DOCK 6: Combining techniques to model RNA–small molecule complexes

With an increasing interest in RNA therapeutics and for targeting RNA to treat disease, there is a need for the tools used in protein-based drug design, particularly DOCKing algorithms, to be extended or adapted for nucleic acids. Here, we have compiled a test set of RNA–ligand complexes to validate the ability of the DOCK suite of programs to successfully recreate experimentally determined binding poses. With the optimized parameters and a minimal scoring function, 70% of the test set with less than seven rotatable ligand bonds and 26% of the test set with less than 13 rotatable bonds can be successfully recreated within 2 Å heavy-atom RMSD. When DOCKed conformations are rescored with the implicit solvent models AMBER generalized Born with solvent-accessible surface area (GB/SA) and Poisson–Boltzmann with solvent-accessible surface area (PB/SA) in combination with explicit water molecules and sodium counterions, the success rate increases to 80% with PB/SA for less than seven rotatable bonds and 58% with AMBER GB/SA and 47% with PB/SA for less than 13 rotatable bonds. These results indicate that DOCK can indeed be useful for structure-based drug design aimed at RNA. Our studies also suggest that RNA-directed ligands often differ from typical protein–ligand complexes in their electrostatic properties, but these differences can be accommodated through the choice of potential function. In addition, in the course of the study, we explore a variety of newly added DOCK functions, demonstrating the ease with which new functions can be added to address new scientific questions.     

Placental transfusion in the naturally born lamb

Neonatal blood volume was measured in 22 full-term lambs using the double label, radioiodinated human serum albumin-125 (RIHSA-125) plasma tag and radiochromium-51 (Cr51) red cell tag dilution technique. Nine lambs (Group I) were born naturally and unassisted. Thirteen lambs were delivered by cesarean section, of which eight (Group II) had early clamping and five (Group III) had late clamping of their umbilical cords. The size of placental transfussion, as reflected in mean red cell volume (RCV) was 36.7 ± 2.1 ml/kg in Group I, which was significantly greater than that of Group II, 29.8 ± 2.0 ml/kg; but smaller than that of Group III, 50.4 ± 2.3 ml/kg. The findings indicate that a partial, rather than a complete, placental transfusion occured in the naturally born lambs. It is suggested that this may reflect Nature's way of regulating the volemic state in the newborn lamb.     

Postmating Reproductive isolation between strains of Drosophila willistoni

Speciation can occur through the presence of reproductive isolation barriers that impede mating, restrict cross-fertilization, or render inviable/sterile hybrid progeny. The D. willistoni subgroup is ideally suited for studies of speciation, with examples of both allopatry and sympatry, a range of isolation barriers, and the availability of one species complete genome sequence to facilitate genetic studies of divergence. D. w. willistoni has the largest geographic distribution among members of the Drosophila willistoni subgroup, spanning from Argentina to the southern United States, including the Caribbean islands. A subspecies of D. w. willistoni, D. w. quechua, is geographically separated by the Andes mountain range and has evolved unidirectional sterility, in that only male offspring of D. w. quechua females × D. w. willistoni males are sterile. Whether D. w. willistoni flies residing east of the Andes belong to one or more D. willistoni subspecies remains unresolved. Here we perform fecundity assays and show that F1 hybrid males produced from crosses between different strains found in Central America, North America, and northern Caribbean islands are reproductively isolated from South American and southern Caribbean island strains as a result of unidirectional hybrid male sterility. Our results show the existence of a reproductive isolation barrier between the northern and southern strains and suggest a subdivision of the previously identified D. willistoni willistoni species into 2 new subspecies.     

Oxylipin biosynthesis reinforces cellular senescence and allows detection of senolysis

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Tools for automated acoustic monitoring within the R package monitoR

The R package monitoR contains tools for managing an acoustic-monitoring program including survey metadata, template creation and manipulation, automated detection and results management. These tools are scalable for use with small projects as well as larger long-term projects and those with expansive spatial extents. Here, we describe typical workflow when using the tools in monitoR. Typical workflow utilizes a generic sequence of functions, with the option for either binary point matching or spectrogram cross-correlation detectors.     

Gastric organoids—an in vitro model system for the study of gastric development and road to personalized medicine

Gastric cancer ranks as the fifth most common human malignancy and the third leading cause of cancer related deaths. Depending on tumor stage, endoscopic or surgical resection supported by perioperative chemotherapy is the only curative option for patients. Due to late clinical manifestation and missing reliable biomarkers, early detection is challenging and overall survival remains poor. Organoids are cell aggregates cultured in three-dimensions that grow with similar characteristics as their tissue-of-origin. Due to their self-renewal and proliferative capacity, organoids can be maintained long term in culture and expanded in many cases in an unlimited fashion. Patient-derived organoid (PDO) libraries function as living biobanks, allowing the in depth analysis of tissue specific function, development and disease. The recent successful establishment of gastric cancer PDOs opens up new perspectives for multiple translational clinical applications. Here, we review different adult stem cell derived gastric organoid model systems and focus on their establishment, phenotypic and genotypic characterizations as well as their use in predicting therapy response. Subject terms: Cancer models, Experimental models of disease     

Activity in salt taste fibers: peripheral mechanism for mediating changes in salt intake

In order to study the role of peripheral taste sensitivity inmediating increases in salt intake of the rat, the effects ofsodium deprivation and adrenalectomy on chorda tympani nerveresponses to taste stimulation were determined. Sodium deprivationresulted in a reduction in whole nerve responsivity to suprathresholdNaCl concentrations requiring a 10-fold increase in concentrationto elicit the same neural signal of control preparations. Saltintake of sodium deprived rats was predicted by adjusting datain a 10-min intake test from control rats for the reduced neuralsignal and lower salivary sodium levels of sodium deprived rats.The whole nerve responses to LiCl and KCl, as well as to NaCl,were reduced after sodium deprivation and adrenalectomy. Themultifiber response of the chorda tympani is comprised of theindividual responses of NaCl sensitive N-best fibers and HCl/NaClsensitive H-best fibers. After sodium deprivation N-best fibers'responses to suprathreshold concentrations of NaCl were reduced;H-best fibers' responses were not affected by sodium deprivation.Future studies will determine the effect of KCl and other saltson responses of N-best and H-best fibers. Applying Beidler'sbiophysical model to the single fiber data suggests that sodiumdeprivation influences receptor mechanisms for NaCl of N-bestfibers and not H-best fibers. Because repeated NaCl stimulationresulted in increased chorda tympani responsivity to NaCl, wesuggest that sodium deprivation may alter the salt receptorsimply by disuse. Altered receptor sensitivity may be an adaptivemechanism to influence salt consumption by a shift in suprathresholdNaCl intensity.     

A novel mutation of presenilin 1 in familial Alzheimer’s disease in Israel detected by denaturing gradient gel electrophoresis

Germline mutations in the presenilin 1 (PS1) gene apparently account for the majority of early-onset, familial Alzheimer’s disease (AD). Using a mutation-screening strategy (denaturing gradient gel electrophoresis; DGGE), we analyzed a large family with early onset AD and seizures. The patients in this family showed a novel missense mutation in exon 5 of the PS1 gene (A to T change in codon 120, altering glutamine to aspartic acid). This novel mutation is located within the second hydrophilic domain of the molecule, a region not particularly involved in previously described germline mutations, and is of unknown biological significance. These results also demonstrate that DGGE can be used effectively to screen for mutations within this gene. Received: 3 July 1996 / Revised: 29 July 1996