Expression of fatty acid synthesis genes and fatty acid accumulation in haematococcus pluvialis under different stressors

<p>Abstract</p> <p>Background</p> <p>Biofuel has been the focus of intensive global research over the past few years. The development of 4^thgeneration biofuel production (algae-to-biofuels) based on metabolic engineering of algae is still in its infancy, one of the main barriers is our lacking of understanding of microalgal growth, metabolism and biofuel production. Although fatty acid (FA) biosynthesis pathway genes have been all cloned and biosynthesis pathway was built up in some higher plants, the molecular mechanism for its regulation in microalgae is far away from elucidation.</p> <p>Results</p> <p>We cloned main key genes for FA biosynthesis in <it>Haematococcus pluvialis</it>, a green microalga as a potential biodiesel feedstock, and investigated the correlations between their expression alternation and FA composition and content detected by GC-MS under different stress treatments, such as nitrogen depletion, salinity, high or low temperature. Our results showed that high temperature, high salinity, and nitrogen depletion treatments played significant roles in promoting microalgal FA synthesis, while FA qualities were not changed much. Correlation analysis showed that acyl carrier protein (ACP), 3-ketoacyl-ACP-synthase (KAS), and acyl-ACP thioesterase (FATA) gene expression had significant correlations with monounsaturated FA (MUFA) synthesis and polyunsaturated FA (PUFA) synthesis.</p> <p>Conclusions</p> <p>We proposed that ACP, KAS, and FATA in <it>H. pluvialis </it>may play an important role in FA synthesis and may be rate limiting genes, which probably could be modified for the further study of metabolic engineering to improve microalgal biofuel quality and production.</p

A Robotic Visual Grasping Design: Rethinking Convolution Neural Network with High-Resolutions

High-resolution representations are important for vision-based robotic grasping problems. Existing works generally encode the input images into low-resolution representations via sub-networks and then recover high-resolution representations. This will lose spatial information, and errors introduced by the decoder will be more serious when multiple types of objects are considered or objects are far away from the camera. To address these issues, we revisit the design paradigm of CNN for robotic perception tasks. We demonstrate that using parallel branches as opposed to serial stacked convolutional layers will be a more powerful design for robotic visual grasping tasks. In particular, guidelines of neural network design are provided for robotic perception tasks, e.g., high-resolution representation and lightweight design, which respond to the challenges in different manipulation scenarios. We then develop a novel grasping visual architecture referred to as HRG-Net, a parallel-branch structure that always maintains a high-resolution representation and repeatedly exchanges information across resolutions. Extensive experiments validate that these two designs can effectively enhance the accuracy of visual-based grasping and accelerate network training. We show a series of comparative experiments in real physical environments at Youtube: https://youtu.be/Jhlsp-xzHFY

Sign language video anonymization

Deaf signers who wish to communicate in their native language frequently share videos on the Web. However, videos cannot preserve privacy—as is often desirable for discussion of sensitive topics—since both hands and face convey critical linguistic information and therefore cannot be obscured without degrading communication. Deaf signers have expressed interest in video anonymization that would preserve linguistic content. However, attempts to develop such technology have thus far shown limited success. We are developing a new method for such anonymization, with input from ASL signers. We modify a motion-based image animation model to generate high-resolution videos with the signer identity changed, but with preservation of linguistically significant motions and facial expressions. An asymmetric encoder-decoder structured image generator is used to generate the high-resolution target frame from the low-resolution source frame based on the optical flow and confidence map. We explicitly guide the model to attain clear generation of hands and face by using bounding boxes to improve the loss computation. FID and KID scores are used for evaluation of the realism of the generated frames. This technology shows great potential for practical applications to benefit deaf signers.Published versio

Cell separation using tilted-angle standing surface acoustic waves

Separation of cells is a critical process for studying cell properties, disease diagnostics, and therapeutics. Cell sorting by acoustic waves offers a means to separate cells on the basis of their size and physical properties in a label-free, contactless, and biocompatible manner. The separation sensitivity and efficiency of currently available acoustic-based approaches, however, are limited, thereby restricting their widespread application in research and health diagnostics. In this work, we introduce a unique configuration of tilted-angle standing surface acoustic waves (taSSAW), which are oriented at an optimally designed inclination to the flow direction in the microfluidic channel. We demonstrate that this design significantly improves the efficiency and sensitivity of acoustic separation techniques. To optimize our device design, we carried out systematic simulations of cell trajectories, matching closely with experimental results. Using numerically optimized design of taSSAW, we successfully separated 2- and 10-µm-diameter polystyrene beads with a separation efficiency of ~99%, and separated 7.3- and 9.9-µm-polystyrene beads with an efficiency of ~97%. We illustrate that taSSAW is capable of effectively separating particles–cells of approximately the same size and density but different compressibility. Finally, we demonstrate the effectiveness of the present technique for biological–biomedical applications by sorting MCF-7 human breast cancer cells from nonmalignant leukocytes, while preserving the integrity of the separated cells. The method introduced here thus offers a unique route for separating circulating tumor cells, and for label-free cell separation with potential applications in biological research, disease diagnostics, and clinical practice.National Institutes of Health (U.S.) (Grant U01HL114476)National Institutes of Health (U.S.) (New Innovator Award 1DP2OD007209-01)National Science Foundation (U.S.). Materials Research Science and Engineering Centers (Program) (Grant DMR-0820404

Improving Negative-Prompt Inversion via Proximal Guidance

DDIM inversion has revealed the remarkable potential of real image editing within diffusion-based methods. However, the accuracy of DDIM reconstruction degrades as larger classifier-free guidance (CFG) scales being used for enhanced editing. Null-text inversion (NTI) optimizes null embeddings to align the reconstruction and inversion trajectories with larger CFG scales, enabling real image editing with cross-attention control. Negative-prompt inversion (NPI) further offers a training-free closed-form solution of NTI. However, it may introduce artifacts and is still constrained by DDIM reconstruction quality. To overcome these limitations, we propose Proximal Negative-Prompt Inversion (ProxNPI), extending the concepts of NTI and NPI. We enhance NPI with a regularization term and reconstruction guidance, which reduces artifacts while capitalizing on its training-free nature. Our method provides an efficient and straightforward approach, effectively addressing real image editing tasks with minimal computational overhead.Comment: Code at https://github.com/phymhan/prompt-to-promp

Acoustic separation of circulating tumor cells

Circulating tumor cells (CTCs) are important targets for cancer biology studies. To further elucidate the role of CTCs in cancer metastasis and prognosis, effective methods for isolating extremely rare tumor cells from peripheral blood must be developed. Acoustic-based methods, which are known to preserve the integrity, functionality, and viability of biological cells using label-free and contact-free sorting, have thus far not been successfully developed to isolate rare CTCs using clinical samples from cancer patients owing to technical constraints, insufficient throughput, and lack of long-term device stability. In this work, we demonstrate the development of an acoustic-based microfluidic device that is capable of high-throughput separation of CTCs from peripheral blood samples obtained from cancer patients. Our method uses tilted-angle standing surface acoustic waves. Parametric numerical simulations were performed to design optimum device geometry, tilt angle, and cell throughput that is more than 20 times higher than previously possible for such devices. We first validated the capability of this device by successfully separating low concentrations (~100 cells/mL) of a variety of cancer cells from cell culture lines from WBCs with a recovery rate better than 83%. We then demonstrated the isolation of CTCs in blood samples obtained from patients with breast cancer. Our acoustic-based separation method thus offers the potential to serve as an invaluable supplemental tool in cancer research, diagnostics, drug efficacy assessment, and therapeutics owing to its excellent biocompatibility, simple design, and label-free automated operation while offering the capability to isolate rare CTCs in a viable state.National Institutes of Health (U.S.) (Grant 1 R01 GM112048-01A1)National Institutes of Health (U.S.) (Grant 1R33EB019785-01)National Science Foundation (U.S.)Penn State Center for Nanoscale Science (Materials Research Science and Engineering Center Grant DMR-0820404)National Institutes of Health (U.S.) (Grant U01HL114476

Taurohyocholic acid acts as a potential predictor of the efficacy of tyrosine kinase inhibitors combined with programmed cell death-1 inhibitors in hepatocellular carcinoma

Background and aims: Tyrosine kinase inhibitors (TKIs) combined with programmed cell death protein-1 (PD-1) have significantly improved survival in patients with unresectable hepatocellular carcinoma (uHCC), but effective biomarkers to predict treatment efficacy are lacking. Peripheral blood bile acids (BAs) are associated with tumor response to therapy, but their roles in HCC remain unclear.Methods: This retrospective study included HCC patients who received first-line TKIs combined with PD-1 inhibitors treatment (combination therapy) in our clinical center from November 2020 to June 2022. The aim of this study was to analyze the changes in plasma BA profiles before and after treatment in both the responding group (Res group) and the non-responding group (Non-Res group). We aimed to explore the potential role of BAs in predicting the response to combination therapy in HCC patients.Results: Fifty-six patients with HCC who underwent combination therapy were included in this study, with 28 designated as responders (Res group) and 28 as non-responders (Non-Res group). There were differences in plasma BA concentrations between the two groups before systemic therapy. Plasma taurohyocholic acid (THCA) levels in the Res group were significantly lower than those in the Non-Res group. Patients with low levels of THCA exhibited superior median progression-free survival (7.6 vs. 4.9 months, p = 0.027) and median overall survival (23.7 vs. 11.6 months, p = 0.006) compared to those of patients with high levels of THCA.Conclusion: Peripheral blood BA metabolism is significantly correlated with combination therapy response and survival in patients with HCC. Our findings emphasize the potential of plasma BAs as biomarkers for predicting combination therapy outcomes and offering novel therapeutic targets for modulating responses to systemic cancer therapy

Transgenerational Epigenetic Inheritance Under Environmental Stress by Genome-Wide DNA Methylation Profiling in Cyanobacterium

Epigenetic modifications such as DNA methylation are well known as connected with many important biological processes. Rapid accumulating evidence shows environmental stress can generate particular defense epigenetic changes across generations in eukaryotes. This transgenerational epigenetic inheritance in animals and plants has gained interest over the last years. Cyanobacteria play very crucial role in the earth, and as the primary producer they can adapt to nearly all diverse environments. However, few knowledge about the genome wide epigenetic information such as methylome information in cyanobacteria, especially under any environment stress, was reported so far. In this study we profiled the genome-wide cytosine methylation from a model cyanobacterium Synechocystis sp. PCC 6803, and explored the possibility of transgenerational epigenetic process in this ancient single-celled prokaryote by comparing the DNA methylomes among normal nitrogen medium cultivation, nitrogen starvation for 72 h and nitrogen recovery for about 12 generations. Our results shows that DNA methylation patterns in nitrogen starvation and nitrogen recovery are much more similar with each other, significantly different from that of the normal nitrogen. This study reveals the difference in global DNA methylation pattern of cyanobacteria between normal and nutrient stress conditions and reports the evidence of transgenerational epigenetic process in cyanobacteria. The results of this study may contribute to a better understanding of epigenetic regulation in prokaryotic adaptation to and survive in the ever changing environment

Stable Expression of Antibiotic-Resistant Gene ble from Streptoalloteichus hindustanus in the Mitochondria of Chlamydomonas reinhardtii

The mitochondrial expression of exogenous antibiotic resistance genes has not been demonstrated successfully to date, which has limited the development of antibiotic resistance genes as selectable markers for mitochondrial site-directed transformation in Chlamydomonas reinhardtii. In this work, the plasmid pBSLPNCB was constructed by inserting the gene ble of Streptoalloteichus hindustanus (Sh ble), encoding a small (14-kilodalton) protective protein into the site between TERMINVREP-Left repeats and the cob gene in a fragment of mitochondrial DNA (mtDNA) of C. reinhardtii. The fusion DNA-construct, which contained TERMINVREP-Left, Sh ble, cob, and partial nd4 sequence, were introduced into the mitochondria of the respiratory deficient dum-1 mutant CC-2654 of C. reinhardtii by biolistic particle delivery system. A large number of transformants were obtained after eight weeks in the dark. Subsequent subculture of the transformants on the selection TAP media containing 3 ìg/mL Zeomycin for 12 months resulted in genetically modified transgenic algae MT-Bs. Sequencing and Southern analyses on the mitochondrial genome of the different MT-B lines revealed that Sh ble gene had been integrated into the mitochondrial genome of C. reinhardtii. Both Western blot, using the anti-BLE monoclonal antibody, and Zeomycin tolerance analysis confirmed the presence of BLE protein in the transgenic algal cells. It indicates that the Sh ble gene can be stably expressed in the mitochondria of C. reinhardtii