Niche separation, dynamics, and transport pattern of trace elements along Antarctic krill (Euphausia superba) to its exclusive predator, mackerel icefish (Champsocephalus gunnari).

In this study, the dynamics of the trophic niches and the accumulation and transfer of four trace elements-Cu, Cd, Zn, and Pb-from Antarctic krill (Euphausia superba) to mackerel icefish (Champsocephalus gunnari) were investigated. The results demonstrated that the average concentrations of Zn, Cu, Cd, and Pb in E. superba were significantly higher than those of the corresponding elements in C. gunnari. These trace elements have a biodilution effect through E. superba to C. gunnari, and Cu has the lowest biomagnification factor among those four trace elements. It is observed that the Cu concentration in E. superba is correlated with its δ15N and δ13C, and the enrichment of Pb in C. gunnari is affected by its δ15N.

Kidney-intrinsic factors determine the severity of ischemia/reperfusion injury in a mouse model of delayed graft function.

Delayed graft function due to transplant ischemia/reperfusion injury adversely affects up to 50% of deceased-donor kidney transplant recipients. However, key factors contributing to the severity of ischemia/reperfusion injury remain unclear. Here, using a clinically relevant mouse model of delayed graft function, we demonstrated that donor genetic background and kidney-intrinsic MyD88/Trif-dependent innate immunity were key determinants of delayed graft function. Functional deterioration of kidney grafts directly corresponded with the duration of cold ischemia time. The graft dysfunction became irreversible after cold ischemia time exceeded six hours. When cold ischemia time reached four hours, kidney grafts displayed histological features reflective of delayed graft function seen in clinical kidney transplantation. Notably, kidneys of B6 mice exhibited significantly more severe histological and functional impairment than kidneys of C3H or BALB/c mice, regardless of recipient strains or alloreactivities. Furthermore, allografts of B6 mice also showed an upregulation of IL-6, neutrophil gelatinase-associated lipocalin, and endoplasmic reticulum stress genes, as well as an increased influx of host neutrophils and memory CD8 T-cells. In contrast, donor MyD88/Trif deficiency inhibited neutrophil influx and decreased the expression of IL-6 and endoplasmic reticulum stress genes, along with improved graft function and prolonged allograft survival. Thus, kidney-intrinsic factors involving genetic characteristics and innate immunity serve as critical determinants of the severity of delayed graft function. This preclinical murine model allows for further investigations of the mechanisms underlying delayed graft function.

Carbapenem-resistant Acinetobacter baumannii from Air and Patients of Intensive Care Units.

To understand the molecular epidemiology and antibiotic resistance of air and clinical isolates of Acinetobacter baumannii , the intensive care unit settings of a hospital in Northern China were surveyed in 2014. Twenty non-duplicate A. baumannii isolates were obtained from patients and five isolates of airborne A. baumannii were obtained from the wards' corridors. Pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to analyze the homology relationships of isolates. Resistance and resistance genes were detected by drug susceptibility test and PCR. The results demonstrated that all isolates can be classified into eight PFGE types and four sequence types (ST208, ST195, ST369 and ST530). A pair of isolates from patients (TAaba004) and from the air (TAaba012) that share 100% similarity in PFGE was identified, indicating that air might be a potential and important transmission route for A. baumannii . More than 80% of the isolates were resistant to carbapenems and aminoglycoside antibiotics. Twenty-four isolates, which were resistant to carbapenems, carried the bla OXA-23-like gene. The data indicated that air might be an alternative way for the transmission of A. baumannii . Hospitals should pay more attention to this route, and design new measures accordingly.

Transcriptome sequencing combined with bioinformatics predicts potential genes and pathways associated with bupivacaine-induced apoptosis.

This study aimed to explore the potential genes and pathways associated with bupivacaine-induced apoptosis. Human neuroblastoma cell line SH-SY5Y was used in this study. The effect of bupivacaine on cell viability of SH-SY5Y was detected by Cell Counting Kit-8. Transcriptome sequencing was performed for SH-SY5Y cells that were treated and untreated with bupivacaine based on the HiSeq 4000 sequencing platform. The sequencing results were analyzed using bioinformatics methods, including differentially expressed genes (DEGs) identification, functional enrichment analysis, protein-protein interaction (PPI) network analysis and module analysis. The cell viability of SH-SY5Y cells decreased significantly after bupivacaine treatment (p < .01). Based on the HiSeq 4000 sequencing platform, we obtained a global overview of the transcriptome of SH-SY5Y treated with/without bupivacaine. Bioinformatics analysis identified 335 up-regulated and 294 down-regulated DEGs in bupivacaine group. They were significantly enriched in cell cycle-associated functions and pathways and cAMP signaling pathway. In the PPI network, proliferating cell nuclear antigen (PCNA), v-Akt murine thymoma viral oncogene homolog 3 (AKT3), cyclin-dependent kinase inhibitor 1A (CDKN1A) and cell division cycle 6 (CDC6) had high topology scores. Module analysis obtained two sub-network modules (cluster 1 and cluster 2). PCNA, CDC6, CDKN1A and AKT3 may play important roles in bupivacaine-induced apoptosis. Additionally, bupivacaine may also induce apoptosis via pathways of cell cycle and cAMP signaling pathway.

[Effects of climate change on potato growth in semi-arid region of Loess Plateau, China].

Based on the 1988-2008 located observation and 2007-2008 encrypted observation of potato growth and the 1957-2008 meteorological observation in semi-arid region of Loess Plateau, this paper studied the effects of climate change on the potato growth in this region. In 1957-2008, the annual precipitation in this region had a descending trend, with a linear fitting rate of the annual precipitation change curves being - 13.359 mm x (10 a)(-1), while the annual mean temperature displayed an ascending trend, with a linear fitting rate of the annual mean temperature change curves being 0.239 degrees C x (10 a)(-1). During potato growth period, the aridity index displayed a marked ascending trend, and the linear fitting rate of the aridity index change curves was 0.102 x (10 a)(-1). The growth rate of potato tuber became faster from the 96th day after sowing, reached the maximum on the 110th day, and turned slower from the 124th day. The interval from sowing to seedling emergence was shortened by 1-2 d x (10 a)(-1), and that from inflorescence formation to reaping and of whole growth period was lengthened by 9-10 d x (10 a) (-1). In the study region, climate warming shortened the vegetative growth stage, but lengthened the reproductive growth stage and whole growth period of potato.

An intracellular conformational sensor assay for Abl T315I.

Conformational change is a common molecular mechanism for the regulation of kinase activities. Small molecule modulators of protein conformations, including allosteric kinase inhibitors, are highly wanted as tools for the interrogation of kinase biology and as selective therapeutic agents. However, straightforward cellular assays monitoring kinase conformations in a manner conducive to high-throughput screening (HTS) are not readily available. Here we describe such an HTS-compatible conformational sensor assay for Abl based on a split luciferase construct. The Abl sensor responds to intramolecular structural rearrangements associated with intracellular Abl deactivation and small molecule inhibition. The intact regulatory CAP-SH3-SH2 domain is required for the full functionality of the sensor. Moreover, a T334I Abl mutant (T315I in Abl1a) was found to be particularly well suited for HTS purposes and mechanistic intracellular studies of T334I mutant inhibitors. We expect that the split luciferase-based conformational sensor approach might be more broadly useful to probe the intracellular activation of other kinases and enzymes in general.

Identification of coumarin derivatives as a novel class of allosteric MEK1 inhibitors.

A homogenous TR-FRET-based in vitro coupling assay for the MAP3Ks-MEK1-ERK2 kinase cascade was established and was used to screen for inhibitors of the ERK/MAPK pathway. A series of coumarin derivatives were identified from the screen. These compounds potently inhibit the activation of the unactivated human MEK1 by upstream MAP3Ks (including BRAF and COT), but do not inhibit the activity of the activated MEK1. In addition, the potency of these compounds in inhibiting MEK1 activation is not affected by varying the ATP concentration, suggesting that these inhibitors are not competitive with ATP. As expected, the coumarin compounds potently inhibit LPS-induced TNFalpha production and ERK phosphorylation in THP-1 cells, with the most potent compound having an IC(50) of 90nM. Molecular modeling studies suggest that these coumarins bind to an allosteric site in the inactive conformation of MEK1. This site has been shown to be utilized by the biarylamine series of MEK inhibitors such as PD318088. Very interestingly, the identified coumarin derivatives are almost identical to a series of inhibitors recently reported that block LPS-induced TNFalpha production. Our findings have therefore raised the possibility that other naturally occurring or synthetic coumarins with anti-cancer and anti-inflammatory activities might exert their biological function through the inhibition of MEK1.

Crystal structures of human HSP90alpha-complexed with dihydroxyphenylpyrazoles.

A series of dihydroxyphenylpyrazole compounds were identified as a unique class of reversible Hsp90 inhibitors. The crystal structures for two of the identified compounds complexed with the N-terminal ATP binding domain of human Hsp90alpha were determined. The dihydroxyphenyl ring of the compounds fits deeply into the adenine binding pocket with the C2 hydroxyl group forming a direct hydrogen bond with the side chain of Asp93. The pyrazole ring forms hydrogen bonds to the backbone carbonyl of Gly97, the hydroxyl group of Thr184 and to a water molecule, which is present in all of the published HSP90 structures. One of the identified compounds (G3130) demonstrated cellular activities (in Her-2 degradation and activation of Hsp70 promoter) consistent with the inhibition of cellular Hsp90 functions.

A time-resolved fluorescence resonance energy transfer-based HTS assay and a surface plasmon resonance-based binding assay for heat shock protein 90 inhibitors.

Heat shock protein 90 (Hsp90) is an ATP-dependent molecular chaperone required for the stability and function of a number of client proteins, many of which are involved in cancer development. The natural products geldanamycin (GM) and radicicol (RD) are known inhibitors of Hsp90, and their derivatives are being developed for the treatment of various cancers. To identify novel Hsp90 inhibitors, a highly robust time-resolved fluorescence resonance energy transfer (TR-FRET)-based HTS assay that measures the binding of biotinylated geldanamycin (biotin-GM) to the His-tagged human Hsp90 N-terminal ATP-binding domain (Hsp90N) was developed. This assay was optimized in 1536-well plates and was used as the primary assay to screen 10(6) compounds. Identified "hits" were then confirmed in a scintillation proximity assay (SPA) and a DEAE membrane-based assay for [(3)H]AAG binding to Hsp90. In addition, a surface plasmon resonance (SPR) assay that measures the direct interaction of Hsp90 with its inhibitors was developed and used to further characterize the identified inhibitors. Several potent and reversible inhibitors of human Hsp90 with K(d) values measured in the high nanomolar range were identified.

The role of transcription initiation factor IIIB subunits in promoter opening probed by photochemical cross-linking.

The core transcription initiation factor (TF) IIIB recruits its conjugate RNA polymerase (pol) III to the promoter and also plays an essential role in promoter opening. TFIIIB assembled with certain deletion mutants of its Brf1 and Bdp1 subunits is competent in pol III recruitment, but the resulting preinitiation complex does not open the promoter. Whether Brf1 and Bdp1 participate in opening the promoter by direct DNA interaction (as sigma subunits of bacterial RNA polymerases do) or indirectly by their action on pol III has been approached by site-specific photochemical protein-DNA cross-linking of TFIIIB-pol III-U6 RNA gene promoter complexes. Brf1, Bdp1, and several pol III subunits can be cross-linked to the nontranscribed strand of the U6 promoter at base pair -9/-8 and +2/+3 (relative to the transcriptional start as +1), respectively the upstream and downstream ends of the DNA segment that opens up into the transcription bubble. Cross-linking of Bdp1 and Brf1 is detected at 0 degrees C in closed preinitiation complexes and at 30 degrees C in complexes that are partly open, but also it is detected in mutant TFIIIB-pol III-DNA complexes that are unable to open the promoter. In contrast, promoter opening-defective TFIIIB mutants generate significant changes of cross-linking of polymerase subunits. The weight of this evidence argues in favor of an indirect mode of action of TFIIIB in promoter opening.