Genomic and signalling pathway characterization of the NZM panel of melanoma cell lines: A valuable model for studying the impact of genetic diversity in melanoma

Melanoma is a disease associated with a very high mutation burden and thus the possibility of a diverse range of oncogenic mechanisms that allow it to evade therapeutic interventions and the immune system. Here, we describe the characterization of a panel of 102 cell lines from metastatic melanomas (the NZM lines), including using whole‐exome and RNA sequencing to analyse genetic variants and gene expression changes in a subset of this panel. Lines possessing all major melanoma genotypes were identified, and hierarchical clustering of gene expression profiles revealed four broad subgroups of cell lines. Immunogenotyping identified a range of HLA haplotypes as well as expression of neoantigens and cancer–testis antigens in the lines. Together, these characteristics make the NZM panel a valuable resource for cell‐based, immunological and xenograft studies to better understand the diversity of melanoma biology and the responses of melanoma to therapeutic interventions.     

Timing and abundance of sporangia production and zoospore release influences the recovery of different Phytophthora species by baiting

Analysis of soil samples using High Throughput Sequencing (HTS) frequently detects more Phytophthora species compared with traditional soil baiting methods. This study investigated whether differences between species in the timing and abundance of sporangial production and zoospore release could be a reason for the lower number of species isolated by baiting. Stems of Eucalyptus marginata were inoculated with ten Phytophthora species (P. nicotianae, P. multivora, P. pseudocryptogea, P. cinnamomi, P. thermophila, P. arenaria, P. heveae, P. constricta, P. gondwanensis and P. versiformis), and lesioned sections for each species were baited separately in water. There were significant differences between species in timing of sporangia production and zoospore release. P. nicotianae, P. pseudocryptogea, P. multivora and P. thermophila released zoospores within 8–12 h and could be isolated from lesioned baits within 1–2 days. In contrast, P. constricta did not produce zoospores for over 48 h and was only isolated 5–7 days after baiting. P. heveae and P. versiformis did not produce zoospores and were not recovered from the baits. When species were paired in the same baiting tub, those that produced zoospores in the shortest time were isolated most frequently, while species slow to produce zoospores, or which produced them in lower numbers, were isolated from few baits or not at all. Thus, species differences in the timing of sporangia production and zoospore release may contribute to the ease of isolation of some Phytophthora species when they are present together with other Phytophthora species in an environmental sample.     

TORC1-regulated protein kinase Npr1 phosphorylates Orm to stimulate complex sphingolipid synthesis

The evolutionarily conserved Orm1 and Orm2 proteins mediate sphingolipid homeostasis. However, the homologous Orm proteins and the signaling pathways modulating their phosphorylation and function are incompletely characterized. Here we demonstrate that inhibition of nutrient-sensitive target of rapamycin complex 1 (TORC1) stimulates Orm phosphorylation and synthesis of complex sphingolipids in Saccharomyces cerevisiae. TORC1 inhibition activates the kinase Npr1 that directly phosphorylates and activates the Orm proteins. Npr1-phosphorylated Orm1 and Orm2 stimulate de novo synthesis of complex sphingolipids downstream of serine palmitoyltransferase. Complex sphingolipids in turn stimulate plasma membrane localization and activity of the nutrient scavenging general amino acid permease 1. Thus activation of Orm and complex sphingolipid synthesis upon TORC1 inhibition is a physiological response to starvation.     

Chemical Constituents from a Soil‐Derived Actinomycete,Actinomadura miaoliensis BCRC 16873, and Their Inhibitory Activities on Lipopolysaccharide‐Induced Tumor Necrosis Factor Production

An investigation on the secondary metabolites from the BuOH extract of the fermentation broth of the thermotolerant polyester‐degrading actinomycete Actinomadura miaoliensis BCRC 16873 was carried out. One previously undescribed α‐pyrone (=pyran‐2‐one) derivative, designated as miaolienone ( 1 ), and a new butanolide, miaolinolide ( 2 ), together with 13 known compounds, 3 – 15 , were obtained. Their structures were established on the basis of extensive 1D‐ and 2D‐NMR analyses in combination with HR‐MS experiments. In addition, the isolated compounds 1 – 15 were evaluated for the inhibitory effects of the isolates on the production of tumor necrosis factor (TNF‐α) induced by lipopolysaccharide (LPS). Among the isolates, 1 and 2 significantly inhibited TNF‐α production in U937 cells in vitro, and the IC₅₀ values were 0.59 and 0.76 μM , respectively. Compounds 3 – 5 displayed moderate inhibitory activities on LPS‐induced TNF‐α production.     

Phytochemical Investigation of Annulohypoxylon ilanense,an Endophytic Fungus Derived from Cinnamomum Species

Cultivation of the fungal strain Annulohypoxylon ilanense, an endophytic fungus isolated from the wood of medicinal plant Cinnamomum species, resulted in the isolation of one new furanoid derivative, ilanefuranone ( 1 ), one new pyrrole alkaloid, ilanepyrrolal ( 2 ), and one new biarylpropanoid derivative, ilanenoid ( 3 ), together with 22 known compounds, of which one α‐tetralone analog, (?)‐(4R)‐3,4‐dihydro‐4,6‐dihydroxynaphthalen‐1(2H)‐one ( 4 ) was isolated for the first time from a natural source. The structures were elucidated on the basis of physicochemical evidence, in‐depth NMR spectroscopic analysis, and high‐resolution mass spectrometry, and the antimycobacterial activities were also evaluated.     

Ubc9 acetylation modulates distinct SUMO target modification and hypoxia response

While numerous small ubiquitin‐like modifier (SUMO) conjugated substrates have been identified, very little is known about the cellular signalling mechanisms that differentially regulate substrate sumoylation. Here, we show that acetylation of SUMO E2 conjugase Ubc9 selectively downregulates the sumoylation of substrates with negatively charged amino acid‐dependent sumoylation motif (NDSM) consisting of clustered acidic residues located downstream from the core ψ‐K‐X‐E/D consensus motif, such as CBP and Elk‐1, but not substrates with core ψ‐K‐X‐E/D motif alone or SUMO‐interacting motif. Ubc9 is acetylated at residue K65 and K65 acetylation attenuates Ubc9 binding to NDSM substrates, causing a reduction in NDSM substrate sumoylation. Furthermore, Ubc9 K65 acetylation can be downregulated by hypoxia via SIRT1, and is correlated with hypoxia‐elicited modulation of sumoylation and target gene expression of CBP and Elk‐1 and cell survival. Our data suggest that Ubc9 acetylation/deacetylation serves as a dynamic switch for NDSM substrate sumoylation and we report a previously undescribed SIRT1/Ubc9 regulatory axis in the modulation of protein sumoylation and the hypoxia response.     

Signaling of Ankle Joint Position by Receptors in Different Muscles

Plots were made of multiunit activity versus ankle joint position for receptors in each of the 12 muscles crossing the cat ankle joint, except peroneus tertius, by recording from populations of afferent fibers in muscle nerves. The discharge was measured 15 or 30 sec after terminating the movements that altered the position of the joint. These recordings were dominated by large-spike activity that would be expected to originate mainly from primary spindle endings. Seven of the 12 muscles also cross other joints. Their responses at a given ankle joint position were so altered by changes in the position of the knee or toe joints that they could not reliably signal the position of the ankle joint. As judged from multiunit recording, receptors in each of the five muscles specific to the ankle joint were influenced by more than one axis of ankle joint displacement.

Single-unit recording from dorsal root filaments was used to determine whether primary or secondary spindle receptors in soleus and tibialis anterior could selectively signal one axis of ankle joint rotation. Individual soleus receptors were tested both on the flexion extension axis and with a combined adduction–eversion movement.

For 38 of the 70 soleus receptors examined (54%), firm adduction–eversion produced a level of activity greater than that caused by 10° of flexion, and for 77% the level of activity was greater than that caused by 5° of flexion. For 168 of the 184 tibialis anterior receptors studied (91%), firm abduction inversion produced a level of activity greater than that caused by 10° of extension. Thus few receptors were found that responded exclusively to one axis of rotation.

One way in which the position of the ankle joint could be specified in the face of multiaxial receptor activity is by examining the receptor discharge from more than one muscle. A suggestion for how the nervous system might do this is given in the discussion.     

Survival of Phytophthora cinnamomi as oospores,stromata, and thick-walled chlamydospores in roots of symptomatic and asymptomatic annual and herbaceous perennial plant species

Studies were conducted to determine how Phytophthora cinnamomi survives during hot and dry Mediterranean summers in areas with limited surviving susceptible hosts.