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Remodeling of the extracellular matrix plays an important role in vascular homeostasis in the basal chordate Botryllus schlosseri, whose large, transparent, extracorporeal vascular network makes it an ideal system for studies of vascular mechanotransduction.

The generation of distinct hematopoietic cell types, including tissue-resident immune cells, distinguishes fetal from adult hematopoiesis. However, the mechanisms underlying differential cell production to generate a layered immune system during hematopoietic development are unclear. Using an irreversible lineage-tracing model, we identify a definitive hematopoietic stem cell (HSC) that supports long-term multilineage reconstitution upon transplantation into adult recipients but does not persist into adulthood in situ. These HSCs are fully multipotent, yet they display both higher lymphoid cell production and greater capacity to generate innate-like B and T lymphocytes as compared to coexisting fetal HSCs and adult HSCs. Thus, these developmentally restricted HSCs (drHSCs) define the origin and generation of early lymphoid cells that play essential roles in establishing self-recognition and tolerance, with important implications for understanding autoimmune disease, allergy, and rejection of transplanted organs.

The bile salt export pump (BSEP) is an ABC-transporter expressed at the canalicular membrane of hepatocytes. Its physiological role is to expel bile salts into the canaliculi from where they drain into the bile duct. Inhibition of this transporter may lead to intrahepatic cholestasis. Predictive computational models of BSEP inhibition may allow for fast identification of potentially harmful compounds in large databases. This article presents a predictive in silicomodel based on physicochemical descriptors that is able to flag compounds as potential BSEP inhibitors. This model was built using a training set of 670 compounds with available BSEP inhibition potencies. It successfully predicted BSEP inhibition for two independent test sets and was in a further step used for a virtual screening experiment. After in vitrotesting of selected candidates, a marketed drug, bromocriptin, was identified for the first time as BSEP inhibitor. This demonstrates the usefulness of the model to identify new BSEP inhibitors and therefore potential cholestasis perpetrators.

Whilst most new drugs are designed to act on a single target or a small number of targets, many do show broad pharmacological activity. In some cases this can be beneficial and necessary for efficacy and in others it can be detrimental, leading to increased safety liability. To probe off‐target pharmacology most drug discovery programs include screening against a broad panel of targets that represent known troublesome pharmacology. Hits against any one of these targets can then be subjected to a risk assessment for potential safety problems in preclinical or clinical studies. In addition, the secondary pharmacology profile can also be thought of as an alternative description of the compound and as such can be used as a method for assessing ‘similarity’. Consequently, inspection of the in vivo findings of pharmacological neighbors can give important insights into potential safety liabilities that are neither identified by pure chemical similarity searches nor by risk assessment on individual targets. Here we show that the pharmacological profile contains additional information as compared to chemical similarity, and also demonstrate how this can be used in the hazard assessment done during drug discovery and development.

Genetic fate-mapping approaches provide a unique opportunity to assess differentiation pathways under physiological conditions. We have recently employed a lineage tracing approach to define hematopoietic differentiation pathways in relation to expression of the tyrosine kinase receptor Flk2.1Based on our examination of reporter activity across all stem, progenitor and mature populations in our Flk2-Cre lineage model, we concluded that all mature blood lineages are derived through a Flk2+intermediate, both at steady-state and under stress conditions. Here, we re-examine in depth our initial conclusions and perform additional experiments to test alternative options of lineage specification. Our data unequivocally support the conclusion that onset of Flk2 expression results in loss of self-renewal but preservation of multilineage differentiation potential. We discuss the implications of these data for defining stem cell identity and lineage potential among hematopoietic populations.

Variable selection is important in QSAR modeling since it can improve model performance and transparency, as well as reduce the computational cost of model fitting and predictions. Which variable selection methods that perform well in QSAR settings is largely unknown. To address this question we, in a total of 1728 benchmarking experiments, rigorously investigated how eight variable selection methods affect the predictive performance and transparency of random forest models fitted to seven QSAR datasets covering different endpoints, descriptors sets, types of response variables, and number of chemical compounds. The results show that univariate variable selection methods are suboptimal and that the number of variables in the benchmarked datasets can be reduced with about 60 % without significant loss in model performance when using multivariate adaptive regression splines MARS and forward selection.

With the ever increasing volume of data available to scientists in drug discovery and development, the opportunity to leverage an increasing amount of these data in the assessment of drug safety is clear. The challenge in an environment of increasing data volume is in the structuring and the analysis of these data, such that decisions can be made without excluding information or overstating their meaning. Informatics and modelling play a crucial role in addressing this challenge in two basic ways: a) the data are structured and analysed in a transparent and objective way; and b) new experiments are designed with the model as part of the design process, much like modern experimental physics. Enhancing the use and impact of informatics and modelling on drug discovery is not simply a matter of increasing processor speed and memory capacity. The transformation of raw data to usable, and useful, information is a scientific, technical and, perhaps most importantly, cultural challenge within drug discovery. This review will highlight some of the history, current approaches and promising future directions in this rapidly expanding area.

Many efforts are currently being made to connect small molecules to target proteins by extracting pharmacological data from bibliographic sources and storing them in annotated chemical libraries. Here, small molecules are further connected to biological pathways, with particular focus to pathways involving members of the nuclear receptor family. The results bring to light the relative importance for molecules on gaining selectivity at the target level, when the target has an intrinsic promiscuity at the pathway level, and highlight the implications for drug discovery to address current challenges related to poor drug efficacy and toxicity. Details on the main limitations encountered during the molecule-to-target-to-pathway annotation process are also discussed.

Bioactive ligands are a valuable and increasingly accessible source of information about protein targets. On the basis of this statement, a list of 25 nuclear receptors was described by a series of bioactive ligands extracted directly from bibliographical sources, stored properly in an annotated chemical library, and mathematically represented using the recently reported SHED molecular descriptors. Analysis of this ligand information allowed for derivation of a threshold of nuclear receptor concern. If the similarity of one molecule to any of the molecules annotated to one particular nuclear receptor is below that threshold, the molecule receives an alert on the probability of having affinity below 10 M for that nuclear receptor. On this basis, a linkage map was constructed that reveals the interaction network of nuclear receptors from the perspective of their active ligands. This ligand-based approach to nuclear receptor profiling was subsequently applied to four external chemical libraries of 10?000 molecules targeted to proteases, kinases, ion channels, and G protein-coupled receptors. The percentage of each library that returned an alert on at least one nuclear receptor was reasonably low and varied between 4.4 and 9.7%. In addition, ligand-based nuclear receptor profiling of a set of 2944 drugs provided an alert for 153 drugs. For some of them, namely, acitretin, telmisartan, phenyltoloxamine, tazarotene, and flumazenil, bibliographical evidence could be found indicating that those drugs may indeed have some potential off-target residual affinity for the nuclear receptors annotated. Overall, the present findings suggest that ligand-based approaches to protein family profiling appear as a promising means toward the establishment of novel tools for in silico pharmacology.

Nuclear receptors form a family of ligand-activated transcription factors that regulate a wide variety of biological processes and are thus generally considered relevant targets in drug discovery. We have constructed an annotated compound library directed to nuclear receptors (NRacl) as a means for integrating the chemical and biological data being generated within this family. Special care has been put in the appropriate storage of annotations by using hierarchical classification schemes for both molecules and nuclear receptors, which takes the ability to extract knowledge from annotated compound libraries to another level. Analysis of NRacl has ultimately led to the identification of scaffolds with highly promiscuous nuclear receptor profiles and to the classification of nuclear receptor groups with similar scaffold promiscuity patterns. This information can be exploited in the design of probing libraries for deorphanization activities as well as for devising screening batteries to address selectivity issues.

This technical paper describes the utilization of a new automated liquid handler from Beckman Coulter, Inc., the Biomek® NX Laboratory Automation Workstation, for genomic and proteomic applications. For genomic applications, methodology for plasmid DNA purification using Promega Wizard® SV 96 reagents was developed for the Biomek NX. A single plate of bacterial pellets can be processed to purified plasmid DNA without user interaction after initial setup. DNA quantity and quality were assessed by spectrophotometric analysis, restriction digestion, PCR (The PCR process is covered by patents owned by Roche Molecular Systems, Inc., and F. Homan La Roche, Ltd.), and capillary sequencing. Additionally, the plasmid preparation method was used to purify plasmid DNA from bacterial clones isolated in a bacterial two-hybrid screening procedure. In this case, the system quickly and efficiently prepared clones for rapid identification of target sequences. For proteomic applications, His-tag proteins were purified from bacterial cultures in a 96-well plate format. Following purification, a Bradford assay was used to determine the quantitative yields of the His-tag protein products in each of the aliquots from the purified samples. The AD 340 Automated Labware Positioner (ALP), an integrated absorbance reader, was used for absorbance measurements in the Bradford assay. Given the placement of this ALP on the deck of the Biomek NX, the entire process of protein purification and quantitation was performed in a complete walk-away automated format. Results obtained when purifying proteins, from both uninduced and induced bacterial cultures, on the worksurface of the Biomek NX will be described. (JALA 2004;9:177-84)

This technical paper describes the utilization of a new automated liquid handler from Beckman Coulter, Inc., the Biomek® NX Laboratory Automation Workstation, for genomic and proteomic applications. For genomic applications, methodology for plasmid DNA purification using Promega Wizard® SV 96 reagents was developed for the Biomek NX. A single plate of bacterial pellets can be processed to purified plasmid DNA without user interaction after initial setup. DNA quantity and quality were assessed by spectrophotometric analysis, restriction digestion, PCR (The PCR process is covered by patents owned by Roche Molecular Systems, Inc., and F. Homan La Roche, Ltd.), and capillary sequencing. Additionally, the plasmid preparation method was used to purify plasmid DNA from bacterial clones isolated in a bacterial two-hybrid screening procedure. In this case, the system quickly and efficiently prepared clones for rapid identification of target sequences. For proteomic applications, His-tag proteins were purified from bacterial cultures in a 96-well plate format. Following purification, a Bradford assay was used to determine the quantitative yields of the His-tag protein products in each of the aliquots from the purified samples. The AD 340 Automated Labware Positioner (ALP), an integrated absorbance reader, was used for absorbance measurements in the Bradford assay. Given the placement of this ALP on the deck of the Biomek NX, the entire process of protein purification and quantitation was performed in a complete walk-away automated format. Results obtained when purifying proteins, from both uninduced and induced bacterial cultures, on the worksurface of the Biomek NX will be described.

The pea chloroplast trnK gene which encodes tRNALys (UUU) was sequenced. TrnK is located 210 bp upstream from the promoter of psbA and immediately downstream from the 3'-end of rbcL. The gene is transcribed from the same DNA strand as psbA and rbcL. A 2447 bp intron with class II features is located in the trnK anticodon loop. The intron contains a 506 amino acid open reading frame which could encode an RNA maturase. The primary transcript of trnK is 2.9 kb long; its 5'-end was identified as a site of transcription initiation by in vitro transcription experiments. The 5'-terminus is adjacent to DNA sequences previously identified as transcription promoter elements. The most abundant trnK transcript is 2.5 kb long with termini corresponding to the 5' and 3' ends of the trnK exons. Intron specific RNAs were not detected. This suggests that RNA processing which produces tRNALys leads to rapid degradation of intron sequences.

We have analyzed the region of the chloroplast genome from P. sativumwhich encodes the 5′-end of psbA. S1nuclease mapping and primer extension analysis of chloroplast RNA revealed psbA transcripts with 5′-termini 92, 93 and 68 nucleotides upstream from the psbA open reading frame. The psbA transcripts with 5′-ends 92–93 nucleotides upstream from the psbA open reading frame can be labeled with alpha-32P-GTP by guanylyltransferase. DNA sequences 10 and 35 bp upstream from the longest psbA transcript showed homology to −10 and −35 consensus promoter sequences in E. coli. Truncated psbA constructs which contain the putative psbA promoter sequences were shown to promote transcription in E. colifrom a site similar to that used by chloroplast RNA polymerase in vivo. Accurate transcription of psbA constructs was also observed in a homologous in vitrotranscription extract from chloroplasts. Sequence analysis of the region upstream from the psbA transcripts revealed a putative 3′-exon of a tRNA-Lys (240 bp upstream) and an unidentified open reading frame (URF, 485 bp upstream). The 3′-end of the URF mRNA was located approximately 240 bp from the 5′-end of the longest psbA transcript indicating that the URF and tRNA-Lys sequence are cotranscribed. Comparison of P. sativumand N. tabacumDNA sequences at the 5′-end of psbA revealed homology between sequences coding for psbA mRNA including 40 bp upstream from the longest psbA transcript. A second region of homology which includes the tRNA-Lys sequence was also located. In contrast the intergenic DNA exhibited extensive divergence in size and sequence. re]19850627 rv]19851211 ac]19851216

No relevant conflicts of interest to declare.

The generation of innate-like immune cells distinguishes fetal hematopoiesis from adult hematopoiesis, but the cellular mechanisms underlying differential cell production during development remain to be established. Specifically, whether differential lymphoid output arises as a consequence of discrete hematopoietic stem cell (HSC) populations present during development or whether the fetal/neonatal microenvironment is required for their production remains to be established. We recently established a Flk2/Flt3 lineage tracing mouse model wherein Flk2-driven expression of Cre recombinase results in the irreversible switching of a ubiquitous dual-color reporter from Tomato to GFP expression. Because the switch from Tom to GFP expression in this model involves an irreversible genetic excision of the Tomato gene, a GFP+ cell can never give rise to Tom+ progeny. Using this model, we have definitively demonstrated that all functional, adult HSC remain Tomato+ and therefore that all developmental precursors of adult HSC lack a history of Flk2 expression. In contrast, adoptive transfer experiments of Tom+ and GFP+ fetal liver Lin-cKit+Sca1+ (KLS) fractions demonstrated that both Tom+ and GFP+ fetal HSC support serial, long-term multilineage reconstitution (LTR) in irradiated adult recipients. We have therefore identified a novel, developmentally restricted HSC that supports long-term multilineage reconstitution upon transplantation into an adult recipient but does not normally persist into adulthood. Developmentally-restricted GFP+ HSC display greater lymphoid potential, and regenerated both innate-like B-1 lymphocytes and Vg3-expressing T lymphocytes to a greater extent than coexisting Tom+ FL and adult HSC. Interestingly, whereas developmental regulation of fetal-specific B-cell subsets appears to be regulated cell-instrinsically, as fetal HSC generated more innate-like B-cells than adult HSC even within an adult environment, T-cell development may be regulated both cell intrinsically and extrinsically, as both the cell-of-origin and the fetal microenvironment regulated the generation of innate-like T-cells. Our results provide direct evidence for a developmentally restricted HSC that gives rise to a layered immune system and describes a novel mechanism underlying the source of developmental hematopoietic waves. As early lymphoid cells play essential roles in establishing self-recognition and tolerance, these findings are critical for understanding the development of autoimmune diseases, allergies, and tolerance induction upon organ transplantation. Furthermore, by uncoupling self-renewal capacity in situ with that observed upon transplantation, our data suggests that transplantation- and/or irradiation-induced cues may allow for the engraftment of developmental HSC populations that do not normally persist in situ. As LTR upon transplantation has served as the prevailing definition of adult HSC origin during development, our data challenge the current conceptual framework of adult HSC origin.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.