expertise France)
Authors: Dah Ter Tiero Elias , Couderc Clotilde , Coulibaly Alou , kouamé Malan Jean-Baptiste , Agboyibor Mawuényégan Kouamivi , Traoré Issa , Maradan Gwenaëlle , Rojas Castro Daniela , Mensah Ephrem , Anoma Camille , Dembélé Keita Bintou , Spire Bruno , Laurent Christian ,   CohMSM Study Group, Couderc Clotilde , Granouillac Bruno , Izard Suzanne , Laurent Christian , March Laura , Peeters Martine , Serrano Laetitia , Berenger Cyril , Bourrelly Michel , Coulaud Pierre-Julien , Maradan Gwenaelle , Mora Marion , Sagaon-Teyssier Luis , Spire Bruno , Bernier Adeline , Palvadeau Paméla , Castro Daniela Rojas , Camara Drissa , Cisse Oumar , Coulibaly Alou , Keita Bintou Dembélé , Diallo Fodié , Diarra Mahamadou , Keita Abdoul Aziz , Maiga Kader , Ouologuem Aly , Traore Fodé , Thomas Aka Niamkey , Anoma Camille , Babo Yoro Stéphane-Alain , Coulibaly Noufo Hamed , Kotchi Rachelle , Kouabenan Patrick , Jean-Baptiste kouamé Malan , Julien Lokrou Kpassou , Dibi N’Guessan Frédéric , Coulibaly Christian , Elias Dah Ter Tiero , Ilboudo Ousseni , Ouedraogo Joseph , Ouedraogo Mamadou , Thio Elisabeth , Toure Juste Rodrigue , Traore Abdoulazziz , Traoré Issa , Yougbare Fiffou , Kokouvi Kouakou , Agbomadji Selom , Agboyibor Mawuényégan Kouamivi , Attiogbe Messan , Mawuli Badjassim Aléda , Lorette Ekon Agbégnigan , Kokouba Anouwarsadat , Mensah Ephrem , Strauss Tablissi Diimiln Joseph , Dagnra Claver Anoumou Yaotsé
Published: May 2019

Background

Although men who have sex with men (MSM) are at high risk of hepatitis B virus (HBV) infection, they do not have access to vaccination in West Africa, which is a highly endemic region. We investigated HBV prevalence and associated factors, as well as acceptability and difficulties of vaccination in MSM enrolled in an operational research program in Burkina Faso, Côte d’Ivoire, Mali, and Togo.

Methods

We followed up 779 MSM in 2015–2018. Participants who were negative for both hepatitis B surface antigen (HBsAg) and antibodies (anti-HBs) at enrollment were offered HBV vaccination. Factors associated with HBV infection were identified using logistic regression models.

Results

Overall, HBV prevalence was 11.2% (95% confidence interval [CI], 9.0%–13.6%). It was lower in Togo than in Côte d’Ivoire (2.7% vs 17.3%; adjusted odds ratio [aOR], 0.12; 95% CI, 0.02–0.28) and higher in participants with 6+ recent male sexual partners (21.0% vs 9.3%; aOR, 1.48; 95% CI, 1.12–1.97). Of 528 participants eligible for vaccination, 484 (91.7%) were willing to be vaccinated and received at least 1 dose (ranging from 68.2% in Abidjan to 96.4% in Bamako; P < .001). Of the latter, 390 (80.6%) received 3 or 4 doses. The proportion of participants for whom the minimum required time between each dose was respected ranged from 10.9% in Bamako to 88.6% in Lomé (P < .001).

Conclusions

MSM in West Africa should be targeted more for HBV screening and vaccination. Although vaccination is well accepted by MSM, greater training of health care workers and education of MSM are required.
8Visual Culture
Authors: Lewis India
Published: May 2019

This chapter addresses books published in the field of visual culture in 2018 and is divided into three sections: 1. Art and the Internet; 2. Art and Society, and 3. Artists and Their Environment. The books under review cover a broad range of subjects within their specialities, but reflect general trends in contemporary writing and study in the field of visual culture. The first section explores how art critics and those in the field are continuing to deal with visual culture’s relationship with the Internet and digital media (Daniel Birnbaum, Michelle Kuo, eds. More Than Real: Art in the Digital Age; Eva Respini, ed., Art in the Age of the Internet: 1989 to Today). The second section looks at books about art in the social sphere (Kim Snepvangers and Donna Mathewson Mitchell, eds., Beyond Community Engagement: Transforming Dialogues in Art, Education, and the Cultural Sphere; Ole Marius Hylland and Erling Bjurström, eds., Aesthetics and Politics: A Nordic Perspective on How Cultural Policy Negotiates the Agency of Music and Arts; Gary Alan Fine, Talking Art: The Culture of Practice and the Practice of Culture in MFA Education). The third and final section looks at how artists negotiate their environment, responding to and altering their surroundings (Sarah Lowndes, Contemporary Artists Working Outside the City: Creative Retreat; Gabriel N. Gee and Alison Vogelaar, eds., Changing Representations of Nature and the City: The 1960s–1970s and Their Legacies).
Characterizing Sources of Resistance to Phytophthora Blight of Pepper Caused by Phytophthora capsici in North Carolina
Authors: Parada-Rojas Camilo H. , Quesada-Ocampo Lina M.
Published: May 2019

Phytophthora blight, caused by Phytophthora capsici, is an important disease of peppers in the United States and worldwide. P. capsici causes crown, root, and fruit rot as well as foliar lesions in peppers. Field trials were conducted in 2015 and 2016 to evaluate 32 commercial and experimental pepper cultivars against a mixed-isolate inoculum in North Carolina. Cultivars Martha-R and Meeting were classified as highly resistant to P. capsici, and Paladin was classified as resistant. Intermediate resistance to P. capsici in the field was observed with Fabuloso, Revolution, Vanguard, Archimedes, Aristotle, Ebano-R, and Declaration. Greenhouse experiments were conducted to determine the response of 48 pepper cultivars when inoculated individually with two isolates from North Carolina and an isolate from Michigan. Isolates exhibited different levels of virulence in pepper cultivars screened for resistance. Landraces CM334 and Fidel as well as the cultivars Martha-R, Meeting, and Intruder were categorized as highly resistant or resistant to the three isolates tested. Overall, highly resistant cultivars tended to respond similarly to field mix inoculations and greenhouse single isolate inoculations.
A Multi-Breed Reference Panel and Additional Rare Variation Maximizes Imputation Accuracy in Cattle
Authors: Rowan Troy N. , Hoff Jesse L. , Crum Tamar E. , Taylor Jeremy F. , Schnabel Robert D. , Decker Jared E.
Published: May 2019

Background

The use of array-based SNP genotyping in the beef and dairy industries has produced an astounding amount of medium-to-low density genomic data in the last decade. While low-density assays work exceptionally well in the context of genomic prediction, they are less useful in mapping and causal variant discovery. This project focuses on maximizing imputation accuracies to the marker set of two high-density research assays, the Illumina Bovine HD, and the GGP-F250 which contains a large proportion of rare and potentially functional variants (~850,000 total SNPs). This 850K SNP set is well-suited for both imputation to sequence-level genotypes and direct downstream analysis.

Results

We find that a large multi-breed composite imputation reference comprised of 36,131 samples with either HD and/or F250 genotypes significantly increases imputation accuracy compared to a standard within-breed reference panel, particularly at low minor allele frequencies. Imputation accuracies were maximized when an individual’s ancestry was adequately represented in the composite reference, particularly with complete 850K genotypes. The addition of rare content from the F250 to our composite reference panel significantly increased the imputation accuracy of rare variants found exclusively on the HD. Additionally, we identify 50,000 variants as an ideal starting density for 850K imputation.

Conclusion

Using high-density genotypes on all available individuals in a multi-breed reference panel maximizes imputation accuracy for all cattle populations. Admixed breeds or those sparsely represented in the composite reference are still imputed at high accuracy which will increase further as the reference panel grows. We expect that the addition of rare variation from the F250 will increase the accuracy of imputation at the sequence level.
A Population Genomics Analysis of the Native Irish Galway Sheep Breed
Authors: McHugo Gillian P. , Browett Sam , Randhawa Imtiaz A. S. , Howard Dawn J. , Mullen Michael P. , Richardson Ian W. , Park Stephen D. E. , Magee David A. , Scraggs Erik , Dover Michael , Correia Carolina N. , Hanrahan James P. , MacHugh David E.
Published: May 2019

The Galway sheep population is the only native Irish sheep breed and represents an important livestock genetic resource, which is currently categorised as “at-risk”. In the present study, comparative population genomics analyses of Galway sheep and other sheep populations of European origin were used to investigate the microevolution and recent genetic history of the breed. These analyses support the hypothesis that British Leicester sheep were used in the formation of the Galway breed and suggest more recent gene flow from the Suffolk sheep breed. When compared to conventional and endangered breeds, the Galway breed was intermediate in effective population size, genomic inbreeding and runs of homozygosity. This indicates that, although the Galway breed is declining, it is still relatively genetically diverse and that conservation and management plans informed by genomic information may aid its recovery. The Galway breed also exhibited distinct genomic signatures of artificial or natural selection when compared to other breeds, which highlighted candidate genes that may be involved in meat and wool production.
Comparison of miRNA profiling methods using synthetic miRNA pools and standardized exRNA samples reveals substantial performance differences
Authors: Godoy Paula M. , Barczak Andrea J. , DeHoff Peter , Srinivasan Srimeenakshi , Das Saumya , Erle David J. , Laurent Louise C.
Published: May 2019

MicroRNAs (miRNAs) found in biofluids play functional roles in health and in disease pathogenesis, underpinning their potential as clinical biomarkers. Several platforms for measurement of extracellular RNAs have recently become available. We evaluated the reproducibility, accuracy, sensitivity, and specificity of four miRNA quantification platforms, including one widely used discovery approach (small RNA-seq) and three targeted platforms (FirePlex, EdgeSeq, and nCounter). Using pools of synthetic miRNAs, we observed that reproducibility was highest for RNA-seq and EdgeSeq, that all three targeted platforms had lower bias than RNA-seq, and that RNA-seq had the best ability to distinguish between present and absent sequences. Overall reproducibility was lower for plasma samples than synthetic miRNA pools. We compared expression of placental miRNAs in plasma from pregnant and non-pregnant women and observed expected differences with RNA-seq and EdgeSeq, but not FirePlex or nCounter. We conclude that differences in performance among miRNA profiling platforms impact their relative utility as potential assay systems for clinical biomarkers.
A Freely Available, Self-Calibrating Software for Automatic Measurement of Freezing Behavior
Authors: Amorim Felippe E. , Moulin Thiago C. , Amaral Olavo B.
Published: May 2019

Freezing behavior is commonly used as a measure of associative fear memory. It can be measured by a trained observer, but this task is time-consuming and subject to variation. Commercially available software packages can also be used to quantify freezing; however, they can be expensive and usually require various parameters to be adjusted by the researcher, leading to additional work and variability in results. With this in mind, we developed Phobos, a freely available, self-calibrating software that measures freezing in a set of videos using a brief manual quantification performed by the user to automatically adjust parameters. To optimize the software, we used four different video sets with different features in order to determine the most relevant parameters, the amount of videos needed for calibration and the minimum criteria to consider it reliable. The results of four different users were compared in order to test intra- and interobserver variability in manual and automated freezing scores. Our results suggest that Phobos can be an inexpensive, simple and reliable tool for measurement of fear-related behavior, with intra- and interuser variability similar to that obtained with manual scoring.
Second Harmonic Generation Spectroscopy of Membrane Probe Dynamics in Gram-Positive Bacteria
Authors: Miller L. N. , Brewer W. T. , Williams J. D. , Fozo E. M. , Calhoun T. R.
Published: May 2019

Bacterial membranes are complex mixtures with dispersity that is dynamic over scales of both space and time. In order to capture adsorption onto and transport within these mixtures, we conduct simultaneous second harmonic generation (SHG) and two photon fluorescence measurements on two different gram-positive bacterial species as the cells uptake membrane-specific probe molecules. Our results show that SHG can not only monitor the movement of small molecules across membrane leaflets, but is also sensitive to higher-level ordering of the molecules within the membrane. Further, we show that the membranes of Staphylococcus aureus remain more dynamic after longer times at room temperature in comparison to Enterococcus faecalis. Our findings provide insight into the variability of activities seen between structurally similar molecules in gram-positive bacteria while also demonstrating the power of SHG to examine these dynamics.

STATEMENT OF SIGNIFICANCE

Bacterial membranes are highly adept at discerning and modifying their interactions with different small molecules in their environment. Here we show how second harmonic generation (SHG) spectroscopy can track the dynamics of structurally similar membrane probes in two gram-positive bacterial species. Our results reveal behavior that is dependent on both the probe molecule and the membrane composition. Specifically, we observe flip-flop between leaflets for one molecule, while the other molecule produces a signal indicative of larger scale ordering in the membrane. These phenomena can all be explained by considering potential differences in the membrane fluidity and surface charge between the two bacterial species. Overall, our work highlights the dynamic differences between bacterial membranes and SHG’s sensitivity to probing these systems.
SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble
Authors: Huh Ruth , Yang Yuchen , Jiang Yuchao , Shen Yin , Li Yun
Published: May 2019

Clustering is an essential step in the analysis of single cell RNA-seq (scRNA-seq) data to shed light on tissue complexity including the number of cell types and transcriptomic signatures of each cell type. Due to its importance, novel methods have been developed recently for this purpose. However, different approaches generate varying estimates regarding the number of clusters and the single-cell level cluster assignments. This type of unsupervised clustering is challenging and it is often times hard to gauge which method to use because none of the existing methods outperform others across all scenarios. We present SAME-clustering, a mixture model-based approach that takes clustering solutions from multiple methods and selects a maximally diverse subset to produce an improved ensemble solution. We tested SAME-clustering across 15 scRNA-seq datasets generated by different platforms, with number of clusters varying from 3 to 15, and number of single cells from 49 to 32,695. Results show that our SAME-clustering ensemble method yields enhanced clustering, in terms of both cluster assignments and number of clusters. The mixture model ensemble clustering is not limited to clustering scRNA-seq data and may be useful to a wide range of clustering applications.
PD-1 expression during acute infection is repressed through a LSD1- Blimp-1 axis
Authors: Bally Alexander P. R. , Neeld Dennis K. , Lu Peiyuan , Majumder Parimal , Tang Yan , Barwick Benjamin G. , Wang Qing , Boss Jeremy M.
Published: May 2019

During prolonged exposure to antigens, such as chronic viral infections, sustained T cell receptor (TCR) signaling can result in T cell exhaustion mediated in part by expression of Programmed cell death-1 (PD-1) encoded by thePdcd1gene. Here, dynamic changes in histone H3K4 modifications at thePdcd1locus during ex vivo and in vivo activation of CD8 T cells, suggested a potential role for the histone H3 lysine 4 demethylase LSD1 in regulating PD-1 expression. CD8 T cells lacking LSD1 expressed higher levels ofPdcd1mRNA following ex vivo stimulation, as well as increased surface levels of PD-1 during acute but not chronic infection with lymphocytic choriomeningitis virus (LCMV). Blimp-1, a known repressor of PD-1, recruited LSD1 to thePdcd1gene during acute but not chronic LCMV infection. Loss of DNA methylation atPdcd1’s promoter proximal regulatory regions is highly correlated with its expression. However, following acute LCMV infection where PD-1 expression levels return to near base line, LSD1-deficient CD8 T cells failed to remethylate thePdcd1locus to the levels of wild-type cells. Finally, in a murine melanoma model, the frequency of PD-1 expressing tumor infiltrating LSD1-deficient CD8 T cells was greater than wild-type. Thus, LSD1 is recruited to thePdcd1locus by Blimp-1, downregulates PD-1 expression by facilitating the removal of activating histone marks, and is important for remethylation of the locus. Together, these data provide insight into the complex regulatory mechanisms governing T cell immunity and the regulation of a critical T cell checkpoint gene.

Key Points

LSD1 suppress PD-1 expression following acute infection or transient induction.

Blimp-1 binding to the Pdcd1 locus is required to recruit LSD1.

LSD1 is required to fully remethylate the PD-1 proximal promoter region.
Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics
Authors: Huang Yiming , Sheth Ravi U , Kaufman Andrew , Wang Harris H
Published: May 2019

Bacterial RNA sequencing (RNA-seq) is a powerful approach for quantitatively delineating the global transcriptional profiles of microbes in order to gain deeper understanding of their physiology and function. Cost-effective bacterial RNA-seq requires efficient physical removal of ribosomal RNA (rRNA), which otherwise dominates transcriptomic reads. However, current methods to effectively deplete rRNA of diverse non-model bacterial species are lacking. Here, we describe a probe and ribonuclease based strategy for bacterial rRNA removal. We implemented the method using either chemically synthesized oligonucleotides or amplicon-based single-stranded DNA probes and validated the technique on three novel gut microbiota isolates from three distinct phyla. We further showed that different probe sets can be used on closely related species. We provide a detailed methods protocol, probe sets for >5,000 common microbes from RefSeq, and an online tool to generate custom probe libraries. This approach lays the groundwork for large-scale and cost-effective bacterial transcriptomics studies.
Transferrin plays a central role to maintain coagulation balance by interacting with clotting factors
Authors: Tang Xiaopeng , Zhang Zhiye , Fang Mingqian , Han Yajun , Wang Sheng , Xue Min , Li Yaxiong , Zhang Li , Wu Jian , Yang Biqing , Lu Qiumin , Du Xiaoping , Lai Ren
Published: May 2019

Coagulation balance is maintained through fine-tuning interactions among clotting factors. Physiological concentrations of clotting factors are huge difference. Especially, coagulation proteases’ concentration (pM to nM) is much lower than their natural inactivator antithrombin III (AT-III, ∼3 μM). Here we show that transferrin (normal plasma concentration ∼40 μM) interacts with fibrinogen, thrombin, FXIIa and AT-III with different affinity to maintain coagulation balance. Normally, transferrin is sequestered by binding with fibrinogen (normal plasma concentration ∼10 μM) with a molar ratio of 4:1. In atherosclerosis, abnormally up-regulated transferrin interacts with and potentiates thrombin/FXIIa and blocks AT-III’s inactivation on coagulation proteases by binding to AT-III, and thus induces hypercoagulability. In mouse models, transferrin-overexpression aggravated atherosclerosis while transferrin-knockdown, anti-transferrin antibody or designed peptides interfering transferrin-thrombin/FXIIa interactions alleviated it. Collectively, these findings identify transferrin as a clotting factor and an adjuster for maintaining coagulation balance and modify the coagulation cascade.
Learning to select actions shapes recurrent dynamics in the corticostriatal system
Authors: Márton Christian D. , Schultz Simon R. , Averbeck Bruno B.
Published: May 2019

Learning to select appropriate actions based on their values is fundamental to adaptive behavior. This form of learning is supported by fronto-striatal systems. The dorsal-lateral prefrontal cortex (dlPFC) and the dorsal striatum (dSTR), which are strongly interconnected, are key nodes in this circuitry. Substantial experimental evidence, including neurophysiological recordings, have shown that neurons in these structures represent key aspects of learning. The computational mechanisms that shape the neurophysiological responses, however, are not clear. To examine this, we developed a recurrent neural network (RNN) model of the dlPFC-dSTR circuit and trained it on an oculomotor sequence learning task. We compared the activity generated by the model to activity recorded from monkey dlPFC and dSTR in the same task. This network consisted of a striatal component which encoded action values, and a prefrontal component which selected appropriate actions. After training, this system was able to autonomously represent and update action values and select actions, thus being able to closely approximate the representational structure in corticostriatal recordings. We found that learning to select the correct actions drove action-sequence representations further apart in activity space, both in the model and in the neural data. The model revealed that learning proceeds by increasing the distance between sequence-specific representations. This makes it more likely that the model will select the appropriate action sequence as learning develops. Our model thus supports the hypothesis that learning in networks drives the neural representations of actions further apart, increasing the probability that the network generates correct actions as learning proceeds. Altogether, this study advances our understanding of how neural circuit dynamics are involved in neural computation, showing how dynamics in the corticostriatal system support task learning.
Measuring mRNA translation in neuronal processes and somata by tRNA-FRET
Authors: Koltun Bella , Ironi Sivan , Gershoni-Emek Noga , Barrera Iliana , Hleihil Mohammad , Nanguneri Siddharth , Sasmal Ranjan , Agasti Sarit S. , Nair Deepak , Rosenblum Kobi
Published: May 2019

In neurons, the specific spatial and temporal localization of protein synthesis is of great importance for function and survival. In this work, we visualized tRNA and protein synthesis events in fixed and live mouse primary cortical culture using fluorescently-labeled tRNAs. We were able to characterize the distribution and movement of tRNAs in different neuronal sub-compartments and to study their association with the ribosome. We found that tRNA motion in neural processes is lower than in somata and corresponds to patterns of slow transport mechanisms, and that larger tRNA puncta co-localize with translational machinery components and are likely the functional fraction. Furthermore, chemical induction of LTP in culture revealed GluR-dependent biphasic up-regulation of mRNA translation with a similar effect in dendrites and somata. Importantly, measurement of protein synthesis in neurons with high resolutions offers new insights into neuronal function in health and disease states.
Loss of the Alzheimer’s-linked bridging integrator 1 (BIN1) protein affects synaptic structure and disrupts tau localisation and release
Authors: Glennon Elizabeth B. , Lau Dawn H-W , Gabriele Rebecca M.C. , Taylor Matthew F. , Troakes Claire , Elliott Christina , Killick Richard , Hanger Diane P. , Perez-Nievas Beatriz G. , Noble Wendy
Published: May 2019

Background

Post-translational modifications of tau modify its interaction with binding partners and cause tau mislocalisation and altered tau function in Alzheimer’s disease (AD). The AD risk gene BIN1, is a binding partner for tau, however the mechanism by which BIN1 influences tau function is not fully understood. We hypothesised that BIN1 modulates AD risk by causing damaging tau mis-sorting to the synapse.

Methods

Tau and BIN1 levels, distribution and interactions were assessed in post-mortem control and AD brain and in primary neurons. In primary neurons, tau was further examined using structured illumination microscopy and immunoblotting following BIN1 knockdown, BIN1-tau interactions were examined using proximity ligation assays and tau release from neurons was measured by sensitive sandwich ELISA.

Results

Proline 216 in tau was identified as critical for tau interaction with the BIN1-SH3 domain, and tau phosphorylation at serine/threonine residues disrupted this interaction. Subcellular fractionation showed that BIN1 is lost from the cytoplasm of AD brain and this correlated with the mislocalisation of phosphorylated tau to synapses. Mimicking BIN1 loss in AD by knockdown of the protein in primary neurons altered the structure of dendritic spines, caused phosphorylated tau to mis-sort to synapses and reduced the physiological release of predominantly dephosphorylated tau.

Conclusions

These data suggest that BIN1 loss in AD allows phosphorylated tau to be mis-sorted to synapses which likely alters the integrity of the post-synapse, alongside reducing the functionally important release of physiological forms of tau.