Insight into molecular profile changes after skeletal muscle contusion using microarray and bioinformatics analyses

Muscle trauma frequently occurs in daily life. However, the molecular mechanisms of muscle healing, which partly depend on the extent of the damage, are not well understood. The present study aimed to investigate gene expression profiles following mild and severe muscle contusion, and to provide more information about the molecular mechanisms underlying the repair process. A total of 33 rats were divided randomly into control (n=3), mild contusion (n=15), and severe contusion (n=15) groups; the contusion groups were further divided into five subgroups (1, 3, 24, 48, and 168 h post-injury; n=3 per subgroup). A total of 2844 and 2298 differentially expressed genes (DEGs) were identified using microarray analyses in the mild and severe contusions, respectively. From the analysis of the 1620 coexpressed genes in mildly and severely contused muscle, we discovered that the gene profiles in functional modules and temporal clusters were similar between the mild and severe contusion groups; moreover, the genes showed time-dependent patterns of expression, which allowed us to identify useful markers of wound age. The functional analyses of genes in the functional modules and temporal clusters were performed, and the hub genes in each module-cluster pair were identified. Interestingly, we found that genes down-regulated at 24-48 h were largely associated with metabolic processes, especially of the oxidative phosphorylation (OXPHOS), which has been rarely reported. These results improve our understanding of the molecular mechanisms underlying muscle repair, and provide a basis for further studies of wound age estimation.

Analysis of sensitivity and specificity: precise recognition of neutrophils during regeneration of contused skeletal muscle in rats

In this report, we applied the TissueFAXS 200 digital pathological analysis system to rapidly and accurately identify neutrophils during regeneration of contused skeletal muscle, and to provide information for follow-up studies on neutrophils to estimate wound age. Rat injury model was established, and skeletal muscle samples were obtained from the control group and contusion groups at 1, 1.5, 2, 3, 4, and 6 h, as well as at 1, 3, 5, and 15 d post-injury (n = 5 per group). The expression of nuclei and neutrophils was detected by hematoxylin and eosin (HE) staining and immunohistochemical (IHC) staining. A total of 20 injury site areas of 0.25 mm² (0.5 mm × 0.5 mm) were then randomly selected at all time points. A TissueFAXS 200 digital pathological analysis system was used to identify the positive and negative numbers. Knowledge of five professional medical workers were considered the gold standard to measure the false positive rate (FPR), false negative rate (FNR), sensitivity, specificity, and area under the curve (AUC) of receiver operating characteristic (ROC) curves. As a result, with a staining area of neutrophils from 8 µm² to 15 µm², the FPR was 4.28%–12.14%, the FNR was 12.42%–64.08%, the sensitivity was 35.92%–87.58%, the specificity was 87.86%–95.72%, the Youden index was 0.316–0.754, the accuracy was 82.80%–88.30%, and the AUC was 0.771–0.826. The AUC was largest when the cut-off value of the staining area was 12 µm². Our results show that this software-based method is more accurate than the human eye in evaluating neutrophil infiltration. Based on the sensitivity and specificity, neutrophils can be accurately identified during regeneration of contused skeletal muscle. The TissueFAXS 200 digital pathological analysis system can also be used to optimize conditions for different cell types under various injury conditions to determine the optimal cut-off value of the staining area and provide optimal conditions for further study. Furthermore, it will provide evidence for forensic pathology cases.

[Chromosomal abnormalities in spontaneous miscarriage specimens detected by combinatorial probe anchor synthesis-based high-throughput low coverage whole genome sequencing]

Objective: To evaluate the application of combinatorial probe anchor synthesis (cPAS)-based high-throughput low coverage whole genome sequencing in chromosomal aberration detection in spontaneous miscarriage. Methods: From September 2015 to May 2017, spontaneous miscarriage samples were collected from Inner Mongolia Maternal and Child Health Care Hospital. Those samples were further analyzed with two independent methods, fluorescence in situ hybridization (FISH) and low coverage whole genome sequencing on the BGISEQ-500 high-throughput platform. The performance of low coverage whole genome sequencing was assessed by comparing to FISH results. Results: In 595 spontaneous miscarried specimens, low coverage whole genome sequencing revealed 144 cases (24.2%, 144/595) chromosomal abnormalities, of which a subset of 137 cases (23.0%, 137/595) were detected as aneuploidies, 2 cases (0.3%, 2/595) as mosaicisms and 5 cases (0.8%, 5/595) as copy number variation (≥5 Mb). Conclusion: cPAS-based high-throughput low coverage whole genome sequencing is a reliable method in detecting chromosomal aberrations inspontaneous abortion tissues, including chromosome aneuploidies, mosaicisms and copy number variation (≥5 Mb).

Wound Age Estimation by Neutrophil Migration Distance

Abstract

Objective To explore the application of neutrophil migration distance for wound age estimation of skeletal muscles in rats, and to provide methodological basis for follow-up study in future. Methods The skeletal muscle contusion model was established in rats, and the control group and the 2, 4, 6 h post-traumatic groups were set. The law of response of neutrophils that participated in the inflammation after injury was detected by immunohistochemical staining, and the relationship between neutrophil migration distance and injury time was detected by TissueFAXS PLUS software. Results The skeletal muscle was obviously infiltrated with neutrophils 2-6 h after injury. The positive rate of neutrophil was （28.75±0.94）% at 2 h post-traumatic, and reached the peak （45.50±3.63）% at 4 h post-traumatic, then decreased to （31.92±1.56）% at 6 h post-traumatic. The neutrophil migration distances increased with the progress of inflammation, and reached （124.80±12.32） μm, （229.03±21.45） μm and （335.04±16.75） μm at 2 h, 4 h and 6 h, respectively. Conclusion There is a relationship of neutrophil infiltrated number and migration distance and wound age within the 2-6 h after skeletal muscle injury, which could be used for the inference of skeletal muscle wound age.

Vitality and wound-age estimation in forensic pathology: review and future prospects

Determining the age of a wound is challenging in forensic pathology, but it can contribute to the reconstruction of crime scenes and lead to arrest of suspects. Forensic scholars have tended to focus on evaluating wound vitality and determining the time elapsed since the wound was sustained. Recent progress in forensic techniques, particularly high-throughput analyses, has enabled evaluation of materials at the cellular and molecular levels, as well as simultaneous assessment of multiple markers. This paper provides an update on wound-age estimation in forensic pathology, summarizes the recent literature, and considers useful additional information provided by each marker. Finally, the future prospects for estimating wound age in forensic practise are discussed with the hope of providing something useful for further study.

Population genetic analysis of the Globalfiler STR loci in 3032 individuals from the Altay Han population of Xinjiang in northwest China

The genetic polymorphisms of 21 autosomal short tandem repeat (STR) loci included in the GlobalFiler™ PCR Amplification Kit were evaluated in 3032 unrelated individuals Altay Han of Xinjiang, northwest China. All of the loci reached the Hardy-Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. SE33 showed the greatest power of discrimination in Altay Han population, whereas TPOX showed the lowest. The combined discrimination power and probability of excluding paternity of the 21 autosomal STR loci were 0.999999999999999999999999889838 and 0.999999996664704, respectively. Both pairwise genetic distance and phylogenetic methods indicated that the Altay Han had the closest genetic relationship with the Han origin and Hui populations. The present results revealed that the GlobalFiler system had a high level of polymorphism in Altay Han population and hence could be a powerful tool for forensic application and population genetic study.

Developmental validation of a 6-dye typing system with 27 loci and application in Han population of China

In this study, a novel 27-locus system (now known as the SureID PanGlobal system), including 24 autosomal STRs (D3S1358, TH01, D21S11, D18S51, Penta E, D12S391, D6S1043, D2S1338, D1S1656, D2S441, D5S818, D13S317, D7S820, D19S433, CSF1PO, Penta D, vWA, D8S1179, TPOX, FGA, D16S539, D22S1045, SE33, D10S1248), two Y-chromosome markers (DYS391 and Y-indel) and the sex determining marker, Amelogenin was developed with six fluorescent dyes labeling. The included STR loci belonged to the core loci in the Combined DNA Index System (CODIS) and the European Standard Set (ESS) as well as some additional loci commonly used in commercial kits and national DNA databases. This paper describes the validation studies conducted with the SureID PanGlobal system using Applied Biosystems 3500 XL Genetic Analyzer for fragment length detection that included the analysis of the following parameters and aspects: PCR conditions, sensitivity, species specificity, inhibition, precision, stutter, DNA mixtures, and stability studies with crime scene samples. The studies demonstrated that the SureID PanGlobal system is reproducible, accurate, sensitive and robust for forensic application and databasing. Additionally, the whole cycling time of the system can finish within 65 minutes, which was developed specifically for rapid and reliable generation of DNA profiles obtained from blood, buccal swabs and forensic stains.

[Comparison of the Skin and Skeletal Muscle Contusion in Rats Induced by Blunt Force with Different Heights]

OBJECTIVES

To explore the differences in the repair process of skin and skeletal muscle after contusion caused by blunt force attack with different heights.

METHODS

Three degrees of contusion were performed on SD rats' right hind limbs by a designed free-dropping device falling from 15, 30 and 50 cm heights, which as a main consideration factor for degree of injury. The repair process of skin and skeletal muscle at 6 h, 24 h, 3 d, 7 d and 13 d after contusion were observed using routine histological methods.

RESULTS

Hematoma within skin and/or muscle was found in the rats' hind limbs after contusion with three different heights. The repair processes were similar at 24 h after contusion. However, with the increase of height, the display degree was more obvious. At 3 d after contusion, the RBC of the hemorrhagic region would be decomposed and elapsed in 15 cm contusion group, but for 30 cm contusion group, it delayed to 7 d. At 13 d after contusion, the similar result was found in 15 cm and 30 cm contusion groups, in contrast, the 50 cm contusion group was still in the proliferative phase.

CONCLUSIONS

With the increase of height, the occurring rate of hematoma within skin and muscle at the same time increases, and the more serious histological appearance after contusion, including inflammation and proliferation, the longer healing process are observed. According to the results of present study and considering forensic application, the contusion model with 50 cm height （2.58 J/cm²） is recommended as the experimental animal model for the future study of wound age estimation on contusion.

Genetic polymorphisms of 17 Y chromosomal STRs in She and Manchu ethnic populations from China

To evaluate the utility of Yfiler haplotype for DNA testing in two ethnic populations of China, a sample of 413 unrelated individuals (152 Shes and 261 Manchus) was determined. In the She and Manchu populations, the haplotype diversity was 0.9990 and 0.9988, respectively, and the discrimination capacity was 0.9474 and 0.9080, respectively. Research results will be valuable for human identification and paternity tests in the two minority regions and for Chinese population genetic study in the future.

Forensic discrimination of three common brands of kitchen knives in China by ICP-AES and infrared absorption

A block of an injury instrument will be left in wounds sometimes, and the suspect instrument can be discriminated by comparison with the block that was left through elemental analysis. In this study, three brands (Shibazi, Zhangxiaoquan, Qiaoxifu) of kitchen knives with forged, chop, and slice application series were analyzed by inductively coupled plasma atomic emission spectroscopy (ICP-AES) and Infrared Absorption to investigate the type, number of elements and the reference range used for comparing. The results show that when regarding one or more element as the discriminative threshold, together with 5% relative standard deviation (RSD) as the reference range, all the samples could be distinguished among different series. Furthermore, within the same series, the discriminative capability could reach up to 88.57% for all samples. In addition, elements with high content, such as Cr, Mn, and C, were useful to discriminate among different series, and trace elements, such as Ni, Si, and Cu, were useful within the same series. However, in practice, it is necessary to evaluate the accuracy of the method by Standard Reference Material (SRM) before an examination is performed.

Haplotype diversity of 17 Y-STR loci in a Chinese Han population sample from Shanxi Province, Northern China

The distribution of 17 Y-chromosome STR loci DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y-GATA-H4, DYS437, DYS438, and DYS448 haplotypes was determined in a population sample of 222 unrelated Chinese Han from Shanxi Province, Northern China. A total of 219 haplotypes were observed, and of these, 216 were unique, while 3 were found two times. The overall haplotype diversity was 0.9999 and the discrimination capacity was 0.9865, indicating a high potential for differentiating between male individuals in this population. Comparison analysis via Analysis of Molecular Variance (AMOVA) and construction of MDS plot revealed that Shanxi Han sample clusters with Chinese origin populations and stands far apart of the non-Chinese populations, justifying the establishment of local databases in Shanxi Han population for any future forensic and genetic epidemiology efforts in this region.

[Polymorphisms of 11 Y-chromosomal short tandem repeat loci in Chongqing Tujia ethnic group and genetic relationships with 16 populations]

OBJECTIVE

To investigate the genetic polymorphisms of 11 Y-chromosomal short tandem repeats (STR) loci in Chongqing Tujia population, and to evaluate their forensic application values and genetic relationships with the other 16 populations of China.

METHODS

Eleven Y-STR loci in 215 unrelated Tujia individuals from Chongqing were amplified with PowerPlex Y System, and the PCR products were analyzed by 310 Genetic Analyzer. Cluster analysis and phylogenic trees were applied to show the genetic distance among the populations.

RESULTS

A total of 195 haplotypes were identified and the overall haplotypes diversity for the 11 Y-STR loci was 0.9942. The gene diversity values (GD) for each locus ranged from 0.3757 (DYS391) to 0.9170 (DYS385a/b). Comparing with other 16 populations, the genetic distance between Tujia and Tibetan was the nearest (0.02467), that between the Tujia and Korean ethnic groups was the farthest (0.25350).

CONCLUSION

The genetic distribution of the 11 Y-STR loci in Chongqing Tujia population showed favorable polymorphisms. They are suitable for forensic identification and paternity testing in the local area. The study of genetic diversity among different populations is useful in understanding their origins, migrations and their relationships.

[The Y-STR polymorphisms and phylogenetic relationships of two minority populations in Liaoning province]

OBJECTIVE

To investigate the genetic polymorphisms of 11 Y-chromosomal short tandem repeats (Y-STR) loci in 484 male individuals from two minority populations, the Hui and Xibe, of Liaoning province, and to evaluate their forensic application values and genetic relationships with other 15 populations of China.

METHODS

Eleven Y-STR loci in all samples were amplified with PowerPlex Y System, and the PCR products were analyzed by 310 Genetic Analyzer. Cluster analysis and neighbor-joining tree were applied to show the genetic distance among the populations.

RESULTS

In Hui people, 187 haplotypes were identified, and the overall haplotype diversity value was 0.9990. The gene diversity values (GD) for each locus ranged from 0.4783(DYS437) to 0.9679(DYS385a/b); In Xibe people, 237 haplotypes were identified, and the overall haplotype diversity value was 0.9984. The GD value for each locus ranged from 0.3618(DYS391) to 0.9686(DYS385a/b). Comparing with 15 reference populations, the genetic distance between the Hui and Xibe was the nearest (0.0257), and that between the Hui and Yi was the farthest (0.1046), while the genetic distance between Xibe and Korean was also the farthest (0.0978). The NJ tree was similar to the results of clustering analysis and all the 17 populations were clustered into 3 groups.

CONCLUSION

The genetic distribution of the 11 Y-STR loci in Liaoning Hui and Xibe ethnic groups showed favorable polymorphisms, therefore are suitable for forensic identification and paternity testing in the local area. The study of haplotype diversity among different populations is useful in understanding their origins, migrations and their relationships.

The time-dependent expressions of IL-1β, COX-2, MCP-1 mRNA in skin wounds of rabbits

In this study, we investigated the time-dependent expression of IL-1beta, COX-2, MCP-1 mRNA after incised wounds in rabbit skin using real-time fluorescent quantitative PCR. The tested wound ages were distributed as following: <0.5h, 0.5h, 1h, 2h, 3h, 4h, 5h, 6h, 8h, 12h, 24h, 2d, 3d, and 7d. The expressions of three markers in postmortem wounds were determined. Comparison of each wound age with control group, expression of IL-1beta mRNA showed that the significant increase occurred at <0.5h (p<0.01), and the peak level at 2h. The expression was almost normalized at 2d. But for COX-2 and MCP-1 mRNA, the significant increase occurred at 1h for COX-2 mRNA, and 3h for MCP-1 mRNA. The expression peak levels were at 3h and 5h, and were almost normalized at 3d and 7d, respectively. There was no significant increase in all postmortem samples for IL-1beta, COX-2, MCP-1 mRNA compared with control group. Thus, the results of these cytokines and enzyme significant increase at different early wound ages implied that the combined investigation could make wound age determination more objective and accurate. Moreover, the three markers could also be used to distinguish the supravital injuries.

Population genetics for Y-chromosomal STRs haplotypes of Chinese Tujia ethnic group

Allele and haplotype frequencies of 11 Y-chromosomal short tandem repeats (STRs) included in the PowerPlex Y Systems (Promega) were determined in a sample of 215 unrelated healthy male individuals of Chinese Tujia ethnic group living in Chongqing (Southwest of China). The gene diversity values of the Y-STRs loci ranged from 0.3757(DYS391) to 0.9170 (DYS385a/b). A total of 195 haplotypes were identified in the Y-STR loci, among which 180 were unique, 11 were found in two individuals, 3 were shared in three individuals and 1 was shared in four individuals. The observed haplotype diversity value and discrimination capacity were 0.9942 and 0.9070, respectively.

Genetic polymorphism of 14 non-CODIS STR loci for forensic use in southeast China population

We investigated 14 polymorphic STR loci (D1S2142, D2S1360, D3S1545, D7S1517, D10S2325, D12S391, D13S1492, D14S306, D15S659, D16S3253, D18S1270, D19S253, D20S470, D21S1437) which are not included in the standard sets of forensic loci (CODIS) in a sample of 216 unrelated healthy southeast Chinese individuals. The studied loci were highly informative and did not show departures from Hardy-Weinberg equilibrium. The accumulated powers of discrimination and power of exclusion for the 14 loci were 99.9999999999 and 99.999998%, respectively. No linkage was observed between the 14 loci and the traditional set of STR markers included in commercially available kits (the AmpFLSTR IdentifilerTM 15 System loci). We thus considered the studied 14 STRs are informative and when necessary, can be used as the candidate genetic markers in the study and application in genetics and forensic practice.

[Twenty Y-STR locus multiplex amplification and genetic polymorphism analysis in Han population in Chaoshan area]

OBJECTIVE

To study genetic polymorphisms of 20 Y-chromosomal short tandem repeats (STR) in Chaoshan Han population, and to evaluate their value in forensic science.

METHODS

Twenty Y-specific STR loci (DYS434, Y-GATA-A10, Y-GATA-H4, DYS438, DYS439, DYS443, DYS444, DYS446, DYS447, DYS448, DYS456, DYS458, DYS460, DYS520, DYS531, DYS557, DYS622, DYS630, DYS635 and DYS709) were amplified by using three fluorescence-labeled multiplex PCR systems and were analyzed by ABI310 genetic analyzer. One hundred and fifty-eight unrelated male individuals of Han population in Chaoshan area were investigated to determine the distribution of allele frequencies and haplotype.

RESULTS

The Y-STR multiplexes developed had followed the published nomenclature and ISFG guidelines for STR analysis. Gene diversity ranged from 0.2506 at DYS434 to 0.8034 at DYS447. A total of 157 different haplotypes were observed, and among these, 156 were unique, while 1 was found for two times. The haplotype diversity value calculated from all 20 loci combined was 0.999998. None of Y-STR allele mutation was observed in the 30 father/ son pairs confirmed by autosomal STR analysis.

CONCLUSION

The results indicate that the 20 Y-STR loci are highly polymorphic and fathership genealogy inheritance are stable. The three fluorescence-labeled multiplex amplification systems that we constructed are suitable for forensic individual identification and paternity testing in Chaoshan area.

Allele frequencies for six miniSTR loci of two ethnic populations in China

Allele frequencies and forensic parameters for the six miniSTR loci D1S1677, D2S441, D4S2364, D10S1248, D14S1434, and D22S1045 were investigated in two ethnic China populations. Allele frequencies for each locus are reported along with nomenclature based on sequence analysis. The polymerase chain reaction (PCR) products contained within the six loci were less than 125 bp in size. All loci showed a moderate degree of polymorphism with observed heterozygosity >0.7 except for D4S2364 and did not show departures from Hardy-Weinberg equilibrium for all two populations. The accumulated powers of discrimination for the six loci were 0.999994, and 0.999996 for Han ethnic, and Korean ethnic minority group, respectively.

Identify the injury implements by SEM/EDX and ICP-AES

The forensic investigator is frequently confronted with the discrimination and deduction of injury implements, which is one of the most important physical testimonies in courts. The usual method used in actual cases is from points of morphology. In the forensic discrimination of injury implements, such as metal implements, the analysis and comparison of elements are expected to provide excellent results, and simultaneous multi-elemental analysis is required to analyze various kinds of elements. This study was designed to establish discrimination and deduction of metal injury implements by scanning electron microscope/energy disperse X-ray microanalyzer (SEM/EDX) and inductively coupled plasma atomic emission spectrometry (ICP-AES). Examined metal particles in five wounds made on the skin of domestic pigs, respectively, using Cu-Zn or Cr-Ni coated and carbon steel kitchen implements by EDX. For carbon steel kitchen implements, analyzed five samples from the back and blade separately in the contents and varieties of elements by ICP-AES. In the wounds by the coated implements, the special particles only containing Cu, Zn or Cr, Ni were found. In the wounds by carbon steel kitchen implements, the particles containing Fe, Cr, Si or Fe, Mn, Si were found. The differences of contents of elements between the back and blade was no significant except No. 5 for carbon steel kitchen implements, and the significant differences of elements exited in Cr, Mn, Si, Cu, Mo among the stainless kitchen knives, Mn, Si among the other kitchen implements and for the blade of No. 5 knife, relative standard deviations (R.S.D.s) were significantly different in Mn, Si, Mo, Ti, S, P, Ni. Using EDX to examine the particles in wounds can deduce the categories of metal injury implements, and we can still deduce the different implements in the same category by ICP-AES.