Contribution of dipole-dipole interactions to the stability of the collagen triple helix

Unveiling sequence-stability and structure-stability relationships is a major goal of protein chemistry and structural biology. Despite the enormous efforts devoted, answers to these issues remain elusive. In principle, collagen represents an ideal system for such investigations due to its simplified sequence and regular structure. However, the definition of the molecular basis of collagen triple helix stability has hitherto proved to be a difficult task. Particularly puzzling is the decoding of the mechanism of triple helix stabilization/destabilization induced by imino acids. Although the propensity-based model, which correlates the propensities of the individual imino acids with the structural requirements of the triple helix, is able to explicate most of the experimental data, it is unable to predict the rather high stability of peptides embedding Gly-Hyp-Hyp triplets. Starting from the available X-ray structures of this polypeptide, we carried out an extensive quantum chemistry analysis of the mutual interactions established by hydroxyproline residues located at the X and Y positions of the Gly-X-Y motif. Our data clearly indicate that the opposing rings of these residues establish significant van der Waals and dipole-dipole interactions that play an important role in triple helix stabilization. These findings suggest that triple helix stabilization can be achieved by distinct structural mechanisms. The interplay of these subtle but recurrent effects dictates the overall stability of this widespread structural motif.     

Structural and spectroscopic comparison of five-coordinate cobalt(II) and nickel(II) thiolato complexes with the related four-coordinate complexes

Five-coordinate thiolato complexes, [L1M(SMeIm)] (M = Co and Ni) (L1 = hydrotris(3,5-diisopropyl-1-pyrazolyl)borate anion and HSMeIm = 2-mercapto-1-methylimidazole), were synthesized. These complexes were compared with the corresponding Cu(II) and Zn(II) complexes with the same ligands and were also compared with the related four-coordinate complexes [L1M(SC₆F₅)] (HSC₆F₅ = pentafluorobenzenthiol). All the complexes were characterized by X-ray crystallography and UV-Vis absorption, IR, ¹H NMR, and other spectroscopic techniques. All five-coordinate thiolato complexes, [L1M(SMeIm)] (M = Co, Ni, and Cu), form a distorted square pyramidal structure with a high spin state, and only [L1Zn(SMeIm)] takes a four-coordinate structure with a distorted tetrahedral configuration. The N21-M-S bond angles of the obtained five-coordinate complexes were proportional to the corresponding d value, which comes from between the equatorial basal plane with N4S ligand donor sets and metal ion. These observations and M-S bond distances affect on UV-Vis and far-IR spectral behavior.     

自然湿地土壤产甲烷菌和甲烷氧化菌多样性的分子检测

自然湿地是CH4排放的重要来源之一。产甲烷菌和甲烷氧化菌是介导自然湿地甲烷循环的重要功能菌群。开展产甲烷菌和甲烷氧化菌多样性的检测研究有助于揭示微生物介导的甲烷循环以及自然湿地甲烷排放的时空异质性。传统基于培养的检测方法已被证实无法充分描述产甲烷菌和甲烷氧化菌的多样性,而分子检测方法为自然湿地土壤产甲烷菌和甲烷氧化菌的多样性检测提供了一种更准确和科学的工具。本文综述了自然湿地土壤产甲烷菌和甲烷氧化菌的定性和定量分子检测方法,包括末端限制性片段长度多态性（T-RFLP）、变性梯度凝胶电泳（DGGE）、荧光原位杂交（FISH）和实时定量PCR（real-time qPCR）,重点分析了分子检测中两类重要的标记基因,总结了不同类型自然湿地产甲烷菌和甲烷氧化菌群落多样性的最新成果,提出了我国在该领域今后应深入研究探讨的一些问题及建议。     

Validation of photo‐identification as a mark–recapture method in the spotted eagle ray Aetobatus narinari

The spotted eagle ray Aetobatus narinari is characterized by pigmentation patterns that are retained for up to 3·5 years. These pigmentations can be used to identify individuals through photo‐identification. Only one study has validated this technique, but no study has estimated the percentage of correct identification of the rays using this technique. In order to carry out demographic research, a reliable photographic identification technique is needed. To achieve this validation for A. narinari, a double‐mark system was established over 11 months and photographs of the dorsal surface of 191 rays were taken. Three body parts with distinctive natural patterns were analysed (dorsal surface of the cephalic region, dorsal surface of the pectoral fins and dorsal surface of the pelvic fins) in order to determine the body part that could be used to give the highest percentage of correct identification. The dorsal surface of the pectoral fins of A. narinari provides the most accurate photo‐identification to distinguish individuals (88·2%).     

2,4-二氯苯酚的矿物表面化学行为研究

矿物质是土壤中的重要组成成分,本实验采用动态反应和平衡反应研究氧化物矿物表面2,4-二氯苯酚(2,4-DCP)的化学行为.结果表明,无定形铁氧化物、针铁矿、α-MnO₂、δ-MnO₂对自然的或外源的有机化合物有较强的氧化能力,其中对2,4二氯苯酚的氧化能力是:δ-MnO₂αMnO₂>无定形铁氧化物、针铁矿.采用分段法估算反应系统的速率,发现氧化锰氧化2,4-二氯苯酚的反应速率是氧化铁的3～50倍,δ-MnO₂氧化2,4-二氯苯酚的速率是α-MnO₂的1.5～3.2倍.根系分泌物由于参与氧化物表面化学反应,对系统2,4-二氯苯酚的氧化过程产生一定影响,α-MnO₂加入根系分泌物后,2,4-二氯苯酚在溶液中的消减速率明显减慢,δ-MnO₂则相反,在根系分泌物共存下溶液中的2,4-二氯苯酚的转化率增加.Cu复合共存可能影响2,4二氯苯酚在矿物表面的键合氧化过程,其中δ-MnO₂对铜吸附能力大于αMnO₂,Cu复合共存对δMnO₂表面2,4-二氯苯酚的氧化影响较大.     

Macroinvertebrate communities of non-glacial high altitude intermittent streams

1. Macroinvertebrate assemblages of five non‐glacial intermittent high altitude headwater streams (above 1400 m – Serra da Estrela, Portugal), with dry periods of different lengths (0–3 months), were investigated in nearly undisturbed conditions to (i) examine spatial differences and identify environmental variables responsible for the observed invertebrate patterns, (ii) assess the association of dry period length with invertebrate community structure and (iii) determine the influence of using different taxonomic identification levels (order, family and genus) to assess invertebrate community patterns. 2. More than 100 macroinvertebrate genera were identified. Insects clearly dominated these communities with more than 95% of total captures and around 95% of the total richness. Diptera were the most rich and abundant group with chironomid occurrences comprising over 70% of macroinvertebrate captures. 3. The highest taxon richness, diversity, EPT (Ephemeroptera + Plecoptera + Trichoptera) and OCH (Odonata + Coleoptera + Heteroptera) genus richness, the greatest number of exclusive and characteristic taxa identified by the Indicator Value (IndVal), and a distinct community structure shown by Canonical Correspondence Analyses (CCA), were found in the only stream that was never totally dry, with pools lasting over summer. Environmental gradients that spatially structured the macroinvertebrate communities were always related to flow variations. 4. Over time, the highest abundances found in these systems were also related to flow variations and maximum genus richness occurred in the connected pools or in isolated pools. Streams with longer dry periods presented a distinct recolonization phase, with higher abundance of the stonefly larvae Nemoura sp. and the presence of the chironomid larvae Krenosmittia sp., possibly arriving from the hyporheos. 5. Taxonomic level of invertebrate identification was vital for recognizing the characteristic taxa (IndVal) of streams yet was not critical for identifying streams with the highest macroinvertebrate richness/diversity or structuring environmental gradients. 6. Overall, this study emphasizes the variability of high altitude intermittent streams macroinvertebrate communities, despite spatial proximity. This variability was probably related to flow intermittency and hydrologic permanence, different vegetation covers and riverbed substrata. Consequently, the establishment of reference conditions should involve long‐term data collections and more detailed physical characterization. Also, these findings have significant implications for accurately predicting the ecological consequences of future climate change in high altitude scenarios.     

Phosphoryl amino acids: Common origin for nucleic acids and protein

A series of compounds (DAP-AA) composed of an amino acid (AA) and a dialkyl phosphoryl group (DAP) is the basic elements of life chemistry. Self-catalysis of DAP-AA gives the self-assembly oligopeptides, even in aqueous medium at 38°C. The oligo-nucleotides could also be assembled from nucleosides' phosphorylation by DAP-AA. DAP-AA acts as the energy source as well as the phosphoryl donor for the synthesis of nuclic Acids and protein. A general expression for the self assembly system is proposed.     

The good,the bad and the ugly: science,aesthetics and environmental assessment

The question is raised, whether there are peculiarly scientific values which can be applied in environmental assessment. The use of the expression scientific interest is traced from its 19th century origins to modern British statutes. It is argued that attempts to replace expert judgements by objective scientific criteria (e.g., indices of biodiversity) can never be completely successful. In particular, interest is an aesthetic atribute particularly valued by scientists but incapable of precise measurement. While science provides the best framework for informed judgements on conservation issues, the judgements of scientists are inevitably distinct from their experimental results. Judgements rest on ethical and aesthetic values such as importance and interest, which are essential constituents of the scientific sub-culture, but which are not uniquely scientific.     

Seasonal variation in ribulose bisphosphate carboxylase activity in Pinus silvestris

Ribulose bisphosphate carboxylase activity was examined in Pinus silvestris L. during successive seasons. The enzyme activities were studied both in seedlings, kept under controlled conditions in a climate chamber, and in needles from a 15-year-old tree in a natural stand. The enzyme activities were analysed in cell-free extracts prepared with Tween 80 as protective agent. The carboxylase activity fluctuated periodically both in the seedlings and in the natural stand. In the seedlings, the weight-related activity in the older needles increased 50–100% (in the cotyledons c. 200%) in the beginning of the “summer”. It decreased as the new shoot developed. The specific activity increased c. 100%. With chlorophyll as base, the activity usually decreased during “summer”. In the developing current needles the carboxylase activity increased when expressed on a weight or on a protein basis. The decrease in weight-related carboxylase activity in the older needles was preceded by, or simultaneous with, loss of total protein. It is suggested that protein, including the carboxylase, is utilized as nitrogen reserve for the new shoot. During hardening by combined photoperiod and thermoperiod, the carboxylase activity decreased when expressed relative to dry weight and protein. Calculated on a chlorophyll basis, the activity was rather constant. In the natural stand the activity in the one- and two-year-old needles increased during spring and summer and decreased during autumn and winter. Even at severe winter stress substantial carboxylase activity remained in the needles. The activity of the enzyme in vivo is discussed with respect to electron transport and net photosynthesis.     

Natural inspired piperine-based ureas and amides as novel antitumor agents towards breast cancer

In this work, the natural piperine moiety was utilised to develop two sets of piperine-based amides (5a–i) and ureas (8a–y) as potential anticancer agents. The anticancer action was assessed against triple negative breast cancer (TNBC) MDA-MB-231, ovarian A2780CP and hepatocellular HepG2 cancer cell lines. In particular, 8q stood out as the most potent anti-proliferative analogue against TNBC MDA-MB-231 cells with IC₅₀ equals 18.7 µM, which is better than that of piperine (IC₅₀ = 47.8 µM) and 5-FU (IC₅₀ = 38.5 µM). Furthermore, 8q was investigated for its possible mechanism of action in MDA-MB-231 cells via Annexin V-FITC apoptosis assay and cell cycle analysis. Moreover, an in-silico analysis has proposed VEGFR-2 as a probable enzymatic target for piperine-based derivatives, and then has explored the binding interactions within VEGFR-2 active site (PDB:4ASD). Finally, an in vitro VEGFR-2 inhibition assay was performed to validate the in silico findings, where 8q showed good VEGFR-2 inhibitory activity with IC₅₀ = 231 nM.