A cost-effective approach to identify conservation priority for 30 × 30 biodiversity target on the premise of food security.

There is a growing consensus on expanding protected and conserved areas for biodiversity conservation. Nevertheless, it remains uncertain where to expand conserved areas as well as what appropriate management modalities to choose. Moreover, conserved areas expansion should be balanced with crop-related food security challenges. We developed a framework to identify cost-effective areas for expanding protected areas and other effective area-based conservation measures (OECMs), and applied it to China. By combining templates for biodiversity conservation priorities at global scale and the priority conservation areas based on 2413 vertebrates' extinction risk in China, we identified areas with high biodiversity conservation value. We then categorized the priority areas according to human impact, indicating the potential cost of management. As a result of combining the two aspects above, we identified the most cost-effective areas for expanding protected areas and OECMs while excluding both the current and predicted croplands that can be used for food security. The results show that China could expand its protected areas to 22.81 % of the country's land area and establish OECMs in areas accounting for 9.82 % and 17.37 % of the country's land area in a cost-effective approach in two scenarios. In the ambitious scenario, protected and conserved areas would account for a maximum of 40.18 % of terrestrial area, with an average 62.67 % coverage of the 2413 species' suitable habitat. To achieve the goals of protected and conserved areas in Kunming-Montreal Global Biodiversity Framework, countries could apply this framework to identify their protected areas and OECM expansion priorities.

Over 1/4 of China's terrestrial area significantly contributed both to biodiversity conservation and carbon neutrality, requiring protection.

Protected areas (PAs) play a crucial role in halting biodiversity loss and mitigating climate change. However, research on the advantages of integrating biodiversity conservation and climate mitigation within PAs remains limited, and there is a deficiency in holistic, scientifically supported management strategies. To address these gaps, we conducted a case study in China, comparing the conservation effectiveness of designating conservation priorities considering either single or multiple objectives, including biodiversity conservation and carbon neutrality. The results showed that integrating multiple values could truly increase the effectiveness of PAs compared to a single value considered. Over 1/4 of China's terrestrial area had a significant contribution for both biodiversity conservation and carbon neutrality, yet remained unprotected. Expanding PAs in these areas holds tremendous win-win biodiversity conservation and carbon neutrality opportunity. We delineated different conservation priorities for comprehensive management and outlined strategies for different types of areas. The framework presented in this study can serve as a reference for other places with comparable scales or management objectives.

Ecologically different earthworm species are the driving force of microbial hotspots influencing Pb uptake by the leafy vegetable Brassica campestris.

Food chain contamination by soil lead (Pb), beginning with Pb uptake by leafy vegetables, is a threat to food safety and poses a potential risk to human health. This study highlights the importance of two ecologically different earthworm species (the anecic species Amynthas aspergillum and the epigeic species Eisenia fetida) as the driving force of microbial hotspots to enhance Pb accumulation in the leafy vegetable Brassica campestris at different Pb contamination levels (0, 100, 500, and 1,000 mg·kg-1). The fingerprints of phospholipid fatty acids (PLFAs) were employed to reveal the microbial mechanism of Pb accumulation involving earthworm-plant interaction, as PLFAs provide a general profile of soil microbial biomass and community structure. The results showed that Gram-positive (G+) bacteria dominated the microbial community. At 0 mg·kg-1 Pb, the presence of earthworms significantly reduced the total PLFAs. The maximum total of PLFAs was found at 100 mg·kg-1 Pb with E. fetida inoculation. A significant shift in the bacterial community was observed in the treatments with E. fetida inoculation at 500 and 1,000 mg·kg-1 Pb, where the G+/G- bacteria ratio was significantly decreased compared to no earthworm inoculation. Principal component analysis (PCA) showed that E. fetida had a greater effect on soil microbial hotspots than A. aspergillum, thus having a greater effect on the Pb uptake by B. campestris. Redundancy analysis (RDA) showed that soil microbial biomass and structure explained 43.0% (R2 = 0.53) of the total variation in Pb uptake by B. campestris, compared to 9.51% of microbial activity. G- bacteria explained 23.2% of the total variation in the Pb uptake by B. campestris, significantly higher than the other microbes. The Mantel test showed that microbial properties significantly influenced Pb uptake by B. campestris under the driving force of earthworms. E. fetida inoculation was favorable for the G- bacterial community, whereas A. aspergillum inoculation was favorable for the fungal community. Both microbial communities facilitated the entry of Pb into the vegetable food chain system. This study delivers novel evidence and meaningful insights into how earthworms prime the microbial mechanism of Pb uptake by leafy vegetables by influencing soil microbial biomass and community composition. Comprehensive metagenomics analysis can be employed in future studies to identify the microbial strains promoting Pb migration and develop effective strategies to mitigate Pb contamination in food chains.

Therapeutic Effects of Baicalin on Diseases Related to Gut-Brain Axis Dysfunctions.

The gut-brain axis is an active area of research. Several representative diseases, including central nervous system disorders (Alzheimer's disease, Parkinson's disease, and depression), metabolic disorders (obesity-related diseases), and intestinal disorders (inflammatory bowel disease and dysbiosis), are associated with the dysfunctional gut-brain axis. Baicalin, a bioactive flavonoid extracted from Scutellaria baicalensis, is reported to exert various pharmacological effects. This narrative review summarizes the molecular mechanisms and potential targets of baicalin in disorders of the gut-brain axis. Baicalin protects the central nervous system through anti-neuroinflammatory and anti-neuronal apoptotic effects, suppresses obesity through anti-inflammatory and antioxidant effects, and alleviates intestinal disorders through regulatory effects on intestinal microorganisms and short-chain fatty acid production. The bioactivities of baicalin are mediated through the gut-brain axis. This review comprehensively summarizes the regulatory role of baicalin in gut-brain axis disorders, laying a foundation for future research, although further confirmatory basic research is required.

A framework for identifying bird conservation priority areas in croplands at national level.

Global biodiversity is declining at an unprecedented rate, and the Post-2020 Global Biodiversity Framework requires each country to fulfill the conservation targets in biodiversity-inclusive spatial planning. Croplands provide habitat and food for many species, making them crucial for biodiversity conservation in addition to food production. Assessing conservation priorities in cropland is a prerequisite to allocate conservation resources and plan actions for better conservation outcomes. Yet quantitative methods to assess cropland conservation priority for biodiversity conservation at a national scale are still lacking. We proposed a framework for identifying the conservation priority in cropland for bird species at a national scale and applied the framework in China. We calculated the suitable habitat for each species and used a complementarity-based approach to designate the irreplaceable conservation priority areas considering richness, threatened level, and conservation percentage targets. We identified cropland taking up 6.76% of China's land area as a bird conservation priority, partially covering the suitable habitat of all the study species. By analyzing the landscape pattern of the priority areas and species' foraging traits, we provided policy-making suggestions according to area-specific characteristics. This framework can be used to identify priority areas for large-scale biodiversity conservation for different countries.

One-third of lands face high conflict risk between biodiversity conservation and human activities in China.

Biodiversity is declining at an unprecedented rate, and conservation is needed in many places including human-dominated landscapes. Evaluation of conflict risk between biodiversity conservation and human activities is a prerequisite for countries to develop strategies to achieve better conservation outcomes. However, quantitative methods to measure the conflict risk in large-scale areas are still lacking. Here we put forward a quantitative model in large-scale areas and produce the first continuum map of conflict risk in China. Our results show that conflict risk hotspots take up 32.86 % of China's terrestrial area, which may affect 42.98 % of China's population and more than 98 % of threaten vertebrates. Although species richness is high in these hotspot regions, only 10.69 % of them are covered by protected areas. Therefore, alternative conservation measures and proactive spatial planning are needed, especially in regions along the coastlines and around the Sichuan Basin. Especially, extraordinary attentions should be paid to urban agglomerations such as the Pearl River Delta and Yangtze River Delta. Compared to previous studies, our study quantifies the conflict risk of every gird cell, enabling the comparison among any locations. The analysis of 500 times generations shows a low sensitivity of the model as the maximum standard deviation is only 0.017. Furthermore, our model can be applied in other countries or at global scale to provide strategies for conflict governance and biodiversity conservation.

Cost-effective priorities for the expansion of global terrestrial protected areas: Setting post-2020 global and national targets.

Biodiversity loss is a social and ecological emergency, and calls have been made for the global expansion of protected areas (PAs) to tackle this crisis. It is unclear, however, where best to locate new PAs to protect biodiversity cost-effectively. To answer this question, we conducted a spatial meta-analysis by overlaying seven global biodiversity templates to identify conservation priority zones. These are then combined with low human impact areas to identify cost-effective zones (CEZs) for PA designation. CEZs cover around 38% of global terrestrial area, of which only 24% is currently covered by existing PAs. To protect more CEZs, we propose three scenarios with conservative, moderate, and ambitious targets, which aim to protect 19, 26, and 43% of global terrestrial area, respectively. These three targets are set for each Convention on Biological Diversity party with spatially explicit CEZs identified, providing valuable decision support for the post-2020 global biodiversity framework.

Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum.

BACKGROUND: Clostridium acetobutylicum is a model organism for both clostridial biology and solvent production. The organism is exposed to its own toxic metabolites butyrate and butanol, which trigger an adaptive stress response. Integrative analysis of proteomic and RNAseq data may provide novel insights into post-transcriptional regulation. RESULTS: The identified iTRAQ-based quantitative stress proteome is made up of 616 proteins with a 15 % genome coverage. The differentially expressed proteome correlated poorly with the corresponding differential RNAseq transcriptome. Up to 31 % of the differentially expressed proteins under stress displayed patterns opposite to those of the transcriptome, thus suggesting significant post-transcriptional regulation. The differential proteome of the translation machinery suggests that cells employ a different subset of ribosomal proteins under stress. Several highly upregulated proteins but with low mRNA levels possessed mRNAs with long 5'UTRs and strong RBS scores, thus supporting the argument that regulatory elements on the long 5'UTRs control their translation. For example, the oxidative stress response rubrerythrin was upregulated only at the protein level up to 40-fold without significant mRNA changes. We also identified many leaderless transcripts, several displaying different transcriptional start sites, thus suggesting mRNA-trimming mechanisms under stress. Downregulation of Rho and partner proteins pointed to changes in transcriptional elongation and termination under stress. CONCLUSIONS: The integrative proteomic-transcriptomic analysis demonstrated complex expression patterns of a large fraction of the proteome. Such patterns could not have been detected with one or the other omic analyses. Our analysis proposes the involvement of specific molecular mechanisms of post-transcriptional regulation to explain the observed complex stress response.

Patterned biofilm formation reveals a mechanism for structural heterogeneity in bacterial biofilms.

Bacterial biofilms are ubiquitous and are the major cause of chronic infections in humans and persistent biofouling in industry. Despite the significance of bacterial biofilms, the mechanism of biofilm formation and associated drug tolerance is still not fully understood. A major challenge in biofilm research is the intrinsic heterogeneity in the biofilm structure, which leads to temporal and spatial variation in cell density and gene expression. To understand and control such structural heterogeneity, surfaces with patterned functional alkanthiols were used in this study to obtain Escherichia coli cell clusters with systematically varied cluster size and distance between clusters. The results from quantitative imaging analysis revealed an interesting phenomenon in which multicellular connections can be formed between cell clusters depending on the size of interacting clusters and the distance between them. In addition, significant differences in patterned biofilm formation were observed between wild-type E. coli RP437 and some of its isogenic mutants, indicating that certain cellular and genetic factors are involved in interactions among cell clusters. In particular, autoinducer-2-mediated quorum sensing was found to be important. Collectively, these results provide missing information that links cell-to-cell signaling and interaction among cell clusters to the structural organization of bacterial biofilms.

Targeted human cerebrospinal fluid proteomics for the validation of multiple Alzheimer's disease biomarker candidates.

There is significant interest in the development of methods to validate novel biomarkers for Alzheimer's disease (AD) diagnosis. Previously, a proteomic panel of cerebrospinal fluid (CSF) biomarker candidates that differentiated AD and non-AD CSF with accuracy higher than 90% was found; information about these CSF proteins can be used to develop multiple reaction monitoring (MRM) based analytical assays, which offer the possibility of quantifying protein expression level changes in samples, as well as, validation among multiple laboratories. Here we report an MRM assay that demonstrates good linearity (average R(2)=0.969) and reproducibility (average coefficient of variance of 6.93%) for the proposed AD CSF biomarkers. MRM quantification results of Aß1-40, Aß1-42, retinol-binding protein and cystatin C correlated well with those from ELISA (average R(2)=0.974). Analysis shows that 12 out of 16 selected targets exhibit the same trend in protein expression as that in literature.

Workflow for quantitative proteomic analysis of Clostridium acetobutylicum ATCC 824 using iTRAQ tags.

Clostridium acetobutylicum (Cac) is an anaerobic, endospore-forming, Gram-positive bacterium with tremendous promise for use as a biocatalyst for the production of fuels and solvents. Cac proteomic sample preparation for shotgun analysis typically involves a multitude of reagents for harsh lysis conditions and to maintain protein solubility. We describe a protein extraction and preparation method for Cac that is compatible with proteomic shotgun analysis using isobaric labeling approaches. The method is applied to the analysis of Cac grown under butanol stress and labeled using iTRAQ 4-plex reagents. This method relies on the use of calcium carbonate to facilitate lysis by sonication and a commercially available kit to remove detergents prior to labeling. This workflow resulted in the identification and quantitation of 566 unique proteins using ProteinPilot software with a false discovery rate of 0.01% for peptide matches and 0.70% for protein matches. Ninety-five proteins were found to have statistically higher expression levels in butanol-stressed Cac as compared to non-stressed Cac. Sixty-one proteins were found to have statistically lower expression levels in stressed versus non-stressed cells. This method may be applicable to other Gram-positive organisms.

Serine phosphorylation is critical for the activation of ubiquitin-specific protease 1 and its interaction with WD40-repeat protein UAF1.

Deubiquitinating enzymes (DUBs) are important for the normal function of a number of cellular processes, including transcriptional regulation, cell cycle control, and DNA damage response. The enzymatic activity of DUB is regulated by different mechanisms. DUBs in several different families are post-translationally modified by phosphorylation. Large-scale phosphoproteomic studies of human DUBs revealed that a majority of ubiquitin-specific proteases (USPs) are phosphorylated. USP1 is a prototypical DUB that requires a specific interaction with a WD40-repeat protein, UAF1, for its catalytic activity. In this study, we show that Ser313 phosphorylation in USP1 is required for its interaction with UAF1 and for the stimulation of USP1's activity. In contrast, two other known USP1 serine phosphorylations (Ser42 and Ser67) are dispensable with respect to the activity of the USP1/UAF1 complex. An S313D phosphomimetic mutation in USP1 can substitute for Ser313 phosphorylation in promoting the formation of the USP1/UAF1 complex. We further demonstrated that CDK1 is responsible for Ser313 phosphorylation, and protein phosphatase treatment of USP1 can lead to inactivation of USP1/UAF1. An inserted domain in USP1 (amino acids 235-408) was found to interact with UAF1, and this interaction is mediated by Ser313 phosphorylation. Our findings revealed an intriguing mechanism of regulating USP1 activity that combines phosphorylation of a key serine residue in USP1 and the specific interaction of USP1 with a WD40-repeat protein UAF1. The pSer313-dependent formation of the USP1/UAF1 complex points to a new approach for inhibiting USP1 activity by disrupting the interaction between the UAF1's WD40-repeat domain and the Ser313-containing phosphopeptide in USP1.

Microtopographic patterns affect Escherichia coli biofilm formation on poly(dimethylsiloxane) surfaces.

Biofilms are involved in 80% of human bacterial infections and are up to 1000 times more tolerant to antibiotics than their planktonic counterparts. To better understand the mechanism of bacteria-surface interactions, polydimethylsiloxane (PDMS) surfaces with microtopographic patterns were tested to study the effects of surface topography on bacterial adhesion and biofilm formation. The patterned PDMS surfaces were prepared by transferring complementary surface topography from a silicon wafer etched via photolithography to introduce 10 µm tall square-shape features. The dimension of protruding square features and the distance between adjacent features were systematically varied. Escherichia coli RP437/pRSH103 (with constitutive expression of red fluorescent protein) was found to preferentially attach and form biofilms in valleys between protruding features even when the dimension of plateaus (top of the square features) is considerably larger than valleys. In addition, significant adhesion of E. coli on plateaus was only observed when the plateaus were bigger than 20 µm × 20 µm for face-up patterns and 40 µm × 40 µm for face-down patterns. This finding suggests that a threshold dimension may be essential for biofilm formation on flat surfaces without physical confinement.

Effects of Trp- and Arg-containing antimicrobial-peptide structure on inhibition of Escherichia coli planktonic growth and biofilm formation.

Biofilms are sessile microbial communities that cause serious chronic infections with high morbidity and mortality. In order to develop more effective approaches for biofilm control, a series of linear cationic antimicrobial peptides (AMPs) with various arginine (Arg or R) and tryptophan (Trp or W) repeats [(RW)(n)-NH(2), where n = 2, 3, or 4] were rigorously compared to correlate their structures with antimicrobial activities affecting the planktonic growth and biofilm formation of Escherichia coli. The chain length of AMPs appears to be important for inhibition of bacterial planktonic growth, since the hexameric and octameric peptides significantly inhibited E. coli growth, while tetrameric peptide did not cause noticeable inhibition. In addition, all AMPs except the tetrameric peptide significantly reduced E. coli biofilm surface coverage and the viability of biofilm cells, when added at inoculation. In addition to inhibition of biofilm formation, significant killing of biofilm cells was observed after a 3-hour treatment of preformed biofilms with hexameric peptide. Interestingly, treatment with the octameric peptide caused significant biofilm dispersion without apparent killing of biofilm cells that remained on the surface; e.g., the surface coverage was reduced by 91.5 + or - 3.5% by 200 microM octameric peptide. The detached biofilm cells, however, were effectively killed by this peptide. Overall, these results suggest that hexameric and octameric peptides are potent inhibitors of both bacterial planktonic growth and biofilm formation, while the octameric peptide can also disperse existing biofilms and kill the detached cells. These results are helpful for designing novel biofilm inhibitors and developing more effective therapeutic methods.

Antimicrobial properties of nanostructured hydrogel webs containing silver.

The need exists for biomaterials that prevent biofilm formation and associated infections. In this report, we have studied the synthesis, processing, and antimicrobial behavior of new silver-containing thermoplastic hydrogel nanofibrous webs. Thermoplastic hydrogels were synthesized from multiblock PEG-POSS polyurethanes (PEG: poly(ethylene gylcol); POSS: polyhedral oligosilsesquioxane) and electrospun into nanofibrous webs (diameter approximately 150 nm), with or without AgNO(3). The nanofibrous hydrogels exhibited unusual shrinkage during water uptake, yielding a uniquely dense structure compared to hydrogels prepared from cast films. Antimicrobial activity was examined using exposure to Escherichia coli with daily refreshment of medium and inoculation to a controlled cell density. Nanofibrous hydrogels without silver featured the most rapid and most extensive biofilm formation, while the silver-containing nanofibrous hydrogel featured outstanding biofilm resistance, with biofilm formation taking hold only after 14 days of incubation in daily refreshed bacterial cultures. We envision application of the unique antimicrobial hydrogels as wound dressings that combine sustained bactericidal properties and lack of volumetric swelling during water uptake.

Antimicrobial dendrimer active against Escherichia coli biofilms.

We have investigated the ability of a previously reported antimicrobial peptide dendrimer (RW)(4D) to inactivate Escherichia coli RP437 in planktonic culture and in biofilms. The results show that the dendrimer inhibits bacterial growth in both planktonic and biofilm states. Live/Dead staining assays reveal that most bacteria in a preformed biofilm lose viability after treatment with this peptide. This result is in marked contrast to most existing reports that antimicrobial peptides are ineffective against mature bacterial biofilms.

Prolonged control of patterned biofilm formation by bio-inert surface chemistry.

A bio-inert surface chemistry was developed that can confine biofilm formation in designed patterns for at least 26 days.

Molecular gradients of bioinertness reveal a mechanistic difference between mammalian cell adhesion and bacterial biofilm formation.

Chemical gradients play an important role in guiding the activities of both eukaryotic and prokaryotic cells. Here, we used molecularly well-defined chemical gradients formed by self-assembled monolayers (SAMs) on gold films to reveal that mammalian cell adhesion and bacterial biofilm formation respond differently to a gradient of surface chemistry that resists cell attachment. Gradient self-assembled monolayers (SAMs) consisting of two mixed alkanethiols were fabricated by differential exposure of the gold film to one alkanethiol, followed by soaking in another alkanethiol solution. A gradient in bioinertness that resisted cell attachment was created on SAMs from a gradient in the surface density of HS(CH2)11(OCH2CH2)3OH, backfilled with either HS(CH2)11OH or HS(CH2)11CH3. Measurements of the amounts of mammalian cells and bacterial biofilms on these gradient surfaces reveal that, for mammalian cells, a critical density of adhesion ligands from absorbed proteins on surfaces exists for supporting maximum adhesion and proliferation, whereas for the bacterium Escherichia coli , the amount of biofilm formed on surfaces increased linearly with the surface density of adhesive groups (methyl or hydroxyl groups) in different media. These results are consistent with mammalian cell adhesion requiring an anchorage via specific molecular recognitions and suggest that biofilms can form by immobilization of bacteria via nonspecific interaction between bacteria and surfaces.

Identifying Escherichia coli genes involved in intrinsic multidrug resistance.

Multidrug resistance is a major cause of clinical failure in treating bacterial infections. Increasing evidence suggests that bacteria can resist multiple antibiotics through intrinsic mechanisms that rely on gene products such as efflux pumps that expel antibiotics and special membrane proteins that block the penetration of drug molecules. In this study, Escherichia coli was used as a model system to explore the genetic basis of intrinsic multidrug resistance. A random mutant library was constructed in E. coli EC100 using transposon mutagenesis. The library was screened by growth measurement to identify the mutants with enhanced or reduced resistance to chloramphenicol (Cm). Out of the 4,000 mutants screened, six mutants were found to be more sensitive to Cm and seven were more resistant compared to the wild-type EC100. Mutations in 12 out of the 13 mutants were identified by inverse polymerase chain reaction. Mutants of the genes rob, garP, bipA, insK, and yhhX were more sensitive to Cm compared to the wild-type EC100, while the mutation of rhaB, yejM, dsdX, nagA, yccE, atpF, or htrB led to higher resistance. Overexpression of rob was found to increase the resistance of E. coli biofilms to tobramycin (Tob) by 2.7-fold, while overexpression of nagA, rhaB, and yccE significantly enhanced the susceptibility of biofilms by 2.2-, 2.5-, and 2.1-fold respectively.

Identifying the important structural elements of brominated furanones for inhibiting biofilm formation by Escherichia coli.

A collection of structurally closely related furanones was synthesized to identify the most important structural elements in brominated furanones for inhibiting the formation of bacterial biofilms. The results suggest that a conjugated exocyclic vinyl bromide on the furanone ring is the most important structural element for the non-toxic but inhibition activity for Escherichia coli biofilm formation. Furanones bearing monosubstituted bromide groups on saturated carbons were found to have a toxic effect that attenuates the bacterial growth.