RESUMEN

Chemical structure extraction from documents remains a hard problem because of both false positive identification of structures during segmentation and errors in the predicted structures. Current approaches rely on handcrafted rules and subroutines that perform reasonably well generally but still routinely encounter situations where recognition rates are not yet satisfactory and systematic improvement is challenging. Complications impacting the performance of current approaches include the diversity in visual styles used by various software to render structures, the frequent use of ad hoc annotations, and other challenges related to image quality, including resolution and noise. We present end-to-end deep learning solutions for both segmenting molecular structures from documents and predicting chemical structures from the segmented images. This deep-learning-based approach does not require any handcrafted features, is learned directly from data, and is robust against variations in image quality and style. Using the deep learning approach described herein, we show that it is possible to perform well on both segmentation and prediction of low-resolution images containing moderately sized molecules found in journal articles and patents.

Asunto(s)

RESUMEN

Tight regulation of microtubule (MT) dynamics is essential for proper chromosome movement during mitosis. Here we show, using mammalian cells, that structure-specific recognition protein 1 (SSRP1) is a novel regulator of MT dynamics. SSRP1 colocalizes with the spindle and midbody MTs, and associates with MTs both in vitro and in vivo. Purified SSRP1 facilitates tubulin polymerization and MT bundling in vitro. Knockdown of SSRP1 inhibits the growth of MTs and leads to disorganized spindle structures, reduction of K-fibers and midbody fibers, disrupted chromosome movement, and attenuated cytokinesis in vivo. These results demonstrate that SSRP1 is crucial for MT growth and spindle assembly during mitosis.

Asunto(s)

RESUMEN

Label-free imaging mass spectrometry is utilized the first time to study lipid-lipid interactions in a model membrane system. Ternary lipid mixtures of cholesterol (CH), sphingomyelin (SM), and phosphatidylcholine (PC) on supported Langmuir-Blodgett films are investigated as a mimic of the cellular membrane. The unique chemical specificity and imaging capability allow identification and localization of each lipid molecule in the membranes. The SM and PC in each ternary mixture vary in their acyl chain saturation with both, either, or neither one double bonded at the same position of their acyl chain. For the ternary mixtures with SM and PC both saturated or unsaturated, all the lipids are evenly distributed in the molecule-specific images. However, domain structures were observed for the two mixtures with either SM or PC unsaturated. In both films, the saturated lipid, whether it is SM or PC, colocalized with CH while the unsaturated lipid was excluded from the CH domains. These results strongly suggest that acyl chain saturation, rather than the specific interactions between SM and CH, is the dominating factor for SM colocalization with CH in the raft areas of the cellular membranes.

Asunto(s)

RESUMEN

The location of each lipid in a palmitoyloleoylphosphatidylcholine/18:0 sphingomyelin/cholesterol monolayer system is laterally resolved using imaging time-of-flight secondary ion mass spectrometry (TOF-SIMS) without the necessity of adding fluorescent labels. This system of coexisting immiscible liquid phases shows cholesterol domains with sizes and shapes comparable to those in the fluorescence microscopy literature. The results show that SM localizes with cholesterol and that palmitoyloleoylphosphatidylcholine is excluded. Moreover, the segregation is not complete, and there is a small amount of both phospholipids distributed throughout.

Asunto(s)

RESUMEN

There is an increased interest in how lipids interact with each other, especially in the lateral separation of lipids into coexisting liquid phases as this is believed to be an attribute of raft formation in cell membranes. ToF-SIMS has shown itself to be an excellent tool for investigating cellular and model membrane systems and will be perhaps the most powerful one for investigating raft formation. Results from our laboratory show the capability of ToF-SIMS at identifying unequivocally the content of coexisting liquid lipid phases. Using supported lipid monolayers we find that the inclusion of dipalmitoylphosphatidylethanolamine (DPPE) to a homogeneous dipalmitoylphosphatidylcholine (DPPC)/cholesterol phase results in the formation of cholesterol-rich domains [A.G. Sostarecz, C.M. McQuaw, A.G. Ewing, N. Winograd, J. Am. Chem. Soc. 126 (2004) 13882]. Also, for DPPE/cholesterol systems a single homogeneous DPPE/cholesterol phase is formed at ~50 mol% cholesterol, whereas DPPC/cholesterol systems form a single phase at 30 mol% cholesterol [C.M. McQuaw, A. Sostarecz, L. Zheng, A.G. Ewing, N. Winograd, Langmuir 21 (2005) 807]. Currently we are exploring the incorporation of sphingomyelin into phospholipid-cholesterol mixtures in an effort to gain a better understanding of its role in raft formation.

RESUMEN

To better understand the influence of cholesterol (CH) on dipalmitoylphosphatidylethanolamine (DPPE), Langmuir-Blodgett (LB) model membranes of DPPE with varying amounts of cholesterol were imaged by time-of-flight secondary ion mass spectrometry (ToF-SIMS) and atomic force microscopy (AFM). Cholesterol has a condensing effect on DPPE that at low cholesterol concentrations results in lateral heterogeneity of the LB monolayer. At 4:1 DPPE/CH, islands of DPPE/CH phase exist with a connected DPPE phase. As the concentration of cholesterol is increased, the percolation threshold is crossed and the DPPE/CH phase islands connect to separate the DPPE phase (2:1 DPPE/CH). Finally, at 50 mol % cholesterol a single homogeneous DPPE/CH phase LB monolayer exists. ToF-SIMS of the DPPE/CH phase provides a lower ion signal for the characteristic lipid fragments and substrate apparently owing to the higher molecular density induced by cholesterol. AFM data indicate that the DPPE/CH phase is lower in height than the DPPE phase. As phosphatidylethanolamine is predominant in the inner lipid leaflet of cellular membranes, this work has implications for the understanding of cholesterol domains in the inner leaflet of cells.

Asunto(s)

RESUMEN

Bombardment with C60+ primary ions of monolayer and multilayer barium arachidate Langmuir-Blodgett (LB) films is investigated. The behavior of cluster versus atomic (Ga+) bombardment is monitored by the barium-cationized arachidate ion (mass-to-charge ratio (m/z) 449) and a characteristic fragment ion (m/z 209) using 1-, 7-, and 15-layer model systems. The removal rate of material from the films is shown to be on the order of several hundred molecules per C60 impact, a value 100-fold larger than Ga+ impact. The enhancement in secondary ion yield is also shown to be larger for the 15-layer film (400x) than for the monolayer film (100x). Moreover, most of the increase in yield is shown to be associated with ejection of sputtered species rather than an increase in ionization probability. High yields associated with cluster bombardment are also shown to be amenable to depth profiling experiments in which the two ions can be monitored as the film is being removed. In this modality, chemical damage associated with bombardment is removed before it can accumulate on the surface. Due to the similarity of fatty acid LB films to cellular membranes, these results suggest that C60+ primary ion beams may improve the prospects for TOF-SIMS studies of biological systems.

Asunto(s)

RESUMEN

Coexisting liquid phases of model membrane systems are chemically identified using imaging time-of-flight secondary ion mass spectrometry (TOF-SIMS). The systems studied were Langmuir-Blodgett (LB) model membranes of cholesterol (CH) with two different phospholipids, one a major component in the outer plasma membrane bilayer leaflet (dipalmitoylphosphatidylcholine (PC)) and the other a major component in the inner leaflet (dipalmitoylphosphatidylethanolamine (PE)). Binary mixtures of CH with each of the phospholipids were investigated, as well as a ternary system. A single homogeneous phase is evident for PC/CH, whereas both systems containing PE show lateral heterogeneity with phospholipid-rich and CH-rich regions. The interaction between CH and the two phospholipids differs due to the disparity between the phospholipid headgroups. Imaging TOF-SIMS offers a novel opportunity to chemically identify and differentiate the specific membrane locations of CH and phospholipid in membrane regions without the use of fluorescent dyes. This unique imaging method has been used to demonstrate the formation of micrometer-size CH domains in phosphatidylethanolamine-rich systems and is further evidence suggesting that CH may facilitate transport and signaling across the two leaflets of the plasma membrane.

Asunto(s)

RESUMEN

Understanding the influence of molecular environment on phospholipids is important in time-of-flight secondary ion mass spectrometry (TOF-SIMS) studies of complex systems such as cellular membranes. Varying the molecular environment of model membrane Langmuir-Blodgett (LB) films is shown to affect the TOF-SIMS signal of the phospholipids in the films. The molecular environment of a LB film of dipalmitoylphosphatidylcholine (DPPC) is changed by varying the film density, varying the sample substrate, and the addition of cholesterol. An increase in film density results in a decrease in the headgroup fragment ion signal at a mass-to-charge ratio of 184 (phosphocholine). Varying the sample substrate increases the secondary ion yield of phosphocholine as does the addition of proton-donating molecules such as cholesterol to the DPPC LB film. Switching from a model system of DPPC and cholesterol to one of dipalmitoylphosphatidylethanolamine (DPPE) and cholesterol demonstrates the ability of cholesterol to also mask the phospholipid headgroup ion signal. TOF-SIMS studies of simplistic phospholipid LB model membrane systems demonstrate the potential use of these systems in TOF-SIMS analysis of cells.

Asunto(s)