bluuebunny/crossref_metadata_2025 huggingface dataset:
Defining and redefining its role in biology: Synthetic biology as an emerging field at the interface of engineering and biology
Authors: Ng Wenfa
Published: January 2018

Synthetic biology is often misunderstood as creation of artificial life or new biology using principles different from those of extant organisms around us. But, fundamentally, the field is about engineering biology in a more efficient and effective way, and endowing new functions in existing organisms using a more refined and predictable approach. Thus, synthetic biology as encapsulated by the field it helps defined, is enhanced recombinant DNA technology, an example of which is modular and orthogonal “standard swappable biological parts”. But, as the field grows and matures, various “allied” fields are subsumed into it such as metabolic engineering, protein engineering, directed evolution, origins of life research, and systems biology, which in totality represents a new perspective of how engineering principles can be utilized to expand, in scope and depth, the realms of questions that biology ask. Two parallel approaches, directed evolution and de novo protein design, are frequently used to engineer new phenotypes into organisms. Similar to evolution but with purposeful use of selection pressure to elicit progressive refinement of specific traits in an efficient manner, directed evolution is a powerful methodology that generates, at the cell level, libraries of mutants of slightly different function such as differing resistance to heavy metals, that upon exertion of continued selection pressure, led to the evolution of a strain capable of thriving under a hostile environment previously inhabitable to the organism. Taking a different approach, de novo protein design taps on advances in biomolecule structure modeling together with bioinformatic sequence search for inserting, in a structure defined manner, specific amino acids (natural or unnatural) in a protein structure to endow desired functionality, where one highly sought function is catalysis of unnatural reactions such as the Diels-Alder reaction. Long chain length DNA synthesis, on the other hand, finds utility in enabling the synthesis of a minimal genome for a bacterium, which demonstrates the huge possibilities of having a microbe with an optimized genome (free of extraneous genes) for biotechnological applications in delivering drugs and fuel at high titer with lower cost. Having assimilated other fields, synthetic biology is again redefining its role as its seeks to use, in an ethical and responsible manner, a new way of adding new functions into organisms through genome editing. For example, CRISPR/Cas9 genome editing holds enormous potential for providing life saving gene editing capability in medical treatments, while enabling fast, easy removal of undesirable genes and prophages from a production microorganism. Synthetic biologists are asking themselves deep questions on how best to regulate this powerful technology that could be as impactful on science and human society as recombinant DNA technology was in 1973.
Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations
Authors: Pascoe Ben , Meric Guillaume , Yahara Koji , Wimaralathna Helen , Murray Susan , Hitchings Matthew D , Sproston Emma L , Carrillo Catherine D , Taboada Eduardo N , Cooper Kerry K , Huynh Steven , Cody Alison J , Jolley Keith A , Maiden Martin CJ , McCarthy Noel D , Didelot Xavier , Parker Craig , Sheppard Samuel K
Published: January 2018

The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distances and genetic distances, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance with past human migration, whereas in Mycobacterium tuberculosis it is the lack of recombination that causes allopatric clusters. In Campylobacter, analyses of genomic data and molecular typing have been successful in determining the reservoir host species, but not geographical origin. We investigated biogeographical variation in highly recombining genes to determine the extent of clustering between genomes from geographically distinct Campylobacter populations. Whole genome sequences from 294 Campylobacter isolates from North America and the UK were analysed. Isolates from within the same country shared more recently recombined DNA than isolates from different countries. Using 15 UK/American pairs of isolates that shared ancestors, we identify regions that have frequently and recently recombined to test their correlation with geographical origin. The seven genes that demonstrated the greatest clustering by geography were used in an attribution model to infer geographical origins and tested using a further 383 UK clinical isolates to detect signatures of recent foreign travel. Patient records indicated that in 46 cases travel abroad had occurred less than two weeks prior to sampling: genomic analysis indicated that 34 (74%) of these isolates were of a non-UK origin. Identification of biogeographical markers in Campylobacter genomes will contribute to improved source attribution of clinical Campylobacter infection and inform intervention strategies to reduce campylobacteriosis.
Strategies for biomedical software management, sharing, and citation
Authors: Katz Daniel S , Niemeyer Kyle E , Smith Arfon M
Published: January 2018

This document is an open response to the NIH Request for Information (RFI): Strategies for NIH Data Management, Sharing, and Citation, Notice Number: NOT-OD-17-015, written by the leaders of the FORCE11 Software Citation Working Group from its inception in mid-2015 through today. This group produced a set of Software Citation Principles and related discussion, which are the basis for this document. Here, we describe research software, summarize the software citation principles, discuss open issues related to software citation, and make recommendations to the NIH.
Congregating behavior and response to resource distribution of the Green House Millipede, Oxidus gracilis
Authors: Bulpitt Gregory
Published: January 2018

Background. Congregating behaviors, though common among many animal species, are little studied among millipedes. It is also unclear to what extent abiotic factors influence the distribution and behavior of millipedes. The species Oxidus gracilis was surveyed around several streams on the island of Mo’orea along with soil moisture, leaf litter cover, and rock cover. Experiments were designed in order to determine how an innate congregating behavior may affect their distributions.

Methods. Fifteen transects were performed in the field, recording O. gracilis abundances and the three environmental factors every 1 m. Forty trials were performed using covered bins filled with soil and five fruits of the Tahitian chestnut tree (Inocarpus fagifer). Ten millipedes were placed in the box and left for an hour, after which the number of individuals per fruit was recorded.

Results. It was found that while none of the three environmental factors were strong indicators of the distribution of O. gracilis , individuals did in fact demonstrate a tendency to congregate in the experimental trials.

Discussion. The lack of significant relationships with the three environmental parameters suggests a generalist behavior of this millipede species, potentially benefitting its invasive nature. The congregating behavior could potentially be for the purposes of mating or defense. Although not studied in this paper, it is possible that conspecific chemical cues are responsible.
Ca2+ dynamics in zebrafish hyper-dorsalization of congenital anomaly
Authors: Tsuruwaka Yusuke , Shimada Eriko
Published: January 2018

Intracellular calcium ion (Ca2+) signaling is deeply involved in development, as demonstrated by the use of various Ca2+ sensors. Ca2+ patterns in wildtype and mutant zebrafish have been reported to date, however, not many zebrafish embryos with congenital anomaly have been studied yet. In the present study, we monitored serial Ca2+ levels of zebrafish embryos which showed inborn hyper-dorsalization using Ca2+ sensor, yellow cameleon, YC2.12. Our results showed clearly elevated Ca2+ levels in the presumptive dorsal part during gastrula period and in the dorsal region during segmentation period. The results suggested that monitoring Ca2+ levels may help to anticipate the region which influences a fate determination prior to morphogenesis.
Reinstatement of Pedicularis delavayi (Orobanchaceae): a species separating from P. siphonantha revealed by phylogenetic analyses
Authors: Yu Wen-Bin , Wang Hong , Liu Min-Lu , Grabovskaya Alisa E. , Li De-Zhu
Published: January 2018

Background. Morphological identification of Pedicularis depends on floral characters because interspecific variations these characters is very large. However, some important characters may be lost during the process of pressing the specimen. Pedicularis delavayi was described from Lijiang, northwestern Yunnan, and it was widely adopted as a variety of P. siphonantha. Unfortunately, the name “P. siphonantha var. delavayi’ incorrectly referred to P. milliana/P. tenuituba in some identified specimens and publications. Moreover, phylogenetic relationships between P. delavayi and P. siphonantha and its allies (P. millana and P. tenuituba) were not fully resolved. Methods. In total, we sampled 75 individuals representing 56 taxa. Of them, 10 taxa were from P. siphonantha group, and 11 individuals of P. delavayi represented 9 populations. One nuclear gene (nrITS) and four chloroplast genes/regions (matK, rbcL, trnH-psbA, and trnL-F) were sequenced for phylogenetic analyses. The nrITS and plastid datasets were combined to analyze. Bayesian Inference (BI) and Maximum Likelihood (ML) methods were used to reconstruct phylogenetic trees. Species identification, morphological comparison and line drawing were based on field observation, dried herbarium specimens and FFA-fixed samples. Results. Phylogenetic analyses showed that the P. siphonantha group was polyphyletic: monophyletic P. delavayi, sister to P. obliquigaleata, fell into clade A; and the remaining species of P. siphonantha group was in clade B as monophyletic (i.e. P. siphonantha lineage). In the P. siphonantha lineage, P. milliana, P. siphonantha, and P. tenuituba (= P. siphonantha var. stictochila) were well supported as monophyletic, and P. dolichosiphon (≡ P. siphonantha var. dolichosiphon) was sister to P. leptosiphon. Morphologically, P. delavayi differs from species of the P. siphonantha lineage in having a long petiole (~ 50 mm) and pedicel (~ 40 mm), a ridged corolla tube, and a folded lower-lip of the corolla. Discussion. Phylogenetic analyses showed evolution of P. delavayi was independent from the P. siphonantha lineage. The long-tubular corollas in P. delavayi and P. siphonantha lineage might be a convergent character. Both morphological and phylogenetic evidence strongly supported to reinstate P. delavayi as an independent species. In addition, P. neolatituba was proposed to reduce as a new synonymy of P. delavayi.
Sponge physiology: the effects of temperature on the regeneration and reaggregation of sponges (Haliclona reniera)
Authors: Runzel Charlotte C
Published: January 2018

Background. Increases in oceanic temperatures are expected to affect the cellular function of ecologically important organisms, such as sponges. Sponges are important to biodiversity, coral reef systems, benthic and spongiverous organisms, and the biomedical industry. Sponges can repair wounds (regeneration) and rebuild their body from separated cells (reaggregation). The rates of regeneration and reaggregation can serve as a proxy for cellular functions. These processes are important to sponge physiology, growth and competition in reef systems. This study will examine how temperature affects the regeneration and reaggregation of Haliclona reniera.

Methods. This study considered the effects of temperature on growth and reaggregation. Percent of reaggregation was measured in a range of temperatures (4-34˚C) for 15 minutes and analyzed using imageJ software. Regeneration rates of wounded sponges were measured in fluctuating (28-32˚C & 28-34˚C) and non-fluctuating (28˚C and 32˚C) oceanic temperatures. The depth and size of H. reniera was measured with transects.

Results. Through observing growth and aggregation rates in a variety of temperatures, this study showed that sponges exposed to average fluctuations at 1m (28-32˚C) had higher regeneration rates than those exposed to high fluctuations (28-34˚C) at 0.5m. Wounded sponges regenerated faster in higher temperatures (32˚C) than in lower temperatures (28˚C). Aggregation cells fit a temperature performance curve with a peak at 29.5˚C, or just above average oceanic temperatures (29˚C). H. reniera was most commonly found at depths of 1m.

Discussion. Although coral and other organisms may be greatly affected by oceanic warming, sponges may persist, depending on how oceanic temperature will fluctuate in the future. H. reniera repaired wounds faster in average temperature with normally occurring fluctuations and aggregated most frequently at temperatures slightly above average (29.5˚C). With IPCC predictions of increased oceanic temperatures and fluctuations, H. reniera may not have ideal oceanic conditions, but will still endure these conditions. With coral reefs affected by climate change conditions, many organisms may die off, perhaps transitioning coral reefs into sponge reefs.
Molecular cloning, sequence characteristics, and tissue expression analysis of the SLC35D3 gene in lean, obese and mini-type pigs
Authors: Li Wen-tong , Liu Ying , Zhou Rong , Yang Ya-lan , Zhang Yan-min , Tang Hui
Published: January 2018

Nowadays, with the development of people's life, obesity become one of the largest health problems today. Solute carrier family 35, member D3 (SLC35D3) protein has been reported to be involved in adipose deposition and metabolic control in mice. Because organ size in pig is comparable to that of the human, the pig is an ideal model that has been used to study diabetes mellitus, atherosclerosis, obesity, and other diseases. To better understand the structure and function of the SLC35D3 gene, the Meishan pig SLC35D3 gene was cloned and characterized, and its expression in different tissues was determined. The SLC35D3 cDNA consisted of a 1272 bp coding sequence that encoded a protein of 243 amino acids with a molecular mass of 44653.9 Da, and 966 bp 3′ untranslated regions. It is a pity that we have not got 5′ untranslated regions. Phylogenetic tree analysis revealed that porcine SLC35D3 had a closer genetic relationship and a shorter evolutionary distance with Vicugna; however, its evolutionary distance with that of the gorilla was longer than that of Vicugna. In addition, we quantified the SLC35D3 mRNA level by real-time polymerase chain reaction and detected expression in the liver, kidney, lung, heart, brain, LM, and spleen, as well as in the leaf lard, SAT, and PAT. In addition, we also tested the expression level of Meishan, Bama and Yorkshire in adipose tissue. The SLC35D3 mRNA level was highest in the leaf lard. These results serve as a foundation for further study on the porcine SLC35D3 gene.
Benthic boom: Understanding larval insect colonization in Moorea, French Polynesia
Authors: LaPaglia Nicholas A
Published: January 2018

Insects are important in assessing ecosystem quality and health. Current climate change models predict that in the next one hundred years, intense storms separated by long periods of drought will frequent French Polynesia. Variation in water availability may be difficult for many stream insects to cope with. Studying insect response after a disturbance as well as assessing their current distribution and abundance can help us understand greater ecological interactions and allow us to make predictions about future assemblages. The recolonization rate and habitat preference of Simuliidae and Chironomidae larvae were measured in a high elevation stream on Moorea, French Polynesia. Insect recolonization was measured 1, 3, and 6 days after an artificial disturbance event, and habitat preference was determined through the use of 3 introduced substrates: streamside moss, synthetic moss, and an empty control. Habitat preference was also evaluated through the comparison of larval densities across both experiments. Ultimately both Simuliidae and Chironomidae larvae were shown to return to baseline abundance 3 days after a disturbance event. Furthermore, chironomids preferred the synthetic moss substrate to all other habitats, while simuliids preferred the empty control compared to the moss treatment. This likely indicates that the chironomids live within the submerged moss while simuliids live on a rocky substrate. It also suggests that both species can live in a variety of environments and can adapt well to changing conditions.
Choosing favorites: the host preference of a vascular epiphyte (Didymoglassum tahitense)
Authors: Klein Zoe
Published: January 2018

Background. The specific relationships between hosts and epiphytes are fairly unknown. Biotic factors contributing to epiphytic distribution have generally been considered secondary predictors to epiphyte growth and range. Invasive species pose risk to the biodiversity of epiphytes by altering the very specific environments epiphytes require to grow, which could ultimately harm the ecosystem as a whole. This study investigates the relationship between a tropical island vascular epiphyte, Didymoglassum tahitense, to wood density, bark phosphorus and host species in order to understand the specific interactions between host and epiphyte. Methods. Epiphytic surveys were conducted on the two native trees N. forsteri and I. fagifer and two invasive trees S. campanulata and P. falcataria to test for D. tahitense abundance and presence. Wood density for all tree species was calculated with the equation density=mass/volume, where volume was found using the displacement method and the mass by calculating dry mass. Phosphorus concentrations in the bark and epiphyte were found using an elemental analyzer. Results. The study found that D. tahitense preferred to live on the two native species N. forsteri and I. fagifer and that no D. tahitense grew on the invasive trees S. campanulata and P. falcataria. Of these four tree species, the two native trees had lower bark density and higher phosphorus concentrations where the invasive trees had higher bark density and lower phosphorus amounts. Discussion. With these findings, I assume that D. tahitense is host specific to species with high phosphorus in their wood.
Understanding of the activity of a protein involved in DNA repair by biochemical, structural and in silico approaches
Authors: Morrone Castrese , Miggiano Riccardo , Serpe Mario , Massarotti Alberto , Valenti Anna , Del Monaco Giovanni , Rossi Mosé , Rossi Franca , Rizzi Menico , Ciaramella Maria , Perugino Giuseppe
Published: January 2018

The repair of DNA from alkylation damage is generally performed by evolutionary conserved protein complexes. However, specific repair of O6-alkylated-guanines is a task of a small class of proteins called AGTs (alkylated DNA-protein alkyl-transferases): by using a single-step reaction mechanism, the alkylic group is irreversibly transferred to a catalytic cysteine in the active site, inducing the in vitro and in vivo inactivation and destabilization of the protein. Although some conformational changes after the alkylation are supposed, a complete picture of structural rearrangements occurring during the reaction cycle is missing. The complete knowledge of these structural movements is a great challenge and a fundamental task for the development of new inhibitors of the human AGT, whose overexpression leads to a resistance in several types of tumor cells to the chemoterapic alkylating agents-based treatment. We used the Sulfolobus solfataricus thermostable ortholog (SsOGT) as a model for AGTs [1], by performing biochemical, structural, molecular dynamics and in silico analysis of ligand-free, DNA-bound and alkylated version of the protein. With this protein, we were able to highlight conformational changes and perturbations of intramolecular interaction occurring during lesion recognition and catalysis, confirming our previous hypothesis that coordination between the N- and C-terminal domains of SsOGT is important for protein activity and stability [2]. All the data allowed us to propose a general model of structural rearrangements occurring during the reaction cycle of AGTs [3], and proposing it as a starting point to design strategies to modulate AGT activity in therapeutic settings.

[1] G. Perugino, A. Vettone, G. Illiano, A. Valenti, M.C. Ferrara, M. Rossi, M. Ciaramella (2012) Activity and regulation of archaeal DNA alkyltransferase: conserved protein involved in repair of DNA alkylation damage. J. Biol. Chem., 287, 4222-4231.

[2] G.Perugino, R.Miggiano, M.Serpe, A.Vettone, A.Valenti, S.Lahiri, F.Rossi, M.Rossi, M. Rizzi, M. Ciaramella (2015) Structure-function relationships governing activity and stability of a DNA alkylation damage repair thermostable protein. Nucleic Acids Res., 43, 8801-8816.

[3] C. Morrone, R. Miggiano, M. Serpe, A. Massarotti, A. Valenti, G. del Monaco, M. Rossi, F. Rossi, M. Rizzi, G. Perugino, M. Ciaramella (2017) Interdomain interactions rearrangements control the reaction steps of a thermostable DNA alkyltransferase. BBA-Gen. Sub., 1861, 2, 86-96.
Vacuolar pH in yeast cells during pseudohyphal growth induced by nitrogen starvation
Authors: Makanae Koji
Published: January 2018

It has been reported that the intracellular pH of the budding yeast Saccharomyces cerevisiae is asymmetric between mother and daughter cells, and this asymmetry in pH underlies replicative aging and rejuvenation. S. cerevisiae growth morphology changes between the yeast form and pseudohyphal form, according to nutrient availability. A previous study reported that the replicative life span of pseudohyphal form cells is longer than that of yeast form cells in S. cerevisiae. However, the intracellular pH of pseudohyphal cells is unknown. To examine the intracellular pH of S. cerevisiae cells during pseudohyphal growth, vital staining was performed with neutral red, which is a pH indicator, of cells growing on nitrogen starvation (SLAD) medium. The results showed that the vacuoles of S. cerevisiae cells during pseudohyphal growth induced by nitrogen starvation formed polar pH gradients. The relationship between cell size and shape and the neutral red staining patterns suggested that the pH of cell vacuoles during pseudohyphal growth changed from uniformly near pH 6.8 to steep gradients of pH from vacuole ends along the long axis of the cell. The results of time-lapse imaging to examine vacuolar dynamics and neutral red staining suggested that the pH gradients were not formed simply by inheritance of vacuolar contents accompanying vacuolar movements.
Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets
Authors: Washburne Alex D , Silverman Justin D , Leff Jonathan W , Bennett Dominic J , Darcy John L , Mukherjee Sayan , Fierer Noah , David Lawrence A
Published: January 2018

Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to investigate how shared evolutionary history affects microbial abundance patterns. Here, we present a method to identify the phylogenetic factors driving patterns in microbial community composition. We use the method, "phylofactorization", to re-analyze datasets from the human body and soil microbial communities, demonstrating how phylofactorization is a dimensionality-reducing tool, an ordination-visualization tool, and an inferential tool for identifying edges in the phylogeny along which putative functional ecological traits may have arisen.
Among-site variability in the stochastic dynamics of East African coral reefs
Authors: Allen Katherine A , Bruno John F , Chong Fiona , Clancy Damian , McClanahan Tim R , Spencer Matthew , Zychaluk Kamila
Published: January 2018

Coral reefs are dynamic systems whose composition is highly influenced by unpredictable biotic and abiotic factors. Understanding the spatial scale at which long-term predictions of reef composition can be made will be crucial for guiding conservation efforts. Using a 22-year time series of benthic composition data from 20 reefs on the Kenyan and Tanzanian coast, we developed Bayesian vector autoregressive state-space models for reef dynamics, incorporating among-site variability, and quantified their long-term behaviour. We estimated that if there were no among-site variability, the total long-term variability would be approximately one third of its current value. Thus, our results showed that among-site variability contributes more to long-term variability in reef composition than does temporal variability. Individual sites were more predictable than previously thought, and predictions based on current snapshots are informative about long-term properties. Our approach allowed us to identify a subset of possible climate refugia sites with high conservation value, where the long-term probability of coral cover \(\leq\) 0.1 was very low. Analytical results show that this probability is most strongly influenced by among-site variability and by interactions among benthic components within sites. These findings suggest that conservation initiatives might be successful at the site scale as well as the regional scale.
Assessing coral health in Moorea, French Polynesia after a regional die-off of the coral antagonist, Dendropoma maxima
Authors: O'Malley Liam
Published: January 2018

Coral reefs are under pressure from numerous anthropogenic and natural threats. A species of vermetid worm, Dendropoma maxima, has a negative interaction with the corals it lives on. Vermetid worm interactions result in structural homogeneity of reef habitats, reduced coral growth, and increased coral death. Dendropoma maxima and corals have a naturally evolved competitive relationship. Therefore, it is inherent that removal of D. maxima from the environment would alleviate stress to coral associated with vermetid worm activity and lead to increased coral growth and survival. A 2015 die-off of D. maxima in French Polynesia is likely to have had direct positive effects to coral and cascading effects on reef community structure. The aim of this investigation was to contribute to the understanding of vermetid worm and coral interactions by quantifying the extent of stress on corals under reduced vermetid worm densities. This study measured D. maxima size and abundance on several coral types and assessed Porites coral health by the presence of pink lesions and growth along edges of coral. Surveys of D. maxima size and Porites coral health occurred at Temae Reef, Moorea in October and November 2016. Live D. maxima were less than half the size of dead D. maxima. Average size of live D. maxima was different between Porites coral and dead coral substrates and between Top or Side positions. There was a strong positive correlation between number of live D. maxima and number of lesions on Porites coral and positive correlation between live D. maxima and percent of coral death. A positive but insignificant correlation between number of live D. maxima and length of new growth was observed. The die-off of D. maxima in 2015 appears to have positively impacted coral health and the results are important to understanding shifts in community structure and ecological health, especially as environmental changes become more frequent in the future.
Distribution and biological implications of plastic pollution on the fringing reef of Mo’orea, French Polynesia
Authors: Connors Elizabeth Janice
Published: January 2018

Plastic pollution has been recognized as a major pollutant of the open ocean, but the extent and impact of plastic pollution on the coral reef environment has yet to be fully understood. In this study, the distribution of both macro- (>5mm) and micro- plastic (<5mm) of a typical coral reef ecosystem— the fringing reef of an isolated South Pacific island, Mo’orea, French Polynesia—was quantified. During the course of the study, macroplastic was found on every beach on the island, and distribution of plastic was categorized by site type and the presence of Turbinaria oranata, a common macroalgae of Mo’orea. Microplastic (plastic pieces <5mm) was found in the water column of the fringing reef of the island, at a concentration of 0.74 plastic pieces per square meter. To test the impact on coral reef organisms of the plastic pollution found in the fringing reef, microplastic was exposed to a species of soft coral, Discosoma spp.in a laboratory setting. The resilience of Discosoma spp.in fluctuating temperatures and rising CO2 levels is well understood, but the effect of plastic pollution on Discosoma spp. and other corallimorphs has never before been analyzed. This study reports for the first time the ingestion of microplastic by the soft coral Discosoma spp. Positively buoyant and negatively buoyant microplastic were both ingested over different time frames. In addition, wild (not experimentally introduced) microplastic was found in the stomach cavity of the organism. These findings indicate that plastic debris are being ingested by Discosoma spp. and may impair the health of this prevalent coral reef organism.
Evidence against a mechanism of allelopathy in the green alga Chlorodesmis fastigiata
Authors: Kumler William E
Published: January 2018

Allelopathic macroalgae have been shown to have significant negative effects on corals via the transfer of toxic compounds. The interaction that takes place between allelopathic macroalgae and other algae, however, has not been studied in detail. Here, the effects of the allelopathic Chlorodesmis fastigiata on other macroalgae were analyzed. These effects were first tested on complete coral and macroalgal individuals over several days, then on small samples of the macroalgal species when exposed to isolated toxins. However, neither experiment found significant negative effects on either Sargassum mangarevense or Boodlea kaeneana due to the interaction between these algae and the toxin produced by C. fastigiata. Distribution and abundance of C. fastigiata was also assessed around the island of Moorea in French Polynesia.
Mechanism of apoptosis induced by quinoxalone from the myxobacterium Stigmatella eracta WXNXJ-B in B16 mouse melanoma cell line
Authors: Wang Dahong , Wei Lanlan , Zhang Shuaiying
Published: January 2018

The biological activities of quinoxalone, a novel small molecular substance isolated from the broth of the myxobacterium Stigmatella eracta WXNXJ-B, was investigated. This study was designed to determine the anti-proliferative, apoptotic property of quinoxalone, using B16 mouse melanoma cells as a model system. The results showed that quinoxalone has antitumor activity and can significantly inhibit the proliferation of B16 cells. The extent and the timing of apoptosis were strongly dependent on the dose. After treating with quinoxalone and staining with Hoechst 33342, B16 cells showed typical apoptotic morphological features such as chromatin condensation by fluorescent microscopy. DNA isolated from B16 cells cultured with quinoxalone showed a typical DNA ladder of apoptosis in agarose gel electrophoresis. Further investigation results showed that the apoptotic machinery of B16 induced by quinoxalone was associated with drop in mitochondrial membrane potential from 5.35% to 23.7%, up-regulation of Bax and down-regulation of Bcl-2 in a dose-dependent manner. And a signiﬁcant increased activation of caspase-3. Our finding suggests that quinoxalone could suppress the growth of B16 cells and reduces cell survival via disturbing mitochondrial membrane potential and inducing apoptosis of tumor cells.
Functional and spinal neuropeptidomic alterations in a new rat surgical model of osteoarthritic pain: A pilot study
Authors: Gervais Julie-Anne , Otis Colombe , Lussier Bertrand , Guillot Martin , Beaudry Francis , Troncy Eric
Published: January 2018

Background. Osteoarthritis is the leading cause of chronic joint pain, causing important productivity and economic losses. It is believed that peripheral and centralized sensitization play a role in the creation and maintenance of a chronic painful state. Different animal models have been employed for the investigation of pain mechanisms and evaluation of potential treatments, but none of them are ideal in terms of reproducibly, reliability and translational value. Methods. In the search for better animal model, this pilot study was performed with the goal of evaluating pain functional outcomes and spinal biomarkers between three surgical rat models of osteoarthritic pain, i.e. destabilization of the medial meniscus, cranial cruciate ligament transection and the combination of both, and comparing those results to the intra-articular injection of monosodium iodoacetate. Six rats were assigned to each model group and a Sham group. Static weight bearing, punctate tactile paw withdrawal threshold, and spinal neuropeptides (substance P, calcitonin gene-related peptide, bradykinin, and somatostatin) were evaluated for each group. Results. Both the monosodium iodoacetate and combination models induced functional alterations in static weight bearing and punctate tactile paw withdrawal threshold, the changes being more persistent in the combination group. Both also produced an increased release of pro-nociceptive and anti-nociceptive neuropeptides at different time-points. When surgical models were compared, the cranial cruciate ligament transection and destabilization of the medial meniscus models were less interesting, with temporary functional alterations, and no significant change in neuropeptides. Discussion. The surgical induction of osteoarthritis was accompanied by quantifiable neurophysiologic changes relating to non-physiologic pain. Comparison with the monosodium iodoacetate model showed that the interest of a surgical model, especially the combination of destabilization of the medial meniscus and cranial cruciate ligament transection, might reside in more persistent and progressive changes, a model that may represent better the human post-traumatic osteoarthritis.
gb4gv: A genome browser for geminivirus
Authors: Ho Eric S , Newsom-Stewart Catherine M , Diarra Lysa , McCauley Caroline S
Published: January 2018

Background: Geminivirus (family Geminiviridae) is a prevalent plant virus that imperils agriculture globally, causing serious damage to the livelihood of farmers, particularly in developing countries. The virus evolves rapidly, attributing to its single-stranded genome propensity, resulting in worldwide circulation of diverse and viable genomes. Genomics is a prominent approach taken by researchers in elucidating the infectious mechanism of the virus. Currently, NCBI Viral Genome website is a popular repository of viral genomes that conveniently provides researchers a centralized data source of genomic information. However, unlike the genome of living organisms, viral genomes most often maintain peculiar characteristics that fit into no single genome architecture. By imposing a unified annotation scheme on the myriad of viral genomes may downplay their hallmark features. For example, virion of Begomovirus prevailing in America encapsulates two similar-sized circular genomes and both are required to maintain virulence. But, the two bipartite genomes are kept separately in NCBI with no explicit association in linking them. Thus, our goal is to build a comprehensive Geminivirus genomics database, namely gb4gv, that not only preserves genomic characteristics of the virus, but also supplements biologically relevant annotations that help to interrogate this virus e.g. the targeted host, putative iterons, siRNA targets etc. Methods: We have employed manual and automatic methods to curate 508 genomes from four major genera of Geminiviruses, and 161 associated satellites obtained from NCBI RefSeq and PubMed databases. Results: These data are available for free access without registration from our website. Besides genomic content, our website provides visualization capability inherited from UCSC Genome Browser. Discussion: With the genomic information readily accessible, we hope that our database will inspire researchers in gaining better understanding about this virus, resulting in insightful strategies to conquer the devastation inflicted agriculture. Availability and Implementation: Database URL: http://gb4gv.lafayette.edu .
Largest baleen whale mass mortality during strong El Niño event is likely related to harmful toxic algal bloom
Authors: Häussermann Verena , Gutstein Carolina S , Beddington Michael , Cassis David , Olavarria Carlos , Dale Andrew C , Valenzuela-Toro Ana M. , Perez-Alvarez MariaJose , Sepúlveda Hector H. , McConnell Kaitlin M. , Horwitz Fanny E , Försterra Günter
Published: January 2018

While large mass mortality events (MMEs) are well known for toothed whales, they have been rare in baleen whales due to their less gregarious behaviour. Although in most cases the cause of mortality has not been conclusively identified, some baleen whale mortality events have been linked to bio-oceanographic conditions, such as harmful algal blooms (HABs).In southern Chile, HABs can be triggered by the ocean-atmosphere phenomenon El Niño. The frequency of the strongest El Niño events is increasing due to climate change. In March 2015, by far the largest reported mass mortality of baleen whales took place in a gulf in southern Chile. Here we show that the synchronous death of at least 343, primarily sei, whales can be attributed to HABs during a building El Niño. Although considered an oceanic species, the sei whales died while feeding near to shore in previously unknown large aggregations. This provides evidence of new feeding grounds for the species. The combination of older and newer remains of whales in the same area indicate that MMEs have occurred more than once in recent years.Large HABs and reports of marine mammal MMEs along the north-east Pacific coast may indicate similar processes in both hemispheres. Increasing MMEs through HABs may become a serious concern in the conservation of endangered whale species.
Remote sensing and geographical information analytical techniques for modelling Ommatissus lybicus (Hemiptera: Tropiduchidae) habitat and population densities
Authors: Al-Kindi Khalifa M , Kwan Paul , Andrew Nigel , Welch Mitchell
Published: January 2018

In order to understand the distribution and prevalence of Ommatissus lybicus (Homoptera: Tropiduchidae) as well as analyse their current biographical patterns and predict their future spread, comprehensive and highly sophisticated information on the environmental, climatic, and agricultural practices are essential. The analytical techniques available in modern spatial analysis packages, such as Remote Sensing and Geographical Information Systems, can help detect and model spatial links and correlations between the presence, absence and density of O. lybicus in response to climatic, environmental and human factors. The main objective of this paper is to review remote sensing and geographical information analytical techniques that can be applied in mapping and modelling the habitat and population density of O. lybicus in Oman. An exhaustive search of related literature revealed that there are few studies linking location-based infestation levels of pests like the O. lybicus with climatic, environmental and human practice related variables in the Middle East. Our review also highlights the accumulated knowledge and addresses the gaps in this area of research. Furthermore, it makes recommendations for future studies, and gives suggestions on monitoring and surveillance sites that are necessary in designing both local and regional level integrated pest management (IPM) policing of palm tree and other affected cultivated crops.
Assessment of accuracy for target detection in 3D-space using eye tracking and computer vision
Authors: Leroux Martin , Achiche Sofiane , Raison Maxime
Published: January 2018

Over the last decade, eye tracking systems have been developed and used in many fields, mostly to identify targets on a screen, i.e. a plane. For novel applications such as the control of robotic devices by the user vision, there is a great interest in developing methods base on eye tracking to identify target points in free three dimensional environments. The objective of this paper is to characterise the accuracy the eye tracking and computer vision combination that was designed recently to overcome many limitations of eye tracking in 3D space. We propose a characterization protocol to assess the behavior of the accuracy of the system over the workspace of a robotic manipulator assistant. Applying this protocol to 33 subjects, we estimated the behavior of the error of the system relatively to the target position on a cylindrical workspace and to the acquisition time. Over our workspace, targets are located on average at 0.84 m and our method shows an accuracy 12.65 times better than the calculation of the 3D point of gaze. With the current accuracy, many potential applications become possible, such as visually controlled robotic assistants in the field of rehabilitation and adaptation engineering.
Concrete vs abstract words – what do you recall better? A study on dual coding theory
Authors: Yui Lin , Ng Roslin , Perera-W.A. Hiran
Published: January 2018

This study was conducted to investigate the theory of dual coding on remembering words, by testing whether concrete words are better recalled than abstract words. A total of 298 (from Asian ethnicity) participants took part in this study. The participants were divided into two groups, where each group was given a list of abstract or concrete words. Then, they were asked to write down as many words as they recall within two minute. The results demonstrated that the participants recalled concrete words better than the abstract words, supporting previous studies.
A novel universal probe library quantitative reverse transcription polymerase chain reaction method to profile immunological gene expression in blood of captive beluga whales (Delphinapterusleucas)
Authors: Tsai Ming-An , Chen I-Hua , Wang Jiann-Hsiung , Chou Shih-Jen , Li Tsung-Hsien , Leu Ming-Yih , Ho Hsiao-Kuan , Yang Wei Cheng
Published: January 2018

Cytokines are fundamental for a functioning immune system, and thus, potentially serve as important indicators of animal health. Quantitation of mRNA using quantitative reverse transcription polymerase chain reaction (qRT-PCR) is an established immunological technique. It is particularly suitable for detecting the expression of proteins against which monoclonal antibodies are not available. In this study, we developed a novel probe-based quantitative gene expression assay for immunological assessment of captive beluga whales ( Delphinapterusleucas ) that is one of the most common cetacean species on display in aquariums worldwide. Six immunologically relevant genes (IL-2Rα, -4, -10, -12, TNFα, and IFNγ) were selected for analysis, and two validated housekeeping genes (PGK1 and RPL4) with stable expression were used as reference genes. Sixteen blood samples were obtained from four animals with different health conditions and stored in RNAlater solution. These samples were used for RNA extraction followed by qRT-PCR analysis. Analysis of gene transcripts was performed by relative quantitation using the comparative Cq method with the integration of amplification efficiency and two reference genes. The expression levels of each gene in the samples from clinically healthy animals were normally distributed. Transcript outliers for IL-2Rα, IL-4, IL-12, TNFα, and IFNγ were noticed in four samples collected from two clinically unhealthy animals. This assay has the potential to identify immune system deviation from normal state, which is caused by health problems. Furthermore, knowing the immune status of captive cetaceans could help both trainers and veterinarians in implementing preventive approaches prior to disease onset.
Freeze-thaw decellularization of the trabecular meshwork in an ex vivo eye perfusion model
Authors: Dang Yalong , Waxman Susannah , Wang Chao , Jensen Adrianna , Loewen Ralitsa T , Bilonick Richard , Loewen Nils A
Published: January 2018

Objective: Trabecular meshwork (TM) is the primary substrate of outflow resistance in glaucomatous eyes. Repopulating diseased TM with fresh, functional TM cells might represent a novel therapeutic breakthrough. Various decellularized TM scaffolds were developed by ablating existing cells with suicide gene therapy or saponin, but always with incomplete cell removal or dissolve the extracellular matrix. We hypothesized that a chemical-free, freeze-thaw method would be able to produce a fully decellularized TM scaffold for cell transplantation.

Materials and Methods: We obtained 24 porcine eyes from a local abattoir, dissected and mounted them in an anterior segment perfusion and pressure transduction system within two hours of sacrifice. After they stabilized for 72 hours, eight eyes each were assigned to freeze-thaw (F) ablation (-80°C×2), to 0.02% saponin (S) treatment, or the control group (C), respectively. The trabecular meshwork was transduced with an eGFP expressing feline immunodeficiency viral (FIV) vector and tracked via fluorescent microscopy to confirm ablation. Following treatment, the eyes were perfused with standard tissue culture medium for 180 hours. We assessed histological changes by hematoxylin and eosin staining. TM cell viability was evaluated with a calcein AM/propidium iodide (PI) assay. We measured IOP and modeled it with a linear mixed effects model using a B-spline function of time with 5 degrees of freedom.

Results: F and S experienced a similar IOP reduction by 30% from baseline (P=0.64). IOP reduction of about 30% occurred in F within 24 hours and in S within 48 hours. Live visualization of eGFP demonstrated that F conferred a complete ablation of all TM cells and only a partial ablation in S. Histological analysis confirmed that no TM cells survived in F while the extracellular matrix remained. The viability assay showed very low PI and no calcein staining in F in contrast to numerous PI-labeled dead TM cells and calcein-labeled viable TM cells in S.

Conclusion: We developed a rapid TM ablation method that uses cyclic freezing that is free of biological or chemical agents and able to produce a decellularized TM scaffold with preserved TM excellular matrix in an organotypic perfusion culture.