bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic diversity and population structure of Gerbera delavayi Franch. revealed by newly developed genic-SSR markers
Authors: Zheng Wei , Xu Xiaodan 
Published: January 2018

Background: Gerbera delavayi Franch., a perennial herb native to southwest China, is of important and special value in textile and culture. Its abaxial leaves have a layer of soft fibers, which can be manually peeled, twisted into a yarn, and applied in textiles for hand-made clothes. The particular craftsmanship, unique all over the world, is a part of the intangible cultural heritage in Yunnan and Sichuan Province. To date, the wild species has become endangered because its leaves are excessively harvested for textile applications. Estimating the genetic variation of plant species is crucial for plant conservation and breeding. So, the aim of this study was to (1) provide an accurate outline of the genetic diversity and population structure of G. delavayi and (2) propose targeted conservation strategies for these wild resources.
Methods: Simple sequence repeats (SSR) markers were developed from the G. delavayi transcriptome for its genetic analysis. A total of 5,179 genic-SSR markers were identified and 350 primer pairs were selected for PCR validation. After primary screening , 19 polymorphic and neutral primer pairs were used to analyze the genetic diversity and population structure of nine wild fireweed populations (a total of 204 individuals) collected from Southwest China.
Results: Moderate genetic diversity (allelic richness (Ar)=3.436, Shannon’s information index (I)=0.789 , observed heterozygosity (Ho)=0.304 , and expected heterozygosity (He)=0.415) and moderate differentiation (FST=0.110, P=0.000) were found among nine populations. The lowest genetic diversity (Ar=2.351, I=0.497, Ho=0.178, and He=0.284) and highest inbreeding (inbreeding coefficient (FIS)=0.365) were both detected within the isolated population PE. Furthermore, high genetic differentiation, limited gene flow, and clear genetic barrier were detected between PE and other populations, showing the significant effects of habitat fragmentation on the genetic differentiation of these G. delavayi populations.
Conclusions: Our results showed that human overexploitation has led to moderate genetic diversity in G.delavayi populations. Furthermore, habitat fragmentation has resulted in clear genetic barrier and high differentiation between the isolated and concentrated populations. Upon the genetic features of wild G. delavayi populations, we proposed several strategies for protecting and utilizing the current wild resources.
Is there a connection between peptide bond geometry and aminoacid residue conformational preferences?
Authors: Balasco Nicole , Esposito Luciana , Vitagliano Luigi 
Published: January 2018

The definition of the structural basis of the conformational preferences of the genetically encoded aminoacid residues is crucial to decipher the physical code of protein folding and would have a huge impact on our understanding of protein structure and function. Indeed, although a large number of computational and experimental investigations have highlighted that the different protein residues show distinct conformational propensities, none of the current hypotheses is able to satisfactorily explain these preferences. In the last decades, we and others have clearly demonstrated that several geometrical parameters of protein backbone (bond angles, peptide bond distortions from planarity, and pyramidalization of the carbonyl carbon atom) are heavily dependent on the local conformation (φ/ψ dihedral angles) [1-8]. Moreover, a correlation between bond distances such as CO and CN has been detected in ultrahigh resolution protein structures [9]. Concerning bond angles, most of these investigations have been focused on the NCαC (τ) angle, shown to be significantly affected by both φ/ψ dihedral angles. In this framework, we here evaluated the impact of the local geometry on the residues conformational preferences by performing statistical analyses on a dataset of non-redundant protein chains selected from the Protein data Bank (PDB). Our data highlight a clear link between residue conformational preferences and local geometry.

References

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Exposure to dense bacteria lawns does not cause the social amoeba Dictyostelium discoideum to carry bacteria through the social stage
Authors: Brock Debra A , Canas Alicia , Jones Kai , Queller David C , Strassmann Joan E 
Published: January 2018

Background. Interactions between eukaryotic amoebae and bacteria are understudied and important. Bacteria inside of amoebae are protected from external forces including antibiotics. An excellent model for bacteria-amoeba interactions is the social amoeba Dictyostelium discoideum and its associated bacteria. A third of wild-collected clones of the soil-dwelling amoeba Dictyostelium discoideum exhibit a suite of characteristics that make them simple farmers of bacteria. They carry bacteria internally through the social spore-making stage. They then release these bacteria to grow and subsequently eat them, prudently stopping before they are entirely consumed so some bacteria can be carried to the next generation. D. discoideum defend their food bacteria with other inedible bacteria that produce compounds toxic to non-farmers. Both carried bacteria and social amoeba hosts have demonstrated co-evolved characteristics. Most farmer clones discovered to date carry inedible Burkholderia in addition to food bacteria, but it is not clear whether or not a preponderance of naïve bacteria might induce the farming state by overwhelming the phagocytic actions of the host amoebae. In this study we address this question with D. discoideum clones that naturally carry bacteria and those that do not. Will naïve bacteria in large numbers succeed in colonizing the amoebae?
Methods. We grew five non-farmer clones and five farmer clones of wild-collected Dictyostelium discoideum on three different concentrations of a highly palatable bacterial food source, Klebsiella pneumoniae. We then tested them to see if they carried bacteria through the social stage.
Results. We found that bacterial density did not have a significant effect on whether or not the clones carried bacteria through the social stage. Even those grown in very dense bacterial cultures were able to shed them successfully unless they were also carrying Burkholderia.
Discussion. Our results indicate that even a preponderance of food bacteria cannot overwhelm the ability of social amoebae to digest and not carry bacteria. Apparently, only the inedible Burkholderia have that effect. This points to the importance of understanding co-infection with multiple bacteria because those that cannot induce carriage can nevertheless become carried, foiling digestive processes, but only in the presence of another bacterium. Future studies of host bacteria interactions should consider using multiple bacteria simultaneously.
­Isochoric refrigeration of food products
Authors: Lyu Chenang , Nastase Gabriel , Ukpai Gideon , Serban Alexandru , Rubinsky Boris 
Published: January 2018

Background: Food preservation is essential to the growing world population, food economy. Freezing is a commonly used method for food preservation. While extending the life of the product, freezing has detrimental effects. It is causing loss of food weight and is causing changes in food quality, e.g. enzymatic browning.
Method: Freezing of food is usually done under constant atmospheric pressure (isobaric). We have developed a new technology in which biological materials are preserved at subfreezing temperatures in an isochoric (constant volume) system. Experiments were performed with a food product, potato, in a thermodynamic isochoric device designed by us, that is robust and has no moving parts.
Results: We have shown that under similar storage conditions, freezing to -5°C, the isochoric preserved potato experienced no weight loss and limited enzymatic browning. In contrast the -5°C isobaric frozen potato experienced substantial weight loss and substantial enzymatic browning. Microscopic analysis, shows that the mechanism responsible for the different results is related to the integrity of the cell and the cell membrane, which are maintain during freezing in the isochoric system and lost during freezing in the isobaric system.
Discussion: The main mechanism of cell damage during isobaric freezing are the increase in extracellular osmolality and the mechanical damage by ice crystals. In contrast, during isochoric freezing the cells in the preserved material are under conditions in which the intracellular osmolality is comparable to the extracellular osmolality and they are not affected by ice mechanical damage. The conditions during isochoric freezing result in improved quality of the preserved food products.
Conclusion: We have shown that the quality of food products preserved by isochoric freezing is better than the quality of food preserved to the same temperature in isobaric conditions. This is only a preliminary study on isochoric preservation of food. However, it illustrates the potential of the technology.
Isolation and characterization of a new cell line of retinoblastoma
Authors: Ghasemi Fariba , Heidari Keshel Saeed , Mirakhorli Mojgan , Roozafzoon Reza , Rajabi Mohammad Taher , Tabatabaie Seid Zia , Farzanfar Farideh , Khoshzaban Ahad , Asadi-Amoli Fahimeh 
Published: January 2018

BACKGROUNDː This article describes the characterization of a new cell line (IRB-1), which was established from an Iranian child with retinoblastoma.
METHODSː Using cell culture techniques, we isolated a clonal population from primary Cultures of retinoblastoma tumor samples and after several passages an established cell line, IRB-1, was obtained. The following techniques were performed: cell proliferation studies by MTT assays, scanning electron microscopy, cell surface analyses by flowcytometry, creation of neurospheres in soft agar and the expression of ABCG2, RAR-α, GFAP, and ACTB genes by real time PCR.
RESULTSː Of total 6 received samples, only a single cell line was successfully isolatedfrom a group E sporadic unilateral retinoblastoma. The primarily enucleated left eye had a differentiated retinoblastoma, with a slight degree of necrosis in pathology report. The adherent cultured cells were in spindle-shaped morphology with similar appendages and pulled neurons. Doubling time is 36 ± 5 hours. After 30 days, the effect of retinoic acid on isolated cells and expression of RAR-α receptor was appeared. Chromosomal abnormalities in chromosomes 3, 9, 10, 11, 14, 16, 17, and 22 were observed. Specific gene expression of ABCG2, RAR-α, and ACTB gene expression of GFAP positive expression of these genes in the control cells were observed. This cell line passaged 132 consecutive times.
Discussionː IRB-1 is a novel human adherent RB cell line, which with interesting characteristics of adherent and flocculent growth and more chromosomal imbalances different from other RB cell lines. A novel human RB cell line, IRB-1, was established from a 1-year old patient with a unilateral sporadic RB at Farabi Hospital- Tehran University Medical Sciences. The cultural characteristics of IRB-1 cell line were comparable to those of Y79 in characteristic.
The hidden anatomy of paranasal sinuses reveals biogeographically distinct morphotypes in the nine-banded armadillos (Dasypus novemcinctus)
Authors: Billet Guillaume , Hautier Lionel , de Thoisy Benoit , Delsuc Frédéric 
Published: January 2018

Background. With their Pan-American distribution, long-nosed armadillos (genus Dasypus) constitute an understudied model for Neotropical biogeography. This genus currently comprises seven recognized species, the nine-banded armadillo (D. novemcinctus) having the widest distribution ranging from Northern Argentina to the South-Eastern US. With their broad diversity of habitats, nine-banded armadillos provide a useful model to explore the effects of climatic and biogeographic events on morphological diversity at a continental scale.
Methods. Based on a sample of 136 skulls of Dasypus spp., including 112 specimens identified as D. novemcinctus, we studied the diversity and pattern of variation of internal paranasal cavities, which were reconstructed virtually using µCT-scanning or observed through bone transparency.
Results. Our qualitative analyses of paranasal sinuses and recesses successfully retrieved a taxonomic differentiation between the traditional species D. kappleri, D. pilosus and D. novemcinctus but failed to recover diagnostic features between the disputed and morphologically similar D. septemcinctus and D. hybridus. Most interestingly, the high variation detected in our large sample of D. novemcinctus showed a clear geographical patterning, with the recognition of three well-separated morphotypes: one ranging from North and Central America and parts of northern South America west of the Andes, one distributed across the Amazonian Basin and central South America, and one restricted to the Guiana Shield.
Discussion. The question as to whether these paranasal morphotypes may represent previously unrecognized species is to be evaluated through a thorough revision of the Dasypus species complex integrating molecular and morphological data. Remarkably, our recognition of a distinct morphotype in the Guiana Shield area is congruent with the recent discovery of a divergent mitogenomic lineage in French Guiana. The inflation of the second medialmost pair of caudal frontal sinuses constitutes an unexpected morphological diagnostic feature for this potentially distinct species. Our results demonstrate the benefits of studying overlooked internal morphological structures in supposedly cryptic species revealed by molecular data. It also illustrates the under-exploited potential of the highly variable paranasal sinuses of armadillos for systematic studies.
Evaluation of a multi-institution mastoidectomy performance instrument
Authors: Kerwin Thomas , Hittle Brad , Stredney Don , De Boeck Paul , Wiet Gregory 
Published: January 2018

Objective: The objective of this work is to obtain validity evidence for an evaluation instrument used to assess the performance level of a mastoidectomy. The instrument has been previously described and had been formulated by a multi-institutional consortium.
Design: Mastoidectomies were performed on a virtual temporal bone system and then rated by experts using a previously described 15 element task-based checklist. Based on the results, a second, similar checklist was created and a second round of rating was performed.
Setting: Twelve otolaryngological surgical training programs in the United States. Participants 66 individuals with a variety of temporal bone dissection experience, from medical students to attending physicians. Raters were attending surgeons from 12 different institutions.
Results: Intraclass correlation (ICC) scores varied greatly between items in the checklist with some being low and some being high. Percentage agreement scores were similar to previous rating instruments. There is strong evidence that a high score on the task- based checklist is necessary for a rater to consider a mastoidectomy to be performed at the level of an expert but a high score is not a sufficient condition.
Conclusions: Rewording of the instrument items to focus on safety does not result in increased reliability of the instrument. The strong result of the Necessary Condition Analysis suggests that going beyond simple correlation measures can give extra insight into grading results. Additionally, we suggest using a multiple point scale instead of a binary pass/fail question combined with descriptive mastery levels.
How do we transition from non-coding to coding?
Authors: Ruiz-Orera Jorge , Villanueva-Cañas José Luis , Blevins William , Albà M.Mar 
Published: January 2018

Recent years have witnessed the discovery of protein–coding genes which appear to have evolved de novo from previously non-coding sequences. This has changed the long-standing view that coding sequences can only evolve from other coding sequences. However, there are still many open questions regarding how new protein-coding sequences can arise from non-genic DNA.
Two prerequisites for the birth of a new functional protein-coding gene are that the corresponding DNA fragment is transcribed and that it is also translated. Transcription is known to be pervasive in the genome, producing a large number of transcripts that do not correspond to conserved protein-coding genes, and which are usually annotated as long non-coding RNAs (lncRNA). Recently, sequencing of ribosome protected fragments (Ribo-Seq) has provided evidence that many of these transcripts actually translate small proteins. We have used mouse non-synonymous and synonymous variation data to estimate the strength of purifying selection acting on the translated open reading frames (ORFs). Whereas a subset of the lncRNAs are likely to actually be true protein-coding genes (and thus previously misclassified), the bulk of lncRNAs code for proteins which show variation patterns consistent with neutral evolution. We also show that the ORFs that have a more favorable, coding-like, sequence composition are more likely to be translated than other ORFs in lncRNAs. This study provides strong evidence that there is a large and ever-changing reservoir of lowly abundant proteins; some of these peptides may become useful and act as seeds for de novo gene evolution.
Cellobiohydrolase B of Aspergillus niger over-expressed in Pichia pastoris stimulates hydrolysis of oil palm empty fruit bunches
Authors: Woon James Sy-Keen , Mackeen Mukram M , Illias Rosli M , Mahadi Nor M , Broughton William J , Abdul Murad Abdul Munir , Abu Bakar Farah Diba 
Published: January 2018

Background. Aspergillus niger along with many other lignocellulolytic fungi, has been widely used as a commercial workhorse for cellulase production. A fungal cellulase system generally includes three major classes of enzymes i.e. β-glucosidases, endoglucanases and cellobiohydrolases. Cellobiohydrolases (CBH) are vital to the degradation of crystalline cellulose present in lignocellulosic biomass. However, A. niger naturally secretes low levels of CBH. Hence, recombinant production of A. niger CBH is desirable to increase CBH production yield and also to allow biochemical characterisation of the recombinant CBH from A. niger.
Methods. In this study, the gene encoding a cellobiohydrolase B (cbhB) from A. niger ATCC 10574 was cloned and expressed in the methylotrophic yeast Pichia pastoris X-33. The recombinant CbhB was purified and characterised to study its biochemical and kinetic characteristics. To evaluate the potential of CbhB in assisting biomass conversion, CbhB was supplemented into a commercial cellulase preparation (Cellic® CTec2) and was used to hydrolyse oil palm empty fruit bunch (OPEFB), one of the most abundant lignocellulosic waste from the palm oil industry. To attain maximum saccharification, enzyme loadings were optimised by response surface methodology and the optimum point was validated experimentally. Hydrolysed OPEFB samples were analysed using attenuated total reflectance FTIR spectroscopy (ATR-FTIR) to screen for any compositional changes upon enzymatic treatment.
Results. Recombinant CbhB was over-expressed as a hyperglycosylated protein attached to N-glycans. CbhB was enzymatically active towards soluble substrates such as 4-methylumbelliferyl-β-D-cellobioside (MUC), p-nitrophenyl-cellobioside (pNPC) and p-nitrophenyl-cellobiotrioside (pNPG3) but was not active towards crystalline substrates like Avicel® and Sigmacell cellulose. Characterisation of purified CbhB using MUC as the model substrate revealed that optimum catalysis occurred at 50 oC and pH 4 but the enzyme was stable between pH 3 to 10 and 30 to 80 oC. Although CbhB on its own was unable to digest crystalline substrates, supplementation of CbhB (0.37%) with Cellic® CTec2 (30%) increased saccharification of OPEFB by 27%. Compositional analyses of the treated OPEFB samples revealed that CbhB complementation reduced peak intensities of both crystalline cellulose Iα and Iβ in the treated OPEFB samples.
Discussion. Since CbhB alone was inactive against crystalline cellulose, these data suggested that it might work synergistically with other components of Cellic® CTec2. CbhB supplements were desirable as they further increased hydrolysis of OPEFB when the performance of Cellic® CTec2 was theoretically capped at an enzyme loading of 34% in this study. Hence, A. niger CbhB was identified as a potential supplementary enzyme for the enzymatic hydrolysis of OPEFB.
Preventive effects of salvia officinalis leaf extract on insulin resistance and inflammation, in high fat diet-induced-obesity mice model
Authors: Ben Khedher Mohamed Raafet , Hammami Mohamed , Arch Jonathan Robert , Hislop David Christopher , Eze Dominic Anthony , Wargent Edward Taynton , Kępczyńska Małgorzata Anna , Zaibi Mohamed Sghaier 
Published: January 2018

Background: Salvia officinalis (sage) is a native plant to the Mediterranean region and has been used for a long time in traditional medicine for various diseases. We investigated possible anti-diabetic, anti-inflammatory and anti-obesity effects of sage methanol (MetOH) extract in a nutritional mouse model of obesity, inflammation and insulin resistance, as well as its effects on lipolysis and lipogenesis in 3T3-L1 cells.
Methods: Diet-induced obese (DIO) mice were treated for 5 weeks with sage methanol extract (100 and 400 mg.kg -1 /day. bid), or rosiglitazone (3 mg.kg -1 /day. bid), as a positive control. Energy expenditure, food intake, body weight, fat mass, liver glycogen and lipid content were evaluated. Blood glucose, and plasma levels of insulin, lipids leptin and pro- and anti-inflammatory cytokines were measured throughout the experiment. The effects of sage MetOH extract on lipolysis and lipogenesis were tested in vitro in 3T3-L1 cells.
Results: After two weeks of treatment, the lower dose of sage MetOH extract decreased blood glucose and plasma insulin levels during an oral glucose tolerance test (OGTT). An insulin tolerance test (ITT), performed at day 29 confirmed that sage improved insulin sensitivity. Groups treated with low dose sage and rosiglitazone showed very similar effects on OGTT and ITT. Sage also improved HOMA-IR, triglycerides and NEFA. Treatment with the low dose increased the plasma levels of the anti-inflammatory cytokines IL-2, IL-4 and IL-10 and reduced the plasma level of the pro-inflammatory cytokines IL-12, TNF-α, and KC/GRO. The GC analysis revealed the presence of two PPARs agonist in sage MetOH extract. In vitro, the extract reduced in a dose-related manner the accumulation of lipid droplets; however no effect on lipolysis was observed.
Conclusions: Sage MetOH extract at low dose exhibits similar effects to rosiglitazone. It improves insulin sensitivity, inhibits lipogenesis in adipocytes and reduces inflammation as judged by plasma cytokines. Sage presents an alternative to pharmaceuticals for the treatment of diabetes and associated inflammation.