Lipoproteomics I: mapping of proteins in low-density lipoprotein using two-dimensional gel electrophoresis and mass spectrometry

The molecular mechanisms underlying the relationship between low-density lipoprotein (LDL) and the risk of atherosclerosis are not clear. Therefore, detailed information about the protein composition of LDL may contribute to reveal its role in atherogenesis and the mechanisms that lead to coronary disease in humans. Here, we sought to map the proteins in human LDL by a proteomic approach. LDL was isolated by two-step discontinuous density-gradient ultracentrifugation and the proteins were separated with two-dimensional gel electrophoresis and identified with peptide mass fingerprinting, using matrix assisted laser desorption/ionization-time of flight-mass spectrometry and with amino acid sequencing using electrospray ionization tandem mass spectrometry. These procedures identified apo B-100, apo C-II, apo C-III (three isoforms), apo E (four isoforms), apo A-I (two isoforms), apo A-IV, apo J and apo M (three isoforms not previously described). In addition, three proteins that have not previously been identified in LDL were found: serum amyloid A-IV (two isoforms), calgranulin A, and lysozyme C. The identities of apo M, calgranulin A, and lysozyme C were confirmed by sequence information obtained after collision-induced dissociation fragmentation of peptides characteristic for these proteins. Moreover, the presence of lysozyme C was further corroborated by demonstrating enriched hydrolytic activity in LDL against Micrococcus lysodeikticus. These results indicate that in addition to the dominating apo B-100, LDL contains a number of other apolipoproteins, many of which occur in different isoforms. The demonstration, for the first time, that LDL contains calgranulin A and lysozyme C raises the possibility that LDL proteins may play hitherto unknown role(s) in immune and inflammatory reactions of the arterial wall.     

Functional sulfurtransferase is associated with mitochondrial complex I from Yarrowia lipolytica, but is not required for assembly of its iron-sulfur clusters

Here, we report that in the obligate aerobic yeast Yarrowia lipolytica, a protein exhibiting rhodanese (thiosulfate:cyanide sulfurtransferase) activity is associated with proton pumping NADH:ubiquinone oxidoreductase (complex I). Complex I is a key enzyme of the mitochondrial respiratory chain that contains eight iron-sulfur clusters. From a rhodanese deletion strain, we purified functional complex I that lacked the additional protein but was fully assembled and displayed no functional defects or changes in EPR signature. In contrast to previous suggestions, this indicated that the sulfurtransferase associated with Y. lipolytica complex I is not required for assembly of its iron-sulfur clusters.     

Carbohydrate utilization in the thoraces of honey bees (Apis mellifera) during early times of flight

Trehalose levels in the thoraces of honey bees did not change significantly during the first 2–4 min of flight. This effect was seen both for bees flown shortly after removal from the hive and for bees which were flown after a 2 hr starvation period. There was also no detectable activation of the trehalose in isolated mitochondria from bees flown for periods of up to 2 min. However, the glucose content of the thoraces of bees flown shortly after removal from the hive dropped dramatically during the first 15 sec of flight. There was no evidence of a transient increase in the glucose content in the thorax at any of the times studied as would be expected if trehalose were hydrolized. The drop in glucose content at early times of flight was not detected if the bees were starved for 2 hr before flight was started. The changes in fructose content of the thoraces with time were similar to those observed for glucose, but were not statistically significant due to variation among individual bees. The sucrose content of bee thoraces varied greatly and no meaningful conclusions could be reached about how it changed as a function of time of flight.     

Proteome analysis of silk gland proteins from the silkworm, Bombyx mori

The silk gland of Bombyx mori is an organ specialized for the synthesis and secretion of silk proteins. We report here the resolution of silk gland proteins by 2-DE and the identification of many of those proteins. This was accomplished by dissecting the glands into several sections, with each exhibiting more than 400 protein spots by 2-DE, of which 100 spots were excised and characterized by in-gel digestion followed by PMF. Ninety-three proteins were tentatively identified. These were then categorized into groups involved in silk protein secretion, transport, lipid metabolism, defense, etc. Western blotting of a 2-DE gel using an antibody of the carotenoid binding protein confirmed the presence of this protein in the silk gland. Proteins including fibroin L-chain and P25 were found as multiple isoforms, some of which contained differential amounts of phosphate residues as analyzed by on-probe dephosphorylation. The current analysis contributes to our understanding of proteins expressed by the silk gland not only of the model lepidopteran B. mori, but also to proteins from other silk-producing insects such as Philosamia cynthia ricini.     

慢性阻塞性肺疾病与非慢性阻塞性肺疾病吸烟者肺组织蛋白质组学比较分析

吸烟是导致慢性阻塞性肺疾病（COPD）发生发展的主要原因之一.但吸烟者是否发生COPD存在个体差异,其机制尚未完全阐明.蛋白质组学研究能够高效率发现疾病相关蛋白并为深入研究疾病的发病机制提供线索.本研究运用二维凝胶电泳（2-DE）和基质辅助激光解吸电离飞行时间质谱(MALDI-TOF-MS)蛋白质组学研究方法结合生物信息学数据,对吸烟COPD患者和非COPD吸烟者肺组织表达的差异蛋白进行筛选和鉴定,共鉴定出24种差异蛋白,涉及基本代谢酶类、氧化应激相关酶类、凝血/纤溶相关蛋白、蛋白降解相关酶以及细胞生长分化相关蛋白等.本研究结果为进一步探索COPD的发病机制提供了新的线索.     

Making noise: Emergent stochasticity in collective motion

Individual-based models of self-propelled particles (SPPs) are a popular and promising approach to explain features of the collective motion of animal aggregations. Many models that capture some features of group motion have been suggested but a common framework has yet to emerge. Key to all of these models is the inclusion of “noise” or stochastic errors in the individual behaviour of the SPPs. Here, we present a fully stochastic SPP model in one dimension that demonstrates a new way of introducing noise into SPP models whilst preserving emergent behaviours of previous models such as coherent groups and spontaneous direction switching. This purely individual-to-individual, local model is related to previous models in the literature and can easily be extended to higher dimensions. Its coarse-grained behaviour qualitatively reproduces recently reported locust movement data. We suggest that our approach offers an alternative to current reasoning about model construction and has the potential to offer mechanistic explanations for emergent properties of animal groups in nature.     

Molecular Basis for the Recognition and Cleavages of IGF-II, TGF-α, and Amylin by Human Insulin-Degrading Enzyme

Insulin-degrading enzyme (IDE) is involved in the clearance of many bioactive peptide substrates, including insulin and amyloid-β, peptides vital to the development of diabetes and Alzheimer's disease, respectively. IDE can also rapidly degrade hormones that are held together by intramolecular disulfide bond(s) without their reduction. Furthermore, IDE exhibits a remarkable ability to preferentially degrade structurally similar peptides such as the selective degradation of insulin-like growth factor (IGF)-II and transforming growth factor-α (TGF-α) over IGF-I and epidermal growth factor, respectively. Here, we used high-accuracy mass spectrometry to identify the cleavage sites of human IGF-II, TGF-α, amylin, reduced amylin, and amyloid-β by human IDE. We also determined the structures of human IDE-IGF-II and IDE-TGF-α at 2.3 Å and IDE-amylin at 2.9 Å. We found that IDE cleaves its substrates at multiple sites in a biased stochastic manner. Furthermore, the presence of a disulfide bond in amylin allows IDE to cut at an additional site in the middle of the peptide (amino acids 18-19). Our amylin-bound IDE structure offers insight into how the structural constraint from a disulfide bond in amylin can alter IDE cleavage sites. Together with NMR structures of amylin and the IGF and epidermal growth factor families, our work also reveals the structural basis of how the high dipole moment of substrates complements the charge distribution of the IDE catalytic chamber for the substrate selectivity. In addition, we show how the ability of substrates to properly anchor their N-terminus to the exosite of IDE and undergo a conformational switch upon binding to the catalytic chamber of IDE can also contribute to the selective degradation of structurally related growth factors.     

Differentiation-dependent expression of hypothetical proteins in the neuroblastoma cell line N1E-115

Several protein cascades, including signaling, cytoskeletal, chaperones, metabolic, and antioxidant proteins, have been shown to be involved in the process of neuronal differentiation (ND) of neuroblastoma cell lines. No systematic approach to detect hitherto unknown and unnamed proteins or structures that have been predicted upon nucleic acid sequences in ND has been published so far. We therefore decided to screen hypothetical protein (HP) expression by protein profiling. Two-dimensional gel electrophoresis with subsequent matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF/TOF) identification was used for expression analysis of undifferentiated and dimethylsulfoxide-induced neuronally differentiated N1E-115 cells. We unambiguously identified six HPs: Q8C520, Q99LF4, Q9CXS1, Q9DAF8, Q91WT0, and Q8C5G2. A prefoldin domain in Q91WT0, a t-SNARE domain in Q9CXS1, and a bromodomain were observed in Q8C5G2. For the three remaining proteins, no putative function using Pfam, BLOCKS, PROSITE, PRINTS, InterPro, Superfamily, CoPS, and ExPASy could be assigned. While two proteins were present in both cell lines, Q9CXS1 was switched off (i.e., undetectably low) in differentiated cells only, and Q9DAF8, Q91WT0, and Q8C5G2 were switched on in differentiated cells exclusively. Herein, using a proteomic approach suitable for screening and identification of HP, we present HP structures that have been only predicted so far based upon nucleic acid sequences. The four differentially regulated HPs may play a putative role in the process of ND.     

Flight Speed of Tethered Reticulitermes flavipes (Kollar) (Isoptera: Rhinotermitidae) Alates

Alates of the Eastern subterranean termite, Reticulitermes flavipes (Kollar) were collected over two flight seasons (2002 and 2004) and flown on flight mills. Data were collected to test if alate mass, colony origin, or gender influenced flight speed. Flight speed ranged from 3.14 to 69.12 cm s⁻¹ and the maximum distance flown by an alate was 458.3 m. Alate mass (P = 0.9406), gender (P = 0.3976), colony origin (P = 0.1244), and the interaction of gender and colony (P = 0.7093) did not significantly influence flight speed. Additionally, an electronic counting device was used to provide instantaneous flight speeds and allowed flight speed to be modeled during acceleration, cruising, and deceleration periods of flight. Mean (±SEM) flight speeds in 2004 were 20.64 (±2.21) cm s⁻¹ (n = 13) for males and 17.76 cm s⁻¹ (n = 1) for the single female flown, falling within the range of the 2002 values.     

Monitoring bird migration with a fixed-beam radar and a thermal-imaging camera

ABSTRACT.   Previous studies using thermal imaging cameras (TI) have used target size as an indicator of target altitude when radar was not available, but this approach may lead to errors if birds that differ greatly in size are actually flying at the same altitude. To overcome this potential difficulty and obtain more accurate measures of the flight altitudes and numbers of individual migrants, we have developed a technique that combines a vertically pointed stationary radar beam and a vertically pointed thermal imaging camera (VERTRAD/TI). The TI provides accurate counts of the birds passing through a fixed, circular sampling area in the TI display, and the radar provides accurate data on their flight altitudes. We analyzed samples of VERTRAD/TI video data collected during nocturnal fall migration in 2000 and 2003 and during the arrival of spring trans-Gulf migration during the daytime in 2003. We used a video peak store (VPS) to make time exposures of target tracks in the video record of the TI and developed criteria to distinguish birds, foraging bats, and insects based on characteristics of the tracks in the VPS images and the altitude of the targets. The TI worked equally well during daytime and nighttime observations and best when skies were clear, because thermal radiance from cloud heat often obscured targets. The VERTRAD/TI system, though costly, is a valuable tool for measuring accurate bird migration traffic rates (the number of birds crossing 1609.34 m [1 statute mile] of front per hour) for different altitudinal strata above 25 m. The technique can be used to estimate the potential risk of migrating birds colliding with man-made obstacles of various heights (e.g., communication and broadcast towers and wind turbines)—a subject of increasing importance to conservation biologists.