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Ri chicken is the most popular backyard chicken breed in Vietnam, but little is known about the growth curve of this breed. This study compared the performances of models with three parameters (Gompertz, Brody, and Logistic) and models containing four parameters (Richards, Bridges, and Janoschek) for describing the growth of Ri chicken. The bodyweight of Ri chicken was recorded weekly from week 1 to week 19. Growth models were fitted using minpack.lm package in R software and Akaike’s information criterion (AIC), Bayesian information criterion (BIC), and root mean square error (RMSE) were used for model comparison. Based on these criteria, the models having four parameters showed better performance than the ones with three parameters, and the Richards model was the best one for males and females. The lowest and highest value of asymmetric weights (α) were obtained by Bridges and Brody models for each of sexes, respectively. Age and weight estimated by the Richard model were 8.46 and 7.51 weeks and 696.88 and 487.58 g for males and for females, respectively. Differences in the growth curves were observed between males and female chicken. Overall, the results suggested using the Richards model for describing the growth curve of Ri chickens. Further studies on the genetics and genomics of the obtained growth parameters are required before using them for the genetic improvement of Ri chickens. Resumo O frango Ri é a raça de frango de quintal mais popular do Vietnã, mas pouco se sabe sobre a curva de crescimento dessa raça. Este estudo comparou o desempenho de modelos com três parâmetros (Gompertz, Brody e Logistic) e modelos contendo quatro parâmetros (Richards, Bridges e Janoschek) para descrever o crescimento do frango Ri. O peso corporal do frango Ri foi registrado semanalmente da semana 1 à semana 19. Os modelos de crescimento foram ajustados usando o pacote minpack.lm no software R e o critério de informação de Akaike (AIC); critério de informação bayesiano (BIC) e erro quadrático médio (RMSE) foram usados para comparação de modelos. Com base nesses critérios, os modelos com quatro parâmetros apresentaram melhor desempenho do que os com três parâmetros, sendo o modelo de Richards o melhor para homens e mulheres. O menor e o maior valor dos pesos assimétricos (α) foram obtidos pelos modelos Bridges e Brody para cada um dos sexos, respectivamente. A idade e o peso estimados pelo modelo de Richard foram de 8,46 e 7,51 semanas e 696,88 e 487,58 g para homens e mulheres, respectivamente. Diferenças nas curvas de crescimento foram observadas entre frangos machos e fêmeas. No geral, os resultados sugeriram o uso do modelo de Richards para descrever a curva de crescimento de frangos Ri. Mais estudos sobre a genética e genômica dos parâmetros de crescimento obtidos são necessários antes de usá-los para o melhoramento genético de frangos Ri.

Based on the previously reported 13-residue antibacterial peptide analog, brevinin-1EMa (FLGWLFKVASKVL, peptide B), we attempted to design a novel class of antiviral peptides. For this goal, we synthesized three peptides with different stapling positions (B–2S, B–8S, and B–5S). The most active antiviral peptide with the specific stapling position (B–5S) was further modified in combination with either cysteine (B–5S3C, B–5S7C, and B–5S10C) or hydrophilic amino acid substitution (Bsub and Bsub-5S). Overall, B, B–5S, and Bsub-5S peptides showed superior antiviral activities against enveloped viruses such as retrovirus, lentivirus, hepatitis C virus, and herpes simplex virus with EC50 values of 1–5 μM. Murine norovirus, a non-enveloped virus, was not susceptible to the virucidal actions of these peptides, suggesting the virus membrane disruption as their main antiviral mechanisms of action. We believe that these three novel peptides could serve as promising candidates for further development of membrane-targeting antiviral drugs in the future.

Dendrobium anosmum Lindl. var. semialba has variants of flower shapes. Currently, it has high economic value and is favored on the market. In this study, the genetic relationship of Dendrobium anosmum Lindl. var. semialba species was determined based on the analysis of chloroplast matK, rbcL gene sequences. The matK and rbcL genes of twelve species were amplified and their DNA sequenced. These DNA sequences were compared, calculated genetic distance and constructed phylogenetic tree. The results showed that 100% of samples were amplified and sequenced successfully. The analysis of matK sequences showed that 12 species had very high genetic similarity with the low genetic distance of 0 - 0.001; the nucleotide sequences were almost unchanged except for one variable nucleotide position in TB1 and TB1 was in a separate branch of the phylogenetic tree. The analysis of rbcL sequences showed that all species had a low genetic distance of 0 - 0.012 and had 7 mutant positions in nucleotide sequences of TB1 and TB5. These species were in a separate branch of the phylogenetic tree while the other species were grouped in the other branch of the phylogenetic tree. The study provided a reliable molecular database of the Dendrobium anosmum Lindl. var. semialba for identification, classification, biodiversity assessment and conservation of genetic resources.

In this study, the usage of α-amylase and wheatgrass powder supplement was investigated to reduce the fermentation duration and fortify the nutritional values of banh bo (white honeycomb cake), an indigenous cake made from rice flour and tapioca starch in Vietnam. The results indicate that the addition of 0.05 wt% and 0.07 wt% α-amylase could significantly reduce total fermentation duration from 11 to 6 h while the fortification with 0.5–2 wt% wheat grass did not significantly influence the process. All the batters exhibited strong non-Newtonian behavior, but higher consistency of batters was obtained with the addition of α-amylase. All the resultant cakes did not display a significant difference in porosity, except the cake of 0.2 wt% wheat grass. The hardness and chewiness values decreased gradually with the increase in added enzyme content, but their increasing trends were observed with the addition of wheatgrass. The supplement of wheatgrass powder significantly increased the contents of chlorophyll and phenolic compounds, which both were responsible for the increments in antioxidant capacity. Hedonic tests indicate that the sensory attributes of the final products were successfully maintained. The study may provide insights in cereal-based fermented foods.

Plastic pollution, and its associated impacts on marine fauna due to chemical contamination, is an area of growing global concern. We analyzed 145 preen gland oil samples from 32 seabird species belonging to 8 families with different foraging habits and life history strategies from around the world for plastic additives and legacy persistent organic pollutants. The additives included two brominated flame retardants (decabromodiphenyl ether, BDE209; decabromo diphenyl ethane, DBDPE) and six benzotriazole UV stabilizers (BUVSs; UVP, UV326, UV329, UV328, UV327, and UV234). Polychlorinated biphenyls (PCBs) and organochlorine pesticides (Dichlorodiphenyltrichloroethane and its metabolites: DDTs and hexachlorocyclohexane: HCHs) were detected ubiquitously. High concentrations of PCBs (up to 20,000 ng/g-lipid) were observed in the seabirds from higher-trophic level taxa. These patterns can be attributed to PCB exposure via their diet and associated biomagnification. DDT concentrations showed strong positive correlations with PCB concentrations, suggesting that DDTs in seabirds are also a result of diet and biomagnification. Plastic additives were detected sporadically as BDE209 and DBDPE were detected in 16 seabirds from 10 species (range: 3–379 ng/g-lipid) and BUVSs were detected in 46% (67) of the examined individuals (range: 2–7,055 ng/g-lipid). UV stabilizers were more frequently detected than flame retardants because UV stabilizers are more widely applied to plastic products. None of the plastic additives were correlated to the presence of PCBs, nor were they explained by the foraging area or trophic level. High concentrations of additives were detected in the species with high levels of plastic in their digestive tracts. In some of these species, such as Hawaiian petrels (Pterodroma sandwichensis) from Hawaii and flesh-footed shearwaters (Ardenna carneipes) from Western Australia, plastics were directly observed in the stomach. For other species, including great shearwaters (Ardenna gravis) from Gough Island, blue petrels (Halobaena caerulea) from Marion Island, and black-footed and Laysan albatrosses (Phoebastria nigripes and P. immutabilis) from Hawaii, plastic ingestion has been documented in literature. These patterns can be explained if the additives are mainly from ingested plastics rather than diet. The detection of BFRs and BUVSs demonstrated that a significant proportion of the examined seabirds accumulated chemicals from ingested plastics.

VEGF inhibitor drugs have been successful, especially in ophthalmology, but not all patients respond to them. Combinations of drugs are likely to be needed for more effective therapies of angiogenesis-related diseases. In this paper we describe naturally occurring combinations of receptors in endothelial cells that might help to understand how cells communicate and to identify targets for drug combinations. We also develop and share a new software tool called DECNEO to identify them.Single-cell gene expression data are used to identify a set of co-expressed endothelial cell receptors, conserved among species (mice and humans) and enriched, within a network, of connections to up-regulated genes. This set includes several receptors previously shown to play a role in angiogenesis. Multiple statistical tests from large datasets, including an independent validation set, support the reproducibility, evolutionary conservation and role in angiogenesis of these naturally occurring combinations of receptors. We also show tissue-specific combinations and, in the case of choroid endothelial cells, consistency with both well-established and recent experimental findings, presented in a separate paper.The results and methods presented here advance the understanding of signaling to endothelial cells. The methods are generally applicable to the decoding of intercellular combinations of signals.

The Kushum is a relatively new breed of horses in Kazakhstan that was established in the middle of the 20th century through a cross between mares of Kazakhstan local horses and stallions of Thoroughbred, Trotter, and Russian Don breeds to supply military horses. To reveal the genetic characteristics of this breed, we investigated haplotypes of mitochondrial DNA (mtDNA) and single-nucleotide polymorphisms of the Y chromosome, as well as genotypes of five functional genes associated with coat color, body composition, and locomotion traits. We detected 10 mtDNA haplotypes that fell into 8 of the 17 major haplogroups of horse mtDNA, indicating a unique haplotype composition with high genetic diversity. We also found two Y-chromosomal haplotypes in Kushum horses, which likely originated from Trotter and/or Don breeds. The findings regarding the mtDNA and Y-chromosomal haplotypes are concordant with the documented maternal and paternal origins of the Kushum horses. The allele frequencies of ASIP, MC1R, and MATP associated with coat color were consistent with the coat color variations of Kushum horses. The allele frequencies of MSTN associated with endurance performance and those of DMRT3 associated with gait suggested that the observed allele frequencies of these genes were the result of selective breeding for these traits. As a result of this study, we were able to obtain useful information for a better understanding of the origin and breeding history of the Kushum horse breed using molecular markers.

Understanding of animal growth is important for the improvement of management and feeding practices; however, little is known about the growth curve in Vietnamese indigenous chicken. This study was performed to determine the most appropriate models for describing the growth curve of Vietnamese Mia chicken. The study evaluated the performances of the Logistic, Gompertz, Richards, and Bridges models of body weights in 224 Mia chickens. Models were fitted using minpack.lm package in R software and Akaike's information criterion and Bayesian information criterion were used for model comparison. Based on these criteria, the Gompertz and Bridges were the best models for males and females, respectively. Estimated asymmetric weights (α) were ranged from 2,241.91 ± 14.74 (g) (Logistic) to 2,623.86 ± 30.23 (g) (Gompertz) for males and from 1,537.36 ± 10.97 (g) (Logistic) and 1,958.36 ± 72.92 (g) (Bridges) for females, respectively. The age at the inflection point was estimated from 9.32 to 10.5 weeks and from 8.51 to 9.86 weeks for males and females, respectively. In conclusion, the Gompertz model is the most suitable model for describing the growth curve of Mia chicken. The parameters obtained from growth models could help define feeding programs to meet nutritional needs from hatching to the age of maximum growth, reproduction programs, and marketing strategies.

Few studies have described the effects of physical disturbance and post-recovery of deep-sea benthic communities. Here, we explore the status of deep-sea sponge ground communities four years after being impacted by an experimental bottom trawl. The diversity and abundance of epibenthic megafauna of two distinct benthic communities in disturbed versus control areas were surveyed using a remotely operated vehicle on the Schulz Bank, Arctic Ocean. Four years after disturbance, megafaunal densities of the shallow (∼600 m depth) and deep (∼1,400 m depth) sites were significantly lower on the disturbed patches compared to the control areas. Multivariate analyses revealed a distinct separation between disturbed and control communities for both sites, with trawling causing 29–58% of the variation. Many epibenthic morphotypes were significantly impacted by the trawl, including ascidians, Geodia parva, Hexactinellida spp., Craniella infrequens, Lissodendoryx complicata, Haliclonia sp. Stylocordyla borealis, Gersemia rubiformis and Actiniaria sp. However, we found some smaller morphospecies to be equally abundant with control transects, including Polymastia thielei, Geodia hentscheli, and Stelletta rhaphidiophora, reflecting lower trawl impact for these morphotypes. Overall, our results suggest that these are fragile ecosystems that require much more time than four years to recover from physical disturbance typical of trawling activities.

The title compound (systematic name: bis{[2-(4-hydroxy-1H-indol-3-yl)ethyl]bis(propan-2-yl)azanium} but-2-enedioate tetrahydrate), 2C16H25N2O+·C4H2O4 2−·4H2O, has a singly protonated DPT cation, one half of a fumarate dianion (completed by a crystallographic centre of symmetry) and two water molecules of crystallization in the asymmetric unit. A series of N—H...O and O—H...O hydrogen bonds form a three-dimensional network in the solid state.

After hatching, juveniles of most sea turtle species undertake long migrations across ocean basins and remain in oceanic habitats for several years. Assessing population abundance and demographic parameters during this oceanic stage is challenging. Two long-recognized deficiencies in population assessment are (i) reliance on trends in numbers of nests or reproductive females at nesting beaches and (ii) ignorance of factors regulating recruitment to the early oceanic stage. To address these critical gaps, we examined 15 years of standardized loggerhead sighting data collected opportunistically by fisheries observers in the Azores archipelago. From 2001 to 2015, 429 loggerheads were sighted during 67,922 km of survey effort. We used a model-based approach to evaluate the influence of environmental factors and present the first estimates of relative abundance of oceanic-stage juvenile sea turtles. During this period, relative abundance of loggerheads in the Azores tracked annual nest abundance at source rookeries in Florida when adjusted for a 3-year lag. This concurrence of abundance patterns indicates that recruitment to the oceanic stage is more dependent on nest abundance at source rookeries than on stochastic processes derived from short term climatic variability, as previously believed.

The following protocol is intended to respond to the requirements set by the European Union’s Marine Strategy Framework Directives (MSFD) for the D10C3 Criteria reported in the Commission Decision (EU), related to the amount of litter ingested by marine animals. Standardized methodologies for extracting litter items ingested from dead sea turtles along with guidelines on data analysis are provided. The protocol starts with the collection of dead sea turtles and classification of samples according to the decomposition status. Turtle necropsy must be performed in authorized centers and the protocol described here explains the best procedure for gastrointestinal (GI) tract isolation. The three parts of the GI (esophagus, stomach, intestine) should be separated, opened lengthways and contents filtered using a 1 mm mesh sieve. The article describes the classification and quantification of ingested litter, classifying GI contents into seven different categories of marine litter and two categories of natural remains. The quantity of ingested litter should be reported as total dry mass (weight in grams, with two decimal places) and abundance (number of items). The protocol proposes two possible scenarios to achieve the Good Environmental Status (GES). First: “There should be less than X% of sea turtles having Y g or more plastic in the GI in samples of 50-100 dead turtles from each sub-region”, where Y is the average weight of plastic ingested and X% is the percentage of sea turtles with more weight (in grams) of plastic than Y. The second one, which considers the food remain versus plastic as a proxy of individual health, is: “There should be less than X% of sea turtles having more weight of plastic (in grams) than food remains in the GI in samples of 50-100 dead turtles from each sub-region”. © 2019 Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License.

The use of plant growth-promoting rhizobacteria as a sustainable alternative for chemical nitrogen fertilizers has been explored for many economically important crops. For one such strain isolated from rice rhizosphere and endosphere, nitrogen-fixing Pseudomonas stutzeri A15, unequivocal evidence of the plant growth-promoting effect and the potential contribution of biological nitrogen fixation (BNF) is still lacking. In this study, we investigated the effect of P. stutzeri A15 inoculation on the growth of rice seedlings in greenhouse conditions. P. stutzeri A15 induced significant growth promotion compared to uninoculated rice seedlings. Furthermore, inoculation with strain A15 performed significantly better than chemical nitrogen fertilization, clearly pointing to the potential of this bacterium as biofertilizer. To assess the contribution of BNF to the plant growth-promoting effect, rice seedlings were also inoculated with a nitrogen fixation-deficient mutant. Our results suggest that BNF (at best) only partially contributes to the stimulation of plant growth.

Although gastroenteritis is the most commonly described manifestation of Edwardsiella tarda infection, the pathogenesis and transient or long-term colonization of the gastrointestinal tract of this organism in human disease is not clear. We describe a rare manifestation of E. tarda infection in a perihepatic abscess in the setting of a patient with perforated cholecystitis and its successful eradication following antibiotic treatment.

The presence of microplastic in marine fishes has been well documented but few studies have directly examined differences between fishes occupying contrasting environmental compartments. In the present study, we investigated the gut contents of 390 fishes belonging to three pelagic (blue jack mackerel, chub mackerel, skipjack tuna) and two deep-sea species (blackbelly rosefish, blackspot seabream) from the Azores archipelago, North-East Atlantic for microplastic contamination. Our results revealed that pelagic species had significantly more microplastic than the deep-water species. In all of the species studied, fragments were the most common plastic shape recovered and we found a significant difference in the type of polymer between the pelagic and deep-water species. In deep-sea fish we found almost exclusively polypropylene, whereas in the pelagic fish, polyethylene was the most abundant polymer type. Overall, the proportion of fish containing plastic items varied across our study species from 3.7% to 16.7% of individuals sampled, and the average abundance of plastic items ranged from 0.04 to 0.22 per individual (the maximum was 4 items recovered in one stomach). Despite the proximity of the Azores archipelago to the North Atlantic subtropical gyre, a region of elevated plastic abundance, the proportion of individuals containing plastic (9.49%) were comparable with data reported elsewhere.

Background Non-small cell lung cancer (NSCLC) accounts for approximately 80-85% of all lung cancer cases, and is characterized by a poor response to chemotherapy and a low survival rate. Treatment targeting the immune checkpoint inhibitor pathway PD-1/PD-L1 has been found to be effective against NSCLC with manageable side effects, but with only 20-25% of patients showing a positive response there is an urgent need for additional immunotherapy options for this group of patients. LAG-3 and PD-1 are often co-expressed and upregulated on T cells leading to immune exhaustion and tumor growth, and co-blockade of the LAG-3 and PD-1 pathways has been shown to synergize to improve T cytotoxic cell responses. Methods In order to perform a comprehensive immunoprofiling of NSCLC tumors we used MultiOmyx™, an immunofluorescence (IF) multiplexing assay that utilize a pair of directly conjugated Cyanine dye-labeled (Cy3, Cy5) antibodies per round of staining. Using a 16-marker panel we have analyzed the proportion of B cells, T cell subtypes, M1/M2-type tumor-associated macrophages, as well as the expression of PD-1, PD-L1, LAG-3, and TIM-3 in 20 samples from patients with NSCLC. Results LAG-3 was found to be expressed mainly on T cytotoxic cells in both subtypes, but the overall density of LAG-3 was 59% higher in squamous cell carcinoma (SCC) tumors compared to adenocarcinoma tumors. In both SCC and adenocarcinoma subtypes TIM-3 was found primarily on tumor-associated macrophages (TAMs), followed by an equal distribution on helper and cytotoxic T cells. When analyzing the proportion of T cytotoxic cells infiltrating into the tumor area, we observed an apparent synergy between LAG-3 and PD-1, suggesting a therapeutic benefit of dual checkpoint blockade of LAG-3 and PD-1 in NSCLC. Conclusion It is our hope that these data will help provide new insights into the biology of NSCLC that can ultimately be used to explore novel immunotherapeutic interventions for lung cancer treatment. Legal entity responsible for the study NeoGenomics. Funding NeoGenomics. Disclosure A. Juncker-Jensen: Full / Part-time employment: NeoGenomics. M. Nagy: Full / Part-time employment: NeoGenomics. J. Kuo: Full / Part-time employment: NeoGenomics. E. Leones: Full / Part-time employment: NeoGenomics. F. Sahafi: Full / Part-time employment: NeoGenomics. K. Pham: Full / Part-time employment: NeoGenomics. E. Parnell: Full / Part-time employment: NeoGenomics.

Cold-water corals and sponges aggregations are important features of the deep sea, recently classified as vulnerable marine ecosystems (VMEs). VMEs increase habitat complexity, believed to act as feeding, reproductive, nursery and refuge areas for a high number of invertebrates and fish species. In the Azores archipelago (NE Atlantic), VMEs are prevalent but their ecological role has not received much attention. The objective of this study was to investigate the importance of VMEs in influencing the distribution of demersal fish in the Azores. With data collected during experimental longline surveys , we modeled the catch of six demersal fish species of commercial value (Helicolenus dactylopterus, Pagellus bogaraveo, Mora moro, Conger conger, Phycis phycis, Pontinus kuhlii) in relation to the presence of VMEs and other environmental factors using General Additive Models (GAMs). Our study demonstrated that total fish catch was higher inside VMEs but the relationship between fish and VMEs varied among fish species. Species specific models showed that catch was strongly influenced by environmental factors, mainly depth, whilst the presence of VMEs was only important for two rockfish species; juvenile and adult P. kuhlii and juvenile H. dactylopterus. Although the association between deep-sea demersal fish and VMEs may be an exception to the rule, we suggest that VMEs act as an important habitat for two commercially important species in the Azores.

Giardia is a single-celled parasite causing significant diarrheal disease in several hundred million people worldwide. Due to limited access to the site of infection in the gastrointestinal tract, our understanding of the dynamics of Giardia infections in the host has remained limited and largely inferred from laboratory culture. To better understand Giardia physiology and colonization in the host, we developed imaging methods to quantify Giardia expressing bioluminescent physiological reporters in two relevant animal models. We discovered that parasites primarily colonize and encyst in the proximal small intestine in discrete, high-density foci. We also show that high parasite density contributes to encystation initiation., Giardia lamblia is a highly prevalent yet understudied protistan parasite causing significant diarrheal disease worldwide. Hosts ingest Giardia cysts from contaminated sources. In the gastrointestinal tract, cysts excyst to become motile trophozoites, colonizing and attaching to the gut epithelium. Trophozoites later differentiate into infectious cysts that are excreted and contaminate the environment. Due to the limited accessibility of the gut, the temporospatial dynamics of giardiasis in the host are largely inferred from laboratory culture and thus may not mirror Giardia physiology in the host. Here, we have developed bioluminescent imaging (BLI) to directly interrogate and quantify the in vivo temporospatial dynamics of Giardia infection, thereby providing an improved murine model to evaluate anti-Giardia drugs. Using BLI, we determined that parasites primarily colonize the proximal small intestine nonuniformly in high-density foci. By imaging encystation-specific bioreporters, we show that encystation initiates shortly after inoculation and continues throughout the duration of infection. Encystation also initiates in high-density foci in the proximal small intestine, and high density contributes to the initiation of encystation in laboratory culture. We suggest that these high-density in vivo foci of colonizing and encysting Giardia likely result in localized disruption to the epithelium. This more accurate visualization of giardiasis redefines the dynamics of the in vivo Giardia life cycle, paving the way for future mechanistic studies of density-dependent parasitic processes in the host. IMPORTANCE Giardia is a single-celled parasite causing significant diarrheal disease in several hundred million people worldwide. Due to limited access to the site of infection in the gastrointestinal tract, our understanding of the dynamics of Giardia infections in the host has remained limited and largely inferred from laboratory culture. To better understand Giardia physiology and colonization in the host, we developed imaging methods to quantify Giardia expressing bioluminescent physiological reporters in two relevant animal models. We discovered that parasites primarily colonize and encyst in the proximal small intestine in discrete, high-density foci. We also show that high parasite density contributes to encystation initiation.

Juvenile oceanic-stage sea turtles are particularly vulnerable to the increasing quantity of plastic coming into the oceans. In this study, we analysed the gastrointestinal tracts of 24 juvenile oceanic-stage loggerheads ( Caretta caretta ) collected off the North Atlantic subtropical gyre, in the Azores region, a key feeding ground for juvenile loggerheads. Twenty individuals were found to have ingested marine debris (83%), composed exclusively of plastic items (primarily polyethylene and polypropylene) identified by μ-Fourier Transform Infrared Spectroscopy. Large microplastics (1–5 mm) represented 25% of the total number of debris and were found in 58% of the individuals sampled. Average number of items was 15.83 ± 6.09 (± SE) per individual, corresponding to a mean dry mass of 1.07 ± 0.41 g. The results of this study demonstrate that plastic pollution acts as another stressor for this critical life stage of loggerhead turtles in the North Atlantic.

Giardiais a highly prevalent, understudied protistan parasite causing significant diarrheal disease worldwide. Its life cycle consists of two stages: infectious cysts ingested from contaminated food or water sources, and motile trophozoites that colonize and attach to the gut epithelium, later encysting to form new cysts that are excreted into the environment. Current understanding of parasite physiology in the host is largely inferred from transcriptomic studies usingGiardiagrown axenically or in co-culture with mammalian cell lines. The dearth of information about the diversity of host-parasite interactions occurring within distinct regions of the gastrointestinal tract has been exacerbated by a lack of methods to directly and non-invasively interrogate disease progression and parasite physiology in live animal hosts. By visualizingGiardiainfections in the mouse gastrointestinal tract using bioluminescent imaging (BLI) of tagged parasites, we recently showed that parasites colonize the gut in high-density foci that may cause localized pathology to the epithelium. Encystation is also initiated in these foci throughout the entire course of infection, yet how the physiology of parasites within high-density foci in the host gut differs from that of cells in laboratory culture is unclear. Here we use BLI to precisely select parasite samples from high-density foci in the proximal intestine to interrogatein vivo Giardiagene expression in the host. Relative to axenic culture, we noted significantly higher expression (> 10-fold) of oxidative stress, membrane transporter, and metabolic and structural genes associated with encystation in the high-density foci. These differences in gene expression within parasite foci in the host may reflect physiological changes associated with high-density growth in localized regions of the gut. We also identified and verified six novel cyst-specific proteins, including new components of the cyst wall that were highly expressed in these foci. Ourin vivotranscriptome data support an emerging view that parasites encyst early in localized regions in the gut, possibly as a consequence of nutrient limitation, and also impact local metabolism and physiology.

The envelope protein VP28 of white spot syndrome virus (WSSV) is considered a candidate antigen for use in a potential vaccine to this important shrimp pathogen (the cause of white spot syndrome, WSS). Here, we used spores of Bacillus subtilis to display VP28 on the spore surface. Trials were conducted to evaluate their ability to protect shrimps against WSSV infection. The gene cotB-vp28 was integrated into the chromosome of the laboratory strain B. subtilis PY79, and expression of CotB-VP28 was detected by Western blotting and immunofluorescence. Expression of CotB-VP28 was equivalent to 1000 molecules per spore. PY79 and CotB-VP28 spores were mixed with pellets for feeding of whiteleg shrimps (Litopenaeus vannamei), followed by WSSV challenge. Superoxidase dismutase (SOD), phenoloxidase activities and mortality rates of the two shrimp groups were evaluated. Groups fed with PY79 and CotB-VP28 spores at day 7 had increased SOD activities of 29% and increased phenoloxidase activities of 15% and 33%, respectively, compared to those of the control group. Fourteen days postchallenge, 35% of vaccinated shrimps had died compared to 49% of those fed naked spores (PY79) and 66% untreated, unchallenged animals. These data suggest that spores expressing VP28 have potential as a prophylactic treatment of WSS.

Malcolm Roy Clarke (1930–2013) was a British teuthologist who made an important contribution to marine science in the Azores archipelago (Portugal). Malcolm started doing research in the Azores from 1980s onward, settling for residency in 2000 after retirement (in 1987). He kept publishing on Azorean cephalopods collaborating in 20% of the peer reviewed works focus- ing on two main areas: dietary studies; and the ecology of cephalopods on seamounts. Since his first visit in 1981, he was involved in the description of the dietary ecology of several cetaceans, seabirds, and large pelagic and deep-water fish. Using his own data, Malcolm revised the association of cephalopods with seamounts, updating and enlarging the different cephalopod groups according to species behaviour and ecology. Malcolm taught several students working in the Azores on cephalopods and beak identification, lecturing the Third International Workshop in Faial (2007). He empowered the recently established research community, by providing important contacts with foreign institutes and informal advice. He collaborated in the regional cetacean stranding network (RACA) and was an active member of the advisory board of the journal Arquipelago—Life and Marine Sciences. But the scientific role of Malcolm Clarke in the Azores went beyond his academic activities. In the last 10 years Malcolm and Dot Clarke dedicated themselves to building and running a museum on Pico Island, showing the biology of the sperm whale and its interaction with squid; a cultural and touristic legacy for future generations to enjoy. Directorate for Education, Science and Culture, of the Regional Government of the Azores (M3.1.2/F/062/2011) info:eu-repo/semantics/publishedVersion

Distribution of fish assemblages and habitat associations of demersal fishes on the Condor seamount were investigated by analyzing in situ video imagery acquired by the Remotely-Operated Vehicles ROV SP 300 and Luso 6000. A total of 51 fish taxa from 32 families were inventoried. Zooplanktivores (10 species) were the most abundant group followed by carnivores (23 species) and benthivores (18 species). Non-metric multidimensional scaling (MDS) analyses were performed on dive segments to visualize the spatial relationships between species and habitat type, substrate type or depth, with depth being the most significant parameter influencing fish distribution. Four major fish groups were identified from their vertical distribution alone: summit species (generally to

a b s t r a c t Knowledge on historical fisheries removal is essential for adopting an ecosystem approach to the man- agement of marine resources. Shore-based whaling was an important economic activity for the Azores archipelago with 23,557 sperm whales (Physeter macrocephalus) captured between 1896 and 1987. The corresponding biomass is unknown because local official fisheries statistics report this extractive compo- nent in number of sperm whales and total oil production. The objective of this study was to estimate total sperm whale biomass removed during shore-based whaling operations using two different methods: (1) a function of length of males and females and (2) a function of oil extraction efficiency. The estimated sperm whale biomass removed from Azorean waters by shore-based whalers between 1896 and 1987 was 361,039 tonnes (250,297-619,561 tonnes). For the period 1950-1987, sperm whale catches repre- sented 29% of the total biomass removed by fisheries, including whaling. At the peak of whaling activity (1950-1957), sperm whale catches were about twice the amount reported by the fisheries sector. The results show that biomass removal by whaling was important in the scope of the regional fisheries. Con- sequently, including sperm whale biomass extractions into the total marine fisheries catch for the Azores is of high relevance for implementing an ecosystem approach to management.

Understanding the link between fish and their habitat is essential for an ecosystem approach to fisheries management. However, determining such relationship is challenging, especially for deep-sea species. In this study, we applied generalized additive models (GAMs) to relate presence–absence and relative abundance data of eight economically-important fish species to environmental variables (depth, slope, aspect, substrate type, bottom temperature, salinity and oxygen saturation). We combined 13 years of catch data collected from systematic longline surveys performed across the region. Overall, presence–absence GAMs performed better than abundance models and predictions made for the observed data successfully predicted the occurrence of the eight deep-sea fish species. Depth was the most influential predictor of all fish species occurrence and abundance distributions, whereas other factors were found to be significant for some species but did not show such a clear influence. Our results predicted that despite the extensive Azores EEZ, the habitats available for the studied deep-sea fish species are highly limited and patchy, restricted to seamounts slopes and summits, offshore banks and island slopes. Despite some identified limitations, our GAMs provide an improved knowledge of the spatial distribution of these commercially important fish species in the region.

Giardiais a highly prevalent, yet understudied protistan parasite causing diarrheal disease worldwide. Hosts ingestGiardiacysts from contaminated sources. In the gastrointestinal tract, cysts excyst to become motile trophozoites, colonizing and attaching to the gut epithelium. Trophozoites later differentiate into infectious cysts that are excreted and contaminate the environment. Due to the limited accessibility of the gut, the temporospatial dynamics of giardiasis in the host is largely inferred from laboratory culture and thus may not mirrorGiardiaphysiology in the host. Here we have developed bioluminescent imaging (BLI) to directly interrogate and quantify thein vivotemporospatial dynamics of giardiasis, thereby providing an improved murine model to evaluate anti-Giardiadrugs. Using BLI, we determined that parasites primarily colonize the proximal small intestine non-uniformly in high-density foci. By imaging encystation-specific bioreporters, we show that encystation initiates shortly after inoculation and continues throughout the entire duration of infection. Encystation also initiates in high-density foci in the proximal small intestine, and high-density laboratory cultures of parasites are also stimulated to encyst. This work overturns the assumption that parasites encyst later during infection as they are dislodged and travel through the colon. We suggest that these high-density regions of parasite colonization likely result in localized pathology to the epithelium, and encystation occurs when trophozoites reach a threshold density due to local nutrient depletion. This more accurate visualization of giardiasis redefines the dynamics ofin vivo Giardialife cycle, paving the way for future mechanistic studies of density-dependent parasitic processes in the host.SignificanceGiardiais a single-celled parasite causing both acute and chronic diarrheal disease in over one billion people worldwide. Due to limited access to the site of infection in the gastrointestinal tract, our understanding of the dynamics ofGiardiainfections in the host has remained limited, and largely inferred from laboratory culture. To better understand giardiasis in the host, we developed imaging methods to quantifyGiardiaexpressing bioluminescent physiological reporters in live mice. We discovered that parasites primarily colonize and encyst in the proximal small intestine in discrete, high-density foci. Furthermore, this work provides evidence of a parasite density-based threshold for the differentiation ofGiardiainto cysts in the host. These findings overturn existing paradigms of giardiasis infection dynamics in the host.

The impact of bottom trawling on cold-water corals (CWC) has been thoroughly studied and shown to be long-lasting; however the effects of bottom longlining on CWC ecosystems have received little attention. The present paper identifies the principal CWC species landed by bottom longlining in Faial (Azores) from 150 to 600 m depth. Data were obtained from a survey of 297 landings during four months coupled with 16 interviews with fishermen. A distinction was made among corals brought on deck directly entangled in the fishing gear (primary by-catch) from corals brought up associated with other larger CWC species or rocks (secondary by-catch). Forty-five (15.2%) of 297 fishing trips surveyed landed coral specimens. The survey recorded 39 different CWC taxa in the by-catch, belonging to five different orders (Scleractinia, Alcyonacea, Antipatharia, Zoanthidea and Anthoathecata). Secondary by-catch included a larger number of species but the total number of corals was in the same order of magnitude for both groups. The taxa most frequently encountered were Leiopathes spp., Errina dabneyiand Dendrophyllia sp. CWC taxa in the by-catch were mostly medium size (10–60 cm), 3-dimensional and branched colonies. Local ecological knowledge of fishermen confirmed that the corals recorded were representative of their past experience and also revealed a general agreement that there has been a decrease of CWC by-catch on traditional fishing grounds. Corals are common by-catch in bottom longline fisheries around the Azores and so conservation measures may be required.

SummaryGenome sequences of diverse free-living protists are essential for understanding eukaryotic evolution and molecular and cell biology. The free-living amoeboflagellate Naegleria gruberi belongs to a varied and ubiquitous protist clade (Heterolobosea) that diverged from other eukaryotic lineages over a billion years ago. Analysis of the 15,727 protein-coding genes encoded by Naegleria's 41 Mb nuclear genome indicates a capacity for both aerobic respiration and anaerobic metabolism with concomitant hydrogen production, with fundamental implications for the evolution of organelle metabolism. The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing us to identify thousands of genes likely present in the pan-eukaryotic ancestor, with 40% likely eukaryotic inventions. Moreover, we construct a comprehensive catalog of amoeboid-motility genes. The Naegleria genome, analyzed in the context of other protists, reveals a remarkably complex ancestral eukaryote with a rich repertoire of cytoskeletal, sexual, signaling, and metabolic modules.PaperClip

The profitability of octopus ongrowing remains limited because low cost artificial diets have not yet been effectively developed. Therefore, alternative, low cost diets are worth exploring. In this study, we have investigated the growth and mortality of octopuses fed strictly on mackerel (Scomber colias), a low cost fish, readily available in the Azores Archipelago. Different weight classes (150-300; 300-600; and 600-1,000 g) were maintained at two stocking densities; 5 versus 12 individuals (ranging between 0.38-2.72 kg m -3 ). The trial lasted 72 days and was performed in an open system composed of large rectangular tanks. Each individual was tagged, and growth was followed weekly. Mean instantaneous growth rate (G) varied between 0.67 and 1.47 (% increase in body weight day -1 ), depending on initial body size. Survival was 100% for octopuses held in tanks at low density. On the other hand, increased aggressive interactions in high density tanks resulted in higher mortality rates (MR), especially for the smallest size class (MR ¼ 66.7%). The results of this study suggest that with a monodiet of mackerel, subadult octopuses of 300 g can reach commercial size (750 g) in 2.5 mo. However, high mortality under elevated stocking densities will hinder commercial profitability with such diet. A proposed approach to increase survival would be to periodically supplement the monodiet with crustacean flesh.

Despite being an exploited and economically important species, little is known about the reproductive behaviour ofLoligo forbesi. During a captive trial performed in a closed seawater system in the Azores, three spawning events were directly witnessed. An account of their main behavioural aspects is given. A number of behavioural components are described for the first time in this species: ‘pair formation’, ‘mate guarding’, ‘egg holding’, ‘egg touching’, ‘white arms’, ‘red accessory nidamental glands’, ‘accentuated testis’, and ‘jockeying and parrying’. The chromatic, locomotor and postural components were very similar to other coastal loliginids observed on spawning grounds. From egg masses recovered on octopus traps, we show that in the Azores spawning activity occurs at least between 25 and 144 m, but greater depths might be expected. We suggest that this squid preferentially deposits egg masses on hard structures probably hiding them in cracks and crevices of volcanic substrata. The existence of spawning aggregations is supported by several factors: (i) these spawning grounds may coincide with the fishing spots, where the exploitation seasonally takes place, given that most individuals caught by fishermen are usually mature (more than 80%); and (ii) mate guarding and jockeying/parrying by males was observed, which is a common feature of spawning aggregation areas, where sperm competition occurs. Furthermore, our results, combined with available published and non-published data further confirmL. forbesias an intermittent spawner. We estimate that throughout their short life cycle, females ofL. forbesiare able to perform up to six spawning events, each composed of an average of ≈2300 eggs.

Pham, Kasey K. [et al.], Major public DNA databases — NCBI GenBank, the DNA DataBank of Japan (DDBJ), and the European Molecular Biology Laboratory (EMBL) — are invaluable biodiversity libraries. Systematists and other biodiversity scientists commonly mine these databases for sequence data to use in phylogenetic studies, but such studies generally use only the taxonomic identity of the sequenced tissue, not the specimen identity. Thus studies that use DNA supermatrices to construct phylogenetic trees with species at the tips typically do not take advantage of the fact that for many individuals in the public DNA databases, several DNA regions have been sampled; and for many species, two or more individuals have been sampled. Thus these studies typically do not make full use of the multigene datasets in public DNA databases to test species coherence and select optimal sequences to represent a species. In this study, we introduce a set of tools developed in the R programming language to construct individual-based trees from NCBI GenBank data and present a set of trees for the genus Carex (Cyperaceae) constructed using these methods. For the more than 770 species for which we found sequence data, our approach recovered an average of 1.85 gene regions per specimen, up to seven for some specimens, and more than 450 species represented by two or more specimens. Depending on the subset of genes analyzed, we found up to 42% of species monophyletic. We introduce a simple tree statistic—the Taxonomic Disparity Index (TDI)—to assist in curating specimen-level datasets and provide code for selecting maximally informative (or, conversely, minimally misleading) sequences as species exemplars. While tailored to the Carex dataset, the approach and code presented in this paper can readily be generalized to constructing individual-level trees from large amounts of data for any species group., Funding for this work was provided by the National Science Foundation (Award #1255901 to ALH andMJWand Award #1256033 to EHR), including an REU supplement that supported KKP’s work.

We describe continuing work to develop restriction endonucleases as tools to enrich targeted genomes of interest from diverse populations. Two approaches were developed in parallel to segregate genomic DNA based on cytosine methylation. First, the methyl-sensitive endonuclease HpaII was used to bind non-CG methylated DNA. Second, a truncated fragment of McrB was used to bind CpG methylated DNA. Enrichment levels of microbial genomes can exceed 100-fold with HpaII allowing improved genomic detection and coverage of otherwise trace microbial genomes from sputum. Additionally, we observe interesting enrichment results that correlate with the methylation states not only of bacteria, but of fungi, viruses, a protist and plants. The methods presented here offer promise for testing biological samples for pathogens and global analysis of population methylomes.

We reported earlier that exposure to exogenous bone morphogenetic protein 7 (BMP7) could strongly inhibit serum starvation–induced apoptosis to C4-2B cell line, a variant of the LNCaP human prostate cancer cell line with propensity for bone metastasis. Whereas serum starvation suppressed the expression of survivin, a member of the inhibitor of apoptosis protein family, its expression was sustained in the presence of BMP7. In this study, we present evidence that BMP7 exposure up-regulated survivin promoter activity, an effect that was associated with activation of Smad, and could be repressed by dominant-negative Smad5. Additionally, serum starvation–induced suppression of c-jun NH2-terminal kinase (JNK) activity in C4-2B cells could be mostly restored by BMP7, and a JNK inhibitor could counteract the antiapoptotic effect of BMP7, without a significant effect on the level of survivin expression. Thus, we identified JNK pathway as another signaling mode for the antiapoptotic function of BMP7. To test the effect of endogenous up-regulation of BMP7, we genetically modulated the C4-2B cell line to overexpress BMP7 protein. Not only was this altered cell line resistant to serum starvation–induced apoptosis but it also exhibited patterns of Smad activation, survivin up-regulation, and JNK activation similar to those of the parental C4-2B cells exposed to exogenous BMP7. Consistent with these in vitro findings of BMP7 action, we acquired correlative results of Smad activation, survivin expression, and JNK activation in the progression of prostate cancer in the conditional Pten deletion mouse model, in which we first obtained the evidence of BMP7 overexpression. (Cancer Res 2006; 66(8): 4285-90)

We investigated the immobilization of actin filaments and its self-assembly in vitro in a continuous-flow system on poly(styrene-maleic acid) (PSMA), poly(methyl methacrylate) (PMMA), poly(t-butyl methacrylate) [P(tBuMA)] polymeric surfaces and along the linear channels. Among these polymeric surfaces, PSMA appeared to be more suitable for supramolecular manipulations as it lacked inherent fluorescence, had good biocompatibility with actin-myosin, and provided sufficient amounts of binding sites for the covalent immobilization of actin. Covalent attachment of G-actin on PSMA polymeric surfaces resulted in stable polymerization followed by alignment of filaments over 1.5 h, along with a greater surface density of the proteins. It is shown that electrostatic condensation of intact F-actin filaments and F-actin/gelsolin filaments with Ba2+ can be successfully used for progressive bundle formation and alignment in the constant flow. Actin bundles retained their ability to support HMM-anti-HMM bead translocation. Long-range cooperative transitions in actin induced by gelsolin represent a structural perturbation of the barbed end and presumably result in regularly organized bundles that secure directional movement. This simple technique for fabrication of self-assembled and aligned F-actin/gelsolin bundles provides a convenient experimental system for nanotechnological applications.

Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence annotation of the reference plant Arabidopsis . Sequencing full-length cDNAs and hybridizations using RNA populations from various tissues to a set of high-density oligonucleotide arrays spanning the entire genome allowed the accurate annotation of thousands of gene structures. We identified 5817 novel transcription units, including a substantial amount of antisense gene transcription, and 40 genes within the genetically defined centromeres. This approach resulted in completion of ∼30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome.

The adhesion of the marine alpha-Proteobacteria Sulfitobacter pontiacus, Sulfitobacter mediterraneus, Sulfitobacter brevis, and Staleya guttiformis to a poly(tert-butyl methacrylate) (PtBMA) polymeric surface generates unusual cell morphological peculiarities following attachment. While the type strains S. pontiacus and S. brevis failed to attach to PtBMA, the vegetative cells of type strain S. mediterraneus underwent morphological conversion into coccoid forms during the attachment over an incubation period of 24-72 h. Type strain St. guttiformis cells formed a multilayered biofilm on the PtBMA surface, presumably facilitated by bacterial production of extracellular polysaccharides. The attachment behavior and fine structure of these coccoid forms have been described using atomic force microscopy. The impact of polymeric surfaces of defined hydrophobicity on the formation of coccoid bodies is discussed.

The distribution of 30 HLA-DRB1 alleles in 85 individuals and of 10 HLA-DQB1 alleles in 91 individuals of the Viet Muong population was studied and compared with those of nine other Asian populations, including 103 Viet Kinh belonging to the major ethnic group in Vietnam. In terms of genetic distance, our data are consistent with a close ethnogeographic relationship between Viet Muong, Buyi and Dai Lue, two Southern Chinese ethnic groups. Conversely, these three populations are distant from the Northern Chinese population. The Viet Kinh belong to an intermediate group, together with North-eastern Thais, Thais and present day Thais. The striking presence of the HLA-DQ1*0502 allele (48% frequency) in the Viet Muongs is possibly anthropological or environmental in origin: the Viet Muongs have been submitted to endemic malaria for centuries, and the survivors carry the protective trait of glucose-6-phosphate dehydrogenase deficiency. This raises the hypothesis of a possible resistance to lethal or severe forms of the disease, where the association with a specific HLA-DQB1 allele may play a role.

Next-generation sequencing (NGS) technologies have raised a challenging de novo genome assembly problem that is further amplified in recently emerged single-cell sequencing projects. While various NGS assemblers can use information from several libraries of read-pairs, most of them were originally developed for a single library and do not fully benefit from multiple libraries. Moreover, most assemblers assume uniform read coverage, condition that does not hold for single-cell projects where utilization of read-pairs is even more challenging. We have developed an exSPAnder algorithm that accurately resolves repeats in the case of both single and multiple libraries of read-pairs in both standard and single-cell assembly projects. Availability and implementation: http://bioinf.spbau.ru/en/spades Contact: ap@bioinf.spbau.ru

An Arabidopsis cDNA clone encoding a DNA-binding protein, RAP-1, was isolated by southwestern screening of an Escherichia coli cDNA expression library. The protein contains a bHLH DNA-binding domain and is homologous to R proteins, regulating anthocyanin biosynthesis. RAP-1 binds to the sequence CACNTG. It is encoded by a single gene, which is expressed to high levels in root and stem and to low levels in leaf and flower. No expression could be detected in siliques. Rap-1 does not correspond to one of the known loci involved in anthocyanin biosynthesis, since it is located at a different map position. In contrast to the maize R protein Lc, RAP-1 did not induce anthocyanin biosynthesis in pea cotyledons. Thus, RAP-1 is a novel member of the bHLH class of DNA-binding proteins.

Esculentin-2EM is a 37-residue, cationic, amphipathic, α-helical antimicrobial peptide isolated from a Korean frog, Glandirama emeljanovi. Many studies revealed that truncation of this peptide results in substantial decreases in its antimicrobial activity. Lee and his colleagues have recently reported that a 23-residue esculentin-2EM analog containing a tryptophanyl substitution at position 16 showed a significant recovery of the antimicrobial activity of the parent peptide. Here we report a new series of 15-residue esculentin-2EM analogs which are constrained into an α-helical conformation via an oct-4-enyl cross-link. The resulting 'stapled' derivatives displayed remarkable increases not only in antimicrobial activity but also in helical content and protease resistance compared to Lee's original 23-residue esculentin-2EM analog. The preliminary data obtained in this work strongly supports the potential of our strategy for the development of a new class of peptide antibiotics.

Proceedings of the 19th International Conference on Radionuclide Metrology and its Applications 17–21 June 2013, Antwerp, Belgium.-- et al., A Certified Reference Material (CRM) for radionuclides in seaweed (Fucus vesiculosus) from the Baltic Sea (IAEA-446) is described and the results of the certification process are presented. The 40K, 137Cs, 234U and 239+240Pu radionuclides were certified for this material, and information values for 12 other radionuclides (90Sr, 99Tc, 210Pb (210Po), 226Ra, 228Ra, 228Th, 230Th, 232Th, 235U, 238U, 239Pu and 240Pu) are presented. The CRM can be used for Quality Assurance/Quality Control of analysis of radionuclides in seaweed and other biota samples, as well as for development and validation of analytical methods, and for training purposes.

Three-dimensional (3D) tissue culture provides a physiologically relevant microenvironment for distinguishing malignant from non-malignant breast cell phenotypes. 3D culture assay can also be used to test novel cancer therapies and predict a differential response to radiation between normal and malignant cells in vivo. However, biological measurements in such complex models are difficult to quantify and current approaches do not allow for in-depth multifaceted assessment of individual colonies or unique sub-populations within the entire culture. This is in part due to the limitations of imaging at a range of depths in 3D culture resulting in optical aberrations and intensity attenuation. Here, we address these limitations by combining sample smearing techniques with high-throughput imaging algorithms to accurately and rapidly quantify imaging features acquired from 3D cultures without the usage of slow confocal microscopy. Multiple high resolution imaging features especially designed to characterize 3D cultures show that non-malignant human breast cells surviving large doses of ionizing radiation acquire a “swelled acinar” phenotype with fewer and larger nuclei, loss of cell connectivity and diffused basement membrane. When integrating these imaging features into hierarchical clustering classification, we could also identify subpopulations of phenotypes from individual human tumor colonies treated with ionizing radiation or/and integrin inhibitors. Such tools have therefore the potential to further characterize cell culture populations after cancer treatment and identify novel phenotypes of resistance.

We describe the sampling of sixty-three uncultured hospital air samples collected over a six-month period and analysis using shotgun metagenomic sequencing. Our primary goals were to determine the longitudinal metagenomic variability of this environment, identify and characterize genomes of potential pathogens and determine whether they are atypical to the hospital airborne metagenome. Air samples were collected from eight locations which included patient wards, the main lobby and outside. The resulting DNA libraries produced 972 million sequences representing 51 gigabases. Hierarchical clustering of samples by the most abundant 50 microbial orders generated three major nodes which primarily clustered by type of location. Because the indoor locations were longitudinally consistent, episodic relative increases in microbial genomic signatures related to the opportunistic pathogens Aspergillus, Penicillium and Stenotrophomonas were identified as outliers at specific locations. Further analysis of microbial reads specific for Stenotrophomonas maltophilia indicated homology to a sequenced multi-drug resistant clinical strain and we observed broad sequence coverage of resistance genes. We demonstrate that a shotgun metagenomic sequencing approach can be used to characterize the resistance determinants of pathogen genomes that are uncharacteristic for an otherwise consistent hospital air microbial metagenomic profile.

One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been improved algorithms for utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in the assembly graph structure. However, the PDBG approach faces difficulties when the variation in the insert sizes is high. To address this problem, we first transform mate-pairs into edge-pair histograms that allow one to better estimate the distance between edges in the assembly graph that represent regions linked by multiple mate-pairs. Further, we combine the ideas of mate-pair transformation and PDBGs to construct new data structures for genome assembly: pathsets and pathset graphs.

Barnacles belong to the Cirripedia group (cirri: cirri, pedia: feet) and are, for the most part, sessile crustaceans that live permanently adhered to a substrate that can be inorganic (rock), organic (coral, molluscs, turtles, whales) and even artificial (plastic, wood) (Southward, 1987). They mainly inhabit marine environments; although some species can resist low salinities in estuarine zones (Arenas, 1971), and are distributed bathymetrically from the high intertidal zone to depths of over 1,000 m (Anderson, 1994). They are gregarious, forming dense “patches” of individuals that can completely cover substrates.

One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in the assembly graph structure. However, the PDBG approach faces difficulties when the variation in the insert sizes is high. To address this problem, we first transform mate-pairs into edge-pair histograms that allow one to better estimate the distance between edges in the assembly graph that represent regions linked by multiple mate-pairs. Further, we combine the ideas of mate-pair transformation and PDBGs to construct new data structures for genome assembly: pathsets and pathset graphs.

Giardia intestinalis is a ubiquitous parasitic protist that is the causative agent of giardiasis, one of the most common protozoan diarrheal diseases in the world. Giardia trophozoites attach to the intestinal epithelium using a specialized and elaborate microtubule structure, the ventral disc. Surrounding the ventral disc is a less characterized putatively contractile structure, the lateral crest, which forms a continuous perimeter seal with the substrate. A better understanding of ventral disc and lateral crest structure, conformational dynamics, and biogenesis is critical for understanding the mechanism of giardial attachment to the host. To determine the components comprising the ventral disc and lateral crest, we used shotgun proteomics to identify proteins in a preparation of isolated ventral discs. Candidate disc-associated proteins, or DAPs, were GFP-tagged using a ligation-independent high-throughput cloning method. Based on disc localization, we identified eighteen novel DAPs, which more than doubles the number of known disc-associated proteins. Ten of the novel DAPs are associated with the lateral crest or outer edge of the disc, and are the first confirmed components of this structure. Using Fluorescence Recovery After Photobleaching (FRAP) with representative novel DAP::GFP strains we found that the newly identified DAPs tested did not recover after photobleaching and are therefore structural components of the ventral disc or lateral crest. Functional analyses of the novel DAPs will be central toward understanding the mechanism of ventral disc-mediated attachment and the mechanism of disc biogenesis during cell division. Since attachment of Giardia to the intestine via the ventral disc is essential for pathogenesis, it is possible that some proteins comprising the disc could be potential drug targets if their loss or disruption interfered with disc biogenesis or function, preventing attachment., Author Summary Giardia is a unicellular intestinal parasite that infects millions of people worldwide each year. Colonization of the small intestine is a critical stage in Giardia infection. Giardia colonizes the intestinal wall using a specialized suction cup-like structure, the ventral disc. Little is known about the protein composition of the disc or about how the disc functions during attachment. We identified and confirmed eighteen new ventral disc proteins in a preparation of isolated discs using modern genomic methods for analyzing protein composition. We imaged these disc proteins in Giardia cells by labeling the proteins with fluorescent tags. A number of these proteins were present on the rim of the ventral disc, a region that appears necessary for the disc to form a seal during attachment to the host. These new ventral disc proteins form the building blocks of the ventral disc structure. Future studies of the roles of the ventral disc proteins either in the assembly of the ventral disc during cell division, or in the functioning of the disc during attachment will enable a better understanding of Giardia's colonization of the host.

An egg mass of Loligo forbesi was observed in the field for the first time while conducting a remotely operated vehicle dive at a depth of 370 m, off the Sao Jorge Island (Azores, north-east Atlantic). This observation allowed the confirmation of two hypotheses previously suggested for the reproduction of this species: (i) that in the Azores this species spawns deeper than the previously recorded 144 m; and that (ii) it is likely that this species prefers to spawn within cavities. The way the observed egg strings suspended from the roof of a cavity, underneath a rocky block, surrounded by sediment, is a feature that interestingly seems to be shared between L. forbesi (in the Azores, all the previous naturally-laid egg masses were recovered from within cavities) and L. vulgaris that inhabit shallower waters off the Madeira archipelago.