Quantification of DNA cleavage specificity in Hi-C experiments

Hi-C experiments produce large numbers of DNA sequence read pairs that are typically analyzed to deduce genomewide interactions between arbitrary loci. A key step in these experiments is the cleavage of cross-linked chromatin with a restriction endonuclease. Although this cleavage should happen specifically at the enzyme''s recognition sequence, an unknown proportion of cleavage events may involve other sequences, owing to the enzyme''s star activity or to random DNA breakage. A quantitative estimation of these non-specific cleavages may enable simulating realistic Hi-C read pairs for validation of downstream analyses, monitoring the reproducibility of experimental conditions and investigating biophysical properties that correlate with DNA cleavage patterns. Here we describe a computational method for analyzing Hi-C read pairs to estimate the fractions of cleavages at different possible targets. The method relies on expressing an observed local target distribution downstream of aligned reads as a linear combination of known conditional local target distributions. We validated this method using Hi-C read pairs obtained by computer simulation. Application of the method to experimental Hi-C datasets from murine cells revealed interesting similarities and differences in patterns of cleavage across the various experiments considered.     

Design of a potent anticancer lead inspired by natural products from traditional Indian medicine

Abstract

Among the plant constituents of Clerodendrum colebrookianum Walp., acteoside, martinoside, and osmanthuside β6 interact with ROCK, a drug target for cancer. In this study, aglycone fragments of these plant constituents (caffeic acid, ferulic acid, and p-coumaric acid) along with the homopiperazine ring of fasudil (standard ROCK inhibitor) were used to design hybrid molecules. The designed molecules interact with the key hinge region residue Met156/Met157 of ROCK I/II in a stable manner according to our docking and molecular dynamics simulations. These compounds were synthesized and tested in vitro in SW480, MDA-MB-231, and A-549 cancer cell lines. The most promising compound was chemically optimized to obtain a thiourea analog, 6a (IC₅₀ = 25?µM), which has >3-fold higher antiproliferative activity than fasudil (IC₅₀ = 87?µM) in SW480 cells. Treatment with this molecule also inhibits the migration of colon cancer cells and induces cell apoptosis. Further, SPR experiments suggests that the binding affinity of 6a with ROCK I protein is better than that of fasudil. Hence, the drug-like natural product analog 6a constitutes a highly promising new anticancer lead.

Communicated by Ramaswamy H. Sarma     

A new species of the genusProbstmayria Ransom, 1907 (Nematoda: Atractidae) from the rhesus macaque,Macaca mulatta

Probstmayria nainitalensis n. sp. is described from the rectum of the rhesus macaque,Macaca mulatta, from Nainital, India. The new form consists of morphologically dissimilar spicules, spicular ratio 1:1.41–1.50, tip of shorter spicule elongate and blunt, six pairs of postanal papillae and a prominent gubernaculum in the male and didelphic ovaries and postequatorial vulva in the female. A key to the species is also furnished.     

Lectin staining of rat testis and epididymis after ligation of excurrent ducts at different levels

Seven rhodamine-conjugated lectins (PNA, RCA I, SBA, Con A, WGA, UEA I, and DBA; see Table 1) were utilized in studying the staining pattern of glycoproteins in rat testis and epididymis after ligation of ductuli efferentes (DE), corpus epididymidis (CE), and vas deferens (VD) for various time periods. Ductuli efferentes ligation caused a widening of seminferous tubules and detachment of spermatids with formation of multinuclear cells. These cells acquired a strong affinity for all lectins. Corpus epididymidis ligation also caused degeneration of spermatids with increased lectin staining in some tubules, but after 7 days another cell population close to the periphery of seminiferous tubules showed an increased nuclear affinity for some lectins followed by a clear degeneration and strong cytoplasmic staining with all lectins. Vas deferens ligation caused no degenerative changes in testicular spermatids. However, the peripheral cell population showed degenerative changes similar to those found after CE ligation. In both cases this was coincident with the formation of spermatic granulomas at the site of ligation. Ductuli efferentes ligation caused a gradual decrease of intratubular content in caput epididymidis, while the contrary was true after CE ligation. The latter was associated with intratubular accumulation of lectin-positive swollen cells and sperm aggregates as well as an increased lectin staining of narrow cells in initial segment and light cells in distal caput. After VD ligation an increased staining of light cells was initially found in distal cauda and distal caput, but, concomitant with distension of the tubules this reaction decreased.(ABSTRACT TRUNCATED AT 250 WORDS)