Rethinking 3D-QSAR

The average error of pIC50 prediction reported for 140 structures in make-and-test applications of topomer CoMFA by four discovery organizations is 0.5. This remarkable accuracy can be understood to result from a topomer pose’s goal of generating field differences only at lattice intersections adjacent to intended structural change

The inevitable QSAR renaissance

QSAR approaches, including recent advances in 3D-QSAR, are advantageous during the lead optimization phase of drug discovery and complementary with bioinformatics and growing data accessibility. Hints for future QSAR practitioners are also offered

Late Paleocene event chronology: unconformities, not diachrony

The chronology of the events associated with the late Paleocene thermal maximum (LPTM, Chron C24r) has been established through the construction of a composite reference section that involved chemomagnetobiostratigraphic correlations and assumed minimum diachrony of biostratigraphic events. On this basis, discrepancies between correlations in different sections were explained by inferred unconformities. However, diachrony between distant sections cannot be ruled out. We report here on two geographically close sections drilled onshore New Jersey that yield different records of chemomagnetobiostratigraphic correlations in the interval representing Chron C24r. Because of their proximity (approximately 40 km apart), diachrony of biostratigraphic events between the two sections can be ruled out. In contrast, the marked lithologic disconformities in the sections explain well the different records of events. We thus conclude that the current relative chronology for Chron C24r is firmly based and that the upper Paleocene-lower Eocene stratigraphic record yields multiple unconformities, with Subzone NP9b rarely sampled. We examine the implications that undeciphered unconformities may have on the identification of proxies for paleoceanographic reconstruction, in particular with regard to the identification of the carbon isotope excursion (CIE) that reflects a dramatic latest Paleocene disturbance of the carbon cycle. We propose biostratigraphic means (short-lived calcareous nannoplankton and planktonic foraminifera taxa) that permit the unequivocal identification of the CIE not only in the oceanic realm but also in neritic settings

An Exceptional Chronologic, Isotopic, and Clay Mineralogic Record of the Latest Paleocene Thermal Maximum, Bass River, NJ, ODP 174AX

A thick, apparently continuous section recording events of the latest Paleocene thermal maximum in a neritic setting was drilled at Bass River State Forest, New Jersey as part of ODP Leg l74AX [Miller, Sugarman, Browning et al., 1998]. Integrated nannofossil and magneto-stratigraphy provides a firm chronology supplemented by planktonic foraminiferal biostratigraphy. This chronologic study indicates that this neritic section rivals the best deep-sea sections in providing a complete record of late Paleocene climatic events. Carbon and oxygen isotopes measured on benthic foraminifera show a major (4.0 %o in carbon, 2.3 %o in oxygen) negative shift correlative with the global latest Paleocene carbon isotope excursion (CIE). A sharp increase in kaolinite content coincides with the isotope shift in the Bass River section, analogous to increases found in several other records. Carbon and oxygen isotopes remain low and kaolinite content remains high for the remainder of the depositional sequence above the CIE (32.5 ft, 9.9 m), which we estimate to represent 300-500 k.y. We interpret these data as indicative of an abrupt shift to a warmer and wetter climate along the North American mid-Atlantic coast, in concert with global events associated with the CIE

Tissue-specific mRNA expression profiling in grape berry tissues

<p>Abstract</p> <p>Background</p> <p>Berries of grape (<it>Vitis vinifera</it>) contain three major tissue types (skin, pulp and seed) all of which contribute to the aroma, color, and flavor characters of wine. The pericarp, which is composed of the exocarp (skin) and mesocarp (pulp), not only functions to protect and feed the developing seed, but also to assist in the dispersal of the mature seed by avian and mammalian vectors. The skin provides volatile and nonvolatile aroma and color compounds, the pulp contributes organic acids and sugars, and the seeds provide condensed tannins, all of which are important to the formation of organoleptic characteristics of wine. In order to understand the transcriptional network responsible for controlling tissue-specific mRNA expression patterns, mRNA expression profiling was conducted on each tissue of mature berries of <it>V. vinifera </it>Cabernet Sauvignon using the Affymetrix GeneChip^®<it>Vitis </it>oligonucleotide microarray ver. 1.0. In order to monitor the influence of water-deficit stress on tissue-specific expression patterns, mRNA expression profiles were also compared from mature berries harvested from vines subjected to well-watered or water-deficit conditions.</p> <p>Results</p> <p>Overall, berry tissues were found to express approximately 76% of genes represented on the <it>Vitis </it>microarray. Approximately 60% of these genes exhibited significant differential expression in one or more of the three major tissue types with more than 28% of genes showing pronounced (2-fold or greater) differences in mRNA expression. The largest difference in tissue-specific expression was observed between the seed and pulp/skin. Exocarp tissue, which is involved in pathogen defense and pigment production, showed higher mRNA abundance relative to other berry tissues for genes involved with flavonoid biosynthesis, pathogen resistance, and cell wall modification. Mesocarp tissue, which is considered a nutritive tissue, exhibited a higher mRNA abundance of genes involved in cell wall function and transport processes. Seeds, which supply essential resources for embryo development, showed higher mRNA abundance of genes encoding phenylpropanoid biosynthetic enzymes, seed storage proteins, and late embryogenesis abundant proteins. Water-deficit stress affected the mRNA abundance of 13% of the genes with differential expression patterns occurring mainly in the pulp and skin. In pulp and seed tissues transcript abundance in most functional categories declined in water-deficit stressed vines relative to well-watered vines with transcripts for storage proteins and novel (no-hit) functional assignments being over represented. In the skin of berries from water-deficit stressed vines, however, transcripts from several functional categories including general phenypropanoid and ethylene metabolism, pathogenesis-related responses, energy, and interaction with the environment were significantly over-represented.</p> <p>Conclusion</p> <p>These results revealed novel insights into the tissue-specific expression mRNA expression patterns of an extensive repertoire of genes expressed in berry tissues. This work also establishes an extensive catalogue of gene expression patterns for future investigations aimed at the dissection of the transcriptional regulatory hierarchies that govern tissue-specific expression patterns associated with tissue differentiation within berries. These results also confirmed that water-deficit stress has a profound effect on mRNA expression patterns particularly associated with the biosynthesis of aroma and color metabolites within skin and pulp tissues that ultimately impact wine quality.</p

Individual Responses for Muscle Activation, Repetitions, and Volume during Three Sets to Failure of High- (80% 1RM) \u3cem\u3eversus\u3c/em\u3e Low-Load (30% 1RM) Forearm Flexion Resistance Exercise

This study compared electromyographic (EMG) amplitude, the number of repetitions completed, and exercise volume during three sets to failure of high- (80% 1RM) versus low-load (30% 1RM) forearm flexion resistance exercise on a subject-by-subject basis. Fifteen men were familiarized, completed forearm flexion 1RM testing. Forty-eight to 72 h later, the subjects completed three sets to failure of dumbbell forearm flexion resistance exercise with 80% (n = 8) or 30% (n = 7) 1RM. EMG amplitude was calculated for every repetition, and the number of repetitions performed and exercise volume were recorded. During sets 1, 2, and 3, one of eight subjects in the 80% 1RM group demonstrated a significant linear relationship for EMG amplitude versus repetition. For the 30% 1RM group, seven, five, and four of seven subjects demonstrated significant linear relationships during sets 1, 2, and 3, respectively. The mean EMG amplitude responses show that the fatigue-induced increases in EMG amplitude for the 30% 1RM group and no change in EMG amplitude for the 80% 1RM group resulted in similar levels of muscle activation in both groups. The numbers of repetitions completed were comparatively greater, while exercise volumes were similar in the 30% versus 80% 1RM group. Our results, in conjunction with those of previous studies in the leg extensors, suggest that there may be muscle specific differences in the responses to high- versus low-load exercise

Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development

BACKGROUND: Grape berry development is a dynamic process that involves a complex series of molecular genetic and biochemical changes divided into three major phases. During initial berry growth (Phase I), berry size increases along a sigmoidal growth curve due to cell division and subsequent cell expansion, and organic acids (mainly malate and tartrate), tannins, and hydroxycinnamates accumulate to peak levels. The second major phase (Phase II) is defined as a lag phase in which cell expansion ceases and sugars begin to accumulate. Véraison (the onset of ripening) marks the beginning of the third major phase (Phase III) in which berries undergo a second period of sigmoidal growth due to additional mesocarp cell expansion, accumulation of anthocyanin pigments for berry color, accumulation of volatile compounds for aroma, softening, peak accumulation of sugars (mainly glucose and fructose), and a decline in organic acid accumulation. In order to understand the transcriptional network responsible for controlling berry development, mRNA expression profiling was conducted on berries of V. vinifera Cabernet Sauvignon using the Affymetrix GeneChip® Vitis oligonucleotide microarray ver. 1.0 spanning seven stages of berry development from small pea size berries (E-L stages 31 to 33 as defined by the modified E-L system), through véraison (E-L stages 34 and 35), to mature berries (E-L stages 36 and 38). Selected metabolites were profiled in parallel with mRNA expression profiling to understand the effect of transcriptional regulatory processes on specific metabolite production that ultimately influence the organoleptic properties of wine. RESULTS: Over the course of berry development whole fruit tissues were found to express an average of 74.5% of probes represented on the Vitis microarray, which has 14,470 Unigenes. Approximately 60% of the expressed transcripts were differentially expressed between at least two out of the seven stages of berry development (28% of transcripts, 4,151 Unigenes, had pronounced (≥2 fold) differences in mRNA expression) illustrating the dynamic nature of the developmental process. The subset of 4,151 Unigenes was split into twenty well-correlated expression profiles. Expression profile patterns included those with declining or increasing mRNA expression over the course of berry development as well as transient peak or trough patterns across various developmental stages as defined by the modified E-L system. These detailed surveys revealed the expression patterns for genes that play key functional roles in phytohormone biosynthesis and response, calcium sequestration, transport and signaling, cell wall metabolism mediating expansion, ripening, and softening, flavonoid metabolism and transport, organic and amino acid metabolism, hexose sugar and triose phosphate metabolism and transport, starch metabolism, photosynthesis, circadian cycles and pathogen resistance. In particular, mRNA expression patterns of transcription factors, abscisic acid (ABA) biosynthesis, and calcium signaling genes identified candidate factors likely to participate in the progression of key developmental events such as véraison and potential candidate genes associated with such processes as auxin partitioning within berry cells, aroma compound production, and pathway regulation and sequestration of flavonoid compounds. Finally, analysis of sugar metabolism gene expression patterns indicated the existence of an alternative pathway for glucose and triose phosphate production that is invoked from véraison to mature berries. CONCLUSION: These results reveal the first high-resolution picture of the transcriptome dynamics that occur during seven stages of grape berry development. This work also establishes an extensive catalog of gene expression patterns for future investigations aimed at the dissection of the transcriptional regulatory hierarchies that govern berry development in a widely grown cultivar of wine grape. More importantly, this analysis identified a set of previously unknown genes potentially involved in critical steps associated with fruit development that can now be subjected to functional testing.National Science Foundation Plant Genome Project (DBI-0217653); Bioinformatics program (DBI-0136561); National Institute of Health Biomedical Research Infrastructure Network (NIH-NCRR P20 RR16464; National Institute of Health IDeA Network of Biomedical Research Excellence (INBRE, RR-03-008); Nevada Agricultural Experimental Statio

A Self-Consistent Vacuum for Misner Space and the Chronology Protection Conjecture

In this paper we find a self-consistent vacuum for Misner space. For this "adapted" Rindler vacuum the renormalized stress-energy tensor is zero throughout the Misner space. A point-like particle detector traveling on a timelike geodesic in a Misner space with this vacuum detects nothing. Misner space with this vacuum thus creates no problems for time travel in and of itself but a time traveler may pose a danger to himself and to the spacetime.Comment: 5 pages, received September 5, 1997, with a note added November 24, 199

The Grizzly, February 4, 1983

Trouble at Cutillo\u27s: Frats Earn Reputation as Animals • Drinking Concerns Richter • Economics Council Sponsors Entrepreneur-Related Forum • President\u27s Corner • Wismer Tries Again • Pfacelift at Pfahler • Bear Blades Burnished Beat Wilmington Twice • Serendipity Celebration Features Films • Writing Center Welcomes Students • Who\u27s Who in Who\u27s Who? • Commentary: Speak Up for Coed Housing • Didja Ever Wonder • Wrestlers Earn Split • Lewis on Wall Street • Disruptive Fans Cause Flare-up at Widener • Top Individual Efforts Mark Gymnastics Team • Interview: Chupein Named to All-League Team • Lady Hoops Still Struggling • Men\u27s Basketball Find Road a Bit Bumpy • Swimmers Maul Terrors of Western Marylandhttps://digitalcommons.ursinus.edu/grizzlynews/1092/thumbnail.jp