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1.
Brulc JM Yeoman CJ Wilson MK Berg Miller ME Jeraldo P Jindou S Goldenfeld N Flint HJ Lamed R Borovok I Vodovnik M Nelson KE Bayer EA White BA 《PloS one》2011,6(10):e25329
Background
The bovine rumen maintains a diverse microbial community that serves to break down indigestible plant substrates. However, those bacteria specifically adapted to degrade cellulose, the major structural component of plant biomass, represent a fraction of the rumen microbiome. Previously, we proposed scaC as a candidate for phylotyping Ruminococcus flavefaciens, one of three major cellulolytic bacterial species isolated from the rumen. In the present report we examine the dynamics and diversity of scaC-types both within and between cattle temporally, following a dietary switch from corn-silage to grass-legume hay. These results were placed in the context of the overall bacterial population dynamics measured using the 16S rRNA.Principal Findings
As many as 117 scaC-types were estimated, although just nineteen were detected in each of three rumens tested, and these collectively accounted for the majority of all types present. Variation in scaC populations was observed between cattle, between planktonic and fiber-associated fractions and temporally over the six-week survey, and appeared related to scaC phylogeny. However, by the sixth week no significant separation of scaC populations was seen between animals, suggesting enrichment of a constrained set of scaC-types. Comparing the amino-acid translation of each scaC-type revealed sequence variation within part of the predicted dockerin module but strong conservation in the N-terminus, where the cohesin module is located.Conclusions
The R. flavefaciens species comprises a multiplicity of scaC-types in-vivo. Enrichment of particular scaC-types temporally, following a dietary switch, and between fractions along with the phylogenetic congruence suggests that functional differences exist between types. Observed differences in dockerin modules suggest at least part of the functional heterogeneity may be conferred by scaC. The polymorphic nature of scaC enables the relative distribution of R. flavefaciens strains to be examined and represents a gene-centric approach to investigating the intraspecific adaptation of an important specialist population. 相似文献2.
Tobias Kuemmerle Jed O. Kaplan Alexander V. Prishchepov Ilya Rylsky Oleh Chaskovskyy Vladimir S. Tikunov Daniel Müller 《Global Change Biology》2015,21(8):3049-3061
Forests often rebound from deforestation following industrialization and urbanization, but for many regions our understanding of where and when forest transitions happened, and how they affected carbon budgets remains poor. One such region is Eastern Europe, where political and socio‐economic conditions changed drastically over the last three centuries, but forest trends have not yet been analyzed in detail. We present a new assessment of historical forest change in the European part of the former Soviet Union and the legacies of these changes on contemporary carbon stocks. To reconstruct forest area, we homogenized statistics at the provincial level for ad 1700–2010 to identify forest transition years and forest trends. We contrast our reconstruction with the KK11 and HYDE 3.1 land change scenarios, and use all three datasets to drive the LPJ dynamic global vegetation model to calculate carbon stock dynamics. Our results revealed that forest transitions in Eastern Europe occurred predominantly in the early 20th century, substantially later than in Western Europe. We also found marked geographic variation in forest transitions, with some areas characterized by relatively stable or continuously declining forest area. Our data suggest extensive deforestation in European Russia already prior to ad 1700, and even greater deforestation in the 18th and 19th centuries than in the KK11 and HYDE scenarios. Based on our reconstruction, cumulative carbon emissions from deforestation were greater before 1700 (60 Pg C) than thereafter (29 Pg C). Summed over our entire study area, forest transitions led to a modest uptake in carbon over recent decades, with our dataset showing the smallest effect (<5.5 Pg C) and a more heterogeneous pattern of source and sink regions. This suggests substantial sequestration potential in regrowing forests of the region, a trend that may be amplified through ongoing land abandonment, climate change, and CO2 fertilization. 相似文献
3.
Ilya G. Kichigin Massimo Giovannotti Alex I. Makunin Bee L. Ng Marsel R. Kabilov Alexey E. Tupikin Vincenzo Caputo Barucchi Andrea Splendiani Paolo Ruggeri Willem Rens Patricia C. M. O’Brien Malcolm A. Ferguson-Smith Alexander S. Graphodatsky Vladimir A. Trifonov 《Molecular genetics and genomics : MGG》2016,291(5):1955-1966
4.
Darshan Kumar Behnam Lak Taina Suntio Helena Vihinen Ilya Belevich Tiina Viita Liu Xiaonan Aki Vartiainen Maria Vartiainen Markku Varjosalo Eija Jokitalo 《Molecular biology of the cell》2021,32(12):1158
The endoplasmic reticulum (ER) is composed of a controlled ratio of sheets and tubules, which are maintained by several proteins with multiple functions. Reticulons (RTNs), especially RTN4, and DP1/Yop1p family members are known to induce ER membrane curvature. RTN4B is the main RTN4 isoform expressed in nonneuronal cells. In this study, we identified FAM134C as a RTN4B interacting protein in mammalian, nonneuronal cells. FAM134C localized specifically to the ER tubules and sheet edges. Ultrastructural analysis revealed that overexpression of FAM134C induced the formation of unbranched, long tubules or dense globular structures composed of heavily branched narrow tubules. In both cases, tubules were nonmotile. ER tubulation was dependent on the reticulon homology domain (RHD) close to the N-terminus. FAM134C plays a role in the autophagy pathway as its level elevated significantly upon amino acid starvation but not during ER stress. Moreover, FAM134C depletion reduced the number and size of autophagic structures and the amount of ER as a cargo within autophagic structures under starvation conditions. Dominant-negative expression of FAM134C forms with mutated RHD or LC3 interacting region also led to a reduced number of autophagic structures. Our results suggest that FAM134C provides a link between regulation of ER architecture and ER turnover by promoting ER tubulation required for subsequent ER fragmentation and engulfment into autophagosomes. 相似文献
5.
Mikhail G. Divashuk Oleg S. Alexandrov Olga V. Razumova Ilya V. Kirov Gennady I. Karlov 《PloS one》2014,9(1)
Hemp (Cannabis sativa L.) was karyotyped using by DAPI/C-banding staining to provide chromosome measurements, and by fluorescence in situ hybridization with probes for 45 rDNA (pTa71), 5S rDNA (pCT4.2), a subtelomeric repeat (CS-1) and the Arabidopsis telomere probes. The karyotype has 18 autosomes plus a sex chromosome pair (XX in female and XY in male plants). The autosomes are difficult to distinguish morphologically, but three pairs could be distinguished using the probes. The Y chromosome is larger than the autosomes, and carries a fully heterochromatic DAPI positive arm and CS-1 repeats only on the less intensely DAPI-stained, euchromatic arm. The X is the largest chromosome of all, and carries CS-1 subtelomeric repeats on both arms. The meiotic configuration of the sex bivalent locates a pseudoautosomal region of the Y chromosome at the end of the euchromatic CS-1-carrying arm. Our molecular cytogenetic study of the C. sativa sex chromosomes is a starting point for helping to make C. sativa a promising model to study sex chromosome evolution. 相似文献
6.
Liat Bahari Yuval Gilad Ilya Borovok Hamutal Kahel-Raifer Bareket Dassa Yakir Nataf Yuval Shoham Raphael Lamed Edward A. Bayer 《Journal of industrial microbiology & biotechnology》2011,38(7):825-832
The composition of the cellulase system in the cellulosome-producing bacterium, Clostridium thermocellum, has been reported to change in response to growth on different carbon sources. Recently, an extensive carbohydrate-sensing
mechanism, purported to regulate the activation of genes coding for polysaccharide-degrading enzymes, was suggested. In this
system, CBM modules, comprising extracellular components of RsgI-like anti-σ factors, were proposed to function as carbohydrate
sensors, through which a set of cellulose utilization genes are activated by the associated σI-like factors. An extracellular module of one of these RsgI-like proteins (Cthe_2119) was annotated as a family 10 glycoside
hydrolase, RsgI6-GH10, and a second putative anti-σ factor (Cthe_1471), related in sequence to Rsi24, was found to contain
a module that resembles a family 5 glycoside hydrolase (termed herein Rsi24C-GH5). The present study examines the relevance
of these two glycoside hydrolases as sensors in this signal-transmission system. The RsgI6-GH10 was found to bind xylan matrices
but exhibited low enzymatic activity on this substrate. In addition, this glycoside hydrolase module was shown to interact
with crystalline cellulose although no hydrolytic activity was detected on cellulosic substrates. Bioinformatic analysis of
the Rsi24C-GH5 showed a glutamate-to-glutamine substitution that would presumably preclude catalytic activity. Indeed, the
recombinant module was shown to bind to cellulose, but showed no hydrolytic activity. These observations suggest that these
two glycoside hydrolases underwent an evolutionary adaptation to function as polysaccharide binding agents rather than enzymatic
components and thus serve in the capacity of extracellular carbohydrate sensors. 相似文献
7.
8.
9.
Declerck P Behets J Lammertyn E Lebeau I Anné J Ollevier F 《Canadian journal of microbiology》2006,52(6):584-590
The presence of high levels of Legionella pneumophila in man-made aquatic systems correlates with the incidence of nosocomial Legionnaires' disease. This requires a rapid, reliable, and sensitive quantification of L. pneumophila concentrations in suspected water systems. In this research, a homologous competitor was developed and evaluated in a L. pneumophila competitive polymerase chain reaction (cPCR) to quantify this human pathogen in a quick, cost-effective, and reliable way. Accuracy of cPCR was evaluated by analyzing cooling tower and tap water samples spiked with known concentrations of L. pneumophila bacteria, in parallel with the standard culture method. Legionella pneumophila amounts detected and calculated from cPCR and culture correlated very well: r = 0.998, P = 0.002 for tap water and r = 0.990, P = 0.009 for cooling tower water. Nevertheless, for both kinds of water samples, mean numbers of L. pneumophila calculated from cPCR results were always higher than those obtained by culture. This study makes it clear that the rapid, sensitive, and cost-effective L. pneumophila cPCR is a promising alternative to the standard time-consuming culture method and expensive real-time PCR to enumerate L. pneumophila bacteria in environmental water samples. 相似文献
10.
Switching of membrane organelles between cytoskeletal transport systems is determined by regulation of the microtubule-based transport 下载免费PDF全文
Intracellular transport of membrane organelles occurs along microtubules (MTs) and actin filaments (AFs). Although transport along each type of the cytoskeletal tracks is well characterized, the switching between the two types of transport is poorly understood because it cannot be observed directly in living cells. To gain insight into the regulation of the switching of membrane organelles between the two major transport systems, we developed a novel approach that combines live cell imaging with computational modeling. Using this approach, we measured the parameters that determine how fast membrane organelles switch back and forth between MTs and AFs (the switching rate constants) and compared these parameters during different signaling states. We show that regulation involves a major change in a single parameter: the transferring rate from AFs onto MTs. This result suggests that MT transport is the defining factor whose regulation determines the choice of the cytoskeletal tracks during the transport of membrane organelles. 相似文献