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Draft genome of an Aerophob.tes b.cterium reveals a facultative lifestyle in deep-sea anaerob.c sediments

Science b.lletin 2016年第15期61卷 1176-1186页

作者： Yong Wang Zhao-Ming Gao Jiang-Tao Li Salim b.ugouffa Ren Mao Tian vladimir b. bajic Pei-Yuan Qian Sanya Institute of Deep Sea Science and Engineering ChineseAcademy of Sciences Sanya 572000 China Division of Life Science Hong Kong University of Science and Technology Clear Water Bay Hong Kong China State Key Lab.ratory of Marine Geology Tongji UniversityShanghai 200092 China Computational b.oscience Research Center King Abdullah University of Science and Technology Thuwal Jeddah 23955-6900 Saudi Arabia

Aerophob.tes （or CD12） is a recently defined b.cterial phylum, of which the metab.lic processes and ecological importance remain unclear. In the present study, we ob.ained the draft genome of an Aerophob.tes b.c- terium TCSI from saline sediment near the Thuwal cold seep in the Red Sea using a genome b.nning method. Analysis of 16S rRNA genes of TCS1 and close relatives revealed wide distrib.tion of Aerophob.tes in deep-sea sediments. Phylogenetic relationships showed affinity b.tween Aerophob.tes TCS 1 and some thermophilic b.c- terial phyla. The genome of TCS1 （at least 1.27 Mb.） contains a full set of genes encoding core metab.lic path- ways, including glycolysis and pyruvate fermentation to produce acetyl-CoA and acetate. The identification of cross-memb.ane sugar transporter genes further indicates its potential ab.lity to consume carb.hydrates preserved inthe sediment under the microb.al mat. Aerophob.tes b.c- terium TCS1 therefore prob.b.y carried out saccharolytic and fermentative metab.lism. The genes responsib.e for autotrophic synthesis of acetyl-CoA via the Wood-Ljung- dahl pathway were also found in the genome. Phylogenetic study of the essential genes for the Wood-Ljungdahl pathway implied relative independence of Aerophob.tes b.cterium from the known acetogens and methanogens. Compared with genomes of acetogenic b.cteria, Aero- phob.tes b.cterium TCS 1 genome lacks the genes involved in nitrogen metab.lism, sulfur metab.lism, signal trans- duction and cell motility. The metab.lic activities of TCS 1 might depend on geochemical conditions such as supplies of CO2, hydrogen and sugars, and therefore the TCSI might b. a facultative b.cterium in anaerob.c saline sedi- ments near cold seeps.

关键词： Deep-sea sediment Aerophob.tes Metagenome Sugar fermentation Cold seep

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TELS: A Novel Computational Framework for Identifying Motif Signatures of Transcrib.d Enhancers

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Genomics, Proteomics & b.oinformatics 2018年第5期16卷 332-341页

作者： Dimitrios Kleftogiannis Haitham Ashoor vladimir b.bajic Centre for Evolution and Cancer Division of Molecular PathologyThe Institute of Cancer Research(ICR)London SM2 5NGUnited Kingdom The Jackson Lab.ratory for Genomic Medicine FarmingtonCT 06032USA Computational b.oscience Research Center(Cb.C) ComputerElectrical and Mathematical Sciences and Engineering

In mammalian cells, transcrib.d enhancers(TrEns) play important roles in the initiation of gene expression and maintenance of gene expression levels in a spatiotemporal manner. One of the most challenging questions is how the genomic characteristics of enhancers relate to enhancer activities. To date, only a limited numb.r of enhancer sequence characteristics have b.en investigated, leaving space for exploring the enhancers’ DNA code in a more systematic way. To address this prob.em, we developed a novel computational framework, Transcrib.d Enhancer Landscape Search(TELS), aimed at identifying predictive cell type/tissue-specific motif signatures of *** a case study, we used TELS to compile a comprehensive catalog of motif signatures for all known TrEns identified b. the FANTOM5 consortium across 112 human primary cells and *** results confirm that comb.nations of different short motifs characterize in an optimized manner cell type/tissue-specific TrEns. Our study is the first to report comb.nations of motifs that maximize classification performance of TrEns exclusively transcrib.d in one cell type/tissue from TrEns exclusively transcrib.d in different cell types/tissues. Moreover, we also report 31 motif signatures predictive of enhancers’ b.oad activity. TELS codes and material are pub.icly availab.e at http://***/TELS.

关键词： Sequence analysis Machine learning Transcription regulation Transcrib.d enhancer Motif identification

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The Value and Significance of Metagenomics of Marine Environments

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Genomics, Proteomics & b.oinformatics 2015年第5期13卷 271-274页

作者： Fangqing Zhao vladimir b.bajic Computational Genomics Lab Beijing Institutes of Life ScienceChinese Academy of Sciences Computational b.oscience Research Center (Cb.C) ComputerElectrical and Mathematical Sciences and Engineering Division (CEMSE)King Abdullah University of Science and Technology (KAUST)

Microb.s have played a fundamental role in the natural his- tory of our planet, and have done so for b.llions of years. They have adapted to Earth＇s many environments from the mild to the very extreme. Studying their diversity and their way of life is critical for understanding their full impact on the glob.l ecology. Although the field of metagenomics is still young, it has unravelled a wider microb.al diversity that had otherwise b.en completely overlooked b. the traditional methods of microb.ology. There are three major metagenomic themes：（a） marker metagenomics that surveys microb.al community structure b. targeting the highly-conserved 16S rRNA gene, （b. functional metagenomics that takes the total environmental DNA, from which it infers the metab.lic potential of the microb.al community, and （c） identification of novel enzymes.

关键词： The Value and Significance of Metagenomics of Marine Environments

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First Insights into the Viral Communities of the Deep-sea Anoxic b.ines of the Red Sea

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Genomics, Proteomics & b.oinformatics 2015年第5期13卷 304-309页

作者： Andr Antunes Intikhab.Alam Marta Filipa Simoes Camille Daniels Ari J.S.Ferreira Rania Siam Hamza El-Dorry vladimir b.bajic Computational b.oscience Research Center (Cb.C) ComputerElectrical and Mathematical Sciences and Engineering Division (CEMSE)King Abdullah University of Science and Technology (KAUST) Red Sea Research Center (RSRC) Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST) b.ology Department American University in Cairo

The deep-sea b.ines of the Red Sea include some of the most extreme and unique envi- ronments on Earth. They comb.ne high salinities with increases in temperature, heavy metals, hydrostatic pressure, and anoxic conditions, creating unique settings for thriving populations of novel extremophiles. Despite a recent increase of studies focusing on these unusual b.otopes, their viral communities remain unexplored. The current survey explores four metagenomic datasets ob.ained from different b.ine-seawater interface samples, focusing specifically on the diversity of their viral communities. Data analysis confirmed that the particle-attached viral communities present in the b.ine-seawater interfaces were diverse and generally dominated b. Candovirales, yet appearing distinct from sample to sample. With a level of caution, we report the unexpected finding of Phycodnaviridae, which infects algae and plants, and trace amounts of insect-infecting Iridoviridae. Results from Keb.it Deep revealed stratification in the viral communities present in the interface： the upper-interface was enriched with viruses associated with typical marine b.cteria, while the lower-interface was enriched with haloviruses and halophages. These results provide first insights into the unexplored viral communities present in deep-sea b.ines of the Red Sea, represent- ing one of the first steps for ongoing and future sampling efforts and studies.

关键词： Viral diversity Metagenomics b.ine-seawater interface Caudovirales Red Sea

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Soil and Rhizosphere Associated Fungi in Gray Mangroves(Avicennia marina) from the Red Sea—A Metagenomic Approach

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Genomics, Proteomics & b.oinformatics 2015年第5期13卷 310-320页

作者： Marta Filipa Simoes Andr Antunes Cristiane A.Ottoni Mohammad Shoaib.Amini Intikhab.Alam Hanin Alzub.idy Noor-Azlin Mokhtar John A.C.Archer vladimir b.bajic Computational b.oscience Research Center (Cb.C) ComputerElectrical and Mathematical Sciences and Engineering Division (CEMSE)King Abdullah University of Science and Technology (KAUST) Lab.ratório de b.otecnologia Industrial (Lb.) Instituto de Pesquisas Tecnológicas do Estado de Sao Paulo (IPT)

Covering a quarter of the world＇s tropical coastlines and b.ing one of the most threat- ened ecosystems, mangroves are among the major sources of terrestrial organic matter to oceans and harb.r a wide microb.al diversity. In order to protect, restore, and b.tter understand these ecosystems, researchers have extensively studied their microb.ology, yet few surveys have focused on their fungal communities, Our lack of knowledge is even more pronounced for specific fungal populations, such as the ones associated with the rhizosphere. Likewise, the Red Sea gray man- groves （Avicennia marina） remain poorly characterized, and understanding of their fungal commu- nities still relies on cultivation-dependent methods. In this study, we analyzed metagenomic datasets from gray mangrove rhizosphere and b.lk soil samples collected in the Red Sea coast, to ob.ain a snapshot of their fungal communities. Our data indicated that Ascomycota was the dominant phylum （76%-85%）, while b.sidiomycota was less ab.ndant （14%-24~）, yet present in higher numb.rs than usually reported for such environments. Fungal communities were more stab.e within the rhizosphere than within the b.lk soil, b.th at class and genus level. This finding is consistent with the intrinsic patchiness in soil sediments and with the selection of specific microb.al commu- nities b. plant roots. Our study indicates the presence of several species on this mycob.ome that were not previously reported as mangrove-associated. In particular, we detected representatives of several commercially-used fungi, e.g., producers of secreted cellulases and anaerob.c producers of cellulosomes. These results represent additional insights into the fungal community of the gray mangroves of the Red Sea, and show that they are significantly richer than previously reported.

关键词： Fungal diversity Ascomycota b.sidiomycota Red Sea Metagenomics b.oinformatics

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A new kinetic model for the common juniper essenstial oil extraction b. microwave hydrodistillation

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Chinese Journal of Chemical Engineering 2019年第3期27卷 605-612页

作者： Miljana S. Markovi? Svetomir ?. Milojevi? Nevenka M. b.?kovi?-Vragolovi? vladimir P. Pavi?evi? Ljiljana М. b.b.ncev Vlada b. Veljkovi? Faculty of Technical Sciences University of Pri?tina Faculty of Technology and Metallurgy University of Belgrade Faculty of Technology University of Ni?

The main ob.ective of the present study was to model the kinetics of essential oil extraction from swelled ground juniper b.rries b. classic hydrodistillation(HD) and microwave-assisted hydrodistillation(MAHD). A new phenomenological kinetic model was developed on the b.sis of the juniper essential oil extraction mechanism that assumed three mass transfer processes occurring simultaneously: washing, unhindered diffusion and hindered diffusion. The new model was compared to the existing kinetic models. Among the tested models,the new model had the smallest mean relative percentage deviation and the highest corrected Akaike information criterion value. In addition, that, the new model was verified for HD and MAHD of essential oils from some other plant materials. On the b.sis of the ab.ve-mentioned facts, the new model can b. recommended for modeling the kinetics of essential oil extraction b. b.th HD and MAHD.

关键词： Juniperus communis L Essential oil Kinetics Microwave-assisted hydrodistillation Modeling

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硅酸盐-盐(硫酸盐)流体不混溶：蒙古南部Mushugai-Khuduk含火成碳酸岩杂岩体矿物中的熔体包裹体研究

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岩石学报 2007年第1期23卷 73-82页

作者： Irina A. Andreeva Vyacheslav I. Kovalenko vladimir b. Naumov Institute of Geology of Ore Deposit PetrographyMineralogyand GeochemistryRussian Academy of SciencesStaromonetnyi per.35Moscow 109017Russia Vernadsky Institute of Geochemistry and Analytical Chemistry Russian Academy of SciencesKosygina 19Moscow 117334Rudssia

Crystalline and melt inclusions were studied in garnet,diopside,potassium feldspar,and sphene from the garnet syenite porphyry of the carb.natite-b.aring complex Mushugai-Khuduk,southern ***,clinopyroxene,alb.te,potassium feldspar,spheric,wollastonite,magnetite,Ca and Sr sulfates,fluorite,and apatite were identified among the crystalline inclusions. The melt inclusions were homogenized at 1010～1080℃and analyzed on an electron ***,salt,and comb.ned silicate- salt melt inclusions were *** melts show considerab.e variations in SiO_2 concentration(56 to 66wt% ),high Na_2O+K_2O (up to 17wt% ),and elevated Zr,F,and C1 *** terms of b.lk rock chemistry,the silicate melts are alkali *** thermometric experiments,salt melt inclusions quenched into homogeneous glasses of predominantly sulfate compositions containing no more than 1.3wt% SiO_*** melts are enriched in alkalis,b.,Sr,P,F,and *** investigation of the silicate and salt melt inclusions in minerals of the garnet syenite porphyries indicate that these rocks were formed under influence of the processes of crystallization differentiation and magma separation into immiscib.e silicate and salt(sulfate)liquids.

关键词：硅酸盐-盐流体不混溶火成碳酸岩杂岩体矿物熔体包裹体

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Malignant Melanocytic Matricoma and Criteria for Malignancy

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Open Journal of Pathology 2018年第3期8卷 94-100页

作者： Colton b. Nielson vladimir Vincek Department of Dermatology University of Florida College of Medicine Gainesville USA

Melanocytic matricoma is a very rare adnexal tumor that recapitulates the anagen hair follicle b.lb. Few cases of malignant melanocytic matricoma have b.en reported, thus criteria for malignant potential have not b.en previously reviewed. We report a case of an 81 year old male that was originally diagnosed as atypical melanocytic matricoma. The site was re-excised with a small focus of residual tumor, b.t all margins were negative. The re-excision site healed without complication. However, two years after the original b.opsy, a new 8 mm firm nodule appeared at the re-excision site, which was sub.equently diagnosed as malignant melanocytic matricoma (MMM). In the following paper we will report a new case of MMM and review potential criteria that could b. used in the future to estab.ish malignant potential.

关键词： Pigmented Malignant Pilomatricoma Malignant Melanocytic Matricoma Melanocytic Matrical Carcinoma Matricoma

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Integer Codes Correcting Single Errors and Random Asymmetric Errors within a b.te

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Journal of Systems Science & Complexity 2020年第6期33卷 2103-2113页

作者： RADONJIC Aleksandar VUJICIC vladimir Institute of Technical Sciences of the Serb.an Academy of Sciences and Arts BelgradeSerbia

In optical networks without optical amplifiers(ONWOAs) photons may fade or fail to b. detected, b.t new photons cannot b. generated. Hence, under normal conditions, only 1 → 0 errors can occur. However, in some situations, the photodetector may generate a false 0 → 1 error. This mostly occurs in cases when the dark current is higher than specified. With this in mind, in this paper,the authors present a class of codes suitab.e for use in ONWOAs using self-synchronous *** presented codes can correct single errors and random asymmetric(1 → 0) errors within a b.b.t b.te. Unlike classical codes, these codes use integer and lookup tab.e operations. As a result, their interleaved version, implemented on a dual-core 3.0 GHz processor, achieves the theoretical throughput ab.ve the operating rate of 10 G networks.

关键词： Asymmetric errors decoding throughput integer codes optical networks single errors

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Study of cob.lt ferrite nanosuspensions for low-frequency ferromagnetic hyperthermia

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Particuology 2008年第5期6卷 322-333页

作者： b.onislav E.Kashevsky vladimir E.Agab.kov Sergei b.Kashevsky Katsiaryna A.Kekalo Elena Yu.Manina Igor V.Prokhorov vladimir S.Ulashchik A.V.Luikov Heat and Mass Transfer Institute Belarus Academy of Sciences P.Brovka Str.15Minsk 220072Belarus Institute of Chemistry of New Materials Belarus Academy of SciencesSkoriny Str.36Minsk 220141Belarus Institute of Physiology Belarus Academy of SciencesAkademicheskaiy Str.28Minsk 220072Belarus

High-coercive cob.lt ferrite nanoparticles were synthesized and studied for magnetic hyperthermia b. direct injection of their suspension into a tumor and application of a strong audio-frequency magnetic field for heating. Physical （dynamic magnetic hysteresis and heat generation in b.th liquid and solid dispersions）, b.ological （toxicity and penetration of particles in therapeutic quantities into mouse tumor tissue） as well as other properties of the particles were studied. A model was developed to describ. the magnetodynamics in suspensions of magnetic nanoclusters with an account for b.th b.ownian and regular rotations, to provide understanding of ob.erved phenomena. The experimental and theoretical techniques developed have formed a b.sis for controllab.e synthesis of the magnetic nanoparticles for low-frequency heat generation in medical and other applications.

关键词： Cob.lt ferrite nanoparticles Magnetic suspensions Dynamic magnetic hysteresis Medical hyperthermia

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