Decoupling global biases and local interactions between cell biological variables.

Analysis of coupled variables is a core concept of cell biological inference, with co-localization of two molecules as a proxy for protein interaction being a ubiquitous example. However, external effectors may influence the observed co-localization independently from the local interaction of two proteins. Such global bias, although biologically meaningful, is often neglected when interpreting co-localization. Here, we describe DeBias, a computational method to quantify and decouple global bias from local interactions between variables by modeling the observed co-localization as the cumulative contribution of a global and a local component. We showcase four applications of DeBias in different areas of cell biology, and demonstrate that the global bias encapsulates fundamental mechanistic insight into cellular behavior. The DeBias software package is freely accessible online via a web-server at https://debias.biohpc.swmed.edu.

Vimentin Intermediate Filaments Template Microtubule Networks to Enhance Persistence in Cell Polarity and Directed Migration.

Increased expression of vimentin intermediate filaments (VIFs) enhances directed cell migration, but the mechanism behind VIFs' effect on motility is not understood. VIFs interact with microtubules, whose organization contributes to polarity maintenance in migrating cells. Here, we characterize the dynamic coordination of VIF and microtubule networks in wounded monolayers of retinal pigment epithelial cells. By genome editing, we fluorescently labeled endogenous vimentin and α-tubulin, and we developed computational image analysis to delineate architecture and interactions of the two networks. Our results show that VIFs assemble an ultrastructural copy of the previously polarized microtubule network. Because the VIF network is long-lived compared to the microtubule network, VIFs template future microtubule growth along previous microtubule tracks, thus providing a feedback mechanism that maintains cell polarity. VIF knockdown prevents cells from polarizing and migrating properly during wound healing. We suggest that VIFs' templating function establishes a memory in microtubule organization that enhances persistence in cell polarization in general and migration in particular.

Protective effect of heme oxygenase-1 on Wistar rats with heart failure through the inhibition of inflammation and amelioration of intestinal microcirculation.

BACKGROUND: Myocardial infarction (MI) has likely contributed to the increased prevalence of heart failure (HF). As a result of reduced cardiac function, splanchnic blood flow decreases, causing ischemia in villi and damage to the intestinal barrier. The induction of heme oxygenase-1 (HO-1) could prevent, or lessen the effects of stress and inflammation. Thus, the effect and mechanism thereof of HO-1 on the intestines of rats with HF was investigated. METHODS: Male Wistar rats with heart failure through ligation of the left coronary artery were identified with an left ventricular ejection fraction of < 45% through echocardiography and then divided into various experimental groups based on the type of peritoneal injection they received [MI: saline; MI + Cobalt protoporphyrin (CoPP): CoPP solution; and MI + Tin mesoporphyrin IX dichloride (SnMP): SnMP solution]. The control group was comprised of rats without coronary ligation. Echocardiography was performed before ligation for a baseline and eight weeks after ligation in order to evaluate the cardiac function of the rats. The bacterial translocation (BT) incidence, mesenteric microcirculation, amount of endotoxins in the vein serum, ileum levels of HO-1, carbon oxide (CO), nitric oxide (NO), interleukin (IL)-10, tumour necrosis factor-α (TNF-α), and the ileum morphology were determined eight weeks after the operation. RESULTS: The rats receiving MI + CoPP injections exhibited a recovery in cardiac function, an amelioration of mesenteric microcirculation and change in morphology, a lower BT incidence, a reduction in serum and ileac NO and TNF-α levels, and an elevation in ileac HO-1, CO, and interleukin-10 (IL-10) levels compared to the MI group (P < 0.05). The rats that received the MI + SnMP injections exhibited results inverse to the MI (P < 0.05) group. CONCLUSIONS: HO-1 exerted a protective effect on the intestines of rats with HF by inhibiting the inflammation and amelioration of microcirculation through the CO pathway. This protective effect could be independent from the recovery of cardiac function.

[Contribution of different processes in wetland soil N2O production in different restoration phases of the Yellow River estuary, China].

By using the method of time-space mutual substitution, the contribution of different processes in wetland soil N2O production was studied in the un-restoration wetland (R0), restoration wetland since 2007 (R2007) and restoration wetland since 2002 (R2002) of the Yellow River estuary to evaluate the effectiveness of the restoration projects. Results showed wetland soil total N2O production had a significant difference in different restoration phases, but the N2O release was the main source. The N2O production in restoration wetland was higher than that in un-restoration wetland. The N2O production wss mainly due to the nitrification and nitrifier denitrification processes, while the denitrification process had great weakening effects on N2O production, which was closely related to the physical and chemical properties of wetland soils in different restoration phases. The non-biological processes made greater contributions to N2O production and these were mainly due to that iron was reductive, while the Yellow River estuary was an area of highly active iron. Although N2O production in wetland soils was the results of biological processes combined with non-biological processes in different restoration phases, non-biological processes had larger influences and should be paid a special attention. There were different influences on wetland soil processes generating N2O between temperature and water content, indicating responses of soil microbial activities to temperature and water content were different. In addition, the N2O production contents ranged from 0.37 +/- 0.08 nmol x (kg x h) (-1) to 9.75 +/- 7.64 nmol x (kg x h) (-1) in marshes of the Yellow River estuary, which was slightly higher than those in the S. alterniflora wetland soils of the Min River estuary, but significantly lower than those in the C. malaccensis wetland soils of the Min River estuary, the grassland soils and the aerobic forest soils. We found that the long-term implements of ecological restoration project in the Yellow River estuary obviously promoted N2O production, so we should consider two factors of landscape restoration and weakening greenhouse gases in the next wetland restoration project.

Using multifocal plane microscopy to reveal novel trafficking processes in the recycling pathway.

A major outstanding issue in cell biology is the lack of understanding of the contribution of tubulovesicular transport carriers (TCs) to intracellular trafficking pathways within 3D cellular environments. This is primarily due to the challenges associated with the use of microscopy techniques to track these highly motile, small compartments. In the present study we have used multifocal plane microscopy with localized photoactivation to overcome these limitations. Using this approach, we have characterized individual components constituting the recycling pathway of the receptor FcRn. Specifically, several different pathways followed by TCs that intersect with larger, relatively static sorting endosomes have been defined. These pathways include a novel 'looping' process in which TCs leave and return to the same sorting endosome. Significantly, TCs with different itineraries can be identified by associations with distinct complements of Rab GTPases, APPL1 and SNX4. These studies provide a framework for further analyses of the recycling pathway.

[Spatial distribution characteristics of Fe and Mn contents in the new-born coastal marshes in the Yellow River estuary].

The spatial distribution characteristics of Fe and Mn contents in soils of nine different vegetation communities, located in the new-born marshes of the northern Yellow River estuary, were studied in May 2009. The results showed that the horizontal distributions of Fe and Mn contents showed an increasing tendency from Sparganiaceae-Potentilla supina marsh to bare flat. The vertical distribution characteristics of Fe and Mn contents in different marsh soils fluctuated significantly with the vegetation succession. The soil parent materials determined the Fe, Mn contents in the new-born marshes, and seawater, vegetations and soil fine particle also had important influences on their contents. Further analysis showed that Fe contents had significant positive correlation with Mn contents (P < 0.01). Fe, Mn contents also showed significant correlations with silt, clay, TN, NO3(-) -N and organic matter (P < 0.05), indicating that Fe and Mn had close relationships with nitrogen, and the contents of soil fine particles and organic matter were the dominant factors affecting the distribution of Fe and Mn in soils. In addition, the Fe contents ranged from 16.49 g x kg(-1) to 33.11 g x kg(-1) and the average was 22.54 g x kg(-1), which was close to the Fe contents in the tidal marshes of north Jiangsu, the Loess Plateau and the China soil background value, but slightly lower than those in the marshes of the Yangtse River estuary, the mangrove swamps and inland lake wetland. The Mn contents ranged from 305.87 mg x kg(-1) to 711.39 mg x kg(-1) and the average was 451.09 mg x kg(-1), which was lower than the Mn contents in the Loess Plateau and the China soil background value. Hydrology and Water Resources Survey Bureau of the Yellow River Estuary, Dongying 257091, China)

Analyses of the recycling receptor, FcRn, in live cells reveal novel pathways for lysosomal delivery.

Lysosomes play a central role in the degradation of proteins and other macromolecules. The mechanisms by which receptors are transferred to lysosomes for constitutive degradation are poorly understood. We have analyzed the processes that lead to the lysosomal delivery of the Fc receptor, FcRn. These studies provide support for a novel pathway for receptor delivery. Specifically, unlike other receptors that enter intraluminal vesicles in late endosomes, FcRn is transferred from the limiting membrane of such endosomes to lysosomes, and is rapidly internalized into the lysosomal lumen. By contrast, LAMP-1 persists on the limiting membrane. Receptor transfer is mediated by tubular extensions from late endosomes to lysosomes, or by interactions of the two participating organelles in kiss-and-linger-like processes, whereas full fusion is rarely observed. The persistence of FcRn on the late endosomal limiting membrane, together with selective transfer to lysosomes, allows this receptor to undergo recycling or degradation. Consequently, late endosomes have functional plasticity, consistent with the presence of the Rab5 GTPase in discrete domains on these compartments.

Targeting the neonatal fc receptor for antigen delivery using engineered fc fragments.

The development of approaches for Ag delivery to the appropriate subcellular compartments of APCs and the optimization of Ag persistence are both of central relevance for the induction of protective immunity or tolerance. The expression of the neonatal Fc receptor, FcRn, in APCs and its localization to the endosomal system suggest that it might serve as a target for Ag delivery using engineered Fc fragment-epitope fusions. The impact of FcRn binding characteristics of an Fc fragment on in vivo persistence allows this property to also be modulated. We have therefore generated recombinant Fc (mouse IgG1-derived) fusions containing the N-terminal epitope of myelin basic protein that is associated with experimental autoimmune encephalomyelitis in H-2(u) mice. The Fc fragments have distinct binding properties for FcRn that result in differences in intracellular trafficking and in vivo half-lives, allowing the impact of these characteristics on CD4(+) T cell responses to be evaluated. To dissect the relative roles of FcRn and the "classical" FcgammaRs in Ag delivery, analogous aglycosylated Fc-MBP fusions have been generated. We show that engineered Fc fragments with increased affinities for FcRn at pH 6.0-7.4 are more effective in delivering Ag to FcRn-expressing APCs in vitro relative to their lower affinity counterparts. However, higher affinity of the FcRn-Fc interaction at near neutral pH results in decreased in vivo persistence. The trade-off between improved FcRn targeting efficiency and lower half-life becomes apparent during analyses of T cell proliferative responses in mice, particularly when Fc-MBP fusions with both FcRn and FcgammaR binding activity are used.

[Land use/land cover change and their ecological effect in small watershed on gully region of the Loess Plateau].

Based on land use data of 1994 and 2004 in Wangdonggou watershed, through developing dynamic model of LUCC and indices of regional ecological environment, this paper quantified the characteristics of LUCC and its ecological effect. The results showed that from 1994 to 2004, farmland decreased while grassland and orchard increased greatly, forest and nonproductive land changed little. The speed of individual land use changes was in the order of grassland > orchard > nonproductive land > farmland > forest land. As to the spatial change, a total of 11 major land use change types were identified, among which the change from farmland to others and form others to forest were the most important land use change. The gravitational center of farmland and orchard moved to the northwest tableland, while those of forest land and grassland moved to the southeast gully land. From 1994 to 2004, owing to LUCC, the ecological environment was improved, but the type of land use and their change took effect differently with both improving and decreasing effect. The decrease of farmland affected ecological environment negatively, while the increase of forest and grassland and orchard improved the ecological environment and its ecosystem service values. Those improving the ecological environment were from other types of land use to forest and orchard, while those worsening the ecological environment were from forest to others and from farmland to nonproductive land.

Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy.

The intracellular events on the recycling pathway that lead from sorting endosomes to exocytosis at the plasma membrane are central to cellular function. However, despite intensive study, these processes are poorly characterized in spatial and dynamic terms. The primary reason for this is that, to date, it has not been possible to visualize rapidly moving intracellular compartments in three dimensions in cells. Here, we use a recently developed imaging setup in which multiple planes can be simultaneously imaged within the cell in conjunction with visualization of the plasma membrane plane by using total internal reflection fluorescence microscopy. This has allowed us to track and characterize intracellular events on the recycling pathway that lead to exocytosis of the MHC Class I-related receptor, FcRn. We observe both direct delivery of tubular and vesicular transport containers (TCs) from sorting endosomes to exocytic sites at the plasma membrane, and indirect pathways in which TCs that are not in proximity to sorting endosomes undergo exocytosis. TCs can also interact with different sorting endosomes before exocytosis. Our data provide insight into the intracellular events that precede exocytic fusion.