Transcriptomic Approaches to Cardiomyocyte-Biomaterial Interactions: A Review.

Biomaterials, essential for supporting, enhancing, and repairing damaged tissues, play a critical role in various medical applications. This Review focuses on the interaction of biomaterials and cardiomyocytes, emphasizing the unique significance of transcriptomic approaches in understanding their interactions, which are pivotal in cardiac bioengineering and regenerative medicine. Transcriptomic approaches serve as powerful tools to investigate how cardiomyocytes respond to biomaterials, shedding light on the gene expression patterns, regulatory pathways, and cellular processes involved in these interactions. Emerging technologies such as bulk RNA-seq, single-cell RNA-seq, single-nucleus RNA-seq, and spatial transcriptomics offer promising avenues for more precise and in-depth investigations. Longitudinal studies, pathway analyses, and machine learning techniques further improve the ability to explore the complex regulatory mechanisms involved. This review also discusses the challenges and opportunities of utilizing transcriptomic techniques in cardiomyocyte-biomaterial research. Although there are ongoing challenges such as costs, cell size limitation, sample differences, and complex analytical process, there exist exciting prospects in comprehensive gene expression analyses, biomaterial design, cardiac disease treatment, and drug testing. These multimodal methodologies have the capacity to deepen our understanding of the intricate interaction network between cardiomyocytes and biomaterials, potentially revolutionizing cardiac research with the aim of promoting heart health, and they are also promising for studying interactions between biomaterials and other cell types.

Exploring the CO2 Electrocatalysis Potential of 2D Metal-Organic Transition Metal-Hexahydroxytriquinoline Frameworks: A DFT Investigation.

Metal-organic frameworks have demonstrated great capacity in catalytic CO2 reduction due to their versatile pore structures, diverse active sites, and functionalization capabilities. In this study, a novel electrocatalytic framework for CO2 reduction was designed and implemented using 2D coordination network-type transition metal-hexahydroxytricyclic quinazoline (TM-HHTQ) materials. Density functional theory calculations were carried out to examine the binding energies between the HHTQ substrate and 10 single TM atoms, ranging from Sc to Zn, which revealed a stable distribution of metal atoms on the HHTQ substrate. The majority of the catalysts exhibited high selectivity for CO2 reduction, except for the Mn-HHTQ catalysts, which only exhibited selectivity at pH values above 4.183. Specifically, Ti and Cr primarily produced HCOOH, with corresponding 0.606 V and 0.236 V overpotentials. Vanadium produced CH4 as the main product with an overpotential of 0.675 V, while Fe formed HCHO with an overpotential of 0.342 V. Therefore, V, Cr, Fe, and Ti exhibit promising potential as electrocatalysts for carbon dioxide reduction due to their favorable product selectivity and low overpotential. Cu mainly produces CH3OH as the primary product, with an overpotential of 0.96 V. Zn primarily produces CO with a relatively high overpotential of 1.046 V. In contrast, catalysts such as Sc, Mn, Ni, and Co, among others, produce multiple products simultaneously at the same rate-limiting step and potential threshold.

Density Functional Study of Electrocatalytic Carbon Dioxide Reduction in Fourth-Period Transition Metal-Tetrahydroxyquinone Organic Framework.

This study investigates the utilisation of organometallic network frameworks composed of fourth-period transition metals and tetrahydroxyquinone (THQ) in electrocatalytic CO2 reduction. Density functional theory (DFT) calculations were employed in analysing binding energies, as well as the stabilities of metal atoms within the THQ frameworks, for transition metal TM-THQs ranging from Y to Cd. The findings demonstrate how metal atoms could be effectively dispersed and held within the THQ frameworks due to sufficiently high binding energies. Most TM-THQ frameworks exhibited favourable selectivity towards CO2 reduction, except for Tc and Ru, which experienced competition from hydrogen evolution reaction (HER) and required solution environments with pH values greater than 5.716 and 8.819, respectively, to exhibit CO2RR selectivity. Notably, the primary product of Y, Ag, and Cd was HCOOH; Mo produced HCHO; Pd yielded CO; and Zr, Nb, Tc, Ru, and Rh predominantly generated CH4. Among the studied frameworks, Zr-THQ displayed values of 1.212 V and 1.043 V, corresponding to the highest limiting potential and overpotential, respectively, while other metal-organic frameworks displayed relatively low ranges of overpotentials from 0.179 V to 0.949 V. Consequently, it is predicted that the TM-THQ framework constructed using a fourth-period transition metal and tetrahydroxyquinone exhibits robust electrocatalytic reduction of CO2 catalytic activity.

The checkmark association between gamma glutamyl-transpeptidase and body mass index in a large Chinese population.

BACKGROUND: Obesity has long been regarded as a risk factor for abnormal liver function, although the quantitative relationship between them is not clear. This study aimed to investigate the relationship between body mass index (BMI) and gamma-glutamyl transpeptidase (GGT) in different gender populations. METHODS: The cross-sectional study included 221,934 people aged over 18 years and under 90 years who underwent physical examinations at Yijishan Hospital in Wuhu City from 2011 to 2016. t-test and Chi-square test were used to compare the differences in demographic characteristics and biochemical indexes between men and women. Linear regression model and smooth curve method were used to investigate the relationship between BMI and GGT. RESULTS: The smooth curve shows a checkmark association between GGT and BMI. After adjusting for confounders, the cut-off BMI for the whole population was 19.5 kg/m2. When BMI was less than 19.5 kg/m2, GGT levels decreased with increasing BMI, and when BMI was greater than 19.5 kg/m2, GGT levels increased with increasing BMI. After gender stratification, there was a checkmark association between male and female GGT levels and BMI, but the trend of male GGT levels changing with BMI was more obvious than that of females. CONCLUSIONS: Our investigation demonstrated that the GGT level in obese Chinese people is significantly higher than that in non-obese people living in Wuhu City. BMI level can be considered as an early warning index for diseases related to liver function injury in the clinic, although the influence of gender difference should be specifically considered.

Dyslipidemia and hyperuricemia: a cross-sectional study of residents in Wuhu, China.

BACKGROUND: While dyslipidemia has been recognized as a potential risk factor for hyperuricemia, there is currently a dearth of large-scale data specifically focused on studying the relationship between these two conditions. To address this gap, the present study analyzed a dataset of 298,891 physical examination records to investigate in greater detail the clinical classification and compositional relationship between hyperuricemia and dyslipidemia. METHODS: For this investigation, a cross-sectional research design was utilized to analyze physical examination data that was gathered from Yijishan Hospital in Wuhu, China between 2011 and 2016. Logistic regression was employed to examine the association between hyperuricemia and dyslipidemia. Furthermore, the association between hyperuricemia and dyslipidemia was evaluated based on the clinical classifications of dyslipidemia and its components. RESULTS: A total of 298,891 participants from China (124,886 [41.8%] females) were included in the study, with an age range of 18 to 90 years (mean [SD]: 47.76 [13.54] years). In multivariate analysis, the odds of hyperuricemia was 1.878 times higher in patients with dyslipidemia compared to those without dyslipidemia (95% confidence interval [CI]: 1.835-1.922). In the clinical classification of dyslipidemia, individuals with hypertriglyceridemia and mixed hyperlipidemia had 1.753 times (95% CI: 1.706-1.802) and 1.925 times (95% CI: 1.870-1.982) higher odds of hyperuricemia, respectively, compared to those without dyslipidemia. Among the components of dyslipidemia, the odds ratios for hyperuricemia in individuals in the fourth quartile compared to those in the first quartile were 3.744 (95% CI: 3.636-3.918) for triglycerides, 1.518 (95% CI: 1.471-1.565) for total cholesterol, and 1.775 (95% CI: 1.718 - 1.833) for non-high-density lipoprotein cholesterol. CONCLUSIONS: Dyslipidemia has been independently linked with hyperuricemia. Moreover, the elevation of triglycerides or total cholesterol levels, including conditions such as hypertriglyceridemia and mixed hyperlipidemia, have been observed to have a positive association with the development of hyperuricemia.

A proof-of-principle study: The potential application of MiniHap biomarkers in ancestry inference based on the QNome nanopore sequencing.

Haplotyped SNPs convey forensic-related information, and microhaplotypes (MHs), as the most representative of this kind of marker, have proved the potential value for human forensics. In recent years, nanopore sequencing technology has developed rapidly, with its outstanding ability to sequence long continuous DNA fragments and obtain phase information, making the detection of longer haplotype marker possible. In this proof-of-principle study, we proposed a new type of forensic marker, MiniHap, based on five or more SNPs within a molecular distance less than 800 bp, and investigated the haplotype data of 56 selected MiniHaps in five Chinese populations using the QNome nanopore sequencing. The sequencing performance, allele (haplotype) frequencies, forensic parameters, effective number of alleles (Ae), and informativeness (In) were subsequently calculated. In addition, we performed principal component analysis (PCA), phylogenetic tree, and structure analysis to investigate the population genetic relationships and ancestry components among the five investigated populations and 26 worldwide populations. MiniHap-04 exhibited remarkable forensic efficacy, with 148 haplotypes reported and the Ae was 66.9268. In addition, the power of discrimination (PD) was 0.9934, the probability of exclusion (PE) was 0.9898, and the In value was 0.7893. Of the 56 loci, 85.71% had PD values above 0.85, 66.07% had PE values above 0.54, 67.86% had Ae values over 7.0%, and 55.36% were with In values above 0.2 across all samples, indicating that most of the MiniHaps are suitable for individual identification, paternity testing, mixture deconvolution, and ancestry inference. Moreover, the results of PCA, phylogenetic tree and structure analysis demonstrated that this MiniHap panel had the competency in continental population ancestry inference, but the differentiation within intracontinental/linguistically restricted subpopulations was not ideal. Such findings suggested that the QNome device for MiniHap detection was feasible and this novel marker has the potential in ancestry inference. Yet, the establishment of a more comprehensive database with sufficient reference population data remains necessary to screen more suitable MiniHaps.

First principles study of a triazine-based covalent organic framework as a high-capacity anode material for Na/K-ion batteries.

The rational design of high-performance anode materials is crucial for the development of rechargeable Na-ion batteries (NIBs) and K-ion batteries (KIBs). In this study, based on density functional theory (DFT) calculations, we have systematically investigated the possibility of a bilayer triazine-based covalent organic framework (bilayer TCOF) as an anode for NIBs and KIBs. The calculation of the electronic band structure shows that the bilayer TCOF is a direct band gap semiconductor with a band gap of 2.01 eV. After the adsorption of Na/K at the most favorable sites, the bilayer TCOF transitions from a semiconductor to a metal state, guaranteeing good electronic conductivity. The low diffusion barriers of the bilayer TCOF are 0.45 and 0.26 eV, respectively, indicating a fast diffusion rate of Na/K ions. In addition, the bilayer TCOF has a theoretical storage capacity of up to 628 mA h g-1. Finally, it is found that the average voltage of the bilayer TCOF for NIBs and KIBs is 0.53 and 0.48 V, respectively. Based on these results, we can conclude that the bilayer TCOF may be a suitable anode material for NIBs and KIBs.

Single-Layer GaInSe3: Promising Water-Splitting Photocatalyst with Solar Conversion Efficiency over 30% from Theoretical Calculations.

Hydrogen energy from solar water-splitting is known as an ideal method with which to address the energy crisis and global environmental pollution. Herein, the first-principles calculations are carried out to study the photocatalytic water-splitting performance of single-layer GaInSe3 under biaxial strains from -2% to +2%. Calculations reveal that single-layer GaInSe3 under various biaxial strains has electronic bandgaps ranging from 1.11 to 1.28 eV under biaxial strain from -2% to +2%, as well as a completely separated valence band maximum and conduction band minimum. Meanwhile, the appropriate band edges for water-splitting and visible optical absorption up to ~3 × 105 cm-1 are obtained under biaxial strains from -2% to 0%. More impressively, the solar conversion efficiency of single-layer GaInSe3 under biaxial strains from -2% to 0% reaches over 30%. The OER of unstrained single-layer GaInSe3 can proceed without co-catalysts. These demonstrate that single-layer GaInSe3 is a viable material for solar water-splitting.

COVID-19 hospitalization increases the risk of developing glioblastoma: a bidirectional Mendelian-randomization study.

Background: As a result of the COVID-19 pandemic, patients with glioblastoma (GBM) are considered a highly vulnerable population. Despite this, the extent of the causative relationship between GBM and COVID-19 infection is uncertain. Methods: Genetic instruments for SARS-CoV-2 infection (38,984 cases and 1,644,784 control individuals), COVID-19 hospitalization (8,316 cases and 1,549,095 control individuals), and COVID-19 severity (4,792 cases and 1,054,664 control individuals) were obtained from a genome-wide association study (GWAS) from European populations. A total of 6,183 GBM cases and 18,169 controls from GWAS were enrolled in our study. Their associations were evaluated by applying Mendelian randomization (MR) including IVW meta-analysis, MR-Egger regression, and weighted-median analysis. To make the conclusions more robust and reliable, sensitivity analyses were performed. Results: Our results showed that genetically predicted COVID-19 hospitalization increases the risk of GBM (OR = 1.202, 95% CI = 1.035-1.395, p = 0.016). In addition, no increased risk of SARS-CoV-2 infection, COVID-19 hospitalization and severity were observed in patients with any type of genetically predicted GBM. Conclusion: Our MR study indicated for the first time that genetically predicted COVID-19 hospitalization was demonstrated as a risk factor for the development of GBM.

Impact of carotid hemodynamics on carotid plaque location: Age difference.

PURPOSE: This study was aimed to investigate the influence of carotid hemodynamics in common carotid artery (CCA) and internal carotid artery (ICA) on carotid plaque location. METHODS: A total of 4444 participants from Anhui Maanshan People's Hospital were selected from December 2013 to December 2018. Doppler ultrasound was used to measure the location of carotid plaque. Patients were divided into four groups according to plaque location: LEFT, RIGHT, BOTH, and NONE. Multiple logistic regression and smooth curve were applied to determine the relationship of carotid plaque location and hemodynamic indexes. RESULTS: Compared with the NONE group, the ratio of artery systolic and diastolic blood flow velocity in right internal carotid (RICA S/D) was a risk factor for LEFT group (OR=1.548) after adjustment; artery systolic and diastolic blood flow velocity ratio of left common carotid artery (LCCA S/D) was a risk factor for RIGHT group (OR=1.250); resistance index of right internal carotid (RICA RI) was a protective factor for BOTH group (OR=0.097), while LCCA S/D and RICA S/D were risk factors for BOTH group (OR=1.201, OR=1.457). Compared with the RIGHT group, artery systolic and diastolic blood flow velocity ratio of right common carotid (RCCA S/D) was the risk factor for the LEFT group (OR=1.463), LCCA S/D and RICA S/D were the risk factors for BOTH group (OR=1.706, OR=2.111). After age stratification, resistance index of right common carotid artery (RCCA RI) and resistance index of left internal carotid artery (LICA RI) were protective factors for BOTH group (OR=0.046, OR=0.042) in group younger than 52. RCCA S/D and RICA S/D were risk factors for BOTH group (OR=1.557, OR=1.843). Resistance index of left common carotid artery (LCCA RI) was a protective factor in the LEFT group compared with the RIGHT group (OR=0.476). In group older than 52, RICA S/D was a risk factor for LEFT group (OR=1.388). LCCA S/D was a risk factor for RIGHT group (OR=1.575). LCCA S/D and RICA S/D were risk factors for BOTH group (OR=1.348, OR=1.311). RICA S/D and RCCA S/D were protective factors in the LEFT group compared with the RIGHT group (OR=0.567, OR=0.680).

Gender-based relationship between serum creatinine and carotid plaque stability: A cross-sectional study in China.

OBJECTIVE: Carotid plaque instability is a risk factor for ischemic stroke, and changes in serum creatinine are associated with carotid plaque. However, the relationship between serum creatinine and carotid plaque stability is not well explained. This study aimed to interpret this relationship for clinical treatment of carotid plaque. METHODS: A total of 4363 subjects aged 29-86 from December 2013 to December 2018 were included in this study. The stability of carotid plaque was determined based on ultrasound echoes and divided into two groups: carotid plaque stable group and carotid plaque unstable group. The relationship between serum creatinine and carotid plaque stability was determined using curve fitting methods as well as logistic regression. RESULTS: After age stratification, there was an inverted U-shaped curve between the stability of right carotid plaque and serum creatinine in males, When serum creatinine levels were less than 84 µmol/L, the probability of carotid plaque instability gradually increased, and the carotid plaque became stable when creatinine levels were greater than 84 µmol/L. The relationship between left carotid female plaque stability and serum creatinine showed a U-shaped curve. When serum creatinine levels were less than 80 µmol/L, the carotid plaque stability stabilized, and the probability increased when creatitine levels were more than 80 µmol/L, as the carotid plaque instability rose. CONCLUSION: There was an inverted U-shaped relationship between the stability of carotid plaque in the right carotid artery and serum creatinine in males, and a U-shaped relationship between the stability of carotid plaque in the left carotid artery and serum creatinine in females.

The V-shaped curve relationship between fasting plasma glucose and human serum albumin in a large health checkup population in China.

BACKGROUND: This study aimed to investigate the relationship between fasting plasma glucose (FPG) and human serum albumin (HSA) in a large health checkup population in China. METHODS: In this cross-sectional health checkup study, we enrolled a population of 284,635 subjects from Wuhu between 2011 and 2016. All participants completed the physical examination, blood biochemical examination, and blood routine examination. RESULTS: The prevalence of diabetes in men and women was 6.11% and 2.98%, respectively. The average level of HSA and FPG was significantly higher in men than in women (48.44 ± 3.25 vs. 47.14 ± 3.22, P < 0.0001; 5.50 ± 1.26 vs. 5.26 ± 0.94, P < 0.0001). There were significant differences in blood biochemistry and blood routine values by gender. After adjusting for confounding factors, the results showed that FPG and HSA were a V-shaped curve, and the threshold value of HSA was 40.7 mmol/L. FPG and HSA still showed a V-shaped curve after stratification by gender and age. In the male group, FPG decreased with HSA when HSA<42.3 mmol/L, and increased when HSA ≥ 42.3 mmol/L. In the female group, FPG decreased with HSA when HSA<35.7 mmol/L, and increased when HSA ≥ 35.7 mmol/L. In the age<65 group, FPG decreased with HSA when HSA<37.5 mmol/L, and increased when HSA ≥ 37.5 mmol/L. In the age ≥ 65 group, FPG decreased with HSA when HSA<43.2 mmol/L, and increased when HSA ≥ 43.2 mmol/L. CONCLUSIONS: A V-shape relationship exists between fasting plasma glucose and human serum albumin among the Chinese health checkup population studied.

CmVCall: An automated and adjustable nanopore analysis pipeline for heteroplasmy detection of the control region in human mitochondrial genome.

Genetic associations between human mitochondrial DNA (mtDNA) heteroplasmy and mitochondrial diseases, aging, and cancer have been elaborated, contributing a lot to the further understanding of mtDNA polymorphic spectrum in anthropology, population, and forensic genetics. In the past decade, heteroplasmy detection using Sanger sequencing and next generation sequencing (NGS) was hampered by the former's inefficiency and the latter's inherent bias due to amplification and mapping of short reads, respectively. Nanopore sequencing stands out for its ability to yield long contiguous segments of DNA, providing a new insight into heterogeneity authentication. In addition to MinION from Oxford Nanopore Technologies, an alternative nanopore sequencer QNome (Qitan Technology) has also been applied to various biological research and the forensic applicability of this platform has been proved recently. In this study, we evaluated the performance of four commonly used variant callers in the heterogeneity authentication of the control region of human mtDNA based on simulations of different ratios generated by mixing QNome nanopore sequencing reads of two synthetic sequences. Then, an open-source and python-based nanopore analytics pipeline, CmVCall was developed and incorporated multiple programs including reads filtering, removal of nuclear mitochondrial sequences (NUMTs), alignment, optional 'Correction' mode, and heterogeneity identification. CmVCall can achieve high precision, accuracy, and recall of 100%, 99.9%, and 92.3% with a 5% heteroplasmy level in 'Correction' mode. Moreover, blood, saliva, and hair shaft samples from monozygotic (MZ) twins were used for heterogeneity evaluation and comparison with the NGS data. Results of MZ twin samples showed that CmVCall could identify more point heteroplasmy sites, revealing significant levels of inter- and intra-individual mtDNA polymorphism. In conclusion, we believe that this analysis pipeline will lay a solid foundation for the development of a comprehensive nanopore analysis pipeline targeting the whole mitochondrial genome.

A multidisciplinary study on the social customs of the Tang Empire in the Medieval Ages.

Multidisciplinary research on human remains can provide important information about population dynamics, culture diffusion, as well as social organization and customs in history. In this study, multidisciplinary analyses were undertaken on a joint burial (M56) in the Shuangzhao cemetery of the Tang Dynasty (618-907 AD), one of the most prosperous dynasties in Chinese history, to shed light on the genetic profile and sociocultural aspects of this dynasty. The archaeological investigation suggested that this burial belonged to the Mid-Tang period and was used by common civilians. The osteological analysis identified the sex, age, and health status of the three individuals excavated from M56, who shared a similar diet inferred from the stable isotopic data. Genomic evidence revealed that these co-buried individuals had no genetic kinship but all belonged to the gene pool of the ancient populations in the Central Plains, represented by Yangshao and Longshan individuals, etc. Multiple lines of evidence, including archaeology, historic records, as well as chemical and genetic analyses, have indicated a very probable familial joint burial of husband and wives. Our study provides insights into the burial customs and social organization of the Tang Dynasty and reconstructs a scenario of civilian life in historic China.

Massively parallel sequencing of 74 microhaplotypes and forensic characteristics in three Chinese Sino-Tibetan populations.

Microhaplotype (MH), as an emerging type of forensic genetic marker in recent years, has the potential to support multiple forensic applications, especially for mixture deconvolution and biogeographic ancestry inference. Herein, we investigated the genotype data of 74 MHs included in a novel MH panel, the Ion AmpliSeq MH-74 Plex Microhaplotype Research Panel, in three Chinese Sino-Tibetan populations (Han, Tibetan, and Yi) using the Ion Torrent semiconductor sequencing. The sequencing performance, allele frequencies, effective number of alleles (Ae), informativeness (In), and forensic parameters were subsequently estimated and calculated. In addition, principal component analysis (PCA) and structure analysis were performed to explore the population relationships among the three populations and the ancestry component distribution. Overall, this novel MH panel is robust and reliable, and has an excellent sequencing performance. The Ae values ranged from 1.0126 to 7.0855 across all samples, and 75.68 % of MHs had Ae values >2.0000. Allele frequencies at some loci varied considerably among the three studied populations, and the mean In value was 0.0195. Moreover, the genetic affinity between Tibetans and Yis was closer than that between Tibetans and Hans. The aforementioned results suggest that the Ion AmpliSeq MH-74 Plex Microhaplotype Research Panel is highly polymorphic in three investigated populations and could be used as an effective tool for human forensics. Although these 74 MHs have demonstrated the competency in continental population stratification, a higher resolution for distinguishing intracontinental subpopulations and a more comprehensive database with sufficient reference population data still remain to be accomplished.

A novel aptamer-G-quadruplex/hemin self-assembling color system: rapid visual diagnosis of invasive fungal infections.

BACKGROUND: The clinical symptoms of invasive fungal infections (IFI) are nonspecific, and early clinical diagnosis is challenging, resulting in high mortality rates. This study reports the development of a novel aptamer-G-quadruplex/hemin self-assembling color system (AGSCS) based on (1 → 3)-ß-D-glucans' detection for rapid, specific and visual diagnosis of IFI. METHODS: We screened high affinity and specificity ssDNA aptamers binding to (1 → 3)-ß-D-glucans, the main components of cell wall from Candida albicans via Systematic Evolution of Ligands by EXponential enrichment. Next, a comparison of diagnostic efficiency of AGSCS and the (1 → 3)-ß-D-glucans assay ("G test") with regard to predicting IFI in 198 clinical serum samples was done. RESULTS: Water-soluble (1 → 3)-ß-D-glucans were successfully isolated from C. albicans ATCC 10,231 strain, and these low degree of polymerization glucans (< 1.7 kD) were targeted for aptamer screening with the complementary sequences of G-quadruplex. Six high affinity single stranded DNA aptamers (A1, A2, A3, A4, A5 and A6) were found. The linear detection range for (1 → 3)-ß-D-glucans stretched from 1.6 pg/mL to 400 pg/mL on a microplate reader, and the detection limit was 3.125 pg/mL using naked eye observation. Using a microplate reader, the sensitivity and specificity of AGSCS for the diagnosis of IFI were 92.68% and 89.65%, respectively, which was higher than that of the G test. CONCLUSION: This newly developed visual diagnostic method for detecting IFI showed promising results and is expected to be developed as a point-of-care testing kit to enable quick and cost effective diagnosis of IFI in the future.

Forensic biogeographical ancestry inference: recent insights and current trends.

BACKGROUND: As a powerful complement to the paradigmatic DNA profiling strategy, biogeographical ancestry inference (BGAI) plays a significant part in human forensic investigation especially when a database hit or eyewitness testimony are not available. It indicates one's biogeographical profile based on known population-specific genetic variations, and thus is crucial for guiding authority investigations to find unknown individuals. Forensic biogeographical ancestry testing exploits much of the recent advances in the understanding of human genomic variation and improving of molecular biology. OBJECTIVE: In this review, recent development of prospective ancestry informative markers (AIMs) and the statistical approaches of inferring biogeographic ancestry from AIMs are elucidated and discussed. METHODS: We highlight the research progress of three potential AIMs (i.e., single nucleotide polymorphisms, microhaplotypes, and Y or mtDNA uniparental markers) and discuss the prospects and challenges of two methods that are commonly used in BGAI. CONCLUSION: While BGAI for forensic purposes has been thriving in recent years, important challenges, such as ethics and responsibilities, data completeness, and ununified standards for evaluation, remain for the use of biogeographical ancestry information in human forensic investigations. To address these issues and fully realize the value of BGAI in forensic investigation, efforts should be made not only by labs/institutions around the world independently, but also by inter-lab/institution collaborations.

Exploring rare differences in mitochondrial genome between MZ twins using Ion Torrent semiconductor sequencing.

Monozygotic (MZ) twins are considered to be genetically identical in that they have the same genomic DNA sequences in theory, and thus cannot be differentiated using forensic standard STR-based DNA profiling. However, a recent study employed deep sequencing to explore extremely rare mutations in the nuclear genome and reported that the mutation analysis could be applied to differentiate between MZ twins. Compared with the nuclear genome, the mitochondrial DNA (mtDNA) exhibits higher mutation rates due to fewer DNA repair mechanisms in the mitochondrial genome (mtGenome) and the lack of proofreading capability of the mtDNA polymerase. In a previous study, we used Illumina ultra-deep sequencing to describe point heteroplasmy (PHP) and nucleotide variant of the mtGenomes in venous blood samples of MZ twins. In the present study, we characterized minor differences of the mtGenomes in three tissue samples from seven sets of MZ twins using Ion Torrent semiconductor sequencing (Thermo Fisher Ion S5 XL system) and commercialized mtGenome sequencing kit (Precision ID mtDNA Whole Genome Panel). PHP was observed in blood samples from one set of MZ twins and in saliva samples from two sets of twins, but it presented in hair shaft samples from all seven sets of MZ twins. Overall, the coding region of the mtGenome exhibits more PHPs than the control region. The results of this study have further attested the competence of mtGenome sequencing in differentiating between MZ twins, and that among the three kinds of samples tested, hair shaft is more likely to accumulate minor differences in the mtGenomes of MZ twins.

Extracellular biomineralization of uranium and its toxicity alleviation to Bacillus thuringiensis X-27.

Uranium biomineralization can slow uranium migration in the environment and thus prevent it from further contaminating the surroundings. Investigations into the uranium species, pH, inorganic phosphate (Pi) concentration, and microbial viability during biomineralization by microorganisms are crucial for understanding the mineralization mechanism. In this study, Bacillus thuringiensis X-27 was isolated from soil contaminated with uranium and was used to investigate the formation process of uranium biominerals induced by X-27. The results showed that as biomineralization proceeded, amorphous uranium-containing deposits were generated and transformed into crystalline minerals outside cells, increasing the overall concentration of uramphite. This is a cumulative rather than abrupt process. Notably, B. thuringiensis X-27 precipitated uranium outside the cell surface within 0.5 h, while the release of Pi into the extracellular environment and the change of pH to alkalescence further promoted the formation of uramphite. In addition, cell viability determination showed that the U(VI) biomineralization induced by B. thuringiensis X-27 was instrumental in alleviating the toxicity of U(VI) to cells. This work offers insight into the mechanism of U(VI) phosphate biomineralization and is a reference for bioremediation-related studies.

The mutation rate of rpoB gene showed an upward trend with the increase of MIRU10, MIRU39 and QUB4156 repetitive number.

BACKGROUND: Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) is a frequently used typing method for identifying the Beijing genotype of Mycobacterium tuberculosis (Mtb), which is easily transformed into rifampicin (RIF) resistance. The RIF resistance of Mtb is considered to be highly related with the mutation of rpoB gene. Therefore, this study aimed to analyze the relationship between the repetitive number of MIRU loci and the mutation of rpoB gene. METHODS: An open-source whole-genome sequencing data of Mtb was used to detect the mutation of rpoB gene and the repetitive number of MIRU loci by bioinformatics methods. Cochran-Armitage analysis was performed to analyze the trend of the rpoB gene mutation rate and the repetitive number of MIRU loci. RESULTS: Among 357 rifampicin-resistant tuberculosis (RR-TB), 304 strains with mutated rpoB genes were detected, and 6 of 67 rifampicin susceptible strains were detected mutations. The rpoB gene mutational rate showed an upward trend with the increase of MIRU10, MIRU39, QUB4156 and MIRU16 repetitive number, but only the repetitive number of MIRU10, MRIU39 and QUB4156 were risk factors for rpoB gene mutation. The Hunter-Gaston discriminatory index (HGDI) of MIRU10 (0.65) and QUB4156 (0.62) was high in the overall sample, while MIRU39 (0.39) and MIRU16 (0.43) showed a moderate discriminatory Power. CONCLUSION: The mutation rate of rpoB gene increases with the addition of repetitive numbers of MIRU10, QUB4156 and MIRU39 loci.