bluuebunny/crossref_metadata_2025_split huggingface dataset:
First Draft Genome of a Brazilian Atlantic Rainforest Burseraceae reveals commercially-promising genes involved in terpenic oleoresins synthesis
Authors: Afonso Luana Ferreira , Amaral Danielle , Uliano-Silva Marcela , Torres André Luiz Quintanilha , Simas Daniel Reis , Rebelo Mauro de Freitas 
Published: November 2018

BackgroundProtiumspecies produce abundant aromatic oleoresins composed mainly of different types of terpenes, which are highly sought after by the flavor and fragrance industry.ResultsHere we present (i) the first draft genome of an endemic tree of the Brazil’s Atlantic Rainforest (Mata Atlântica),Protium kleiniiCuatrec., (ii) a first characterization of its genes involved in the terpene pathways, and (iii) the composition of the resin’s volatile fraction. The de novo draft genome was assembled using Illumina paired-end-only data, totalizing 407 Mb in size present in 229,912 scaffolds. The N50 is 2.60 Kb and the longest scaffold is 52.26 Kb. Despite its fragmentation, we were able to infer 53,538 gene models of which 5,434 were complete. The draft genome of P. kleinii presents 76.67 % (62.01 % complete and 14.66 % partial) of plant-core BUSCO genes. InterProScan was able to assign at least one Gene Ontology annotation and one Pfam domain for 13,629 and 26,469 sequences, respectively. We were able to identify 116 enzymes involved in terpene biosynthesis, such as monoterpenesα-terpineol, 1,8-cineole, geraniol, (+)-neomenthol and (+)-(R)-limonene. Through the phylogenetic analysis of the Terpene Synthases gene family, three candidates of limonene synthase were identified. Chemical analysis of the resin’s volatile fraction identified four monoterpenes: terpinolene, limonene,α-pinene andα-phellandrene.ConclusionThese results provide resources for further studies to identify the molecular bases of the main aroma compounds and new biotechnological approaches to their production.
Patterns and mechanisms of diminishing returns from beneficial mutations
Authors: Wei Xinzhu , Zhang Jianzhi 
Published: November 2018

ABSTRACTDiminishing returns epistasis causes the benefit of the same advantageous mutation smaller in fitter genotypes, and is frequently observed in experimental evolution. However, its occurrence in other contexts, environment-dependence, and mechanistic basis are unclear. Here we address these questions using 1005 sequenced segregants generated from a yeast cross. Under each of 47 examined environments, 66-92% of tested polymorphisms exhibit diminishing returns epistasis. Surprisingly, improving environment quality also reduces the benefits of advantageous mutations even when fitness is controlled for, indicating the necessity to revise the global epistasis hypothesis. We propose that diminishing returns originates from the modular organization of life where the contribution of each functional module to fitness is determined jointly by the genotype and environment and has an upper limit, and demonstrate that our model predictions match empirical observations. These findings broaden the concept of diminishing returns epistasis, reveal its generality and potential cause, and have important evolutionary implications.
Source-sink dynamics could sustain HIV epidemics in rural communities in sub-Saharan Africa: the case of Malawi
Authors: Okano Justin T. , Sharp Katie , Palk Laurence , Blower Sally 
Published: November 2018

AbstractBackground:Approximately 25.5 million individuals are infected with HIV in sub-Saharan Africa (SSA). Epidemics in this region are generalized, show substantial geographic variation in prevalence, and are driven by heterosexual transmission; populations are highly mobile. We propose that generalized HIV epidemics should be viewed as a series of micro-epidemics occurring in multiple connected communities. Using a mathematical model, we test the hypothesis that travel can sustain HIV micro-epidemics in communities where transmission is too low to be self-sustaining. We use Malawi as a case study.Methods:We first conduct a mapping exercise to visualize geographic variation in HIV prevalence and population-level mobility. We construct maps by spatially interpolating georeferenced HIV-testing and mobility data from a nationally representative population-level survey: the 2015-16 Malawi Demographic and Health Survey. To test our hypothesis, we construct a novel HIV epidemic model that includes three transmission pathways: resident-to-resident, visitor-caused and travel-related. The model consists of communities functioning as “sources” and “sinks”. A community is a source if transmission is high enough to be self-sustaining, and a sink if it is not.Results:HIV prevalence ranges from zero to 27%. Mobility is high, 27% of the population took a trip lasting at least a month in the previous year. Prevalence is higher in urban centers than rural areas, but long-duration travel is higher in rural areas than urban centers. We show that a source-community can sustain a micro-epidemic in a sink-community, but only if specific epidemiological and demographic threshold conditions are met. The threshold depends upon the level of transmission in the source- and sink-communities, as well as the relative sizes of the two communities. The larger the source than the sink, the lower transmission in the source-community needs to be for sustainability.Discussion:Our results support our hypothesis, and suggest that it may be rather easy for large urban communities to sustain HIV micro-epidemics in small rural communities; this may be occurring in northern Malawi. Visitor-generated and travel-related transmission may also be sustaining micro-epidemics in rural communities in other SSA countries with highly-mobile populations. It is essential to consider mobility when developing HIV elimination strategies.
Genetic loss of the ubiquitin ligase RNF126, an AID interacting partner and modifier, affects strand targeting during somatic hypermutation of antibody genes
Authors: Economos Nicholas , Delker Rebecca K , Stavropoulos Pete , Papavasiliou F. Nina 
Published: November 2018

AbstractActivation-induced cytidine deaminase (AID) initiates somatic hypermutation (SHM) and class switch recombination (CSR) in B lymphocytes by catalyzing the introduction of deoxyuracil: deoxyguanine mismatches into the DNA of the transcribed Ig locus. Repair pathways then process these mismatches to produce point mutations in the Ig variable region or double-stranded DNA breaks in the switch region followed by deletional recombination. It has been suggested that post-translational modifications on AID mediate a number of these different decisions, ranging from global targeting (Ig vs the genome), local targeting (variable vs switch region; transcribed vs non-transcribed strand) as well as process-appropriate DNA repair. Here we demonstrate that absence of RNF126, an E3 ligase shown to mono-ubiquitylate AID, results in a specific strand targeting defect in SHM, producing substantial G>C bias; strickingly, loss of RNF126 was also associated with tandem indels within the variable region (JH4 intron) but only a slight increase in the types of chromosomal translocations that are characteristic of deregulated AID. Conversely, these findings suggest that mono-ubiquitination of AID, likely in situ, is necessary for the proper removal of the protein from the non-transcribed strand, thus producing both optimal patterns of SHM and also limiting the number of indels within the target locus.
Premovement suppression of corticospinal excitability may be a necessary part of movement preparation
Authors: Ibáñez J. , Hannah R. , Rocchi L. , Rothwell J.C. 
Published: November 2018

ABSTRACTIn a warned reaction time (RT) task, corticospinal excitability (CSE) decreases in task-related muscles at the time of the imperative signal (preparatory inhibition). Because RT tasks emphasise speed of response, it is impossible to distinguish whether preparatory inhibition reflects a mechanism preventing premature reactions, or whether it is an inherent part of movement preparation. We used transcranial magnetic stimulation (TMS) to study CSE changes preceding RT movements and movements that were either self-paced (SP) or performed at predictable times to coincide with an external event (PT). Results show that CSE changes over a similar temporal profile in all cases, suggesting that preparatory inhibition is a necessary state in planned movements allowing the transition between rest and movement. Additionally, TMS given shortly before the times to move speeded the onset of movements in both RT and SP contexts, suggesting that their initiation depends on a form of trigger that can be conditioned by external signals. On the contrary, PT movements do not show this effect, suggesting the use of a mechanistically different triggering strategy. This relative immunity of PT tasks to be biased by external events may reflect a mechanism that ensures priority of internal predictive signals to trigger movement onset.
A novel model plant to study the light control of seed germination
Authors: Mérai Zsuzsanna , Graeber Kai , Wilhelmsson Per , Ullrich Kristian K. , Arshad Waheed , Grosche Christopher , Tarkowská Danuše , Turečková Veronika , Strnad Miroslav , Rensing Stefan A. , Leubner-Metzger Gerhard , Scheid Ortrun Mittelsten 
Published: November 2018

AbstractTiming of seed germination is crucial for seed plants and coordinated by internal and external cues, reflecting adaptations to different habitats. Physiological and molecular studies with lettuce andArabidopsis thalianahave documented a strict requirement for light to initiate germination and identified many receptors, signalling cascades, and hormonal control elements. In contrast, seed germination of several other plants is inhibited by light, but the molecular basis of this converse response is unknown. We describeAethionema arabicum(Brassicaceae) as a suitable model plant to investigate the mechanism of germination inhibition by light, as it comprises accessions with natural variation between light-sensitive and light-neutral responses. Inhibition is independent of light wavelength and increases with light intensity and duration. Gibberellins and abscisic acid are involved in the control of germination as in Arabidopsis, but transcriptome comparisons of light- and dark-exposedAethionema arabicumseeds revealed that expression of genes for key regulators upon light exposure undergo converse changes, resulting in antipodal hormone regulation. This illustrates that similar modular components of a pathway in light-inhibited, light-neutral and light requiring germination among the Brassicaceae have been assembled by evolution to produce divergent pathways, likely as adaptive traits.HighlightIn contrast to light requirement for Arabidopsis seed germination, germination of severalAethionema arabicumaccessions is inhibited by light, due to antipodal transcriptional regulation of hormone balance.
Runs of Homozygosity in sub-Saharan African populations provide insights into a complex demographic and health history
Authors: Ceballos Francisco C. , Hazelhurst Scott , Ramsay Michele 
Published: November 2018

AbstractThe study of runs of homozygosity (ROH), contiguous regions in the genome where an individual is homozygous across all sites, can shed light on the demographic history and cultural practices. We present a fine-scale ROH analysis of 1679 individuals from 28 sub-Saharan African (SSA) populations along with 1384 individuals from 17 world-wide populations. Using high-density SNP coverage, we could accurately obtain ROH as low as 300Kb using PLINK software. The analyses showed a heterogeneous distribution of autozygosity across SSA, revealing a complex demographic history. They highlight differences between African groups and can differentiate between the impact of consanguineous practices (e.g. among the Somali) and endogamy (e.g. among several Khoe-San groups1). The genomic distribution of ROH was analysed through the identification of ROH islands and regions of heterozygosity (RHZ). These homozygosity cold and hotspots harbour multiple protein coding genes. Studying ROH therefore not only sheds light on population history, but can also be used to study genetic variation related to the health of extant populations.
Comprehensive and quantitative analysis of white and brown adipose tissue by shotgun lipidomics
Authors: Grzybek Michal , Palladini Alessandra , Alexaki Vasileia I , Surma Michal A. , Simons Kai , Chavakis Triantafyllos , Klose Christian , Coskun Ünal 
Published: November 2018

AbstractShotgun lipidomics enables an extensive analysis of lipids from tissues and fluids. Each specimen requires appropriate extraction and processing procedures to ensure good coverage and reproducible quantification of the lipidome. Adipose tissue (AT) has become a research focus with regard to its involvement in obesity-related pathologies. However, the quantification of the AT lipidome is particularly challenging due to the predominance of triacylglycerides, which elicit high ion suppression of the remaining lipid classes. We present a new and validated method for shotgun lipidomics of AT, which tailors the lipid extraction procedure to the target specimen and features high reproducibility with a linear dynamic range of at least 4 orders of magnitude for all lipid classes. Utilizing this method, we observed tissue-specific and diet-related differences in three AT types (brown, gonadal, inguinal subcutaneous) from lean and obese mice. Brown AT exhibited a distinct lipidomic profile with the greatest lipid class diversity and responded to high-fat diet by altering its lipid composition, which shifted towards that of white AT. Moreover, diet-induced obesity promoted an overall remodelling of the lipidome, where all three AT types featured a significant increase in longer and more unsaturated triacylglyceride and phospholipid species.The here presented method facilitates reproducible systematic lipidomic profiling of AT and could be integrated with further –omics approaches used in (pre-)clinical research, in order to advance the understanding of the molecular metabolic dynamics involved in the pathogenesis of obesity-associated disorders.
The AGC protein kinase UNICORN controls planar growth by attenuating PDK1 inArabidopsis thaliana
Authors: Scholz Sebastian , Pleßmann Janys , Hüttl Regina , Wassmer Katrin , Enugutti Balaji , Schneitz Kay 
Published: November 2018

AbstractTissue morphogenesis critically depends on the coordination of cellular growth patterns. In plants, many organs consist of clonally distinct cell layers, such as the epidermis, whose cells undergo divisions that are oriented along the plane of the layer. The developmental control of such planar growth is poorly understood. We have previously identified the Arabidopsis AGCVIII-class protein kinase UNICORN (UCN) as a central regulator of this process. Plants lackingUCNactivity show spontaneous formation of ectopic multicellular protrusions in integuments and malformed petals indicating thatUCNsuppresses uncontrolled growth in those tissues. In the current model UCN regulates planar growth of integuments in part by directly repressing the putative transcription factor ABERRANT TESTA SHAPE (ATS). Here we report on the identification of3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1(PDK1) as a novel factor involved inUCN-mediated growth control. PDK1 constitutes a basic component of signaling mediated by AGC protein kinases throughout eukaryotes. ArabidopsisPDK1is implied in stress responses and growth promotion. Here we show that loss-of-function mutations inPDK1suppress aberrant growth in integuments and petals ofucnmutants. Additional genetic, in vitro, and cell biological data support the view that UCN functions by repressing PDK1. Furthermore, our data indicate thatPDK1is indirectly required for deregulated growth caused byATSoverexpression. Our findings support a model proposing that UCN suppresses ectopic growth in integuments through two independent processes: the attenuation of the protein kinase PDK1 in the cytoplasm and the repression of the transcription factor ATS in the nucleus.Author SummaryPlant organs, such as petals or roots, are composites of distinct cell layers. As a rule, cells making up a layer, for example the epidermis, the outermost layer of a tissue, divide “within the plane” of the layer. This cellular behavior results in the two-dimensional sheet-like or planar growth of the cell layer. The mechanism orchestrating such a growth pattern is poorly understood. In particular, it is unclear how uncontrolled and “out-of-plane” growth is avoided. Here we provide insight into this process. Our data indicate that higher than normal activity of a central regulator of growth and stress responses results in wavy and malformed petals and in protrusion-like aberrant outgrowths in the tissue that will develop into the seed coat. It is therefore important to keep this factor in check to allow proper formation of those tissues. We further show that a protein called UNICORN attenuates the activity of this regulator thereby ensuring the sheet-like growth of young petals or the developing seed coat.
Neural distinctiveness declines with age in auditory cortex and is associated with auditory GABA levels
Authors: Lalwani Poortata , Gagnon Holly , Cassady Kaitlin , Simmonite Molly , Peltier Scott , Seidler Rachael D. , Taylor Stephan F. , Weissman Daniel H. , Polk Thad A. 
Published: November 2018

AbstractNeural activation patterns in the ventral visual cortex in response to different categories of visual stimuli (e.g., faces vs. houses) are less selective, or distinctive, in older adults than in younger adults, a phenomenon known as age-related neural dedifferentiation. Previous work in animals suggests that age-related reductions of the inhibitory neurotransmitter, gamma aminobutyric acid (GABA), may play a role in this age-related decline in neural distinctiveness. In this study, we investigated whether neural dedifferentiation extends to auditory cortex and whether individual differences in GABA are associated with individual differences in neural distinctiveness in humans. 20 healthy young adults (ages 18-29) and 23 healthy older adults (over 65) completed a functional magnetic resonance imaging (fMRI) scan, during which neural activity was estimated while they listened to foreign speech and music. GABA levels in the auditory, ventrovisual and sensorimotor cortex were estimated in the same individuals in a separate magnetic resonance spectroscopy (MRS) scan. Relative to the younger adults, the older adults exhibited both (1) less distinct activation patterns for music vs. speech stimuli and (2) lower GABA levels in the auditory cortex. Also, individual differences in auditory GABA levels (but not ventrovisual or sensorimotor GABA levels) predicted individual differences in neural distinctiveness in the auditory cortex in the older adults. These results demonstrate that age-related neural dedifferentiation extends to the auditory cortex and suggest that declining GABA levels may play a role in neural dedifferentiation in older adults.Significance StatementPrior work has revealed age-related neural dedifferentiation in the visual cortex. GABA levels also decline with age in several parts of the human cortex. Here, we report that these two age-related changes are linked; neural dedifferentiation is associated with lower GABA levels in older adults. We also show that age-related neural dedifferentiation extends to auditory cortex, suggesting that it may be a general feature of the aging brain. These findings provide novel insights into the neurochemical basis of age-related neural dedifferentiation in humans and also offer a potential new avenue for investigating age-related declines in central auditory processing.
The lipid phosphatase-like protein PLPPR1 increases cell adhesion by modulating RhoA/Rac1 activity
Authors: Iweka Chinyere Agbaegbu , Tilve Sharada , Mencio Caitlin , Katagiri Yasuhiro , Geller Herbert M 
Published: November 2018

ABSTRACTPhospholipid Phosphatase-Related Protein Type 1 (PLPPR1) is a member of a family of lipid phosphatase related proteins, integral membrane proteins characterized by six transmembrane domains. PLPPR1 is enriched in the brain and recent data indicate potential pleiotropic functions in several different contexts. An inherent ability of PLPPR1 is to induce membrane protrusions, and we have previously reported that members within this family may act in concert. However, the mechanism by which PLPPR1 produces these actions is not yet understood. Here, we report that exogenous expression of PLPPR1 reduces cell motility and increases cell adhesion to the ECM substrate by altering cytoskeletal dynamics and modulating RhoA and Rac1 activity through association with RhoGDI. This signaling also allows overexpression of PLPPR1 to overcome the inhibitory activity of CSPGs and LPA on neurites. Together, these results establish a novel signaling pathway for the PLPPR1 protein.SUMMARYPLPPR1 increases cell adhesion and decreases cell motility by modulating RhoA and Rac1 activation through its association with RhoGDI.
Eating habits of Polish university students depending on the direction of studies and gender
Authors: Kowalska Anna Sylwia , Tarnowska Agnieszka 
Published: November 2018

Purpose
The purpose of this paper is to evaluate the eating habits of students in the field of management and engineering of food products compared to students from faculties not related to food science. Furthermore, another aim is to conduct gender-wise assessment to determine the type of eating habit, i.e., careful or binge eating.

Design/methodology/approach
The research involved 400 students from all years of study. The survey was conducted in 2017–2018 and the selection of the sample was intentional. The research used a questionnaire form. Additionally, χ2 test was performed to assess the statistical independence of characteristics.

Findings
It is found that most students who pledge proper nutrition are women. The majority of respondents ate 3–4 meals in day and regular consumption of breakfast was declared among 42 percent of respondents. The consumption of sweet snacks between meals is reaffirmed by the half of the respondents. Students of the food sciences more often than others believed that they eat healthier and more regularly, although students of non-food directions most often declared intake of five or more meals a day.

Research limitations/implications
An important limitation of the conducted study is a relatively small research sample. It consisted of university students from one of the largest academic centers in Poland. The results cannot be generalized to all students in this country. In the future, a similar survey should be conducted on a larger scale and cover all similar fields of management and engineering of food products in Poland. In addition, it would be worth expanding the research and examine graduates who found employment in the food industry.

Practical implications
The results of the conducted research are a good source of information on the differences in the way of feeding studying women and men. While such studies are not very revealing, the comparison between students in food and non-food fields can be considered a novelty. The described results can be used by the students themselves, but above all, by the authorities of universities conducting food science programs.

Social implications
The students do not eat properly which can lead to nutritional deficiencies and can deteriorate mental and physical endurance damaging overall health.

Originality/value
The described research is important due to the observed deteriorating eating habits and growing overweight of young adults in developed countries like Poland. They show that education of food technologists, even at the academic level, does not always allow to avoid mistakes in their own nutrition.