Publications by authors named "Biqing Liang"

12 Publications

  • Page 1 of 1

YPIBP: A repository for phosphoinositide-binding proteins in yeast.

Comput Struct Biotechnol J 2021 24;19:3692-3707. Epub 2021 Jun 24.

Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan.

Phosphoinositides (PIs) are a family of eight lipids consisting of phosphatidylinositol (PtdIns) and its seven phosphorylated forms. PIs have important regulatory functions in the cell including lipid signaling, protein transport, and membrane trafficking. Yeast has been recognized as a eukaryotic model system to study lipid-protein interactions. Hundreds of yeast PI-binding proteins have been identified, but this research knowledge remains scattered. Besides, the complete PI-binding spectrum and potential PI-binding domains have not been interlinked. No comprehensive databases are available to support the lipid-protein interaction research on phosphoinositides. Here we constructed the first knowledgebase of Yeast Phosphoinositide-Binding Proteins (YPIBP), a repository consisting of 679 PI-binding proteins collected from high-throughput proteome-array and lipid-array studies, QuickGO, and a rigorous literature mining. The YPIBP also contains protein domain information in categories of lipid-binding domains, lipid-related domains and other domains. The YPIBP provides search and browse modes along with two enrichment analyses (PI-binding enrichment analysis and domain enrichment analysis). An interactive visualization is given to summarize the PI-domain-protein interactome. Finally, three case studies were given to demonstrate the utility of YPIBP. The YPIBP knowledgebase consolidates the present knowledge and provides new insights of the PI-binding proteins by bringing comprehensive and in-depth interaction network of the PI-binding proteins. YPIBP is available at http://cosbi7.ee.ncku.edu.tw/YPIBP/.
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http://dx.doi.org/10.1016/j.csbj.2021.06.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8261538PMC
June 2021

Systematic Analysis of Phosphatidylinositol-5-phosphate-Interacting Proteins Using Yeast Proteome Microarrays.

Anal Chem 2021 01 11;93(2):868-877. Epub 2020 Dec 11.

Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan.

We used yeast proteome microarrays (∼5800 purified proteins) to conduct a high-throughput and systematic screening of PI5P-interacting proteins with PI5P-tagged fluorescent liposomal nanovesicles. Lissamine rhodamine B-dipalmitoyl phosphatidylethanol was incorporated into the liposome bilayer to provide the nanovesicles with fluorescence without any encapsulants, which not only made the liposome fabrication much easier without the need for purification but also improved the chip-probing quality. A special chip assay was washed very gently without the traditional spin-dry step. Forty-five PI5P-interacting proteins were identified in triplicate with this special chip assay. Subsequently, we used flow cytometry to validate these interactions, and a total of 41 PI5P-interacting proteins were confirmed. Enrichment analysis revealed that these proteins have significant functions associated with ribosome biogenesis, rRNA processing, ribosome binding, GTP binding, and hydrolase activity. Their component enrichment is located in the nucleolus. The InterPro domain analysis indicated that PI5P-interacting proteins are enriched in the P-loop containing nucleoside triphosphate hydrolases domain (P-loop). Additionally, using the MEME program, we identified a consensus motif (IVGPAGTGKSTLF) that contains the Walker A sequence, a well-known nucleotide-binding motif. Furthermore, using a quartz crystal microbalance, both the consensus motif and Walker A motif showed strong affinities to PI5P-containing liposomes but not to PI5P-deprived liposomes or PI-containing liposomes. Additionally, the glycine (G6) and lysine (K7) residues of the Walker A motif (-GPAGTGKS-) were found to be critical to the PI5P-binding ability. This study not only identified an additional set of PI5P-interacting proteins but also revealed the strong PI5P-binding affinity ( = 1.81 × 10 M) of the Walker A motif beyond the motif's nucleotide-binding characteristic.
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http://dx.doi.org/10.1021/acs.analchem.0c03463DOI Listing
January 2021

Systematic changes of bone hydroxyapatite along a charring temperature gradient: An integrative study with dissolution behavior.

Sci Total Environ 2021 Apr 3;766:142601. Epub 2020 Oct 3.

Material Science Group, National Synchrotron Radiation Research Center, Hsinchu, Taiwan.

The applicability of bone char as a long-term phosphorus nutrient source was assessed by integrating their mineral transformation and physicochemical properties with their dissolution behavior. We have explored synchrotron-based spectroscopic and imaging techniques (FTIR, XRD, and TXM) to investigate the physicochemical changes of bone and bone char along a charring temperature gradient (300-1200 °C) and used a lab incubation experiment to study their dissolution behaviors in solutions of different pH (4, 6, and 6.9). The thermal decomposition of inorganic carbonate (CO) and the loss of organic components rendered a crystallographic rearrangement (blueshift of the PO peak) and mineral transformation with increasing temperatures. The mineral transformation from B-type to AB- and A-type carbonate substitution occurred mainly at <700 °C, while the transformation from carbonated hydroxyapatite (CHAp) to more mineralogically and chemically stable HAp occurred at >800 °C. The loss of inorganic carbonate and the increase of structural OH with increasing temperatures explained the change of pH buffering capacity and increase of pH and their dissolution behaviors. The higher peak area ratios of phosphate to carbonate and phosphate to amide I band with increasing temperatures corroborated the higher stability and resistivity to acidic dissolution by bone chars made at higher temperatures. Our findings suggest that bone char made at low to intermediate temperatures can be a substantial source of phosphorus for soil fertility via waste management and recycling. The bone char made at 500 °C exhibited a high pH buffering capacity in acidic and near-neutral solutions. The 700 °C bone char was proposed as a suitable liming agent for raising the soil pH and abating soil acidity. Our study has underpinned the systematic changes of bone char and interlinked the charring effect with their dissolution behavior, providing a scientific base for understanding the applicability of different bone chars as suitable P-fertilizers.
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http://dx.doi.org/10.1016/j.scitotenv.2020.142601DOI Listing
April 2021

Black carbon enriches short-range-order ferrihydrite in Amazonian Dark Earth: Interplay mechanism and environmental implications.

Sci Total Environ 2020 Jul 24;725:138195. Epub 2020 Mar 24.

Life Science Group, National Synchrotron Radiation Center, Hsinchu, Taiwan; Department of Optics and Photonics, National Central University, Chung-Li, Taiwan; Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan. Electronic address:

Our study underpins the mechanism of organo-mineral interaction between black carbon (BC, biochar) and associated minerals in the historical BC-rich Amazonian Dark Earth (ADE) by using synchrotron-based microscopic (TXM), microspectroscopic (μFTIR) and spectroscopic (XAS and μ-diffraction) approaches. The BC-rich ADE contained over 100% more poorly crystalline minerals than the adjacent tropical soil. Linear combination fitting of k-spacing in the X-ray Absorption Spectra (XAS) revealed that ferrihydrite contributed to 81.1% of the Fe-minerals in BC. A small but distinct peak was observed at 5.7 Å in the extended X-ray absorption fine structure k oscillation of BC, revealing the presence of FeC (including Fe-O-C) covalent bonds. No FeC path was yielded by the XAS fitting when an obvious peak downshift of the first (FeFe) shell was observed, suggesting that the availability of inner-sphere FeC complexation was limited to the BC surface and interphase region. The main minerals for organo-mineral complexation were short-range-order (SRO) ferrihydrite on BC instead of corner-sharing FeO octahedra. Compared to ADE, the coordination number of the first (FeFe) and second (FeFe) shell was higher in BC, revealing a higher degree of order in coordination between the neighboring Fe mineral crystals. Black C limited the progressive aging of amorphous Fe phases and greatly enriched SRO ferrihydrite in the redox-fluctuating and high-leaching environment. The transformation of SRO ferrihydrite into the more crystalline Fe oxides was controlled by the local pH environment. A strong signal from the complexed phenolic group (aryl-OH, 1241 cm) and a distinct band of inner-sphere complexation (Fe-aryl C, 1380-1384 cm) were identified in the FTIR spectra. The enrichment of poorly crystalline minerals can have positive feedback on the long-term stabilization of BC. The scale-up application of biochar to agricultural and ecological systems may have a long-lasting impact on the enrichment and transformation of the SRO minerals in the soil.
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http://dx.doi.org/10.1016/j.scitotenv.2020.138195DOI Listing
July 2020

Temporal physicochemical changes and transformation of biochar in a rice paddy: Insights from a 9-year field experiment.

Sci Total Environ 2020 Jun 6;721:137670. Epub 2020 Mar 6.

Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China. Electronic address:

Biochar application to soil has attracted extensive attention worldwide due to its carbon (C) sequestration and fertility-enhancing properties. However, the lack of biochar accumulation in highly disturbed agroecosystems challenges the perceived long-term stability of biochars in soil. This 9-year field experiment was conducted in rice paddy fields to understand the temporal degradation of biochars produced from two contrasting feedstocks (rice straw vs. bamboo) at a high temperature (600 °C). Obvious physical alterations, surface oxidation, and transformation of condensed aromatic C occurred in biochars in the disturbed paddy field with frequent redox cycles. Increase in O/C atomic ratio, levels of high-temperature-sensitive degradable components, H/C ratio, and linear alkyl-C content were observed, which were indicative of time-dependent molecular changes and degradative transformation of biochars. Biochar degradation was characterized by the loss of labile C at an early stage and the degradation of aromatic C at a later stage. Based on the massive loss of C content in biochars (10.3-11.8%) and considerable degradation of aromatic C (5.0-8.7%) in 9 years, we argue that current biphasic C dynamic models probably overestimate the stability of biochars in agroecosystems such as rice paddy fields. Long-term field experiments (>5 years) are required to assess biochar's potential for C sequestration. This study provides long-term field data regarding the temporal changes in biochar physicochemical properties, which may facilitate the development of a robust assessment scheme on the long-term persistence of biochars in agroecosystems.
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http://dx.doi.org/10.1016/j.scitotenv.2020.137670DOI Listing
June 2020

Biochar drives microbially-mediated rice production by increasing soil carbon.

J Hazard Mater 2020 04 13;387:121680. Epub 2019 Nov 13.

Institute of Environmental Science and Technology, College of Environment and Resource Science, Zhejiang University, Hangzhou, 310029, PR China. Electronic address:

The effects of an on-site biomass (rice straw) equivalent biochar-returning strategy (RSC) on rice yield, soil nutrients and bacterial community composition were examined in a four-year field trial (2013-2016) conducted in a paddy field in south China. Three treatments were set up including annual on-site biomass return (RS, rice straw at 8 t ha yr), annual on-site biomass equivalent biochar-return (RSC, rice straw biochar at 2.8 t ha yr with a 35 % carbonization rate) and control (CK, no rice straw or biochar added). Results showed that a low rate of biochar application (RSC) could significantly increase rice yield in four successive years. The increase in rice yield was mainly attributed to the increase in soil potassium and magnesium contents resulting from the presence of the unique surface functional groups of biochar. As a result of biochar amendment, soil bacterial cooperative relationships were improved in the RSC, compared to those in the RS treatment. Our study indicated that RSC might be promoted as a promising strategy to enhance rice productivity and soil fertility in a sustainable way.
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http://dx.doi.org/10.1016/j.jhazmat.2019.121680DOI Listing
April 2020

Fast Projection Matching for X-ray Tomography.

Sci Rep 2017 06 16;7(1):3691. Epub 2017 Jun 16.

Collection Management Department, National Taiwan Museum, 10047, Taipei, Taiwan.

X-ray 3D tomographic techniques are powerful tools for investigating the morphology and internal structures of specimens. A common strategy for obtaining 3D tomography is to capture a series of 2D projections from different X-ray illumination angles of specimens mounted on a finely calibrated rotational stage. However, the reconstruction quality of 3D tomography relies on the precision and stability of the rotational stage, i.e. the accurate alignment of the 2D projections in the correct three-dimensional positions. This is a crucial problem for nano-tomographic techniques due to the non-negligible mechanical imperfection of the rotational stages at the nanometer level which significantly degrades the spatial resolution of reconstructed 3-D tomography. Even when using an X-ray micro-CT with a highly stabilized rotational stage, thermal effects caused by the CT system are not negligible and may cause sample drift. Here, we propose a markerless image auto-alignment algorithm based on an iterative method. This algorithm reduces the traditional projection matching method into two simplified matching problems and it is much faster and more reliable than traditional methods. This algorithm can greatly decrease hardware requirements for both nano-tomography and data processing and can be easily applied to other tomographic techniques, such as X-ray micro-CT and electron tomography.
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http://dx.doi.org/10.1038/s41598-017-04020-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473817PMC
June 2017

Cyanophycin mediates the accumulation and storage of fixed carbon in non-heterocystous filamentous cyanobacteria from coniform mats.

PLoS One 2014 7;9(2):e88142. Epub 2014 Feb 7.

Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

Thin, filamentous, non-heterocystous, benthic cyanobacteria (Subsection III) from some marine, lacustrine and thermal environments aggregate into macroscopic cones and conical stromatolites. We investigate the uptake and storage of inorganic carbon by cone-forming cyanobacteria from Yellowstone National Park using high-resolution stable isotope mapping of labeled carbon (H(13)CO3 (-)) and immunoassays. Observations and incubation experiments in actively photosynthesizing enrichment cultures and field samples reveal the presence of abundant cyanophycin granules in the active growth layer of cones. These ultrastructurally heterogeneous granules rapidly accumulate newly fixed carbon and store 18% of the total particulate labeled carbon after 120 mins of incubation. The intracellular distribution of labeled carbon during the incubation experiment demonstrates an unexpectedly large contribution of PEP carboxylase to carbon fixation, and a large flow of carbon and nitrogen toward cyanophycin in thin filamentous, non-heterocystous cyanobacteria. This pattern does not occur in obvious response to a changing N or C status. Instead, it may suggest an unusual interplay between the regulation of carbon concentration mechanisms and accumulation of photorespiratory products that facilitates uptake of inorganic C and reduces photorespiration in the dense, surface-attached communities of cyanobacteria from Subsection III.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0088142PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3917874PMC
May 2015

Reaction-diffusion model of nutrient uptake in a biofilm: theory and experiment.

J Theor Biol 2011 Nov 10;289:90-5. Epub 2011 Aug 10.

Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

Microbes in natural settings typically live attached to surfaces in complex communities called biofilms. Despite the many advantages of biofilm formation, communal living forces microbes to compete with one another for resources. Here we combine mathematical models with stable isotope techniques to test a reaction-diffusion model of competition in a photosynthetic biofilm. In this model, a nutrient is transported through the mat by diffusion and is consumed at a rate proportional to its local concentration. When the nutrient is supplied from the surface of the biofilm, the balance between diffusion and consumption gives rise to gradients of nutrient availability, resulting in gradients of nutrient uptake. To test this model, a biofilm was incubated for a fixed amount of time with an isotopically labeled nutrient that was incorporated into cellular biomass. Thus, the concentration of labeled nutrient in a cell is a measure of the mean rate of nutrient incorporation over the course of the experiment. Comparison of this measurement to the solution of the reaction-diffusion model in the biofilm confirms the presence of gradients in nutrient uptake with the predicted shape. The excellent agreement between theory and experiment lends strong support to this one-parameter model of reaction and diffusion of nutrients in a biofilm. Having validated this model empirically, we discuss how these dynamics may arise from diffusion through a reactive heterogeneous medium. More generally, this result identifies stable isotope techniques as a powerful tool to test quantitative models of chemical transport through biofilms.
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http://dx.doi.org/10.1016/j.jtbi.2011.08.004DOI Listing
November 2011

Speciation and long- and short-term molecular-level dynamics of soil organic sulfur studied by X-ray absorption near-edge structure spectroscopy.

J Environ Qual 2011 May-Jun;40(3):704-18

Department of Crop and soil Sciences, Ithaca, NY 14853, USA.

We investigated speciation, oxidative state changes, and long- and short-term molecular-level dynamics of organic S after 365 d of aerobic incubation with and without the addition of sugarcane residue using XANES spectroscopy. Soil samples were collected from the upper 15 cm of undisturbed grasslands since 1880, from undisturbed grasslands since 1931, and from cultivated fields since 1880 in the western United States. We found three distinct groups of organosulfur compounds in these grassland-derived soils: (i) strongly reduced (S to S) organic S that encompasses thiols, monosulfides, disulfides, polysulfides, and thiophenes; (ii) organic S in intermediate oxidation (S to S) states, which include sulfoxides and sulfonates; and (iii) strongly oxidized (S) organic S, which comprises ester-SO-S. The first two groups represent S directly linked to C and accounted for 80% of the total organic S detected by XANES from the undisturbed soils. Aerobic incubation without the addition of sugarcane residue led to a 21% decline in organanosulfur compounds directly linked to C and to up to an 82% increase inorganic S directly bonded to O. Among the C-bonded S compounds, low-valence thiols, sulfides, thiophenic S, and intermediate-valence sulfoxide S seem to be highly susceptible to microbial attack and may represent the most reactive components of organic S pool in these grassland soils. Sulfonate S exhibited a much lower short-term reactivity. The incorporation of sugarcane residue resulted in an increase in organosulfur compounds directly bonded to C at the early stage of incubation. However, similar to soils incubated without residue addition, the proportion of organic S directly linked to C continued to decline with increasing duration of aerobic incubation, whereas the proportion of organic S directly bonded to O showed a steady rise.
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http://dx.doi.org/10.2134/jeq2010.0061DOI Listing
June 2011

Amazonian anthrosols support similar microbial communities that differ distinctly from those extant in adjacent, unmodified soils of the same mineralogy.

Microb Ecol 2010 Jul 24;60(1):192-205. Epub 2010 Jun 24.

Department of Crop and Soil Sciences, Cornell University, 722 Bradfield Hall, Ithaca, NY 14853, USA.

We compared the microbial community composition in soils from the Brazilian Amazon with two contrasting histories; anthrosols and their adjacent non-anthrosol soils of the same mineralogy. The anthrosols, also known as the Amazonian Dark Earths or terra preta, were managed by the indigenous pre-Colombian Indians between 500 and 8,700 years before present and are characterized by unusually high cation exchange capacity, phosphorus (P), and calcium (Ca) contents, and soil carbon pools that contain a high proportion of incompletely combusted biomass as biochar or black carbon (BC). We sampled paired anthrosol and unmodified soils from four locations in the Manaus, Brazil, region that differed in their current land use and soil type. Community DNA was extracted from sampled soils and characterized by use of denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism. DNA bands of interest from Bacteria and Archaea DGGE gels were cloned and sequenced. In cluster analyses of the DNA fingerprints, microbial communities from the anthrosols grouped together regardless of current land use or soil type and were distinct from those in their respective, paired adjacent soils. For the Archaea, the anthrosol communities diverged from the adjacent soils by over 90%. A greater overall richness was observed for Bacteria sequences as compared with those of the Archaea. Most of the sequences obtained were novel and matched those in databases at less than 98% similarity. Several sequences obtained only from the anthrosols grouped at 93% similarity with the Verrucomicrobia, a genus commonly found in rice paddies in the tropics. Sequences closely related to Proteobacteria and Cyanobacteria sp. were recovered only from adjacent soil samples. Sequences related to Pseudomonas, Acidobacteria, and Flexibacter sp. were recovered from both anthrosols and adjacent soils. The strong similarities among the microbial communities present in the anthrosols for both the Bacteria and Archaea suggests that the microbial community composition in these soils is controlled more strongly by their historical soil management than by soil type or current land use. The anthrosols had consistently higher concentrations of incompletely combusted organic black carbon material (BC), higher soil pH, and higher concentrations of P and Ca compared to their respective adjacent soils. Such characteristics may help to explain the longevity and distinctiveness of the anthrosols in the Amazonian landscape and guide us in recreating soils with sustained high fertility in otherwise nutrient-poor soils in modern times.
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http://dx.doi.org/10.1007/s00248-010-9689-3DOI Listing
July 2010

Morphological record of oxygenic photosynthesis in conical stromatolites.

Proc Natl Acad Sci U S A 2009 Jul 29;106(27):10939-43. Epub 2009 Jun 29.

Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Conical stromatolites are thought to be robust indicators of the presence of photosynthetic and phototactic microbes in aquatic environments as early as 3.5 billion years ago. However, phototaxis alone cannot explain the ubiquity of disrupted, curled, and contorted laminae in the crests of many Mesoproterozoic, Paleoproterozoic, and some Archean conical stromatolites. Here, we demonstrate that cyanobacterial production of oxygen in the tips of modern conical aggregates creates contorted laminae and submillimeter-to-millimeter-scale enmeshed bubbles. Similarly sized fossil bubbles and contorted laminae may be present only in the crestal zones of some conical stromatolites 2.7 billion years old or younger. This implies not only that cyanobacteria built Proterozoic conical stromatolites but also that fossil bubbles may constrain the timing of the evolution of oxygenic photosynthesis.
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http://dx.doi.org/10.1073/pnas.0900885106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2708726PMC
July 2009