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Biology subjects

Ma, L.

Publications and source records attributed to Ma, L..

At least 307 records · Page 17Linked to original sources

Embedded Enzyme Nanoclusters Depolymerize Polyesters via Chain-End Mediated Processive Degradation

Many bioactive elements, long perceived as non-viable for material development, are now emerging as viable building blocks to encode material lifecycle and to ensure our harmonious existence with nature. Yet, there is a significant knowledge gap on how bio-elements interface with synthetic counterparts and function outside of their native environments. Here, we show that when enzymes are dispersed as nanoclusters confined within macromolecular matrices, their reaction kinetics, pathway, and substrate selectivity can be modulated to achieve programmable polymer degradation down to repolymerizable small molecules. Specifically, when enzyme nanoclusters are dispersed in trace amount (~0.02 wt%) in polyesters, i.e. poly(caprolactone) (PCL) and poly(lactic acid) (PLA), chain-end mediated processive depolymerization can be realized, leading to scalable bioactive plastics for efficient sorting, such as recovery of precious metal filler from flexible electronics. Present studies demonstrate that when the enzyme is confined at dimensions similar to that of polymer chains, their behaviors are governed by the polymer conformation, segmental dynamic and thermal history, highlighting the importance to consider bioactive plastics differently from solution enzymology.

bioengineering↗

Autotransporters drive biofilm formation and auto-aggregation in the diderm Firmicute Veillonella parvula

The Negativicutes are a clade of Firmicutes that have retained the ancestral diderm character and possess an outer membrane. One of the best studied Negativicute, Veillonella parvula, is an anaerobic commensal and opportunistic pathogen inhabiting complex human microbial communities, including the gut and the dental plaque microbiota. Whereas adhesion and biofilm capacity of V. parvula is expected to be crucial for its maintenance and development in these environments, studies of V. parvula adhesion have been hindered by the lack of efficient genetic tools to perform functional analyses in this bacterium. Here, we took advantage of a recently described naturally transformable V. parvula isolate, SKV38, and adapted tools developed for the closely related Clostridia spp. to perform random transposon and targeted mutagenesis to identify V. parvula genes involved in biofilm formation. We show that type V secreted autotransporters -typically found in diderm bacteria-are the main determinants of V. parvula auto-aggregation and biofilm formation, which compete with each other for binding either to cells or to surfaces, with strong consequences on V. parvula biofilm formation capacity. We also show that inactivation of the gene coding for a poorly characterized metal-dependent phosphohydrolase HD domain protein conserved in the Firmicutes and their closely related diderm phyla inhibits autotransporter-mediated biofilm formation. This study paves the way for further molecular characterization of V. parvula interactions with other bacteria and the host within complex microbiota environments.

microbiology↗

Proteogenomics analysis of non-coding region encoded peptides in normal tissues and five cancer types

Previous proteogenomics studies have identified peptides encoded by non-coding sequences such as pseudogenes and long non-coding RNAs (lncRNAs) in healthy human tissues as well as in cancers. However, these studies are either limited to analyze only healthy or cancerous tissues, lacking direct comparison between them. In this study, we used an established proteogenomics analysis workflow to analyze proteomics data from 926 cancer samples of five cancer types and 31 different healthy human tissues. We observed the protein level expression of pseudogenes can be classified as ubiquitous or lineage expression. The ubiquitously translated pseudogenes are homologous to house-keeping genes. Our results suggest there is common mechanism underlying the translation of pseudogenes in both normal and tumors. Moreover, we discovered several translated non-coding genes such as DGCR5 and RHOXF1P3 that were up-regulated in tumors compared to normal. These translated pseudogenes imply the biological function of pseudogenes extends to protein level yet to be studied. Further, from the non-coding region encoded peptides specifically detected in tumors we have predicted a large number of potential neoantigens which can be developed as cancer vaccine.

bioinformatics↗

Atlas of ACE2 gene expression in mammals reveals novel insights in transmission of SARS-Cov-2

BackgroundCOVID-19 has become a worldwide pandemic. It is caused by a novel coronavirus named SARS-CoV-2 with elusive origin. SARS-CoV-2 infects mammalian cells by binding to ACE2, a transmembrane protein. Therefore, the conservation of ACE2 and its expression pattern across mammalian species, which are yet to be comprehensively investigated, may provide valuable insights into tracing potential hosts of SARS-CoV-2. MethodsWe analyzed gene conservation of ACE2 across mammals and collected more than 140 transcriptome datasets from human and common mammalian species, including presumed hosts of SARS-CoV-2 and other animals in close contact with humans. In order to enable comparisons across species and tissues, we used a unified pipeline to quantify and normalize ACE2 expression levels. ResultsWe first found high conservation of ACE2 genes among common mammals at both DNA and peptide levels, suggesting that a broad range of mammalian species can potentially be the hosts of SARS-CoV-2. Next, we showed that high level of ACE2 expression in certain human tissues is consistent with clinical symptoms of COVID-19 patients. Furthermore, we observed that ACE2 expressed in a species-specific manner in the mammals examined. Notably, high expression in skin and eyes in cat and dog suggested that these animals may play roles in transmitting SARS-CoV-2 to humans. ConclusionsThrough building the first atlas of ACE2 expression in pets and livestock, we identified species and tissues susceptible to SARS-CoV-2 infection, yielding novel insights into the viral transmission.

genomics↗

Reactive oxygen species as important regulators of cell division

Currently, the role of reactive oxygen species (ROS) in plant growth is a topic of interest. In this study, we discuss the role of ROS in cell division. We analyzed ROS impact on the stiffness of plant cell walls and whether ROS play an important role in Brassica napus ability to adapt to cold stress. Cultivated sterile seedlings and calli of cold-tolerant cultivar 16NTS309 were subjected to cold stress at 25{degrees}C and 4{degrees}C, respectively. Under normal conditions, O2.- mainly accumulated in the leaf edges, shoot apical meristem, leaf primordia, root tips, lateral root primordia, calli of meristematic nodular tissues, cambia, vascular bundles and root primordia, which are characterized by high division rates. After exposure to cold stress, the malondialdehyde and ROS (O2.-) contents in roots, stems and leaves of cultivar 16NTS309 were significantly higher than under non-cold conditions (P < 0.05). ROS (O2.-) were not only distributed in these zones, but also in other cells, at higher levels than under normal conditions. A strong ROS-based staining appeared in the cell wall. The results support a dual role for apoplastic ROS, in which they have direct effects on the stiffness of the cell wall, because ROS cleave cell-wall, and act as wall loosening agents, thereby either promoting or restricting cellular division. This promotes the appearance of new shoots and a strong root system, allowing plants to adapt to cold stress.

plant biology↗

Autophagy-associated Production of Antimicrobial Peptides hBD1 and LL37 Exhibits Anti-Bacillus Calmette-Guerin Effects in Lung Epithelial Cells.

Antimicrobial peptides (AMPs) constitute important groups of bactericidal polypeptides against various microorganisms that exhibit their anti-bacteria activity through cleavage of precursor peptides into the active form of 50-100 amino acids in length. Various AMP cleavage mechanisms have been reported in different cell types; however, those in Mycobacterium tuberculosis (MTB)-infected lung epithelial cells remain unknown. In the present study, we found that MTB-infected lung epithelial cells expressed high level of the AMPs hBD1 and LL37 to kill intracellular MTB as the first-line immune barrier against MTB infection. Notably, their production in the lung epithelial cells was closely related to the function of autophagosomes and lysosomes. Experimental induction of autophagy in lung epithelial cells could enhance the expression of active hBD1 and LL37 at the post-transcriptional level, whereas silencing of these two active AMPs could decrease the bactericidal effect of autophagy. These findings indicated that cleavage of peptide precursors to form active AMPs might constitute a previously unrecognized antibacterial mechanism of autophagy. Author summaryLM and RW conceived and designed the experiments; RW performed the experiments and analyzed the data; QW analyzed the data and contributed reagents/materials/analysis tools; HL performed the experiments; XZ, JY, YL and ZH analyzed the data. LM and RW drafted the manuscript.

immunology↗

Endonuclease activity of RecJ from extremely alkaliphilic Bacillus alcalophilus

At present, all documented RecJs are exonucleases, degrading single-stranded nucleic acids. Here, we report a novel RecJ, from the extremely alkaliphilic bacterium Bacillus alcalophilus (BaRecJ), which possesses endonuclease activity and can cleave supercoiled DNA. BaRecJ contains the typical DHH and DHHA1 domains, which are conserved in all RecJs, and a functionally unknown PIWI-like domain at the C-terminus. The endonuclease activity originates from the C-terminal domain of BaRecJ which contains PIWI-like domain, and the exonuclease activity from the DHH and DHHA1 domains. Mutational analysis reveals that several important residues affect the endonuclease activity of BaRecJ. Moreover, BaRecJ cleaves specific target sequences at moderate temperature when directed by a phosphorothioate-modified single-stranded DNA (S-modified ssDNA) guide. These findings suggest that BaRecJ is substantially different from any reported RecJs and has the potential to be developed as a new gene editing tool.

microbiology↗

Microbial redox activity mediated anaerobic pyrite oxidation under circumneutral conditions

In modern Earth, anaerobic pyrite oxidation under circumneutral conditions also has great impact on the fate of nitrate in aquifers and sediments, as well as the transportation of toxic metals. However, the mechanism of how microbes mediated this process is still being debated. Electrochemical analysis on pyrite cubic electrode showed that, its oxidation threshold under anaerobic circumneutral conditions (ca. 200 mV) was much lower than that at aerobic acidic conditions (ca. 650 mV), implying possible direct pyrite oxidation by high redox potential cellular components. Sole substrate (pyrite) microbial enrichment cultures with EDTA addition showed higher oxidation rate (0.092 d-1) than that of EDTA-free cultures (0.019 d-1), suggesting that ligands producing pathway was much preferred by microbes than maintaining acidic micro-environments. This hypothesis was supported by amplicon and metagenomic sequencing data, which demonstrated discrepant bacteria involving iron-sulfur oxidation and metabolic potentials in cultures with/without EDTA addition. A concept model was proposed based on experimental data considering different reaction stages and microbial communities. The results shed lights on the potential interactions between microbes and pyrite, which may serve as a model for explaining subsurface pyrite oxidation and optimizing anaerobic pyrite oxidation-based pollutant removal processes. TOC art O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/952168v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@14c7a01org.highwire.dtl.DTLVardef@1de10bdorg.highwire.dtl.DTLVardef@1ceb4dorg.highwire.dtl.DTLVardef@9c27fc_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Acquisition of Innate Odor Preference Depends on Spontaneous and Experiential Activities During Critical Period

Animals possess inborn ability to recognize certain odors, which enables them to seek food, avoid predators and find mates even in the absence of prior experiences. The establishment of innate odor preference has been thought to be genetically hardwired. Here we report that the acquisition of innate odor recognition requires spontaneous neural activity and is influenced by sensory experience during early postnatal development. Genetic silencing of mouse olfactory sensory neurons during the developmental critical period has little impact on odor sensitivity, odor discrimination and recognition later in life. However, it abolishes innate odor preference and alters the patterns of activation in brain centers. Moreover, exposure to an innately aversive odor during the critical period abolishes aversion in adulthood in an odor specific manner. The loss of innate aversion is associated with broadened projection of OSNs expressing the cognate receptor such that they innervate ectopic glomeruli in the olfactory bulb. These results indicate that a delicate balance of neural activity is required during critical period in establishing innate odor preference and that ectopic projection is a convergent mechanism to alter innate odor valence.

neuroscience↗

Encoding Innately Recognized Odors via a Generalized Population Code

Odors carrying intrinsic values often trigger instinctive aversive or attractive responses. It is not known how innate valence is encoded. An intuitive model suggests that the information is conveyed through specific channels in hardwired circuits along the olfactory pathway, insulated from influences of other odors, to trigger innate responses. Here we show that in mice, mixing innately aversive or attractive odors with a neutral odor, and surprisingly, mixing two odors with the same valence, abolish the innate behavioral responses. Recordings from the olfactory bulb indicate that odors are not masked at the level of peripheral activation and glomeruli independently encode components in the mixture. In contrast, crosstalk among the mitral/tufted cells changes their patterns of activity such that those elicited by the mixtures can no longer be linearly decoded as separate components. The changes in behavioral and mitral/tufted cell responses are associated with reduced activation of brain areas linked to odor preferences. Thus, crosstalk among odor channels at the earliest processing stage in the olfactory pathway leads to re-coding of odor identity to abolish valence associated with the odors. These results are inconsistent with insulated labeled lines and support a model of a common mechanism of odor recognition for both innate and learned valence associations.

neuroscience↗

Crystal structure of the giant panda MHC class I complex: first insights into the viral peptide presentation profile in the bear family

The viral cytotoxic T lymphocyte (CTL) epitope peptides presented by classical MHC-I molecules require the assembly of a peptide-MHC-I-{beta}2m (aka pMHC-I) trimolecular complex for TCR recognition, which is the critical activation link for triggering antiviral T cell immunity. Ursidae includes 5 genera and 8 species; however, research on T cell immunology in this family, especially structural immunology, is lacking. In this study, the structure of the key trimolecular complex pMHC-1 (aka pAime-128), which binds a peptide from canine distemper virus, was solved for the first time using giant panda as a representative species of Ursidae. The structural characteristics of the giant panda pMHC-I complex, including the unique pockets in the peptide-binding groove (PBG), were analyzed in detail. Comparing the panda pMHC-I to others in the bear family and extending the comparison to other mammals revealed distinct features. The interaction between MHC-I and {beta}2m, the features of pAime-128 involved in TCR docking and CD8 binding, the anchor sites in the PBG, and the CTL epitopes of potential viruses that infect pandas were concretely clarified. Unique features of pMHC-I viral antigen presentation in the panda were revealed by solving the three-dimensional structure of pAime-128. The distinct characteristics of pAime-128 indicate an unusual event that emerged during the evolution of the MHC system in the bear family. These results provide a new platform for research on panda CTL immunity and the design of vaccines for application in the bear family. IMPORTANCEUrsidae includes 5 genera and 8 species; however, the study of its immunology, especially structural immunology, is extremely rare to date. In this paper, we first crystallized the key complex pMHC-I, taking the giant panda as its representative species. Structural characteristics of the giant panda pMHC-I complexes, contains the unique pockets of PBG were analyzed in detail. Comparison of the panda pMHC-I in the bear family and other mammals, almost definite features was displayed. Meanwhile, the interaction between HC and LV, the unique features of pMHC-I in the CD8 binding and TCR docking, validation of anchor site in the PBG, and epitopes of potential viruses infected with the pandas, were concretely clarified. These unique characteristics of pMHC-I clearly indicate an unusual situation during the evolution of MHC molecules in the endangered pandas. These results also provide a novel platform for further study of panda T cell immunology and vaccines.

immunology↗

Counteracting Genome Instability by p53-dependent Mintosis

Entosis was proposed to promote aneuploidy and genome instability by cell-in-cell mediated engulfment in tumor cells. We reported here, in epithelial cells, that entosis coupled with mitotic arrest functions to counteract genome instability by targeting aneuploid mitotic progenies for engulfment and elimination. We found that the formation of cell-in-cell structures associated with prolonged mitosis, which was sufficient to induce entosis. This process was controlled by the tumor suppressor p53 (wild type) that upregulates Rnd3 expression in response to DNA damages associated with prolonged metaphase. Rnd3 compartmentalized RhoA activities accumulated during prolonged metaphase to drive cell-in-cell formation. Remarkably, this prolonged mitosis-induced entosis (mintosis) selectively targets non-diploid progenies for internalization, blockade of which increased aneuploidy. Thus, our work uncovered a heretofore unrecognized mechanism of mitotic surveillance for entosis, which eliminates newly-born abnormal daughter cells in a p53-depedent way to maintain genome integrity.

cell biology↗

Simultaneous Determination of Contents of Flavonol Glycosides and Terpene Lactones in Ginkgo Biloba Tablets by Ultra High Performance Liquid Chromatography Tandem Single Quadrupole Mass Spectrometry Detector

Ginkgo biloba leaf tablets is an effective ingredient in the treatment of cardiovascular and cerebrovascular diseases. In the process of drug production, the quality of ginkgo preparations is often controlled by measuring the content of seven ingredients in ginkgo leaves. To establish UPLC-MS multicomponent analysis method for ginkgo biloba tablets and to simultaneously determine the contents of quercetin (QUE), isorhamnetin(ISO), kaempferol(KAE) and GinkgolideA (GA),ginkgolideB(GB),ginkgolideC(GC) and bilobalide (BB) in ginkgo tablets. Waters Xbridge C18(4.6x150mm,3.5um) column was used, mobile phase A was acetonitrile and mobile phase B was water (containing 0.10% formic acid). The injection volume was 10L.Negative ion mode monitoring was conducted with ESI. Scanning range:m/z100[~]1400.The detection ions of the seven tested components includem/z301.0(QUE),m/z284.9(KAE),m/z315.1(ISO),m/z453.1(GA),m/z423.1(G B),m/z439.0(GC)and m/z325.0(BB), respectively. Within a space of 10min, flavonoids and terpene lactones in ginkgo biloba tablets were completely separated. The peak area exhibited an excellent linear relationship with the concentration. The sample recovery rate ranged from 91.74% to 109.77%.Precision RSDs of within-day and between-day were lower than 2.879% and 3.928% respectively. The method for determination of seven components in ginkgo biloba tablets displays good repeatability, recovery rate and precision, for which it can be applied to quality control of ginkgo biloba tablets.

biochemistry↗

Niacin Stimulates Mammary Gland Development in Pubertal Mice through Activation of the AKT/mTOR and ERK1/2 Signaling Pathways

Previous studies have shown the effects of vitamins on the development of the mammary gland. However, the role of niacin in this process has not been reported. Therefore, the aim of this study was to investigate the effects of niacin on mammary gland development in pubertal mice and to use a mouse mammary epithelial cell line to study the underlying mechanism. The results showed that niacin could activate the AKT/mTOR and ERK signaling pathways by the Gi protein-coupled receptor and increase phosphorylation of 4EBP1 to promote the synthesis of cell proliferation markers, leading to the dissociation of the Rb-E2F1 complex in mMECs. In addition, 0.5% niacin promoted mammary duct development, increased the expression of cyclin D1/D3 and PCNA, and activated Akt/mTOR and ERK1/2 in the mammary glands of pubertal mice. These results strongly suggest that niacin stimulates mammary gland development in pubertal mice through the Akt/mTOR and ERK1/2 signaling pathways and that the Gi protein-coupled receptor is essential for this function.

developmental biology↗

Dual Roles of the Retinal Pigment Epithelium and Lens in Cavefish Eye Degeneration

Astyanax mexicanus consists of two forms, a sighted surface dwelling form (surface fish) and a blind cave-dwelling form (cavefish). Embryonic eyes are initially formed in cavefish but they are subsequently arrested in growth and degenerate during larval development. Previous lens transplantation studies have shown that the lens plays a central role in cavefish eye loss. However, several lines of evidence suggest that additional factors, such as the retinal pigment epithelium (RPE), which is morphologically altered in cavefish, could also be involved in the eye regression process. To explore the role of the RPE in cavefish eye degeneration, we generated an albino eyed (AE) strain by artificial selection for hybrid individuals with large eyes and a depigmented RPE. The AE strain exhibited an RPE lacking pigment granules and showed reduced expression of the RPE specific enzyme retinol isomerase, allowing eye development to be studied by lens ablation in an RPE background resembling cavefish. We found that lens ablation in the AE strain had stronger negative effects on eye growth than in surface fish, suggesting that an intact RPE is required for normal eye development. We also found that the AE strain develops a cartilaginous sclera lacking boney ossicles, a trait similar to cavefish. Extrapolation of the results to cavefish suggests that the RPE and lens have dual roles in eye degeneration, and that deficiencies in the RPE may be associated with evolutionary changes in scleral ossification.

developmental biology↗

Diversity and complexity of the large surface protein family in the compacted genomes of various Pneumocystis species

Pneumocystis, a major opportunistic pathogen in patients with a broad range of immunodeficiencies, contains abundant surface proteins encoded by a multi-copy gene family, termed the major surface glycoprotein (Msg) gene superfamily. This superfamily has been identified in all Pneumocystis species characterized to date, highlighting its important role in Pneumocystis biology. In this report, through a comprehensive and in-depth characterization of 459 msg genes from 7 Pneumocystis species, we demonstrate, for the first time, the phylogeny and evolution of conserved domains in Msg proteins, and provide detailed description of the classification, unique characteristics and phylogenetic relatedness of five Msg families. We further describe the relative expression levels of individual msg families in two rodent Pneumocystis species, the substantial variability of the msg repertoires in P. carinii from laboratory and wild rats, and the distinct features of the expression site for the classic msg genes in Pneumocystis from 8 mammalian host species. Our analysis suggests a wide variety of functions for this superfamily, not only conferring antigenic variation to allow immune evasion but also mediating life-stage development, optimizing cell mobility and adhesion, and adapting to specific host niches or environmental conditions. This study provides a rich source of information that lays the foundation for the continued experimental exploration of the functions of the Msg superfamily in Pneumocystis biology.

molecular biology↗

The Brassica napus Wall-Associated Kinase-Like (WAKL) gene Rlm9 provides race-specific blackleg resistance

In plants, race-specific defense against microbial pathogens is facilitated by resistance (R) genes which correspond to specific pathogen avirulence (Avr) genes. This study reports the cloning of a blackleg R gene from Brassica napus (canola); Rlm9, which encodes a wall-associated kinase-like (WAKL) protein, a newly-discovered class of race-specific plant RLK resistance genes. Rlm9 provides race-specific resistance against isolates of Leptosphaeria maculans carrying the corresponding avirulence gene AvrLm5-9, representing only the second WAKL-type R gene described to date. The Rlm9 protein is predicted to be cell membrane-bound yet appears to have no direct interaction with AvrLm5-9. Rlm9 forms part of a distinct evolutionary family of RLK proteins in B. napus, and while little is yet known about WAKL function, the Brassica-Leptosphaeria pathosystem may prove to be a model system by which the mechanism of fungal avirulence protein recognition by WAKL-type R genes can be determined.

plant biology↗

A Hypomorphic Cystathionine β-Synthase Gene Contributes to Cavefish Eye Loss by Disrupting Optic Vasculature

Vestigial structures are key indicators of evolutionary descent but the mechanisms underlying their development are poorly understood. This study examines vestigial eye formation in the teleost Astyanax mexicanus, which consists of a sighted surface-dwelling morph and different populations of blind cave morphs. Cavefish embryos initially develop optic primordia but vestigial eyes are formed during larval development. Multiple genetic factors are involved in cavefish eye loss but none of the mutated genes have been identified. Here we identify cystathionine {beta}-synthase (cbsa), which encodes the key enzyme of the transsulfuration pathway, as a mutated gene responsible for eye degeneration in multiple cavefish populations. The inactivation of cbsa affects eye development by inducing accumulation of the transsulfuration intermediate homocysteine and defects in optic vasculature, including aneurysms and eye hemorrhages, leading to oxygen deficiency. Our findings suggest that localized modifications in the circulatory system and hypoxia had important roles in the evolution of vestigial eyes in blind cavefish.

developmental biology↗