Molecular chaperones maximize the native state yield on biological times by driving substrates out of equilibrium

Chakrabarti, Shaon,Hyeon, Changbong,Ye, Xiang,Lorimer, George H.,Thirumalai, D. National Academy of Sciences 2017 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.114 No.51

<P><B>Significance</B></P><P>Molecular chaperones have evolved to assist the folding of proteins and RNA, thus avoiding the deleterious consequences of misfolding. Thus, it is expected that increasing chaperone concentrations should enhance the yield of native states. While this has been observed in GroEL-mediated protein folding, experiments on <I>Tetrahymena</I> ribozyme folding assisted by CYT-19 surprisingly show the opposite trend. Here, we reconcile these divergent experimental observations by developing a unified theory of chaperone-assisted protein and RNA folding. We show that these ATP-fueled machines drive their substrates out of equilibrium, maximizing the nonequilibrium native yield in a given time rather than the absolute yield or folding rate. The theory predicts that in vivo the number of chaperones is regulated to optimize their functions.</P><P>Molecular chaperones facilitate the folding of proteins and RNA in vivo. Under physiological conditions, the in vitro folding of <I>Tetrahymena</I> ribozyme by the RNA chaperone CYT-19 behaves paradoxically; increasing the chaperone concentration reduces the yield of native ribozymes. In contrast, the protein chaperone GroEL works as expected; the yield of the native substrate increases with chaperone concentration. The discrepant chaperone-assisted ribozyme folding thus contradicts the expectation that it operates as an efficient annealing machine. To resolve this paradox, we propose a minimal stochastic model based on the Iterative Annealing Mechanism (IAM) that offers a unified description of chaperone-mediated folding of both proteins and RNA. Our theory provides a general relation that quantitatively predicts how the yield of native states depends on chaperone concentration. Although the absolute yield of native states decreases in the <I>Tetrahymena</I> ribozyme, the product of the folding rate and the steady-state native yield increases in both cases. By using energy from ATP hydrolysis, both CYT-19 and GroEL drive their substrate concentrations far out of equilibrium, thus maximizing the native yield in a short time. This also holds when the substrate concentration exceeds that of GroEL. Our findings satisfy the expectation that proteins and RNA be folded by chaperones on biologically relevant time scales, even if the final yield is lower than what equilibrium thermodynamics would dictate. The theory predicts that the quantity of chaperones in vivo has evolved to optimize native state production of the folded states of RNA and proteins in a given time.</P>

A dual path encoder-decoder network for placental vessel segmentation in fetoscopic surgery

YunBo Rao,Tian Tan,Shaoning Zeng,Zhanglin Chen,Jihong Sun 한국인터넷정보학회 2024 KSII Transactions on Internet and Information Syst Vol.18 No.1

A fetoscope is an optical endoscope, which is often applied in fetoscopic laser photocoagulation to treat twin-to-twin transfusion syndrome. In an operation, the clinician needs to observe the abnormal placental vessels through the endoscope, so as to guide the operation. However, low-quality imaging and narrow field of view of the fetoscope increase the difficulty of the operation. Introducing an accurate placental vessel segmentation of fetoscopic images can assist the fetoscopic laser photocoagulation and help identify the abnormal vessels. This study proposes a method to solve the above problems. A novel encoder-decoder network with a dual-path structure is proposed to segment the placental vessels in fetoscopic images. In particular, we introduce a channel attention mechanism and a continuous convolution structure to obtain multi-scale features with their weights. Moreover, a switching connection is inserted between the corresponding blocks of the two paths to strengthen their relationship. According to the results of a set of blood vessel segmentation experiments conducted on a public fetoscopic image dataset, our method has achieved higher scores than the current mainstream segmentation methods, raising the dice similarity coefficient, intersection over union, and pixel accuracy by 5.80%, 8.39% and 0.62%, respectively.

Evaluate and Predict Concentration of Particulate Matter (PM10) Using Machine Learning Approach

M. F. Mridha,Md. Abdul Hamid,Shaon Hossain Sani,Akramkhan Rony,Seungmin Oh,Jinsul Kim 한국디지털콘텐츠학회 2019 The Journal of Contents Computing Vol.1 No.1

Particulate matter (PM10) is a general term used for a mixture of solid particles and liquid droplets. PM10 is the most significant air pollutant associated with diseases and death compared to other measured criteria pollutants. In this paper, we have focused on PM10 concentration at Dhaka city in Bangladesh. With the help of our proposed predictive model to predict hourly criteria air pollutant concentrations. The ambient air quality data were collected from October 2016 to March 2019. We have used Artificial Neural Network (ANN) to fill the missing value of our Dataset. And we have used Ensemble model (StackNet) to predict PM10. The average correlation coefficient (R) and root-mean square error (RMSE) values when comparing predictions and measurements were 0.94 and 26.14, respectively.

Cultivable Bacterial Community Analysis of Dairy Activated Sludge for Value Addition to Dairy Wastewater

Tethi Biswas,Debasmita Chatterjee,Sinchini Barman,Sinchini Barman,Amrita Chakraborty,Nabanita Halder,Srimoyee Banerjee,Shaon Ray Chaudhuri 한국미생물·생명공학회 2019 한국미생물·생명공학회지 Vol.47 No.4

Analysis of bacterial communities based on their 16S rDNA sequences revealed the predominance of Proteobacteria (Aeromonas sp., Acinetobacter sp. and Thaueraamino aromatica sp.) and uncultured bacterium in activated sludge from the effluent treatment plant (ETP) of Mother Dairy, Calcutta (India). Each isolate was used for bioremediation of dairy wastewater with simultaneous conversion of nitrogenous pollutants into ammonia. A consortium developed using seven of these isolates and three Bacillus strains from different environmental origins could reduce 93% nitrate with simultaneous production of ammonia (626 μg/100 ml) within 20 h in non-aerated, immobilized conditions as compared to 82% nitrate reduction producing 2.4 μg/100 ml ammonia in 96 h with extensive aeration in a conventional ETP. The treated ammonia- rich effluent could be used instead of freshwater and fertilizer during cultivation of mung bean with 1.6-fold increase in grain yield. The ETP with the surrounding agricultural land makes this process a zero liquid discharge technology for using the biofertilizer generated. In addition, the process requires minimal energy supporting sustained environmental health. This method is thus proposed as an alternative approach for small-scale dairy ETPs.

Cultivable Bacterial Community Analysis of Dairy Activated Sludge for Value Addition to Dairy Wastewater

Biswas, Tethi,Chatterjee, Debasmita,Barman, Sinchini,Chakraborty, Amrita,Halder, Nabanita,Banerjee, Srimoyee,Chaudhuri, Shaon Ray The Korean Society for Microbiology and Biotechnol 2019 한국미생물·생명공학회지 Vol.47 No.4

Analysis of bacterial communities based on their 16S rDNA sequences revealed the predominance of Proteobacteria (Aeromonas sp., Acinetobacter sp. and Thaueraamino aromatica sp.) and uncultured bacterium in activated sludge from the effluent treatment plant (ETP) of Mother Dairy, Calcutta (India). Each isolate was used for bioremediation of dairy wastewater with simultaneous conversion of nitrogenous pollutants into ammonia. A consortium developed using seven of these isolates and three Bacillus strains from different environmental origins could reduce 93% nitrate with simultaneous production of ammonia (626 ㎍/100 ml) within 20 h in non-aerated, immobilized conditions as compared to 82% nitrate reduction producing 2.4 ㎍/100 ml ammonia in 96 h with extensive aeration in a conventional ETP. The treated ammonia-rich effluent could be used instead of freshwater and fertilizer during cultivation of mung bean with 1.6-fold increase in grain yield. The ETP with the surrounding agricultural land makes this process a zero liquid discharge technology for using the biofertilizer generated. In addition, the process requires minimal energy supporting sustained environmental health. This method is thus proposed as an alternative approach for small-scale dairy ETPs.

Understanding Bacterial Biofilm Stimulation Using Different Methods - a Criterion for Selecting Epiphytes by Plants

Bhushan, Shashi,Gogoi, Mandakini,Bora, Abhispa,Ghosh, Sourav,Barman, Sinchini,Biswas, Tethi,Sudarshan, Mathummal,Thakur, Ashoke Ranjan,Mukherjee, Indranil,Dey, Subrata Kumar,Chaudhuri, Shaon Ray The Korean Society for Microbiology and Biotechnol 2019 한국미생물·생명공학회지 Vol.47 No.2

Earlier studies by our group revealed that gallic acid in phytochemicals stimulated biofilm production in epiphytes, while caffeic acid in phytochemicals inhibited biofilm production in non-epiphytes. It is well documented that antimicrobial secretion by some epiphytic bacteria inhibits non-epiphytic bacterial growth on leaf surfaces. These selection criteria help plants choose their microbial inhabitants. Calcium and iron in phytochemicals also stimulate biofilm formation and thus, may be selection criteria adopted by plants with respect to their native epiphytic population. Furthermore, the processing of leaves during phytochemical extraction impacts the composition of the extract, and therefore its ability to affect bacterial biofilm formation. Computation of the Hurst exponent using biofilm thickness data obtained from the Ellipsometry of Brewster Angle Microscopic (BAM) images is an efficient tool for understanding the impact of phytochemicals on epiphytic and non-epiphytic populations when compared to fluorescent microscopy, scanning electron microscopy, and staining techniques. To the best of our knowledge, this is the first report that uses the Hurst exponent to elucidate the mechanism involved in plant microbe interaction.

Understanding Bacterial Biofilm Stimulation Using Different Methods – a Criterion for Selecting Epiphytes by Plants

Shashi Bhushan,Mandakini Gogoi,Abhispa Bora,Sourav Ghosh,Sinchini Barman,Tethi Biswas,Mathummal Sudarshan,Ashoke Ranjan Thakur,Indranil Mukherjee,Subrata Kumar Dey,Shaon Ray Chaudhuri 한국미생물·생명공학회 2019 한국미생물·생명공학회지 Vol.47 No.2

Earlier studies by our group revealed that gallic acid in phytochemicals stimulated biofilm production in epiphytes, while caffeic acid in phytochemicals inhibited biofilm production in non-epiphytes. It is well documented that antimicrobial secretion by some epiphytic bacteria inhibits non-epiphytic bacterial growth on leaf surfaces. These selection criteria help plants choose their microbial inhabitants. Calcium and iron in phytochemicals also stimulate biofilm formation and thus, may be selection criteria adopted by plants with respect to their native epiphytic population. Furthermore, the processing of leaves during phytochemical extraction impacts the composition of the extract, and therefore its ability to affect bacterial biofilm formation. Computation of the Hurst exponent using biofilm thickness data obtained from the Ellipsometry of Brewster Angle Microscopic (BAM) images is an efficient tool for understanding the impact of phytochemicals on epiphytic and non-epiphytic populations when compared to fluorescent microscopy, scanning electron microscopy, and staining techniques. To the best of our knowledge, this is the first report that uses the Hurst exponent to elucidate the mechanism involved in plant microbe interaction.