Anguillid eels

Anguillid eels have fascinated humans for centuries, but our knowledge of these mysterious fish is still scant. There are 19 species or subspecies in the genus Anguilla, which are found globally, except in the eastern Pacific and southern Atlantic. Their common label 'freshwater eels' is a misnomer - all anguillids are facultatively catadromous, born in marine environments, developing in continental waters, with a proportion never entering freshwater at all. Anguillid eels have several life history traits that have allowed them to exploit a broad range of habitats. As such, anguillid eels play an important ecological role in both marine and freshwater environments as well as being commercially valuable. Because of this, anguillid eels are under threat from multiple stressors, such as barriers to migration, pollution, parasites, disease, climate change and unsustainable exploitation. Six species are listed as Threatened in the Red List of Threatened Species, and four are listed as Data Deficient. Strengthening conservation and management of these species is essential, and further research provides an exciting opportunity to develop a greater understanding of this mysterious clade of fish.

Analysing detection gaps in acoustic telemetry data to infer differential movement patterns in fish

A wide array of technologies are available for gaining insight into the movement of wild aquatic animals. Although acoustic telemetry can lack the fine-scale spatial resolution of some satellite tracking technologies, the substantially longer battery life can yield important long-term data on individual behavior and movement for low per-unit cost. Typically, however, receiver arrays are designed to maximize spatial coverage at the cost of positional accuracy leading to potentially longer detection gaps as individuals move out of range between monitored locations. This is particularly true when these technologies are deployed to monitor species in hard-to-access locations.Here, we develop a novel approach to analyzing acoustic telemetry data, using the timing and duration of gaps between animal detections to infer different behaviors. Using the durations between detections at the same and different receiver locations (i.e., detection gaps), we classify behaviors into "restricted" or potential wider "out-of-range" movements synonymous with longer distance dispersal. We apply this method to investigate spatial and temporal segregation of inferred movement patterns in two sympatric species of reef shark within a large, remote, marine protected area (MPA). Response variables were generated using network analysis, and drivers of these movements were identified using generalized linear mixed models and multimodel inference.Species, diel period, and season were significant predictors of "out-of-range" movements. Silvertip sharks were overall more likely to undertake "out-of-range" movements, compared with gray reef sharks, indicating spatial segregation, and corroborating previous stable isotope work between these two species. High individual variability in "out-of-range" movements in both species was also identified.We present a novel gap analysis of telemetry data to help infer differential movement and space use patterns where acoustic coverage is imperfect and other tracking methods are impractical at scale. In remote locations, inference may be the best available tool and this approach shows that acoustic telemetry gap analysis can be used for comparative studies in fish ecology, or combined with other research techniques to better understand functional mechanisms driving behavior.

A phase 2 trial of consolidation pembrolizumab following concurrent chemoradiation for patients with unresectable stage III non-small cell lung cancer: Hoosier Cancer Research Network LUN 14-179

BACKGROUND

Five-year overall survival (OS) for patients with unresectable stage III non-small cell lung cancer (NSCLC) is poor. Until recently, a standard of care was concurrent chemoradiation alone. Patients with metastatic NSCLC treated with anti-programmed death 1 antibodies have demonstrated improved OS. This trial evaluated pembrolizumab as consolidation therapy after concurrent chemoradiation in patients with unresectable stage III disease.

METHODS

Patients with unresectable stage III NSCLC received concurrent chemoradiation with cisplatin and etoposide, cisplatin and pemetrexed, or carboplatin and paclitaxel and 59.4 to 66.6 Gy of radiation. Patients with nonprogression of disease were enrolled and received pembrolizumab (200 mg intravenously every 3 weeks for up to 12 months). The primary endpoint was the time to metastatic disease or death (TMDD). Secondary endpoints included progression-free survival (PFS) and OS.

RESULTS

The median follow-up for 93 patients (92 for efficacy) was 32.2 months (range, 1.2-46.6 months). The median TMDD was 30.7 months (95% confidence interval [CI], 18.7 months to not reached), which was significantly longer than the historical control of 12 months (P < .0001). The median PFS was 18.7 months (95% CI, 12.4-33.8 months), and the median OS was 35.8 months (95% CI, 24.2 months to not reached). The 1-, 2-, and 3-year OS estimates were 81.2%, 62.0%, and 48.5%, respectively. Forty patients (43.5%) completed 12 months of treatment (median number of cycles, 13.5). Symptomatic pneumonitis (grade 2 or higher) was noted in 16 patients (17.2%); these cases included 4 grade 3 events (4.3%), 1 grade 4 event (1.1%), and 1 grade 5 event (1.1%).

CONCLUSIONS

Consolidation pembrolizumab after concurrent chemoradiation improves TMDD, PFS, and OS in comparison with historical controls of chemoradiation alone. Rates of grade 3 to 5 pneumonitis were similar to those reported with chemoradiation alone.

NWChem: Past, present, and future

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

The effect of meals of varying nutritional composition on subjective and physiological markers of nausea in response to optokinetic motion

BACKGROUND

Protein ingestion has been shown to decrease subjective and physiological markers of nausea.

AIM

To elucidate the importance of drink palatability and nutritional composition in preventing subjective symptoms of nausea, decreased normal gastric electrogastrographic activity, and withdrawal of vagal tone in response to optokinetic motion.

METHODS

Participants received a liquid high protein/low carbohydrate, moderate protein/high carbohydrate, low protein/high carbohydrate or water meal 30 min prior to exposure to an optokinetic drum. Subjective symptoms of nausea, electrogastrograms and cardiac vagal tone were measured during the 30-min post-drink rest period, a 10-min baseline period in the stationary drum, and during a 16-min drum rotation period.

RESULTS

Regardless of nutritional composition, a pleasant taste predicted a reduction of the subjective experience of nausea. Subjective symptoms were significantly more severe in the moderate protein/high carbohydrate and water groups compared to the high protein/low carbohydrate and low protein/high carbohydrate groups. Electrogastrographic indicators of nausea were reduced in the high protein/low carbohydrate and low protein/high carbohydrate groups versus water, while cardiac vagal tone was reduced in the high protein/low carbohydrate and moderate protein/high carbohydrate groups versus the low protein/high carbohydrate and water groups.

CONCLUSIONS

Palatability and high protein meals appear to be important factors in attenuating the nausea associated with exposure to optokinetic motion.

Protein-predominant meals inhibit the development of gastric tachyarrhythmia, nausea and the symptoms of motion sickness

BACKGROUND

Meal ingestion has been suggested to reduce susceptibility to the development of gastric tachyarrhythmia, the abnormal activity of the stomach that frequently accompanies nausea.

AIM

To determine the types of meal that are most effective in preventing the development of gastric tachyarrhythmia, nausea and the symptoms of motion sickness provoked by a rotating optokinetic drum.

METHOD

Participants received a carbohydrate beverage, a protein-predominant beverage or nothing immediately before exposure to the rotating drum. Subjective symptoms of motion sickness and electrogastrograms were collected during a 6-min baseline period and a subsequent 16-min drum rotation period.

RESULTS

Subjective symptoms of motion sickness scores were significantly more severe during the no-meal condition than during either the protein or carbohydrate condition. Central, peripheral and, to some extent, gastrointestinal symptoms were more severe during the carbohydrate condition than during the protein condition. Gastric tachyarrhythmia increased significantly less from baseline to drum rotation during both the protein and carbohydrate conditions than during the no-meal condition.

CONCLUSIONS

Liquid protein-predominant meals were most effective in suppressing both the development of gastric tachyarrhythmia and the entire spectrum of motion sickness symptoms, including nausea.

Dynamic microscopy of nanoscale cluster growth at the solid-liquid interface

Dynamic processes at the solid-liquid interface are of key importance across broad areas of science and technology. Electrochemical deposition of copper, for example, is used for metallization in integrated circuits, and a detailed understanding of nucleation, growth and coalescence is essential in optimizing the final microstructure. Our understanding of processes at the solid-vapour interface has advanced tremendously over the past decade due to the routine availability of real-time, high-resolution imaging techniques yielding data that can be compared quantitatively with theory. However, the difficulty of studying the solid-liquid interface leaves our understanding of processes there less complete. Here we analyse dynamic observations--recorded in situ using a novel transmission electron microscopy technique--of the nucleation and growth of nanoscale copper clusters during electrodeposition. We follow in real time the evolution of individual clusters, and compare their development with simulations incorporating the basic physics of electrodeposition during the early stages of growth. The experimental technique developed here is applicable to a broad range of dynamic phenomena at the solid-liquid interface.

The Leu-132 of the Ste4(Gbeta) subunit is essential for proper coupling of the G protein with the Ste2 alpha factor receptor during the mating pheromone response in yeast

In order to identify amino acid residues of Ste4p involved in receptor recognition and/or receptor-G protein coupling, we employed random in vitro mutagenesis and a genetic screening to isolate mutant Ste4p subunits with altered pheromone response. We generated a plasmid library containing randomly mutagenized Ste4 ORFs, followed by phenotypic selection of ste4p mutants by altered alpha pheromone response in yeast cells. Subsequently, we analyzed mutant ste4-10 which has a replacement of the almost universally conserved leucine 132 by phenylalanine. This residue lies in the first blade of the beta propeller structure proposed by crystallographic analysis. By overexpression experiments we found that mutant ste4p subunit triggers the mating pathway at wild type levels in both wild type and receptorless strains. When expressed in a ste4 background, however, the mutant G protein is activated inefficiently by mating pheromone in both a and alpha cells. The mutant ste4-10p was tested in the two-hybrid system and found to be defective in its interaction with the Gpa1p, but has a normal association with the C-termini end of the Ste2p receptor. These observations strongly suggest that the Leu-132 of the Ste4p subunit is essential for efficient activation of the G protein by the pheromone-stimulated receptor and that this domain could be an important point for physical interaction between the Gbeta and the Galpha subunits.

A genetic selection for isolating cDNAs encoding secreted proteins

We describe a simple, rapid technique for simultaneously isolating large numbers of cDNAs encoding secreted proteins. The technique makes use of a facile genetic selection performed in a strain of Saccharomyces cerevisiae deleted for its endogenous invertase gene. A cDNA cloning vector which carries a modified invertase gene lacking its leader sequence is used in conjunction with this strain. Heterologous secreted genes fused appropriately upstream of this defective invertase provide the necessary signals to restore secretion, allowing the yeast to grow on sugars such as sucrose or raffinose. This microbial growth selection facilitates scanning cDNA libraries containing millions of clones, enabling the wholesale identification of novel secreted proteins without the need for specific bioassays. The technique is similar to one previously described (Klein et al. (1996) Proc. Natl. Acad. Sci. USA 93, 7108-7113). We describe results using a cDNA library derived from activated human peripheral blood mononuclear cells (PBMC). Genes identified from this library encoded signal sequences of proteins of diverse structure, function, and cellular location such as cytokines, type 1 and type 2 transmembrane proteins, and proteins found in intracellular organelles. In addition, a number of novel secreted proteins were identified, including a chemokine and a novel G-protein-coupled receptor. Since signal sequences possess features conserved throughout evolution, the procedure can be used to isolate genes encoding secreted proteins from both eukaryotes and prokaryotes.

Histidine patch thioredoxins. Mutant forms of thioredoxin with metal chelating affinity that provide for convenient purifications of thioredoxin fusion proteins

A cluster of surface amino acid residues on Escherichia coli thioredoxin were systematically mutated in order to provide the molecule with an ability to chelate metal ions. The combined effect of two histidine mutants, E30H and Q62H, gave thioredoxin the capacity to bind to nickel ions immobilized on iminodiacetic acid- and nitrilotriacetic acid-Sepharose resins. Even though these two histidines were more than 30 residues apart in thioredoxin's primary sequence, they were found to satisfy the geometric constraints for metal ion coordination as a result of the thioredoxin tertiary fold. A third histidine mutation, S1H, provided additional metal ion chelation affinity, but the native histidine at position 6 of thioredoxin was found not to participate in binding. All of the histidine mutants exhibited decreased thermal stability as compared with wild-type thioredoxin; however, the introduction of an additional mutation, D26A, increased their melting temperatures beyond that of wild-type thioredoxin. The metal chelating abilities of these histidine mutants of thioredoxin were successfully utilized for convenient purifications of human interleukin-8 and -11 expressed in E. coli as soluble thioredoxin fusion proteins.

Post-translational modification of a monocyte-specific chemoattractant synthesized by glioma, osteosarcoma, and vascular smooth muscle cells

Chemotaxis is an important step in monocyte recruitment in inflammation, wound healing, and tumor growth. We reported previously that monocyte chemotactic activity secreted by malignant cells and normal smooth muscle cells is associated with a protein or family of proteins that are related to the monocyte-specific smooth muscle cell-derived chemotactic factor (SMC-CF) (Graves, D. T., Jiang, Y. L., Williamson, M. J., and Valente, A. J. (1989) Science 245, 1490-1493). Similar monocyte chemotactic proteins (MCP-1) produced by U-105MG human glioma cells have also been identified (Yoshimura, T., Robinson, E. A., Tanaka, S., Appella, E., Kuratsu, J., and Leonard, E. J. (1989) J. Exp. Med. 169, 1449-1459). We now report that the MCP-1 gene is expressed in MG-63 human osteosarcoma and vascular smooth muscle cells and that SMC-CF antiserum specifically immunoprecipitates proteins synthesized by U-105MG glioma cells. Experiments were undertaken to elucidate the processing pathway of MCP-1/SMC-CF-like proteins in each of these cell types. These experiments demonstrate that larger MCP-1/SMC-CF-like proteins are derived from a Mr = 9000 precursor. Post-translational modification involves the addition of O-linked carbohydrates and sialic acid residues. Differences in carbohydrate processing account for the heterogeneity in MCP-1/SMC-CF-like proteins produced by different cell types. Secretion of these proteins occurs rapidly following processing events in the endoplasmic reticulum-Golgi compartment.

Identification of monocyte chemotactic activity produced by malignant cells

Human malignant cells secrete low molecular size proteins that attract peripheral blood monocytes and may be responsible for the accumulation of tumor-associated macrophages observed in vivo. Similar chemotactic proteins are secreted by cultured vascular smooth muscle cells. The predominant monocyte chemoattractants produced by tumor cells of differing origin were demonstrated to be related to smooth muscle cell-derived chemotactic factor. Thus, a single class of chemotactic proteins is produced by different cell types, which suggests a common mechanism for the recruitment of monocytes and macrophages. These results are significant in view of the potential of macrophages to affect tumor growth.

Colorimetric plasma assay for the bentiromide test (BT-PABA) for exocrine pancreatic insufficiency

Bentiromide is a synthetic peptide, N-benzoyl-L-tyrosyl-p-aminobenzoic acid, which has been used as a test for exocrine pancreatic function. Following oral administration, bentiromide is hydrolyzed by chymotrypsin to yield free p-aminobenzoic acid (PABA) which is absorbed, conjugated and excreted in the urine. The PABA conjugates reach their peak levels in blood in 90-120 min. Healthy individuals have higher levels of PABA than patients with pancreatic insufficiency. A simple, accurate, and precise method for the determination of PABA in blood has been developed and validated. The plasma (1 ml) is deproteinized by perchloric acid. The conjugates are hydrolyzed and the total PABA is determined colorimetrically by the Bratton-Marshall test. The standard curve in plasma is linear up to 8 micrograms/ml of PABA. A similar semimicro method using 200 microliter of plasma suitable for pediatric samples shows comparable results. Average analytical recovery is 97% and precision studies of pooled within-run and total between-run showed CV% of 5.0 and 5.7%, respectively.

Isolation, identification, and synthesis of the major sulpiride metabolite in primates

The major metabolite of sulpiride, N-[(1-ethyl-2-pyrrolidinyl)methyl]-5-sulfamoyl-2-anisamide (I), in the monkey is N-[(1-ethyl-5-oxo-2-pyrrolidinyl)methyl]-5-sulfamoyl-2-anisamide (II). It is also a metabolite in other laboratory animal species and possibly at very low levels in humans. Treatment of the urine from a monkey dosed orally with 14C-I by dry column chromatography and high-pressure liquid chromatography (HPLC) produced the major metabolite in pure form. Characterization of the purified 14C-radiolabeled metabolite by proton NMR, TLC, HPLC, and chemical ionization mass spectroscopy, along with subsequent comparison of a synthetically prepared sample, gave unequivocal structural confirmation.

High-performance liquid chromatographic microdetermination of indoprofen in human milk

A previously reported high-performance liquid chromatographic (HPLC) method for indoprofen determination in physiological fluids was modified and extended to provide quantitative data on drug concentrations in human milk samples at a low nanogram per milliliter level. The reversed-phase HPLC technique was modified to give a better separation of the drug and milk components. To achieve the necessary cleanup for low level determination, the milk samples required protein precipitation, liquid-liquid drug extraction, and concentration. Excellent indoprofen recovery was obtained with this technique; the average recovery from 20 milk samples spiked with various nanogram drug levels was 95%. The analytical technique showed excellent reproducibility; the calibration solutions over 15 days had a relative standard deviation of 3.2%. Results for indoprofen levels in milk and plasma samples from seven subjects who received either a single or multiple oral drug dose are presented.