Target Region Research Articles

Fine mapping and candidate gene mining of QSc/Sl.cib-7H for spike compactness and length and its pleiotropic effects on yield-related traits in barley (Hordeum vulgare L.).

A major locus for spike compactness and length was mapped on chromosome 7H and its pleiotropic effects, candidate genes and transcriptional regulatory network were analyzed. Spike compactness (SC) and length (SL) are important traits of barley (Hordeum vulgare L.) due to their close association with grain yield. In this study, a major SC and SL locus QSc/Sl.cib-7H was primarily identified on chromosome 7H by bulked segregant analysis, and further fine mapped to a recombination cold spot expanding 244.36-388.09Mb by developing a secondary population using residual heterozygous lines. This region is much more accurate than previously reported spike compactness loci on chromosome 7H.The strong effects of QSc/Sl.cib-7H on SL and SC were validated in two pair of near isogenic lines (NILs) and diverse genetic backgrounds. QSc/Sl.cib-7H exhibited pleiotropic effects on plant height (PH), thousand grain weight and grain length, and did not significantly influence the spikelet number of main spike (SMS) and grain width. Transcriptome analysis based on NILs showed that regulation of SC and SL might be related to the plant circadian rhythm pathway. The candidate genes were mined by analyzing variants and expression patterns of genes in the target region employing multiple genome and transcriptome data. This study takes a further step towards cloning of QSc/Sl.cib-7H, and the data obtained and the developed molecular markers will facilitate its utilization in barley breeding.

Attention model of EEG signals based on reinforcement learning

BackgroundApplying convolutional neural networks to a large number of EEG signal samples is computationally expensive because the computational complexity is linearly proportional to the number of dimensions of the EEG signal. We propose a new Gated Recurrent Unit (GRU) network model based on reinforcement learning, which considers the implementation of attention mechanisms in Electroencephalogram (EEG) signal processing scenarios as a reinforcement learning problem.MethodsThe model can adaptively select target regions or position sequences from inputs and effectively extract information from EEG signals of different resolutions at multiple scales. Just as convolutional neural networks benefit from translation invariance, our proposed network also has a certain degree of translation invariance, making its computational complexity independent of the EEG signal dimension, thus maintaining a lower learning cost. Although the introduction of reinforcement learning makes the model non differentiable, we use policy gradient methods to achieve end-to-end learning of the model.ResultsWe evaluated our proposed model on publicly available EEG dataset (BCI Competition IV-2a). The proposed model outperforms the current state-of-the-art techniques in the BCI Competition IV- 2a dataset with an accuracy of 86.78 and 71.54% for the subject-dependent and subject-independent modes, respectively.ConclusionIn the field of EEG signal processing, attention models that combine reinforcement learning principles can focus on key features, automatically filter out noise and redundant data, and improve the accuracy of signal decoding.

SETDB1 activity is globally directed by H3K14 acetylation via its Triple Tudor Domain.

SETDB1 (SET domain bifurcated histone lysine methyltransferase 1) is a major protein lysine methyltransferasetrimethylating lysine 9 on histone H3 (H3K9) which isinvolved in heterochromatin formation and silencing of repeat elements (REs). It contains a unique Triple Tudor Domain (3TD), which specifically binds the dual modification of H3K14ac in the presence of H3K9me1/2/3. Here, we explored the role of the 3TD H3-tail interaction for the H3K9 methylation activity of SETDB1. We generated a binding reduced 3TD mutant and demonstrate in biochemical methylation assays on peptides and recombinant nucleosomes containing H3K14ac and H3K14ac analogs, respectively, that H3K14 acetylation is crucial for the 3TD mediated recruitment of SETDB1. We also observe this effect in cells where SETDB1 binding and activity is globally correlated with H3K14ac, and knockout of the H3K14 acetyltransferase HBO1 causes a drastic reduction in H3K9me3 levels at SETDB1 dependent sites. Regions with DNA hypomethylation after SETDB1 knockout also show an enrichment in SETDB1-dependent H3K9me3 and H3K14ac. Further analyses revealed that 3TD is particularly important at specific target regions like L1M REs, where H3K9me3 cannot be efficiently reconstituted by the 3TD mutant of SETDB1. In summary, our data demonstrate that the H3K9me3 and H3K14ac are not antagonistic marks but rather the presence of H3K14ac is required for SETDB1 recruitment via 3TD binding to H3K9me1/2/3-K14ac regionsand establishment of H3K9me3.

Abstract A016: YBX1 is a negative regulator of post-transcriptional program associated with invasion and metastasis in cSCC

Abstract Y-box binding protein 1 (YB-1), which is encoded by YBX1 gene, is a multifunctional cold-shock protein that binds both DNA and RNA to orchestrate transcription as well as RNA processing and translation. Recently, we demonstrated that YBX1 is a post-transcriptional effector required for the maintenance of epidermal homeostasis. Although it was well known that YBX1 plays prominent pro-oncogenic roles in malignant transformation and cell invasion in a wide variety of cancers, the role of YBX1 in cutaneous squamous cell carcinoma (SCC) is poorly understood. Here, we report that YBX1 protein level is higher in SCC tumor compared with non-neoplastic skin, but it goes down during tumor progression, in invasive and metastatic states. Indeed, both in vitro and in vivo experiments show that YBX1 acts as an antagonist of SCC progression, inhibiting its migration, invasiveness and metastasis. YBX1 is predominantly found in the cytoplasm of SCC cells. Therefore, we focused on the role of YBX1 as a posttranscriptional regulator and performed an eCLIP-seq (crosslinking immunoprecipitation sequencing) to identify its direct RNA targets. We found that YBX1 binds pro-invasive RNA associated with cell-cell and cell-matrix adhesions. From the integration of eCLIP-seq data with RNA-Bisulfite Seq data, an increased number of m5C modifications was observed to be located within the 3'UTR and CDS of tumor-enriched YBX1 target regions. Upon silencing of YBX1, polysome fractionation analysis revealed that YBX1 KD regulates targets involved in cancer motility, revealing that the loss of function of YBX1 promotes migration and invasion at the post-transcriptional Citation Format: Stefano Sol, Anna Mandinova, Fabiana Boncimino, Kristina Todorova, Emery Di Cicco, Toma Tebaldi, Giorgia Bucciarelli. YBX1 is a negative regulator of post-transcriptional program associated with invasion and metastasis in cSCC [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr A016.

Abstract A014: A methylation state specific targeted background depletion technique for enrichment of ctDNA fraction

Abstract Liquid biopsy continues to be a focus of the cancer diagnostics industry, primarily due to the non-invasive nature of sample collection, however the low levels of circulating tumor DNA (ctDNA) remain a challenge. Methylation has emerged as a promising biomarker for detecting ctDNA, yet detecting the cancerous signal in an excess of non-cancerous, unmethylated cfDNA in the background has been proven difficult. Harbinger Health has developed a novel method that depletes unmethylated background at the CpG-level from specific genomic regions of interest, resulting in an enrichment of the ctDNA fraction. We developed a background cfDNA depletion method that utilizes the endonuclease activity and the specificity of CRISPR/Cas12a to remove unmethylated DNA fragments at ctDNA methylation biomarker sites. First, we identified cancer-informative regions that showed consistent contiguous elevated methylation states in cancer compared to normal samples. We then designed guide RNAs that specifically bind and cut unmethylated CpG sites within the target regions. Cas depletion of bisulfite-converted DNA enriches cancer informative signal for bioanalysis. To test validity of our Cas complex designs, we created model samples that mimic fully unmethylated and fully methylated species. We spiked these cfDNA models into a background of genomic DNA from 5% to 0.01%. In triplicate, we examined cutting efficiency, multiplexing and specificity of Cas to unmethylated species of model DNA. Results were assessed using qPCR by comparing differences in Ct with and without Cas treatment. Additionally, we applied this depletion step during our library preparation process to show utility in methylation analysis of low tumor content liquid biopsy samples. Using both the model sample dilution series and bisulfite converted cfDNA samples, which represent a range of cancerous and background methylation signal, we deplete unmethylated targets using Cas prior to indexing PCR. This rendered unmethylated targets non-amplifiable, removing them from analysis. Results were assessed using both qPCR and sequencing data, such as methylated read counts over the target region. We demonstrated our analytical approach efficiently depletes non-cancer cfDNA by on average 9-fold, which increases the fraction of ctDNA signal and can be multiplexed. This background signal depletion driven by CRISPR is sensitive and specific, maintaining methylated DNA signal detection down to 0.01% at inputs of 10ng DNA. Our Cas-mediated depletion of background signal method has proven useful for enriching rare methylated fragments over background by improving the signal to noise ratio. This technique is novel by harnessing the specificity of CRISPR to target DNA in both a sequence and methylation state specific manner. The depletion of precise methylation states at the CpG-level make it suitable for use in multiple bioassays. Citation Format: Caitlin Gilley, Miguel Williams, Emily Neaga, Sarah Falotico, Kade Pettie, Anthony Shuber. A methylation state specific targeted background depletion technique for enrichment of ctDNA fraction [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A014.

Comparison of Universal mtDNA Primers in Species Identification of Animals in a Sample with Severely Degraded DNA

Analysis of mitochondrial DNA, specifically the cytochrome b gene (cyt b), has become an essential tool for species identification. In the case of degraded samples, in which DNA is fractionated, universal primers, which are highly effective at amplifying the target region, are necessary. The material analysed in this study was a keychain made of bone, which was secured at a border crossing due to the suspicion that it was made of ivory. Due to processing of the bone and the likelihood of DNA degradation, five pairs of universal primers with different product lengths (from 148 to 990 base pairs) were used for species identification. Fragments of mtDNA from the cyt b and the 12S rRNA and 16S rRNA subunits were analysed. The analysis showed that only one pair of primers (L15601/H15748) enabled identification of the species, which is very common in samples with highly degraded DNA. The material was bone tissue belonging to the species Bos taurus (cattle). Species identification by molecular methods is extremely important in analysis of material when the species cannot be identified on the basis of morphological characteristics.

Saturation profiling of drug-resistant genetic variants using prime editing.

Methods to characterize the functional effects of genetic variants of uncertain significance (VUSs) have been limited by incomplete coverage of the mutational space. In clinical oncology, drug resistance arising from VUSs can prevent optimal treatment. Here we introduce PEER-seq, a high-throughput method based on prime editing that can evaluate the functional effects of single-nucleotide variants (SNVs). PEER-seq introduces both intended SNVs and synonymous marker mutations using prime editing and deep sequences the endogenous target regions to identify the introduced SNVs. We generate and functionally evaluate 2,476 SNVs in the epidermal growth factor receptor gene (EGFR), including 99% of all possible variants in the canonical tyrosine kinase domain. We determined resistance profiles of 95% of all possible EGFR protein variants encoded in the whole tyrosine kinase domain against the common tyrosine kinase inhibitors afatinib, osimertinib and osimertinib in the presence of the co-occurring substitution T790M, in PC-9 cells. Our study has the potential to substantially improve the precision of therapeutic choices in clinical settings.

Prediction of Lead Molecule Esculetin of Tridax procumbens against Zika Virus Envelope Protein

In the existing field of science, it is necessary for Siddha, Ayurveda therapists, to understand the interactions and to treat the target regions of the human system effectively. One of the most significant nightmares for scientists and medical professionals has been the Zika virus. Since the bite of the Aedes mosquito species has infected people worldwide with the Zika virus (Flavivirus). The human mechanism and infection control interactions of the Zika virus are still unclear. In addition, some herbal products may give a pathway to the treat the zika virus. Many herbs aim to regulate various diseases, but the herb Tridax procumbens has a key collection of pharmacological values for diseases. Traditional health practitioners have struggled to grasp the precise mechanism of linking existence and how to treat the disease, so the current Ayurinformatics approach and the evolving field are an idea of a modern medical science system. Here we examine the interaction of flavonoids procumbenetin and esculetin of Tridax procumbens with zika virus in silico docking and molecular simulation and ADME and toxicity profile for the drug candidate. Hereby we conclude that these two compounds have the property to suppress the ZIKA virus and are stable and active with ZIKA virus. Molecular docking of Esculetin and Procumbenetin with ZIKV 5JHM, they bind with each other on active site pockets ASP98, ARG99, GLY100, TRP101, GLY102, ASN103, GLY104, CYS105, GLY106, LEU107, PHE108, GLY109.

Joint anatomical, histological and imaging investigation of the midbrain target region for superolateral medial forebrain bundle (slMFB) DBS.

Deep Brain Stimulation (DBS) of the superolateral branch of the medial forebrain bundle (slMFB) is currently being researched in clinical trials and open case series as a therapeutic option for treatment resistant major depressive disorder (TR-MDD) and treatment resistant obsessive-compulsive disorder (TR-OCD). There are numerous publications describing stimulation in such proximity to the ventral tegmental area (VTA) and open questions remain concerning the stimulation target and its functional environment. As of right now, we are not aware of any publications that compare the typical electrode placements with the histologically supported tractographic depiction of the target structure. We used three cadaver midbrain samples with presumed unaltered anatomy. After fixation, staining and slicing, the histological samples were warped to the MNI (Montreal Neurological Institute) big brain environment. Utilizing a tractographic atlas, a qualitative analysis of the typical slMFB stimulation site in the lateral VTA utilizing a subset of clinically implanted DBS electrodes in n=12 patients, successfully implanted for TR-OCD was performed. A joint qualitative overlay analysis of predominantly tyrosine-hydroxylase stained histology at different resolutions in an anatomical common space was achieved. Localization of the DBS-lead bodies was found in the typical positions in front of the red nuclei in the lateral VTA. DBS lead tip region positions explained the oculomotor side effects of stimulation related to para-nigral or parabrachial pigmented sub-nuclei of the VTA, respectively. The location of active electrode contacts suggest downstream and antidromic effects on the greater VTA related medial forebrain bundle system. This is the first dedicated joint histopathological overlay analysis of DBS electrodes targeting the slMFB and lateral VTA in a common anatomical space. This analysis might serve to better understand the DBS target region for this procedure.

YOLO-APDM: Improved YOLOv8 for Road Target Detection in Infrared Images

A new algorithm called YOLO-APDM is proposed to address low quality and multi-scale target detection issues in infrared road scenes. The method reconstructs the neck section of the algorithm using the multi-scale attentional feature fusion idea. Based on this reconstruction, the P2 detection layer is established, which optimizes network structure, enhances multi-scale feature fusion performance, and expands the detection network’s capacity for multi-scale complicated targets. Replacing YOLOv8’s C2f module with C2f-DCNv3 increases the network’s ability to focus on the target region while lowering the amount of model parameters. The MSCA mechanism is added after the backbone’s SPPF module to improve the model’s detection performance by directing the network’s detection resources to the major road target detection zone. Experimental results show that on the FLIR_ADAS_v2 dataset retaining eight main categories, using YOLO-APDM compared to YOLOv8n, mAP@0.5 and mAP@0.5:0.95 increased by 6.6% and 5.0%, respectively. On the M3FD dataset, mAP@0.5 and mAP@0.5 increased by 8.1% and 5.9%, respectively. The number of model parameters and model size were reduced by 8.6% and 4.8%, respectively. The design requirements of the high-precision detection of infrared road targets were achieved while considering the requirements of model complexity control.

Efficient transformer tracking with adaptive attention

AbstractRecently, several trackers utilising Transformer architecture have shown significant performance improvement. However, the high computational cost of multi‐head attention, a core component in the Transformer, has limited real‐time running speed, which is crucial for tracking tasks. Additionally, the global mechanism of multi‐head attention makes it susceptible to distractors with similar semantic information to the target. To address these issues, the authors propose a novel adaptive attention that enhances features through the spatial sparse attention mechanism with less than 1/4 of the computational complexity of multi‐head attention. Our adaptive attention sets a perception range around each element in the feature map based on the target scale in the previous tracking result and adaptively searches for the information of interest. This allows the module to focus on the target region rather than background distractors. Based on adaptive attention, the authors build an efficient transformer tracking framework. It can perform deep interaction between search and template features to activate target information and aggregate multi‐level interaction features to enhance the representation ability. The evaluation results on seven benchmarks show that the authors’ tracker achieves outstanding performance with a speed of 43 fps and significant advantages in hard circumstances.

GPe Projections to the Retrorubral Field Give Rise to Diverging GABAergic and DAergic Circuits.

The external segment of the globus pallidus (GPe) is involved in the modulation of motor output and limbic components of behavior. The circuitry by which the GPe contributes to limbic components of behavior remains unknown. While many investigations have focused on the local circuitry within the basal ganglia, numerous GPe projections to target regions outside of the basal ganglia including the midbrain, thalamus, and cortex exist and remain largely unexplored. Here, by anatomical and electrophysiological means we investigate the projections of the GPe to the Retrorubral Field (RRF), a dopaminergic nucleus in the caudal midbrain, in both male and female mice. We find that the GPe targets both GABAergic and DAergic neurons in the RRF (RRFDA and RRFGABA). Viral-assisted circuit mapping to trace the cell-type specific projection patterns of RRFDA and RRFGABA populations revealed diverging pathways. The connectivity of GPe-recipient RRFDA neurons followed the traditional medial forebrain bundle path, innervating the ventral striatum and to a lesser extent the dorsal striatum. GPe-recipient RRFGABA neurons, on the other hand, displayed broad projections targeting numerous brain regions involved in limbic function including the parabrachial nucleus, amygdala, and hypothalamus. These contrasting projection profiles reveal multiple nodes by which the GPe is disynaptically connected to the limbic system, representing novel access points for the GPe to modulate limbic components of behavior.Significance Statement Progress in our understanding of GPe composition, circuits, and functions has allowed for a greater appreciation of the role of the GPe in shaping behavior. Here, we elaborate on the connectivity of the GPe with the RRF, the third-largest dopaminergic nucleus of the ventral midbrain. We reveal the targeting of both RRFDA and RRFGABA neurons by the GPe and demonstrate the vast non-overlapping projection profiles of RRFDA and RRFGABA Via the multi-level limbic connectivity of the RRF, these results add a novel branch of circuitry to the GPe, which may represent the foundation for some of its non-motor functions.

In situ isotropic 3D imaging of vasculature perfusion specimens using x-ray microscopic dual-energy CT.

Ex vivo x-ray angiography provides high-resolution, three-dimensional information on vascular phenotypes down to the level of capillaries. Sample preparation for ex vivo angiography starts with the removal of blood from the vascular system, followed by perfusion with an x-ray dense contrast agent mixed with a carrier such as gelatine or a polymer. Subsequently, the vascular micro-architecture of harvested organs is imaged in the intact fixed organ. In the present study, we present novel microscopic dual-energy CT (microDECT) imaging protocols that allow to visualise and analyse microvasculature in situ with reference to the morphology of hard and soft tissue. We show that the spectral contrast of µAngiofil and Micropaque barium sulphate in perfused specimens allows for the effective separation of vasculature from mineralised skeletal tissues. Furthermore, we demonstrate the counterstaining of perfused specimens using established x-ray dense contrast agents to depict blood vessels together with the morphology of soft tissue. Phosphotungstic acid (PTA) is used as a counterstain that shows excellent spectral contrast in both µAngiofil and Micropaque barium sulphate-perfused specimens. A novel Sorensen-buffered PTA protocol is introduced as a counterstain for µAngiofil specimens, as the polyurethane polymer is susceptible to artefacts when using conventional staining solutions. Finally, we demonstrate that counterstained samples can be automatically processed into three separate image channels (skeletal tissue, vasculature and stained soft tissue), which offers multiple new options for data analysis. The presented microDECT workflows are suited as tools to screen and quantify microvasculature and can be implemented in various correlative imaging pipelines to target regions of interest for downstream light microscopic investigation.

Ultrafast imaging of laser-induced modifications in planar targets via single-shot in-line holography

Abstract We present a holographic single-shot coherent diffractive imaging method based on in-line holography that allows the ultrafast characterization of 2D transmission maps of semi-transparent planar targets such as foils in amplitude and phase. Holographic information is obtained from the interference of the transmitted primary beam with the fields scattered from the modified or unknown target regions. A specialized iterative phase retrieval is used to incorporate the holographic nature of the approach and to accelerate and improve convergence. The achievable quality and reproducibility of the reconstructed transmission maps as well as optimal setup parameters are investigated using realistic pre-characterized reference targets. We used non-circular laser-induced hole structures in 30 nm thin gold foils that represent the final state of a laser modification and show that the far field error of the reconstructed diffraction images can be used to estimate and optimize the reconstruction quality in the object plane in order to obtain accurate and reproducible transmission maps. Our results mark the important first step towards the full spatio-temporal analysis of all stages of laser material modification or laser ablation in two-color pump probe experiments, including

Realizable seismic cloak via polar metamaterials

Transformation elastodynamics can be used to redirect incident waves to mitigate harmful vibrations in the target region. Under the specific Brun–Guenneau–Movchan gauge, the elastic tensor of the transformed domain lacks minor symmetry. Here, we propose a physically realizable seismic cloak composed of lattice-based polar metamaterials capable of exhibiting asymmetric stresses. Both static and dynamic simulations validate the cloaking performance. A metric is calculated to quantify the protective effects, and results demonstrate satisfactory cloaking and aseismic protection across a wide frequency band.

Heat application in live cell imaging.

Thermal heating of biological samples allows to reversibly manipulate cellular processes with high temporal and spatial resolution. Manifold heating techniques in combination with live-cell imaging were developed, commonly tailored to customized applications. They include Peltier elements and microfluidics for homogenous sample heating as well as infrared lasers and radiation absorption by nanostructures for spot heating. A prerequisite of all techniques is that the induced temperature changes are measured precisely which can be the main challenge considering subcellular structures or multicellular organisms as target regions. This article discusses heating and temperature sensing techniques for live-cell imaging, leading to future applications in cell biology.

The EU project VAXaction: tacking effectively vaccine hesitancy in Europe

Abstract The main objective of VAX-ACTION is to support EU Member States and relevant stakeholders to implement the results of tailored, evidence-based interventions aimed to reduce vaccine hesitancy. Based on the evaluation of effectiveness of these interventions, which will be conducted in selected target regions in EU member states, recommendations will be drawn through diverse dissemination strategies to allow scaling up good practices to other member States, but also to the USA and Canada, where gaps in implementation strategies also have prevented effective, evidence-based interventions aimed to better deal with vaccine hesitancy. The first phase of the research involved some relevant systematic reviews with the aim of: 1. to map public health evidence and research results on large-scale vaccination programs in Europe and north America; 2. to map interventions aimed to address vaccine hesitancy regarding new and well-stablished vaccines and vaccination programs (Covid-19, mpox, national immunizations programs for children) in Europe and north America; 3. to identify successful and unsuccessful interventions designs aimed to address vaccine hesitancy, including challenges in the implementation, evaluation designs, and the feasibility of scaling-up solutions that are context-sensitive; 4. to identify significant similarities or dissimilarities in the designs and outcomes of interventions aimed to address vaccine hesitancy in northern countries where political and academic concern towards this phenomenon is growing; 5. to identify the extent to which ‘grounding’ (bottom-up) experiences aimed to address vaccine hesitancy are evidence-based, build on current international knowledge and guidelines, and whether they are internationally reported; 6. to systematize the mapping of interventions aimed to address vaccine hesitancy in the northern hemisphere in a way that can be shared and used by third parties. This contribution will illustrate the results of the first phase of the project.

The evolution of spatial and temporal distribution of rainfall erosivity in Henan Province, central China

With the advancement of urbanization, there has been a significant reduction in cultivated land, accompanied by soil erosion. Concurrently, the regularity of rainfall in recent years has been erratic, adversely impacting the grain economy and agricultural development in certain regions. Henan Province, spanning the basins of the Yangtze River, the Yellow River, the Huaihe River, and the Haihe River, possesses complex hydrological conditions and serves as a pivotal agricultural zone in China. Therefore, this paper utilizes daily rainfall data collected over 54 years (1969–2022) from 112 rain measuring stations in Henan Province to calculate the rainfall erosivity using the Zhang model and the erosivity model from the first national water survey. Meanwhile, spatial analysis was performed using the Kriging interpolation method in the ArcGIS Geostatistical Wizard, resulting in detailed spatial distribution maps of rainfall and rainfall erosivity. The study also employed Wavelet and Mann–Kendall tests to analyze the abrupt changes, trends and periodicity of rainfall and rainfall erosivity within the target region. The findings indicate that the average rainfall (1969–2022) in Henan province was 718.26 mm, while the average rainfall erosivity (R) was 3213.46 MJ mm/(hm2 h). R values are positively correlated with rainfall intensity and volume, displaying an annual upward trend. Spatially, R values increase gradually from northwest to southeast, closely aligning with topographical variations. Additionally, the analysis revealed a predominant periodic cycle of 54 years in the precipitation patterns. These results offer valuable insights for environmental and agricultural management in other regions of central China.

Can eDNA Present in Aquatic Environments of Rural Areas Help Identify Species Diversity in the Order Anura?

Paddy fields are classified as wetland environments, and they comprise freshwater ecosystems. They are ecologically important habitats and breeding grounds for many aquatic insects, amphibians, and reptiles. However, paddy field ecosystems are constantly threatened by climate change and the indiscriminate use of pesticides. The metabarcode analysis of eDNA (environmental DNA) method is highly effective at accumulating information on many organisms that inhabit paddy field ecosystems. It can indirectly identify the existence of taxa that are no longer found in the target ecosystem due to behavioral characteristics, such as those exhibited by amphibians. In the metabarcoding results of this study, genes of five species of frogs were found, but it was impossible to confirm all of the frogs’ taxa, morphological pictures, and croak sounds. On the other hand, some frog taxa were only found in the metabarcoding analysis. The eDNA of the frogs found only in the metabarcoding analysis is estimated to have been introduced from nearby areas inhabited by frogs rather than the target region. Due to the powerful analytical resolution of eDNA metabarcoding, this eDNA-based paddy field search is expected to help investigate the biodiversity in agricultural ecosystems.

Canine Multiple System Degeneration Associated with Sequence Variants in SERAC1

Canine multiple system degeneration (CMSD) is an early onset, progressive movement disorder affecting Kerry Blue Terriers and Chinese Crested dogs. The associated pathologic lesions include degeneration of the cerebellum, caudate nucleus, and substantia nigra. CMSD is inherited as an autosomal recessive trait in both dog breeds. Previous linkage mapping localized the CMSD locus to a 15 MB region on canine chromosome 1 (CFA1). Next-generation sequencing was used to generate whole-genome sequences from the DNA of an affected dog from each breed. The resulting sequence reads were aligned to the NCBI canine reference genome (build 3.1). Among the homozygous sequence variants within the CFA1 target region, a nonsense variant in exon 15 of SERAC1 was identified in the affected Kerry Blue Terrier, while in the Chinese Crested dog, a 4 bp deletion in the SERAC1 exon 4 acceptor splice site was found. RT-PCR showed that this deletion resulted in exon 4 skipping. Genotyping of large cohorts of Kerry Blue Terriers and Chinese Crested dogs for the respective breed-specific SERAC1 variants showed complete concordance between genotype and disease phenotype. Genotype–phenotype concordance was also observed in offspring generated by cross breeding between SERAC1-heterozygous Kerry Blue Terrier and Chinese Crested dogs, with only the compound heterozygotes exhibiting the disease phenotype, further confirming the recessive inheritance of CMSD. Variants in human SERAC1 are associated with disorders with a range of ages of disease onset and patterns of clinical signs, but that are all characterized by movement abnormalities similar to those of the dogs with CMSD. Canine CMSD could serve as a valuable model to elucidate the mechanisms underlying SERAC1-deficiency disorders and to evaluate potential therapeutic interventions.