-
[show abstract]
[hide abstract]
ABSTRACT: Numerous applications such as financial transactions (e.g., stock trading)
are write-heavy in nature. The shift from reads to writes in web applications
has also been accelerating in recent years. Write-ahead-logging is a common
approach for providing recovery capability while improving performance in most
storage systems. However, the separation of log and application data incurs
write overheads observed in write-heavy environments and hence adversely
affects the write throughput and recovery time in the system. In this paper, we
introduce LogBase - a scalable log-structured database system that adopts
log-only storage for removing the write bottleneck and supporting fast system
recovery. LogBase is designed to be dynamically deployed on commodity clusters
to take advantage of elastic scaling property of cloud environments. LogBase
provides in-memory multiversion indexes for supporting efficient access to data
maintained in the log. LogBase also supports transactions that bundle read and
write operations spanning across multiple records. We implemented the proposed
system and compared it with HBase and a disk-based log-structured
record-oriented system modeled after RAMCloud. The experimental results show
that LogBase is able to provide sustained write throughput, efficient data
access out of the cache, and effective system recovery.
06/2012;
-
[show abstract]
[hide abstract]
ABSTRACT: The atmospheric boundary layer (ABL) is an important physical characteristic of the Earth’s atmosphere. Compared with the
typical ABL, the ABL in arid regions has distinct features and is formed by particular mechanisms. In this paper, the depth
of the diurnal and nocturnal ABLs and their related thermodynamic features of land surface processes, including net radiation,
the ground-air temperature difference and sensible heat flux, under typical summer and winter conditions are discussed on
the basis of comprehensive observations of the ABL and thermodynamic processes at the land surface carried out in the extreme
arid zone of Dunhuang. The relationships of the ABL depth in the development and maintenance stages with these thermodynamic
features are also investigated. The results show that the depth of the ABL is closely correlated with the thermodynamic features
in both development and maintenance stages and more energy is consumed in the development stage. Further analysis indicates
that wind velocity also affects ABL development, especially the development of a stable boundary layer in winter. Taken together,
the analysis results indicate that extremely strong thermodynamic processes at the land surface are the main driving factor
for the formation of a deep ABL in an arid region.
Keywordsarid region–deep atmospheric boundary layer–development and maintenance–thermodynamic process at the land surface–main driving factor
Science China Earth Science 05/2012; 54(10):1586-1594. · 0.70 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: This study developed a simple and rapid purification method for plasma membrane with high yields from adherent cells. The plasma membrane (PM) sheets could be absorbed specifically by the cationic silica-magnetite nanocomposites (CSMN) under acidic conditions, and recovered directly in cell-lysis-buffer with no need for precipitation. The binding between CSMN and PM sheets was confirmed by electron microscopy. Western blot analysis demonstrated a >10-fold relative enrichment factor. Up to 422 integral membrane proteins were identified from 10(7) Huh7 cells. Notably, we found 29 Ras family proteins by classification according to their biological functions. The whole enrichment procedure took <30 min. The CSMN-based procedure demonstrates a simple, economical and efficient enrichment of integral PM proteins in proteomic study.
Proteomics 09/2011; 11(17):3482-90. · 4.43 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: In this report, trypsin was immobilized on silica-coated fiberglass core in microchip to form a core-changeable bioreactor for highly efficient proteolysis. To prepare the fiber core, a layer of organic-inorganic hybrid silica coating was prepared on the surface of a piece of glass fiber by a sol-gel method with tetraethoxysilane (TEOS) and 3-aminopropyltriethoxysilane (APTES) as precursors. Subsequently, trypsin was immobilized on the coating with the aid of glutaraldehyde. Prior to use, the enzyme-immobilized fiber was inserted into the channel of a microchip to form an in-channel fiber bioreactor. The novel bioreactor can be regenerated by changing its fiber core. The scanning electron microscopy images of the cross-section of a trypsin-immobilized fiber indicated that a layer of approximately 1mum thick film formed on the glass substrate. The feasibility and performance of the unique bioreactor were demonstrated by the tryptic digestion of bovine serum albumin (BSA) and cytochrome c (Cyt-c) and the digestion time was significantly reduced to less than 10s. The digests were identified by MALDI-TOF MS with sequence coverages of 45% (BSA) and 77% (Cyt-c) that were comparable to those obtained by 12-h conventional in-solution tryptic digestion. The fiber-based microchip bioreactor provides a promising platform for the high-throughput protein identification.
Talanta 04/2009; 77(5):1767-73. · 3.79 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Alternating current (AC) has been employed to enhance the efficiency of chymotryptic proteolysis for peptide mapping. It was allowed to flow through the mixture solution of proteins and chymotrypsin via a pair of platinum wire electrodes. Bovine serum albumin (BSA) and cytochrome c (Cyt-c) were digested by the novel proteolysis approach to demonstrate its feasibility and performance. The results indicated that AC significantly accelerated in-solution chymotryptic proteolysis and the digestion time was substantially reduced to 5 min. The digests were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with sequence coverages of 46% (BSA) and 90% (Cyt-c) that were much better than those obtained by using 12-h conventional in-solution chymotryptic proteolysis. In addition, AC-assisted chymotryptic proteolysis was employed to digest human serum to demonstrate its suitability to complex protein sample. The present proteolysis strategy is simple and efficient and will find a wide range of applications in proteomic research.
Journal of proteomics 02/2009; 72(4):640-7. · 5.07 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: In this report, alternating current-assisted on-plate proteolysis has been developed for rapid peptide mapping. Protein solutions containing trypsin were allowed to digest directly on the spots of a stainless steel MALDI plate with the assistance of low-voltage alternating current electricity. Alternating current (AC) was allowed to pass through the protein solutions via the MALDI plate and a platinum disc electrode. The feasibility and performance of the novel proteolysis approach were investigated by the digestion of BSA and cytochrome c (Cyt-c). It was demonstrated that AC substantially enhanced the efficiency of proteolysis and the digestion time was significantly reduced to 5 min. The digests were identified by MALDI-TOF MS with sequence coverages of 42% (BSA) and 77% (Cyt-c) that were comparable to those obtained by using conventional in-solution tryptic digestion. The present proteolysis strategy is simple and efficient, offering great promise for MALDI-TOF MS peptide mapping.
Proteomics 11/2008; 8(22):4637-41. · 4.43 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Infrared (IR) radiation was employed to enhance the efficiency of chymotryptic proteolysis for peptide mapping in this work. Protein solutions containing chymotrypsin in sealed transparent Eppendorf tubes were allowed to digest under an IR lamp at 37 degrees C. BSA and cytochrome c (Cyt- c) were digested by IR-assisted chymotryptic proteolysis to demonstrate the feasibility and performance of the novel digestion approach and the digestion time was significantly reduced to 5 min. The obtained digests were further identified by MALDI-TOF MS with the sequence coverages that were comparable to those obtained by using conventional in-solution digestion. The suitability of IR-assisted chymotryptic proteolysis to complex proteins was demonstrated by digesting human serum. The present proteolysis strategy is simple and efficient, offering great promise for high-throughput protein identification.
Journal of Proteome Research 11/2008; 7(11):5049-54. · 5.11 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Sinusoidal alternating voltages (typically 5 V) were employed to enhance the efficiency of proteolysis for peptide mapping in this work. Protein solutions containing trypsin were allowed to digest with the assistance of alternating electric fields (AEFs) between a pair of platinum wire electrodes in Eppendorf tubes. The feasibility and performance of the novel proteolysis approach were investigated by the digestion of several standard proteins. It was demonstrated that AEFs significantly accelerated in-solution proteolysis and the digestion time was substantially reduced to 5 min. The digests were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) with sequence coverages that were comparable to those obtained by using conventional 12-h in-solution proteolysis. The suitability of AEF-assisted proteolysis to real protein samples was demonstrated by digesting and identifying human serum albumin in gel separated from human serum by sodium dodecyl sulphate/polyacrylamide gel electrophoresis (SDS-PAGE). The present proteolysis strategy is simple and efficient and will find a wide range of applications in protein identification.
Rapid Communications in Mass Spectrometry 10/2008; 22(20):3225-32. · 2.79 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: In this report, infrared (IR)-assisted on-plate proteolysis has been developed for rapid peptide mapping. Protein solutions containing trypsin were allowed to digest directly on the spots of matrix-assisted laser desorption/ionization (MALDI) plates under IR radiation. The feasibility and performance of the novel proteolysis approach were investigated by the digestion of bovine serum albumin (BSA) and cytochrome c (Cyt-c). It was demonstrated that IR radiation substantially enhanced the efficiency of proteolysis and the digestion time was significantly reduced to 5 min. The digests were identified by MALDI time-of-flight mass spectrometry with sequence coverages of 55 (BSA) and 75% (Cyt-c) that were comparable to those obtained by using conventional in-solution tryptic digestion. The suitability of IR-assisted on-plate proteolysis to complex proteins was demonstrated by digesting human serum and casein extracted from commercially available milk sample. The present proteolysis strategy is simple and efficient, offering great promise for high-throughput protein identification.
Analytical Chemistry 08/2008; 80(14):5640-7. · 5.86 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: In this report, infrared (IR) radiation was employed to enhance the efficiency of tryptic proteolysis for peptide mapping. Protein solutions containing trypsin in sealed transparent Eppendorf tubes were allowed to digest under an IR lamp at 37 degrees C. The feasibility and performance of the novel proteolysis approach were demonstrated by the digestion of BSA and myoglobin (MYO) and the digestion time was significantly reduced to 5 min. The obtained digests were identified by MALDI-TOF MS with the sequence coverages of 69% (BSA) and 90% (MYO) that were much better than those obtained by conventional in-solution tryptic digestion. The present IR-assisted proteolysis strategy is simple and efficient, offering great promise for high-throughput protein identification.
Proteomics 08/2008; 8(13):2579-82. · 4.43 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: In this report, a core-changeable needle enzymatic reactor was developed for highly efficient proteolysis. A piece of enzyme-immobilized fiber core was inserted into the needle of a syringe pump to form a flow-through bioreactor. The novel in-needle bioreactor could be regenerated by changing its fiber core. The feasibility and performance of the unique bioreactor were demonstrated by the tryptic digestion of BSA and lysozyme and the digestion time was significantly reduced to less than 5 s. The digests were identified by MALDI-TOF MS with sequence coverages comparable to those obtained by the conventional in-solution tryptic digestion. The present in-needle bioreactor provides a promising platform for the high-throughput protein identification.
Proteomics 06/2008; 8(9):1785-8. · 4.43 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: In this report, a four-component nanocomposite, trypsin-immobilized polyaniline-coated Fe(3)O(4)/carbon nanotube composite, was synthesized for highly efficient protein digestion. Fe(3)O(4) was deposited by the chemical coprecipitation of Fe(2+) and Fe(3+) in an alkaline solution containing carbon nanotubes (CNTs) to prepare nano-Fe(3)O(4)/CNT composite. Subsequently, polyaniline (PA) was assembled on the Fe(3)O(4)/CNT composite by the in situ polymerization of aniline in the presence of trypsin to obtain trypsin-immobilized PA/Fe(3)O(4)/CNT nanocomposite. The novel 1D superparamagnetic biomaterial has been characterized by TEM, SEM, XRD, and magnetometric analysis. The feasibility and performance of the unique magnetic biomaterial have been demonstrated by the tryptic digestion of bovine serum albumin, myoglobin, and lysozyme within 5min. The digests were identified by MALDI-TOF MS with sequence coverages that were comparable to those obtained from the conventional in-solution tryptic digestion. The present biocomposite offers considerable promise for protein analysis due to its high magnetic responsivity and excellent dispersibility. It can be easily isolated from the digests with the aid of an external magnetic field. Because the enzyme-immobilized nanocomposite can be prepared by a simple two-step deposition approach at low cost, it may find a wide range of biological applications including proteome research.
Analytica chimica acta 05/2008; 612(2):182-9. · 4.31 Impact Factor
-
Huali Shen,
Gang Cheng,
Huizhi Fan,
Jie Zhang,
Xiangmin Zhang,
Haojie Lu,
Chunli Liu,
Fengxia Sun,
Hong Jin,
Xuejiao Xu, [......], Sheng Wang,
Caiyun Fang,
Huimin Bao,
Yan Wang,
Jing Wang,
Hua Zhong,
Ziniu Yu,
Yinkun Liu,
Zhaoyou Tang,
Pengyuan Yang
[show abstract]
[hide abstract]
ABSTRACT: We report for the first time an expressed proteome for human hepatocellular carcinoma (HCC) in nude mice model. Most cases of human liver cancer are HCC with highly metastatic ability. Therefore, the early prediction or diagnosis and effective treatment are the key points of research. We have previously successfully established a human HCC nude mice model (LCI-D20) with high metastasis potential. To understand better the tumor biology of HCC it is worth to explore the relativity of all expressed protein profiles in the LCI-D20 HCC nude mice model. With advanced proteomics technologies, we have carried out a proteomic analysis with following stages: protein sample preparation of cancer tissue, including total cellular extraction and sequential fractionation, 2-DE and 2-D LC separation, ESI/MALDI-MS/MS identification, as well as data-dependent bioinformatics. The identified proteins were classified bioinformatically respective to their function, biological process and intracellular localization. Some important proteins found in HCC, e.g. metabolism enzymes, proteins regulating cell motility, signaling proteins, and heat shock proteins, are discussed in terms of their metastasis.
PROTEOMICS 02/2006; 6(2):528-37. · 4.51 Impact Factor
