Historical ecology of the Raja Ampat Archipelago, Papua Province, Indonesia

This work presents a review of the status of marine resources of the Raja Ampat Archipelago, Papua Province, Indonesia, based on narratives of early European expeditions in various museums and libraries in Europe, Canada, and local archives in Papua. More than 500 pertinent documents on the study area were identified and located in various European museums and at the University of British Columbia library. About half of these were scanned (25,000 pages), which yielded the equivalent of 900 pages of text (or 4% of the total number of pages scanned) with observations on abundance and impact of the human population on the marine ecosystem within 2 degrees North and 2 degrees South between 127 degrees and 132 degrees East. In general, these observations, which spanned the period from 1810 to the present, suggest a decrease in the perceived occurrences of turtles, fish, and invertebrates; perceived abundance of turtles, fish, and algae; percieved subsistence exploitation of marine resources; and an increase in perceived commercial exploitation of marine resources. We conclude with a discussion of the problems and potential of contents analysis, and its use in the historical reconstruction of broad biodiversity trends.     

Extreme sensitivity to Yondelis (Trabectedin, ET-743) in low passaged sarcoma cell lines correlates with mutated p53

Yondelis (Trabectedin, ET-743) is a marine anticancer agent currently in Phase II/III development in patients with advanced pretreated soft tissue sarcoma. In the present study, we generated a panel of low passaged tumor cell lines from samples explanted from chemonaive sarcoma patients with different tumor types. We assessed in vitro sensitivity/resistance to Trabectedin and doxorubicin in a panel of sarcoma cell lines and examined the correlation between molecular alterations in DNA repair genes and sensitivity to Trabectedin. We treated cell lines with Trabectedin and doxorubicin in both 96-h and clonogenic assays. In both assays, well-defined groups of resistant and sensitive cell lines were observed. Resistance to Trabectedin did not correlate with resistance to doxorubicin, indicating that the two drugs may have different mechanisms of resistance. p53 mutations and deletions correlated with extreme sensitivity (IC50 < 1 nM) to Trabectedin (P < 0.01). In a pair of isogenic cell lines differing only in the presence or absence of wild-type p53, the absence of p53 rendered cells threefold more sensitive to Trabectedin.     

A model for the recognition of protein kinases based on the entropy of 3D van der Waals interactions

The study and prediction of kinase function (kinomics) is of major importance for proteome research due to the widespread distribution of kinases. However, the prediction of protein function based on the similarity between a functionally annotated 3D template and a query structure may fail, for instance, if a similar protein structure cannot be identified. Alternatively, function can be assigned using 3D-structural empirical parameters. In previous studies, we introduced parameters based on electrostatic entropy (Proteins 2004, 56, 715) and molecular vibration entropy (Bioinformatics 2003, 19, 2079) but ignored other important factors such as van der Waals (vdw) interactions. In the work described here, we define 3D-vdw entropies (degrees theta(k)) and use them for the first time to derive a classifier for protein kinases. The model classifies correctly 88.0% of proteins in training and more than 85.0% of proteins in validation studies. Principal components analysis of heterogeneous proteins demonstrated that degrees theta(k) codify information that is different to that described by other bulk or folding parameters. In additional validation experiments, the model recognized 129 out of 142 kinases (90.8%) and 592 out of 677 non-kinases (87.4%) not used above. This study provides a basis for further consideration of degrees theta(k) as parameters for the empirical search for structure-function relationships.     

Competing Lipid-Protein and Protein-Protein Interactions Determine Clustering and Gating Patterns in the Potassium Channel from Streptomyces lividans (KcsA)

There is increasing evidence to support the notion that membrane proteins, instead of being isolated components floating in a fluid lipid environment, can be assembled into supramolecular complexes that take part in a variety of cooperative cellular functions. The interplay between lipid-protein and protein-protein interactions is expected to be a determinant factor in the assembly and dynamics of such membrane complexes. Here we report on a role of anionic phospholipids in determining the extent of clustering of KcsA, a model potassium channel. Assembly/disassembly of channel clusters occurs, at least partly, as a consequence of competing lipid-protein and protein-protein interactions at nonannular lipid binding sites on the channel surface and brings about profound changes in the gating properties of the channel. Our results suggest that these latter effects of anionic lipids are mediated via the Trp⁶⁷–Glu⁷¹–Asp⁸⁰ inactivation triad within the channel structure and its bearing on the selectivity filter.     

Toward an early marker of metabolic dysfunction: omentin-1 in prepubertal children

Omentin-1 is a recently recognized adipokine primarily originating in visceral adipose tissue. We posited that circulating omentin-1 could be an early marker of metabolic dysfunction. To this end, we examined the associations between circulating omentin-1, body fat (bioelectric impedance), an endocrine-metabolic profile (homeostasis model assessment for insulin resistance (HOMA(IR)), serum lipids, high-molecular-weight (HMW) adiponectin and blood pressure (BP)) and family history of obesity and diabetes in asymptomatic prepubertal children (n = 161; 77 boys and 84 girls; age 7 ± 1 year) with a normal distribution of height and weight. Increased circulating omentin-1 was associated with a poorer metabolic profile, with relatively higher HOMA(IR), fasting triacylglycerol, BP and familial prevalence of diabetes (all P < 0.005 to P < 0.0001), and relatively lower fraction of HMW adiponectin (P < 0.005), whereas no relationship was found with body weight or fat or with family history of obesity. All these associations were independent of age, gender and fat mass. In conclusion, circulating omentin-1 may become a marker of metabolic dysfunction integrating insulin sensitivity, markers of adipose-tissue metabolism and BP as early as in prepubertal childhood.     

Engineering defensin α‐helix to produce high‐affinity SARS‐CoV‐2 spike protein binding ligands

The binding of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) spike protein to the angiotensin‐converting enzyme 2 (ACE2) receptor expressed on the host cells is a critical initial step for viral infection. This interaction is blocked through competitive inhibition by soluble ACE2 protein. Therefore, developing high‐affinity and cost‐effective ACE2 mimetic ligands that disrupt this protein–protein interaction is a promising strategy for viral diagnostics and therapy. We employed human and plant defensins, a class of small (2–5 kDa) and highly stable proteins containing solvent‐exposed alpha‐helix, conformationally constrained by two disulfide bonds. Therefore, we engineered the amino acid residues on the constrained alpha‐helix of defensins to mimic the critical residues on the ACE2 helix 1 that interact with the SARS‐CoV‐2 spike protein. The engineered proteins (h‐deface2, p‐deface2, and p‐deface2‐MUT) were soluble and purified to homogeneity with a high yield from a bacterial expression system. The proteins demonstrated exceptional thermostability (Tm 70.7°C), high‐affinity binding to the spike protein with apparent K _d values of 54.4 ± 11.3, 33.5 ± 8.2, and 14.4 ± 3.5 nM for h‐deface2, p‐deface2, and p‐deface2‐MUT, respectively, and were used in a diagnostic assay that detected SARS‐CoV‐2 neutralizing antibodies. This work addresses the challenge of developing helical ACE2 mimetics by demonstrating that defensins provide promising scaffolds to engineer alpha‐helices in a constrained form for designing of high‐affinity ligands.     

Comparative biochemical profiling during the stages of acquisition and development of somatic embryogenesis in African oil palm (Elaeis guineensis Jacq.)

In this study, the different stages of somatic embryogenesis (SE) of the African oil palm (Elaeis guineensis Jacq.) were characterized biochemically. The total soluble sugars, starch, total free amino acids, and total proteins were extracted, identified and quantified at various stages of embryogenesis: zygotic embryos (initial explants), primary calluses, embryogenic calluses, calluses with pro-embryos, globular embryos, differentiated somatic embryos, and regenerated plants. It was found that at the onset of induction of SE, the level of soluble sugars in the tissues of the explants fell by half. During this period, the total soluble sugars present in the cultures consisted basically of glucose and fructose. In the process of regeneration and maturation, the concentrations of soluble sugars gradually increased, reaching the highest values in the last two stages of development. At this stage, the disaccharide sucrose accounts for more than 80 % of the composition of total soluble sugars in the explants. Compared to starch, we found that the concentrations thereof in developing tissues are inversely proportional to that of soluble sugars virtually throughout embryogenic development. As for free amino acids, we found that after 30 days of induction until formation of the embryogenic calluses, there is an accentuated synthesis of total free amino acids in the explant tissue. In this stage, there was a significant increase in the levels of alanine and serine in the tissues. However, after the formation of the embryogenic calluses, the levels of total free amino acids present in the cultures become stabile and remain constant until the end of cultivation. Similar results were found for total protein, which also showed a significant increase at the onset of induction, undergoing slight changes during the remainder of the cultivation.