Identification of a novel inhibitor of JAK2 tyrosine kinase by structure-based virtual screening

Janus kinase 2 (JAK2) plays a crucial role in the pathomechanism of myeloproliferative disorders and hematologic malignancies. A somatic mutation of JAK2 (Val617Phe) was previously shown to occur in 98% of patients with polycythemia vera and 50% of patients with essential thrombocythemia and primary myelofibrosis. Thus, effective JAK2 kinase inhibitors may be of significant therapeutic importance. Here, we applied a structure-based virtual screen to identify novel JAK2 inhibitors. One JAK2 inhibitor in particular, G6, demonstrated remarkable potency as well as specificity, which makes it as a potential lead candidate against diseases related to elevated JAK2 tyrosine kinase activity.     

Recombination and Repair: Ku starts at the end

Genetic evidence suggests that the Ku DNA-end-binding protein complex is central to the recombination-based repair of double-strand breaks that protects DNA from radiation and underlies antibody gene rearrangement.     

Cloning, sequence analysis, and expression in Escherichia coli of the gene encoding an alpha-amino acid ester hydrolase from Acetobacter turbidans.

The alpha-amino acid ester hydrolase from Acetobacter turbidans ATCC 9325 is capable of hydrolyzing and synthesizing beta-lactam antibiotics, such as cephalexin and ampicillin. N-terminal amino acid sequencing of the purified alpha-amino acid ester hydrolase allowed cloning and genetic characterization of the corresponding gene from an A. turbidans genomic library. The gene, designated aehA, encodes a polypeptide with a molecular weight of 72,000. Comparison of the determined N-terminal sequence and the deduced amino acid sequence indicated the presence of an N-terminal leader sequence of 40 amino acids. The aehA gene was subcloned in the pET9 expression plasmid and expressed in Escherichia coli. The recombinant protein was purified and found to be dimeric with subunits of 70 kDa. A sequence similarity search revealed 26% identity with a glutaryl 7-ACA acylase precursor from Bacillus laterosporus, but no homology was found with other known penicillin or cephalosporin acylases. There was some similarity to serine proteases, including the conservation of the active site motif, GXSYXG. Together with database searches, this suggested that the alpha-amino acid ester hydrolase is a beta-lactam antibiotic acylase that belongs to a class of hydrolases that is different from the Ntn hydrolase superfamily to which the well-characterized penicillin acylase from E. coli belongs. The alpha-amino acid ester hydrolase of A. turbidans represents a subclass of this new class of beta-lactam antibiotic acylases.     

Proteomics analysis of human intestinal organoids during hypoxia and reoxygenation as a model to study ischemia-reperfusion injury

Intestinal ischemia-reperfusion (IR) injury is associated with high mortality rates, which have not improved in the past decades despite advanced insight in its pathophysiology using in vivo animal and human models. The inability to translate previous findings to effective therapies emphasizes the need for a physiologically relevant in vitro model to thoroughly investigate mechanisms of IR-induced epithelial injury and test potential therapies. In this study, we demonstrate the use of human small intestinal organoids to model IR injury by exposing organoids to hypoxia and reoxygenation (HR). A mass-spectrometry-based proteomics approach was applied to characterize organoid differentiation and decipher protein dynamics and molecular mechanisms of IR injury in crypt-like and villus-like human intestinal organoids. We showed successful separation of organoids exhibiting a crypt-like proliferative phenotype, and organoids exhibiting a villus-like phenotype, enriched for enterocytes and goblet cells. Functional enrichment analysis of significantly changing proteins during HR revealed that processes related to mitochondrial metabolism and organization, other metabolic processes, and the immune response were altered in both organoid phenotypes. Changes in protein metabolism, as well as mitophagy pathway and protection against oxidative stress were more pronounced in crypt-like organoids, whereas cellular stress and cell death associated protein changes were more pronounced in villus-like organoids. Profile analysis highlighted several interesting proteins showing a consistent temporal profile during HR in organoids from different origin, such as NDRG1, SDF4 or DMBT1. This study demonstrates that the HR response in human intestinal organoids recapitulates properties of the in vivo IR response. Our findings provide a framework for further investigations to elucidate underlying mechanisms of IR injury in crypt and/or villus separately, and a model to test therapeutics to prevent IR injury.Subject terms: Mechanisms of disease, Proteomics     

Occurrence of Bondar's Nesting Whitefly,Paraleyrodes bondari (Hemiptera: Aleyrodidae), on cassava in Uganda

Cassava is a valued calorific source to millions of Africans who eat it daily and a vital staple for their food security. One of the key constraints to this crop is whiteflies which are both a vector of viral diseases and a direct pest. Although the African cassava whitefly is known to cause physical damage on cassava with considerable tuberous yield loss, a recent whitefly outbreak caused unusually severe damage, which prompted the current reported investigation. Molecular identification of whitefly adults sampled from the affected cassava field revealed the presence of a new whitefly species, Paraleyrodes bondari. This communication is the first report of the occurrence of P. bondari on cassava in Uganda.     

The behavioral context of visual displays in common marmosets (Callithrix jacchus)

Communication is important in social species, and may occur with the use of visual, olfactory or auditory signals. However, visual communication may be hampered in species that are arboreal have elaborate facial coloring and live in small groups. The common marmoset fits these criteria and may have limited visual communication. Nonetheless, some (contradictive) propositions concerning visual displays in the common marmoset have been made, yet quantitative data are lacking. The aim of this study was to assign a behavioral context to different visual displays using pre–post‐event‐analyses. Focal observations were conducted on 16 captive adult and sub‐adult marmosets in three different family groups. Based on behavioral elements with an unambiguous meaning, four different behavioral contexts were distinguished: aggression, fear, affiliation, and play behavior. Visual displays concerned behavior that included facial expressions, body postures, and pilo‐erection of the fur. Visual displays related to aggression, fear, and play/affiliation were consistent with the literature. We propose that the visual display “pilo‐erection tip of tail” is related to fear. Individuals receiving these fear signals showed a higher rate of affiliative behavior. This study indicates that several visual displays may provide cues or signals of particular social contexts. Since the three displays of fear elicited an affiliative response, they may communicate a request of anxiety reduction or signal an external referent. Concluding, common marmosets, despite being arboreal and living in small groups, use several visual displays to communicate with conspecifics and their facial coloration may not hamper, but actually promote the visibility of visual displays. Am. J. Primatol. 75:1084–1095, 2013. © 2013 The Authors. American Journal of Primatology Published by Wiley Periodicals, Inc.     

The Moves of a Bajau Middlewoman: Understanding the Disparity between Trade Networks and Marine Conservation

At the interface of Indonesia and Malaysia, border-crossing maritime trade appears to elude attempts to conserve marine resources. In Berau district (East Kalimantan) attempts to protect coastal waters from illegal fishing and trade fail to correspond with mobile trade networks. In this article, I describe how a female Bajau trader acts out her (illegal) trade network in practice. The article draws on 18 months of ethnographic research, during which I joined the trader along her travels through the coastal zone of northeastern Kalimantan. Using a performative network approach, I explore the trader's network as a continuously generated effect of practice and movement. Following her trading practices, I show that the performance of her network requires the ceaseless movement of people and things, in travelling (mobility) as well as in the reshaping of relations (fluidity). The trader's network is enmeshed in historically grown relations of kinship, ethnicity, and patron–client associations across the sea. These socially and spatially mobile associations are at odds with conservationists’ preoccupation with a spatial fixation of people, places, and borders. By showing how relations of loyalty, debt, and affiliation systematically transgress these borders, I demonstrate the significance of a relational approach to marine conservation that takes into account the mobility and interdependency of maritime networks. Such an approach may help to redress the hegemony of place-based approaches in marine conservation.     

Temporal and spatial variability in soil nutrient status of a former beach plain

As part of a research project on the variation in life-history characteristics within a population of Plantago major L. ssp. pleiosperma, seasonal and spatial variability in the availability of macronutrients (N, P, and K) were examined on a small scale in the 0–25 cm soil depth at a primary beach plain site, embanked since 1966. On the basis of distinct differences, among other things, in plant biomass, an a priori division into three different types of microhabitat occurring in a mosaic distribution pattern was made: an overall low-lying area (subsite 1) with slightly elevated patches of 0.5 to 1.5 m in diameter (subsite 2) and rather large patches, 20 to 40 m in diameter, of sea buckthorn shrubs, with small and relatively open spots (subsite 3) in the transitional zone from lower area into scrub. All three subsite types were studied within a total area of approximately 2000 m². Three methods of analysis were applied: an inventory survey (sampling once at the start of the growing season), an analysis of the seasonal variation (sampling at approximately monthly intervals during the period April-November), and an assessment of nitrogen mineralization potentials in the laboratory (sampling once at the beginning of the growing season). All three procedures clearly demonstrated the occurrence of differences in the availability of nutrients over very short distances, i.e. a pronounced spatial variability among subsites. Particularly the availability of N and P appeared to have increased at the subsites 2 and 3, when compared to subsite 1. This small-scale differentiation in soil properties has occurred in an essentially homogeneous parent material (e.g. in texture and carbonate content) over a period of about 20 years. Besides a spatial variability, statistically significant temporal fluctuations were observed in the availability of N, P, and K. Relative fluctuations of mineral N (as indicated by the range/mean ratio) were especially large at the subsites 2 and 3.