bluuebunny/crossref_metadata_2025 huggingface dataset:
Lectins: an effective tool for screening of potential cancer biomarkers
Authors: Hashim Onn Haji , Jayapalan Jaime Jacqueline , Lee Cheng-Siang
Published: January 2018

In recent years, the use of lectins for screening of potential biomarkers has gained increased importance in cancer research, given the development in glycobiology that highlights altered structural changes of glycans in cancer associated processes. Lectins, having the properties of recognizing specific carbohydrate moieties of glycoconjugates, have become an effective tool for detection of new cancer biomarkers in complex bodily fluids and tissues. The specificity of lectins provides an added advantage of selecting peptides that are differently glycosylated and aberrantly expressed in cancer patients, many of which are not possibly detected using conventional methods because of their low abundance in bodily fluids. When coupled with mass spectrometry, research utilizing lectins, which are mainly from plants and fungi, has led to identification of numerous potential cancer biomarkers that may be used in the future. This article reviews lectin-based methods that are commonly adopted in cancer biomarker discovery research.
Short COI markers for freshwater macroinvertebrate metabarcoding
Authors: Vamos Ecaterina Edith , Elbrecht Vasco , Leese Florian
Published: January 2018

Species diversity of metazoan bulk samples can be rapidly assessed using Cytochrome c oxidase I (COI) metabarcoding. However, in cases where only degraded DNA is available, e.g. from poorly conserved museum specimens, eDNA filtered from water or gut content analyses, universal primer sets that amplify only a short COI fragment are advantageous. Using PrimerMiner, we optimised two universal primer sets targeting freshwater macroinvertebrates based on NCBI and BOLD reference sequences. The fwh1 and fwh2 primer sets targeting a 178 and 205 bp region were tested in vivo by sequencing previously used freshwater macroinvertebrate mock communities of known composition and three monitoring samples from Romanian streams. They were further evaluated in silico for their suitability to amplify other insect groups. The fwh1 primer sets showed the most consistent amplification in silico and in vivo , detecting 92% of the taxa present in the mock communities, and allowing clear differentiation between the three macroinvertebrate communities from the Romanian streams. In silico analysis indicates that the short primers are likely to perform well even for non-freshwater insects. Comparing the performance of the new fwh1 primer sets to a highly degenerate primer set targeting a longer fragment (BF2/BR2) revealed that efficiency is slightly lower for the new primer set. Nevertheless, the shorter new primer pairs might be useful for studies that have to rely on degraded or poorly conserved DNA and thus be of importance for biomonitoring, conservation biological or molecular ecological studies. Furthermore, our study highlights the need for in silico evaluation of primer sets in order to detect design errors in primers (fwhR2) and find optimal universal primer sets for the target taxa of interest.
Diversity of cultivated aerobic poly-hydrolytic bacteria in saline alkaline soils
Authors: Sorokin Dmitry Y. , Kolganova Tatiana V. , Khijniak Tatiana V. , Jones Brian E. , Kublanov Ilya V.
Published: January 2018

Alkaline saline soils known also as “soda solonchaks” represent a natural soda habitat which differed from soda lake sediments by higher aeration and lower humidity. The microbiology of soda soils, in contrast to the more intensively studied soda lakes, remains poorly explored. In this work we present information on the diversity of culturable aerobic haloalkalitolerant bacteria with various hydrolytic activities from soda soils at different locations in Central Asia and Africa. In total, 180 isolates were obtained by using media with various polymers at pH 10 and 0.6 M total Na+. According to the 16S rRNA gene sequences analysis, most of the isolates belonged to Firmicutes and Actinobacteria. Most isolates possessed multiple hydrolytic activities, including endoglucanase, xylanase, amylase and protease. The pH profiling of selected representatives of actinobacteria and endospore-forming bacteria showed, that the former were facultative alkaliphiles, while the latter were mostly obligate alkaliphiles. The hydrolases of both groups were active at a broad pH range from 6 to 11. Overall, this work demonstrated the presence of a rich hydrolytic bacterial community in soda soils which might be explored further for production of haloalkalistable hydrolases.
The role of self-incompatibility systems in the prevention of bi-parental inbreeding
Authors: Furstenau Tara N , Cartwright Reed A
Published: January 2018

Hermaphroditic plants experience inbreeding through both self-fertilization and bi-parental inbreeding. Therefore, many plant species have evolved either heteromorphic (morphology-based) or homomorphic (molecular-based) self-incompatibility (SI) systems. These SI systems limit extreme inbreeding through self-fertilization and, in the case of homomorphic SI systems, have the potential to limit bi-parental inbreeding, which is common when dispersal is restricted to a local region. Homomorphic SI species are prevalent across the angiosperms, and it is often assumed that the potential to reduce bi-parental inbreeding may be a factor in their success. To test this assumption, we developed a spatially-explicit, individual-based simulation of plant populations with either heteromorphic SI or one of three different types of homomorphic SI. In our simulations, we varied dispersal distance and the presence of inbreeding depression. We found that autozygosity in the homomorphic SI populations was significantly lower than in the heteromorphic SI populations and that this reduction was due to bi-parental inbreeding avoidance. As expected, the differences between the homomorphic and heteromorphic SI populations were more pronounced when seed and pollen dispersal was limited. However, levels of homozygosity and inbreeding depression between these plant populations were not different. At low dispersal, homomorphic SI populations also suffered reduced female fecundity and had smaller census population sizes. Our results suggest that bi-parental inbreeding avoidance was unlikely to be a major driver in the evolution of homomorphic SI systems.
The evolution of aminoacyl-tRNA synthetases in chromerids
Authors: Sharaf Abdoallah , Jiroutová Kateřina , Obornik Miroslav
Published: January 2018

Aminoacyl-tRNA synthetases (aaRS) are enzymes that catalyze the ligation of tRNAs to their cognate amino acids. There are aaRSs specific to each of the 20 standard amino acids. These enzymes are divided into two classes, class I and class II, which are unrelated in both sequence and structure. aaRSs can function in multiple sub-cellular compartments due to the phenomenon of dual targeting. We searched the total predicted proteins of Chromera velia and Vitrella brassicaformis for aaRSs proteins. Phylogenetic analyses of all available 21 aaRSs sequences were performed using maximum likelihood and Bayesian inference. Computer predictions of the intracellular location of the identified enzymes were performed to test the multiple targeting hypothesis. Fifty genes encoding aaRS were identified in C. velia, while only 38 aaRSs were found in V. brassicaformis. Forty-five percent of C. velia’s aaRss are encoded by three distinct loci, whereas 35% of aaRSs are encoded by two distinct loci. Interestingly, both tryRS and trpRS are encoded by only one locus and valRS is encoded by five loci. In contrast, 70% of the V. brassicaformis aaRSs are encoded by just two distinct loci. Most of the molecular phylogenies of aaRSs indicate that for each aaRS the evolutionary pattern is different and eukaryotic genes are usually retained. Targeting predictions show that particular enzymes are not often used in the compartments where they originate.
Fungi found in Mediterranean and North Sea sponges: How specific are they?
Authors: Naim Mohd Azrul , Smidt Hauke , Sipkema Detmer
Published: January 2018

Fungi and other eukaryotes represent one of the last frontiers of microbial diversity in the sponge holobiont. In this study we employed pyrosequencing of 18S ribosomal RNA gene amplicons containing the V7 and V8 hypervariable regions to explore the fungal diversity of seven sponge species from the North Sea and the Mediterranean Sea. For most sponges, fungi were present at a low relative abundance averaging 0.75% of the 18S rRNA gene reads. In total, 44 fungal OTUs (operational taxonomic units) were detected in sponges, and 28 of these OTUs were also found in seawater. Twenty-two of the sponge-associated OTUs were identified as yeasts (mainly Malasseziales), representing 84% of the fungal reads. Several OTUs were related to fungal sequences previously retrieved from other sponges, but all OTUs were also related to fungi from other biological sources, such as seawater, sediments, lakes and anaerobic digesters. Therefore our data, supported by currently available data, point into the direction of mostly accidental presence of fungi in sponges and do not support the existence of a sponge-specific fungal community.
Cancer spatial evolution in a changing microenvironment
Authors: Jiang Xiaowei , Tomlinson Ian PM
Published: January 2018

Cancer development as an ecological and evolutionary process is poorly understood, which includes early cancer evolution, malignancy and metastasis. It was hypothesised that the tumour microenvironment (TME) plays a critical role in this process. Unfortunately, in most cancer modelling studies the TME is ignored or considered static and different cancers are often studied in isolation. There is a lack of a general theory of cancer adaptive evolution (CAE). Here I establish a genetic and phenotypic model of cancer three-dimensional (3D) spatial evolution in a changing TME. With 3D individual-based simulations I show how cancer cells adapt to diverse changing TME conditions and selection intensities. I am able to capture key histological characteristics of various cancer forms including complex dynamics of spatial-temporal heterogeneity of subclonal fitness and subclonal mixing, ball-like and non-ball-like subclonal structures. Moreover, I identify key evolutionary and phylogenetic patterns of CAE under various combinations of phenotypic, genetic, population genetic and changing TME conditions. I show classical drivers, mini drivers, Darwinian and neutral/nearly neutral evolution and cost of complexity. I demonstrate the importance of ecology in CAE. I show that there are fundamental differences in the mode of CAE when the TME is changing, which is the limiting factor of CAE. Finally, I discuss important implications for cancer evolution theories and cancer personalised medicine.
Arsenophonus and Sodalis replacements shape evolution of symbiosis in louse flies
Authors: Šochová Eva , Husník Filip , Nováková Eva , Halajian Ali , Hypša Václav
Published: January 2018

Symbiotic interactions between insects and bacteria are ubiquitous and form a continuum from loose facultative symbiosis to greatly intimate and stable obligate symbiosis. In blood-sucking insects living exclusively on vertebrate blood, obligate endosymbionts are essential for hosts and hypothesized to supplement B-vitamins and cofactors missing from their blood diet. The role and distribution of facultative endosymbionts and their evolutionary significance as seeds of obligate symbioses are much less understood. Here, using phylogenetic approaches, we focus on the Hippoboscidae phylogeny as well as the stability and dynamics of obligate symbioses within this bloodsucking group. In particular, we demonstrate a new potentially obligate lineage of Sodalis co-evolving with the Olfersini subclade of Hippoboscidae. We also show several likely facultative Sodalis lineages closely related to Sodalis praecaptivus (HS strain) and suggest repeated acquisition of novel symbionts from the environment. Similar to Sodalis, Arsenophonus endosymbionts also form both obligate endosymbiotic lineages co-evolving with their hosts (Ornithomyini and Ornithoica groups) as well as possibly facultative infections incongruent with the Hippoboscidae phylogeny. Finally, we reveal substantial diversity of Wolbachia strains detected in Hippoboscidae samples falling into three supergroups: A, B, and the most common F. Altogether, our results prove the associations between Hippoboscoidea and their symbiotic bacteria to undergo surprisingly dynamic, yet selective, evolutionary processes strongly shaped by repeated endosymbiont replacements. Interestingly, obligate symbionts only originate from two endosymbiont genera, Arsenophonus and Sodalis, suggesting that the host is either highly selective about its future obligate symbionts or that these two lineages are the most competitive when establishing symbioses in louse flies.
Single phase computed tomography is equivalent to dual phase method for localizing hyperfunctioning parathyroid glands in patients with primary hyperparathyroidism: A retrospective review
Authors: Moron Fanny , Delumpa Alfred , Chetta Justin , Guffey Danielle , Dunaway David
Published: January 2018

Objective: This study aims to compare the sensitivity of dual phase (non-contrast and arterial) versus single phase (arterial) CT for detection of hyper-functioning parathyroid glands in patients with primary hyperparathyroidism. Methods: The CT scans of thirty-two patients who have biochemical evidence of primary hyperparathyroidism, pathologically proven parathyroid adenomas, and pre-operative multiphase parathyroid imaging were evaluated retrospectively in order to compare the adequacy of single phase vs. dual phase CT scans for the detection of parathyroid adenomas. Results: The parathyroid adenomas were localized in 83% of cases on single arterial phase CT and 80% of cases on dual phase CT. The specificity for localization of parathyroid tumor was 96% for single phase CT and 97% for dual phase CT. The results were not significantly different (p=0.695). These results are similar to those found in the literature for multiphase CT of 55-94%. Conclusions: Our study supports the use of a single arterial phase CT for the detection of hyperfunctioning parathyroid adenomas. Advances in knowledge: A single arterial phase CT has similar sensitivity for localizing parathyroid adenomas as dual phase CT and significantly reduces radiation dose to the patient.
Examining publication bias – A simulation-based evaluation of statistical tests on publication bias
Authors: Schneck Andreas
Published: January 2018

Background

Publication bias is a form of scientific misconduct. It threatens the validity of research results and the credibility of science. Although several tests on publication bias exist, no in-depth evaluations are available that suggest which test to use for the specific research problem.

Methods

In the study at hand four tests on publication bias, Egger’s test (FAT), p-uniform, the test of excess significance (TES), as well as the caliper test, were evaluated in a Monte Carlo simulation. Two different types of publication bias, as well as its degree (0%, 50%, 100%), were simulated. The type of publication bias was defined either as file-drawer, meaning the repeated analysis of new datasets, or p-hacking, meaning the inclusion of covariates in order to obtain a significant result. In addition, the underlying effect (β = 0, 0.5, 1, 1.5), effect heterogeneity, and the number of observations in the simulated primary studies (N =100, 500), as well as in the number of observations for the publication bias tests (K =100, 1000), were varied.

Results

All tests evaluated were able to identify publication bias both in the file-drawer and p-hacking condition. The false positive rates were, with the exception of the 15%- and 20%-caliper test, unbiased. The FAT had the largest statistical power in the file-drawer conditions, whereas under p-hacking the TES was, except under effect heterogeneity, slightly better. The caliper test was, however, inferior to the other tests under effect homogeneity and had a decent statistical power only in conditions with 1000 primary studies.

Discussion

The FAT is recommended as a test for publication bias in standard meta-analyses with no or only small effect heterogeneity. If no clear direction of publication bias is suspected the TES is the first alternative to the FAT. The 5%-caliper tests is recommended under conditions of effect heterogeneity, which may be found if publication bias is examined in a discipline-wide setting when primary studies cover different research problems.
The urban heat island effect is closely related to cicada density in metropolitan Seoul
Authors: Nguyen Hoa Q. , Kim Yuseob , Jang Yikweon
Published: January 2018

Background. Cryptotympana atrata and Hyalessa fuscata are the most abundant cicada species in the Korean Peninsula, where their population densities are higher in urban areas than in rural ones. The urban heat island (UHI) effect, wherein human activities cause urban areas to be significantly warmer than surrounding rural areas, may underlie this difference. We predicted a positive relationship between the degrees of UHI in urban areas and population densities of C. atrata and H. fuscata.

Methods. To test this prediction, we examined cicada population densities in three groups: those of high and low UHI areas within metropolitan Seoul, and suburban areas. Enumeration surveys of cicada exuviae were conducted from July to August, 2015.

Results. C. atrata and H. fuscata constituted almost 30% and 70% of the cicada populations, respectively, collected across all sampling localities. No significant difference in species composition was observed, regardless of groups, but the densities of the two species were significantly higher in urban areas with high UHI than in other groups. Specifically, densities of C. atrata in high UHI areas were approximately seven and four times higher compared to those in low UHI and in suburban groups, respectively. The order of magnitude was greater in H. fuscata, where densities in high UHI group were respectively 22 and six times higher than those in low UHI and in suburban groups.

Discussion. These results suggest that the UHI effect may be closely linked to high cicada densities in metropolitan Seoul, although the underlying mechanism for this remains unclear.
Effect of tire leachate on the invasive mosquito Aedes albopictus and the native congener Aedes triseriatus
Authors: Villena Oswaldo , Terry Ivana , Iwata Kayoko , Landa Edward , LaDeau Shannon , Leisnham Paul
Published: January 2018

Discarded vehicle tire casings are an important artificial habitat for the developmental stages of numerous vector mosquitoes. Discarded vehicle tires degrade under ultraviolet light and leach numerous soluble metals (e.g., barium, cadmium, zinc) and organic substances (e.g., benzothiazole and its derivatives [BTs], polyaromatic hydrocarbons [PAHs]) that could affect mosquito larvae that inhabit the tire casing. This study examined the relationship between soluble zinc, a common marker of tire leachate, on mosquito densities in tire habitats in the field, and tested the effects of tire leachate on the survival and development of newly hatched Aedes albopictus and Aedes triseriatus larvae in a controlled laboratory dose-response experiment. In the field, zinc concentrations were as high as 7.26 mg/L in a single tire and averaged as high as 2.39 (SE±1.17) mg/L among tires at a single site. A. albopictus (37/42 tires, 81.1%) and A. triseriatus (23/42, 54.8%) were the most widespread mosquito species, co-occurred in over half (22/42, 52.4%) of all tires, and A. triseriatus was only collected without A. albopictus in one tire. A. triseriatus was more strongly negatively associated with zinc concentration than A. albopictus, and another common mosquito, C. pipiens, which was found in 17 tires. In the laboratory experiment, A. albopictus per capita rate of population change (l’) was over 1.0, indicating positive population growth, from 0 to 10,000 mg/L tire leachate, corresponding to 8.9 mg/L zinc concentration, but steeply declined to zero from 50,000 to 100,000 mg/L tire leachate (44.5-89.0 mg/L zinc). In contrast, A. triseriatus l’ declined at the lower concentration of 100 mg/L tire leachate (0.05 mg/L zinc), and was zero at 500, 10,000, 50,000 and 100,000 mg/L tire leachate. These results indicate that tire leachate can have severe negative effects on populations of container utilizing mosquitoes at concentrations commonly found in the field. Superior tolerance to tire leachate of A. albopictus compared to A. triseriatus, and possibly other native mosquito species, may have facilitated the replacement of these native species as A. albopictus has invaded North America and other regions around the world.
Asymmetric responses to simulated global warming by populations of Colobanthus quitensis along a latitudinal gradient
Authors: Acuña-Rodríguez Ian S. , Torres-Díaz Cristian , Hereme Rasme , Molina-Montenegro Marco A.
Published: January 2018

The increase in temperature as consequence of the recent global warming has been reported to generate new ice-free areas in the Antarctic continent, propitiating the colonization and spread of plant populations. Consequently, antarctic vascular plants have been observed extending their southern distribution. But as the environmental conditions toward southern localities are progressively far apart from these species’ physiological optimum, the colonization of new sites and ecophysiological responses could be decreased. However, if processes of local adaptation are the main cause of the observed southern expansion, those populations could appear constrained to respond positively to the expected global warming. Using individuals from the southern tip of South America, the South Shetland Islands and the Antarctic Peninsula, we assess with a long term experiment (3 years) under controlled conditions if the responsiveness of Colobanthus quitensis populations to the expected global warming, is related with their different foliar traits and photoprotective mechanisms along their latitudinal gradient. In addition, we tested if the release of the stress condition by the global warming in theses cold environments increase the ecophysiological performance. For this, we describe the latitudinal pattern of net photosynthetic capacity, biomass accumulation, and number of flowers under current and future temperatures -by warming- respective to each site of origin after three growing seasons. Overall, was showed a clinal trend was found in the foliar traits and photoprotective mechanisms in the evaluated C. quitensis populations. On the other hand, an asymmetric response to warming was observed for southern populations in all ecophysiological traits evaluated, suggesting that low temperature is limiting the performance of C. quitensis populations, mainly in those from southern. Our results suggest that under a global warming scenario those plant populations that inhabiting cold zones at high latitudes could be improved in their ecophysiological performance, enhancing the size of populations or their spread.
Detection and analysis of PM2.5 microbial aerosol in Chicken Houses in Shandong Province, China
Authors: Yang Wenhao , Guo Mengjiao , Liu Guijun , Yu Gaoshui , Wang Peng , Chai Tongjie , Wang Hairong
Published: January 2018

To evaluate the environmental quality of different poultry houses, the concentrations and compositions of microbial aerosols and PM2.5 were measured. Results showed that the concentrations of airborne bacteria, airborne fungi and airborne Escherichia coli in poultry houses were 0.167-4.484 × 104 CFU/m3, 0.236-4.735 × 103 CFU/m3, and 0-33.0 CFU/m3, respectively. Distributions of bacteria and fungi at levels 5 and 6 of the Andersen sampler were 11.4%-34.3% and 16.8%-37.5%, respectively. Conditional pathogenic bacteria including Klebsiella pneumoniae, Staphylococcus epidermidis, Enterococcus and Aerococcus viridans, were detected at the aforementioned level, in particle sizes similar to PM2.5 and with PM2.5 concentrations in poultry houses of 114-230 μg/m3 . In PM2.5, the chief bacteria genera were Faecalibacterium, Bacteroides, and Escherichia, whereas the dominant genus of fungus was Aspergillus. Importantly, the relative abundances of Escherichia and Corynebacterium in broiler houses were 3.1% and 1.94%, respectively, which were greater than those in layer houses. However, the percentages of Aspergillus and Penicillium were 13.5% and 0.56%, with a relatively high level in layer houses . Altogether, results revealed that the ambient air quality in poultry houses had a relatively high abundance of conditional pathogenic bacteria and concentration of PM2.5, which could threaten the health of animals and workers.
The effects of allogenic stem cells in a murine model of hind limb diabetic ischemic tissue
Authors: Álvarez García Jesús , García Gómez-Heras Soledad , Riera del Moral Luis , Largo Carlota , García-Olmo Damián , García-Arranz Mariano
Published: January 2018

Background: Diabetes is one of the major risk factors for peripheral arterial disease. In patients in whom surgery cannot be performed, cell therapy may be an alternative treatment. Since time is crucial for these patients, we propose the use of allogenic mesenchymal cells. Methods: We obtained mesenchymal cells derived from the fat tissue of a healthy Sprague-Dawley rat. Previous diabetic induction with streptozotocin in 40 male Sprague-Dawley rats, ligation plus left iliac and femoral artery sections were performed as a previously described model of ischemia. After 10 days of follow-up, macroscopic and histo-pathological analysis was performed to evaluate angiogenic and inflammatory parameters in the repair of the injured limb. All samples were evaluated by the same blind researcher. Statistical analysis was performed using the SPSS v.11.5 program (p <0.05). Results: Seventy percent of the rats treated with streptozotocin met the criteria for diabetes. Macroscopically, cell-treated rats presented better general and lower ischemic clinical status, and histologically, a better trend towards angiogenesis, greater infiltration of type 2 macrophages and a shortening of the inflammatory process. However, only the inflammatory variables were statistically significant. No immunological reaction was observed with the use of allogeneic cells. Discussion: The application of allogeneic ASCs in a hind limb ischemic model in diabetic animals shows no rejection reactions and a reduction in inflammatory parameters in favor of better repair of damaged tissue. These results are consistent with other lines of research in allogeneic cell therapy. This approach might be a safe, effective treatment option that makes it feasible to avoid the time involved in the process of isolation, expansion and production of the use of autologous cells.
Different definitions of species presence to refine estimates of local species richness
Authors: Ruete Alejandro , Pärt Tomas , Berg Åke , Knape Jonas , Arlt Debora
Published: January 2018

Abstract

Aim To improve predictions of spatial and temporal patterns of species richness it is important to consider how species presence at a site is defined. This is because this definition affects our estimate of species richness, which should be aligned with the aims of the study, e.g. estimating richness of the breeding community. Here we explore the sensitivity of species richness estimates to criteria for defining presence of species (e.g. in relation to number of days present during the breeding season) at 107 wetlands.

Innovation We use opportunistic citizen science data of high density (a total of 151,817 observations of 77 wetland bird species; i.e. about 16 observations per day) to build site-occupancy models calculating occupancy probabilities at a high temporal resolution (e.g. daily occupancies) to derive probabilistic estimates of seasonal site use of each species. We introduce a new way for defining species presence by using different criteria related to the number of days the species are required to be present at local sites. We compared patterns of species richness when using these different criteria of species inclusions.

Main conclusion While estimates of local species richness derived from high temporal resolution occupancy models are robust to observational bias, these estimates are sensitive to restrictions concerning the number of days of presence required during the breeding season. Unlike complete local species lists, summaries of seasonal site use and different presence criteria allow identifying differences between sites and amplifying the variability in species richness among sites. Thus, this approach allows filtering out species according to their phenology and migration behaviour (e.g. passer-by species) and could improve the explanatory power of environmental variables on predictive models.
Land snails of Leptopoma Pfeiffer, 1847 in Sabah, Northern Borneo (Caenogastropoda: Cyclophoridae): an analysis of molecular phylogeny and variations in shell form due to geography
Authors: Phung Chee-Chean , Heng Pooi-San , Liew Thor-Seng
Published: January 2018

Leptopoma is a species rich genus with approximately 100 species documented according to shell morphology and animal anatomy. Many of the Leptopoma species are described in terms of shell size, shape, sculpture and colour patterns of a small number of examined materials. However, the implications of the inter- and intra-species variations in shell form to the taxonomy of Leptopoma species and the congruency of its current shell based taxonomy with its molecular phylogeny are still unclear. Over the last decade, more than 900 collection lots consisting of more than 4000 Leptopoma specimens have been obtained in Sabah and deposited in BORNEENSIS at Universiti Malaysia Sabah. Access to this collection gave us the opportunity to examine the geographical variations in shell forms and the phylogenetic relationship of Leptopoma species in Sabah. The phylogenetic relationship of three Leptopoma species was first estimated by performing maximum likelihood and Bayesian analysis based on mitochondrial genes (16S and COI) and nuclear gene (ITS-1). After this, a total of six quantitative shell characters (i.e. shell height, shell width, aperture height, aperture width, shell spire height, and ratio of shell height and width) and three qualitative shell characters (i.e. shell colour patterns, spiral ridges, and dark ring band in aperture) of the specimens were mapped across the phylogenetic tree and tested for phylogenetic signals. Data on shell characters of Leptopoma sericatum and Leptopoma pellucidum from two different locations (i.e. Balambangan Island and Kinabatangan) where both species occurred sympatrically were then obtained to examine the geographical variations in shell form. The molecular phylogenetic analyses suggested that each of the three Leptopoma species was monophyletic and indicated congruence with one of the shell characters (i.e. shell spiral ridges) in the current morphological-based classification. Other qualitative and quantitative shell characters were incongruent with the Leptopoma species phylogeny. Although the geographical variation analyses suggested some of the shell characters indicating inter-species differences between the two Leptopoma species, these also pointed to intra-species differences between populations from different locations. This study provides an initiation to resolve the taxonomy conundrum for the remaining 100 little known Leptopoma species from other regions and highlights a need to assess variations in shell characters before they could be used in species classification.
Hand posture comparison in Synergy Space
Authors: Bhatt Nayan , SKM Varadhan
Published: January 2018

In studies of human movement control, an important question is how the central nervous system (CNS) controls movements in the presence of a large number of degrees of freedom (DoFs) at all levels of the control architecture. It is known that CNS groups the multiple DoFs into representative functional units also called synergies for simplification of the task. Hence, comparing two different hand postures in the synergy space, rather than joint angle space may provide insightful information about efforts needed (in terms of synergy components) to transform from one hand posture to another hand posture. Working with synergy space may also provide information about how CNS deals with system with multiple DoFs. We developed an index called posture similarity index (PSI) which measures the similarity of two postures by projecting hand posture from the joint angles into the synergy space. A large value of PSI represents high similarity between postures whereas a lower value represents less similarity between postures. This index uses principle of synergies and nicely captures effort required for kinematic transformation. Using this index as a feature, possible set of representative postures can be identified. The other hand postures can be derived from a possible set of representative postures with relatively less efforts for kinematic transformation.
An identical mechanism governs self-nonself discrimination and effector class regulation
Authors: Usharauli David , Kamala Tirumalai
Published: January 2018

Prevailing immunological dogma dictates self-nonself discrimination, meaning to respond or not, and effector class regulation, meaning choosing the most effective response, are two separate decisions the immune system makes when faced with a new antigen. Representing a cardinal departure from the past, our model instead predicts both self-nonself discrimination and effector class regulation are in fact one and the same process controlled by Foxp3+ regulatory T cells (Tregs) whose antigen-specific repertoire is entirely maintained by commensal microbiota-derived cross-reactive antigens.
Environmental suitability for Lutzomyia (Nyssomyia) whitmani (Diptera: Psychodidae: Phlebotominae) and the occurrence of American Cutaneous Leishmaniasis in Brazil
Authors: Costa Simone Miranda , Cordeiro José Luis Passos , Rangel Elizabeth Ferreira
Published: January 2018

Leishmaniasis represents an important public health problem in Brazil. The continuous process of urbanization and expansion of human activities in forest areas impacts natural habitats, modifying the ecology of some species of Leishmania, as well as its vectors and reservoirs and, consequently, changes the epidemiological pattern and contribute to the expansion of American Cutaneous Leishmaniasis (ACL) in Brazil. In epidemiology of ACL, we highlight Lutzomyia (Nyssomyia) whitmani, the main vector of ACL, transmitting two dermotropic Leishmania spp.: Leishmania (Viannia) braziliensis and Leishmania (Viannia) shawi. We used the maximum entropy niche modeling approach (MAXENT) to evaluate the environmental suitability of L. (N.) whitmani and the transmission of ACL in Brazil, in addition to designing models for a future scenario of climate change. MAXENT was used under the "auto-features" mode and the default settings, with 100-fold repetition (bootstrap). The logistic output was used with higher values in the Habitat Suitability Map, representing more favorable conditions for the occurrence of L. (N.) whitmani and human cases of ACL. Two models were developed: Lutzomyia whitmani model (LWM) and American Cutaneous Leishmaniasis model (ACLM). LWM identified that the species "prefers" (more appropriate habitat) regions with moderate Annual Precipitation (AP), between 1,000 - 1,600 mm, intermediate vegetation density (NDVI) values, Mean Temperature of The Coldest Quarter (MTCQ), between 15°C - 21°C, and Annual Mean Temperature (AMT), between 19°C - 24°C. ACLM indicates that ACL is strongly associated with areas of intermediate density vegetation, areas with Annual Precipitation (AP) between 800 and 1200 mm, MTCQ above 16 ° C and AMT below 23°C. The results obtained in this study are discussed in terms of epidemiology and surveillance of ACL in future scenarios in Brazil.
DNA barcoding revealing the mislabeling of fish in a highly tourist capital in Brazil
Authors: Staffen Clisten Fátima , Staffen Mari Dalva , Becker Mariana Londero , Löfgren Sara Emelie , Muniz Yara Costa Netto , Freitas Renato Hajenius Aché , Marrero Andrea Rita
Published: January 2018

The consumption of raw fish has been increasing considerably in the West, since it has an appeal to be potentially healthier (omega 3 and 6, essential amino acids and vitamins). However this potential benefit, as well as the taste, value and even the risk of extinction is different between species of fish, constituting grounds for fraud. Through the Project "Cat by Hare", using the principles of the DNA barcode, we revealed mislabelling of fish in japanese restaurants and fishmarkets in Florianópolis, a highly tourist capital in Brazil. We sequenced the COI gene of 65 samples from fishmongers and 80 from restaurants and we diagnosed 34\% of fraud in fishmongers and 17\% in restaurants. This different percentage is related to the restaurants selling only two species (Tuna and Salmon) and one category of fish called "white fish" that can be any species that has whitish musculature. We discussed that frauds may have occurred for different reasons: to circumvent surveillance on threatened species; to sell fish with sizes smaller than allowed or species that are being highly captured as being a low captured one at any time (law of supply); to induce product consumption using species with better taste. It should be noted that some substitutions are derived from incorrect identification and are not a fraud per se, due to confusion of popular names or misunderstanding of sellers. Therefore, we suggest the implementation of a systematic regulatory program conducted by governmental agencies to reduce mislabelling to avoid further damage to the community (in health and financial issues) and fish stocks
lncRNA H19 mediates TGF-β1-induced epithelial to mesenchymal transition in bovine epithelial cells through PI3K/AKT Signaling Pathway
Authors: yang wei , li xuezhong , qi shaopei , li xueru , zhou kun , qing suzhu , zhang yong , Gao Mingqing
Published: January 2018

Increased levels of long noncoding RNA H19 (H19) have been observed in many inflammatory and organ fibrosis diseases including ulcerative colitis, osteoarthritis, liver fibrosis, renal fibrosis and pulmonary fibrosis. However, the role of H19 in bovine mastitis and mastitis-caused fibrosis is still unclear. In our study, H19 was characterized as a novel regulator of EMT induced by transforming growth factor-β1 (TGF-β1) in bovine mammary alveolar cell-T (MAC-T) cell line. We found that H19 was highly expressed in bovine mastitis tissues and inflammatory MAC-T cells induced by virulence factors of pathogens. TGF-β1 was also highly expressed in inflammatory MAC-T cells, and exogenous TGF-β1 could induce EMT, enhance extracellular matrix protein expression, and upregulate H19 expression in epithelial cells. Stable expression of H19 significantly promotes EMT progression and expression of ECM protein induced by TGF-β1 in MAC-T cells. Furthermore, by using a specific inhibitor of the PI3K/AKT pathway, we demonstrated that TGF-β1 upregulated H19 expression through PI3K/AKT pathway. All these observations imply that the lncRNA H19 modulated TGF-β1-induced epithelial to mesenchymal transition in bovine epithelial cells through PI3K/AKT signaling pathway, which suggests that mammary epithelial cells might be one source for myofibroblasts in vivo in the mammary glands under an inflammatory condition, thereby contributing to mammary gland fibrosis.
A world of opportunities with nanopore sequencing
Authors: Leggett Richard M , Clark Matthew D
Published: January 2018

Oxford Nanopore Technologies' MinION sequencer was launched in pre-release form in 2014 and represents an exciting new sequencing paradigm. The device offers multi-kilobase reads and a streamed mode of operation that allows processing of reads as they are generated. Crucially, it is an extremely compact device that is powered from the USB port of a laptop computer, enabling it to be taken out of the lab and facilitating previously impossible in-field sequencing experiments to be contemplated. Many of the initial publications concerning the platform focussed on provision of tools to access and analyse the new sequence formats and then demonstrating the assembly of microbial genomes. More recently, as throughput and accuracy have increased, it has been possible to consider work involving more complex genomes and metagenomes. With the release of the high throughput GridION X5 and PromethION platforms the sequencing of large genomes will become more cost efficient, and enable the leveraging of extremely long (>100kb) reads for resolution of complex genomic structures. This review provides a brief overview of nanopore sequencing technology, describes the growing range of nanopore bioinformatics tools and highlights some of the most influential publications that have emerged over the last two years. Finally, we look to the future and the potential the platform has to disrupt work in human, microbiome and plant genomics.
In-silico interaction studies on the efflux pumps suggest polymyxins to be better substrate for RND efflux pumps in multi-drug resistant strains of Acinetobacter baumannii
Authors: Verma Privita , Tiwari Vishvanath
Published: January 2018

Bacterial efflux pumps have emerged as antibiotic resistance determinants and confers multidrug resistance to a broad range of antimicrobials as well as non-antibiotic substances by potentially extruding them out. These are also associated with the virulence and biofilm formation. Thus, development of inhibitors against these effective antibacterial targets can be a highly beneficial approach in order to reverse the multidrug resistance (MDR) in the clinical relevant strains. A keen study on the efflux of foregoing or commonly used antibiotics will contribute in finding substrates that could bind efficiently with these efflux pumps. In the present study, we have explored efflux pumps belonging to Resistance-Nodulation-Division (RND) family as they are found prevalent in gram negative pathogens such as A. baumannii. The two RND efflux pumps under consideration are AdeABC and AcrAB-TolC. For comparative analysis, a non-RND family efflux pump i.e. NorM is selected here. We employed a series of computational techniques ranging from molecular docking to binding free energy estimation and molecular dynamics simulations to determine the binding affinity for different classess of drugs namely aminoglycosides, polymyxins, β-lactams, tetracyclines, glycylcyclines, quinolones and metronidazole against the efflux pumps under study. Our results revealed that class polymyxins has the highest binding affinity with the RND efflux pumps i.e. AcrAB-TolC and AdeABC as well as non-RND efflux pump (NorM). The experimental data was found to much extent in accordance with the binding free energy scores obtained from our in silico analysis. To recapitulate the outcome, polymyxins can possibly be the most efficient substrate for both RND and non-RND efflux pumps, thus, can be used as a reference drug for designing potent efflux pump inhibitors against multi-drug resistant strains.
Patterns of temporal variation in growth rate from a mainland population of Anolis nebulosus (Squamata: Dactyloidae), in the Mexican Pacific Coast
Authors: Ramírez Bautista Aurelio , Hernández-Salinas Uriel , Cruz Elizalde Raciel
Published: January 2018

In this study we used three nonlinear regression models: Von Bertalanffy, logistic-by-length, and logistic-by-weight to describe the pattern of growth of hatchling, juvenile, and adult of the lizard Anolis nebulosus in a tropical dry forest near of the Mexican Pacific coast during a period of 1989 and 1990. Von Bertalanffy and logistic-by-length models showed the best fit to the growth data for males and females of three age classes from marked and recaptured lizards in these years. The characteristic parameter of growth (r) and asymptotic growth (A1) extracted from these models indicated that males grow faster than females, but the latter reach a slightly larger size than males. The growth curves revealed that males reach minimum size at sexual maturity at 35 mm in snout-vent length (SVL), at an age of seven months, while females reach sexual maturity at 37 mm of SVL at nine months. Comparisons of growth rate between wet and dry seasons and years revealed that hatchlings and juveniles of both sexes had higher growth during the wet season for both years. Although there was no significant variation between measured environmental variables or in the food availability, the weight of evidence suggests that environmental variation has an influence on the growth of A. nebulosus of this population. Results indicate that variation on growth patterns observed may result from a combination of environmental factors, such as food availability, predation pressure and some reproductive characteristics as size at sexual maturity and size of hatchlings at birth.
Are extinction opinions extinct?
Authors: Lee Tamsin E , Bowman Clive , Roberts David L
Published: January 2018

Extinction models vary in the information they require, the simplest considering the rate of certain sightings only. More complicated methods include uncertain sightings and allow for variation in the reliability of uncertain sightings. Generally extinction models require expert opinion, either as a prior belief that a species is extinct, or to establish the quality of a sighting record, or both. Is this subjectivity necessary?

We present two models to explore whether the individual quality of sightings, judged by experts, is strongly informative of the probability of extinction: the `quality breakpoint method' and the `quality as variance method'. For the first method we use the Barbary lion as an exemplar. For the second method we use the Barbary lion, Alaotra grebe, Jamaican petrel and Pohnpei starling as exemplars.

The `quality breakpoint method' uses certain and uncertain sighting records, and the quality of uncertain records, to establish whether a change point in the rate of sightings can be established using a simultaneous Bayesian optimisation with a non-informative prior. For the Barbary lion, there is a change in subjective quality of sightings around 1930. Unexpectedly sighting quality increases after this date. This suggests that including quality scores from experts can lead to irregular effects and may not offer reliable results. As an alternative, we use quality as a measure of variance around the sightings, not a change in quality. This leads to predictions with larger standard deviations, however the results remain consistent across any prior belief of extinction. Nonetheless, replacing actual quality scores with random quality scores showed little difference, inferring that the quality scores from experts are superfluous.

Therefore, we deem the expensive process of obtaining pooled expert estimates as unnecessary and even when used we recommend that sighting data should have minimal input from experts in terms of assessing the sighting quality at a fine scale. Rather, sightings should be classed as certain or uncertain, using a framework that is as independent of human bias as possible.