白洋淀湖滨湿地岸边带氨氧化古菌与氨氧化细菌的分布特性

摘要：本研究通过分子生物学分析方法,以amoA基因为标记,考察了氨氧化古菌（Ammonia-Oxidizing Archaea, AOA）和氨氧化细菌（Ammonia-Oxidizing Bacteria,AOB）在华北平原的白洋淀这一典型湖泊的湖滨湿地岸边带系统中的生物多样性和丰度分布。在前人的研究中,氨氧化古菌在海洋、原生态土壤和人为干扰土壤等环境中主导氨氧化过程的完成。但本研究发现,在湿地岸边带系统中氨氧化过程并不是完全由氨氧化古菌主导完成,即氨氧化古菌和氨氧化细菌在不同区域分别占据主导地位。根据主导微生物的不同,可以将湿地岸边带区域划分为陆相区、中间区和湖相区。在湿地岸边带陆相区,氨氧化古菌主导氨氧化过程,氨氧化古菌的amoA基因丰度是氨氧化细菌的526倍（AOA：1.23?108每克干土;AOB：2.34?105每克干土）;在岸边带湖相区,氨氧化细菌主导氨氧化过程,氨氧化古菌的amoA基因丰度只有氨氧化细菌的1/50倍（AOA：3.17?106每克干土;AOB：1.39?108每克干土）;在岸边带中间区,两种微生物对氨氧化过程的贡献相当,二者的amoA基因丰度也相当 (AOA：9.83?106, AOB：4.08?106)。研究还发现,湿地中间区的微生物生物多样性高于陆相区和湖相区。在湿地中间区,氨氧化古菌和氨氧化细菌的生物多样性都最高,分别有5和7个操作分类单元（OTUs）;相比之下,岸边带陆相区和湖相区的多样性依次降低,陆相区的氨氧化古菌和氨氧化细菌分别有3和6个操作分类单元,湖相区的氨氧化古菌和氨氧化细菌分别有2和6个分类单元。本研究的两个结论进一步反映了湿地岸边带极强的空间异质性。     

Charge Generation and Recombination in an Organic Solar Cell with Low Energetic Offsets

Organic bulk heterojunction (BHJ) solar cells require energetic offsets between the donor and acceptor to obtain high short‐circuit currents (J_SC) and fill factors (FF). However, it is necessary to reduce the energetic offsets to achieve high open‐circuit voltages (V_OC). Recently, reports have highlighted BHJ blends that are pushing at the accepted limits of energetic offsets necessary for high efficiency. Unfortunately, most of these BHJs have modest FF values. How the energetic offset impacts the solar cell characteristics thus remains poorly understood. Here, a comprehensive characterization of the losses in a polymer:fullerene BHJ blend, PIPCP:phenyl‐C61‐butyric acid methyl ester (PC₆₁BM), that achieves a high V_OC (0.9 V) with very low energy losses (E_loss = 0.52 eV) from the energy of absorbed photons, a respectable J_SC (13 mA cm^?2), but a limited FF (54%) is reported. Despite the low energetic offset, the system does not suffer from field‐dependent generation and instead it is characterized by very fast nongeminate recombination and the presence of shallow traps. The charge‐carrier losses are attributed to suboptimal morphology due to high miscibility between PIPCP and PC₆₁BM. These results hold promise that given the appropriate morphology, the J_SC, V_OC, and FF can all be improved, even with very low energetic offsets.     

Factors influencing the natural regeneration of the pioneering shrub Calligonum mongolicum in sand dune stabilization plantations in arid deserts of northwest China

Calligonum mongolicum is a successful pioneer shrub to combat desertification, which is widely used for vegetation restoration in the desert regions of northwest China. In order to reveal the limitations to natural regeneration of C. mongolicum by asexual and sexual reproduction, following the process of sand dune stabilization, we assessed clonal shoots, seedling emergence, soil seed bank density, and soil physical characteristics in mobile and stabilized sand dunes. Controlled field and pot experiments were also conducted to assess germination and seedling emergence in different dune soil types and seed burial depths. The population density of mature C. mongolicum was significantly different after sand dune stabilization. Juvenile density of C. mongolicm was much lower in stabilized sand dunes than mobile sand dune. There was no significant difference in soil seed bank density at three soil depths between mobile and stabilized sand dunes, while the emergence of seedlings in stabilized dunes was much lower than emergence in mobile dunes. There was no clonal propagation found in stabilized dunes, and very few C. mongolicum seedlings were established on stabilized sand dunes. Soil clay and silt content, air‐filled porosity, and soil surface compaction were significantly changed from mobile sand dune to stabilized dunes. Seedling emergence of C. mongolicm was highly dependent on soil physical condition. These results indicated that changes in soil physical condition limited clonal propagation and seedling emergence of C. mongolicum in stabilized sand dunes. Seed bank density was not a limiting factor; however, poor seedling establishment limited C. mongolicum's further natural regeneration in stabilized sand dunes. Therefore, clonal propagation may be the most important mode for population expansion in mobile sand dunes. As a pioneer species C. mongolicum is well adapted to propagate in mobile sand dune conditions, it appears unlikely to survive naturally in stabilized sand dune plantations.     

High-throughput profiling of point mutations across the HIV-1 genome

Background

The HIV-1 pandemic is not the result of a static pathogen but a large genetically diverse and dynamic viral population. The virus is characterized by a highly mutable genome rendering efforts to design a universal vaccine a significant challenge and drives the emergence of drug resistant variants upon antiviral pressure. Gaining a comprehensive understanding of the mutational tolerance of each HIV-1 genomic position is therefore of critical importance.

Results

Here we combine high-density mutagenesis with the power of next-generation sequencing to gauge the replication capacity and therefore mutational tolerability of single point mutations across the entire HIV-1 genome. We were able to achieve the evaluation of point mutational effects on viral replicative capacity for 5,553 individual HIV-1 nucleotide positions – representing 57% of the viral genome. Replicative capacity was assessed at 3,943 nucleotide positions for a single alternate base change, 1,459 nucleotide positions for two alternate base changes, and 151 nucleotide positions for all three possible alternate base changes. This resulted in the study of how a total of 7,314 individual point mutations impact HIV-1 replication on a single experimental platform. We further utilize the dataset for a focused structural analysis on a capsid inhibitor binding pocket.

Conclusion

The approach presented here can be applied to any pathogen that can be genetically manipulated in a laboratory setting. Furthermore, the methodology can be utilized under externally applied selection conditions, such as drug or immune pressure, to identify genetic elements that contribute to drug or host interactions, and therefore mutational routes of pathogen resistance and escape.

     

Independent Relationship between Amyloid Precursor Protein (APP) Dimerization and γ-Secretase Processivity

Altered production of β-amyloid (Aβ) from the amyloid precursor protein (APP) is closely associated with Alzheimer’s disease (AD). APP has a number of homo- and hetero-dimerizing domains, and studies have suggested that dimerization of β-secretase derived APP carboxyl terminal fragment (CTFβ, C99) impairs processive cleavage by γ-secretase increasing production of long Aβs (e.g., Aβ1-42, 43). Other studies report that APP CTFβ dimers are not γ-secretase substrates. We revisited this issue due to observations made with an artificial APP mutant referred to as 3xK-APP, which contains three lysine residues at the border of the APP ectodomain and transmembrane domain (TMD). This mutant, which dramatically increases production of long Aβ, was found to form SDS-stable APP dimers, once again suggesting a mechanistic link between dimerization and increased production of long Aβ. To further evaluate how multimerization of substrate affects both initial γ-secretase cleavage and subsequent processivity, we generated recombinant wild type- (WT) and 3xK-C100 substrates, isolated monomeric, dimeric and trimeric forms of these proteins, and evaluated both ε-cleavage site utilization and Aβ production. These show that multimerization significantly impedes γ-secretase cleavage, irrespective of substrate sequence. Further, the monomeric form of the 3xK-C100 mutant increased long Aβ production without altering the initial ε-cleavage utilization. These data confirm and extend previous studies showing that dimeric substrates are not efficient γ-secretase substrates, and demonstrate that primary sequence determinants within APP substrate alter γ-secretase processivity.     

Peroxisome-generated succinate induces lipid accumulation and oxidative stress in the kidneys of diabetic mice

Diabetes normally causes lipid accumulation and oxidative stress in the kidneys, which plays a critical role in the onset of diabetic nephropathy; however, the mechanism by which dysregulated fatty acid metabolism increases lipid and reactive oxygen species (ROS) formation in the diabetic kidney is not clear. As succinate is remarkably increased in the diabetic kidney, and accumulation of succinate suppresses mitochondrial fatty acid oxidation and increases ROS formation, we hypothesized that succinate might play a role in inducing lipid and ROS accumulation in the diabetic kidney. Here we demonstrate a novel mechanism by which diabetes induces lipid and ROS accumulation in the kidney of diabetic animals. We show that enhanced oxidation of dicarboxylic acids by peroxisomes leads to lipid and ROS accumulation in the kidney of diabetic mice via the metabolite succinate. Furthermore, specific suppression of peroxisomal β-oxidation improved diabetes-induced nephropathy by reducing succinate generation and attenuating lipid and ROS accumulation in the kidneys of the diabetic mice. We suggest that peroxisome-generated succinate acts as a pathological molecule inducing lipid and ROS accumulation in kidney, and that specifically targeting peroxisomal β-oxidation might be an effective strategy in treating diabetic nephropathy and related metabolic disorders.