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3D in vitro tumor models have recently been investigated as they can recapitulate key features in the tumor microenvironment. Reconstruction of a biomimetic scaffold is critical in these models. However, most current methods focus on modulating local properties, e.g. micro- and nano-scaled topographies, without capturing the global millimeter or intermediate mesoscale features. Here we introduced a method for modulating the collagen I-based extracellular matrix structure by disruption of fibrillogenesis and the gelation process through mechanical agitation. With this method, we generated collagen scaffolds that are thickened and wavy at a larger scale while featuring global softness. Thickened collagen patches were interconnected with loose collagen networks, highly resembling collagen architecture in the tumor stroma. This thickened collagen network promoted tumor cell dissemination. In addition, this novel modified scaffold triggered differences in morphology and migratory behaviors of tumor cells. Altogether, our method for altered collagen architecture paves new ways for studying in detail cell behavior in physiologically relevant biological processes. STATEMENT OF SIGNIFICANCE: Tumor progression usually involves chronic tissue damage and repair processes. Hallmarks of tumors are highly overlapped with those of wound healing. To mimic the tumor milieu, collagen-based scaffolds are widely used. These scaffolds focus on modulating microscale topographies and mechanics, lacking global architecture similarity compared with in vivo architecture. Here we introduced one type of thick collagen bundles that mimics ECM architecture in human skin scars. These thickened collagen bundles are long and wavy while featuring global softness. This collagen architecture imposes fewer steric restraints and promotes tumor cell dissemination. Our findings demonstrate a distinct picture of cell behaviors and intercellular interactions, highlighting the importance of collagen architecture and spatial heterogeneity of the tumor microenvironment.

Ductal carcinoma in situ (DCIS) is a precancerous stage breast cancer, where abnormal cells are contained within the duct, but have not invaded into the surrounding tissue. However, only 30–40% of ...

Archival storage in DNA is one of the most challenging themes in rapidly growing information technology. In addition, its practical applications are more difficult due to complicated data analysis,...

Tumor emboli – aggregates of tumor cell within vessels – pose a clinical challenge as they are associated with increased metastasis and tumor recurrence. When growing within a vessel, tumor emboli are subject to a unique mechanical constraint provided by the tubular geometry of the vessel. Current models of tumor emboli use unconstrained multicellular tumor spheroids, which neglect this mechanical interplay. Here, we modelled a lymphatic vessel as a 200 μm-diameter channel in either a stiff or soft, bioinert agarose matrix, and we modelled colon or breast cancer tumor emboli with aggregates of HCT116 or SUM149PT cells, respectively. The stiff vessel model constrained the tumor emboli to the cylindrical geometry, which led to continuous growth of the emboli, in contrast to the growth plateau that unconstrained spheroids exhibit. Emboli morphology in the soft vessel model, however, was dependent on the magnitude of mechanical mismatch between the vessel matrix and the cell aggregates. In general, when the elastic modulus of the vessel was greater than the emboli (Eves / Eemb > 1), the emboli were constrained to grow within the vessel geometry, and when the elastic modulus of the vessel was less than the emboli (0 < Eves / Eemb < 1), the emboli bulged into the matrix. Inhibitors of myosin-related force generation decreased the elastic modulus and/or increased the stress relaxation of the tumor cell aggregates, effectively increasing the mechanical mismatch. The increased mechanical mismatch after drug treatment was correlated with increased confinement of tumor emboli growth along the vessel, which may translate to increased tumor burden due to the increased tumor volume within the diffusion distance of nutrients and oxygen.INSIGHT BOXThe growth of tumor emboli—aggregates of tumor cells within vessels—is associated with aggressive cancer progression and metastasis. Models of their growth have not taken into account their biomechanical context, where radial expansion is constrained, but lengthwise expansion is free in the vessel. Here, we modelled the vessel geometry with a cylindrical microchannel in a hydrogel. In contrast to unconstrained or fully embedded aggregates, vessel-like constraint promotes growth of emboli in our model. The growth advantage is increased when the matrix is stiffened or actomyosin contractility weakened, both of which effectively increase the magnitude of mechanical constraint. This study sheds light on increased tumor burden in vessel-based growth and indicates a need to study tumor progression in similar environments.

Sickle cell disease (SCD) is a genetic condition that causes abnormalities in hemoglobin mechanics. Those affected are at high risk of vaso-occlusive crisis (VOC), which can induce life-threatening symptoms. The development of measurements related to vaso-occlusion facilitates the diagnosis of the patient's disease state. To complement existing readouts, we design a microfluidic-informatics analytical system with varied confined geometries for the quantification of sickle cell disease occlusion. We detect an increase in physical occlusion events in the most severe hemoglobin SS group. We use bioinformatics and modeling to quantify the

Stromal collagen is upregulated surrounding a solid tumor and presents as dense, thick, linearized, and aligned bundles. The collagen bundles are continually remodeled during tumor progression, and their orientation with respect to the tumor boundary has been correlated with invasive state. Currently, reconstituted-collagen gels are the standard in vitro tumor cell-extracellular matrix interaction model. The reticular, dense, and isotropic nanofiber (~900 nm-diameter, on average) gels do not, however, recapitulate the in vivo structural features of collagen bundling and alignment. Here, we present a rapid and simple method to fabricate bundles of collagen type I, whose average thickness may be varied between about 4 μm and 9 μm dependent upon diluent temperature and ionic strength. The durability and versatility of the collagen bundles was demonstrated with their incorporation into two in vitro models where the thickness and alignment of the collagen bundles resembled various in vivo arrangements. First, collagen bundles aligned by a microfluidic device elicited cancer cell contact guidance and enhanced their directional migration. Second, the presence of the collagen bundles in a bio-inert agarose hydrogel was shown to provide a route for cancer cell outgrowth. The unique structural features of the collagen bundles advance the physiological relevance of in vitro collagen-based tumor models for accurately capturing tumor cell-extracellular matrix interactions. Statement of significance Collagen in the tumor microenvironment is upregulated and remodeled into dense, thick, and aligned bundles that are associated with invasive state. Current collagen-based in vitro models are based on reticular, isotropic nanofiber gels that do not fully recapitulate in vivo tumor stromal collagen. We present a simple and robust method of rapidly fabricating cell-scale collagen bundles that better mimic the remodeled collagen surrounding a tumor. Interacting with the bundles, cancer cells exhibited drastically different phenotypic behaviors, compared to nanofiber scaffolds. This work reveals the importance of microscale architecture of in vitro tumor models. The collagen bundles provide physiologically relevant collagen morphologies that may be easily incorporated into existing models of tumor cell-extracellular matrix interactions.

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International audience; Plant immunity is activated upon pathogen perception and often affects growth and yield when it is constitutively active. How plants fine-tune immune homeostasis in their natural habitats remains elusive. Here, we discover a conserved immune suppression network in cereals that orchestrates immune homeostasis, centering on a Ca2+-sensor, RESISTANCE OF RICE TO DISEASES1 (ROD1). ROD1 promotes reactive oxygen species (ROS) scavenging by stimulating catalase activity, and its protein stability is regulated by ubiquitination. ROD1 disruption confers resistance to multiple pathogens, whereas a natural ROD1 allele prevalent in indica rice with agroecology-specific distribution enhances resistance without yield penalty. The fungal effector AvrPiz-t structurally mimics ROD1 and activates the same ROS-scavenging cascade to suppress host immunity and promote virulence. We thus reveal a molecular framework adopted by both host and pathogen that integrates Ca2+ sensing and ROS homeostasis to suppress plant immunity, suggesting a principle for breeding disease-resistant, high-yield crops.

Drug treatment against liver cancer has limited efficacy due to heterogeneous response among liver cancer subtypes. In addition, the functional biophysical phenotypes which arise from this heterogeneity and contribute to aggressive invasive behavior remain poorly understood. This study interrogated how heterogeneity in liver cancer subtypes contributes to differences in invasive phenotypes and drug response. Utilizing histological analysis, quantitative 2D invasion metrics, reconstituted 3D hydrogels, and bioinformatics, our study linked cytoskeletal dynamics to differential invasion profiles and drug resistance in liver cancer subtypes. We investigated cytoskeletal regulation in 2D and 3D culture environments using two liver cancer cell lines, SNU-475 and HepG2, chosen for their distinct cytoskeletal features and invasion profiles. For SNU-475 cells, a model for aggressive liver cancer, many cytoskeletal inhibitors abrogated 2D migration but only some suppressed 3D migration. For HepG2 cells, cytoskeletal inhibition did not significantly affect 3D migration but did affect proliferative capabilities and spheroid core growth. This study highlights cytoskeleton driven phenotypic variation, their consequences and coexistence within the same tumor, as well as efficacy of targeting biophysical phenotypes that may be masked in traditional screens against tumor growth.

The bacterial genus Staphylococcus comprises a large group of pathogenic and nonpathogenic species associated with an array of host species. Staphylococci are differentiated into coagulase-positive or coagulase-negative groups based on the capacity to promote clotting of plasma, a phenotype historically associated with the ability to cause disease. However, the genetic basis of this important diagnostic and pathogenic trait across the genus has not been examined to date. Here, we selected 54 representative staphylococcal species and subspecies to examine coagulation of plasma derived from six representative host species. In total, 13 staphylococcal species mediated coagulation of plasma from at least one host species including one previously identified as coagulase negative (Staphylococcus condimenti). Comparative genomic analysis revealed that coagulase activity correlated with the presence of a gene (vwb) encoding the von Willebrand binding protein (vWbp) whereas only the Staphylococcus aureus complex contained a gene encoding staphylocoagulase (Coa), the classical mediator of coagulation. Importantly, S. aureus retained vwb-dependent coagulase activity in an S. aureus strain deleted for coa whereas deletion of vwb in Staphylococcus pseudintermedius resulted in loss of coagulase activity. Whole-genome-based phylogenetic reconstruction of the Staphylococcus genus revealed that the vwb gene has been acquired on at least four different occasions during the evolution of the Staphylococcus genus followed by allelic diversification via mutation and recombination. Allelic variants of vWbp from selected coagulase-positive staphylococci mediated coagulation in a host-dependent manner indicative of host-adaptive evolution. Taken together, we have determined the genetic and evolutionary basis of staphylococcal coagulation, revealing vWbp to be its archetypal determinant. IMPORTANCE The ability of some species of staphylococci to promote coagulation of plasma is a key pathogenic and diagnostic trait. Here, we provide a comprehensive analysis of the coagulase positivity of the staphylococci and its evolutionary genetic basis. We demonstrate that the von Willebrand binding protein rather than staphylocoagulase is the archetypal coagulation factor of the staphylococci and that the vwb gene has been acquired several times independently during the evolution of the staphylococci. Subsequently, vwb has undergone adaptive diversification to facilitate host-specific functionality. Our findings provide important insights into the evolution of pathogenicity among the staphylococci and the genetic basis for a defining diagnostic phenotype.

With the increasing of extreme weathers, cities, especially the small- and medium-sized urban rivers with the protection areas less than 200 square hectares, are experiencing significantly more flood disasters worldwide. Heavy snowfalls and rainfalls can rapidly overflow these rivers and cause floods due to the their unique geographic locations and fast runoff and confluence. Therefore, it is particularly important to accurately predict the short-to-medium term water levels of such rivers for reducing and avoiding urban floods. In the present work, a particle swarm optimization (PSO)-support vector machine (SVM) water level predication model was constructed by combining PSO and SVM and trained with the meteorological data of Wuhan, China, and the water level data of Yangtze River. The PSO-SVM model is able to lower mean square error (MSE) 70.47% and increase coefficient of determination (R2) 7.02% of the prediction results, as compared with SVM model alone. The highly accurate PSO-SVM model can be used to predict river water level real-time using the hourly weather and water level data, which thereby provides quantitative data support for urban flood control, construction management of water projects, improving response efficiency and reducing safety risks.

Plant immunity is activated upon pathogen perception and often affects growth and yield when it is constitutively active. How plants fine-tune immune homeostasis in their natural habitats remains elusive. Here, we discover a conserved immune suppression network in cereals that orchestrates immune homeostasis, centering on a Ca

Ductal carcinoma

The leaf of Nelumbo nucifera (Family Nelumbonaceae) has been widely included in the diet of Chinese people from the time of the Min Dynasty. In this study, a randomized double-blind trial (n = 60) was performed to determine the effects of extract from sun dried Nelumbo nucifera leaves (NnEx), which included quercetin-3-glucuronide (Q3GA) as the main components, in overweight patients (24 kg/m2

With more and more large-scale scientific facilities are built, more and more HPC requirements are needed in IHEP. RDMA is a technology that allows servers in a network to exchange data in main memory without involving the processor, cache or operating system of either server, which can provide high bandwidth and low latency. There are two RDMA technologies which were InfiniBand and a relative newcomer called RoCE – RDMA over Converged Ethernet. This paper introduces the RoCE technology, we research and compare the performance of both IB and RoCE in IHEP data center, and we also evaluate the application scenarios of RoCE which can support our future technology selection in HEPS. In the end, we present our future plan.

The bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo), belonging to Xanthomonas sp., causes one of the most destructive vascular diseases in rice worldwide, particularly in Asia and Africa. To better understand Xoo pathogenesis, we performed genome sequencing of the Korea race 1 strain DY89031 (J18) and analyzed the phylogenetic tree of 63 Xoo strains. We found that the rich diversity of evolutionary features is likely associated with the rice cultivation regions. Further, virulence effector proteins secreted by the type III secretion system (T3SS) of Xoo showed pathogenesis divergence. The genome of DY89031 shows a remarkable difference from that of the widely prevailed Philippines race 6 strain PXO99A, which is avirulent to rice Xa21, a well-known disease resistance (R) gene that can be broken down by DY89031. Interestingly, plant inoculation experiments with the PXO99A transformants expressing the DY89031 genes enabled us to identify additional TAL (transcription activator-like) and non-TAL effectors that may support DY89031-specific virulence. Characterization of DY89031 genome and identification of new effectors will facilitate the investigation of the rice-Xoo interaction and new mechanisms involved.

Pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) in plants enable them to respond to pathogens by activating the production of defence metabolites that orchestrate immune responses

Ductal carcinoma in situ (DCIS) is a pre-cancerous stage breast cancer, where abnormal cells are contained within the duct, but have not invaded into the surrounding tissue. However, only 30-40% of DCIS cases are likely to progress into an invasive ductal carcinoma (IDC), while the remainder are innocuous. Since little is known about what contributes to the transition from DCIS to IDC, clinicians and patients tend to opt for treatment, leading to concerns of overdiagnosis and overtreatment. In vitro models are currently being used to probe how DCIS transitions into IDC, but many models do not take into consideration the macroscopic tissue architecture and the biomechanical properties of the microenvironment. Here, we developed an organotypic mammary duct model by molding a channel within a collagen matrix and lining it with a basement membrane. By adjusting the concentration of collagen, we effectively modulated the stiffness and morphological properties of the matrix and examined how an assortment of breast cells responded to changing density and stiffness of the matrix. We first validated the model using two established, phenotypically divergent breast cancer cell lines by demonstrating the ability of the cells to either invade (MDA-MB-231) or cluster (MCF7). We then examined how cells of the isogenic MCF10 series—spanning the range from healthy to aggressive—behaved within our model and observed distinct characteristics of breast cancer progression such as hyperplasia and invasion, in response to collagen concentration. Our results show that the model can recapitulate different stages of breast cancer progression and that the MCF10 series is adaptable to physiologically relevant in vitro studies, demonstrating the potential of both the model and cell lines to elucidate key factors that may contribute to understanding the transition from DCIS to IDC.IMPACT STATEMENTThe success of early preventative measures for breast cancer has left patients susceptible to overdiagnosis and overtreatment. Limited knowledge of factors driving an invasive transition has inspired the development of in vitro models that accurately capture this phenomenon. However, current models tend to neglect the macroscopic architecture and biomechanical properties of the mammary duct. Here, we introduce an organotypic model that recapitulates the cylindrical geometry of the tissue and the altered stroma seen in tumor microenvironments. Our model was able to capture distinct features associated with breast cancer progression, demonstrating its potential to uncover novel insights into disease progression.

Stromal collagen surrounding a solid tumor tends to present as dense, thick bundles. The collagen bundles are remodeled during tumor progression: first tangential to the tumor boundary (indicating growth) and later perpendicular to the tumor boundary (indicating likely metastasis). Current reconstituted-collagenin vitrotumor models are unable to recapitulate thein vivostructural features of collagen bundling and alignment. Here, we present a rapid yet simple procedure to fabricate collagen bundles with an average thickness of 9 μm, compared to the reticular dense collagen nanofiber (∼900 nm-diameter, on average) prepared using common protocols. The versatility of the collagen bundles was demonstrated with their incorporation into twoin vitromodels where the thickness and alignment of the collagen bundles resembled the variousin vivoarrangements. First, collagen bundles aligned by a microfluidic device elicited cancer cell contact guidance and enhanced their directional migration. Second, the presence of the collagen bundles in a bio-inert agarose hydrogel was shown to provide a highway for cancer cell invasion. The unique structural features of the collagen bundles advance the physiological relevance ofin vitrocollagen-based tumor models for accurately capturing cancer cell-stroma interactions.

Unique elastomeric rotary actuators based on pneumatically driven peristaltic motion are demonstrated. Using silicone-based wheels, these motors enable a new class of soft locomotion not found in nature, which is capable of withstanding impact, traversing irregular terrain, and operating in water. For soft robotics, this work marks progress toward providing torque without bending actuators.

Biophysical properties of the extracellular matrix (ECM) are known to play a significant role in cell behavior. To gain a better understanding of the effects of the biophysical microenvironment on cell behavior, the practical challenge is longitudinally monitoring behavioral variations within a population to make statistically powerful assessments. Population-level measurements mask heterogeneity in cell responses, and large-scale individual cell measurements are often performed in a one-time, snapshot manner after removing cells from their matrix. Here we present an easy and low-cost method for large-scale, longitudinal studies of heterogeneous cell behavior in 3D hydrogel matrices. Using a platform we term “the drop-patterning chip”, thousands of cells were simultaneously transferred from microwell arrays and fully embedded, only using the force of gravity, in precise patterns in 3D collagen I or Matrigel. This method allows for throughputs approaching 2D patterning methods that lack phenotypic information on cell-matrix interactions, and does not rely on special equipment and cell treatments that may result in a proximal stiff surface. With a large and yet well-organized group of cells captured in 3D matrices, we demonstrated the capability of locating selected individual cells and monitoring cell division, migration, and proliferation for multiple days.

Cancer heterogeneity includes cancer cell genetic heterogeneity and heterogeneity in the tumor microenvironment (TME)—both stromal cells and extracellular matrix (ECM). Determining which combinations of the vast array of possibly interacting heterogeneities drive tumor progression presents a major multi-disciplinary challenge in cancer research. To make effective treatment decisions this challenge must be addressed. The practical challenge is assessing cellular heterogeneity in a statistically powerful way with respect to targeted TME characteristics. Here we present a simple, but extensible, and low-cost method for conducting mid- to high-throughput and long-term studies of heterogeneous cell responses to various biomechanical stimuli in 3D models mimicking the biomechanical properties of the ECM. Using a platform we term “the drop-patterning chip” thousands of cells are simultaneously transferred from microwells and fully embedded, only using the force of gravity, in precise patterns in 3D. This method allows for throughputs approaching flow-through methods, which lack phenotypic information on cell-matrix interactions, and does not rely on expensive or harsh patterning forces, which often times also result in a proximal stiff surface.

A new strategy based on enantioselective acylation properties of relatively unknown penicillin G acylase from Alcaligenes faecalis has been developed for the production of pharmacologically interesting enantiomerically pure d -phenylalanine. In order to get high reaction rate and enantioselectivity, two key factors (pH and temperature) and eight different acyl donors were optimized, and the optimal acylation reaction was carried out at pH 10, 35 °C, using phenylacetamide as the acyl donor. This enantioselective acylating method is also illustrated by the effective production of five different p-substituted phenylalanine derivatives in enantiopure.

A facile pretreatment method was developed to obtain high specific activity of PGA from recombinant E. coli cells for preparing immobilized enzyme with high activity, which coupled selective extraction of PGA with butyl acetate and adsorption of butyl acetate with active carbon. Butyl acetate (5%, v/v) led to a 92.0% release of PGA, the specific activity of which in the extracting solution was twice that obtained by sonication. The negative effect on PGA immobilization due to residual butyl acetate in the extracting solution was removed by adding active carbon (8%, w/v). The final PGA solution meets requirement for industrial immobilization while eliminating the high cost of a traditional purification process. This pretreatment method developed in this work is simple, highly performing and cost-effective. It has been employed in a 10 tons/year immobilized PGA production line.

For the traditional steganographic method of Jsteg, the emmbedment of secret message is completed by dividing cover-image into nonoverlapping blocks of 8×8 pixels, discrete cosine transform (DCT) transforming, and using the standard 8×8 quantization table to quantize. In this paper, a novel steganographic method based on the JPEG quantization table modification is presented. Instead of dividing cover-image into 8×8 blocks, nonoverlapping blocks of 16×16 pixels is used. Both theoretical anlysis and experiment results show that the new methods has larger steganography capacity and better stego-image quality, compared with the method of Jsteg and Chang’s.

In this work, fatty acid ethyl esters were produced from the lipase-catalyzed irreversible transesterification reaction between Jatropha oil and diethyl carbonate (DEC). Response surface methodology (RSM) based on central composite design (CCD) was used to optimize the five important reaction variables for the irreversible transesterification of Jatropha oil in a solvent-free system. The optimum conditions for the transesterification were a reaction time of 13.3 h, a temperature of 44.5 °C, a lipase amount of 13.7% (w/w), a DEC to Jatropha oil molar ratio of 3.75:1 and no need for adding water. The optimal predicted yield of fatty acid esters was 97.7% and the actual value was 96.2%. The results showed that the RSM based on CCD was adaptable for a fatty acid esters yield study for the current transesterification system.

Papain was purified from spray-dried Carica papaya latex using aqueous two-phase system (ATPS). Then it was recovered from PEG phase by in situ immobilization or preparing cross-linked enzyme aggregates (CLEAs). The Plackett-Burman design and the central composite design (CCD) together with the response surface methodology (RSM) were used to optimize the APTS processes. The highly purified papain (96–100%) was achieved under the optimized conditions: 40% (w/w) 15 mg/ml enzyme solution, 14.33–17.65% (w/w) PEG 6000, 14.27–14.42% (w/w) NaH2PO4/K2HPO4 and pH 5.77–6.30 at 20°C. An in situ enzyme immobilization approach, carried out by directly dispersing aminated supports and chitosan beads into the PEG phase, was investigated to recover papain, in which a high immobilization yield (>90%) and activity recovery (>40%) was obtained. Moreover, CLEAs were successfully used in recovering papain from PEG phase with a hydrolytic activity hundreds times higher than the carrier-bound immobilized papain.

An esterase, Sso2518, from Sulfolobus solfataricus P2 was over-expressed in E. coli. and characterized after purification. The maximum activity was at pH 7.5 and 50 degrees C. The half life of Sso2518 was about 30 min at 85 degrees C and the enzyme was activated by Cu(2+). The catalytic triad of Sso2518 was comprised of residues Ser151, Asp176, and His328. Sso2518 showed the highest activity with p-nitrophenyl caproate (C6) and could also hydrolyze olive oil. Under native conditions, Sso2518 consists of 125 kDa homotrimers.

An efficient and compact red laser at 458 nm is generated by intracavity frequency doubling of a continuous wave (CW) laser operation of a diode pumped Nd:LuVO4 laser at 916 nm under the condition of suppression the higher gain transition near 1064 nm. With 30 W diode pump power and a frequency doubling crystal LBO, as high as 9.6 W of CW output power at 458 nm is achieved, corresponding to an optical-to-optical conversion efficiency of 32.0% and the output power stability in 8 hours is better than 2.35%. To the best of our knowledge, this it the highest conversion efficiency of watt-level laser at 458 nm generated by intracavity frequency doubling of a diode pumped Nd:LuVO4 laser at 916 nm.