Discovery of human autophagy initiation kinase ULK1 inhibitors by multi-directional in silico screening strategies

Autophagy is a self-catabolic mechanism employed by cancer cells to acquire nutrients and energy in times of stress conditions, thereby leading to its progression and survival. Thus, autophagy inhibition has emerged as a new paradigm in the area of cancer treatment. Here, we leverage multi-dimensional screening campaigns aim to identify potent inhibitors against an early and an essential autophagic kinase, ULK1 from DrugBank database. In particular, receptor-based hypothesis, pharmacophore hypothesis, e-pharmacophore hypothesis and shape similarity-based screening algorithm were employed. Of note, the results of the different algorithm were then integrated to eliminate the false positive prediction. Moreover, the inhibitory activities and PK/PD parameters of the leads were tested by Glide and Qikprop algorithm. This resulted in a set of four hits namely; DB12686, DB08341, DB07936, and DB07163. Finally, molecular dynamics simulation was performed using the GROMACS package, to validate the binding kinetics of the hit compound. The compound activity in vitro was assessed by PASS algorithm, highlights the anti-cancer activities of the hits. The structural insights reveal existence of functional moieties such as piperidine carboxamide, benzenesulfonamide, benzamide, and isoindolone in the resultant hits which plays a major role in the anti-cancer activity. Overall, we strongly believe that these ULK1 antagonists could be novel and potent drug candidates for future cancer therapeutics.     

The use of X-ray densitometry to evaluate the wood density profile of Tectona grandis trees growing in fast-growth plantations

Tectona grandis (teak) is an important commercial tree species that is widely used in tropical dendrochronology due to the formation of climate-sensitive annual growth rings. However, young trees growing in plantation conditions exhibit poor ring visibility during the first years of growth, limiting the dendrochronology application. In the present study, we use x-ray densitometry to determine the wood density profile between and within annual rings and at the sapwood-heartwood boundary in trees from fast-growth plantations. The resulting wood density profiles (WDP) can be categorized as uniform, stable growth, unstable growth, and false. The annual ring boundaries were indistinct in trees less than 8 years old. In mature trees, the annual ring boundaries are more defined. In relation to the sapwood-heartwood boundary, the WDP showed a decrease in the wood density; however, this decrease is influenced by the annual ring boundary when the two boundaries coincide. The identification of annual rings in trees growing in fast-growth plantations should be combined with X-ray densitometry and visual identification if wood density data are necessary for deriving other analysis, as climate change, from annual ring.     

Drought leads to reproductive quiescence in smooth-billed anis: Phenotypic evidence for opportunistic breeding and reproductive readiness

Previous studies have suggested that the smooth-billed ani (Crotophaga ani, Linnaeus, 1758) breeds opportunistically following unpredictable rainfall in drought areas. To obtain proof of this phenomenon, the present study described and compared reproductive morphology and cell proliferation in the gonads of free-living smooth-billed anis during a wet season (April to June 2012) and the following dry season (July to September 2012) in a semiarid area using light and electron microscopy (transmission and scanning) and the AgNOR method. The morphological findings indicated distinct levels of reproductive activity related to seasonal changes. Morphological and morphometric analyses of the gonads confirmed intense gametogenic activity during the wet season, whereas gonadal involution occurred after rainfall ceased. The sizes of the testes and ovaries were significantly reduced compared to those in the wet season. The volumetric fraction of the seminiferous tubules in the testis decreased considerably, and no preovulatory follicles were detected in the ovary in the dry season. Moreover, the AgNOR count in the gonads revealed a significant decline in cell recruitment for gametogenesis after rainfall ceased. The histological findings indicated partial gonadal activation throughout the dry season. The analysis of the seminiferous epithelium confirmed the early testicular recrudescence phase, and sporadic postovulatory follicles indicated random ovulation during this time. The excurrent ducts and the oviduct also underwent remarkable involution in the dry season. Taken together, these findings confirm opportunistic breeding by smooth-billed anis in a semiarid habitat and suggest that gonadal recrudescence has been established as a reproductive strategy to cope with unexpected precipitation events.     

A new species of Characidium (Characiformes: Crenuchidae) from the rio Madeira basin,Brazil

This study describes Characidium nambiquara, a new species from the upper rio Guaporé, rio Madeira basin, Brazil. The new species differs from most congeners by the presence of isthmus and area between the contralateral pectoral-fin bases completely naked. From congeners with some degree of scaleless ventral surface of the body C. nambiquara differs by having 10 circumpeduncular scales. The new species is also distinguished from congeners by the spotted colour pattern on body of the large-sized specimens and by having black dashes on all fins and conspicuous midlateral longitudinal dark stripe or conspicuous vertical bars absent. Characidium nambiquara further differs from most congeners by the presence of 34–36 pored scales on the lateral line, 3 horizontal scale rows above the lateral line and 3 horizontal scale rows from the lateral line to the midventral scale series. Remarks on intraspecific colour variation within the genus, not related to sexual dimorphism, are also provided.     

Geographic variation in life-history traits of the endemic kite skate Dipturus chilensis (Batoidea: Rajidae), along its distribution in the fjords and channels of southern Chile

Life-history traits of kite skates Dipturus chilensis were examined from two regions (c. 2286 km apart) in the sheltered fjords and channels of southern Chile. A total of 482 and 403 specimens were collected from the southern fjords (c. 42–46° S) and the fjords of Chilean Patagonia (c. 51–54° S), from September 2003 to 2004, respectively. Vertebra marginal increment analysis indicated an annual deposition of growth rings which was completed during the winter months. For each region, von Bertalanffy growth parameters showed that females attained a larger asymptotic size, L_∞, had a lower growth coefficient, K, and lived longer than males. Growth analysis indicated that D. chilensis from the Patagonian fjords had a longer life span (females: 22 v. 21 years; males 19 v. 17 years), attained a larger L_∞ (females: 150 v. 136 cm; males: 122 v. 118 cm total length, L_T) and had a lower K value (females: 0·087 v. 0·104; males: 0·110 v. 0·116) than their counterparts in the southern fjords. Comparisons with previous studies indicated that D. chilensis from both southern and Patagonian sheltered fjords had larger L_∞, and grew more slowly than their counterparts from central-southern Chile (L_∞= 119–123 cm, K= 0·123–0·127), suggesting latitudinal variations in growth. Females attained sexual maturity later than males in both regions. For both sexes, lengths at 50% maturity (L_50%) between regions were similar (females: c. 103 cm; males: c. 87 cm L_T); however, D. chilensis from Patagonia appeared to mature 1 year earlier (females: 13 v. 14 years; males: 10 v. 11 years). Specimens from Patagonia had a lower ovarian fecundity than those from the southern fjords. An increase in the proportion of mature females and males during summer, suggests that the reproductive peak occurs in this season, and no regional differences were found. The size of the egg cases increased with maternal L_T and these were longer in Patagonia. The information provided here represents the first evidence of regional variations in life-history traits for elasmobranchs in the south-eastern Pacific.     

Intraspecific variation in a generalist herbivore accounts for differential induction and impact of host plant defences

Plants and herbivores are thought to be engaged in a coevolutionary arms race: rising frequencies of plants with anti-herbivore defences exert pressure on herbivores to resist or circumvent these defences and vice versa. Owing to its frequency-dependent character, the arms race hypothesis predicts that herbivores exhibit genetic variation for traits that determine how they deal with the defences of a given host plant phenotype. Here, we show the existence of distinct variation within a single herbivore species, the spider mite Tetranychus urticae, in traits that lead to resistance or susceptibility to jasmonate (JA)-dependent defences of a host plant but also in traits responsible for induction or repression of JA defences. We characterized three distinct lines of T. urticae that differentially induced JA-related defence genes and metabolites while feeding on tomato plants (Solanum lycopersicum). These lines were also differently affected by induced JA defences. The first line, which induced JA-dependent tomato defences, was susceptible to those defences; the second line also induced JA defences but was resistant to them; and the third, although susceptible to JA defences, repressed induction. We hypothesize that such intraspecific variation is common among herbivores living in environments with a diversity of plants that impose diverse selection pressure.     

The taxonomic implications of cranial shape variation in Homo erectus

The taxonomic status of Homo erectus sensu lato has been a source of debate since the early 1980s, when a series of publications suggested that the early African fossils may represent a separate species, H. ergaster. To gain further resolution regarding this debate, 3D geometric morphometric data were used to quantify overall shape variation in the cranial vault within H. erectus using a new metric, the sum of squared pairwise Procrustes distances (SSD). Bootstrapping methods were used to compare the H. erectus SSD to a broad range of human and nonhuman primate samples in order to ascertain whether variation in H. erectus most clearly resembles that seen in one or more species. The reference taxa included relevant phylogenetic, ecological, and temporal analogs including humans, apes, and both extant and extinct papionin monkeys. The mean cranial shapes of different temporogeographic subsets of H. erectus fossils were then tested for significance using exact randomization tests and compared to the distances between regional groups of modern humans and subspecies/species of the ape and papionin monkey taxa. To gauge the influence of sexual dimorphism on levels of variation, comparisons were also made between the mean cranial shapes of single-sex samples for the reference taxa. Results indicate that variation in H. erectus is most comparable to single species of papionin monkeys and the genus Pan, which included two species. However, H. erectus encompasses a limited range of variation given its extensive geographic and temporal range, leading to the conclusion that only one species should be recognized. In addition, there are significant differences between the African/Georgian and Asian H. erectus samples, but not between H. ergaster (Georgia+Africa, excluding OH 9 and Daka) and H. erectus sensu stricto. This finding is in line with expectations for intraspecific variation in a long-lived species with a wide, but probably discontinuous, geographic distribution.