Prioritizing conservation sites for multi-pond systems to maintain protection of water quality in a fragmented agricultural catchment.

Precise targeting of conservation practices to the most effective sites in multi-pond systems (MPSs) is critical for resource optimization and water quality improvement. Previous studies generally prioritized ponds for conservation practices considering nutrient removal efficiency. However, they have frequently overlooked the role of ponds in sediment interception and the impact of human activities and environmental factors around the pond.

Regulation of Precise DNA Repair by Nuclear Actin Polymerization: A Chance for Improving Gene Therapy?

Although more difficult to detect than in the cytoplasm, it is now clear that actin polymerization occurs in the nucleus and that it plays a role in the specific processes of the nucleus such as transcription, replication, and DNA repair. A number of studies suggest that nuclear actin polymerization is promoting precise DNA repair by homologous recombination, which could potentially be of help for precise genome editing and gene therapy. This review summarizes the findings and describes the challenges and chances in the field.

UAV-based modelling of vegetation recovery under extreme habitat stresses in the water level fluctuation zone of the Three Gorges Reservoir, China.

Impoundment of the Three Gorges Reservoir on the upper Yangtze River has remarkably altered hydrological regime within the dammed reaches, triggering structural and functional changes of the riparian ecosystem. Up to date, how vegetation recovers in response to compound habitat stresses in the water level fluctuation zone remains inexplicitly understood. In this study, plant above-ground biomass (AGB) in a selected water level fluctuation zone was quantified to depict its spatial and temporal pattern using unmanned aerial vehicle (UAV)-derived multispectral images and screened empirical models.

Sedimentary geochemistry mediated by a specific hydrological regime in the water level fluctuation zone of the Three Gorges Reservoir, China.

The water level fluctuation zone (WLFZ) of the Three Gorges Reservoir (TGR) acts as an important sink for inflowing suspended sediment loads over the inundation periods following regular dam operations. This study depicts the sedimentary geochemical dynamics along a sedimentary profile based on the determined chronology and explores its links to the specific hydrological regime created by dam flow regulation and riverine seasonal suspended sediment dynamics. A compact 345-cm-long sediment core was extracted near the base water level (145.

Soil aggregate disintegration effects on soil erodibility in the water level fluctuation zone of the Three Gorges Reservoir, China.

Spatial hydrological alterations can affect soil structural stability. Over time, forces induced by water weaken soil aggregates and this has a negative implication to soil health. The Three Gorges Reservoir (TGR) in particular, experienced a long-term hydrological condition and repetitive seasonal water level fluctuations that could affect soil health.

Sangerbox: A comprehensive, interaction-friendly clinical bioinformatics analysis platform.

In recent decades, with the continuous development of high-throughput sequencing technology, data volume in medical research has increased, at the same time, almost all clinical researchers have their own independent omics data, which provided a better condition for data mining and a deeper understanding of gene functions. However, for these large amounts of data, many common and cutting-edge effective bioinformatics research methods still cannot be widely used. This has encouraged the establishment of many analytical platforms, a portion of databases or platforms were designed to solve the special analysis needs of users, for instance, MG RAST, IMG/M, Qiita, BIGSdb, and TRAPR were developed for specific omics research, and some databases or servers provide solutions for special problems solutions.

Engineered FnCas12a with enhanced activity through directional evolution in human cells.

Clustered regularly interspaced short palindromic repeat-Cas12a has been harnessed to manipulate the human genome; however, low cleavage efficiency and stringent protospacer adjacent motif hinder the use of Cas12a-based therapy and applications. Here, we have described a directional evolving and screening system in human cells to identify novel FnCas12a variants with high activity. By using this system, we identified IV-79 (enhanced activity FnCas12a, eaFnCas12a), which possessed higher DNA cleavage activity than WT FnCas12a.

Boosting activity of high-fidelity CRISPR/Cas9 variants using a tRNA-processing system in human cells.

CRISPR/Cas9 nucleases are widely used for genome editing but can induce unwanted off-target mutations. High-fidelity Cas9 variants have been identified; however, they often have reduced activity, constraining their utility, which presents a major challenge for their use in research applications and therapeutics. Here we developed a tRNA-processing system to restore the activity of multiple high-fidelity Cas9 variants in human cells, including SpCas9-HF1, eSpCas9, and xCas9.

Efficient Human Genome Editing Using SaCas9 Ribonucleoprotein Complexes.

Genome editing using RNA-guided nucleases in their ribonucleoprotein (RNP) form represents a promising strategy for gene modification and therapy because they are free of exogenous DNA integration and have reduced toxicity in vivo and ex vivo. However, genome editing by Cas9 nuclease from Staphylococcus aureus (SaCas9) has not been reported in its RNP form, which recognizes a longer protospacer adjacent motif (PAM), 5'-NNGRRT-3', compared with Streptococcus pyogenes Cas9 (SpCas9) of 5'-NGG-3' PAM. Here, SaCas9-RNP-mediated genome editing is reported in human cells.

Basic and Clinical Application of Adeno-Associated Virus-Mediated Genome Editing.

Traditional gene therapy (gene replacement) has made a breakthrough in treating inherited diseases. Adeno-associated virus (AAV) has emerged as a highly promising vector with innate ability, boosting the development of gene replacement and gene targeting. With the recent advance of engineered nucleases that work efficiently in human cells, AAV mediated-genome editing with nucleases has raised hopes for gene therapy of inherited and non-inherited diseases.

Engineering the Direct Repeat Sequence of crRNA for Optimization of FnCpf1-Mediated Genome Editing in Human Cells.

FnCpf1-mediated genome-editing technologies have enabled a broad range of research and medical applications. Recently, we reported that FnCpf1 possesses activity in human cells and recognizes a more compatible PAM (protospacer adjacent motif, 5'-KYTV-3'), compared with the other two commonly used Cpf1 enzymes (AsCpf1 and LbCpf1), which requires a 5'-TTTN-3' PAM. However, due to the efficiency and fidelity, FnCpf1-based clinical and basic applications remain a challenge.

Particle size differentiation explains flow regulation controls on sediment sorting in the water-level fluctuation zone of the Three Gorges Reservoir, China.

The Three Gorges Dam has significantly interrupted fluvial continuity and modified the mass transfer regime along river continuums. Flow regulation following regular dam operations drives dramatic hydrological regime shifts, which facilitates sediment dispersal in the water-level fluctuation zone over episodic inundation periods. How flow regulation modulates sediment redistribution, however, remains unclear.

Sedimentary chronology reinterpreted from Changshou Lake of the Three Gorges Reservoir Area reveals natural and anthropogenic controls on sediment production.

Sedimentary archives preserved in geomorphic sinks provide records of historical sediment dynamics and its related natural and anthropogenic controls. This study reinterpreted sedimentary processes in Changshou Lake of the Three Gorges Reservoir Area in China by combining a rainfall erosivity index with multiple tracing proxies, and the impacts of natural and anthropogenic drivers on sediment production were also explored. Erosive rainfalls with low frequency and large magnitude in the rainy season contribute to a substantial proportion of annual total rainfall, which thus can be used to infer erosion and sediment yield events.

Recapitulating X-Linked Juvenile Retinoschisis in Mouse Model by Knock-In Patient-Specific Novel Mutation.

X-linked juvenile retinoschisis (XLRS) is a retinal disease caused by mutations in the gene encoding retinoschisin (RS1), which leads to a significant proportion of visual impairment and blindness. To develop personalized genome editing based gene therapy, knock-in animal disease models that have the exact mutation identified in the patients is extremely crucial, and that the way which genome editing in knock-in animals could be easily transferred to the patients. Here we recruited a family diagnosed with XLRS and identified the causative mutation (, p.

SaCas9 Requires 5'-NNGRRT-3' PAM for Sufficient Cleavage and Possesses Higher Cleavage Activity than SpCas9 or FnCpf1 in Human Cells.

CRISPR/Cas9-mediated gene therapy holds great promise for the treatment of human diseases. The protospacer adjacent motif (PAM), the sequence adjacent to the target sequence, is an essential targeting component for the design of CRISPR/Cas9-mediated gene editing. However, currently, very few studies have attempted to directly study the PAM sequence in human cells.

[Genome-editing: focus on the off-target effects].

Breakthroughs of genome-editing in recent years have paved the way to develop new therapeutic strategies. These genome-editing tools mainly include Zinc-finger nucleases (ZFNs), Transcription activator-like effector nucleases (TALENs), and clustered regulatory interspaced short palindromic repeat (CRISPR)/Cas-based RNA-guided DNA endonucleases. However, off-target effects are still the major issue in genome editing, and limit the application in gene therapy.

A 'new lease of life': FnCpf1 possesses DNA cleavage activity for genome editing in human cells.

Cpf1 nucleases were recently reported to be highly specific and programmable nucleases with efficiencies comparable to those of SpCas9. AsCpf1 and LbCpf1 require a single crRNA and recognize a 5'-TTTN-3' protospacer adjacent motif (PAM) at the 5' end of the protospacer for genome editing. For widespread application in precision site-specific human genome editing, the range of sequences that AsCpf1 and LbCpf1 can recognize is limited due to the size of this PAM.

Sediment transfer at different spatial and temporal scales in the Sichuan Hilly Basin, China: Synthesizing data from multiple approaches and preliminary interpretation in the context of climatic and anthropogenic drivers.

Quantifying sediment production and transfer at different spatial and temporal scales in a changing environment is critical in understanding the potential effects of climatic and anthropogenic drivers. Accordingly, estimates of soil erosion and sediment production at hillslope field, first-order small catchment (<0.25km) and river basin scales in the Sichuan Hilly Basin of Southwestern China, generated using a variety of techniques, including fallout radionuclide tracing, runoff plot observations, core chronology dating and conventional sediment flux monitoring, were synthesized and interpreted in the context of potential climatic and human controls.

Linking sedimentary total organic carbon to Pb chronology from Changshou Lake in the Three Gorges Reservoir Region, China.

The influences of total organic carbon (TOC) and total nitrogen (TN) on Lead-210 (Pb) dating have recently been of increasing concern in lacustrine research. Sediment core from Changshou Lake in the Longxi catchment was investigated for influence of TOC on Pb dating. Lead-210 excess (Pb), Cesium-137 (Cs) activities, TOC, TN, and particle size were measured.

Flow regulation manipulates contemporary seasonal sedimentary dynamics in the reservoir fluctuation zone of the Three Gorges Reservoir, China.

Since the launch of the Three Gorges Dam on the Yangtze River, a distinctive reservoir fluctuation zone has been created and significantly modified by regular dam operations. Sediment redistribution within this artificial landscape differs substantially from that in natural fluvial riparian zones, due to a specific hydrological regime comprising steps of water impoundment with increasing magnitudes and seasonal water level fluctuation holding a range of sediment fluxes. This study reinterpreted post-dam sedimentary dynamics in the reservoir fluctuation zone by stratigraphy determination of a 345-cm long sediment core, and related it to impact of the hydrological regime.

Sedimentation and associated trace metal enrichment in the riparian zone of the Three Gorges Reservoir, China.

Impoundment of the Three Gorges Reservoir has created an artificial riparian zone with a vertical height of 30 m and a total area of 349 km(2), which has been subjected to seasonal inundation and exposure due to regular reservoir impoundment and the occurrence of natural floods. The significant alteration of hydrologic regime has caused numerous environmental changes. The present study investigated the magnitude and spatial pattern of sedimentation and metal enrichment in a typical section of the riparian zone, composed of bench terraces with previous agricultural land uses, and explored their links to the changed hydrologic regime.

Assessment of runoff and sediment yields using the AnnAGNPS model in a Three-Gorge watershed of China.

Soil erosion has been recognized as one of the major threats to our environment and water quality worldwide, especially in China. To mitigate nonpoint source water quality problems caused by soil erosion, best management practices (BMPs) and/or conservation programs have been adopted. Watershed models, such as the Annualized Agricultural Non-Point Source Pollutant Loading model (AnnAGNPS), have been developed to aid in the evaluation of watershed response to watershed management practices.