Influence of surface water and groundwater on functional traits and trade-off strategies of oasis communities at the end of the Keriya River, China.

Plant functional traits reflect the capacity of plants to adapt to their environment and the underlying optimization mechanisms. However, few studies have investigated trade-off strategies for functional traits in desert-wetland ecosystems, the mechanisms by which surface water disturbance and groundwater depth drive functional trait variation at the community scale, and the roles of intraspecific and interspecific variation. Therefore, this study analyzed specific differences in community-weighted mean traits among habitat types and obtained the relative contribution of intraspecific and interspecific variation by decomposing community-weighted mean traits, focusing on the Daliyabuyi Oasis in the hinterland of the Taklamakan Desert. We also explored the mechanisms by which surface water and groundwater influence different sources of variability specifically. The results showed that plant height, relative chlorophyll content, leaf thickness, leaf nitrogen content, and nitrogen-phosphorus ratio were the key traits reflecting habitat differences. As the groundwater depth becomes shallower and surface water disturbance intensifies, plant communities tend to have higher leaf nitrogen content, nitrogen-phosphorus ratio, and relative chlorophyll content and lower height. Surface water, groundwater, soil water content, and total soil nitrogen can influence interspecific and intraspecific variation in these traits through direct and indirect effects. As arid to wet habitats change, plant trade-off strategies for resources will shift from conservative to acquisitive. The study concluded that community functional traits are mainly contributed by interspecific variation, but consideration of intraspecific variation and the covariation effects that exist between it and interspecific variation can help to further enhance the understanding of the response of community traits in desert-wetland ecosystems to environmental change. Surface water disturbance has a non-negligible contribution to this adaptation process and plays a higher role than groundwater depth.

Effects of meteorological factors and groundwater depths on sap flow density of Populus euphratica in a desert oasis, Taklamakan Desert, China.

Accurate estimation of desert vegetation transpiration is key to regulating desert water resources of desert ecosystems. Sap flow density (SFD) can indirectly reflect a tree's transpiration consumption, and it has been affected by climate warming and groundwater depths in desert ecosystems. Sap flow responses to meteorological conditions and groundwater depths are further affected by tree of different sizes. However, how meteorological factors and groundwater depths affects tree sap flow among tree sizes remains poorly understand. In this study, a 50 × 50 m P. euphratica stand was selected as a sample plot in the hinterland of the Taklamakan Desert, and the SFD of P. euphratica of different sizes was measured continuously using the thermal diffusion technique from May to October of 2021 and 2022. The results showed that SFD of large P. euphratica was consistently higher than that of small P. euphratica in 2021 and 2022. and the SFD of P. euphratica was significantly and positively correlated with solar radiation (Rad) and vapor pressure deficit (VPD), and the correlation was higher than that of the air temperature (Ta) and relative humidity (RH), and also showed a strong non-linear relationship. Analysis of the hour-by-hour relationship between P. euphratica SFD and VPD and Rad showed a strong hysteresis. Throughout the growing season, there was no significant relationship between SFD of P. euphratica and groundwater depth, VPD and Rad were still the main controlling factors of SFD in different groundwater depths. However, during the period of relative groundwater deficit, the effect of groundwater depth on the SFD of P. euphratica increased, and the small P. euphratica was more sensitive, indicating that the small P. euphratica was more susceptible to groundwater changes. This study emphasized that Rad and VPD were the main drivers of SFD during the growing season, as well as differences in the response of different sizes of P. euphratica to groundwater changes. The results of the study provide a scientific basis for future modeling of transpiration consumption in P. euphratica forests in desert oases, as well as the regulation and allocation of water resources.

Comprehensive Assessment of 16S rRNA Gene Amplicon Sequencing for Microbiome Profiling across Multiple Habitats.

The 16S rRNA gene works as a rapid and effective marker for the identification of microorganisms in complex communities; hence, a huge number of microbiomes have been surveyed by 16S amplicon-based sequencing. The resolution of the 16S rRNA gene is always considered only at the genus level; however, it has not been verified on a wide range of microbes yet. To fully explore the ability and potential of the 16S rRNA gene in microbial profiling, here, we propose Qscore, a comprehensive method to evaluate the performance of amplicons by integrating the amplification rate, multitier taxonomic annotation, sequence type, and length. Our in silico assessment by a "global view" of 35,889 microbe species across multiple reference databases summarizes the optimal sequencing strategy for 16S short reads. On the other hand, since microbes are unevenly distributed according to their habitats, we also provide the recommended configuration for 16 typical ecosystems based on the Qscores of 157,390 microbiomes in the Microbiome Search Engine (MSE). Detailed data simulation further proves that the 16S amplicons produced with Qscore-suggested parameters exhibit high precision in microbiome profiling, which is close to that of shotgun metagenomes under CAMI metrics. Therefore, by reconsidering the precision of 16S-based microbiome profiling, our work not only enables the high-quality reusability of massive sequence legacy that has already been produced but is also significant for guiding microbiome studies in the future. We have implemented the Qscore as an online service at http://qscore.single-cell.cn to parse the recommended sequencing strategy for specific habitats or expected microbial structures. IMPORTANCE 16S rRNA has long been used as a biomarker to identify distinct microbes from complex communities. However, due to the influence of the amplification region, sequencing type, sequence processing, and reference database, the accuracy of 16S rRNA has not been fully verified on a global range. More importantly, the microbial composition of different habitats varies greatly, and it is necessary to adopt different strategies according to the corresponding target microbes to achieve optimal analytical performance. Here, we developed Qscore, which evaluates the comprehensive performance of 16S amplicons from multiple perspectives, thus providing the best sequencing strategies for common ecological environments by using big data.

The combined effect of surface water and groundwater on environmental heterogeneity reveals the basis of beta diversity pattern in desert oasis communities.

Beta diversity indicates the species turnover with respect to a particular environmental gradient. It is crucial for understanding biodiversity maintenance mechanisms and for prescribing conservation measures. In this study, we aimed to reveal the drivers of beta diversity patterns in desert hinterland oasis communities by establishing three types of surface water disturbance and groundwater depth gradients. The results indicated that the dominant factor driving the beta diversity pattern within the same gradient shifted from soil organic matter to pH, as groundwater depth became shallower and surface water disturbance increased. Among the different gradients, surface water disturbance can have important effects on communities where original water resource conditions are extremely scarce. Under the premise that all habitats are disturbed by low surface water, differences in groundwater depth dominated the shifts in the community species composition. However, when groundwater depth in each habitat was shallow, surface water disturbance had little effect on the change in species composition. For the two components of beta diversity, the main drivers of species turnover pattern was the unique effects of surface water disturbance and soil environmental differences, and the main driver of species nestedness pattern was the common effect of multiple environmental pressures. The results of this study suggest that increasing the disturbance of surface water in dry areas with the help of river flooding will help in promoting vegetation restoration and alleviating the degradation of oases. They also confirm that surface water and groundwater mutually drive the establishment of desert oasis communities. Equal focus on both factors can contribute to the rational ecological recovery of dryland oases and prevent biodiversity loss.

A Potent Micron Neoantigen Tumor Vaccine GP-Neoantigen Induces Robust Antitumor Activity in Multiple Tumor Models.

Therapeutic tumor neoantigen vaccines have been widely studied given their good safety profile and ability to avoid central thymic tolerance. However, targeting antigen-presenting cells (APCs) and inducing robust neoantigen-specific cellular immunity remain challenges. Here, a safe and broad-spectrum neoantigen vaccine delivery system is proposed (GP-Neoantigen) based on ß-1,3-glucan particles (GPs) derived from Saccharomyces cerevisiae and coupling peptide antigens with GPs through convenient click chemistry. The prepared system has a highly uniform particle size and high APC targeting specificity. In mice, the vaccine system induced a robust specific CD8+ T cell immune response and humoral immune response against various conjugated peptide antigens and showed strong tumor growth inhibitory activity in EG7·OVA lymphoma, B16F10 melanoma, 4T1 breast cancer, and CT26 colon cancer models. The combination of the toll-like receptors (TLRs) agonist PolyI:C and CpG 2395 further enhanced the antitumor response of the particle system, achieving complete tumor clearance in multiple mouse models and inducing long-term rejection of reinoculated tumors. These results provide the broad possibility for its further clinical promotion and personalized vaccine treatment.

P22 virus-like particles as an effective antigen delivery nanoplatform for cancer immunotherapy.

As a new strategy for cancer immunotherapy, therapeutic cancer vaccines have been greatly improved in recent years. However, addressing the needs to quickly and efficiently elicit a high-intensity immune response against neoantigen peptides, especially to induce an effective cytotoxic lymphocyte (CTL) reaction, remain challenges in this field. In this study, virus-like particles (VLPs) derived from the phage P22 were adopted to load peptide antigens on the surface, to test whether VLP technology can be used as a platform for efficient peptide antigen delivery by therapeutic cancer vaccines. The B and T epitopes (OVAB peptide and OVAT peptide) of ovalbumin (OVA) were used here as model antigens and fused individually at the C terminus of the coat protein (CP), which allowed display on the surface of P22 particles to form two types of vaccine particles (VLP-OVAB and VLP-OVAT). Subsequent experiments showed that VLP-OVAB induced an antibody titer against the peptide antigen as high as 5.0 × 105 and that VLP-OVAT induced highly effective cross-presentation and then strongly activated a T epitope-specific CTL response. Mouse tumor model experiments showed that VLP-OVAT could significantly inhibit tumor growth by increasing the proportions of CD4+ T cells, CD8+ T cells and effector memory T cells (TEM cells) and lowering the proportion of myeloid-derived suppressor cells (MDSCs) among tumor-infiltrating lymphocytes and splenocytes. Compared with other chemically synthesized nanomaterials, VLPs have obvious advantages as vaccine carriers due to their clear chemical composition, fixed spatial structure, excellent biocompatibility, and relatively high potential for clinical translation. Therefore, this platform may lay a solid foundation for the design and preparation of personalized therapeutic vaccines based on neoantigen peptides.

PEG Linker Improves Antitumor Efficacy and Safety of Affibody-Based Drug Conjugates.

Antibody drug conjugates (ADCs) have become an important modality of clinical cancer treatment. However, traditional ADCs have some limitations, such as reduced permeability in solid tumors due to the high molecular weight of monoclonal antibodies, difficulty in preparation and heterogeneity of products due to the high drug/antibody ratio (4-8 small molecules per antibody). Miniaturized ADCs may be a potential solution, although their short circulation half-life may lead to new problems. In this study, we propose a novel design strategy for miniaturized ADCs in which drug molecules and small ligand proteins are site-specifically coupled via a bifunctional poly(ethylene glycol) (PEG) chain. The results showed that the inserted PEG chains significantly prolonged the circulation half-life but also obviously reduced the cytotoxicity of the conjugates. Compared with the conjugate ZHER2-SMCC-MMAE (HM), which has no PEG insertion, ZHER2-PEG4K-MMAE (HP4KM) and ZHER2-PEG10K-MMAE (HP10KM) with 4 or 10 kDa PEG insertions have 2.5- and 11.2-fold half-life extensions and 4.5- and 22-fold in vitro cytotoxicity reductions, respectively. The combined effect leads to HP10KM having the most ideal tumor therapeutic ability at the same dosages in the animal model, and its off-target toxicity was also reduced by more than 4 times compared with that of HM. These results may indicate that prolonging the half-life is very helpful in improving the therapeutic capacity of miniaturized ADCs. In the future, the design of better strategies that can prolong half-life without affecting cytotoxicity may be useful for further improving the therapeutic potential of these molecules.