Generation of a new class of hNK(2) receptor ligands using the 'fragment approach'

The so called 'fragment approach' was applied in the search for new leads as selective hNK(2) antagonists. A first round of structural space exploration through the use of bond rigidity as scaffold to support the fragments, afforded 27a as 200 nM hNK(2) ligand. Further refinement gave MEN 14933 as a 16 nM hNK(2) ligand, selective versus hNK(1), of a novel class. Conformational analysis was used to study results and plan future work.     

Ultrastructure of testicular macrophages in aging mice

Testicular macrophages of aging mice were studied by TEM. Testicular macrophages retained with Leydig cells the close morphological relationships observed in the adult young animals, but digitations were not found. Lipofuscin granules like those of the Leydig cells from aging mice were observed in the cytoplasm. These organelles were generally absent in the testicular macrophages of young adult mice. Testicular macrophages did not display phagocytosis of the lipofuscin granules. In addition, the latter were not found in the intercellular spaces. These observations indicated that lipofuscin granules were formed, at least in a great part, within testicular macrophages as a consequence of metabolic changes occurring with age. Fine lamellar organization was seen in the lipofuscin granules of both Leydig cells and testicular macrophages. Frequently, lipofuscin granules originated from secondary lysosomes containing lipidic vacuoles only. Together with accumulation of the lipofuscin granules, changes of testicular macrophage fine morphology were observed. Endoplasmic reticulum and Golgi apparatus became poorly developed, and coated vesicles were rarely found. Fewer mitochondria were encountered, but their ultrastructure was not altered. These results suggest that in testicular macrophages lipofuscin accumulation is associated with a functional involution.     

Determination of amphetamine-derived designer drugs in human urine by SPE extraction and capillary electrophoresis with mass spectrometry detection

In recent years, a number of newer designer drugs have entered the illicit drug market. The methylenedioxy-derivates of amphetamine represent the largest group of designer drugs. This paper describes a method for screening for and quantification of ten 2,5-methylenedioxy-derivates of amphetamine and phenylethylamine in human urine, using capillary electrophoresis coupled to electrospray ionisation-mass spectrometry (CE-ESI-MS). Prior to CE-MS analysis, a simple solid-phase extraction (SPE) was used for sample cleanup. The method was validates according to international guidelines.     

Acrylamide-agarose copolymers: improved resolution of high molecular mass proteins in two-dimensional gel electrophoresis

A method was developed in order to analyse high molecular mass proteins by two-dimensional (2-D) electrophoresis using a copolymer of acrylamide and allyl agarose instead of Bis cross-linked polyacrylamide (PA) gels in sodium dodecyl sulphate-electrophoresis. In this work, the matrix composition was optimised to improve the resolution of proteins larger than 200 kDa. The new gel type does not entrap large proteins and protein complexes at the application site. Mechanical properties were investigated through rheological measurements, which suggested the formation of a highly entangled elastomeric soft gel. A high 2-D resolution of proteins, extracted from membranes of red blood cells, was obtained in these gels. An example of tryptic digestion, peptide extraction and matrix-assisted laser desorption/ionisation-time of flight mass spectrometry was reported. The results demonstrate that the new gel is fully compatible with mass spectrometry protein analysis.     

Deep learning architectures for prediction of nucleosome positioning from sequences data

Background

Nucleosomes are DNA-histone complex, each wrapping about 150 pairs of double-stranded DNA. Their function is fundamental for one of the primary functions of Chromatin i.e. packing the DNA into the nucleus of the Eukaryote cells. Several biological studies have shown that the nucleosome positioning influences the regulation of cell type-specific gene activities. Moreover, computational studies have shown evidence of sequence specificity concerning the DNA fragment wrapped into nucleosomes, clearly underlined by the organization of particular DNA substrings. As the main consequence, the identification of nucleosomes on a genomic scale has been successfully performed by computational methods using a sequence features representation.

Results

In this work, we propose a deep learning model for nucleosome identification. Our model stacks convolutional layers and Long Short-term Memories to automatically extract features from short- and long-range dependencies in a sequence. Using this model we are able to avoid the feature extraction and selection steps while improving the classification performances.

Conclusions

Results computed on eleven data sets of five different organisms, from Yeast to Human, show the superiority of the proposed method with respect to the state of the art recently presented in the literature.

     

Annual flower strips support pollinators and potentially enhance red clover seed yield

Ecological intensification provides opportunity to increase agricultural productivity while minimizing negative environmental impacts, by supporting ecosystem services such as crop pollination and biological pest control. For this we need to develop targeted management solutions that provide critical resources to service‐providing organisms at the right time and place. We tested whether annual strips of early flowering phacelia Phacelia tanacetifolia support pollinators and natural enemies of seed weevils Protapion spp., by attracting and offering nectar and pollen before the crop flowers. This was expected to increase yield of red clover Trifolium pratense seed. We monitored insect pollinators, pests, natural enemies and seed yields in a total of 50 clover fields along a landscape heterogeneity gradient, over 2 years and across two regions in southern Sweden. About half of the fields were sown with flower strips of 125–2,000 m². The clover fields were pollinated by 60% bumble bees Bombus spp. and 40% honey bees Apis mellifera. The clover seed yield was negatively associated with weevil density, but was unrelated to bee species richness and density. Flower strips enhanced bumble bees species richness in the clover fields, with the strongest influence in heterogeneous landscapes. There were few detectable differences between crop fields with and without flower strips. However, long‐tongued bumble bees were redistributed toward field interiors and during phacelia bloom honey bees toward field edges. Clover seed yield also increased with increasing size of the flower strip. We conclude that annual flower strips of early flower resources can support bumble bee species richness and, if sufficiently large, possibly also increase crop yields. However, clover seed yield was mainly limited by weevil infestation, which was not influenced by the annual flower strips. A future goal should be to design targeted measures for pest control.     

Early events of liver regeneration in rats: a multiparametric analysis

5-Bromodeoxyuridine (BrdU), a synthetic analogue of thymidine, has been utilized in vivo to detect the proliferation which occurs in the liver after two-thirds surgical hepatectomy. Immunocytochemical detection of BrdU incorporation has been carried out at both the morphological and flow cytometrical level, while structural changes of regenerating liver have been investigated, using Mallory-Azan-stained paraffin sections, by means of an image analyser. The results obtained show that in vivo DNA synthesis progression throughout S phase follows a pattern similar to that previously described in vitro in both 3T3 fibroblasts and Friend erythroleukemia cells and also demonstrate a precise correlation between morphological patterns of BrdU incorporating cells and their lobular distribution. Moreover, the activation of at least two proliferation waves can be detected from 18 to 34 h after hepatectomy: the former, starting from adjacent regions of contiguous lobules, apparently induces an irregular increase of lobular dimension; the latter, involving both inner and peripheral lobular domains, seems to be correlated with the appearance of nodule-like structures at the lobule periphery. In view of these results the role of the hepatic acinus and the hypothesis of a streaming of parenchymal cells during liver regeneration have been discussed.     

Immunoaffinity purification and characterization of diamine oxidase from Cicer

Antiserum specific for diamine oxidase (DAO;EC 1.4.3.6) from Lens culinaris cross-reacted with DAO from several other members of the Leguminosae when tested by agar double diffusion. Antibodies purified by affinity chromatography were used to make an immunoadsorbent for the one-step purification of DAO from various species of the Leguminosae. This technique has made it possible to purify in one step the already characterized DAO from pea and lentil, and the unknown diamine oxidase from Cicer arietinum. This enzyme was partially characterized; it showed a pH optimum of 7.5 with putrescine as substrate and followed typical Michaelis-Menten kinetics with a K_m of 2.4 × 10^?4 M. Copper ligands and carbonyl group-directed reagents inhibited the enzyme.     

In vivo conversion of [4-14C]sitosterol and [22,23-3H]sitosterol to stigmasterol in barley seedlings

Six-day-old barley seedlings were allowed to take up [4-¹⁴C]sitosterol and [22, 23-³H]sitosterol for 2.5 hr and the incorporation into the sterol fractions was determined after 0, 6, 12 and 24 hr. Sitosterol was readily incorporated into every sterol class. The ³H/¹⁴C ratio in the free forms dropped when compared with the ³H/¹⁴C ratio of the administered sitosterol. In the free sterol, radioactive stigmasterol, showing a ³H/¹⁴C ratio half that of the sitosterol ³H/¹⁴C ratio, was isolated and its radiochemical purity established by dilution with carrier material and crystallization to constant specific activity.     

Modulation of human neuronal alpha 1E-type calcium channel by alpha 2delta -subunit

Calcium channels are composed of a pore-forming subunit,₁, and at least two auxiliarysubunits, - and₂-subunits. It is well knownthat -subunits regulate most of the properties of the channel. Thefunction of ₂-subunit isless understood. In this study, the effects of the calcium channel₂-subunit on the neuronal_1E voltage-gated calciumchannel expressed in Xenopus oocyteswas investigated without and with simultaneous coexpression of eitherthe _1b- or the_2a-subunit. Most aspects of_1E function were affected by₂. Thus₂ caused a shift in thecurrent-voltage and conductance-voltage curves toward more positivepotentials and accelerated activation, deactivation, and theinstallation of the inactivation process. In addition, the efficiencywith which charge movement is coupled to pore opening assessed bydetermining ratios of limiting conductance to limiting charge movementwas decreased by ₂ byfactors that ranged from 1.6 (P < 0.01) for _1E-channels to 3.0 (P < 0.005) for_1E1b-channels. These results indicate that₂ facilitates the expressionand the maturation of_1E-channels and converts thesechannels into molecules responding more rapidly to voltage.