Apop-1, a Novel Protein Inducing Cyclophilin D-dependent but Bax/Bak-related Channel-independent Apoptosis

In the intrinsic pathway of apoptosis, mitochondria play a crucial role by releasing cytochrome c from the intermembrane space into the cytoplasm. Cytochrome c release through Bax/Bak-dependent channels in mitochondria has been well documented. In contrast, cyclophilin D (CypD), an important component of permeability transition pore-dependent protein release, remains largely undefined, and no apoptogenic proteins that act specifically in a CypD-dependent manner have been reported to date. Here, we describe a novel and evolutionarily conserved protein, apoptogenic protein (Apop). Mouse Apop-1 expression induces apoptotic death by releasing cytochrome c from mitochondria into the cytosolic space followed by activation of caspase-9 and -3. Apop-1-induced apoptosis is not blocked by Bcl-2 or Bcl-xL, inhibitors of Bax/Bak-dependent channels, whereas it is completely blocked by cyclosporin A, an inhibitor of permeability transition pore. Cells lacking CypD were resistant to Apop-induced apoptosis. Moreover, inhibition of Apop expression prevented the cell death induced by apoptosis-inducing substances. Our findings, thus, indicate that the expression of Apop-1 induces apoptosis though CypD-dependent pathway and that Apop-1 plays roles in cell death under physiological conditions

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Synthesis of an Alternated Heterobimetallic Supramolecular Polymer Based on Ru(II) and Fe(II)

A heterobimetallic supramolecular polymer (polyRuFe) with alternately complexed Ru(II) and Fe(II) is prepared following a stepwise synthetic route through harnessing first the strongly binding metal ion Ru(II) and then the weakly binding metal ion Fe(II). A high yield of product is achieved in each step. The heterometal ions are incorporated into the polymer chain in identical coordination environments formed by two 2,2′:6′,2″-terpyridine moieties. Characterization is accomplished by NMR spectroscopy, MALDI–TOF mass spectrometry, UV–Vis spectroscopy, and cyclic voltammetry. PolyRuFe shows a wide optical window (λ = 311–577 nm) and a broad distinct reversible redox nature of two types, originated from the coupling of the two heterometallic segments into the polymer chain. Such characteristics of polyRuFe suggest its potential for various electrochemical and electro-optical applications

Synthesis of DPA dendron encapsulated gold clusters with metal-assembling function

Gold clusters modified with first, second and third generation dendritic polyphenylazomethines (DPA) were synthesized by an exchanged reaction of corresponding DPA dendron thiols. Measurements by high performance perfect sizer (HPPS) and TEM reveal that their diameters increase with a change in the chain length of the modifying molecules from the first to third generation. These gold clusters with DPA dendrons exhibit coordination quantitatively to metal ions such as Fe3+, Sn2+, etc., because of their imine groups; this then resulted in self-aggregation to form a large sphere