Influence of habitat types and seasons on the composition and diversity of spontaneous species in the rural-urban fringe of Chengdu City, China.

The rural-urban fringe (RUF) is the indistinct boundary zone outside the urban area. It is also a highly vulnerable, sensitive, and ecologically valuable space, owing to the complex demographic composition, unbalanced economic development, and dramatic changes in land use and ecosystems. Different plants spontaneously emerge across RUF areas, playing an important ecological role in regulating climate and providing varied habitats for plants and animals.

Rational Design of Advanced Gene Delivery Carriers: Macrophage Phenotype Matters.

Nucleic acid delivery in hard-to-transfect macrophages have attracted increasing attention in diverse applications such as defence against bacterial infection. Regulated by microenvironments in specific applications, macrophages have a heterogenous nature and exist in different phenotypes with diverse functions, e.g.

Natural agents derived Pickering emulsion enabled by silica nanoparticles with enhanced antibacterial activity against drug-resistant bacteria.

The emergence of antibiotic-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) has become a global health challenge due to the overuse of antibiotics. Natural substances including enzymes and essential oils have shown great potential as alternative treatment options. However, the combinational use of these natural agents remains challenging due to the denaturation of enzymes upon direct contact with oil.

Characterizing identity by descent segments in Chinese interpopulation unrelated individual pairs.

Identity by descent (IBD) segments, uninterrupted DNA segments derived from the same ancestral chromosomes, are widely used as indicators of relationships in genetics. A great deal of research focuses on IBD segments between related pairs, while the statistical analyses of segments in irrelevant individuals are rare. In this study, we investigated the basic informative features of IBD segments in unrelated pairs in Chinese populations from the 1000 Genome Project.

Designing Peptide-Based Nanoinhibitors of Programmed Cell Death Ligand 1 (PD-L1) for Enhanced Chemo-immunotherapy.

The combination of immune checkpoint blockade (ICB) and chemotherapy has shown significant potential in the clinical treatment of various cancers. However, circulating regeneration of PD-L1 within tumor cells greatly limits the efficiency of chemo-immunotherapy and consequent patient response rates. Herein, we report the synthesis of a nanoparticle-based PD-L1 inhibitor (FRS) with a rational design for effective endogenous PD-L1 suppression.

Development of a 39 MM-InDel multiplex assay for the forensic application.

Insertion/deletion polymorphisms (InDels) are a category of highly prevalent markers in the human genome, characterized by their distinctive attributes, including short amplicon sizes and low mutation rates, which have shown great potential in forensic applications. Multi-allelic InDel and multi-InDel markers, collectively abbreviated as MM-InDels, were developed to enhance polymorphism by the introduction of novel alleles. Nevertheless, the relatively low mutation rates of InDels, coupled with the founder effect, result in distinct allele frequency distributions among populations.

Validation of phylogenetic informative Y-InDels in Y-chromosomal haplogroup O-M175.

The Y-chromosomal haplogroup tree, which consists of a group of Y-chromosomal loci with phylogenetic information, has been widely applied in anthropology, archaeology and population genetics. With the continuous updating of the phylogenetic structure, Y-chromosomal haplogroup tree provides more information for recalling the biogeographical origin of Y chromosomes. Generally, Y-chromosomal insertion-deletion polymorphisms (Y-InDels) are genetically stable as Y-chromosomal single nucleotide polymorphisms (Y-SNPs), and therefore carry mutations that can accumulate over generations.

Development of a multiplex panel with 31 multi-allelic InDels for forensic DNA typing.

Insertion/Deletion (InDel) polymorphic genetic markers are abundant in human genomes. Diallelic InDel markers have been widely studied for forensic purposes, yet the low polymorphic information content limits their application and current InDel panels remain to be improved. In this study, multi-allelic InDels located out of low complexity sequence regions were selected in the datasets from East Asian populations, and a multiplex amplification system containing 31 multi-allelic InDel markers and the Amelogenin marker (FA-HID32plex) was constructed and optimized.

Investigation of Linear Amplification Using Abasic Site-Containing Primers Coupled to Routine STR Typing for LT-DNA Analysis.

Obtaining a full short tandem repeat (STR) profile from a low template DNA (LT-DNA) still presents a challenge for conventional methods due to significant stochastic effects and polymerase slippage. A novel amplification method with a lower cost and higher accuracy is required to improve the DNA amount. Previous studies suggested that DNA polymerases without bypass activity could not perform processive DNA synthesis beyond abasic sites in vitro and our results showed a lack of bypass activity for Phusion, Pfu and KAPA DNA polymerases in this study.

Application of machine learning for ancestry inference using multi-InDel markers.

Ancestry inference through population stratification plays an important role in forensic applications. Specifically, ancestry information inferred from forensic DNA evidence can provide vital clues for criminal investigations. Current advances in ancestry inference mostly focus on ancestry informative markers.

Identification and assessment of a subset of Y-SNPs with recurrent mutation for forensic purpose.

Y chromosome has an important role in the forensic practice due to its unique paternal inheritance pattern. Y-chromosomal single nucleotide polymorphisms (Y-SNPs) could provide supplementary information while the application of Y-chromosomal STR (Y-STR) haplotypes encounter their limitations. Y-SNPs with recurrent mutation can be seen in different Y-chromosomal haplogroups, which might help discriminate different paternal pedigrees.

Application of ITO Method in Determination of Special Half-Sibling Relationship.

Objectives: To identify whether the relationship between Zhang A, Zhang B, Zhang C and Zhang X is the half-sibling relationship whose mother is sister (hereinafter referred to as the special half-sibling relationship) or the common first cousin relationship and discuss the application of ITO method in discriminating the special kinship.

Methods: DNA was extracted from blood stain of four identified individuals, PowerPlex 21 System and AGCU 21+1 STR kit were used to detect autosomal STR genetic markers. Investigator Argus X-12 QS kit was used to detect the X chromosome STR genetic markers, the special half-sibling index (SHSI) and first cousin index (FCI) and their likelihood ratio (LR) were calculated by ITO method.

Assessing Autosomal InDel Loci With Multiple Insertions or Deletions of Random DNA Sequences in Human Genome.

Multiple mutational events of insertion/deletion occurring at or around InDel sites could form multi-allelic InDels and multi-InDels (abbreviated as MM-InDels), while InDels with random DNA sequences could imply a unique mutation event at these loci. In this study, preliminary investigation of MM-InDels with random sequences was conducted using high-throughput phased data from the 1000 Genomes Project. A total of 3,599 multi-allelic InDels and 6,375 multi-InDels were filtered with multiple alleles.

Quantum dots' size matters for balancing their quantity and quality in label materials to improve lateral flow immunoassay performance for C-reactive protein determination.

Incorporating quantum dots (QDs) into dendritic mesoporous silica nanoparticles (DMSNs) for signal amplification of label materials represents an efficient strategy to improve the performance of lateral flow immunoassays (LFIAs). In this work, it is found that the CdSe/ZnS QD's size matters for balancing their loading amount and quantum yields (QYs) in the DMSNs-QDs based label materials and ultimately determining the performance of LFIA. The impacts of three CdSe/ZnS QDs with diameters of 9.

Identification and Characterization of Nine Novel X-Chromosomal Short Tandem Repeats on Xp21.1, Xq21.31, and Xq23 Regions.

The application of X-chromosomal short tandem repeats (X-STRs) has been recognized as a powerful tool in complex kinship testing. To support further development of X-STR analysis in forensic use, we identified nine novel X-STRs, which could be clustered into three linkage groups on Xp21.1, Xq21.

Superstructured Macroporous Carbon Rods Composed of Defective Graphitic Nanosheets for Efficient Oxygen Reduction Reaction.

Rationally designed carbon materials with superstructures are promising candidates in applications such as electrocatalysis. However, the synthesis of highly porous carbon superstructures with macropores and carbon defects from a simple crystalline solid remains challenging. In this work, superstructured macroporous carbon rods composed of defective graphitic nanosheets are synthesized by direct carbonization of crystalline poly tannic acid (PTA) rods as precursors.

Variants in linkage status at D5S818 detected by multiple STR kits comparison and Sanger sequencing.

Background: D5S818 discrepancies have been reported in forensic parental testing due to null alleles. However, more cases may be ignored since proportional null alleles were missed without detection of heredity discrepancy between parents and offspring.

Results: In this study, null allele 12 at D5S818 was detected by the PowerPlex 21 System with a higher occurrence rate on the basis of review on 2824 samples from the 1282 routine cases in Chinese Han population.

Calculation of the Paternity Index for STR with tri-allelic patterns in paternity testing.

The calculation of the paternity index (PI) value of common bi-allelic genotypes at STR loci has been standardized in paternity cases. However, for tri-allelic patterns, a rare category of genotyping aberration in forensic practice, the statistical analysis in paternity testing remains disputed. The Type 1 tri-allelic pattern generally results from somatic mutation in the early stage of individual development.

Evaluation of one-step RT-PCR multiplex assay for body fluid identification.

The discrimination of body fluid stains provides crucial evidence during the investigation of criminal cases. Previous studies have demonstrated the practical value of mRNA profiling in body fluid identification. Conventional strategy of mRNA profiling entails reverse transcription and PCR amplification in two separate procedures with different buffer systems.

A 16-plex Y-SNP typing system based on allele-specific PCR for the genotyping of Chinese Y-chromosomal haplogroups.

Y-chromosomal SNP (Y-SNP), with its stable inheritance and low mutation, can provide Supplementary information in forensic investigation. While commonly used Y-chromosomal STR haplotypes show their limitations, typing of Y-SNP would become a powerful complement. In this study, a 16-plex Y-SNP typing system based on allele-specific PCR (AS-PCR) was developed to discriminate four dominant Y-chromosomal haplogroups (C-M130, D-CTS3946, N-M231, and O-M175) and 12 predominant sub-haplogroups of O-M175 (O1a-M119, O1a1a1a-CTS3265, O1b-M268, O1b1a2-Page59, O2-M122, O2a1-L127.

Development of a multiplex system for the identification of forensically relevant body fluids.

Currently, mRNA profiling is widely investigated for forensic body fluid identification, while it is still required to advance the approach for those casework samples of limited quantity or low quality. The inclusion of circular RNAs (circRNAs) can facilitate the detection of mRNA markers in forensic body fluid identification. In this study, a multiplex assay for forensic body fluid identification (F18plex assay) was developed by incorporating 14 tissue-specific mRNA markers with circRNAs expression, 2 mRNA markers with high abundance and 2 housekeeping markers for the discrimination of the most common forensic body fluids, including blood, menstrual blood, saliva, vaginal secretion, semen and urine.

Characterizing Y-STRs in the Evaluation of Population Differentiation Using the Mean of Allele Frequency Difference between Populations.

Y-chromosomal short tandem repeats (Y-STRs) are widely used in human research for the evaluation of population substructure or population differentiation. Previous studies show that several haplotype sets can be used for the evaluation of population differentiation. However, little is known about whether each Y-STR in these sets performs well during this procedure.

Characterization of the extra copy of TPOX locus with tri-allelic pattern.

Background: An STR locus with tri-allelic pattern is occasionally observed in routine forensic casework. The extra copy of TPOX locus with tri-allelic pattern in populations has been assumed to be inserted into an X chromosome, which took place forth before the Bantu expansion in Africa. Nonetheless, the exact location of the duplication and the form of rearrangement in the human genome has not been clarified yet.

Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems.

Rare variants are widely observed in human genome and sequence variations at primer binding sites might impair the process of PCR amplification resulting in dropouts of alleles, named as null alleles. In this study, 5 cases from routine paternity testing using PowerPlex21 System for STR genotyping were considered to harbor null alleles at TH01, FGA, D5S818, D8S1179, and D16S539, respectively. The dropout of alleles was confirmed by using alternative commercial kits AGCU Expressmarker 22 PCR amplification kit and AmpFℓSTR.