bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation Modelling of Marine Diesel Engine Cooling System
Authors: Stanivuk Tatjana , Lalić Branko , Žanić Mikuličić Jelena , Šundov Marko
Published: April 2021

Every internal combustion engine operates on the principle of converting thermal energy into mechanical work. During fuel combustion in the engine cylinders, the heat is released. It also has its negative effects; one is overheating of the engine cylinders and the engine in general. Since the engine parts are made of metal with its own thermal characteristics, the optimal temperature must be achieved in order to protect the components from overheating and, thus, from undesirable consequences of overheating. For this purpose, cooling medium is used as a means of maintaining the optimum temperature. Keeping the system functional as long as possible and minimizing possible deviations are very complex and difficult tasks. The complexity of the marine cooling system requires finding the optimal modes of operation, which results in an increased use of simulation models. This paper indicates advantages of using system dynamics as a tool for simulating certain events in a very realistic and economically acceptable way to prevent negative consequences for the entire marine system. System dynamics became an indispensable segment of designing various systems as well as the diesel engine cooling system.
Assessment of Potential Negative Impact of the System of Factors on the Ship's Operational Condition During Transportation of Oversized and Heavy Cargoes
Authors: Onyshchenko Svitlana , Shibaev Olexandr , Melnyk Oleksiy
Published: April 2021

The potential risks to vessels and crew in merchant shipping stem from human error, vulnerability to environmental influences, failure of shipboard systems and equipment. In case of transportation of heavy and oversized cargo, the preceding list can be expanded to include potential hazards directly associated with the cargo. This study identified a system of potential negative events in the transportation of oversized and heavy cargo under the influence of multiple factors. Negative events are divided into two categories: those occurring during loading/unloading and those occurring during transportation. The consequences of these negative events for cargo and operational condition of the ship are also identified. Six basic options for the operational condition of the vessel in the transportation process of oversized and heavy cargo have been determined. The conceptual model of the combination of factors affecting the operational condition of the vessel during the transportation of oversized and heavy cargo is formulated, and the chain of formation of the probability of negative events during the transportation of oversized and heavy cargo is identified and mathematically described. A basic pattern of relationship between various negative events occurring during transportation of oversized and heavy cargoes and ship's operational conditions is established. The obtained results allow the probability of possible negative events and change of ship's condition due to such influences during the transportation of the cargo category concerned to be estimated in practice, taking into account the specifics of a particular port, vessel and shipping line.
Application of Smart Technologies in Croatian Marinas
Authors: Maglić Livia , Grbčić Ana , Maglić Lovro , Gundić Ana
Published: April 2021

The objective of this research is to analyse smart technologies implemented in Croatian marinas and their impact upon the safety and service quality improvement, sustainability, and environmental protection, as well as energy consumption and operations optimisation. Key performance indicators and a definition of smart marina concept have been derived based on the smart port concept. The analysis has been conducted on a sample of 78 marinas in six different counties along the Croatian coast. Ultimately, the SWOT analysis has been performed in order to determine the advantages and disadvantages of introducing smart technologies in marina management. The results indicate that the Croatian marinas are undergoing a revolution in terms of facilitating booking management process and achieving greater safety and service quality, but still need to improve in the field of monitoring and controlling nautical tourism impact upon the environment.
Cumulative Analysis of Port State Control Based on Paris MoU Inspections
Authors: Bolat Firat , Alpaslan Selcuk
Published: April 2021

The Port State Control (PSC) was established to control ships entering ports or coastal facilities under its jurisdiction, with inspections by PSC officers aiming to determine whether ships meet safety and pollution prevention requirements and comply with the standards prescribed under the relevant international conventions. Annual reports based on PSC’s inspection reports are published under each memorandum of understanding (MoU) regime. The detailed inspection reports within the scope of the PSC, that contain a variety of information about vessels, and the processing and sharing of such information with other regional MoUs are intended to reduce the number of non-conforming practices in the global maritime system. In addition, PSCs publish lists of black, gray and white (BGW) flags, with the classification depending on the number of ship deficiencies and detentions. The classification is an indication of the quality of national flags. When a ship is found to have deficiencies, the inspection takes longer, and when the deficiencies are serious, the vessel is detained. Detention periods mean financial losses for the operator and loss of reputation for the flag state. Hence, the lists of black, gray and white flags published by the regional regimes are important in terms of reflecting the reputation of different countries. For these purposes, in this study, the inspections and detentions under the Paris MoU in 2019 have been examined and analyzed by countries and regions. Countries are categorized by UN geographical regions. In particular, the goal of the study was to identify the flag countries of the most frequently inspected and detained ships in 2019, as well as to determine the strategic measures developed by the countries and establish their differences and similarities compared to inspections and detentions in 2018.  In addition, the global COVID-19 pandemic in 2019 had a lockdown effect in the maritime domain and a profound effect on society, economy and health worldwide. The result of this study is the prediction of PSC efficiency in terms of the COVID-19 pandemic and the effect of the pandemic on the order of countries in the flag lists.
Yesterday's Tomorrow
Authors: Adamczak Bini
Published: April 2021

How the communist revolution failed, presented in a series of catastrophes.

The communist project in the twentieth century grew out of utopian desires to oppose class structures and abolish oppression. The attempts to realize these ideals, however, became a series of colossal failures. In Yesterday's Tomorrow, Bini Adamczak examines these catastrophes, proceeding in reverse chronological order from 1939 to 1917: the Hitler–Stalin Pact, the Great Terror of 1937, the failure of the European Left to prevent National Socialism, Stalin's rise to power, and the bloody defeat of the rebellion at Kronstadt. In the process, she seeks a future that never happened.

If Adamczak framed communism as a fairy tale with the possibility of a happy ending in her earlier book Communism for Kids, here she offers a tragedy for grownups. She describes the deportation of exiled anti-fascists back to Nazi Germany—a betrayal of communists by communists; the initial incredulity of European Communists at the news of the Hitler-Stalin pact; Stalin's state socialist terror plan, with quotas for executions instead of crops; the disappearance of class and the emergence of tactical and economic calculus; the withering into unrecognizability and impossibility of the revolution's successes; and the cheap promise that “next time it will be democratic.” What weighs on the possibility of communist desire, Adamczak writes, is not just the end of history, but first and foremost, the end of the revolution. Not just 1989, but also, even more so, 1939, 1938, and back to 1924, to 1917. Only if we understand this history can we work toward a better future.
Creating and controlling visual environments using BonVision
Authors: Lopes Gonçalo , Farrell Karolina , Horrocks Edward AB , Lee Chi-Yu , Morimoto Mai M , Muzzu Tomaso , Papanikolaou Amalia , Rodrigues Fabio R , Wheatcroft Thomas , Zucca Stefano , Solomon Samuel G , Saleem Aman B
Published: April 2021

Real-time rendering of closed-loop visual environments is important for next-generation understanding of brain function and behaviour, but is often prohibitively difficult for non-experts to implement and is limited to few laboratories worldwide. We developed BonVision as an easy-to-use open-source software for the display of virtual or augmented reality, as well as standard visual stimuli. BonVision has been tested on humans and mice, and is capable of supporting new experimental designs in other animal models of vision. As the architecture is based on the open-source Bonsai graphical programming language, BonVision benefits from native integration with experimental hardware. BonVision therefore enables easy implementation of closed-loop experiments, including real-time interaction with deep neural networks, and communication with behavioural and physiological measurement and manipulation devices.
Soft Bigram distance for names matching
Authors: Hadwan Mohammed , Al-Hagery Mohammed A. , Al-Sanabani Maher , Al-Hagree Salah
Published: April 2021

Background

Bi-gram distance (BI-DIST) is a recent approach to measure the distance between two strings that have an important role in a wide range of applications in various areas. The importance of BI-DIST is due to its representational and computational efficiency, which has led to extensive research to further enhance its efficiency. However, developing an algorithm that can measure the distance of strings accurately and efficiently has posed a major challenge to many developers. Consequently, this research aims to design an algorithm that can match the names accurately. BI-DIST distance is considered the best orthographic measure for names identification; nevertheless, it lacks a distance scale between the name bigrams.

Methods

In this research, the Soft Bigram Distance (Soft-Bidist) measure is proposed. It is an extension of BI-DIST by softening the scale of comparison among the name Bigrams for improving the name matching. Different datasets are used to demonstrate the efficiency of the proposed method.

Results

The results show that Soft-Bidist outperforms the compared algorithms using different name matching datasets.
Identification of a novel autophagy signature for predicting survival in patients with lung adenocarcinoma
Authors: Duan Jin , Lei Youming , Lv Guoli , Liu Yinqiang , Zhao Wei , Yang Qingmei , Su Xiaona , Song Zhijian , Lu Leilei , Shi Yunfei
Published: April 2021

Background

Lung adenocarcinoma (LUAD) is the most commonhistological lung cancer subtype, with an overall five-year survivalrate of only 17%. In this study, we aimed to identify autophagy-related genes (ARGs) and develop an LUAD prognostic signature.

Methods

In this study, we obtained ARGs from three databases and downloaded gene expression profiles from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. We used TCGA-LUAD (n = 490) for a training and testing dataset, and GSE50081 (n = 127) as the external validation dataset.The least absolute shrinkage and selection operator (LASSO) Cox and multivariate Cox regression models were used to generate an autophagy-related signature. We performed gene set enrichment analysis (GSEA) and immune cell analysis between the high- and low-risk groups. A nomogram was built to guide the individual treatment for LUAD patients.

Results

We identified a total of 83 differentially expressed ARGs (DEARGs) from the TCGA-LUAD dataset, including 33 upregulated DEARGs and 50 downregulated DEARGs, both with thresholds of adjusted P < 0.05 and |Fold change| > 1.5. Using LASSO and multivariate Cox regression analyses, we identified 10 ARGs that we used to build a prognostic signature with areas under the curve (AUCs) of 0.705, 0.715, and 0.778 at 1, 3, and 5 years, respectively. Using the risk score formula, the LUAD patients were divided into low- or high-risk groups. Our GSEA results suggested that the low-risk group were enriched in metabolism and immune-related pathways, while the high-risk group was involved in tumorigenesis and tumor progression pathways. Immune cell analysis revealed that, when compared to the high-risk group, the low-risk group had a lower cell fraction of M0- and M1- macrophages, and higher CD4 and PD-L1 expression levels.

Conclusion

Our identified robust signature may provide novel insight into underlying autophagy mechanisms as well as therapeutic strategies for LUAD treatment.
A novel Tick Carousel Assay for testing efficacy of repellents on Amblyomma americanum L.
Authors: Luker Hailey A. , Rodriguez Stacy , Kandel Yashoda , Vulcan Julia , Hansen Immo A.
Published: April 2021

Ticks are important vectors of human and veterinary diseases. A primary way ticks gain access to human hosts is by engaging to clothing. Repellents or acaricides sprayed onto fabric are used to deter ticks’ access to human hosts. However, there are a limited amount of standardized laboratory assays that can determine the potency and efficacy of repellents. We present a novel fabric-engagement assay referred to as the ‘Tick Carousel Assay’. This assay utilizes fabric brushing past ticks located on an artificial grass patch and measures tick engagements to fabric over time. After screening a variety of tick species, we used the lone star tick (Amblyomma americanum) to test the efficacy of four commonly used active ingredients in repellents: DEET, Picaridin, IR3535, and Oil of Lemon Eucalyptus. Repellency was tested immediately, after three hours, and six hours post application to fabric. Our data show that each repellent we tested significantly reduced the number of tick engagements to fabric for at least 6 hours. We did not find significant differences in repellent efficacy between the four active ingredients tested directly and three hours after application. After six hours, Oil of Lemon Eucalyptus repelled ticks more than the other active ingredients. We show that our Tick Carousel Assay provides an affordable, repeatable, and standardized way to compare and test repellent efficacy on treated fabrics. Our results confirm that commonly used repellents applied to fabric are an effective way to reduce tick engagement.
Genome-wide identification and expression analysis of the EXO70 gene family in grape (Vitis vinifera L)
Authors: Wang Han , Ma Zong-Huan , Mao Juan , Chen Bai-Hong
Published: April 2021

EXO70 is the pivotal protein subunit of exocyst, which has a very crucial role in enhancing the shielding effect of the cell wall, resisting abiotic and hormonal stresses. This experiment aims to identify family members of the EXO70 gene family in grape and predict the characteristics of this gene family, so as to lay the foundation of further exploring the mechanism of resisting abiotic and hormone stresses of VvEXO70s. Therefore, the Vitis vinifera ‘Red Globe’ tube plantlet were used as materials. Bioinformatics was used to inquire VvEXO70 genes family members, gene structure, system evolution, cis-acting elements, subcellular and chromosomal localization, collinearity, selective pressure, codon bias and tissue expression. All of VvEXO70s had the conserved pfam03081 domain which maybe necessary for interacting with other proteins. Microarray analysis suggested that most genes expressed to varying degrees in tendrils, leaves, seeds, buds, roots and stems. Quantitative Real-Time PCR (qRT-PCR) showed that the expression levels of all genes with 5 mM salicylic acid (SA), 0.1 mM methy jasmonate (MeJA), 20% PEG6000 and 4 °C for 24 h were higher than for 12 h. With 20% PEG6000 treatment about 24 h, the relative expression of VvEXO70-02 was significantly up-regulated and 361 times higher than CK. All genes’ relative expression was higher at 12 h than that at 24 h after treatment with 7 mM hydrogen peroxide (H2O2) and 0.1 mM ethylene (ETH). In conclusion, the expression levels of 14 VvEXO70 genes are distinguishing under these treatments, which play an important role in the regulation of anti-stress signals in grape. All of these test results provide a reference for the future research on the potential function analysis and plant breeding of VvEXO70 genes.
Fast computational mutation-response scanning of proteins
Authors: Echave Julian
Published: April 2021

Studying the effect of perturbations on protein structure is a basic approach in protein research. Important problems, such as predicting pathological mutations and understanding patterns of structural evolution, have been addressed by computational simulations that model mutations using forces and predict the resulting deformations. In single mutation-response scanning simulations, a sensitivity matrix is obtained by averaging deformations over point mutations. In double mutation-response scanning simulations, a compensation matrix is obtained by minimizing deformations over pairs of mutations. These very useful simulation-based methods may be too slow to deal with large proteins, protein complexes, or large protein databases. To address this issue, I derived analytical closed formulas to calculate the sensitivity and compensation matrices directly, without simulations. Here, I present these derivations and show that the resulting analytical methods are much faster than their simulation counterparts.
«АГРАРНУЮ ИСТОРИЮ НАДО ИЗУЧАТЬ НЕ ПО КНИГАМ, НО НОГАМИ»: ВОСПОМИНАНИЯ В.М. ЛАВРОВСКОГО О Е.А. КОСМИНСКОМ И ИХ НАУЧНОЙ КОМАНДИРОВКЕ В АНГЛИЮ 1925–1926 ГОДОВ, "Средние века"
Authors: Земляков М.В. , Селиванова О.В.
Published: April 2021

Авторы публикации знакомят читателя с воспоминаниями и впечатлениями В.М. Лавровского о посещении им Великобритании в ходе научной командировки 1925 г. (совместно с Е.А. Косминским). Этот документ из личного фонда исследователя в Архиве РАН (АРАН) никогда ранее не публиковался. Во вступительной статье рассматривается краткая научная биография каждого из ученых на фоне зарождения и развития советской исторической науки в 1920-х – 1960-х годах. Особое внимание авторами уделяется вопросам, касающимся способов решения различных исследовательских задач в ходе этих командировок, общения советских и английских историков на международных конференциях, семинарах, коллоквиумах, а также политики советского правительства и научных организаций в области заграничных командировок в 1925–1960 гг. Эти воспоминания особенно ценны сведениями, которые обычно нельзя отыскать в официальных научных отчетах: личными впечатлениями ученого от посещения английских городов (в первую очередь – Лондона) и графств, библиотек, архивов, научных учреждений и университетов; от неформального общения с коллегами – профессорами, молодыми исследователями и студентами, – и обсуждения развития научных, культурных и дипломатических отношений СССР и Великобритании.
ОБРАЗЫ ФРАНЦИИ В ПОЛЕМИЧЕСКИХ СОЧИНЕНИЯХ ФРАНЦУЗСКИХ АВТОРОВ ПЕРВОЙ ПОЛОВИНЫ XV ВЕКА, "Средние века"
Authors: Бароне В.А.
Published: April 2021

Статья посвящена анализу представлений о Франции в трактатах французских полемистов первой половины XV в. Показано, что Французское королевство этого времени соотносилось с термином «государство», понимаемом не только в частно-правовом, но и в публичном аспектах. Делаются выводы о восприятии Франции авторами исследуемых сочинений в качестве родины. Акцентируется внимание на том, что помимо идеи Природы («естественная любовь» человека к отчизне, которая предопределяет круг его обязанностей), патриотические взгляды полемистов основывались также на представлениях о «гражданском» долге и обязанностях каждого перед государством как «делом общественным».
Differences in elastase hydrolysates of elastin from ligamentum nuchae
Authors: Ledvina M. , Bartoš F.
Published: July 2002

By means of molecular exclusive chromatography, a marked difference in the distribution of desmosine and isodesmosine in the products of proteolysis has been found between the partial enzymatic hydrolysates of elastin from the bovine nuchal ligament prepared by two different methods. In the preparation which was treated with hot NaOH the prevailing portion was localized in a macromolecular fraction corresponding to the void volume. An increased precipitation of this fraction with trichloracetic acid has been noticed. The autoclaved material forms substantial amounts of the coacervate during the digestion.
ESR study of the primary electron donor in highly 13C‐enriched Chlorobium limicola f. thiosulfatophilum
Authors: Wasielewski Michael R. , Smith Ursula H. , Norris James R.
Published: July 2002

The photo‐induced electron spin resonance signal of the primary donor P840+ in unit membrane fractions of the title photosynthetic bacterium was measured. Bacteria containing natural isotopic abundances and 82% 13C‐enrichment were examined. Second moment analysis of the lineshape of the 13C‐enriched P840+ signal shows that P840+ consists of two bacteriochlorophyll a‐type macrocycles. The data thus obtained are independent of difficulties in interpreting either peak‐to‐peak linewidths or ENDOR data with respect to intermolecular spin delocalization.
A novel type of energetics in a marine alkali‐tolerant bacterium
Authors: Chernyak B.V. , Dibrov P.A. , Glagolev A.N. , Sherman M.Yu. , Skulachev V.P.
Published: July 2002

Motility of a marine alkali‐tolerant bacterium, Vibrio alginolyticus, can be observed in the presence of high concentrations of a protonophorous uncoupler, CCCP. Motility in the CCCP‐containing media is completely inhibited by decrease in extracellular [Na+] or by monensin‐induced increase in intracellular [Na+]. A mutant has been selected that grows only in media supplemented with a substrate such as acetate requiring no Δ
Na to be transported into the cell. Motility of the mutant was found to be completely inhibited by CCCP. Cyanide, CCCP and vanadate added separately or in twos inhibit motility only partially. The three poisons added together completely paralyse the cells. In this inhibitor cocktail, arsenate can substitute for CCCP + vanadate; cyanide can be replaced by anaerobiosis. It is concluded that (i) Δ
Na rather than Δ
NH powers the flagellar motor of V. alginolyticus in the presence of CCCP, and (ii) in addition to the Na+‐motive respiratory chain [Tokuda, H. and Unemoto, T. (1982) J. Biol. Chem. 257, 10007–10014] there is a vanadate and arsenate‐sensitive oxygen‐independent mechanism of Δ
Na generation, presumably an ion‐motive ATPase. A suggestion is put forward that circulation of Na+ can replace that of H+ in V. alginolyticus, Δ
Na being formed by the Na+‐motive respiratory chain and utilized by Na+‐solute symporters, the Na+‐driven flagellar motor and maybe by a reverse ion‐motive ATPase.
Pyridoxal‐5′‐phosphate as a probe for rotational diffusion
Authors: Cornish Timothy J. , Ledbetter John W.
Published: July 2002

Its usefulness in measuring the slow rotation of proteins and micelles was demonstrated.
Dissociation of human neutrophil membrane depolarization, respiratory burst stimulation and phospholipid metabolism by quinacrine
Authors: Tauber Alfred I. , Simons Elizabeth R.
Published: July 2002

Human neutrophils generate a respiratory burst with the elaboration of toxic oxygen metabolites upon appropriate stimulation. Subsequent to receptor—ligand interaction, the activation pathway of this burst is unknown. Here, attempts to correlate phospholipid turnover have demonstrated dissociation of lipid flux and burst activation. Quinacrine inhibited membrane depolarization, superoxide (O−
2) generation, and net phosphatidylserine production with ID
50‐values of 16 μM, 73 μM and >500 μM, respectively. The inhibitory profiles of these neutrophil activation parameters demonstrate a dissociation between membrane depolarization, respiratory burst stimulation, and phospholipid turnover.
The coupling of ethylene biosynthesis to a transmembrane, electrogenic proton flux
Authors: John Philip
Published: July 2002

It is proposed that the reactions which lead to the generation of ethylene from 1‐aminocyclopropane—1‐carboxylic acid are arranged asymmetrically in the plasma membrane of plant cells so that ethylene biosynthesis is coupled to an inwardly directed, electrogenic flow of protons. According to this model a membrane potential (outside positive is required for ethylene biosynthesis. This proposed requirement is indicated by previous observations of a marked sensitivity of ethylene biosynthesis to the protonophore 2,4‐dinitrophenol, and by its unusually strict dependence on membrane integrity.
Purification and characterization of cell wall lytic enzyme released by mating gametes of Chlamydomonas reinhardtii
Authors: Matsuda Yoshihiro , Yamasaki Atsuko , Tatsuaki Saito , Yamaguchi Tetsuya
Published: July 2002

A cell wall lytic enzyme of Chlamydomonas reinhardtii has been purified and identified as a single glycopolypeptide subunit of 62 kDa by SDS—polyacrylamide gel electrophoresis. It is released into culture medium by mating gametes as a large aggregate of subunits. The purified enzyme shows a pH optimum at about 7.5 and 35°C. Metal ion chelators and SH‐blocking agents inhibit the activity. The activity is also diminished by α2‐macroglobulin.
Characterization of protein kinases in mitotic and meiotic cell extracts
Authors: Halleck Margaret S. , Lumley-Sapanski Katherine , Reed Jon A. , Iyer Anand P. , Mastro Andrea M. , Schlegel Robert A.
Published: July 2002

A number of protein kinases have been separated and identified in extracts from mitotic and interphase culture cells and from mature and immature amphibian oocytes using nondenaturing polyacrylamide gel electrophoresis followed by in situ phosphorylation assays. Certain of these protein kinase activities appear to correlate with the biological activity of extracts, assayed by their ability to induce meiotic maturation following injection into Xenopus oocytes. These results are consistent with the notion that protein phosphorylation/dephosphorylation may be integral to the mechanisms of both nuclear membrane breakdown and chromosome condensation, events common and distinctive to mitosis and meiosis.
Amino‐terminal sequence of ethylene‐induced bean leaf chitinase reveals similarities to sugar‐binding domains of wheat germ agglutinin
Authors: Lucas John , Menschen Agnes , Lottspeich Fritz , Voegeli Urs , Boiler Thomas
Published: July 2002

Chitinase has been reported for many plant species. A role in plant defense has been suggested for plant chitinases, due to their ability to degrade fungal cell wall chitin. Increased levels of chitinase are induced in bean plants by the plant hormone ethylene [(1983) Planta 157, 22‐31]. The amino acid sequence of positions 1–30 of ethylene‐induced bean leaf chitinase was determined and found to possess considerable sequence homology to wheat germ agglutinin and hevein. The implication of a lectin‐related structure for the enzymatic specificity of chitinase is discussed.
The effect of insulin and noradrenaline on the uptake of 2‐[1‐14C]deoxyglucose in vivo by brown adipose tissue and other glucose‐utilising tissues of the mouse
Authors: Cooney Gregory J. , Caterson Ian D. , Newsholme Eric A.
Published: July 2002

The uptake of 2‐[1‐14C]deoxyglucose in vivo by brown adipose tissue was greater than that of brain or heart in control mice on a whole tissue basis. When mice were treated with noradrenaline the rate of uptake of 2‐[1‐14C]deoxyglucose by brown adipose tissue was increased 6‐fold with the only other change occurring in heart where a 5‐fold increase was observed. After administration of insulin the uptake of 2‐[1‐14C]deoxyglucose in vivo was increased in heart, brown adipose tissue, white adipose tissue and muscle. The amount of 2‐[1‐14C]deoxyglucose taken up by brown adipose tissue compared to other tissues and the changes in this uptake after administration of noradrenaline or insulin suggest that brown adipose tissue is capable of playing a quantitatively important role in glucose removal from the blood.
The complete amino acid sequence of a bacteriochlorophyll a binding polypeptide isolated from the cytoplasmic membrane of the green photosynthetic bacterium Chloroflexus aurantiacus
Authors: Wechsler Thomas , Brunisholz René , Suter Franz , Fuller R.Clinton , Zuber Herbert
Published: July 2002

A polypeptide soluble in organic solvents was isolated from whole membrane fractions of the green thermophilic bacterium Chloroflexus aurantiacus by chromatography on Sephadex LH‐60, Whatman DE‐32 and Bio Gel P‐10. The complete amino acid sequence of this 4.9 kDa polypeptide (44 amino acid residues) was determined. The polypeptide shows a 3‐domain structure, similar to the domain structure of the antenna BChI polypeptides of purple photosynthetic bacteria, and sequence homologies (27–39%) to the light‐harvesting α‐polypeptides of the B870 (890) antenna complexes from purple bacteria. Therefore, the 4.9 kDa polypeptide is designated B(808‐866)‐α. The typical His residue (conserved His residue identified in all antenna polypeptides of purple bacteria as possible BChI binding site) is found within the hydrophobic domain, which extends from Asn 10 to Leu 30.
A new tool to study genetic expression using 2‐D electrophoresis data: the functional map concept
Authors: Rabilloud T. , Vincens P. , Tarroux P.
Published: July 2002

A method derived from general computerized data analysis techniques is used here first to tabulate the characteristics of individual peptide spots observed by two‐dimensional electrophoresis and to compare these characteristics among spots. Multivariate analysis of such data arrays then leads to the grouping of spots in an n‐dimensional space, according to their expression characteristics. Such maps display zones which are characteristic of the tissue studied. These functional maps provide a powerful analytical tool for describing such functional interactions and also for predicting the function of unidentified peptides observed on the electrophoresis gels.
Identification of a 68 kDa protein which copurifies with type‐1 protein phosphatase as albumin
Authors: Villa-Moruzzi Emma , Meyer Helmut E. , Heilmeyer Ludwig M.G.
Published: July 2002

Proteins of 60–70 kDa copurify with some preparations of type‐1 or type‐2 phosphatases. In our system chromatography on polylysine‐Affi‐Gel 10 separates a 68 kDa protein from rabbit muscle glycogen particle phosphorylase phosphatase. The separation affects neither the activity nor the size of the phosphatase. The 68 kDa protein, although pure by SDS gel electrophoresis criteria, still displays phosphatase activity of approx. 6–8 . However, rechromatography either on Bio‐Gel A‐0.5 m or on Blue Sepharose CL‐6B followed by gel filtration shows that the activity is due to a contamination with phosphatases of type 1 and type 2, displaying a molecular mass of 35 kDa, which can be totally removed from the 68 kDa protein. The amino acid composition of the 68 kDa protein is identical to that of rabbit serum albumin, within the limits of variation of the method. Furthermore, the sequence of the 38 N‐terminal amino acids is the same in the isolated 68 kDa protein and in rabbit serum albumin.
Extrachromosomal DNA from a dicot plant Vigna radiata
Authors: Bhattacharyya Nisan , Roy Pranab
Published: July 2002

Extrachromosomal DNA was isolated from germinated mung bean as well as from its callus culture. Methods followed for the isolation of cccDNA gave a heterogeneous mixture of DNA from 4.2 kb to 140 bp in size. Hybridization with a repetitive DNA probe from mung bean chromosomal DNA showed extensive dispersion, similar in chromosomal and extrachromosomal locations. An electron micrograph of purified extrachromosomal DNA revealed some circular DNA molecules with hanging tails.
Complete amino acid sequence of poplar plastocyanin b
Authors: Dimitrov Mitko I. , Egorov Caesii A. , Donchev Anthony A. , Atanasov Boris P.
Published: July 2002

A second type of plastocyanin, plastocyanin b (PCb) was isolated from leaves of poplar Populus nigra var. Italica. The complete amino acid sequence of 99 residues in the single polypeptide chain of plastocyanin b has been determined: DVLLGADDG SLAFVPSEFS GEKIVFK NNAGFPHN FDEDPSGV DSKISMSEE DLLNAKGETF EVALSKGEY FYCSPHQGA GMVGKVVN The sequence obviously demonstrates, that PCb, in comparison with the known plastocyanin, plastocyanin a (PCa), has 12 amino acid replacements (underlined letters): Ile 1→Val, Ile 21‐Ser 22‐Pro 23→Val‐Pro‐Ala, Ile 39‐Val 40→Val‐Leu, Ser 45‐Ile 46→ Ala‐Val, Ala 52→Val, Asn 76→Asp, Ser 81→Thr and Thr 97→Ile. The replacements at positions 40 and 76 of PCb are probably essential for differences in its redox and electrochemical properties, respectively.
Unusual solvent isotope effects on the aminoacylase‐catalyzed hydrolysis of acetylamino acids
Authors: Henseling Johannes , Röhm Klaus-Heinrich
Published: July 2002

The deuterium solvent isotope effect on hydrolysis of acetylamino acids catalyzed by porcine kidney aminoacylase I (EC 3.5.1.14) was studied. With Ac‐L‐Met, a ‘standard’ aminoacylase substrate, the effect was normal at low pH (k
cat(D)/k
cat(H) = 0.7 at pH 6), virtually absent at neutrality, and distinctly inverse (k
cat(D)/K
cat(H) = 1.4) at pH 9. Km was not significantly affected. The rates of Ac‐L‐Phe hydrolysis in D2O considerably exceeded those in H2O at any pH between 6.5 and 9. We explain this unusual effect of D2O on aminoacylase I catalysis by an inverse equilibrium effect partially cancelling or, at high pH, reversing a normal isotope effect on k
cat.
Apparent identity of cerebral tyrosylsulfotransferase activities using either a cholecystokinin derivative or an acidic amino acid polymer as substrate
Authors: Vargas Froylan , Schwartz Jean-Charles
Published: July 2002

The tyrosylsulfotransferase activities of rat cerebral fractions transferring [35S]sultate groups from 3'‐phosphoadenosine 5'‐[35S]phosphosulfate to either Boc‐cholecystokinin‐8 (in non‐sulfated form) or the acidic amino acid polymer (Glu, Ala, Tyr)
n
(6:3:1) were compared. They appear similar regarding subcellular distribution (both being enriched in the microsomal fraction) and inhibition by an excess of the acidic amino acid polymer, NaCl or 2,6‐dichloro 4‐nitrophenol. These results obtained with artificial substrates suggest that identical (or closely similar) tyrosylsulfotransferases are responsible for sulfation of tyrosine residues of several secretory proteins from various tissues.
The primary structures of ribosomal proteins L16, L23 and L33 from the archaebacterium Halobacterium marismortui
Authors: Hatakeyama Tomomitsu , Hatakeyama Tamiko , Kimura Makoto
Published: July 2002

The complete amino acid sequences of ribosomal proteins L16, L23 and L33 from the archaebacterium Halobacterium marismortui were determined. The sequences were established by manual sequencing of peptides produced with several proteases as well as by cleavage with dilute HCl. Proteins L16, L23 and L33 consist of 119, 154 and 69 amino acid residues, and their molecular masses are 13538, 16812 and 7620 Da, respectively. The comparison of their sequences with those of ribosomal proteins from other organisms revealed that L23 and L33 are related to eubacterial ribosomal proteins from Escherichia coli and Bacillus stearothermophilus, while protein L16 was found to be homologous to a eukaryotic ribosomal protein from yeast. These results provide information about the special phylogenetic position of archaebacteria.
Electroporation: High frequency of occurrence of a transient high‐permeability state in erythrocytes and intact yeast
Authors: Weaver James C. , Harrison Gail I. , Bliss Jonathan G. , Mourant Judith R. , Powell Kevin T.
Published: July 2002

We present the first determinations of population distributions of macromolecule uptake due to electroporation, the percentage of cells which participate and, for the yeast, the subpopulation of cells whose membranes exhibit significant recovery following macromolecule uptake. Flow cytometry is used to measure the uptake of a first test molecule (green fluorescence, FITC‐dextran; 70 kDa) and also, for the yeast, the subsequent uptake of a second, much smaller, test molecule (red fluorescence, propidium iodide; 660 Da), which provides a measure of membrane recovery. A dramatic 20% (erythrocytes) to 75% (intact Schizosaccharomyces pombe) of cells can take up the first test molecule within 5 min of a pulse.
Truncated glucagon‐like peptide‐1 (proglucagon 78–107 amide), an intestinal insulin‐releasing peptide, has specific receptors on rat insulinoma cells (RIN 5AH)
Authors: Ørskov Cathrine , Nielsen Jens Høiriis
Published: July 2002

We studied binding of 125I‐labelled truncated‐glucagon‐like peptide‐1 (proglucagon 78–107 amide) to a cloned rat insulin‐producing cell line, RIN 5AH, in monolayer culture. Interaction of the peptide with pancreatic insulinoma cells was saturable and time dependent. Half‐maximal binding was obtained when the cells were incubated in the presence of 3.3 × 10−9 mol/l unlabelled truncated‐glucagon‐like peptide‐1 (proglucagon 78–107 amide). Neither glucagon, full‐length glucagon‐like peptide‐1 (proglucagon 72–107 amide) nor gastric inhibitory peptide competed for binding in concentrations up to 10−6 mol/l.
Characterization of purinoceptors present on human liver plasma membranes
Authors: Keppens Stefaan , Vandekerckhove Ann , De Wulf Henri
Published: July 2002

Using ATPα35S as radioligand, we have detected the presence of specific purinoceptors on human liver plasma membranes. They are characterized by a K
d value of 0.19 μM and a B
max of 24 pmol/mg membrane protein. These purinoceptors belong to the P2Y subclass as demonstrated by the high degree of similarity with rat liver purinoceptors, previously shown to be P2Y[(1986) Biochem. J. 240, 367–371] and known to be involved in the control of liver glycogenolysis.
Processing of transcripts of a dimeric tRNA gene in yeast uses the nuclease responsible for maturation of the 3′ termini upon 5 S and 37 S precursor rRNAs
Authors: Piper Peter W. , Stråby Kerstin B.
Published: July 2002

The rna82 mutation of Saccharomyces cerevisiae inactivates an RNA processing activity responsible for maturation of 3′‐terminal sequences upon 5 S and 37 S ribosomal RNA precursors. This study describes a difference in the processing of transcripts of an S. cerevisiae dimeric tRNA gene (tRNAArg‐tRNAAsp) in RNA polymerase III in vitro transcription extracts prepared from rna82 and wild‐type cells. The mutant extract accumulated additional processing intermediates containing tRNAArg sequences as compared to the extract from wild‐type cells. The structure of these intermediates revealed a defect in removal of the 10 nucleotides left 3′ to the tRNAArg sequence by the RNase P cleavage immediately 5′ to tRNAAsp. This is the first demonstration of a mutational defect affecting maturation of 3′ sequences upon a eukaryotic tRNA precursor.
Highly potent and small neuropeptide Y agonist obtained by linking NPY 1–4 via spacer to α‐helical NPY 25–36
Authors: Beck Annette , Jung Günther , Gaida Wolfgang , Köppen Herbert , Lang Rudolph , Schnorrenberg Gerd
Published: July 2002

Analogues of neuropeptide Y (NPY) containing small N‐ and C‐terminal segments linked via flexible spacer arms were found to exhibit receptor binding affinity constants almost as high as NPY as well as post‐ and presynaptic NPY‐agonistic activities. One of the most active analogues contains N‐terminal NPY segment 1–4 linked via ε‐aminocaproic acid (Aca) to the C‐terminal partially α‐helical peptide amide segment 25–36. NPY 1–4‐Aca‐25–36 is the first highly potent NPY agonist, which is of considerably reduced size in comparison to the native hormone. The analogues are accessible by solid‐phase synthesis using Fmoc strategy.
Distribution of serotonin 5‐HT1C receptor mRNA in adult rat brain
Authors: Hoffman Beth J. , Mezey Eva
Published: July 2002

Based on in situ hybridization histochemistry (ISHH), we describe the anatomical distribution of the serotonin 5‐HT1C receptor mRNA. In addition to the very high levels in epithelial cells of the choroid plexus, 5‐HT1C receptor mRNA is found throughout the limbic system, in catecholaminergic cells and in serotonergic neurons. Receptor transcripts are also present in the hypothalamus, numerous motor nuclei and the subthalamus. Our results correlate well with serotonin (5‐HT) innervation and receptor binding. Receptor mRNA is present in many brain structures in addition to regions previously shown to have 5‐HT1C receptor binding. The distribution of this receptor mRNA suggests that the 5‐HT1C receptor may mediate a number of the central effects of 5‐HT.
11‐cis retinal formation in the light catalyzed by a retinal‐binding protein from the honeybee retina
Authors: Cugnoli C. , Mantovani R. , Fioravanti R. , Pepe I.
Published: July 2002

Retinal‐binding protein; Photoisomerase; Retinal‐isomerase; Rhodopsin regeneration; Visual pigment renewal
Exercise modulates the insulin‐induced translocation of glucose transporters in rat skeletal muscle
Authors: Douen Andre G. , Ramlal Toolsie , Cartee Gregory D. , Klip Amira
Published: July 2002

Insulin and acute exercise (45 min of treadmill run) increased glucose uptake into perfused rat hindlimbs 5‐fold and 3.2‐fold, respectively. Following exercise, insulin treatment resulted in a further increase in glucose uptake. The subcellular distribution of the muscle glucose transporters GLUT‐1 and GLUT‐4 was determined in plasma membranes and intracellular membranes. Neither exercise nor exercise→ insulin treatment altered the distribution of GLUT‐1 transporters in these medmbrane fractions. In contrast, exercise, insulin and exercise→ insulin treatment caused comparable increases in GLUT‐4 transporters in the plasma membrane. The results suggest that exercise might limit insulin‐induced GLUT‐4 recruitment and that following exercise, insulin may alter the intrinsic activity of plasma membrane glucose transporters.
The 18S ribosomal RNA sequence of the sea anemone Ammonia sulcata and its evolutionary position among other eukaryotes
Authors: Hendriks Lydia , Van de Peer Yves , Van Herck Martine , Neefs Jean-Marc , De Wachter Rupert
Published: July 2002

Evolutionary trees based on partial small ribosomal subunit RNA sequences of 22 metazoa species have been published [(1988) Science 239, 748‐753]. In these trees, cnidarians (Radiata) seemed to have evolved independently from the Bilateria, which is in contradiction with the general evolutionary view. In order to further investigate this problem, the complete srRNA sequence of the sea anemone Ammonia sulcata was determined and evolutionary trees were constructed using a matrix optimization method. In the tree thus obtained the sea anemone and Bilateria together form a monophyletic cluster, with the sea anemone forming the first line of descent of the metazoan group.
Closely related isozymes of alcohol dehydrogenase Carboxymethylation: γ1γ1 differs widely from both β1β1 and its equine equivalence EE
Authors: Johansson Jan , Vallee Bert L. , Jörnvall Hans
Published: July 2002

Human γ1γ1 alcohol dehydrogenase is quite insensitive to inactivation by iodoacetate, its equine counterpart EE highly sensitive, and the human β1β1 form intermediately sensitive. Imidazole hardly influences the iodoacetate inactivation of γ1γ1, enhances that of EE and decreases that of β1β1. In all isozymes metal‐binding Cys residues are the most reactive, but the patterns for those binding the active site zinc atom differ. In phosphate, Cys‐46 is most sensitive in EE and γ1γ1, Cys‐174 in β1β1. This difference appears to correlate with the absence or presence, respectively, of an extra methyl group in the side‐chain at position 48 (Ser in EE and γ1γ1, Thr in β1β1). In imidazole, the reactivity in β1β1 is shifted to Cys‐46, while the specificity is enhanced in EE and decreased in γ1γ1. Thus, the inactivations illustrate large defferences among structures closely related.
A novel natriuretic peptide isolated from eel cardiac ventricles
Authors: Takei Toshio , Takahashi Akiyoshi , Watanabe Takushi X. , Nakajima Kiichiro , Sakakibara Shumpei
Published: July 2002

A new natriuretic peptide, which exhibits the entire spectrum of actions known to be characteristics of atrial and brain natriuretic peptides (ANP and BNP), was isolated from eel cardiac ventricles and has been named ventricular natriuretic peptide (VNP). The primary structure of eel VNP is characterized by its uniquely long C‐ terminal ‘tall’ that extends from the second half‐cystine. Thus, eel VNP appears to be a novel natriuretic peptide of a type not found in mammals. With respect to natriuretic (rat) and vasodepressor (rat and eel) activities, eel VNP is much more potent than human ANP in eels and almost equipotent in rats. Strong tachyphylaxis is observed for the vasodepressor effect in both rats and eels, whereas it is not observed for the natriuretic effect in rats.
Decline of signal transduction by phospholipase Cγ1 in IMR 90 human diploid fibroblasts at high population doubling levels
Authors: Choudhury Goutam Ghosh , Sylvia Victor L. , Sakaguchi Alan Y.
Published: July 2002

During cellular senescence in vitro, the cells do not respond mitogenically to serum growth factors at high population doubling levels. Phospholipase C activity in low PDL IMR 90 cells showed a 4.7‐fold stimulation in response to 10% serum compared to 3.3‐fold in high PDL cells when measured in whole cell extracts. Immunoaffinity purified tyrosine phosphorylated protein fraction showed a greater increase (5.2‐fold) in phospholipase C activity in low PDL than high PDL cells (2.1‐fold) in response to serum. Serum stimulated PLCγ1 activity was diminished in high PDL cells. Immunokinase assay of PLCγ1 immunoprecipitates from serum stimulated IMR 90 fibroblasts suggested that diminished enzymatic activity in high PDL cells is not due to less receptor coupled tyrosine phosphorylated PLCγ1 enzyme. Serum stimulated [3H]thymidine incorporation into DNA declined in parallel with the activity of PLCγ1, suggesting that its activation might play significant roles in this in vitro model for cellular senescence.
Ordered binding model as a general mechanistic mechanism for secondary active transport systems
Authors: Yamato Ichiro
Published: July 2002

The mechanistic mechanism of secondary active transport processes has not been fully elucidated. Based on substrate binding, studies dependent on coupling cation concentrations of the glutamate, melibiose, lactose and proline transport carriers in Escherichia coli, the ordered binding mechanism was proposed as the energy coupling mechanism of the transport systems. This ordered binding mechanism satisfactorily explained the properties of the secondary active transport systems. Thus, this mechanism as the general energy coupling mechanism for the transport systems is discussed.
rol A modulates the sensitivity to auxin of the proton translocation catalyzed by the plasma membrane H+‐ATPase in transformed tobacco
Authors: Vansuyt Gérard , Vilaine Françoise , Tepfer Mark , Rossignol Michel
Published: July 2002

In order to investigate the effect of the rol A gene product on the plasma membrane response to auxin, a clone of rol A‐transformed tobacco was prepared. Auxin sensitivity was measured by the auxin concentration which induced the highest stimulation of H+‐ATPase‐mediated proton translocation on isolated plasma membrane vesicles. Both transformed and control plants exhibited identical auxin‐sensitivity changes during vegetative and induction to flowering periods. However the sensitivity of flowering‐transformed plants Was 100‐times higher than that of control plants. Consistent observations were also made when using rol A+B+C‐transformed plants. These results suggest that the rol A gene product could either participate in or affect the reception/transduction pathway of auxin signal at the plasma membrane.