Biology subjects

Zou, S.

Publications and source records attributed to Zou, S..

36 records · Page 2Linked to original sources

bioRxiv2024

Avirulence depletion assay: combining R gene-mediated selection with bulk sequencing for rapid avirulence gene identification in wheat powdery mildew

Wheat production is threatened by multiple fungal pathogens, such as the wheat powdery mildew fungus (Blumeria graminis f. sp. tritici, Bgt). Wheat resistance breeding frequently relies on the use of resistance (R) genes that encode diverse immune receptors which detect specific avirulence (AVR) effectors and subsequently induce an immune response. While R gene cloning has accelerated recently, AVR identification in many pathogens including Bgt lags behind, preventing pathogen-informed deployment of resistance sources. Here we describe a new "avirulence depletion (AD) assay" for rapid identification of AVR genes in Bgt. This assay relies on the selection of a segregating, haploid F1 progeny population on a resistant host, followed by bulk sequencing, thereby allowing rapid avirulence candidate gene identification with high mapping resolution. In a proof-of- concept experiment we mapped the AVR component of the wheat immune receptor Pm3a to a 25kb genomic interval in Bgt harboring a single effector, the previously described AvrPm3a2/f2. Subsequently, we applied the AD assay to map the unknown AVR effector recognized by the Pm60 immune receptor. We show that AvrPm60 is encoded by three tandemly arrayed, nearly identical effector genes that trigger an immune response upon co- expression with Pm60 and its alleles Pm60a and Pm60b. We furthermore provide evidence that Pm60 outperforms Pm60a and Pm60b through more efficient recognition of AvrPm60 effectors, suggesting it should be prioritized for wheat breeding. Finally, we show that virulence towards Pm60 is caused by simultaneous deletion of all AvrPm60 gene paralogs and that isolates lacking AvrPm60 are especially prevalent in the US thereby limiting the potential of Pm60 in this region. The AD assay is a powerful new tool for rapid and inexpensive AVR identification in Bgt with the potential to contribute to pathogen-informed breeding decisions for the use of novel R genes and regionally tailored gene deployment.

plant biology↗

bioRxiv2024

A self-adaptive and versatile tool for eliminating multiple undesirable variations from transcriptome

Accurate identification of true biological signals from diverse undesirable variations in large-scale transcriptomes is essential for downstream discoveries. Herein, we develop a universal deep neural network, called DeepAdapter, to eliminate various undesirable variations from transcriptomic data. The innovation of our approach lies in automatic learning of the corresponding denoising strategies to adapt to different situations. The data-driven strategies are flexible and highly attuned to the transcriptomic data that requires denoising, yielding significant improvement in reducing undesirable variation originating from batches, sequencing platforms, and bio-samples with varied purity beyond manually designed schemes. Comprehensive evaluations across multiple batches, different RNA measurement technologies and heterogeneous bio-samples demonstrate that DeepAdapter can robustly correct diverse undesirable variations and accurately preserve biological signals. Our findings indicate that DeepAdapter can act as a versatile tool for the comprehensive denoising of the large and heterogeneous transcriptome across a wide variety of application scenarios.

bioinformatics↗

bioRxiv2024

Screening of associated bacteria of Alexandrium catenella on affecting PSTs production and influence mechanism

Alexandrium causes serious food safety and human death due to paralytic shellfish toxins (PSTs) production. The associated bacteria can affect PSTs production of Alexandrium. However, the influencing mechanism is still unclear. Here we firstly screened functional associated bacteria for affecting PSTs production of Alexandrium catenella in Yangtze Estuary and further studied their influence on physiological process and molecular regulation of A. catenella. Thirteen bacteria strains for affecting PSTs production of A. catenella were selected. The A. catenella strains co-cultured with different functional associated bacteria all produced more PSTs than axenic strain with antibiotic treatment. Compared with axenic A. catenella, the non-axenic A. catenella produced more algal cells, soluble sugar, soluble protein and neutral lipid. By RNA-seq, it was found that non-axenic A. catenella produced more upregulated functional genes than axenic A. catenella. The biosynthesis of cofactors and spliceosome were the dominant different pathways between axenic and non-axenic A. catenella strains. The sxtA expression was closely related with Arginine and proline metabolism, Arginine biosynthesis, Fatty acid biosynthesis, TCA cycle and Glutathione metabolism, which were all downregulated in axenic A. catenella. Meantime, the non-axenic A. catenella under nitrogen deprivation produced less PSTs and functional genes than non-axenic strain under common culture condition, indicating the nitrogen significance for PSTs production. The detailed signal molecular released by associated bacteria for regulating PSTs of A. catenella needs to be further studied.

ecology↗

bioRxiv2024

Comparison and Evaluation of Neutralization of Clinically Frequently Used Antimicrobial Agents Using Three Different Culture Media in Simulated Blood Cultures

The performance of BACT/ALERT FA/FN Plu (France) blood culture containing a novel resin, DL (China) blood culture containing common resin, and adsorbent-free Thermo (USA) blood culture relying on dilution for antimicrobial neutralization at %peak serum concentration was evaluated by measuring the recovery of organisms and time to detection (TTD) in nine simulated microorganism-antimicrobial combination blood cultures.There was a significant difference in recovery rates between the aerobic media: 35/40 (87.5%) for BACT/ALERT media, 15/35 (42.9%) for DL media, and 5/40 (12.5%) for Thermo media; whereas, there was no statistical difference in TTD between FA Plus media and DL aerobic media. The recovery rates of the anaerobic media were 32/35 (91.4%) for BACT/ALERT media, 1/35 (2.9%) for DL media, and 5/35 (14.3%) for Thermo media, with significant differences only between BACT/ALERT FN Plus media and the others. Among the seven main antimicrobial categories, only BACT/ALERT FA/FN Plus culture media showed high recovery of microorganisms, except for carbapenems. The DL culture media exhibited a relatively high recovery rate of piperacillin/tazobactam, levofloxacin, and gentamicin only in aerobic media, and Thermo media only displayed the recovery of gentamicin.BACT/ALERT FA/FN Plus culture media with novel resin showed absolute advantages over DL and Thermo culture media and, thus, can be selectively applied clinically with prior use of antimicrobials before pathogen detection. DL culture media containing common resin outperformed adsorbent-free dilution-based Thermo culture media, which can be a backup option. We should focus on improving the neutralization of carbapenems with low efficiency in all three media.

microbiology↗

bioRxiv2023

Mecp2 Fine-tunes Quiescence Exit by Targeting Nuclear Receptors

Quiescence (G0) maintenance and exit are crucial for tissue homeostasis and regeneration in mammals. Here, we show that methyl-CpG binding protein 2 (Mecp2) expression is cell cycle-dependent and negatively regulates quiescence exit in cultured cells and in an injury-induced liver regeneration mouse model. Specifically, acute reduction of Mecp2 is required for efficient quiescence exit, as deletion of Mecp2 accelerates, while overexpression of Mecp2 delays quiescence exit, and forced expression of Mecp2 after Mecp2 conditional knockout rescues cell cycle reentry. The E3 ligase Nedd4 mediates the ubiquitination and degradation of Mecp2, and thus facilitates quiescence exit. Genome-wide study uncovered the dual role of Mecp2 in preventing quiescence exit by transcriptionally activating metabolic genes while repressing proliferation-associated genes. Particularly, disruption of two nuclear receptors (NRs), Rara or Nr1h3, accelerates quiescence exit, mimicking the Mecp2 depletion phenotype. Our studies unravel a previously unrecognized role for Mecp2 as an essential regulator of quiescence exit and tissue regeneration.

cell biology↗

bioRxiv2023

Analysis of the heterogeneity and complexity of murine extraorbital lacrimal gland via single-cell RNA sequencing

PurposeThe lacrimal gland is essential for maintaining ocular surface health and avoiding external damage by secreting the aqueous layer of the tear film. However, a healthy lacrimal glands inventory of cell types and heterogeneity remains understudied. MethodsHere, 10X genome-based single-cell RNA sequencing was used to generate an unbiased classification of cellular diversity in the extraorbital lacrimal gland (ELG) of C57BL/6J mice. From 48,077 high-quality cells, an atlas of cell heterogeneity was produced, and cell types were defined by classic marker genes. The possible functions of these cells and the pseudotime trajectories for certain cell populations were analyzed through bioinformatics. In addition, a preliminary analysis of the cell-cell communication network in ELG was performed. ResultsOver 41 subclasses of cells were identified, including 9 kinds of glandular epithelial cells, 7 kinds of fibroblasts, 10 kinds of myeloid-derived immune cells, at least 10 kinds of lymphoid-derived immune cells, 3 kinds of vascular-associated cell subsets, and 2 kinds of Schwann cells. Analysis of cell-cell communication networks revealed that innate lymphoid cells were closely associated with other cells. ConclusionsThis study provides the first comprehensive transcriptome atlas and related database of mouse ELG. This resource can aid in a deeper understanding of lacrimal gland biology and pathophysiology of its related diseases.

bioinformatics↗

bioRxiv2022

Investigation of a mathematical model describing global cancer growth and treatment: An inhomogeneous model based on the generalized logistic equation

Tumor growth is manifestation of the evolution of a complex system. Researchers have limited scope of modelling studies on specific aspects or stages of the process. It has led to unsatisfactory explanation of clinical observations. We hereby demonstrated that an inhomogeneous model built on the generalized logistic equation could serve better. It was developed to describe the whole process of tumor progression, clinically observed independence of index tumor growth from spread of the disease and growth deceleration during early stage of solid tumors. It was validated by simulating the coexistence of exponential and sigmoidal growth in chronic lymphocytic leukaemia, theories of tumor heterogeneity, as well as by accommodating notions pertaining to tumor treatment and prognosis. We thought therefore it was an interesting and not unjustifiable description of actual tumor growth in human body and hoped it might encourage more researchers to look at tumor modelling from a clinical perspective.

cancer biology↗

bioRxiv2021

Continental-scale Hyperspectral tree species classification in the National Ecological Observatory Network

Advances in remote sensing imagery and machine learning applications unlock the potential for developing algorithms for species classification at the level of individual tree crowns at unprecedented scales. However, most approaches to date focus on site-specific applications and a small number of taxonomic groups. Little is known about how well these approaches generalize across broader geographic areas and ecosystems. Leveraging field surveys and hyperspectral remote sensing data from the National Ecological Observatory Network (NEON), we developed a continental-extent model for tree species classification that can be applied to the network, including a wide range of US terrestrial ecosystems. We compared the performance of a model trained with data from 27 NEON sites to models trained with data from each individual site, evaluating advantages and challenges posed by training species classifiers at the US scale. We evaluated the effect of geographic location, topography, and ecological conditions on the accuracy and precision of species predictions (72 out of 77 species). On average, the general model resulted in good overall classification accuracy (micro-F1 score), with better accuracy than site-specific classifiers (average individual tree level accuracy of 0.77 for the general model and 0.70 for site-specific models). Aggregating species to the genus-level increased accuracy to 0.83. Regions with more species exhibited lower classification accuracy. Predicted species were more likely to be confused with congeneric and co-occurring species and confusion was highest for trees with structural damage and in complex closed-canopy forests. The model produced accurate estimates of uncertainty, correctly identifying trees where confusion was likely. Using only data from NEON, this single integrated classifier can make predictions for 20% of all tree species found in forest ecosystems across the entire US, which make up to roughly 90% of the upper canopy of the studied ecosystems. This suggests the potential for integrating information from multiple datasets and locations to develop broad scale general models for species classification from hyperspectral imaging.

ecology↗

bioRxiv2021

Functional and Highly Crosslinkable HIV-1 Envelope Glycoproteins Enriched in a Pretriggered Conformation

Binding to the receptor, CD4, drives the pretriggered, "closed" (State-1) conformation of the human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer into more "open" conformations (States 2 and 3). Broadly neutralizing antibodies, which are elicited inefficiently, mostly recognize the State-1 Env conformation, whereas the more commonly elicited poorly neutralizing antibodies recognize States 2/3. HIV-1 Env metastability has created challenges for defining the State-1 structure and developing immunogens mimicking this labile conformation. The availability of functional State-1 Envs that can be efficiently crosslinked at lysine and/or acidic amino acid residues might assist these endeavors. To that end, we modified HIV-1AD8 Env, which exhibits an intermediate level of triggerability by CD4. We introduced lysine/acidic residues at positions that exhibit such polymorphisms in natural HIV-1 strains. Env changes that were tolerated with respect to gp120-gp41 processing, subunit association and virus entry were further combined. Two common polymorphisms, Q114E and Q567K, as well as a known variant, A582T, additively rendered pseudoviruses resistant to cold, soluble CD4 and a CD4-mimetic compound, phenotypes indicative of stabilization of the pretriggered State-1 Env conformation. Combining these changes resulted in two lysine-rich HIV-1AD8 Env variants (E.2 and AE.2) with neutralization- and cold-resistant phenotypes comparable to those of natural, less triggerable Tier 2/3 HIV-1 isolates. Compared with these and the parental Envs, the E.2 and AE.2 Envs were cleaved more efficiently and exhibited stronger gp120-trimer association in detergent lysates. These highly crosslinkable Envs enriched in a pretriggered conformation should assist characterization of the structure and immunogenicity of this labile state. IMPORTANCEThe development of an efficient vaccine is critical for combating HIV-1 infection worldwide. However, the instability of the pretriggered shape (State 1) of the viral envelope glycoprotein (Env) makes it difficult to raise neutralizing antibodies against HIV-1. Here, by introducing multiple changes in Env, we derived two HIV-1 Env variants that are enriched in State 1 and can be efficiently crosslinked to maintain this shape. These Env complexes are more stable in detergent, assisting their purification. Thus, our study provides a path to a better characterization of the native pretriggered Env, which should assist vaccine development.

molecular biology↗

bioRxiv2021

Mechanistic insights into dynamic mutual regulation of USP14 and proteasome

Proteasomal degradation of ubiquitylated proteins is sophisticatedly regulated at multiple levels1-3. A primary regulatory checkpoint is the removal of ubiquitin chains from substrates by the deubiquitylating enzyme USP14 that associates reversibly with the proteasome. How USP14 is activated and regulates the proteasome function remains unknown4-7. Here we report cryo-electron microscopy (cryo-EM) structures of human USP14 in complex with the 26S proteasome in nine conformational states at 3.0-3.6 [A] resolution, captured during polyubiquitylated protein degradation. Time-resolved cryo-EM analysis of the conformational continuum revealed two parallel pathways of proteasome state transitions induced by USP14 and captured transient conversion of substrate-engaged intermediates into substrate-inhibited intermediates. On the substrate-engaged pathway, USP14 activation allosterically reprograms conformational landscape of the AAA-ATPase motor and stimulates opening of the core particle gate8-10, enabling observation of a near-complete cycle of asymmetric ATP hydrolysis around the ATPase ring during processive substrate unfolding. Dynamic USP14-ATPase interactions decouple the ATPase activity from RPN11-catalysed deubiquitylation11-13 and kinetically introduce three regulatory checkpoints on the proteasome, at the steps of ubiquitin recognition, substrate translocation initiation and ubiquitin chain recycling. These findings provide unprecedented insights into the complete functional cycles of USP14-regulated proteasome and of USP14 activation-deubiquitylation-disassembly and establish mechanistic foundations for USP14-targeted therapeutic discovery.

biochemistry↗

bioRxiv2020

Coupling between ribotypic and phenotypic traits of protists across life-cycle stages and temperatures

Relationships between ribotypic and phenotypic traits of protists across life-cycle stages remain largely unknown. Herein, we used single cells of two soil and two marine ciliate species to examine phenotypic and ribotypic traits and their relationships across lag, log, plateau, cystic stages and temperatures. We found that Colpoda inflata and C. steinii demonstrated allometric relationships between 18S rDNA copy number per cell (CNPC), cell volume (CV), and macronuclear volume across all life-cycle stages. Integrating previously reported data of Euplotes vannus and Strombidium sulcatum indicated taxon-dependent rDNA CNPC-CV functions. Ciliate and prokaryote data analysis revealed that the rRNA CNPC followed a unified power-law function, only if the rRNA-deficient resting cysts were not considered. Hence, a theoretical framework was proposed to estimate the relative quantity of resting cysts in the protistan populations with total cellular rDNA and rRNA copy numbers. Using rDNA CNPC was a better predictor of growth rate at a given temperature than rRNA CNPC and CV, suggesting replication of redundant rDNA operons as a key factor that slows cell division. Single-cell high throughput sequencing and analysis after correcting sequencing errors revealed multiple rDNA and rRNA variants per cell. Both encystment and temperature affected the number of rDNA and rRNA variants in several cases. The divergence of rDNA and rRNA sequence in a single cell ranged from 1% to 10%, depending on species. These findings have important implications for inferring cell-based biological traits (e.g., species richness, abundance and biomass, activity, and community structure) of protists using molecular approaches. ImportanceBased on phenotypic traits, traditional surveys usually characterize organismal richness, abundance, biomass, and growth potential to describe diversity, organization and function of protistan populations and communities. The ribosomal RNA gene (rDNA) and its transcripts have been widely used as molecular markers in ecological studies of protists. Nevertheless, the manner in which these molecules relate to cellular (organismal) and physiological traits remains poorly understood, which could lead to misinterpretations of protistan diversity and ecology. The current research highlights the dynamic nature of cellular rDNA and rRNA contents, which tightly couple with multiple phenotypic traits in ciliated protists. We demonstrate that quantity of resting cysts and maximum growth rate of a population can be theoretically estimated using ribotypic trait-based models. The intra-individual sequence polymorphisms of rDNA and rRNA can be influenced by encystment and temperature, which should be considered when interpreting species-level diversity and community structure of microbial eukaryotes.

molecular biology↗

bioRxiv2020

Multiple Mechanisms of HIV-1 resistance to PGT135 in Chinese Subtype B' Slow Progressor

In our study, we describe a slow progressor CBJC515 from whom we constructed pseudoviruses expressing autologous Env. We surprisingly found all the pseudoviruses were resistant to PGT135. By making site-directed mutations and chimeric Env constructs, we found the early 05 strains escaped from PGT135 by losing the N332 glycan site, while the later 06 and 08 strains may escape with the retention of key epitopes through the change of V1/V4/C2 region or by N398/N611 glycan, which was selected as unique N-glycosylation site of CBJC515 compared with CBJC437 whose viruses were also harboring key epitopes but sensitive to PGT135. These findings provide insights into how HIV-1 can escape from N332-directed broadly neutralizing antibody (bNAb) responses without changing the epitope itself, and these ways may be useful to prolong the exposures of bNAb epitopes and contribute to bNAb development. Furthermore, our chimeric experiments also allowed us to explore the co-evolution and retention of functionality among regions. We confirmed that the V1V2 region has a wide range of effectiveness in interfering with the function of envelope protein and the V3 region can promote protein function recovery and buffer the harmful polymorphisms in the other regions contributing to the Env antigenic diversity. These results may provide some clues for the design of vaccines against HIV-1 strains. IMPORTANCEOur findings of mechanisms escaping from PGT135 verified the extensive role of long V1 region in mediating escape from V3-bNAbs. In addition, we also found multiple additional ways suggested that extreme variation may be needed by HIV-1 to escape from PGT135 without changing the epitope itself. Although the V3-glycan bNAb responses are among the most promising vaccine targets, as they are commonly elicited during infection, our findings indicated there may be additional difficulties to be taken into account in immunogen design, such as the consideration of other regions and some glycosylation sites affecting the mask of key epitopes, as well as the selection pressure that may be required by other bNAbs. Our chimeric experiment also highlighted the key role of V3 region in contributing to the maintenance of Env diversity by buffering deleterious polymorphisms, which may be helpful for vaccine design.

immunology↗

bioRxiv2020

Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus in China (SARS-CoV-2)

A new coronavirus SARS-CoV-2 has caused over 9.2 million infection cases and 475758 deaths worldwide. Due to the rapid dissemination and the unavailability of specific therapy, there is a desperate need for vaccines to combat the epidemic of SARS-CoV-2. An in silico approach based on the available virus genome was applied to identify 19 high immunogenic B-cell epitopes and 499 human-leukocyte-antigen (HLA) restricted T-cell epitopes. Thirty multi-epitope peptide vaccines were designed by iNeo Suite, and manufactured by solid-phase synthesis. Docking analysis showed stable hydrogen bonds of epitopes with their corresponding HLA alleles. When four vaccine peptide candidates from the spike protein of SARS-CoV-2 were selected to immunize mice, a significantly larger amount of IgG in serum as well as an increase of CD19+ cells in ILNs was observed in peptide-immunized mice compared to the control mice. The ratio of IFN-{gamma}-secreting lymphocytes in CD4+ or CD8+ cells in the peptides-immunized mice were higher than that in the control mice. There were also a larger number of IFN-{gamma}-secreting T cells in spleen in the peptides-immunized mice. This study screened antigenic B-cell and T-cell epitopes in all encoded proteins of SARS-CoV-2, and further designed multi-epitope based peptide vaccine against viral structural proteins. The obtained vaccine peptides successfully elicited specific humoral and cellular immune responses in mice. Primate experiments and clinical trial are urgently required to validate the efficacy and safety of these vaccine peptides. ImportanceSo far, a new coronavirus SARS-CoV-2 has caused over 9.2 million infection cases and 475758 deaths worldwide. Due to the rapid dissemination and the unavailability of specific therapy, there is a desperate need for vaccines to combat the epidemic of SARS-CoV-2. Different from the development approaches for traditional vaccines, the development of our peptide vaccine is faster and simpler. In this study, we performed an in silico approach to identify the antigenic B-cell epitopes and human-leukocyte-antigen (HLA) restricted T-cell epitopes, and designed a panel of multi-epitope peptide vaccines. The resulting SARS-CoV-2 multi-epitope peptide vaccine could elicit specific humoral and cellular immune responses in mice efficiently, displaying its great potential in our fight of COVID-19.

bioinformatics↗

bioRxiv2020

Clinically applicable histopathological diagnosis system for gastric cancer detection using deep learning

Gastric cancer is among the most malignant tumours with the highest incidence and mortality rates. The early detection and accurate histopathological diagnosis of gastric cancer are essential factors that can help increase the chances of successful treatment. While the worldwide shortage of pathologists has imposed burdens on current histopathology services, it also offers a unique opportunity for the use of artificial intelligence assistance systems to alleviate the workload and increase diagnostic accuracy. To the best of our knowledge, there has not been a clinically applicable histopathological assistance system with high accuracy that can generalize to whole slide images created with diverse digital scanner models from different hospitals. Here, we report a clinically applicable artificial intelligence assistance system developed at the Chinese PLA General Hospital, China, using a deep convolutional neural network trained with 2,123 pixel-level annotated H&E-stained whole slide images. The model achieved a sensitivity near 100% and an average specificity of 80.6% on a real-world test dataset, which included 3,212 whole slide images digitalized with three scanner models. We showed that the system could aid pathologists in improving diagnostic accuracy and preventing misdiagnoses. Moreover, we demonstrated that our system could perform robustly with 1,582 whole slide images from two other medical centres. Our study suggests the feasibility and benefits of using histopathological artificial intelligence assistance systems in routine practice scenarios.Competing Interest StatementXiaoqing Zhang is the founder of Thorough Images. Shuhao Wang is the co-founder and chief technology officer (CTO) of Thorough Images. Calvin Ku, Cancheng Liu, Zhuo Sun, Gang Xu, Yuefeng Wang are algorithm researchers of Thorough Images. All remaining authors have declared no conflicts of interest.View Full Text

pathology↗

bioRxiv2020

New intranuclear symbiotic bacteria from macronucleus of Paramecium putrinum -- Candidatus Gortzia yakutica

Holospora-like bacteria are obligate intracellular Alphaproteobacteria, inhabiting nuclei of Paramecium ciliates and other protists. Alphaproteobacteria have drawn significant attention, as both closest existing relatives of bacteria that gave rise to mitochondria, as well as a class of intracellular bacteria with numerous important pathogens. HLB clade includes two genera - Holospora (Hafkine 1980) and candidatus Gortzia (Boscaro 2013). These bacteria have a peculiar life cycle with two morphological forms, a strict specificity to the host species and the type of nucleus they inhabit. Here we describe a new species of HLB - candidatus Gortzia yakutica sp. nov., a symbiont from macronucleus of Paramecium putrinum, the first known HLB for this Paramecium species. The new symbiont shows morphological similarities with other HLB. The phylogenetic analysis of SSU rDNA gene places it into candidatus Gortzia clade.

microbiology↗

bioRxiv2019

Comparison of SVM and Spectral Embedding in Promoter Biobricks' Categorizing and Clustering

BackgroundIn organisms genomes, promoters are short DNA sequences on the upstream of structural genes, with the function of controlling genes transcription. Promoters can be roughly divided into two classes: constitutive promoters and inducible promoters. Promoters with clear functional annotations are practical synthetic biology biobricks. Many statistical and machine learning methods have been introduced to predict the functions of candidate promoters. Spectral Eigenmap has been proved to be an effective clustering method to classify biobricks, while support vector machine (SVM) is a powerful machine learning algorithm, especially when dataset is small. MethodsThe two algorithms: spectral embedding and SVM are applied to the same dataset with 375 prokaryotic promoters. For spectral embedding, a Laplacian matrix is built with edit distance, followed by K-Means Clustering. The sequences are represented by numeric vector to serve as dataset for SVM trainning. ResultsSVM achieved a high predicting accuracy of 93.07% in 10-fold cross validation for classification of promoters transcriptional functions. Laplacian eigenmap (spectral embedding) based on editing distance may not be capable for extracting discriminative features for this task. AvailabilityCodes, datasets and some important matrices are available on github https://github.com/shangjieZou/Promoter-transcriptional-predictor/tree/source-code

bioinformatics↗

bioRxiv2018

Regulation by HSP70/90 in the different tissues and testis development of male cattle (Cattle-yak and Yak)

HSP70/90 play important role in testis develop and spermatozoa regulation, but the contact of HSP70/90 with infertility in cattle is unclear. Here, we focus on male cattle-yak and yak, which to investigate the expression and localization of HSP70/90 in different tissues, and explore the influence of HSP70/90 to infertility. In our study, a total of 54 cattle (24 cattle-yak and 30 yak) were examined. The HSP90 mRNA of cattle-yak was cloned first and found amino acid variation in HSP90, which led to difference at protein spatial structure compare with yak. To investigate whether the expression of HSP70/90 mRNA and protein are different in cattle-yak and yak, we used real-time quantitative PCR (qRT-PCR) and Western blot (WB) to examine them. We found that the expression level of HSP70/90 mRNA and protein are disparity in different tissues and testis development stages, and obviously high expression was observed in testicle during juvenile and adult, Moreover, it s interestingly in which the HSP70 expression is significant high in yak whereas HSP90 in cattle-yak (P<0.01). On this bases, we detect the location of HSP70/90 in testis by immunohistochemical (IHC) and immunofluorescence (IF), the results demonstrate that HSP70/90 were located in the epithelial cells, spermatogenic cells and mesenchymal cells. In summary, our study proved the expression of HSP70/90 are different in tissues, and the expression of HSP90 is obviously high in testis of cattle-yak, which propose that the infertility of cattle-yak may cause from up-regulating of HSP90.

biochemistry↗

bioRxiv2018

Ammonium Pretreatment and Addition Improve Stability of Environmental Parameters and Biogas Production under Anaerobic Co-digestion of Rice Straw and Dairy Manure

This paper optimized the anaerobic digestion (AD) pretreatment process, identified the relationship between stability of environmental factors and biogas production under ammonium hydroxide (NH3{middle dot}H2O) pretreatment and analyzed the reason of NH3{middle dot}H2O pretreatment to increase biogas production. Variable coefficients (CVs) of environmental factors were calculated to study the stability of environmental factors during AD process. The effect of initial AD environment factors on the stability of environmental factors during AD process was analyzed by redundancy analysis. Path analysis was used to analyze the response relationship the stability of environmental factors between and total biogas production (TBP). Results showed that pretreatment at 8% for 4 days, the TBP produced the highest value (302.5mL/g TS) and significantly higher than the other values (P < 0.01). NH3{middle dot}H2O pretreatment had effect on the initial AD environment factors and the environment factors during AD process. Under the NH3{middle dot}H2O pretreatment conditions, the stability of environment factors during AD process was affected by initial AD environment factors, while they had direct and indirect influences on the TBP. This research concluded that NH3{middle dot}H2O pretreatment improved TBP via changing the initial environment of AD and the stability of environment factors during AD process, as well as the response relationship among initial AD environment factors and the stability of environment factors during AD process and biogas production, the changes improved the stability of environmental factors and made the environment more suitable for AD.

bioengineering↗