OPEN leaf: an open-source cloud-based phenotyping system for tracking dynamic changes at leaf-specific resolution in Arabidopsis

The first draft of the Arabidopsis genome was released more than 20 years ago and despite intensive molecular research, more than 30% of Arabidopsis genes remained uncharacterized or without an assigned function. This is in part due to gene redundancy within gene families or the essential nature of genes, where their deletion results in lethality (i.e., the dark genome). High-throughput plant phenotyping (HTPP) offers an automated and unbiased approach to characterize subtle or transient phenotypes resulting from gene redundancy or inducible gene silencing; however, access to commercial HTPP platforms remains limited. Here we describe the design and implementation of OPEN leaf, an open-source phenotyping system with cloud connectivity and remote bilateral communication to facilitate data collection, sharing and processing. OPEN leaf, coupled with our SMART imaging processing pipeline was able to consistently document and quantify dynamic changes at the whole rosette level and leaf-specific resolution when plants experienced changes in nutrient availability. Our data also demonstrate that VIS sensors remain underutilized and can be used in high-throughput screens to identify and characterize previously unidentified phenotypes in a leaf-specific time-dependent manner. Moreover, the modular and open-source design of OPEN leaf allows seamless integration of additional sensors based on users and experimental needs.

Dimension-agnostic and granularity-based spatially variable gene identification using BSP

Identifying spatially variable genes (SVGs) is critical in linking molecular cell functions with tissue phenotypes. Spatially resolved transcriptomics captures cellular-level gene expression with corresponding spatial coordinates in two or three dimensions and can be used to infer SVGs effectively. However, current computational methods may not achieve reliable results and often cannot handle three-dimensional spatial transcriptomic data. Here we introduce BSP (big-small patch), a non-parametric model by comparing gene expression pattens at two spatial granularities to identify SVGs from two or three-dimensional spatial transcriptomics data in a fast and robust manner. This method has been extensively tested in simulations, demonstrating superior accuracy, robustness, and high efficiency. BSP is further validated by substantiated biological discoveries in cancer, neural science, rheumatoid arthritis, and kidney studies with various types of spatial transcriptomics technologies.

Dimension-agnostic and granularity-based spatially variable gene identification

Identifying spatially variable genes (SVGs) is critical in linking molecular cell functions with tissue phenotypes. Spatially resolved transcriptomics captures cellular-level gene expression with corresponding spatial coordinates in two or three dimensions and can be used to infer SVGs effectively. However, current computational methods may not achieve reliable results and often cannot handle three-dimensional spatial transcriptomic data. Here we introduce BSP (big-small patch), a spatial granularity-guided and non-parametric model to identify SVGs from two or three-dimensional spatial transcriptomics data in a fast and robust manner. This new method has been extensively tested in simulations, demonstrating superior accuracy, robustness, and high efficiency. BSP is further validated by substantiated biological discoveries in cancer, neural science, rheumatoid arthritis, and kidney studies with various types of spatial transcriptomics technologies.

FASTAptameR 2.0: A web tool for combinatorial sequence selections

Combinatorial selections are powerful strategies for identifying biopolymers with specific biological, biomedical, or chemical characteristics. Unfortunately, most available software tools for high-throughput sequencing analysis have high entrance barriers for many users because they require extensive programming expertise. FASTAptameR 2.0 is an R-based reimplementation of FASTAptamer designed to minimize this barrier while maintaining the ability to answer complex sequence-level and population-level questions. This open-source toolkit features a user-friendly web tool, interactive graphics, up to 100 times faster clustering, an expanded module set, and an extensive user guide. FASTAptameR 2.0 accepts diverse input polymer types and can be applied to any sequence-encoded selection.

A self-attention based message passing neural network for predicting molecular lipophilicity and aqueous solubility

Efficient and accurate prediction of molecular properties, such as lipophilicity and solubility, is highly desirable for rational compound design in chemical and pharmaceutical industries. To this end, we build and apply a graph-neural-network framework called self-attention-based message-passing neural network (SAMPN) to study the relationship between chemical properties and structures in an interpretable way. The main advantages of SAMPN are that it directly uses chemical graphs and breaks the black-box mold of many machine/deep learning methods. Specifically, its attention mechanism indicates the degree to which each atom of the molecule contributes to the property of interest, and these results are easily visualized. Further, SAMPN outperforms random forests and the deep learning framework MPN from Deepchem. In addition, another formulation of SAMPN (Multi-SAMPN) can simultaneously predict multiple chemical properties with higher accuracy and efficiency than other models that predict one specific chemical property. Moreover, SAMPN can generate chemically visible and interpretable results, which can help researchers discover new pharmaceuticals and materials. The source code of the SAMPN prediction pipeline is freely available at Github (https://github.com/tbwxmu/SAMPN).

Effects of cholecystokinin on cytosolic calcium in pancreatic duct segments and ductal cells

Although the gastrointestinal peptide cholecystokinin (CCK) has been shown to increase bicarbonate and water secretion and potentiate the effects of secretin on pancreatic ducts, CCK receptors have not been identified on pancreatic ductal epithelium. The effects of CCK octapeptide (CCK-8) on cytosolic calcium were evaluated on microscopically dissected rat pancreatic duct segments and single rat duct cells from the established ARIP cell line. By use of fluorescence microscopy in fura-2-loaded duct segments or single cells, intracellular calcium concentration was measured in response to CCK-8 (4 x 10(-12)-4 x 10(-8) M). CCK-8 significantly increased cytosolic calcium up to 50-fold over baseline. The greatest increase occurred with the highest concentration of CCK-8 (4 x 10(-8) M). Oscillations were observed in experiments performed in buffer containing 0.68 mM physiological calcium. In another series of experiments performed in the presence of ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid to deplete extracellular calcium, CCK-8 treatment still resulted in significant increases in cytosolic calcium; however, oscillations were abolished. Since cytosolic calcium increased in the absence of extracellular calcium, the initial calcium rise most likely was from cytosolic stores. Our findings of CCK-8-stimulated increases in cytosolic calcium in microdissected pancreatic ducts suggest the presence of CCK receptors, a characteristic that was not lost in cultured pancreatic ductal cells. In addition, in ARIP cells, the CCK-8-induced increase in cytosolic calcium was abolished by pretreatment with the selective CCK-B receptor antagonist L-365,260 but not by the CCK-A receptor antagonist L-364,718.

Effects of gastrin and difluoromethylornithine on growth of human colon cancer

The effect of difluoromethylornithine (DFMO), a specific inhibitor of ornithine decarboxylase activity, was evaluated in vivo and in vitro on the growth of a gastrin-sensitive human colon carcinoma (WiDr). In vivo, mice bearing the tumor treated with pentagastrin had larger tumors with higher ornithine decarboxylase activity and polyamine content (P < 0.05) than mice not treated with pentagastrin. Difluoromethylornithine treatment significantly decreased ornithine decarboxylase in both the pentagastrin-treated and the untreated animals; however, DFMO had no effect on tumor volume, weight, protein, or DNA content. In cell culture, gastrin treatment increased WiDr cell number and [3H]thymidine incorporation in the presence or absence of serum. In serum-free conditions, however, gastrin stimulated cell growth without concomitantly increasing ODC activity. DFMO, on the other hand, decreased both ODC activity and growth. These studies suggest that the trophic effect of gastrin on WiDr human colon cancer is independent of ODC activity. Since gastrin treatment increased ODC activity in vivo, gastrin may interact in vitro with other factors present in serum that can alter ODC activity.

Trophic effects of unsulfated cholecystokinin on mouse pancreas and human pancreatic cancer

The effect of unsulfated cholecystokinin on pancreatic growth was evaluated in two experimental models in vivo and in vitro. Mice were injected with sulfated cholecystokinin (CCKs) or unsulfated cholecystokinin (CCKu) (10 or 20 micrograms/kg) or vehicle twice daily for 15 days. Animals were then killed and pancreatic weights, protein, amylase, and DNA content were evaluated. In vitro, growth was evaluated by DNA synthesis and viable cell counts. MIA PaCa-2 and BxPC-3 human pancreatic cancer cells were treated with CCKs or CCKu (10(-12) to 10(-9) M) for 48 or 72 h in the presence of [3H]thymidine to evaluate DNA synthesis. Viable cell counts were performed on both cell lines grown in the presence or absence of unsulfated CCK (10(-12) to 10(-9) M) for 96 h. Pancreatic weight, protein, amylase, and DNA were significantly increased in animals treated with either CCKs or CCKu. However, pancreatic weight, protein, and amylase were significantly higher in mice treated with CCKs compared to CCKu (p less than 0.005). DNA content and index of hyperplasia were the same whether mice were treated with CCKs or CCKu. CCKu was as potent a stimulus for DNA synthesis as CCKs in MIA PaCa-2 and BxPC-3 cells. Finally, CCKu increased cell counts in both pancreatic cancer cell lines. These data suggest that the mechanisms responsible for CCK-induced growth of normal pancreas and pancreatic cancer may differ from those that regulate secretion.

Effects of fat and fiber on human colon cancer xenografted to athymic nude mice

The effects of unsaturated fat and fiber (cellulose) on the growth of human colon cancer explanted to athymic nude mice was evaluated. Eighty-seven male nude mice bearing xenografts of human HT29 or WiDr colon cancer were divided into three groups of equal weight and tumor volume. Each group was fed one of three diets: normal fat/no fiber (N/N), high fat/no fiber (H/N) or high fat/high fiber (H/H). To equalize caloric intake, animals in the H/N group received 4 g of food per day and the other animals were fed 5 g of food per day. At sacrifice tumor volume and weight was recorded, and tumors were analyzed for protein and DNA content and ornithine decarboxylase activity. Tumor volume, weight, and protein were greater in the H/N group compared to the N/N group for both colon cancer cell lines. Tumor DNA content was greater in the HT29 H/N group compared to the N/N group (P less than 0.05) and tumor ornithine decarboxylase activity in the WiDr H/N group was greater than the N/N animals (P less than 0.002). The tumor growth-promoting effects of the high unsaturated fat diet were attenuated by the addition of fiber. Animal weight was higher in the H/N group compared to the N/N and H/H groups. This study suggested that a high-fat diet stimulated and fiber decreased the growth of human colon cancer explanted to athymic nude mice. The growth-promoting effects of a high-fat diet in colorectal cancer may be due in part to a circulating trophic factor since these tumors were remote from the large intestine.

Effects of cholecystokinin on cytosolic calcium in human pancreatic cancer cells

Cholecystokinin (CCK) has been shown to increase cytosolic calcium and stimulate enzyme release from pancreatic acinar cells and a rat acinar cell line, AR42J. CCK is also trophic to normal pancreas and pancreatic cancer; however, the cellular mechanisms which regulate CCK-stimulated growth are unknown. The effect of CCK on intracellular calcium was evaluated in four human pancreatic cancer cell lines known to grow in response to CCK but not secrete enzymes (SW-1990, MIA PaCa-2, BXPC-3 and PANC-1) and a rat acinar cell line (AR42J) shown to secrete enzymes but not grow with CCK. By using single cell fluorescence microscopy in fura-2 loaded cells, intracellular calcium [Ca2+]i was measured. After obtaining baseline fluorescent cell images, synthetic CCK-octapeptide (CCK8) was added to the cells and images of cell fluorescence captured. [Ca2+]i of the rat acinar cells increased (603%) over the baseline within the first minute after the addition of CCK (4.10(-13) M to 4.10(-10) M) in 77% of cells tested. In contrast [Ca2+]i failed to significantly change in the human cancer cells treated with CCK. To further localize the defect in hormone signal transduction in cancer cells, cells were suspended in low calcium media and the plasma membranes were selectively permeabilized with digitonin. Media free calcium concentration was continuously monitored by fura-2 fluorescence. Addition of inositol 1,4,5-trisphosphate (IP3) resulted in a marked increase in medium calcium concentration indicating IP3 was capable of releasing calcium from intracellular stores in both the AR42J rat acinar cell line and in the human pancreas cancer cell lines. In conclusion, CCK does not increase cytosolic calcium in human pancreatic cancer cells in contrast to rat acinar cells although all contain IP3-sensitive intracellular Ca2+ pools. Our results suggest that growth promoting and secretory effects of CCK on pancreatic cells may occur via two independent signalling pathways.

CCK stimulates growth of six human pancreatic cancer cell lines in serum-free medium

The growth responses of six human pancreatic cancer cell lines (SW-1990, PANC-1, MIA PaCa-2, BxPC-3, RWP-2 and CAPAN-2) to cholecystokinin (CCK) were evaluated in serum-free medium (SFM). In each experiment cells were initially plated in media containing fetal calf serum (FCS) grown for 48-72 h, and then washed with saline. Cells were incubated for an additional 72 to 96 h in medium devoid of FCS in the absence (control) or presence of synthetic CCK analogue (Thr4,Nle7)CCK9 (10(-13) to 10(-9) M), or CCK8 (10(-12) to 10(-9) M), or CCK39 (10(-12) to 10(-9) M). Viable cell counts were performed with a hemocytometer. Growth of each cell line was stimulated in the presence of CCK in serum-free medium, although the magnitude of responses differed. The concentrations of (Thr4,Nle7)CCK9 which stimulated the greatest increase in cell counts as compared to controls for each cell line were: SW-1990, 39% (10(-12) M, P less than 0.05); PANC-1, 45% (10(-9) M, P less than 0.005); MIA PaCa-2, 42% (10(-12) M, P less than 0.005); BxPC-3, 32% (10(-13) M, P less than 0.05); RWP-2, 37% (10(-11) M, P less than 0.005). Maximal response to CCK8 occurred at the 10(-9) M dose for each cell line: MIA PaCa-2, 40% (P less than 0.025); PANC-1, 85% (P less than 0.001); RWP-2, 68% (P less than 0.001) and CAPAN-2, 52% (P less than 0.001). The maximal increase in cell count with CCK39 ranged from 44-74% and occurred with either 10(-11) or 10(-10) M. CCK8 in SFM also stimulated cell growth as well as or better than FCS alone in three out of four pancreatic cell lines.(ABSTRACT TRUNCATED AT 250 WORDS)